@article {pmid41526934,
year = {2026},
author = {Fallahzadeh, A and Mahmoodi, T and Kwon, S and Liu, M and Nolan, A},
title = {Multi-omics of oxidative stress and particulate matter exposure: a systematic review.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-025-03487-0},
pmid = {41526934},
issn = {1465-993X},
support = {U01 -OH012069; -OH011855; -OH011300//Centers for Disease Control and Prevention Foundation/ ; UL1TR001445; KL2TR001446/TR/NCATS NIH HHS/United States ; },
abstract = {BACKGROUND: Exposure to particulate matter (PM) is a significant public health concern associated with respiratory, cardiovascular, and metabolic diseases. Oxidative stress is a key biological mechanism mediating the harmful effects of PM exposure. However, a comprehensive review of relating PM exposure to omics layers of oxidative stress has been lacking. We aimed to systematically review the current evidence on the associations between PM exposure and the multi-omics signatures of oxidative stress.

METHODS: We conducted a systematic review of studies published between January 2021 and March 2024 in PubMed and Web of Science, following a registered protocol (PROSPERO ID: CRD42024617742). Eligible studies assessed the impact of PM exposure on oxidative stress-related omics in adult human populations. Data on exposure assessment, study characteristics, and omics outcomes were extracted, and the risk of bias was evaluated using the Newcastle-Ottawa Scale and Cochrane's.

RESULTS: Seventy-seven studies were included. PM exposure was consistently associated with oxidative stress markers across multiple omics platforms. Studies on the analytes showed that PM was associated with an increase in oxidative markers. Metabolomics studies revealed alterations in pro-oxidant metabolites (e.g., eicosanoids, ceramides) and disruptions in antioxidant pathways (e.g., glutathione, vitamin C, and E metabolism). PM exposure was also linked to changes in energy metabolism, fatty acid oxidation, and detoxification pathways. Genomics studies reported differential methylation in genes involved in oxidative stress and inflammation. Microbiome studies suggest that PM exposure alters the composition of gut and nasal microbiota, favoring a pro-oxidative profile. However, some studies reported no significant associations, highlighting heterogeneity in findings.

CONCLUSION: Our systematic review demonstrates that PM exposure affects multiple molecular pathways related to oxidative stress across diverse omics platforms. These findings highlight the complex responses to PM, underscoring the need for integrative multi-omics approaches to fully understand the health impacts of air pollution.},
}

@article {pmid41526899,
year = {2026},
author = {Jia, K and Chen, Y and Dai, D and Xie, Y and Peng, H and Cao, Y and Zou, H and Qiu, C and Tan, Y and Zhang, X and Lu, Z and Yin, X and Peng, Z and Li, J and Shen, L},
title = {Impact of Helicobacter pylori infection on gut and intratumoral microbiome and its association with immunotherapy response in gastrointestinal cancer.},
journal = {BMC medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12916-025-04575-0},
pmid = {41526899},
issn = {1741-7015},
support = {823B2069//National Natural Science Foundation of China/ ; 82203881//National Natural Science Foundation of China/ ; U22A20327//National Natural Science Foundation of China/ ; 7222021//Beijing Natural Science Foundation/ ; QMS20201102//Beijing Hospitals Authority Youth Programme/ ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) infection is associated with enhanced efficacy of immunotherapy in gastric cancer (GC). However, the mechanisms underlying this enhancement are not fully understood.

METHODS: We recruited 218 GC patients, 134 esophageal squamous cell carcinoma (ESCC) patients, and 86 dMMR/MSI-H colorectal cancer (CC) patients and collected their stool and tumor samples to analyze the gut and intratumoral microbiome. We assessed microbial diversity and composition and correlated these findings with clinical outcomes to evaluate the relationship between H. pylori status, microbiome alterations, and immunotherapy efficacy.

RESULTS: H. pylori-positive patients showed higher alpha diversity and unique microbial signatures, which were associated with increased immune-related progression-free survival (irPFS) and overall survival (irOS). In addition, we found that the abundance of 45 gut microbiome species was significantly different between the two groups. The gut microbiome of the H. pylori-positive GC group was enriched with species such as Clostridium leptum, Oscillibacter sp. ER4, and Ruminococcus bromii, which were associated with improved treatment response. However, they predicted poor prognosis in patients with esophageal squamous cell carcinoma and colorectal cancer patients with dMMR/MSI-H. Microbial co-occurrence network revealed significantly distinct interaction patterns among the groups. In addition, we found enhanced L-arginine biosynthesis in the gut microbiome of H. pylori-positive GC. In terms of intratumoral bacteria, we identified two genera, Streptococcus and Granulicatella, that were mutually exclusive with H. pylori infection in GC. Enhanced L-lysine fermentation to acetate and butanoate was observed among intratumoral bacteria, suggesting potential metabolic shifts in the tumor microenvironment. Incorporating H. pylori infection status into the microbiome-based prediction model further improved the accuracy of predicting immunotherapy outcomes in GC.

CONCLUSION: These findings suggest that H. pylori had significant effects on the structure and functional activity of gut and intratumoral microbiome, some of which may affect the efficacy of immunotherapy. The clinical value of H. pylori infection status should be considered when establishing a prediction model for immunotherapy efficacy based on gut microbiome.},
}

@article {pmid41526636,
year = {2026},
author = {Neff, HA and Yıldız-Altay, Ü and Salam, N and Ward, DV and Shepard, D and Ramirez-Ortiz, ZG and Richmond, JM},
title = {Gut dysbiosis in a murine model of cutaneous lupus erythematosus correlates with antigen-specific T cells and antigen-presenting cells in skin.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-34741-6},
pmid = {41526636},
issn = {2045-2322},
support = {Mechanisms & Targets Award//Lupus Research Alliance/ ; Mechanisms & Targets Award//Lupus Research Alliance/ ; },
abstract = {The commensal organisms constituting the human microbiome are increasingly appreciated to fortify epithelial barriers and modulate host immunity. Dysbiosis of both single strains and communities can contribute to inflammatory conditions. Here, we sought to characterize potential dysbiosis in our inducible mouse model of cutaneous lupus erythematosus (CLE). We hypothesized that gut dysbiosis would occur based on several studies that found lower Firmicutes/Bacteroidetes (F/B) ratios and decreased diversity in systemic lupus erythematosus (SLE) cohorts compared to healthy counterparts, a mouse study that identified Ro60 commensal orthologs that can trigger onset of lupus-like disease, and a study of CLE that identified outgrowth of Staphylococcus aureus in the skin. Using whole genome shotgun sequencing, we identified differences in pre- and post-irradiation cohorts, particularly an increase in Duncaniella, a decrease in Prevotella, and a reduction in alpha diversity following irradiation. Baseline alterations in CLE mice gut bacteria compared to littermate controls were also extant, including trends toward increased Parabacterides distasonis and Bacteroides acidifaciens in CLE mice. Importantly, we noted an increase in Phocaeicola sartorii in CLE mice compared to littermate controls post-disease induction. We examined the mycobiome in our mice and noted a reduction of Colletotrichum tofieldiae specifically in CLE mice post-disease induction, and a trend towards increased Periglandula ipomoeae. Last, we correlated abundance of genera and species with flow cytometry data obtained from the skin, lymph node and spleen, and identified specific strains that correlated with presence of antigen-specific T cells and different antigen presenting cell populations. Thus, our model exhibits similar changes to other models of lupus-like disease, and our data identify potential novel strains/species that could be modified for CLE and/or SLE treatment such as through generation of probiotics or specific antimicrobial agents.},
}

@article {pmid41526566,
year = {2026},
author = {Swarte, JC and Zhang, S and Bakker, SJL and Björk, JR and Weersma, RK},
title = {The gut microbiome in solid-organ and haematopoietic-stem-cell transplantation.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {41526566},
issn = {1740-1534},
abstract = {Solid-organ transplantation (for example, kidney or liver) and haematopoietic-stem-cell transplantation have revolutionized treatment of end-stage organ failure and haematological malignancies. However, long-term outcomes are often undermined by complications such as allograft rejection, graft-versus-host disease in haematopoietic-stem-cell recipients, opportunistic infections, adverse effects of drugs and decreased quality of life. Emerging evidence now highlights the gut microbiome and its metabolites (such as short-chain fatty acids) as a potentially modifiable factor influencing transplantation outcomes. Transplantation recipients frequently exhibit gut dysbiosis, which has been linked to graft function, risk of infection (for example, vulnerability to multidrug-resistant bacteria), immune-mediated complications and patient survival. Furthermore, pharmacomicrobiomics studies indicate that microorganisms can metabolize immunosuppressive drugs into less active forms (such as the conversion of the immunosuppressive drug tacrolimus into less active or toxic forms through keto-reduction, glucuronidation or deconjugation) or can activate prodrugs (such as the conversion of mycophenolate mofetil into mycophenolic acid), thereby modulating drug efficacy and safety. Here, we discuss how the intestinal ecosystem is altered and persistently shaped by transplantation-related factors and immunosuppression and how these changes correlate with clinical outcomes. We provide a perspective on leveraging microbiome insights, through biomarkers or microbiome-targeted interventions, to improve outcomes in solid-organ and stem-cell transplantation.},
}

@article {pmid41526497,
year = {2026},
author = {Iktilat, K and Levin, G and Isacson, M and Turjeman, S and Tzemah-Shahar, R and Gamliel, G and Louzoun, Y and Koren, O and Agmon, M},
title = {Integrating gut microbiota and violence exposure metrics to classify psychological distress in middle-aged adults.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-025-01319-2},
pmid = {41526497},
issn = {2730-664X},
abstract = {BACKGROUND: Exposure to violence and psychological distress are positively correlated across populations. Microbiota-gut-brain crosstalk research supports that the microbiota is affected by environmental stressors and may influence mental state. Accordingly, we explored how the microbiota relates to exposure to violence and distress in midlife, a pivotal yet underexplored period. This life stage is marked by emerging vulnerability to chronic stress and mental health decline yet offers opportunities for early identification and intervention.

METHODS: We characterized the fecal microbiota of a previosly snowball-recruited Israeli-Muslim cohort (n = 305, 40-65 yrs) exposed to ongoing and increasing violence (during adulthood) and examined correlations with subjective reports of exposure to violence and psychological distress. We then used machine learning to leverage microbiota profiles and exposure to violence, classifying individuals into high- and low-distress categories.

RESULTS: We identify unique microbial signatures associated with increasing exposure to violence and distress. Some associated bacteria were previously identified in the literature, while others were not yet described in the context of the gut-brain axis. Microbial profiles associated with violence and distress are largely non-overlapping, yet we are able to classify participants into high- and low distress categories using a combination of microbiota and violence variables. This combined model outperforms those using only microbiota or demographics, but its classification accuracy remains modest (with a median area-under-the-curve of 0.595 (IQR 0.045).

CONCLUSIONS: This research sheds light on the microbiota-gut-brain axis, highlighting that psychological distress and exposure to violence are differentially associated with microbiota composition in midlife. These cross-sectional findings, together with moderate classification into distress classes based on the microbiome, suggest that holistic, context-aware approaches would benefit proactive mental health interventions.},
}

@article {pmid41526493,
year = {2026},
author = {Smith, DR and Haq, S and Niu, M and Malla, S and Saha, R and Peer, A and Bianco, P and Romanova, S and Samuelson, DR and Knoell, DL},
title = {ZIP8 loss impairs macrophage-mediated phagolysosomal removal of bacteria and is overcome by butyrate supplementation.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-025-09504-8},
pmid = {41526493},
issn = {2399-3642},
support = {5R35GM143009//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; },
abstract = {Zinc deficiency impacts billions of people and contributes significantly to the increased incidence of community-acquired pneumonia worldwide. Myeloid cells require the zinc transporter ZIP8 for proper host defense. Previously, we observed that infection with S.pneumoniae in myeloid-specific Zip8 knockout mice (Zip8KO) results in increased bacterial burden and mortality despite increased recruitment of macrophages into the lung. Here, we reveal that the lungs of infected Zip8KO mice generate a unique population of dysfunctional macrophages with defects in phagolysosomal function and cell survival. In particular, Zip8KO bone marrow-derived macrophages have increased bacterial accumulation due to deficits in lysosomal number and function via defective mTORC1/TFEB signaling. Knowing that labile Zn cannot enter the cytosol through ZIP8 and that ZIP8 loss impairs butanoate synthesis by the gut microbiome, both previously reported by our group, we reveal an alternative treatment strategy via extended oral phenylbutyrate supplementation. Despite ongoing ZIP8-mediated impairment of lung host defense, phenylbutyrate restored macrophage-mediated bacterial clearance and improved host outcomes. Given the high incidence of diet-induced Zn deficiency and the rs13107325 ZIP8 defective variant allele in humans, future investigations that foster preventive, patient-centered treatment strategies that counter immune dysfunction due to Zn dyshomeostasis are warranted.},
}

@article {pmid41526416,
year = {2026},
author = {Hasan, R and Shaikh, MTM and Rawat, S and Singh, V and Tamang, R and Choudhury, S},
title = {Intratumoral microbiome signatures in a North Central Indian colorectal cancer cohort: identification of novel prognostic biomarkers and functional pathways.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1815},
pmid = {41526416},
issn = {2045-2322},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/mortality ; India/epidemiology ; Female ; Male ; Middle Aged ; Prognosis ; *Biomarkers, Tumor/genetics ; RNA, Ribosomal, 16S/genetics ; Aged ; *Gastrointestinal Microbiome ; Adult ; Cohort Studies ; *Microbiota ; Bacteria/genetics/classification ; },
abstract = {Colorectal cancer (CRC) remains a major global health burden, with emerging evidence implicating gut and oral microbiome dysbiosis in its pathogenesis. This comparative observational study aimed to investigate intratumoral microbial signatures in early-onset CRC (EOCRC) and their association with clinical outcomes. In fact, till date there is no comprehensive study yet that directly compares the microbiome of EOCRC patients in North Central India to other EOCRC groups globally. We analysed 50 matched tumor and adjacent normal tissues (obtained from the same patient) using 16S rRNA amplicon sequencing. Taxonomic and functional analyses were conducted using DESeq2, LEfSe, and KEGG pathway prediction (via PICRUSt2). Our findings revealed distinct intratumoral enrichment of oral pathobionts such as Leptotrichia buccalis and Filifactor alocis, which showed significant correlation with mortality risk. Caldilinea aerophila was detected for the first time in human tumor tissue and was strongly associated with advanced TNM stages (p = 0.01; 83% specificity) in North Central Indian population. LEfSe analysis identified an overrepresentation of Actinomycetales. KEGG pathway analysis revealed enrichment of MAPK signaling, styrene, and aminobenzoate degradation pathways. Depletion of Lactobacillus plantarum and presence of dietary-linked microbes suggest microbial modulation by lifestyle. These findings highlight novel microbial biomarkers and immune-related pathways with potential prognostic implications in this regional CRC cohort.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/mortality
India/epidemiology
Female
Male
Middle Aged
Prognosis
*Biomarkers, Tumor/genetics
RNA, Ribosomal, 16S/genetics
Aged
*Gastrointestinal Microbiome
Adult
Cohort Studies
*Microbiota
Bacteria/genetics/classification

@article {pmid41526369,
year = {2026},
author = {Fu, W and Sun, C and Sun, B and Li, P and Ding, X and Guo, Q and Yuan, J and Lai, H},
title = {Flavonoid-mediated bacterial spermidine biosynthesis enhances vitamin accumulation in tomato fruits.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-68244-9},
pmid = {41526369},
issn = {2041-1723},
abstract = {Rhizosphere microbes benefit plant growth and health. How plant-microbe interactions regulate fruit quality remains poorly understood. Here, we elucidate the multi-level modulation of vitamin accumulation in tomato by flavonoid-mediated crosstalk between host plants and rhizosphere microbes. SlMYB12-overexpressing plants with up-regulated flavonoid biosynthesis accumulate higher levels of vitamins C and B6 in fruits compared to wild-type plants grown in natural soil. Flavonoid-mediated improvement of fruit quality depends on the presence of soil microbiomes and relates to rhizosphere enrichment of key taxa (e.g. Lysobacter). Multi-omics analyses reveal that flavonoids attract Lysobacter soli by stimulating its twitching motility and spermidine biosynthesis, which in turn boosts vitamin accumulation in fruits across tomato cultivars and soil types. RpoN acts as a dual regulator in L. soli that is responsive to flavonoids, controlling bacterial motility and spermidine production. Our study provides insight into flavonoid-mediated rhizosphere signalling and underscores plant-microbiome orchestration for improved tomato fruit quality.},
}

@article {pmid41526362,
year = {2026},
author = {Ascandari, A and Aminu, S and Benhida, R and Daoud, R},
title = {Cross-cohort resistome and virulome gradients structure the colorectal cancer microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00905-5},
pmid = {41526362},
issn = {2055-5008},
abstract = {The gut microbiome is increasingly implicated in colorectal cancer (CRC), yet the functional signatures associated with disease progression remain poorly resolved across populations. We performed an assembly-based metagenomic analysis of more than 500 samples from three geographically distinct cohorts to characterize resistome and virulome patterns associated with CRC. Using a cross-validated modeling framework based on Partial Least Squares (PLS) regression, we identified two reproducible latent functional gradients that structured variation in antimicrobial-resistance and virulence-factor profiles. One gradient was enriched for adhesion, efflux, and biofilm-associated functions, while the second reflected immunomodulatory and barrier-related pathways. These components were statistically robust, directionally stable across cohorts, and consistent with functional themes frequently reported in CRC microbiome studies. To summarize variation along these gradients, we derived an exploratory Dual-Axis Index (DAI) based on the two stable PLS components. Although its discriminative performance was moderate, the DAI provided an interpretable low-dimensional representation of how resistome-virulome patterns differed across healthy, adenoma, and carcinoma states. These results suggest that functional gene profiles in CRC are organized along reproducible statistical axes, and highlight functional modules, such as adhesion-, iron-associated, and immune-interaction pathways that may complement taxonomic or metabolic biomarkers in future multimodal approaches. Our work provides a reproducible, assembly-based framework for examining the functional organization of CRC-associated microbiomes across diverse populations.},
}

@article {pmid41526019,
year = {2026},
author = {Donaubauer, AJ and Frey, B and Agaimy, A and Lange, F and Mogge, L and Fietkau, R and Iro, H and Munoz, LE and Weber, M and Kesting, M and Gaipl, US and Haderlein, M and Müller, S},
title = {Definition of predictive and prognostic immune biomarkers for salivary gland cancer from the intratumoural and systemic immune status: detailed protocol of the prospective, observatory ImmoGlandula study.},
journal = {BMJ open},
volume = {16},
number = {1},
pages = {e100021},
doi = {10.1136/bmjopen-2025-100021},
pmid = {41526019},
issn = {2044-6055},
mesh = {Humans ; *Salivary Gland Neoplasms/immunology/therapy/pathology ; Prospective Studies ; Prognosis ; *Biomarkers, Tumor/immunology ; Immunotherapy ; Observational Studies as Topic ; Female ; },
abstract = {INTRODUCTION: Salivary gland carcinomas (SGC) are rare tumours. The term SGC is not more than an umbrella for a variety of histogenetically, morphologically and biologically distinct entities. Accordingly, SGCs have not been sufficiently investigated to date. Their rarity makes it difficult to reach high patient numbers for individual entities in clinical studies, leading to pooling patients with different histological subtypes to attain sufficient participants. The different histological subtypes of SGC differ significantly in their clinicopathological features, such as their grading, their occurrence and their outcome. SGCs are usually stratified into low-grade, intermediate-grade or high-grade tumours. In most kinds of SGC, specific targetable molecular markers are lacking. The inclusion of immunotherapy (IT), however, might improve the outcome of patients suffering from high-grade SGCs. In order to integrate IT as a therapeutic option for SGC and to facilitate therapeutic decisions based on tumour (immune) biology, predictive and prognostic immunological biomarkers are indispensable.

METHODS AND ANALYSIS: In this prospective study, 500 patients will be enrolled, who are distributed in three arms. The observational cohort includes patients with malignant salivary gland tumours, whereas patients with benign tumours of a salivary gland are grouped in the control group 1. In the control cohort, 2 patients do not have a salivary gland tumour but have a planned functional surgery of the nose or ear or a maxillofacial surgery. The local immune status from the tumour tissue and the microbiome will be sampled before treatment. In addition, the systemic immune status from peripheral blood will be analysed before and after surgery and after the adjuvant and definitive chemoradiotherapy, if applicable. Clinical baseline characteristics and outcome parameters will additionally be collected. Data mining and modelling approaches will finally be applied to identify interactions of local and systemic immune parameters and to define predictive and prognostic immune signatures based on the evaluated immune markers.

ETHICS AND DISSEMINATION: Approval from the institutional review board of the Friedrich-Alexander-Universität Erlangen-Nürnberg was granted in September 2023 (application number 23-292-B). The results will be disseminated to the scientific audience and the general public via presentations at conferences and publication in peer-reviewed journals.

TRIAL REGISTRATION NUMBER: NCT06047236.},
}

Humans
*Salivary Gland Neoplasms/immunology/therapy/pathology
Prospective Studies
Prognosis
*Biomarkers, Tumor/immunology
Immunotherapy
Observational Studies as Topic
Female

@article {pmid41525802,
year = {2026},
author = {Cheng, C and Xu, S and Liu, Z and Zhang, H and Yang, Y and Zhang, Y and Ge, E and Xu, J and Zhu, Q and Li, X and Yu, B and Liu, M and Guo, Y},
title = {Microbial community differences between healthy and Ustilago-infected oats.},
journal = {Genomics},
volume = {},
number = {},
pages = {111202},
doi = {10.1016/j.ygeno.2026.111202},
pmid = {41525802},
issn = {1089-8646},
abstract = {Ustilago, a pathogenic fungus, poses a serious threat to oat growth and yield. However, the species composition, abundance, and distribution of microbial communities in Ustilago-infected oats remain poorly characterized. In this study, we conducted 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing and biochemical assays to compare microbial profiles and physiological traits between healthy (n = 60) and Ustilago-infected oats (n = 60). Our analyses revealed higher bacterial diversity in healthy oats, particularly in the spikes and stems. Significant shifts in microbial community structure were observed across all tissues in diseased plants. While the microbiome of healthy oats predominantly comprised beneficial bacteria, including Exiguobacterium indicum, infected plants were largely colonized by pathogens, including Ustilago hordei, Pyrenophora chaetomioides, and Curtobacterium flaccumfaciens pv. flaccumfaciens, suggesting the occurrence of disease-driven microbial restructuring. Functional predictions indicated that enriched pathways were primarily associated with metabolism, followed by genetic information processing and environmental signal transduction. Malondialdehyde content was significantly lower in most healthy oat tissues compared to Ustilago-infected oats, whereas the activities of the antioxidant enzymes superoxide dismutase and peroxidase were markedly higher. These results implied that Ustilago infection induced severe oxidative damage to membrane systems, likely compromising the plant's ability to scavenge superoxide ions and hydrogen peroxide, thereby reducing overall plant health.},
}

@article {pmid41525776,
year = {2026},
author = {, and Proctor, LM},
title = {Integrating microbiomes into One Health: insights from the 2025 One Health World Microbiome Partnership Summit.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101319},
doi = {10.1016/j.lanmic.2025.101319},
pmid = {41525776},
issn = {2666-5247},
}

@article {pmid41525625,
year = {2026},
author = {Weng, Q and Hu, M and Peng, G and Lu, W and Wang, H and Zhu, J},
title = {Variational Bayesian Multi-Output Gaussian Process Regression for Metabolic Profiles Prediction with Microbiome Data.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2026.3653067},
pmid = {41525625},
issn = {2998-4165},
abstract = {Understanding the pivotal role of the human microbiome in health necessitates accurate metabolite prediction, which is crucial for unraveling the intricate interplay between the gut microbiome and human health. This study introduces an innovative approach, Variational Bayesian Multi-Output Gaussian Process Regression (VBMOGPR), to address the challenges posed by the complex, high-dimensional nature of microbiome data. VBMOGPR predicts microbial metabolites, quantifies the model confidence, and incorporates uncertainty estimates. Employing a Bayesian framework with Automatic Relevance Determination (ARD) for feature selection enhances interpretability and performance. Comparative analysis across 14 datasets within a meta-database demonstrated the superiority of VBMOGPR, marking a significant advancement in metabolite prediction and its implications for microbiome impact on human health. In addition, we confirmed that VBMOGPR could tap the potential microbial metabolic association.},
}

@article {pmid41525344,
year = {2026},
author = {van der Ploeg, GR and White, FTG and Jakobsen, RR and Westerhuis, JA and Heintz-Buschart, A and Smilde, AK},
title = {ACMTF-R: Supervised multi-omics data integration uncovering shared and distinct outcome-associated variation.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0339650},
pmid = {41525344},
issn = {1932-6203},
mesh = {Female ; Humans ; Pregnancy ; Algorithms ; Metabolomics/methods ; Milk, Human/microbiology/metabolism ; *Multiomics ; Feces/microbiology ; Infant ; },
abstract = {The rapid growth of high-dimensional biological data has necessitated advanced data fusion techniques to integrate and interpret complex multi-omics and longitudinal datasets. Shared and unshared structure across such datasets can be identified in an unsupervised manner with Advanced Coupled Matrix and Tensor Factorization (ACMTF), but this cannot be related to an outcome. Conversely, N-way Partial Least Squares (NPLS) is supervised and captures outcome-associated variation but cannot identify shared and unshared structure. To bridge the gap between data exploration and prediction, we introduce ACMTF-Regression (ACMTF-R), an extension of ACMTF that incorporates a regression step, allowing for the simultaneous decomposition of multi-way data while explicitly capturing variation associated with a dependent variable. We present a detailed mathematical formulation of ACMTF-R, including its optimisation algorithm and implementation. Through extensive simulations, we systematically evaluate its ability to recover a small [Formula: see text]-related component shared between multiple blocks, its robustness to noise, and the impact of the tuning parameter ([Formula: see text]) which controls the balance between data exploration and outcome prediction. Our results demonstrate that ACMTF-R can robustly identify the [Formula: see text]-related component, correctly identifying outcome-associated shared and distinct variation, distinguishing it from existing approaches such as NPLS and ACMTF. The development of ACMTF-R was motivated by a real-world dataset investigating how maternal pre-pregnancy BMI affects the human milk microbiome, human milk metabolome, and infant faecal microbiome. Emerging evidence suggests that inter-generational transfer of maternal obesity may affect multiple omics layers, highlighting the need to identify outcome-associated variation. The applicability of ACMTF-R is therefore validated by applying it to this multi-omics dataset. ACMTF-R successfully identifies novel mother-infant relationships associated with maternal pre-pregnancy BMI, underscoring its utility in multi-omics research. Our findings establish ACMTF-R as a versatile tool for multi-way data fusion, offering new insights into complex biological systems by integrating common, local, and distinct variation in the context of a dependent variable.},
}

Female
Humans
Pregnancy
Algorithms
Metabolomics/methods
Milk, Human/microbiology/metabolism
*Multiomics
Feces/microbiology
Infant

@article {pmid41525336,
year = {2026},
author = {Li, X and Smart, CE and Millard, K and Bell, KJ},
title = {Nutrition and healthy lifestyles for children and adolescents with early-stage type 1 diabetes.},
journal = {Hormone research in paediatrics},
volume = {},
number = {},
pages = {1-20},
doi = {10.1159/000550434},
pmid = {41525336},
issn = {1663-2826},
abstract = {Increasingly children and adolescents are being identified in early-stage type 1 diabetes (T1D), defined as two or more islet autoantibodies without hyperglycemia (above diagnostic threshold) or reliance on intensive insulin therapy. They require clinical monitoring and care. Healthy lifestyle education is recommended in guidelines, however evidence synthesis to inform clinical practice is lacking. Therefore, this review summarizes current evidence on nutrition, lifestyle to delay progression to stage 3 T1D; and proposes lifestyle strategies for children and adolescents with early-stage T1D. Specifically, we suggest a key focus on reducing beta-cell stress, promoting a healthy gut microbiome and establishing healthy lifestyles and relationships with food, prior to the introduction of intensive insulin therapy. As secondary prevention of T1D is an emerging research area and randomized controlled trials are scarce, evidence has been largely drawn from prospective cohort studies and routine clinical care for stage 3 T1D. A balanced and varied diet, limiting intake of foods containing high amounts of saturated fat and added sugar, and moderate levels of physical activity, are likely beneficial for overall health in children and adolescents with early-stage T1D. Low glycemic index (GI) diets may be protective against progression to stage 3 T1D.},
}

@article {pmid41525322,
year = {2026},
author = {Karagiannis, TT and Chen, Y and Bald, S and Tai, A and Reed, ER and Milman, S and Andersen, SL and Perls, TT and Segrè, D and Sebastiani, P and Short, MI},
title = {Integrative analysis across metagenomic taxonomic classifiers: A case study of the gut microbiome in aging and longevity in the Integrative Longevity Omics Study.},
journal = {PLoS computational biology},
volume = {22},
number = {1},
pages = {e1013883},
doi = {10.1371/journal.pcbi.1013883},
pmid = {41525322},
issn = {1553-7358},
abstract = {There are various well-validated taxonomic classifiers for profiling shotgun metagenomics data, with two popular methods, MetaPhlAn (marker-gene-based) and Kraken (k-mer-based), at the forefront of many studies. Despite differences between classification approaches and calls for the development of consensus methods, most analyses of shotgun metagenomics data for microbiome studies use a single taxonomic classifier. In this study, we compare inferences from two broadly used classifiers, MetaPhlAn4 and Kraken2, applied to stool metagenomic samples from participants in the Integrative Longevity Omics study to measure associations of taxonomic diversity and relative abundance with age, replicating analyses in an independent cohort. We also introduce consensus and meta-analytic approaches to compare and integrate results from multiple classifiers. While many results are consistent across the two classifiers, we find classifier-specific inferences that would be lost when using one classifier alone. Both classifiers captured similar age-associated changes in diversity across cohorts, with variability in species alpha diversity driven by differences by classifier. When using a correlated meta-analysis approach (AdjMaxP) across classifiers, differential abundance analysis captures more age-associated taxa, including 17 taxa robustly age-associated across cohorts. This study emphasizes the value of employing multiple classifiers and recommends novel approaches that facilitate the integration of results from multiple methodologies.},
}

@article {pmid41525151,
year = {2026},
author = {Walsh, SK and Armet, AM and Nikolaeva, DD and Mota, JF and Lucey, AJ and Oliero, M and Walter, J},
title = {Optimizing Dietary Fiber Intake: Strategies for Human Nutrition and Food Science.},
journal = {Annual review of food science and technology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-food-052824-044842},
pmid = {41525151},
issn = {1941-1421},
abstract = {Adequate dietary fiber intake from plant foods is critical for the prevention of noncommunicable chronic diseases (NCDs). However, across industrialized nations, consumption remains insufficient to meet established intake recommendations. This gap provides a strong rationale to include functional fibers into processed foods or use them as supplements, although their effectiveness in reducing NCD risk is inconclusive . In this review, we examine current nutritional strategies to optimize fiber intake, spanning whole-plant foods, processed foods made or enriched with fiber-containing ingredients, and fiber supplements. We examine the structure and physicochemical properties of the fiber types represented in these strategies and explore the mechanisms by which they influence the gut microbiome and NCD risk markers. Drawing on evidence from human intervention studies, we critically assess the strengths and limitations of each strategy to improve health outcomes and propose a framework for the effective and systematic integration of fiber into nutrition and food science.},
}

@article {pmid41525137,
year = {2026},
author = {Jackson, SA and Hrab, P and Zdouc, MM and Clarke, DJ and Dobson, ADW},
title = {New insights into the microbiome of the deep-sea sponge Inflatella pellicula and the secondary metabolic potential of metagenome-assembled genomes and the wider microbiome.},
journal = {Microbial genomics},
volume = {12},
number = {1},
pages = {},
pmid = {41525137},
issn = {2057-5858},
mesh = {*Porifera/microbiology ; Animals ; *Metagenome ; *Microbiota/genetics ; Secondary Metabolism/genetics ; Phylogeny ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Multigene Family ; Genome, Bacterial ; Sequence Analysis, DNA ; },
abstract = {Marine sponges are found in all of the world's oceans, from the surface waters to the deepest abyssal zones. The marine sponge holobiont is a rich source of microbial and chemical diversity. Up to 63 bacterial phyla have been observed to be associated with sponges, and thousands of unique natural products have been extracted from sponges or their microbial symbionts. However, sponges from the deep sea and their associated microbial communities are relatively understudied, largely due to sampling-associated difficulties. Secondary metabolism biosynthetic gene clusters are phylogenetically distinct and hold the potential to produce novel chemistry with potential pharmacological or industrial utility. In order to gain further insights into the microbiome of the deep-sea sponge Inflatella pellicula, the metagenome of this sponge, sampled from a depth of 2,900 m, was sequenced. A large fraction of the sequence reads appeared to be 'biological dark matter' and could not be taxonomically classified. Further, unlike similar studies from different marine ecosystems, relatively few metagenome-assembled genomes (MAGs) could be assembled, and relatively few secondary metabolism biosynthetic gene clusters were identified. The identified clusters were, however, very dissimilar to known characterized clusters, but some shared similarities with clusters annotated in MAGs assembled from sponge metagenomes from disparate geographic locations. Therefore, renewed efforts to cultivate the hosts of these gene clusters may yield valuable small-molecule natural products.},
}

*Porifera/microbiology
Animals
*Metagenome
*Microbiota/genetics
Secondary Metabolism/genetics
Phylogeny
*Bacteria/genetics/classification/metabolism/isolation & purification
Multigene Family
Genome, Bacterial
Sequence Analysis, DNA

@article {pmid41525049,
year = {2026},
author = {Nishu, and Verma, K and Noor, SA and Mathur, V},
title = {Aboveground insect herbivory shapes plant-soil feedback and ecosystem resilience.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {41525049},
issn = {2676-8607},
abstract = {The interaction between plants and their surrounding soil ecosystems is complex, with plant-soil feedback acting as legacy effects from previous plants, influencing subsequent plant growth and insect interactions. Recent studies have shown that experiments focusing on individual factors in isolation do not accurately predict the outcomes of these complex interactions. Aboveground herbivores impact the development of root exudates and their surrounding microbiome, suggesting that herbivory indirectly shapes belowground biotic communities. Such impact of insect herbivory on plant-soil feedback is a crucial area of ecological research. Most studies focus on root-associated organisms and their influence on foliar herbivorous insects, and little attention has been given to the reverse interaction-how foliar herbivory affects the soil environment and PSF. This study explores the bidirectional influence of herbivory and PSF, revealing that aboveground insect herbivory can significantly alter plant-soil feedback mechanisms, influencing not only plant performance but also the broader community structure. A holistic approach that integrates soil microbial complexity with insect herbivory is needed to better predict community-level outcomes and enhance plant protection strategies. Our study thus highlighted the need for a community-based perspective when studying interactions among plants, insects and soil microorganisms.},
}

@article {pmid41525005,
year = {2026},
author = {Mir, PA and Kumar, N and Bhutia, GT and Chaudhary, P and Kaur, G and Gupta, SK},
title = {The aging gut-glia-immune axis in alzheimer's disease: microbiome-derived mediators of neuroinflammation and therapeutic innovation.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {41525005},
issn = {2509-2723},
abstract = {Alzheimer's disease (AD), the most common cause of dementia in the aging population, is marked by amyloid-beta (Aβ) plaques, tau tangles, and progressive neuronal degeneration, placing heavy clinical and socioeconomic burdens on healthcare worldwide. Aging remains the strongest risk factor, with chronic low-grade inflammation, oxidative stress, mitochondrial dysfunction, and impaired proteostasis creating a vulnerable brain environment that accelerates AD onset and progression. Recent evidence highlights the gut-glia-immune axis as a critical pathway linking age-related microbiome changes to glial dysfunction. Microbial metabolites, such as short-chain fatty acids and tryptophan derivatives, regulate microglial maturation, astrocytic activity, and neuroimmune signaling. However, age-associated dysbiosis disrupts glial homeostasis, amplifies neuroinflammation, and impairs amyloid clearance, thereby worsening neurodegeneration. Preclinical models including germ-free mice and fecal microbiota transplantation along with clinical studies of elderly AD patients, provide compelling evidence of microbiome-driven modulation of disease. From a therapeutic perspective, microbiome-targeted interventions including probiotics, prebiotics, synbiotics, and microbiota-directed small molecules offer promising strategies to restore glial balance, reduce inflammation, and protect cognitive function. This review highlights the therapeutic potential of probiotics, synbiotics, and fecal microbiota transplantation for mitigating neuroinflammation and cognitive decline in Alzheimer's disease. However, given the multifactorial nature of neurodegenerative disorders, these strategies are unlikely to be universally effective and must be tailored to individual patient profiles.},
}

@article {pmid41524878,
year = {2026},
author = {Ohsawa, M and Nishi, H and Hamai, Y and Emi, M and Ibuki, Y and Komatsuzawa, H and Kawaguchi, H and Okada, M},
title = {Relationship Between the Oral Microbiome and Treatment Efficacy in Esophageal Squamous Cell Carcinoma.},
journal = {Annals of surgical oncology},
volume = {},
number = {},
pages = {},
pmid = {41524878},
issn = {1534-4681},
abstract = {BACKGROUND: As the relationship between oral microbiota and treatment efficacy in esophageal cancer remains unexplored, we aimed to clarify it using metagenomic analysis.

PATIENTS AND METHODS: Of the 140 consecutive patients with esophageal squamous cell carcinoma (ESCC) who underwent esophagectomy with R0 resection at Hiroshima University Hospital between April 2020 and May 2024, 74 who received neoadjuvant therapy were included in this study. 16S rRNA gene from oral tongue coating samples was amplified using polymerase chain reaction and subjected to next-generation sequencing. The oral microbiome data were analyzed using QIIME2 and linear discriminant analysis effect size, and the relationship between the oral microbiota and treatment efficacy and prognosis was assessed.

RESULTS: Alpha diversity of the oral microbiota was significantly correlated with the pathological response. Univariate and multivariate analyses showed that the alpha diversity of the oral microbiome (high versus low) was a significant predictor of a good pathological response. Patients with high alpha diversity had significantly improved recurrence-free survival and overall survival compared with those with low alpha diversity. Furthermore, eight bacterial groups (Lactobacillales, Peptostreptococcales-Tissierellales, Bifidobacteriaceae, Erysipelotrichaceae, Lactobacillaceae, Anaerovoracaceae, Staphylococcaceae, and Aerococcaceae) were significantly more abundant in individuals who responded well to neoadjuvant therapy and two bacterial groups (Streptococcaceae and Corynebacteriaceae) were significantly more abundant in poor responders.

CONCLUSIONS: Our results demonstrate a correlation between the oral microbiome and ESCC treatment efficacy, suggesting that it is a significant prognostic factor. Our findings may also help predict the efficacy of esophageal cancer treatment.},
}

@article {pmid41461908,
year = {2025},
author = {, and Alberts, T and Albritton, CF and Alcazar, R and Aljabri, Z and Alvarez, M and Aradhey, A and Ayalew, M and Azizian, N and Balayah, Y and Ball, DD and Barragan, E and Beshoar, C and Best, L and Biggane, E and Biggane, J and Blick, J and Blosser, M and Brown, AK and Campbell, MC and Canizares, Z and Chanhuhwa, FN and Chen, Y and Chin, DR and Chowdhury, K and Collins, T and Compton, B and Da Silva, J and Davis, NR and DeCaro, N and Delgadillo, F and Deng, Y and Duncan, J and Egwu, AC and Ekalle, GD and Elnawam, N and Enke, R and Ewhe, N and Ferrel, MA and Fierst, J and Freymiller, G and Fuller, K and Fulton-Wright, L and Gaysinskaya, V and Gill, T and Gillespie, E and Gonzalez Moreno, P and Goodwin, S and Graham, N and Graham, ME and Graves, JL and Grob, E and Gutierrez, R and Hager, A and Hakim, ST and Harris, A and Hoffman, AM and Hoffmann, T and Horton, AM and Hughes, A and Humphries, EM and Ikechi-Konkwo, JS and Ishtiaq, A and Jackson, R and James, JR and James, K and Jamison, SA and Jimenez, A and Johnson, R and Kauffman, A and Kaur, H and Kc, K and Keeton, A and Kelly, OE and Kerr, J and Kucher, N and Kuehu, DL and Larson, WA and Lee, J and Lee, A and Leek, JT and Lemaic, D and Liburd, LE and Lopez, AF and Mahmanzar, M and Mamae, K and Manjikian, R and Marone, M and Marquez, K and Martinson, A and Mavruk Eskipehlivan, S and Medrano, A and Melendrez-Vallard, M and Meller, R and Méndez, LB and Mendez Gonzalez, MP and Mesquita, N and Miller, CM and Mohd-Ibrahim, I and Mortensen, P and Mosher, S and Muja, A and Nasrin, N and Nasu, M and Nguyen, MH and Nguyen, BT and Nishiguchi, M and O'Connor, LM and Okie, D and Olowookorun, T and Ostrovsky, A and Ozuna, K and Pandey, A and Patel, SB and Paul, G and Pawar, S and Pearson, A and Petrik, D and Platero, J and Pontino, C and Pratap, AP and Pratap, S and Qin, Y and Rai, SK and Ray, N and Repesh, E and Rhinehardt, K and Roche, B and Rodriguez, A and Roy, S and Roy, S and Sawa, A and Schatz, MC and Sen, SK and Serikawa, R and Smith, T and Smith, L and Sniezek, J and Stewart, RD and Suarez-Martinez, EB and Taganna, J and Tan, FJ and Tsotakos, N and Udolisa, N and Ulbricht, K and Veo, T and Vessio, J and Walker, L and Wang, O and Wang, Q and Wappel, R and Wesby, K and Whitford, M and Wild, N and Xie, X and Yang, H and York, S and Zirkle, L},
title = {Unearthing soil biodiversity through collaborative genomic research and education.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {41461908},
issn = {1546-1718},
support = {2011934//National Science Foundation (NSF)/ ; U24 HG013013/HG/NHGRI NIH HHS/United States ; 75N92022P00232//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5T34GM151403//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; 2221924//National Science Foundation (NSF)/ ; 1839895//National Science Foundation (NSF)/ ; 2000157//National Science Foundation (NSF)/ ; U24HG013013//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 75N92023P00302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {The BioDIGS project is a nationwide initiative involving students, researchers and educators across more than 40 research and teaching institutions. Participants lead sample collection, computational analysis and results interpretation to understand the relationships between the soil microbiome, environment and health.},
}

@article {pmid40045571,
year = {2026},
author = {Kim, DS and Kim, EH and Kim, JY and Kim, DH and Choi, YJ and Jeong, J and Sung, YH and Woo, DC and Kim, CJ and Lee, JC and Yun, M and Jeong, JY and Rho, JK},
title = {The Profile of Gut Microbiota in Carcinogenesis Driven by Mutant EGFR in Non-Small Cell Lung Cancer.},
journal = {Cancer research and treatment},
volume = {58},
number = {1},
pages = {115-127},
doi = {10.4143/crt.2024.1177},
pmid = {40045571},
issn = {2005-9256},
support = {2022IP0029//Asan Institute for Life Science/ ; RS-2023-00261982//Korea Health Industry Development Institute/Republic of Korea ; HR21C0198//Ministry of Health and Welfare/ ; },
mesh = {*Gastrointestinal Microbiome/genetics ; Animals ; ErbB Receptors/genetics ; *Lung Neoplasms/genetics/pathology/microbiology ; Humans ; Mice ; *Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology ; Mutation ; *Carcinogenesis/genetics ; Mice, Transgenic ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Feces/microbiology ; Female ; },
abstract = {PURPOSE: Accumulating evidence has clarified that gut dysbiosis is involved in lung cancer development and progression. Although the relationship between tumors and gut microbiota has been extensively studied using clinical samples, no studies have examined the association between mutant epidermal growth factor receptor (EGFR)-induced lung carcinogenesis and dysbiosis in gut microbiota. Therefore, we investigated the gut microbiota profiles in stool samples from human lung-specific conditional EGFR-mutant transgenic mice during lung tumor carcinogenesis.

MATERIALS AND METHODS: Stool samples were collected before tamoxifen treatment (V1) and at each time point following mutant EGFR expression in lung tissue (V2) and lung tumor appearance (V3). Fecal 16S rRNA taxonomy was analyzed to assess microbial diversity, composition, and dynamic changes at each time point.

RESULTS: We found that microbiota richness and diversity were significantly elevated when tumors developed and grew in the lung. Phylogenetic analysis of the microbial community revealed that Lachnospiraceae, Ruminococcaceae, Porphyromonadaceae, Rhodospirillaceae, Odoribacteraceae, and Desulfovibrionaceae showed a significant increase at the V3 stage compared to the V1 stage at the family level. In contrast, Lactobacillaceae, Bacteroidaceae, Muribaculaceae, Coriobacteriaceae, and Rikenellaceae significantly decreased at the V3 stage compared to the V1 stage. Furthermore, Lactobacillus species, also known as short chain fatty acid-producing bacteria, were relatively abundant at the V1 stage but were depleted with the occurrence of lung tumors at the V3 stage.

CONCLUSION: Changes in gut microbiota, such as Lactobacillus species, may be a predictive factor for the emergence and progression of tumors in an animal model of lung adenocarcinoma induced by mutant EGFR.},
}

*Gastrointestinal Microbiome/genetics
Animals
ErbB Receptors/genetics
*Lung Neoplasms/genetics/pathology/microbiology
Humans
Mice
*Carcinoma, Non-Small-Cell Lung/genetics/pathology/microbiology
Mutation
*Carcinogenesis/genetics
Mice, Transgenic
Dysbiosis/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny
Feces/microbiology
Female

@article {pmid41524843,
year = {2026},
author = {Haysom-McDowell, A and Paudel, KR and Mehndiratta, S and Singh, M and Malik, MZ and Kokkinis, S and Pakan, PD and Williams, FE and Singh, SK and Dua, K and De Rubis, G},
title = {Fisetin-loaded Nanoemulsion and Fecal Microbiome Extract Enhance In Vitro Inhibition of Non-Small Cell Lung Cancer Progression.},
journal = {Cell biochemistry and biophysics},
volume = {},
number = {},
pages = {},
pmid = {41524843},
issn = {1559-0283},
}

@article {pmid41524809,
year = {2026},
author = {Singh, G and Aran, KR},
title = {Rethinking on bile acid-brain axis: decoding neurotoxic and neuroprotective landscape in aging and Alzheimer's disease.},
journal = {Biogerontology},
volume = {27},
number = {1},
pages = {37},
pmid = {41524809},
issn = {1573-6768},
mesh = {Humans ; *Alzheimer Disease/metabolism/drug therapy/pathology ; *Bile Acids and Salts/metabolism ; *Aging/metabolism ; *Brain/metabolism/pathology ; Animals ; Gastrointestinal Microbiome ; Neuroprotective Agents ; Neuroprotection ; },
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative condition in which aging serves as the predominant risk factor. Emerging research underscores the importance of bile acids (BAs), traditionally recognized for their role in digestion, as key signaling mediators involved in both systemic metabolism and neural communication. Disruption of bile acid (BA) metabolism during aging arises from altered hepatic synthesis, gut microbial imbalance, and defective receptor signaling. These changes have been implicated in several neurodegenerative processes, including Aβ accumulation, tau protein abnormalities, mitochondrial impairment, and disturbances in immune regulation. Aging induces a shift in BA composition toward more cytotoxic species, contributing to blood-brain barrier disruption and enhanced neuronal damage. Multi-omics analyses have identified distinct BA signatures in plasma and cerebrospinal fluid of individuals with mild cognitive impairment and AD. These alterations show strong correlations with brain atrophy and progressive cognitive decline. Experimental and early clinical findings suggest potential neuroprotective effects of hydrophilic BAs such as ursodeoxycholic acid and tauroursodeoxycholic acid, along with therapeutic opportunities through modulation of BA receptors and microbiome-driven BA regulation. In the current era of AD research, the gut-liver-brain BA axis emerges as a novel mechanistic framework linking systemic metabolic aging to neurodegeneration. This review examines the molecular pathways through which BA dysregulation influences aging and AD, emphasizing its therapeutic relevance and supporting the development of biomarker-based and precision medicine approaches for neurodegenerative disorders.},
}

Humans
*Alzheimer Disease/metabolism/drug therapy/pathology
*Bile Acids and Salts/metabolism
*Aging/metabolism
*Brain/metabolism/pathology
Animals
Gastrointestinal Microbiome
Neuroprotective Agents
Neuroprotection

@article {pmid41524665,
year = {2026},
author = {Pibaque, P and Porporato, G and Cescutti, S and Cruz-Flores, A and Busche, T and Winker, A and Rapp, TM and Bergkamp, P and Doneva, A and Chakarov, N},
title = {Domination Versus Sisterhoods in the Blood Microbiota of Migrating Birds: Patterns of Within- and Between-Individual Blood Parasite Diversity Revealed Through Metabarcoding.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70056},
pmid = {41524665},
issn = {1749-4877},
abstract = {Avian blood parasites of the genera Plasmodium, Haemoproteus, and Leucocytozoon are typically identified through Sanger sequencing of a partial cytochrome b fragment, the MalAvi barcoding region. This approach limits the detection of mixed infections and the relative frequencies of co-infecting parasites. In contrast, next-generation sequencing (NGS) can resolve these problems but has been underused for haemosporidian lineage identification in samples from the wild. We used an improved PCR protocol and sequencing with Illumina MiSeq to determine haemosporidian assemblages in wild birds captured at a migration stopover site in Bulgaria, Europe. From 406 samples obtained from 52 bird species, we detected 81 haemosporidian lineages in 131 infected samples from 32 species (32% prevalence). On average, individuals were infected with 2.4 lineages, with 59 birds infected by a single lineage, and 21 birds infected with 5-9 lineages. A subset of samples was Illumina- and Sanger-sequenced in parallel, finding mixed infections in 72 samples and 8× higher detection rate of mixed and co-infections through high-throughput sequencing. Both methods identified the same dominant (co-infecting) lineage (91%). Metabarcoding identified common mixed infections of sister lineage groups ("sisterhoods") known for prevalent lineages and morphospecies, including Plasmodium relictum p_SGS1, Haemoproteus motacillae h_YWT2, and Haemoproteus parabelopolskyi h_SYAT01. Some other lineages appeared consistently more dominant. Our study shows that in some host communities, metabarcoding can reveal a great diversity of mixed infections. This opens new horizons to the study of assemblages of haemosporidian parasites, their interactions within individual hosts, and co-evolution with other members of the blood microbiome and the hosts.},
}

@article {pmid41524491,
year = {2026},
author = {},
title = {Correction to "The Microbiome in Hidradenitis Suppurativa Tunnels: A Systematic Review".},
journal = {International journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/ijd.70241},
pmid = {41524491},
issn = {1365-4632},
}

@article {pmid41524460,
year = {2026},
author = {Li, X and Yang, M and Jones, DL and Du, X and Liu, J and Guo, X and Tang, Z},
title = {Rhizosphere Metabolites and Microbial Communities Shape Lettuce Responses to Oxytetracycline Stress.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c10653},
pmid = {41524460},
issn = {1520-5118},
abstract = {Oxytetracycline (OTC), a persistent antibiotic frequently detected in agricultural soils, can influence plant growth and rhizosphere ecology. Using lettuce (Lactuca sativa L.) as a model, this study compared the effects of OTC under hydroponic and soil cultivation systems and integrated physiological, metabolomic, and microbiome analyses. Hydroponic exposure consistently inhibited growth, whereas soil culture showed a biphasic, dose-dependent pattern─low OTC doses stimulated growth while high doses suppressed it. In soil systems, OTC exposure reprogrammed rhizosphere metabolites and reshaped microbial networks, enriching taxa associated with OTC degradation and plant growth promotion (Chryseolinea, Nitrospira, Devosia, Haliangium). Structural equation modeling indicated that rhizosphere diversity and metabolite profiles mediate plant biomass responses. These findings reveal that rhizosphere metabolite-microbe networks play a key role in modulating plant hormetic responses to antibiotic stress, providing mechanistic insight into antibiotic-plant-microbe interactions in agroecosystems.},
}

@article {pmid41524424,
year = {2026},
author = {Grundmann, CO and Tomo, CJ and Hershelman, JL and Wolfe, BE and Sanchez, LM},
title = {Spatial metabolomics reveals the role of penicillic acid in cheese-rind microbiome disruption by a spoilage fungus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0130525},
doi = {10.1128/msystems.01305-25},
pmid = {41524424},
issn = {2379-5077},
abstract = {Microbial interactions in cheese rinds influence community structure, food safety, and product quality. But the chemical mechanisms that mediate microbial interactions in cheeses and other fermented foods are generally not known. Here, we investigate how the spoilage mold Aspergillus westerdijkiae chemically inhibits beneficial cheese-rind bacteria using a combination of omics technologies. In cheese-rind community and co-culture experiments, A. westerdijkiae strongly inhibited most cheese-rind community members. In co-culture with Staphylococcus equorum, A. westerdijkiae strongly affected bacterial gene expression, including upregulation of a putative bceAB gene cluster that is associated with resistance to antimicrobial compounds in other bacteria. Mass spectrometry imaging revealed spatially localized production of secondary metabolites, including penicillic acid and ochratoxin B at the fungal-bacterial interface with Brachybacterium alimentarium. Integration of liquid chromatography-tandem mass spectrometry and genome annotations confirmed the presence of additional bioactive metabolites, such as notoamides and circumdatins. Fungal metabolic responses varied by bacterial partner, suggesting species-specific chemical strategies. Notably, penicillic acid levels increased 2.5-fold during interaction with B. alimentarium, and experiments with purified penicillic acid showed inhibition in a dose-dependent manner against this rind bacterium. These findings show that A. westerdijkiae deploys a context-dependent suite of mycotoxins and other metabolites, disrupting microbial community assembly in cheese rinds.IMPORTANCEThis study identifies the chemical mechanisms underlying the negative impacts of Aspergillus westerdijkiae on cheese-rind development, revealing how specialized metabolites like penicillic acid and ochratoxin B influence rind bacterial communities. By integrating biosynthetic gene cluster analyses with mass spectrometry, we demonstrate how chemical communication shapes microbial interactions, with possible implications for food safety and cheese quality. Understanding these interactions is essential for assessing the risks of fungal-driven spoilage and mycotoxin production in cheese-rind maturation. Beyond cheese, these findings contribute to broader microbiome ecology, emphasizing how secondary metabolites mediate microbial competition in natural and fermented food environments.},
}

@article {pmid41524423,
year = {2026},
author = {Benedict, EE and Agee, W and Hink, T and Parrish, KL and Reske, KA and Peacock, K and Bosserman, RE and Valencia, A and Saluja, A and Ovchiyan, E and Arter, O and Jolani, K and Dubberke, ER and Dantas, G and Kwon, JH},
title = {Community-associated quinolone-resistant and extended-spectrum beta-lactamase-producing Escherichia coli isolates are similar to clinical infection isolates by sequence type and resistome.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0159125},
doi = {10.1128/msystems.01591-25},
pmid = {41524423},
issn = {2379-5077},
abstract = {Escherichia coli is a public health threat capable of causing multiple types of infection, carrying a variety of antimicrobial resistance genes (ARGs), and disseminating ARGs to other microbes. Since ARG-carrying E. coli can exist as a commensal gut microbe, intestinal E. coli in community-associated (CA) members presents an under-appreciated reservoir of ARGs. We cultured 75 CA E. coli isolates from stool of 64 patients lacking inpatient healthcare exposures >24 hours in the previous 12 weeks. Remnant stool submitted to the Barnes-Jewish Hospital (BJH) microbiology laboratory for Clostridioides difficile testing was plated to MacConkey agar with ciprofloxacin and extended-spectrum beta-lactamase (ESBL) Chrome Agar to isolate resistant E. coli colonies, which were whole-genome sequenced. Isolates were compared to ESBL E. coli genomes published by Mahmud et al. (B. Mahmud, M. A. Wallace, K. A. Reske, K. Alvarado, et al., mSystems 7:e00519-22, 2022, https://doi.org/10.1128/msystems.00519-22), which were collected from bloodstream and urinary tract infections. We identified ESBL genes and quinolone resistance elements in E. coli isolates from all patients, 32 (50%) of whom had no recent antibiotic exposure. Sequence type (ST) 131 isolates carried more quinolone resistance elements but fewer ESBL genes than other STs. Eleven patients carried two distinct E. coli lineages simultaneously. CA ESBL E. coli displayed a lower diversity of beta-lactamase genes but similar rates of antibiotic resistance genes compared to ESBL E. coli reported by Mahmud et al. (https://doi.org/10.1128/msystems.00519-22). Carriage of resistance elements without recent antimicrobial exposure suggests the presence of circulating, resistant E. coli. Our results show the continually evolving resistance profile of CA E. coli, demonstrating the importance of characterizing antimicrobial resistance in the community.IMPORTANCEAntimicrobial-resistant Escherichia coli presents a substantial threat to public health, limiting treatment options and potentially horizontally transferring its resistance to other members of the gut microbiome. Resistance to quinolones and beta-lactams, specifically, hinders treatment of urinary tract and gastrointestinal infections, both commonly caused by E. coli. Tracking successful lineages, such as ST131, within the healthcare setting can inform clinicians about resistance patterns among their patients, but this work shows that other STs present an even higher antimicrobial resistance burden than ST131. In addition to monitoring multiple lineages of antimicrobial-resistant E. coli, it is necessary to identify and understand community-associated carriage of this organism, as evidenced by the increasing prevalence of community-associated ESBL E. coli carriage and our specific results showing similar resistance burdens within the clinic and community. This work presents insight into antimicrobial-resistant E. coli among those without significant healthcare exposures, providing important community-focused surveillance that is currently lacking.},
}

@article {pmid41524397,
year = {2026},
author = {Kozik, AJ},
title = {Out of the box: toward new frameworks for understanding human microbiomes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0100024},
doi = {10.1128/msphere.01000-24},
pmid = {41524397},
issn = {2379-5042},
abstract = {The study of the human microbiome (mirroring broader practice across biomedical science), has historically defaulted to the use of simplified, socially constructed "boxes," such as racial and ethnic labels, that fail to accurately capture human variation and fundamentally misdirect the search for mechanisms to explain differences in health outcomes. Five years ago, I proposed a "frameshift," a fundamental conceptual shift away from relying on these categories and toward a more nuanced, careful approach to the complexity of human variation. Moving "out of the box" means tackling the difficult but essential work of analyzing microbial variation through a systems lens, connecting large-scale ecosocial drivers to individual mechanisms and outcomes. In this Full Circle review, I discuss rapid progress in the field toward this new framework and argue that by adopting transdisciplinary methods, we can generate more accurate, actionable, and equitable solutions for human health.},
}

@article {pmid41524293,
year = {2026},
author = {Sassun, R and Brucchi, F and Sileo, A and Vignati, B and Crippa, J and Achilli, P and Maggioni, D and Spinelli, A and Montroni, I and Hawkins, AT and Mari, G},
title = {Recurrent left-sided diverticulitis after surgery: A systematic review and single arm meta-analysis.},
journal = {Colorectal disease : the official journal of the Association of Coloproctology of Great Britain and Ireland},
volume = {28},
number = {1},
pages = {e70368},
doi = {10.1111/codi.70368},
pmid = {41524293},
issn = {1463-1318},
mesh = {Humans ; Recurrence ; *Diverticulitis, Colonic/surgery ; Elective Surgical Procedures/adverse effects/statistics & numerical data ; Male ; Female ; *Colectomy/adverse effects ; Middle Aged ; *Postoperative Complications/etiology ; Aged ; Surgical Stomas/statistics & numerical data ; },
abstract = {INTRODUCTION: Recurrent diverticulitis after resection remains a key concern despite advances in minimally invasive surgery. These recurrences may result from incomplete resection of the diseased segment, unrecognized synchronous diverticulosis or ongoing alterations in colonic motility and microbiome composition. This systematic review and single-arm meta-analysis aimed to estimate long-term recurrence and stoma rates following elective surgery for left-sided diverticulitis.

METHODS: Following PRISMA guidelines and PROSPERO registration, PubMed, Cochrane and Scopus databases were searched (2000-2025) for studies reporting recurrence after elective resection. Single-arm meta-analysis of proportions was performed using random-effects models. Quality was assessed using the JBI Checklist, while subgroup and sensitivity analyses explored heterogeneity. A comparative meta-analysis with medical treatment was not performed due to selection bias, crossover and lack of standardized non-operative protocols.

RESULTS: Twenty-four studies (7,525 patients; mean follow-up 53 months) were included. Pooled recurrence rate was 6.2% (95% CI: 4.8-8.0%; I[2] = 80.6%), with no difference between RCTs (6.3%) and observational studies (6.1%) or complicated vs. uncomplicated disease. Stoma rate (16 studies, 6,400 patients) was 17.1% (95% CI: 8.4-31.9%; I[2] = 99.3%), significantly higher in complicated (31.0%) than uncomplicated (5.5%) cases (p = 0.009) and significantly lower post-2020 (8.0% vs. 31.2%; p = 0.003). Quality was high in 92% of studies, while sensitivity analyses confirmed robustness.

CONCLUSIONS: Surgical resection achieves durable control with low recurrence and stoma rates. Research priorities include standardized definitions of recurrence, assessing long-term QOL and exploring microbiome influences to refine patient selection and minimize residual risk.},
}

Humans
Recurrence
*Diverticulitis, Colonic/surgery
Elective Surgical Procedures/adverse effects/statistics & numerical data
Male
Female
*Colectomy/adverse effects
Middle Aged
*Postoperative Complications/etiology
Aged
Surgical Stomas/statistics & numerical data

@article {pmid41524247,
year = {2026},
author = {Mir, HD and Giorgini, G and Santos-García, I and Dumais, E and Rodríguez-Cueto, C and de Lago, E and Silvestri, C and Flamand, N and Fernández-Ruiz, J and Di Marzo, V},
title = {Defining the Intestinal eCBome and Oxylipin Signaling Systems in a TDP-43 Mouse Model of Frontotemporal Dementia.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {2},
pages = {e71306},
pmid = {41524247},
issn = {1530-6860},
support = {RTI-2018-098885-B-100//Federación Española de Enfermedades Raras (FEDER)/ ; PID2021-128906OB-I00//Federación Española de Enfermedades Raras (FEDER)/ ; //Canada Excellence Research Chairs, Government of Canada (CERC)/ ; CFREF-2014-00001//UL|Sentinelle Nord, Université Laval (Sentinel North)/ ; },
mesh = {Animals ; Mice ; *Endocannabinoids/metabolism ; Disease Models, Animal ; *Oxylipins/metabolism ; Gastrointestinal Microbiome ; *Frontotemporal Dementia/metabolism/genetics/pathology ; *Signal Transduction ; *DNA-Binding Proteins/genetics/metabolism ; Male ; Mice, Inbred C57BL ; Mice, Transgenic ; },
abstract = {Frontotemporal dementia (FTD) is a group of early onset and progressive disorders, characterized by degeneration in the frontal and temporal lobes, and subsequent deterioration in cognition, personality, social behavior, and language, with aggregates of the RNA-binding protein TDP-43 being present in ~45% of the cases. We reported alterations of the endocannabinoidome (eCBome) in the brain of a TDP-43 mouse model of FTD. Here we investigated the small intestinal eCBome, oxylipins, and, preliminarily, the gut microbiome. The duodenum, jejunum, and ileum of TDP-43 overexpressing versus wildtype mice were investigated. Lipid mediators were measured by HPLC-MS/MS, and mRNA expression of genes involved in eCBome mediator action and metabolism, or intestinal permeability and inflammation, was analyzed by qPCR. Intestinal content microbiota composition and fecal short-chain fatty acids were studied by 16S DNA sequencing and GC-FID, respectively. Alterations were observed in TDP-43 mice for polyunsaturated fatty acids, N-acyl-ethanolamines, and oxylipins in the duodenum and the jejunum, and for oxylipins and 2-monoacylglycerols in the ileum. Regarding the receptors, mRNA expression of Cnr1 and Gpr119 was increased in the ileum, and that of Pparg in the duodenum, where Gpr55 was instead down-regulated. Regarding the enzymes, Faah and Napepld expression was increased in the ileum. Preliminary gut microbiota data suggest increases of Paraprevotella and Monoglobus in the feces, of DNF00809 in the ileum, and of Butyricicoccus, Candidatus_Arthromitus, and Oscillospira in the cecum, where Paraprevotella, Mucispirillum, and Akkermansia were instead decreased. Fecal acetic, butyric, and isobutyric acid were reduced. We suggest the existence of lipid signal-mediated gut-brain interactions in FTD.},
}

Animals
Mice
*Endocannabinoids/metabolism
Disease Models, Animal
*Oxylipins/metabolism
Gastrointestinal Microbiome
*Frontotemporal Dementia/metabolism/genetics/pathology
*Signal Transduction
*DNA-Binding Proteins/genetics/metabolism
Male
Mice, Inbred C57BL
Mice, Transgenic

@article {pmid41524133,
year = {2026},
author = {Santos, YR and Andréo-Filho, N and Lopes, PS and Leite-Silva, VR},
title = {A review of skin microbiome and new challenges to cosmetic microbiome-friendly formulations.},
journal = {International journal of cosmetic science},
volume = {},
number = {},
pages = {},
doi = {10.1111/ics.70073},
pmid = {41524133},
issn = {1468-2494},
abstract = {Human skin is a complex ecosystem that hosts diverse species of microorganisms. Unbalanced conditions caused by intrinsic and/or extrinsic factors can lead to dysbiosis, presenting symptoms, such as dryness, high transepidermal water loss, reduced barrier protection, premature ageing, and in severe cases, inflammatory dermatoses. Strategies to maintain the skin microbiome balance are becoming increasingly suggested, with prebiotic, probiotic, or postbiotic ingredients promoting the diversity and relative abundance of important microorganisms. Topical products directly influence this balance, both traditional ingredients and specific active ingredients. The concentration and combination of these ingredients, as well as the pH of the final product, are extrinsic characteristics that can affect homeostatic skin condition. Focused on repairing or preserving the skin microbiota, microbiome-friendly cosmetics are gaining prominence in the cosmetics industry, with a focus on reducing or replacing ingredients with adverse effects on skin microbiota or adding positive compounds for the microbiota. This review approaches the main characteristics of the skin microbiome, in symbiosis and dysbiosis, elucidates strategies for skin microbiota rebalance, and addresses the challenges of developing microbiome-friendly products through studies of the interaction between skin microbiome and substantial classes of cosmetic ingredients, such as surfactants, lipophilic compounds, preservatives, fragrances, vitamins, and UV filters. The presented findings elucidate the relationship between the host, the skin microbiome, and the use of cosmetics, which could serve as a tool for the development of microbiome-friendly cosmetics. Given the growing popularity of this topic, we also highlight the need for further research focused on the dynamics between the skin microbiome and cosmetic ingredients.},
}

@article {pmid41524110,
year = {2026},
author = {Ogawa, M and Isobe, Y and Uchino, H and Hirayama, M and Kato, T and Negishi, K and Arita, M},
title = {The Microbiome Modulates Corneal Wound Healing via the Induction of Cholesterol Sulfotransferase Pathway.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {2},
pages = {e71429},
pmid = {41524110},
issn = {1530-6860},
support = {JPMJER2101//MEXT, Japan Science and Technology Agency (JST)/ ; 22zf0127007//Japan Agency for Medical Research and Development (AMED)/ ; 21ae0121036//Japan Agency for Medical Research and Development (AMED)/ ; 22KJ3143//MEXT, Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Animals ; *Sulfotransferases/metabolism/genetics ; Mice ; *Wound Healing/physiology/drug effects ; Mice, Knockout ; Humans ; *Microbiota/physiology ; Mice, Inbred C57BL ; *Corneal Injuries/microbiology/metabolism/pathology/drug therapy ; Cholesterol Esters/metabolism ; *Cornea/metabolism/microbiology ; Anti-Bacterial Agents/pharmacology ; Cholesterol/metabolism ; Male ; },
abstract = {The ocular surface is in direct contact with the external environment and is susceptible to injury from dust, dryness, or other foreign objects. Once corneal injury occurs, a local inflammatory response is triggered, followed by effective repair of the epithelial layer. In this study, we demonstrated that antibiotic treatment delayed corneal wound healing in mice. LC-MS/MS-based untargeted lipidomics and qPCR analyses revealed that the levels of cholesterol sulfate (CS) and the CS-synthesizing enzyme SULT2B1 were significantly upregulated by antibiotic treatment, and SULT2B1 knockout mice exhibited accelerated corneal wound healing along with increased recruitment of neutrophils and eosinophils. Topical application of CS delayed corneal wound healing. In vitro scratch assays revealed that CS delayed the wound healing of human corneal epithelial cells, potentially by inhibiting the DOCK2-Rac pathway. These results highlight the role of commensal bacteria in controlling corneal wound healing via the cholesterol-sulfotransferase pathway.},
}

Animals
*Sulfotransferases/metabolism/genetics
Mice
*Wound Healing/physiology/drug effects
Mice, Knockout
Humans
*Microbiota/physiology
Mice, Inbred C57BL
*Corneal Injuries/microbiology/metabolism/pathology/drug therapy
Cholesterol Esters/metabolism
*Cornea/metabolism/microbiology
Anti-Bacterial Agents/pharmacology
Cholesterol/metabolism
Male

@article {pmid41523970,
year = {2025},
author = {Xu, C and Kong, L and Mou, T and Tang, A and Hu, S and Lai, J},
title = {Vitamin B12 and Affective Disorders: A Focus on the Gut-Brain Axis.},
journal = {Alpha psychiatry},
volume = {26},
number = {6},
pages = {49138},
pmid = {41523970},
issn = {2757-8038},
abstract = {Accumulating evidence highlights the role of Vitamin B12 (VitB12) in the pathophysiology of affective disorders. However, its influence on brain function and the underlying mechanisms remain incompletely understood. In humans, VitB12 is obtained solely from dietary sources, primarily animal-based foods. VitB12 deficiency leads to the accumulation of homocysteine, a known contributor to emotional and behavioral dysregulation. VitB12 plays a critical role in maintaining neuron stability, synapsis plasticity, and regulating neuroinflammation by modulating key bioactive factors. These processes help to alleviate hippocampal damage, mitigate blood-brain barrier disruption, reduce oxidative stress, and enhance both structural and functional connectivity-collectively contributing to resilience against affective disorders. VitB12 from both diet and microbial sources is essential to gut homeostasis. Within the gut lumen, it stabilizes gut microbial communities, promotes short-chain fatty acid (SCFA) production, and supports neurotransmitter metabolism (e.g., serotonin and dopamine) via its role in S-adenosyl-l-methionine biosynthesis. Crucially, VitB12, gut microbiota, SCFAs, intestinal mucosa, and vagal nerve signaling interact synergistically within the gut-brain axis (GBA) to maintain gut microenvironment stability, protect the gut-blood barrier, and suppress neuroinflammatory cascades, eventually reducing the susceptibility to affective disorders. This review synthesizes current evidence on the involvement of VitB12 in the GBA, its association with mood regulation, and its potential as a nutritional adjunct in managing affective disorders. By elucidating this integrative mechanism, we provide new insights into targeting the GBA to improve clinical outcomes in affective disorders.},
}

@article {pmid41523930,
year = {2025},
author = {Kanaya, A and Luković, E and Emala, C and Mikami, M},
title = {Effects of chronic allergic lung inflammation on gut microbiota and depression-like behavior in mice.},
journal = {Exploration of asthma & allergy},
volume = {3},
number = {},
pages = {},
pmid = {41523930},
issn = {2837-5076},
support = {K08 HL143052/HL/NHLBI NIH HHS/United States ; },
abstract = {AIM: Emerging epidemiological studies have reported a link between allergic diseases, including asthma, and depression. Evidently, the gut microbiota is involved in the pathogenesis of asthma and depression. Therefore, we investigated whether allergic lung inflammation in mice causes gut microbial dysbiosis, via the gut-brain axis, which is potentially associated with depression.

METHODS: Wild-type C57BL/6J female mice were sensitized with intranasal house dust mite (HDM) antigen or phosphate-buffered saline (PBS) for 6 weeks to induce chronic allergic lung inflammation. Sucrose preference tests were performed for assessing depression. Fecal samples were collected, and 16S ribosomal RNA gene sequencing was performed to detect differences in gut microbiota composition between the HDM and PBS groups. The distance calculation, clustering of operational taxonomic units, rarefaction analysis, and estimator calculation (α- and β-diversity) were performed.

RESULTS: There was a significant difference in β-diversity (Bray-Curtis dissimilarity, F-statistics = 6.16, p = 0.001) of the gut microbiota between HDM and PBS groups. However, there was no difference in the α-diversity. We observed multiple differentially abundant bacteria in the HDM and PBS groups. The order class Clostridia (p = 0.0036) and genus Faecalibaculum (p = 0.028) were more abundant in the HDM group, whereas the phylum Firmicutes (p = 0.037) and genera Dubosiella (p = 0.00024) and Turicibacter (p = 0.037) were more abundant in the PBS group. Notably, the relative abundance of some bacteria was correlated with the sucrose preference test results.

CONCLUSIONS: Six weeks of intranasal HDM administration to mimic the chronic status of lung inflammation in asthma changed the gut microbiome in mice and was associated with depression-like behavioral changes.},
}

@article {pmid41523773,
year = {2025},
author = {Martín Giménez, VM and García Menéndez, S and Sanz, RL and Schiavone, M and Ferder, L and Inserra, F and Manucha, W},
title = {Potential role of nanopharmacology in reducing neuroinflammation associated with hypertension and metabolic disorders.},
journal = {World journal of experimental medicine},
volume = {15},
number = {3},
pages = {106743},
pmid = {41523773},
issn = {2220-315X},
abstract = {Hypertension disrupts cerebral blood flow, leading to endothelial dysfunction, breakdown of the blood-brain barrier (BBB), and inflammatory cell infiltration. This cascade triggers glial cell activation, increases oxidative stress, and causes pro-inflammatory cytokine release, creating a neurotoxic environment. In this context, we explore the intricate connection between hypertension, neuroinflammation, and neurodegeneration, as well as how hypertension interacts with other metabolic disorders, such as obesity and diabetes, to further worsen neuroinflammation. Additionally, we discuss the role of the renin-angiotensin-aldosterone system, the impact of the microbiome, and the potential contribution of chronic infections in exacerbating neuroinflammation. It is essential to emphasize the potential of nanotechnology to transform therapeutic approaches. Nanoparticle-based drug delivery systems can enhance the bioavailability and selectivity of antihypertensive drugs, antioxidants, and neuroprotective compounds, enabling targeted delivery across the BBB. By combining effective blood pressure management with nanotechnology-enabled therapies that modulate inflammation, oxidative stress, and protein aggregation, we can explore new avenues for preventing and treating hypertension and metabolic disorder-associated neurodegenerative conditions. Ultimately, hypertension significantly contributes to neuroinflammation and neurodegeneration by promoting neuronal cell death, primarily through impaired cerebral blood flow and disruption of the BBB. The interaction of hypertension with metabolic disorders exacerbates these effects. However, advancements in our understanding and new technologies reveal promising nanopharmacological approaches for targeted drug delivery to the brain, thereby improving treatment outcomes, enhancing adherence, and reducing side effects.},
}

@article {pmid41523758,
year = {2025},
author = {Khan, AS and Kamthan, M and Ali, A},
title = {Understanding the intricate interactions between microbiota and host.},
journal = {World journal of experimental medicine},
volume = {15},
number = {3},
pages = {101277},
pmid = {41523758},
issn = {2220-315X},
abstract = {The review examines the intricate relationship between the microbiota and its host, highlighting how these microbial communities influence various physiological functions beyond simple coexistence. The microbiota plays a crucial role in regulating the immune system, metabolism, and overall health. We explore the diverse microbial populations inhabiting different body regions and their essential contributions to maintaining balance within the host. Recent research has uncovered molecular mechanisms that govern microbiota-host interactions, offering new insights into how these microbes support health and, conversely, how imbalances known as dysbiosis can increase susceptibility to diseases. While much attention has been given to the gut microbiota, this review also explores the influence of microbes in other parts of the body, including their effects on various organs and tissues. Additionally, we discuss emerging evidence on the gut-brain axis, illustrating how the microbiota can impact brain function and behavior. Understanding this connection could open new possibilities for treating neurological and psychological disorders. Finally, we evaluate microbiota-based therapies such as probiotics and fecal microbiota transplantation, emphasizing the importance of personalized approaches. By integrating findings from multiple disciplines, this review provides a comprehensive perspective on the microbiota's vital role in human health and its potential as a therapeutic target.},
}

@article {pmid41523692,
year = {2026},
author = {Nosal, BM and Aksenov, A and Andersen, C and Lee, EC and Zhou, Y and Chun, OK},
title = {The gut-bone axis: potential influence of anthocyanins and implications for postmenopausal osteoporosis.},
journal = {Food science and biotechnology},
volume = {35},
number = {1},
pages = {13-25},
pmid = {41523692},
issn = {2092-6456},
abstract = {With the aging population worldwide and increased life expectancy, the risk of postmenopausal osteoporosis (PMO) is an increased public health concern. Current treatments for PMO have declined in use over the past decade which has led to an increased focus on finding dietary agents that possess antioxidant and anti-inflammatory properties for prophylaxis and treatment of osteoporosis. Anthocyanins (ACNs) have been shown to exert therapeutic effects in chronic diseases due to their antioxidant and anti-inflammatory properties. ACNs are also thought to be involved in modulating the gut microbiome owing to their prebiotic properties. The gut microbiome has been implicated as a potential target for osteoporosis prevention and treatment since it can modulate immune and endocrine systems, which influence bone metabolism. This review summarizes findings related to ACNs' influence on the gut-bone axis, with a focus on the immune and endocrine systems and potential implications for PMO prevention.},
}

@article {pmid41523651,
year = {2026},
author = {Sitohang, IBS and Legiawati, L and Widaty, S and Nilasari, H and Agustin, T and Chairunnisa, S and Manurung, THP},
title = {Comparative Profile of Microbiome in Normal Skin and Acne Vulgaris Skin Patients.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {1-7},
pmid = {41523651},
issn = {1178-7015},
abstract = {INTRODUCTION: Changes in the skin microbiome are associated with acne vulgaris (AV), a condition characterized by comedones, papules, and pustules. While some bacteria have been studied, many others remain unexplored, highlighting the need to understand the microbiome differences between acne-prone and normal skin. This study aimed to compare skin microbiome profiles between AV patients and healthy individuals and to explore associations with microbial diversity and specific bacterial populations involved in AV pathogenesis.

METHODS: A total of 144 participants were recruited, comprising 36 AV patients and 108 healthy controls. Skin samples were collected from the left cheek after standardized preconditioning. DNA was extracted using the DNeasy PowerSoil Kit™, and the V3-V4 region of 16S rRNA was amplified and sequenced. Microbial diversity was assessed by the Shannon index, and correlations with sebum levels were analyzed.

RESULTS: The results revealed significant differences in microbial diversity, with AV patients exhibiting a markedly lower Shannon index compared to controls, indicating decreased microbial diversity and potential dysbiosis. While the relative abundance of Cutibacterium acnes, a bacterium commonly associated with AV, showed no significant differences between the two groups, the prevalence of Staphylococcus epidermidis was notably higher in AV patients. This suggests that S. epidermidis may play a complex role in the inflammatory processes associated with AV. Moreover, the study identified a negative correlation between microbial diversity and sebum levels, suggesting that increased sebum production may favor the growth of S. epidermidis, potentially exacerbating the condition.

CONCLUSION: These findings highlight the interaction between host factors and microbial composition. This study emphasizes the role of skin microbiome dysbiosis in acne vulgaris and provides insights for future microbiome-based therapeutic strategies. Further research is needed to clarify microbial mechanisms and potential interventions targeting the microbiome in the management of acne vulgaris.},
}

@article {pmid41523287,
year = {2026},
author = {Fang, S and Wang, S and Liu, Y and Zhu, C and Wang, S and Xu, F},
title = {Clinical Safety and Tolerability of Bifidobacterium bifidum BBi32: An 8-Week Randomized, Double-Blind, Placebo-Controlled Trial With Genomic and In Vitro Corroboration.},
journal = {Food science & nutrition},
volume = {14},
number = {1},
pages = {e71420},
pmid = {41523287},
issn = {2048-7177},
abstract = {Bifidobacterium bifidum BBi32, isolated from a healthy infant, underwent a multi-tiered safety assessment to evaluate its genetic features, in vitro properties, and effects on gut microbiota and host biomarkers. Whole-genome sequencing (WGS) and functional annotation were performed alongside in vitro assays assessing acid and bile tolerance, mucin degradation, hemolysis, Caco-2 cytotoxicity, and antibiotic susceptibility. Acute oral toxicity was tested in mice. A randomized, double-blind, placebo-controlled clinical trial (n = 40, 8 weeks) evaluated tolerability and exploratory endpoints, including hematology, liver and renal function, LL-37 levels, gastrointestinal symptom scores, and 16S rRNA-based microbiome profiling. The BBi32 genome comprised a 2.2 Mbp circular chromosome with 99.99% average nucleotide identity to the type strain, no plasmids, and no acquired antimicrobial resistance or virulence genes. Functional categories were enriched for ABC transporters, purine metabolism, and defense mechanisms. BBi32 demonstrated tolerance to acid and bile, lacked mucin-degrading, or hemolytic activity, showed no cytotoxicity to Caco-2 cells, and was susceptible to most antibiotics. Acute toxicity test yielded an LD50 > 2 × 10[10] CFU/kg with no adverse effects. In the clinical trial, daily BBi32 administration (3 × 10[10] CFU) was well tolerated, with no hematological or hepatic abnormalities. Compared with placebo, BBi32 reduced uric acid, urea, and creatinine levels, increased LL-37, and improved gastrointestinal symptom scores. Microbiome analysis revealed higher alpha diversity, distinct community clustering, enrichment of Romboutsia, and predicted functional shifts toward amino acid biosynthesis and peptidase activity. Genomic, in vitro, toxicological, and clinical data collectively indicate that BBi32 meets key safety criteria and favorably modulates host and microbiome biomarkers, supporting its probiotic potential.},
}

@article {pmid41523278,
year = {2026},
author = {Ji, G and Li, C and Yao, Z and Li, Z and Yang, B and Hu, L and Yu, H and Jiang, T and Wang, S and Wang, H},
title = {Therapeutic Potential of Irpex lacteus Polysaccharides in Lupus Nephritis: Insights From Gut Microbiota and Metabolomics Analysis in MRL/Lpr Mice.},
journal = {Food science & nutrition},
volume = {14},
number = {1},
pages = {e71446},
pmid = {41523278},
issn = {2048-7177},
abstract = {Polysaccharides from Irpex lacteus (PCP) were evaluated for their therapeutic effects on lupus nephritis (LN) in MRL/lpr mice. After 8-week interventions with low- and high-dose PCP, we systematically evaluated the therapeutic efficacy by measuring the levels of autoantibodies, the expression of inflammatory cytokines, and renal function-related parameters. Finally, 16S rDNA gut microbiome sequencing with metabolomics analysis was used to explore the pharmacological mechanism of PCP intervention in LN. PCP could reverse the phenotype of MRL/lpr mice, reduce autoantibody levels, alleviate inflammatory responses, and improve renal function. Gut microbiome analysis found that PCP can improve gut microbiota composition and abundance of two phyla (Firmicutes, Bacteroidota) and five genera (Lachnospiraceae NK4A136 group, Alistipes, Butyricicoccus, Bacteroides, Lactobacillus), which play an important role in the process of PCP intervention on metabolism in MRL/lpr mice. UHPLC-MS untargeted metabolomics showed that PCP significantly affects multiple key differential metabolites, including Linoleic acid, L-Phenylalanine, L-Tyrosine, and 56 other metabolites. These metabolites are primarily involved in metabolic pathways such as tryptophan metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, tyrosine metabolism, linoleic acid metabolism, and arachidonic acid metabolism. Correlation analysis between gut microbiota and differential metabolites reveals a close relationship, suggesting that gut microbiota promoting host metabolism may be one of the mechanisms by which PCP treats LN. PCP alleviates LN by modulating the "microbiota-metabolism axis," reducing autoantibodies, inflammation, and renal damage, while reshaping gut microbiota and regulating key metabolic pathways.},
}

@article {pmid41523242,
year = {2025},
author = {Qi, W and Tian, L and Li, Z and Xu, J and Wang, T},
title = {Pathogen spectrum and management strategies for opportunistic infections in lung cancer in the immunotherapy era: recent advances from fungi to mycobacteria.},
journal = {American journal of cancer research},
volume = {15},
number = {12},
pages = {5140-5167},
pmid = {41523242},
issn = {2156-6976},
abstract = {Lung cancer is one of the most common cancers and the leading cause of cancer death worldwide. Opportunistic infections (OI) are increasingly recognized in this population due to disease-related immune dysfunction and treatment-induced immunosuppression. Compared with the chemotherapy era, the use of immune checkpoint inhibitors and targeted agents has shifted the OI profile. Pneumocystis jirovecii pneumonia (PJP) and invasive pulmonary aspergillosis (IPA) are reported more often in older adults and patients with lymphopenia, while tuberculosis (TB) and nontuberculous mycobacteria (NTM) cluster in those with structural lung disease (e.g., bronchiectasis, cavities) and prolonged immunosuppression. High-risk features include absolute lymphocyte count <500/µL, corticosteroids ≥20 mg prednisone-equivalent for ≥4 weeks, airway obstruction, prior TB, chronic obstructive pulmonary disease/interstitial lung disease (ILD), and recent broad-spectrum antibiotics. Diagnosis should integrate high-resolution computed tomography (HRCT) patterns (e.g., diffuse ground-glass for PJP; nodules with halo sign for IPA), microbiology [bronchoalveolar lavage fluid (BALF) culture/microscopy, galactomannan (GM)/β-D-glucan (BDG)], and metagenomic next-generation sequencing, interpreted against host factors and treatment timeline, while carefully distinguishing immune-related pneumonitis and TKI-associated ILD. Prophylaxis with TMP-SMX is recommended for high-risk patients; voriconazole (or isavuconazole) is first-line for IPA with attention to drug-drug interactions; TB/NTM regimens require coordination with anticancer therapy, especially where rifamycins interact with TKIs. Vaccination (influenza, pneumococcus, zoster) and antimicrobial stewardship are essential. Future work should validate risk scores prospectively and clarify microbiome-immunotherapy-infection relationships.},
}

@article {pmid41523241,
year = {2025},
author = {Wang, Y and Sun, W and Li, H and Xu, F and Cui, W},
title = {Decoding the metastatic nexus: how chronic stress reprograms neuroendocrine-metabolic-microbiome circuits to fuel tumor metastasis.},
journal = {American journal of cancer research},
volume = {15},
number = {12},
pages = {5058-5083},
pmid = {41523241},
issn = {2156-6976},
abstract = {Metastasis, the leading cause of death in patients with solid tumors, involves the spread of cancer cells to distant organs. While genetic and environmental factors contribute, chronic stress is a crucial factor in metastatic progression by disrupting neuroendocrine, immune, metabolic, and microbial homeostasis. This review synthesizes evidence linking chronic stress to tumor metastasis through three pathways: (1) direct effects on tumor cell metabolism, (2) remodeling of the tumor microenvironment, and (3) dysregulation of the gut microbiota. Describe how activation of the hypothalamic-pituitary-adrenal axis and sympathetic nervous system influence epithelial-mesenchymal transition, immune evasion, and angiogenesis via β-adrenergic and glucocorticoid receptor signaling. Explore how microbial metabolites and barrier dysfunction influence immune and neuroendocrine circuits, creating a pro-metastatic loop. Finally, we highlight therapeutic strategies, including psychological interventions and pharmacologic approaches, to alleviate chronic stress. This review proposes a mechanistic framework linking neuroendocrine signaling, metabolic reprogramming, and the microbiome-immune axis.},
}

@article {pmid41523132,
year = {2025},
author = {Arita, R},
title = {Targeted therapies for meibomian gland dysfunction - The role of antibiotics in meibomian gland dysfunction management.},
journal = {Taiwan journal of ophthalmology},
volume = {15},
number = {4},
pages = {516-525},
pmid = {41523132},
issn = {2211-5072},
abstract = {Meibomian gland dysfunction (MGD) is a leading cause of evaporative dry eye, significantly impairing the quality of life. Bacterial proliferation and inflammation play central roles in the pathogenesis of MGD, creating a vicious cycle of gland obstruction and ocular surface instability. Antibiotics, particularly tetracyclines (e.g. doxycycline and minocycline), and macrolides (e.g. azithromycin and erythromycin), are widely used as adjunctive therapy for moderate-to-severe or refractory MGD. This review conducted a comprehensive literature search of PubMed, focusing on original peer-reviewed articles published in English that reported on the efficacy and/or safety of oral or topical antibiotics for MGD or blepharitis. Eligible studies were identified using the specific search terms, screened by title and abstract, and selected based on predefined inclusion and exclusion criteria. Relevant data were extracted and synthesized, with an emphasis on randomized controlled trials and comparative studies. The review indicates that both oral and topical antibiotics improve subjective symptoms, tear film stability, ocular surface staining, meibum quality, and lid margin abnormalities in the short term. Oral azithromycin may be at least as effective as doxycycline, with a shorter treatment course and fewer adverse events, while topical azithromycin offers similar or superior efficacy to systemic regimens with reduced systemic exposure. However, benefits are usually limited to active treatment periods, and optimal dosing and duration remain uncertain. Long-term efficacy, safety, risk of resistance, and effects on the ocular microbiome require further investigation. Antibiotics should be used judiciously as part of a comprehensive, individualized management strategy for MGD.},
}

@article {pmid41523060,
year = {2025},
author = {Agrawal, R and Shah, M and Srivastava, V and Naik, SR and Patel, NR and Dwivedy, S and Mehta, M and Patel, BJ and Makkad, RS},
title = {An In vitro Study of the Isolation of Candidal Strains in Patients at Increased Risk of Oral Squamous Cell Carcinoma.},
journal = {Journal of pharmacy & bioallied sciences},
volume = {17},
number = {Suppl 4},
pages = {S2870-S2872},
pmid = {41523060},
issn = {0976-4879},
abstract = {BACKGROUND: OSCC stands as a prominent oral malignancy that develops because of lifestyle behavior and microbial activity. The pathogenesis of OSCC receives attention through modern research since Candida species reportedly contribute to the development of OSCC through inflammatory responses and nitrosamine generation and epithelial tissue malformation.

MATERIALS AND METHODS: Sixty subjects participated in this in vitro study, which was separated into two distinct groups: Group A with 30 patients who had high OSCC risk oral lesions (leukoplakia and erythroplakia) and Group B which included 30 healthy subjects. A laboratory research involved collecting samples through swabs from saliva and mucosa, which were subsequently cultured on Sabouraud Dextrose Agar (SDA) alongside CHROMagar for fungal detection. The researchers identified isolated colonies by checking their ability to form germ tubes combined with carbohydrate assimilation tests.

RESULTS: Out of the 30 Group A samples, 80% (24/30) demonstrated candidal growth where Candida albicans constituted 70.8% of strains and Candida tropicalis made up 16.7% alongside Candida glabrata counting for 12.5%. The overall candidal growth among participants in Group B was limited to 30% (9/30) as C. albicans constituted 88.9%, whereas C. glabrata accounted for 11.1%. The incidence of candidal colonization proved markedly higher among the high-risk group compared to controls according to statistical analysis (P = 0.002).

CONCLUSION: The numbers of Candida species, particularly C. albicans, rise substantially within the oral environments of patients dealing with potentially malignant disorders. The obtained data support the possibility that oral cancer development may be related to candidal colonization, thus demanding additional studies on this association.},
}

@article {pmid41523026,
year = {2025},
author = {Sahu, M and Agarwal, G and Jain, G and Saad, T and Qureshi, MA and Mishra, S},
title = {Determination of Gut Microbiome Patterns Associated with Developing Active Tuberculosis in a Case-Control Study.},
journal = {Journal of pharmacy & bioallied sciences},
volume = {17},
number = {Suppl 4},
pages = {S3069-S3071},
pmid = {41523026},
issn = {0976-4879},
abstract = {BACKGROUND: The gut microbiome plays a critical role in modulating systemic immunity and may influence susceptibility to infectious diseases, such as tuberculosis (TB). This study aimed to compare gut microbial profiles between individuals with active pulmonary TB and healthy controls to identify potential microbial signatures associated with disease development.

METHODS: A hospital-based case-control study was conducted with 90 participants: 45 treatment-naïve TB patients and 45 healthy controls. Stool samples were collected and analyzed using 16S rRNA sequencing. Microbial diversity was assessed using the Shannon index, and relative abundances of key bacterial phyla were compared. Statistical analysis included Mann-Whitney U tests and LEfSe for differential taxa identification.

RESULTS: TB patients showed significantly lower alpha diversity (Shannon index: 2.91 ± 0.37) compared to controls (3.81 ± 0.28, P < 0.001). The relative abundance of Proteobacteria was significantly higher in TB cases, while Firmicutes and Bacteroidetes were more abundant in controls. These findings indicate a pro-inflammatory gut microbiota shift in active TB.

CONCLUSION: Active tuberculosis is associated with gut microbial dysbiosis, marked by reduced diversity and altered bacterial composition. These microbial signatures could aid in early diagnosis and serve as future targets for microbiome-based interventions.},
}

@article {pmid41522762,
year = {2025},
author = {Yang, H and Liu, X and Yuan, D and Li, H and Mu, X},
title = {A prognostic nomogram for colorectal cancer: integrating blood microbiome and clinical factors.},
journal = {Journal of gastrointestinal oncology},
volume = {16},
number = {6},
pages = {2651-2663},
pmid = {41522762},
issn = {2078-6891},
abstract = {BACKGROUND: The microbiota is pivotal in colorectal cancer (CRC), yet the prognostic value of the blood microbiome and its utility in clinical prediction models remain poorly explored. This study aims to develop a blood microbiome-associated prognostic score (MAPS) that integrates blood microbiome data with clinical factors to improve the accuracy of CRC prognosis prediction and enhance our understanding of the tumor microenvironment (TME).

METHODS: We analyzed whole-genome and transcriptomic sequencing data of CRC patients from The Cancer Genome Atlas (TCGA). A MAPS was developed from blood microbiome data using the least absolute shrinkage and selection operator (LASSO) Cox regression algorithm. A nomogram integrating MAPS and key clinical factors was constructed to predict overall survival (OS). Its predictive accuracy was validated via time-dependent receiver operating characteristic (ROC) analysis, yielding area under the curve (AUC) values for 1-, 3-, and 5-year OS. Underlying mechanisms were investigated through gene set enrichment analysis (GSEA) and immune cell infiltration estimation from matched RNA sequencing (RNA-seq) data.

RESULTS: The MAPS, comprising seven key blood microbes, was an independent prognostic factor. The integrative nomogram demonstrated robust predictive performance, with AUCs of 0.800, 0.805, and 0.755 for predicting 1-, 3-, and 5-year OS, respectively. Mechanistically, the high-MAPS subgroup exhibited enriched pro-tumorigenic pathways (e.g., inflammatory response, hypoxia) and an immunosuppressive TME characterized by increased Treg cell infiltration. We further identified S100A8 and PROK2 as potential therapeutic targets.

CONCLUSIONS: Our study delivers a validated prognostic nomogram based on the blood microbiome and elucidates its link to an immunosuppressive TME, highlighting its dual utility in patient stratification and target discovery.},
}

@article {pmid41522496,
year = {2026},
author = {Gedam, PA and Khandagale, K and Barvkar, VT and Bhandari, S and Patil, S and Wayal, S and Bhangare, I and Bhagat, KP and Landage, K and Kale, R and Bhoite, V and More, S and Mahajan, V and Gawande, S},
title = {Microbial allies: shaping growth, physiology, and rhizosphere dynamics of onion (Allium cepa L.).},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20566},
pmid = {41522496},
issn = {2167-8359},
mesh = {*Rhizosphere ; *Onions/microbiology/growth & development/physiology ; *Soil Microbiology ; Fertilizers ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {The present study investigates the dual impact of microbial biofertilizers on the phenotypic performance and rhizosphere microbiome composition in an onion crop. A pot experiment was conducted with seven treatments of microbial inoculants, such as Azotobacter, Azospirillum, Piriformospora indica, phosphate solubilizing bacteria (PSB), and control treatments with and without chemical fertilizers. The growth, physiological, and biochemical traits of onion were assessed alongside rhizospheric soil microbiome profiling using 16S rRNA metagenomic sequencing. Significant enhancement in plant height, leaf number, leaf area, chlorophyll content, photosynthetic rate, and antioxidant enzyme activity with low leaf temperature was observed in plants inoculated with Azotobacter and Azospirillum. Notably, the Azotobacter treatment yielded a significant enhancement in the bulb phenol content. Rhizosphere metagenomic analysis revealed 17 dominant phyla, with Actinobacteria (25.3%), Proteobacteria (22.2%), Firmicutes (12.8%), and Chloroflexi (11.02%) comprising over 70% of the total microbiome. Alpha and beta diversity metrics indicated that microbial inoculation, especially with Azospirillum and PSB, enriched the soil microbial community structure. Distinct clustering and correlations with specific microbial taxa such as Candidatus Nitrososphaera and Pseudomonas were observed in response to individual biofertilizer treatments. This study highlights the potential of biofertilizers not only in enhancing onion growth and development but also in modulating beneficial rhizosphere microbial communities. Integrating biofertilizers into onion production systems could reduce the dependency on chemical fertilizers and promote sustainable crop management.},
}

*Rhizosphere
*Onions/microbiology/growth & development/physiology
*Soil Microbiology
Fertilizers
*Microbiota
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification

@article {pmid41522492,
year = {2026},
author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R},
title = {Cross-sectional comparative shotgun metagenomic analysis of the subgingival resistome in healthy subjects and patients with periodontitis from four countries.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2610588},
pmid = {41522492},
issn = {2000-2297},
abstract = {BACKGROUND: The oral cavity is a known reservoir of antibiotic resistance genes (ARGs), but little is known about their subgingival distribution across health states and regions.

OBJECTIVE: This study aimed to characterize and compare the subgingival resistome and mobile genetic elements (MGEs) in healthy subjects (HS) and periodontitis patients (PP) from Belgium, Chile, Peru and Spain.

DESIGN: Subgingival samples pooled from the deepest site of each quadrant of 40 HS and 40 PP were analyzed via shotgun metagenomic sequencing. After human DNA depletion, the microbial composition was assessed with MetaPhlAn 4.0; ARGs were identified using MEGAHIT and AMRFinderPlus; and MGEs with MGEfinder.

RESULTS: ARG richness was significantly higher in PP (mean 3.98) than in HS (2.15). PP from Peru showed more ARGs than HS from Chile and Spain. In total, 28 ARGs were found, conferring resistance to eight antibiotic classes. β-lactam, tetracycline and aminoglycoside resistance were more abundant in PP. Macrolide resistance was lower in Chilean samples than in Peruvian and Spanish ones. Additionally, 99 MGE-associated genes were detected, with 16 differing by diagnosis and 78 by country.

CONCLUSIONS: Subgingival resistome profiles vary significantly by periodontal status and geography, underscoring the influence of clinical and regional factors on antimicrobial resistance in the oral microbiome.},
}

@article {pmid41522487,
year = {2026},
author = {Al Qassab, M and Chaarani, N and Hamou, A and Harb, R and Jradi, A and Zeineddine, M and Ghadieh, HE and Khattar, ZA and Azar, S and Kanaan, A and Harb, F},
title = {The Gut Microbiota-Insulin Resistance Axis: Mechanisms, Clinical Implications, and Therapeutic Potential.},
journal = {FASEB bioAdvances},
volume = {8},
number = {1},
pages = {e70080},
pmid = {41522487},
issn = {2573-9832},
abstract = {Emerging evidence highlights the pivotal role of the gut microbiota (GM) in regulating host metabolism and contributing to the development of insulin resistance (IR). Gut dysbiosis alters the production of critical metabolites, including short-chain fatty acids (SCFAs), bile acids, indole derivatives, and trimethylamine N-oxide (TMAO), which influence intestinal barrier integrity, inflammatory pathways, and glucose homeostasis. Recent clinical and translational studies indicate that SCFAs can improve fasting insulin and HOMA-IR, although the magnitude of benefit varies substantially across individuals, highlighting ongoing controversy surrounding their metabolic effects. Altered microbial regulation of bile-acid metabolism has also been implicated in impaired lipid and glucose signaling, reinforcing the relevance of FXR- and TGR5-mediated pathways in IR. Elevated TMAO levels have further been associated with adverse metabolic outcomes, though debate persists regarding its causal role versus its function as a diet-dependent biomarker. Microbiota-targeted strategies, including dietary fiber, probiotics, and fecal microbiota transplantation (FMT), show potential to modulate these metabolic pathways, yet clinical results remain inconsistent. This narrative review synthesizes recent mechanistic discoveries and clinical findings on microbiota-derived metabolites in IR, highlights key controversies, and outlines future priorities for translating microbiome science into effective and personalized interventions for metabolic disease prevention and management.},
}

@article {pmid41522466,
year = {2026},
author = {Jain, V},
title = {Gut microbiome in biliary atresia.},
journal = {World journal of pediatric surgery},
volume = {9},
number = {1},
pages = {e001068},
pmid = {41522466},
issn = {2516-5410},
abstract = {Biliary atresia (BA) is a progressive cholangiopathy of infancy and the leading cause of pediatric liver transplantation. Despite surgical intervention with the Kasai portoenterostomy, long-term outcomes remain poor, with many patients progressing to cirrhosis. Emerging evidence implicates the gut microbiota-a dynamic ecosystem crucial to immune development and liver homeostasis-in BA pathogenesis and clinical progression. This review synthesizes current literature on gut microbiota composition in BA before and after the Kasai procedure, highlighting consistent patterns of dysbiosis, including pathobiont expansion and depletion of beneficial microbes such as Bifidobacterium. The review explores associations between microbial profiles and clinical outcomes-highlighting potential mechanisms involving bile acid metabolism, microbial translocation, and immune modulation. Further understanding of gut-liver-microbiota interactions in BA may inform microbiome-targeted therapies to improve native liver survival.},
}

@article {pmid41522445,
year = {2025},
author = {Glazunova, E and Molodtsova, P and Grabarnik, I and Kurnosov, A and Bikaeva, I and Shipulin, G and Zlobovskaya, O},
title = {Healthy human gut microbiome: Towards standardized research.},
journal = {AIMS microbiology},
volume = {11},
number = {4},
pages = {786-820},
pmid = {41522445},
issn = {2471-1888},
abstract = {OBJECTIVE: An increasing number of international researchers are focusing on the taxonomic composition of fecal microbiota and its correlation with disorders. Thousands of researchers compare conditionally healthy cohorts to those with specific diseases to identify potential markers. However, clinical application requires assessing the feasibility of synthesizing these findings and establishing reference intervals for normal gut flora, at least at higher taxonomic levels.

DESIGN: This study involves a systematic review and meta-analysis of human gut microbiota research based on 16S rRNA gene next-generation sequencing (NGS). Relevant research was sourced following the PRISMA guidelines. Descriptive statistics, linear regression analysis by weighted least squares method, Mann-Whitney test, and Benjamini-Hochberg procedure adjustments were employed. The study has been registered with PROSPERO (CRD42023431467).

RESULTS: Of the 4,346 studies initially identified, 86 publications involving 20,748 unique participants met the quality criteria and were included in the analysis of the impact of fecal sample preparation on taxonomic composition. The phylotype composition, in relation to preprocessing methods and cohort locations, are presented as relative abundances (%): Bacillota (median 49.5-59.6%), Bacteroidota (28.0-33.4%), Pseudomonadota (3.4-5.9%), Actinomycetota (2.3-3.7%), Verrucomicrobiota (0.5-1.0%), Fusobacteriota (maximum 4.6%), and Euryarchaeota (maximum 2.11%). The content of 27 key family-level representatives was also evaluated. The well-known hypothesis regarding the influence of the homogenization stage on taxonomic composition was examined using generalized results.

CONCLUSION: While supported by a strong theoretical basis and evidence from individual practical cases, none of the phyla showed a statistically significant association and consistent relationship with sample preparation or cohort location when generalizing across studies after the two exceptionally large cohorts exclusion, both originating from a single research group. These findings underscore the need for strict methodological standardization in microbiome studies. Key features of the 16S NGS process accounting for these results are outlined, along with proposed optimizations for microbiome research.},
}

@article {pmid41522435,
year = {2025},
author = {Zalila-Kolsi, I},
title = {Engineered bacteria as living therapeutics: Next-generation precision tools for health, industry, environment, and agriculture.},
journal = {AIMS microbiology},
volume = {11},
number = {4},
pages = {946-962},
pmid = {41522435},
issn = {2471-1888},
abstract = {Synthetic biology has revolutionized precision medicine by enabling the development of engineered bacteria as living therapeutics, dynamic biological systems capable of sensing, responding to, and functioning within complex physiological environments. These microbial platforms offer unprecedented adaptability, allowing for real-time detection of disease signals and targeted therapeutic delivery. This review explores recent innovations in microbial engineering across medical, industrial, environmental, and agricultural domains. Key advances include CRISPR-Cas systems, synthetic gene circuits, and modular plasmid architectures that provide fine-tuned control over microbial behavior and therapeutic output. The integration of computational modeling and machine learning has further accelerated design, optimization, and scalability. Despite these breakthroughs, challenges persist in maintaining genetic stability, ensuring biosafety, and achieving reproducibility in clinical and industrial settings. Ethical and regulatory frameworks are evolving to address dual-use concerns, public perception, and global policy disparities. Looking forward, the convergence of synthetic biology with nanotechnology, materials science, and personalized medicine is paving the way for intelligent, responsive, and sustainable solutions to global health and environmental challenges. Engineered bacteria are poised to become transformative tools not only in disease treatment but also in diagnostics, biomanufacturing, pollution mitigation, and sustainable agriculture.},
}

@article {pmid41522308,
year = {2025},
author = {Henry, GD and Diaz, N and Phillips, CD and Lentz, AC and Perito, P and Natale, R and Bennett, N and Stuart, AR and Henry, CJ and Chung, PH},
title = {Methods and early findings from a study comparing next-generation sequencing versus traditional cultures for penile implants concerning for low-grade infection.},
journal = {Translational andrology and urology},
volume = {14},
number = {12},
pages = {3945-3951},
pmid = {41522308},
issn = {2223-4691},
abstract = {Microbial culture is the current standard of care to choose therapeutic antibiotics for infection occurring with inflatable penile prostheses (IPPs). However, next-generation sequencing (NGS) of DNA has proven beneficial for analysis of biofilm composition and relative abundance of specific microorganisms. The main goal of this study is to evaluate whether NGS compared to microbial culture can better guide the management and antibiotic selection and device survival rates. We hypothesize that identifying microbial composition with NGS, as compared with traditional culture, will lead to better therapeutic strategies resulting in improved patient outcomes and device survival. In this present manuscript, we describe the overall study methodology and analyze device survival rates, classify clinical presentations of IPP infections, and determine infected implant microbial composition and antibiotic resistance among an early patient cohort. These early results included 18- to 80-year-old consecutive male patients who received antimicrobial treatment without surgical replacement for at least 7 days since identification of infected IPPs. Subjects were randomized into two analytic arms: traditional culture and NGS. Throughout the study, investigators and patients completed questionnaires to provide data for comparison. To date, of the 9 patients enrolled in the study, 6 eventually underwent device removal due to worsening infection within 7 days of initiating empiric antibiotic treatment. Six patients were seen in a clinic setting, while 3 were seen in the hospital/emergency department: 7 implants were primary, while 2 were secondary. All subjects received a Coloplast IPP but had differing reservoirs and reservoir locations. In cases where penile shaft tenderness was present, the implanted IPP was more often removed within 7 days. In contrast, when no tenderness was reported, the device remained viable for at least 10 days. As of this report, 11 active sites have participated in the study, with ongoing patient enrollment aimed at reaching sufficient sample sizes for statistical comparison. Penile shaft tenderness was a common presentation among patients whose early antibiotic treatment for IPP infection failed. Recruitment of additional patients to this prospective, randomized controlled trial will help to identify favorable presentations of IPP infection. Additional data will allow comparison of implantation outcomes between NGS and traditional culture.},
}

@article {pmid41521788,
year = {2026},
author = {Hernandez-Rovira, B and Villamaria, E and Oh, J and Ozarslan, B and Wyles, S},
title = {Topical Carboxytherapy Modulates the Skin Microbiome Following CO2 Laser Resurfacing: A Pilot Study.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {1},
pages = {e70668},
doi = {10.1111/jocd.70668},
pmid = {41521788},
issn = {1473-2165},
support = {//Lumisque Skincare, LLC/ ; },
}

@article {pmid41521690,
year = {2026},
author = {Bailey, AM and Hofseth, LJ},
title = {Microplastics in Early Onset Carcinogenesis.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgaf093},
pmid = {41521690},
issn = {1460-2180},
abstract = {Plastics have become integral to modern life, but their persistence has generated vast quantities of microplastics (MPs, <5 mm) and nanoplastics (NPs, <1 µm) that now contaminate food, water, air, and human tissues. Although not yet classified as carcinogens by the International Agency for Research on Cancer, accumulating experimental and epidemiologic evidence raises concern that MPs may contribute to cancer development. Global plastic production has risen from 2 megatons in 1950 to more than 450 megatons annually in 2022, leaving behind pervasive waste that fragments into MPs and NPs. These particles act as xenobiotics, carrying toxic additives and adsorbed pollutants, provoking oxidative stress, chronic inflammation, DNA damage, and microbiome disruption; all processes central to carcinogenesis. MPs have been detected in human cancers, and animal studies show tissue accumulation, fibrosis, and genomic instability following exposure. Importantly, the proliferation of plastics parallels a global rise in early-onset cancers (diagnosed before age 50), suggesting a possible, though unproven, temporal association. Individuals born after the 1950s plastic boom have experienced continuous MP exposure beginning in utero, potentially predisposing them to carcinogenic pathways later in life. In this review, we integrate human biomonitoring data, experimental findings, and clinical observations to evaluate the emerging hypothesis that chronic MP exposure contributes to cancer risk. While causality has not been established, the biological plausibility and mounting evidence underscore the urgent need for mechanistic and epidemiologic studies to clarify the role of MPs and NPs in cancer development. It also underscores an urgent need for research into causal pathways and preventive mechanisms.},
}

@article {pmid41521588,
year = {2026},
author = {Alolod, GAL and Guzman, JPMD and Bermeo-Capunong, MRA and Konishi, K and Koiwai, K and Kondo, H and Hirono, I},
title = {Metagenomic Insights on the Progression of White Muscle Disease in Kuruma Shrimp (Penaeus japonicus) Caused by Photobacterium damselae subsp. damselae.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70117},
doi = {10.1111/jfd.70117},
pmid = {41521588},
issn = {1365-2761},
support = {22H00379//Japan Society for the Promotion of Science/ ; JPMJSA1806//Japan Science and Technology Agency/ ; },
abstract = {Kuruma shrimp (Penaeus japonicus) is an economically important shrimp perennially affected by diseases. In 2022, White Muscle Disease (WMD) was first characterised in this Penaeid species, caused by Photobacterium damselae subsp. damselae (Pdd). In this study, muscular and gut microbiome dynamics and their function in the disease progression are investigated by 16S rRNA metagenome sequencing using Illumina sequencing technologies. Alpha diversity indices showed that Pdd infection in the muscle, stomach, and intestine did not significantly change bacterial diversity between control and infected groups at all time points observed (Days 0, 1, 3, 5, 7 and 10). In the infected samples, the Shannon and Simpson indices increased starting Day 5 (D5), in congruence with the first observation of muscle whitening. Bacterial composition for the infected group at the genus level revealed that Photobacterium and Vibrio have increased their relative abundance in the muscle at Day 5 (D5) until Day 7 (D7), but declined at Day 10 (D10). As for stomach samples, Photobacterium declined in abundance and later increased significantly at Day 7 (D7). Photobacterium in the intestinal samples from the infected group increased at Day 5 (D5) but later decreased at Day 7 (D7). Meanwhile, linear discriminant analysis Effect Size (LEfSe) identified that most taxa belong to phylum Pseudomonadota, which can be potential markers for WMD. Moreover, the temporal dynamics of the amplicon sequencing variant ASV2, confirmed to be 100% homologous to the WMD-P3 strain used in this study, were characterised. For all tissues, the logarithmic relative abundance is considered high and very apparent in infected samples collected at Day 7 (D7). Overall, our study provides an understanding of the muscle and gut microbial community, specifically at the genus level, distinguished between WMD-infected and healthy Kuruma shrimps.},
}

@article {pmid41521409,
year = {2025},
author = {Lindsay, J and Yeoh, D and Teh, BW and Reynolds, GK and Henden, A and McQuilten, Z and Wheeler, M and Hamilton, A and Nelson, A and Nakagaki, M and Sandhu, S and Slavin, MA and , },
title = {Consensus guidelines for antibacterial prophylaxis in patients with neutropenia.},
journal = {Internal medicine journal},
volume = {55 Suppl 7},
number = {},
pages = {115-135},
doi = {10.1111/imj.70250},
pmid = {41521409},
issn = {1445-5994},
mesh = {Humans ; *Antibiotic Prophylaxis/standards/methods ; *Neutropenia/drug therapy/chemically induced ; *Anti-Bacterial Agents/therapeutic use ; *Consensus ; Australia/epidemiology ; Neoplasms/drug therapy ; *Practice Guidelines as Topic/standards ; },
abstract = {Since the publication of the Australian consensus guidelines in 2011, the routine use of prophylactic antibiotics in patients with neutropenia has remained controversial, because of concern that the risks of promoting antimicrobial resistance outweighed the level of evidence that their use reduced mortality. Populations at risk have changed over this period and now include a multitude of new cancer therapies, such as targeted cancer therapies and immunotherapies. Emerging understanding about the importance and role of the microbiome in defining treatment response and patterns of antibiotic resistance has also expanded. In addition, the management of neutropenic fever has improved significantly through the development and routine implementation of sepsis pathways. These updated consensus guidelines review recent evidence for the use of antibacterial prophylaxis in adults and children receiving cancer therapies associated with neutropenia. Recommendations presented in these guidelines were based on evaluating current evidence for the benefits and harms of antibacterial prophylaxis while considering the current Australian and New Zealand healthcare setting. In most circumstances, the potential harm of antibiotic resistance, adverse effects of antibiotics and disruption to the microbiome, outweighed the benefit of reducing the incidence of infection, without a benefit in mortality.},
}

Humans
*Antibiotic Prophylaxis/standards/methods
*Neutropenia/drug therapy/chemically induced
*Anti-Bacterial Agents/therapeutic use
*Consensus
Australia/epidemiology
Neoplasms/drug therapy
*Practice Guidelines as Topic/standards

@article {pmid41521406,
year = {2025},
author = {Douglas, AP and Cooley, L and McMullan, B and Kinsella, P and Laundy, N and Yap, N and Bupha-Intr, O and Alcorn, K and Bajel, A and Weinkove, R and Legg, A and Roberts, JA and Trubiano, JA and Conyers, R and Thursky, KA and , },
title = {Consensus guidelines for initial management of neutropenic fever.},
journal = {Internal medicine journal},
volume = {55 Suppl 7},
number = {},
pages = {43-67},
doi = {10.1111/imj.70248},
pmid = {41521406},
issn = {1445-5994},
mesh = {Humans ; *Consensus ; *Neutropenia/therapy/diagnosis ; *Anti-Bacterial Agents/therapeutic use ; *Fever/diagnosis/therapy/etiology/drug therapy ; *Disease Management ; *Practice Guidelines as Topic/standards ; Adult ; },
abstract = {This update of the Australasian consensus guidelines for the initial empiric management of neutropenic fever occurs in the context of major changes in cancer treatment paradigms, as well as advances in the management of sepsis and new models of care for infections since the last version of these guidelines in 2011. Acknowledging the important role of antimicrobials in the disruption of the gut microbiome and emerging antimicrobial resistance, as well as the changing epidemiology of antimicrobial resistance more broadly, these guidelines address current evidence for optimal empiric neutropenic fever therapy. A writing group - including adult and paediatric representatives across infectious diseases, microbiology, haematology, transplant and oncology, as well as across craft groups, including medicine, nursing and pharmacy - was developed to produce and address key management questions. This was overseen by a steering committee, which included consumer representation. Using an extensive review of the literature, these guidelines provide consensus recommendations with evidence grading for initial empiric management of neutropenic fever in adults and children, including recommended investigations, antimicrobial therapy and approach to patients with beta-lactam allergy or risk factors for multidrug-resistant infection. Management beyond the first 72 h is discussed in separate chapters of this issue: the Subsequent Management (for high-risk neutropenic fever) and Ambulatory Management (for low-risk neutropenic fever) chapters.},
}

Humans
*Consensus
*Neutropenia/therapy/diagnosis
*Anti-Bacterial Agents/therapeutic use
*Fever/diagnosis/therapy/etiology/drug therapy
*Disease Management
*Practice Guidelines as Topic/standards
Adult

@article {pmid41521300,
year = {2026},
author = {Deng, W and Chen, D and Wei, Y and Chen, W and Chen, K and Zhong, H and He, X},
title = {Washed microbiota transplantation relieves atopic dermatitis via gut-skin microbiome rebalancing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04717-1},
pmid = {41521300},
issn = {1471-2180},
support = {2022B1111070006//Key-Area Research and Development Program of Guangdong Province/ ; 82300440//National Natural Science Foundation of China Youth Program/ ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease in which dysbiosis of gut and skin microbiota contributes to pathogenesis and severity. Washed microbiota transplantation (WMT)-an improved form of fecal microbiota transplantation with enhanced safety and microbiota quality control-has shown efficacy in a single reported adolescent case. However, clinical data on WMT in AD and its effects on the skin and gut microbiota remain limited.

METHODS: Twenty-three patients with moderate-to-severe AD received at least two courses of WMT between January 2022 and December 2023. Disease activity was evaluated using the SCORing Atopic Dermatitis (SCORAD) index, the Eczema Area and Severity Index (EASI), the Numeric Rating Scale (NRS) for itch, and the Dermatology Life Quality Index (DLQI). Peripheral blood counts, cytokine profiles, lymphocyte subsets, and gut and skin microbiota were assessed before and after treatment.

RESULTS: WMT was well tolerated (58 sessions; 5.2% mild adverse events) and significantly improved SCORAD, EASI, DLQI, and NRS scores, with greater EASI reductions in adults than in children. Absolute basophil counts decreased significantly after treatment, whereas other hematologic and cytokine parameters remained stable. Gut microbiota showed an increased Gut Microbiome Health Index, a decreased Microbial Dysbiosis Index, and enrichment of short-chain fatty acid-producing taxa, including the Eubacterium coprostanoligenes group, Lachnospiraceae, and Coprococcus. Skin microbiota shifted from Staphylococcus dominance to higher abundances of Acinetobacter, Perlucidibaca, and other potentially protective genera, inversely correlating with disease severity and systemic inflammation.

CONCLUSIONS: WMT appears safe and effective in alleviating clinical manifestations of AD while reshaping both gut and skin microbiota. These parallel microbial shifts support the gut-skin axis as a therapeutic target and highlight WMT as a promising microbiota-centered intervention for immune-mediated skin diseases.},
}

@article {pmid41521238,
year = {2026},
author = {Zhoua, J and Leia, K and Zhang, P and Wang, Z and Wang, W},
title = {Probiotics regulate the intestinal microbiome to promote growth in juvenile Salmo trutta fario.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35054-y},
pmid = {41521238},
issn = {2045-2322},
support = {CARS-46//China Agriculture Research System of Specialty Freshwater Fish/ ; },
}

@article {pmid41521228,
year = {2026},
author = {Sharma, S and Seekatz, A and Alizadeh, M and Hassan, H and Yitabrek, A and Pratt, S and Abdelaziz, K},
title = {Early-life supplementation of poultry-derived lactobacilli drives microbial succession and gut immune modulation in broiler chickens.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35177-2},
pmid = {41521228},
issn = {2045-2322},
support = {SC-1700628//USDA National Institute of Food and Agriculture Hatch Project/ ; 2016204//South Carolina Department of Agriculture (ACRE CGP)/ ; },
abstract = {While probiotic supplementation via feed or drinking water is well known to improve poultry gut health by modulating the microbiota and enhancing immune function, the effects of in ovo supplementation remain largely unexplored. In this study, we investigated the effects of administering a lactobacilli cocktail in ovo (embryonic day 18), post-hatch, and in combination on gut immunity and the succession of the cecal microbiota in broilers over 5 weeks. 16S rRNA gene-based sequencing of cecal contents revealed a steady increase in Shannon diversity during the first 2 weeks (PERMANOVA, p < 0.005), with community structure stabilizing by week 3 across all groups. In ovo administration of lactobacilli improved early hatch rates and modulated microbial composition during early succession, including reductions in Klebsiella and Enterococcus, and enrichment of Lactobacillus, during the first two weeks (MaAsLin2, q < 0.25). These microbiome shifts were accompanied by a reduction in the expression of the pro-inflammatory cytokines, including interferon gamma (IFN-γ), interleukin-1β (IL-1β), and IL-8 in the cecal tonsils. These findings highlight the transient yet critical role of early-life probiotic interventions in shaping gut microbial colonization and immune response in broiler chickens. More importantly, a single in ovo lactobacilli dose yielded effects comparable to weekly oral or combined administration.},
}

@article {pmid41521189,
year = {2026},
author = {Vardeman, ET and Cheng, HP and Vandebroek, I and Kennelly, EJ},
title = {The effects of the Caribbean medicinal plant Argemone mexicana on Gardnerella vaginalis using a co-culture method with vaginal Lactobacillus spp.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-26731-5},
pmid = {41521189},
issn = {2045-2322},
support = {F31AT011471//National Institutes of Health, NCCIH/ ; },
abstract = {Bacterial vaginosis (BV) is caused by vaginal microbiome dysbiosis, when beneficial Lactobacillus species are no longer dominant and are replaced by harmful anaerobic bacteria such as Gardnerella vaginalis. In Caribbean cultures, women use plants topically, such as Argemone mexicana, to treat several vaginal infections, including BV. There has been little research into how traditional botanical extracts affect the vaginal microbiota, especially as these extracts are often prepared in different ways for the same condition. This study aims to evaluate the effect of botanical preparations using an in vitro co-culture assay with beneficial Lactobacillus species and BV-causing Gardnerella vaginalis. This is an application of an in vitro co-culture assay to assess the effect of botanical preparations on the vaginal microbiota. We hypothesized that variations in the chemical composition of these preparations would affect the composition of vaginal microbiota. Argemone mexicana extractions were tested using an in vitro co-culture method with Gardnerella vaginalis and one of three vaginal Lactobacillus species and evaluated by UPLC-qToF-MS for metabolomic chemical analysis. Aqueous extractions that did not have significant antibacterial effect compared to the control in monoculture suppressed the growth of Gardnerella vaginalis in co-culture with Lactobacillus, supporting the traditional Dominican use of this plant. These results are likely related to the presence of berberine and polysaccharides in the aqueous extractions.},
}

@article {pmid41521071,
year = {2026},
author = {Kwon, ES},
title = {Integrating Perspectives on Aging: From Mechanistic Causes to Therapeutic Interventions.},
journal = {BMB reports},
volume = {},
number = {},
pages = {},
pmid = {41521071},
issn = {1976-670X},
abstract = {Aging poses one of the most urgent biomedical challenges of the 21st century, increasing vulnerability to chronic diseases and limiting healthspan in aging populations. Recent advances in aging research are transforming our understanding of aging from an inevitable decline to a multidimensional and potentially modifiable biological process. This special issue presents five invited reviews that collectively illustrate the recent progress in aging research. These articles introduce emerging concepts that shed light on the fundamental causes of aging, including the genetic architecture underlying human aging, senescence-driven fibrotic scarring arising from imperfect tissue repair, and the progressive erosion of epigenetic information in the brain. They further highlight promising avenues for intervention-such as epigenetic rejuvenation, the bidirectional interplay between the aging gut microbiome and host physiology, and the emergence of precision geronutrition. By integrating genetic, molecular, cellular, microbial, and nutritional perspectives, this collection emphasizes a future where extending human healthspan is both realistic and scientifically attainable.},
}

@article {pmid41520913,
year = {2026},
author = {Yang, X and Liu, Y and Miao, K},
title = {Microbiome-Modulated Immunotherapy in Oncology: Current Applications and Future Prospects.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2026.01.001},
pmid = {41520913},
issn = {1096-3650},
abstract = {Cancer immunotherapy has transformed oncology, yet therapeutic efficacy remains heterogeneous and frequently limited by primary or acquired resistance. Increasing evidence demonstrates that both intra- and extratumoral microbiota critically modulate antitumor immunity, influencing clinical responses of immunotherapy and immune-related adverse events (irAEs). Microbial communities regulate the tumor immune microenvironment through multiple mechanisms, including microbe-associated molecular patterns, microbial metabolites, and outer membrane vesicles, acting on tumor or immune cells. These insights have fostered the development of microbiome-based applications in oncology, ranging from predictive biomarkers to therapeutic interventions such as engineered bacteria, fecal microbiota transplantation, probiotics, prebiotics, outer membrane vesicles, bacteriophages, and dietary modulation. Early-phase clinical studies indicate that microbiota-targeted strategies can enhance immunotherapy efficacy or mitigate irAEs, although strain specificity, interindividual variability, and safety remain significant challenges. Future progress will require mechanistic elucidation, integration of multi-omics analyses, standardization of methodologies, and personalized intervention frameworks to translate microbiome modulation into clinically actionable, precision immunotherapy.},
}

@article {pmid41520880,
year = {2026},
author = {Tham, TN and Huong, NTL and Kim, QN and Kieu, NTD and Huy, NT},
title = {The Role of the Gut Microbiome in Childhood Obesity: Mechanistic Insights and Community-Based Interventions.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {102911},
doi = {10.1016/j.clnesp.2026.102911},
pmid = {41520880},
issn = {2405-4577},
abstract = {Childhood obesity remains a critical issue, yet traditional efforts focusing on diet and exercise have failed. This review proposes that gut microbiota dysbiosis is not an association, but rather a potentially causal and actionable mechanism underlying childhood obesity. An altered gut microbiome, defined by diminished diversity and specific changes, such as a higher Firmicutes/Bacteroidetes ratio, is a primary contributor to excess weight because of its ability to enhance energy overconsumption, dysregulate production of short-chain fatty acids, regulate appetite, and induce chronic low-grade inflammation. This overview seeks to provide a synthesis of mechanistic evidence and controversies of the gut microbiome as a targetable leverage point, by assessing the microbial signatures of obesity and reflect on the evidence to date and what it implies about the effort: A quest for a singular "obesity microbe" is unlikely to provide success. The unexplained complexity of the host and environment, the lack of a high-quality standard, and evidence of functional microbial pathways and metabolites provide a more fruitful focus. Among other things, this article suggests using high-fiber, whole food dietary strategies to modify the microbiome, the targeted use of evidence-based multi-strain probiotics, and designing school and public health policies to create protective microbiome public health policies. The childhood obesity demands that future efforts focus on the integration of large, multi-omic, longitudinal studies, and the implementation of high-fidelity long-term randomized controlled trial designs that establish the causative relationships, uniform structure to the protocols and enable the implementation of high-impact, equity-based, scalable precision nutrition methodologies.},
}

@article {pmid41520868,
year = {2026},
author = {Bajinka, O and Jallow, L and Ozdemir, G},
title = {A multi-target therapeutic framework for Alzheimer's disease: an integrative mechanistic review.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2026.01.010},
pmid = {41520868},
issn = {1873-7544},
abstract = {BACKGROUND: Alzheimer's disease (AD) is increasingly recognized as a multifactorial network disorder in which amyloid and tau pathology interact with mitochondrial dysfunction, neuroinflammation, metabolic impairment, vascular dysregulation, and synaptic failure. This review provides an integrative, systems-level synthesis of these mechanisms with emphasis on diagnostic and therapeutic implications.

METHODS: A structured narrative review was conducted using PubMed, Scopus, Web of Science, and Embase (2010-2025). Eligible studies included clinical trials, biomarker validation studies, cohort analyses, and mechanistic investigations. Evidence was synthesized by mechanistic domain with focus on cross-system interactions and translational relevance.

FINDINGS: Convergent data indicate that soluble Aβ species, tau propagation, glial dysregulation, insulin resistance, mitochondrial bioenergetic failure, lipid imbalance, and BBB dysfunction form a self-reinforcing neurodegenerative network. Diagnostic advances-including plasma p-tau181/217, Aβ42/40 ratio, GFAP, sTREM2, neuronal exosomes, and multimodal machine-learning models-enable earlier staging and refinement of therapeutic selection. Therapeutic development is shifting from linear amyloid removal to multi-target strategies incorporating anti-tau agents, glial-modulating compounds, metabolic and microbiome interventions, medical nutrition, and multidomain lifestyle programs. Across trials, combined strategies targeting interacting mechanisms demonstrate stronger biomarker and cognitive effects than single-axis approaches.

CONCLUSIONS: AD management requires a systems-oriented therapeutic architecture in which interventions are selected based on mechanistic dominance, biomarker stage, and potential synergy. We outline a multi-target strategy integrating amyloid/tau modulation, neuroimmune regulation, metabolic-vascular stabilization, and synaptic support. Future work should prioritize biomarker-guided stratification, treatment sequencing, and prevention-oriented combination designs.},
}

@article {pmid41520514,
year = {2026},
author = {Kharb, A and Zhu, X},
title = {Unlocking therapeutic impacts of the gut microbiota with computational tools.},
journal = {Current opinion in biotechnology},
volume = {97},
number = {},
pages = {103431},
doi = {10.1016/j.copbio.2025.103431},
pmid = {41520514},
issn = {1879-0429},
abstract = {The human gut microbiota, particularly the intestinal microbiota, shapes host physiology, disease risk, and therapeutic outcomes through complex metabolic and enzymatic activities. Recent advances in molecular omics, metabolomics, enzyme bioinformatics, and artificial intelligence (AI) have created unprecedented opportunities to elucidate its therapeutic roles to further enable precision microbiome medicine for personalized prevention, diagnosis, and treatment. In this review, we highlight emerging applications that leverage molecular omics and metabolomics technologies to dissect gut microbial functions, along with developments in enzyme bioinformatics and AI tools that reveal gut microbial species, enzymes, and metabolic pathways impacting human health. Finally, we discuss perspectives on data standardization, functional annotation, and interpretability, and how emerging tools are accelerating translational microbiome research.},
}

@article {pmid41520466,
year = {2026},
author = {Rapaka, D and Saniotis, A and Thatayaone, M and Bitra, VR},
title = {Neuroendocrine signaling as a pathological seed for the female bias of Alzheimer's disease and the concept of estrobolome.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {195},
number = {},
pages = {118999},
doi = {10.1016/j.biopha.2026.118999},
pmid = {41520466},
issn = {1950-6007},
abstract = {The prevalence of Alzheimer's disease (AD) is anticipated to escalate with the global increase in life expectancy. Although sex-based differences in AD have been previously documented, doubts persist regarding the relationship between sex and pathophysiological pathways. Sex hormones may contribute to these disparities, with a heightened risk of AD-related dementia associated with oophorectomy before menopause. We cannot ascertain if estrogens alone are solely accountable for this accelerated pathological progression of the disease. Estrogens are regulated by the gut microbiota. Thus, the gut-estrogen-brain axis appears to be implicated as a potential new influencer in the pathophysiology of AD, as the female microbiome differs from the male gut microbiome. This suggests it could be a risk factor for the higher prevalence of AD in women. This review speculates on the possible mechanisms for AD prevalence in women, including both anatomical and neuroendocrinological perspectives.},
}

@article {pmid41520335,
year = {2026},
author = {Sang, J and Li, S and Xu, C and Pan, X and Zhu, Y and Li, Y and Ma, C and Zhang, Y and Chen, S and Qiu, Q and Si, H and Huang, Z and Wang, J and Jiao, J and Li, Z},
title = {Rumen microbiome biogeography and ventral epithelial architecture in three ruminant species.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116779},
doi = {10.1016/j.celrep.2025.116779},
pmid = {41520335},
issn = {2211-1247},
abstract = {Ruminants thrive in diverse ecosystems by leveraging their rumen microbiome to ferment fibrous plants. However, the spatial biogeography of rumen microbiome and the genetic diversity of the ventral rumen epithelium remain unknown. Here, we present a multi-omics study in roe deer, sika deer, and sheep, integrating region-resolved microbiome and metabolome across 11 ruminal sacs, as well as single-cell RNA sequencing (scRNA-seq), assay for transposase-accessible chromatin using sequencing (ATAC-seq), and bulk RNA sequencing (RNA-seq) of ventral epithelium. We reveal species-specific microbial compositions and metabolic capacities contributing to differences in short-chain fatty acid and vitamin B production. We uncover functional divergence, genomic specialization, and metabolic changes across the microbiome of distinct ruminal sacs. Single-cell profiling reveals changes of immune responses and structural remodeling of the ruminal ventral epithelium. We demonstrate that vitamin B12 promotes epithelial growth and we identify genes enhancing stem cell differentiation. Our results highlight variation in microbial ecology and epithelial architecture among three ruminant species, offering insights to improve livestock productivity.},
}

@article {pmid41520334,
year = {2026},
author = {Peng, Z and Zhang, H and Ding, Y and Liu, Z and Xie, M},
title = {Prior high fiber intake impinges on the cellular responses of mesenteric adipose and intestinal tissues to subsequent high fat feeding.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116801},
doi = {10.1016/j.celrep.2025.116801},
pmid = {41520334},
issn = {2211-1247},
abstract = {While high-fiber diets (HfiDs) promote weight loss, their long-term efficacy is limited by rapid weight regain upon returning to high-fat diets (HFDs). Using C57BL/6J mice in diet-switching paradigms, we characterized tissue-specific responses to HfiD-to-HFD transitions through single-nucleus and spatial transcriptomics. HfiD pre-feeding enhanced mesenteric white adipose tissue progenitor/adipocyte sensitivity to subsequent HFD exposure. In the intestine, HfiD prevented HFD-induced immune-enterocyte expansion in the duodenum and reversed the enterocyte-to-goblet cell shift in the colon while maintaining persistent epigenetic reprogramming. Although HfiD-induced microbiome changes were largely reversed by HFD, we identified sexually dimorphic remodeling of adipose cell populations during diet transitions. Our findings demonstrate that prior HfiD feeding fundamentally reprograms adipose and intestinal responses to subsequent HFD challenge, providing mechanistic insights into dietary intervention outcomes. This work establishes a spatiotemporal resource for understanding tissue plasticity during dietary changes, offering new perspectives for obesity management strategies.},
}

@article {pmid41520313,
year = {2026},
author = {Chai, Y and Zhou, Y and Peng, H and Jiang, Y and Dai, J and Liu, J},
title = {Comparative efficacy of hyperthermic chemotherapy and BCG instillation in non-muscle invasive bladder cancer: a systematic review and meta-analysis.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {41520313},
issn = {1573-2584},
support = {2023YFS0257//Science & Technology Department of Sichuan Province/ ; },
abstract = {OBJECTIVE: To systematically evaluate the comparative efficacy and safety of hyperthermic intravesical chemotherapy (HIVEC) versus bacillus Calmette-Guérin (BCG) instillation in patients with non-muscle-invasive bladder cancer (NMIBC).

METHODS: A systematic literature search was conducted across PubMed, Embase, the Cochrane Library, and CBM from inception to June 30, 2025, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. The study protocol was registered in the International Prospective Register of Systematic Reviews (PROSPERO) under registration number CRD420251075299. Randomized controlled trials and cohort studies comparing HIVEC with BCG in NMIBC patients were included. Primary outcomes were 24-month recurrence-free survival (RFS), progression-free survival (PFS), and overall survival (OS). Secondary outcomes included adverse events. Risk ratios (RRs) or hazard ratios (HRs) with 95% confidence intervals (CIs) were pooled using fixed- or random-effects models.

RESULTS: Seven studies involving 820 patients were included. The meta-analysis showed no significant differences between HIVEC and BCG in 24-month RFS (RR = 1.01, 95% CI: 0.90-1.12), PFS (RR = 1.00, 95% CI: 0.95-1.05), or OS (RR = 0.99, 95% CI: 0.91-1.09). However, BCG was associated with a significantly higher incidence of dysuria (RR = 1.38, 95% CI: 0.57-3.37). No significant differences were observed in other adverse events such as urinary tract infection, hematuria, or pain.

CONCLUSION: HIVEC demonstrates comparable oncological efficacy to BCG in terms of 24-month RFS, PFS, and OS for NMIBC patients, while offering a better tolerability profile with a significantly lower risk of dysuria. These findings support HIVEC as a valuable alternative treatment option, particularly in the context of BCG shortages or for BCG-intolerant patients.},
}

@article {pmid41520283,
year = {2026},
author = {Duquesnoy, M and Chassaing, B},
title = {MBRA 3.0: integrating the mucus environment for advanced high-throughput in vitro intestinal microbiome modeling.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612804},
doi = {10.1080/19490976.2026.2612804},
pmid = {41520283},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Mucus/microbiology/metabolism ; *Intestinal Mucosa/microbiology/metabolism ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Models, Biological ; Colon/microbiology ; High-Throughput Screening Assays/methods ; },
abstract = {The colonic mucus layer is a dynamic barrier that plays central roles in intestinal health, and recent studies highlight that it harbors a distinct and functionally critical microbial community. However, most in vitro gut models fail to recapitulate this mucosal niche, limiting mechanistic investigation of microbiota-mucus interactions. Here, we developed the MBRA 3.0 system, a next-generation chemostat engineered to integrate mucus-coated carriers and enable high-throughput dissection of spatial microbiome dynamics. Using fecal microbiota from eight human donors, we report that mucus addition does not impact total bacterial density but selectively shapes microbial community structure, metabolic output, and pro-inflammatory potential in a donor-dependent manner. Notably, MBRA 3.0 resolves stable, compositionally distinct mucus-associated and luminal communities, mirroring in vivo spatial heterogeneity. Integration of this mucosal niche also modulates short-chain fatty acid (SCFA) profiles and inflammatory signatures, highlighting the relevance of the spatial context for intestinal microbiota research. Hence, MBRA 3.0 offers a scalable and customizable platform to model mucus-microbiota interactions, advancing our understanding of gut ecology and supporting translational discovery in gastrointestinal health and disease.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Mucus/microbiology/metabolism
*Intestinal Mucosa/microbiology/metabolism
*Bacteria/classification/genetics/isolation & purification/metabolism
Feces/microbiology
Fatty Acids, Volatile/metabolism
Models, Biological
Colon/microbiology
High-Throughput Screening Assays/methods

@article {pmid41520282,
year = {2026},
author = {Yin, Q and Gupta, S and Muller, E and Almeida, A},
title = {The human gut microbiome in enteric infections: from association to translation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2612836},
doi = {10.1080/19490976.2026.2612836},
pmid = {41520282},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; Bacteria/genetics/classification/isolation & purification ; Host-Pathogen Interactions ; Animals ; },
abstract = {Enteric infections remain a leading global cause of morbidity, mortality and economic loss, increasingly compounded by the rise of antimicrobial resistance. The gut microbiome - spanning bacteria, archaea, fungi, protists and viruses - is now recognized as an important mediator that shapes susceptibility to infection, pathogen expansion and disease severity through mechanisms such as colonization resistance, resource competition and immune modulation. Conversely, the gut microbial community can facilitate enteric infection through other processes such as cross-feeding and horizontal gene transfer. In this review, we synthesize correlative and mechanistic evidence currently available on microbiome-pathogen interactions; outline host, environmental and socioeconomic modifiers that affect disease risk across the life course; and evaluate current clinical applications. We highlight key limitations in the field and identify priority areas for future research to refine causal models of microbiome-pathogen ecology and enable targeted diagnostics and therapeutics for preventing and managing enteric infections.},
}

Humans
*Gastrointestinal Microbiome
Bacteria/genetics/classification/isolation & purification
Host-Pathogen Interactions
Animals

@article {pmid41520281,
year = {2026},
author = {Tang, TWH and Ullah, K and Lee, JJ and Chen, HC and Hsieh, PCH},
title = {Comparative insights into the gut-heart axis: cross-species and cross-population perspectives.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2611617},
doi = {10.1080/19490976.2025.2611617},
pmid = {41520281},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Cardiovascular Diseases/microbiology ; *Heart/physiology ; Swine ; Bacteria/classification/metabolism/genetics/isolation & purification ; Host Microbial Interactions ; Species Specificity ; *Gastrointestinal Tract/microbiology ; Disease Models, Animal ; },
abstract = {Gut microbiota research has rapidly expanded our understanding of host-microbe interactions in cardiovascular diseases, yet translation of these insights remains challenged by species-specific differences and substantial population heterogeneity. In this review, we synthesize current evidence across rodents, swine, non-human primates, and multi-ethnic human cohorts to delineate conserved versus context-dependent features of the gut-heart axis. Rodent models remain indispensable for mechanistic discovery, enabling causal testing through germ-free, antibiotic-treated, and humanized microbiota platforms, whereas large-animal models better replicate human cardiac anatomy, physiology, and microbial ecology. Human studies provide essential clinical relevance, demonstrating that patients with myocardial infarction, coronary artery disease, atrial fibrillation, and heart failure harbor distinct microbial and metabolite signatures. However, these findings vary across populations due to differences in diet, lifestyle, host genetics, medication exposure, and environmental transitions. Despite taxonomic variability, several functional pathways, most notably short-chain fatty acid production, bile acid biotransformation, and aromatic amino acid metabolism generating molecules such as trimethylamine-N-oxide and phenylacetylglutamine, consistently associate with cardiovascular risk. At the same time, population-specific features, including glycan-microbe interactions shaped by ABO and FUT2 genotypes, diet-responsive metabolite profiles, and variable drug-microbiome interactions, highlight the importance of genetic and environmental context. By integrating cross-species and cross-population evidence, this review outlines a framework for identifying robust microbial pathways, clarifying their translational boundaries, and guiding the development of microbiota-informed diagnostics and interventions that account for biological, cultural, and environmental diversity.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Cardiovascular Diseases/microbiology
*Heart/physiology
Swine
Bacteria/classification/metabolism/genetics/isolation & purification
Host Microbial Interactions
Species Specificity
*Gastrointestinal Tract/microbiology
Disease Models, Animal

@article {pmid41520196,
year = {2026},
author = {Verburgt, CM and Dunn, KA and Bielawski, JP and Otley, AR and Heyman, MB and Sunseri, W and Shouval, DS and Boneh, RS and de Meij, T and Hyams, JS and Denson, LA and Kugathasan, S and Benninga, MA and de Jonge, WJ and Van Limbergen, JE},
title = {Timing is Everything: Lessons Learned for Building Microbiome-Based Models in Pediatric Crohn's Disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izaf313},
pmid = {41520196},
issn = {1536-4844},
support = {//CIHR-SPOR-Chronic Diseases/ ; //Canadian Institutes of Health Research [CIHR]-Canadian Association of Gastroenterology-Crohn's Colitis Canada New Investigator Award [2015-2019] Crohn/ ; 585718//Colitis Foundation of America, Pro-Kiids/ ; TKI-LSH-ADT-2021-AMC-26344//Health Holland TKI grant/ ; },
}

@article {pmid41520073,
year = {2026},
author = {Alam, N and Yaseen, G and Chandio, MA and Khan, RA and Nasir, MF and Shenawa, E},
title = {Discordance between preoperative urine culture and intraoperative stone/pelvis culture as a predictor of post-PCNL sepsis: a single-center retrospective analysis for targeted antibiotic stewardship.},
journal = {International urology and nephrology},
volume = {},
number = {},
pages = {},
pmid = {41520073},
issn = {1573-2584},
abstract = {PURPOSE: To evaluate the diagnostic accuracy of preoperative midstream urine culture (PMUC) against intraoperative stone and pelvic urine cultures, and to determine if culture discordance independently predicts sepsis following percutaneous nephrolithotomy (PCNL).

METHODS: This retrospective cohort study analyzed 250 adult patients undergoing PCNL between January 2023 and October 2025. All participants had both PMUC and intraoperative stone/pelvic urine cultures. The primary outcome was post-PCNL sepsis defined by Sepsis-3 criteria. Diagnostic performance metrics were calculated, and the association between discordance and sepsis was assessed using multivariable logistic regression, LASSO penalization, and propensity-score matching to adjust for confounders.

RESULTS: Culture discordance was observed in 30% (75/250) of patients. The sensitivity of PMUC for detecting upper urinary tract colonization was only 48%. Sepsis occurred in 6.8% of the total cohort but was significantly more frequent in the discordant group (17.3 vs 2.3%, p < 0.0001). In multivariable analysis, discordance remained the strongest independent predictor of sepsis (adjusted OR 6.23, 95% CI 2.20-17.62, p < 0.001), displacing stone burden and operative time. Notably, patients with sterile preoperative urine but positive intraoperative cultures accounted for 92.3% of sepsis events within the discordant group.

CONCLUSION: PMUC is an unreliable surrogate for the upper tract microbiome, failing to detect colonization in over half of cases. Culture discordance is a robust predictor of post-PCNL sepsis, driven by untreated bacterial biofilms within stones. Routine intraoperative culturing is essential for targeted antibiotic stewardship to mitigate septic complications.},
}

@article {pmid41519984,
year = {2026},
author = {Cronin, B and Kandel, S and McElroy, T and Syed, S and Swinton, C and Corley, C and Sridharan, V and Robeson, MS and Allen, AR},
title = {Changes in gut, microbiome, and cognition after doxorubicin, cyclophosphamide, and paclitaxel chemotherapy treatment.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-33903-w},
pmid = {41519984},
issn = {2045-2322},
support = {1R01CA258673/GF/NIH HHS/United States ; },
abstract = {Over 317,000 new cases of breast cancer will be diagnosed in 2025, making it the most diagnosed cancer among women in the United States. Advancements in treatment options such as chemotherapy and radiation have resulted in a 5-year survival rate of 91%. Upwards of 78% of the 4.1 million breast cancer survivors currently living in the United States report chemotherapy induced cognitive impairment (CICI), or "chemobrain". CICI defined as an impairment in memory, learning, executive function, and attention following chemotherapy treatment. There is a need for a better understanding of the long-term side effects of these treatments and the impact these may have on the quality of life for these survivors. In this study, we used a translational mouse model to study cognitive decline via intraperitoneal injections of the combination chemotherapy AC-T: Doxorubicin (DOX), Cyclophosphamide (CYP), and Paclitaxel (PTX). Mice underwent behavior tests to assess social memory and anxiety 30 days after the last AC-T injection. AC-T treated mice revealed behavioral deficits in social memory and an increase in anxiety-like behavior. RNA-sequencing and western blot analysis revealed negatively altered expression of transcripts associated with neurogenesis, axonal guidance, neurotransmission, and protein IEGs such as Arc, c-Fos, and Egr-1, respectively. Proteomics indicated increases in inflammatory markers in intestinal tissue, which also coincided with changes in intestinal morphology of AC-T treated mice. The gut microbiota of AC-T treated mice showed became dysbiotic. This study provides a multi-omic overview of the effects of AC-T treatment on cognition and intestinal inflammation and morphology.},
}

@article {pmid41519975,
year = {2026},
author = {Christoffersen, SN and Østergaard, SK and de Jonge, N and Pertoldi, C and Sørensen, JG and Noer, NK and Kristensen, TN and Nielsen, JL and Bahrndorff, S},
title = {Arctic Insects Show a Highly Dynamic Microbiome Shaped by Abiotic and Biotic Variables.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02685-z},
pmid = {41519975},
issn = {1432-184X},
abstract = {Arctic regions are inhabited by terrestrial ectotherms that have adapted to an extreme environment where food resources are limited. The host associated microbiome may partly explain their ability to live under these conditions, but very little is known about the microbiome of Arctic ectotherms. We investigate how the bacterial community of the Greenlandic seed bug (Nysius groenlandicus) and damsel bug (Nabis flavomarginatus) is affected by different abiotic and biotic factors (time, acclimation temperature, humidity, and diet) under both field and laboratory conditions. We found large differences in the bacterial composition and diversity between the two species including species-specific presence of potentially symbiotic bacteria. The bacterial community of both species changed across the season, which may be explained by the changing climatic conditions, such as temperature and humidity. This was further supported by results from the laboratory experiments. We also found that diet changed the bacterial composition in both species and that bacteria could be transferred from prey to predator. Together, these results show that the bacterial community of some Arctic insects are highly dynamic and modulated by different abiotic and biotic factors, suggesting that the microbiome plays an important role for these organisms to persist in an extreme and resource-limited Arctic environment.},
}

@article {pmid41519950,
year = {2026},
author = {Ye, X and Zhang, T and Zhou, J and Zhao, C and Wu, J},
title = {The gut microbial profile and circulating metabolism are associated with functional constipation in children.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41519950},
issn = {1530-0447},
abstract = {BACKGROUND: A growing body of evidence highlights the link between gut microbiome imbalances and constipation. However, the role of gut microbiota and its metabolic interactions in pediatric functional constipation (FC) remains incompletely understood.

METHODS: We recruited a total of 40 children with FC and 40 healthy children (CONT). 16SrRNA and metagenomic sequencing were used to evaluate the changes in the gut microbiota structure and gene function in FC patients. Differences in serum metabolite levels were analyzed via targeted metabolomic sequencing.

RESULTS: The FC group exhibited a decrease in gut microbiota diversity, an increase in Bacteroides and Prevotella abundances, depletion of genera such as Lactobacillus and Bifidobacterium and an imbalance of related metabolic activities. Metabolomic analysis revealed that the levels of several metabolites, including taurine and glycochenodeoxycholic acid, which are involved in bile acid (BA) metabolic pathways, differed between the FC and CONT groups. Differences in metabolite levels were associated with changes in the abundances of specific bacteria and with intestinal dysfunction in FC patients.

CONCLUSION: FC in children is associated with distinct gut microbiota alterations and dysregulated BA metabolism. These findings provide potential therapeutic targets for modulating the gut microbiome and metabolic pathways in FC management.

IMPACT: This study offers a comprehensive perspective on the intricate relationship between microbial composition and metabolic pathways in the context of functional constipation in children. This study focuses on children, highlighting how disruptions in bile acid metabolism due to gut microbiota disorders are linked to the occurrence of functional constipation. These findings suggest that disturbances in bile acid metabolism may play a role in the mechanisms underlying functional constipation by impairing intestinal secretion and transport functions. This study offers a new way to study the effects of the gut microbiota, bile acid metabolism, and the gut‒brain axis.},
}

@article {pmid41519893,
year = {2026},
author = {Schaefer-Dreyer, P and Behrens, W and Winkel, A and Pott, PC and Paulsen, M and Stanislawski, N and Tanisik, F and Melk, A and Schmidt, BMW and Lucas, H and Heiden, S and Klopp, N and Illig, T and Blume, H and Blume, C and Yang, I and Stiesch, M},
title = {Effects of cigarette smoking on the oral microbiome in adolescents.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {1348},
pmid = {41519893},
issn = {2045-2322},
mesh = {Humans ; Adolescent ; *Microbiota ; Male ; Female ; *Mouth/microbiology ; *Cigarette Smoking/adverse effects ; *Bacteria/genetics/classification ; RNA, Ribosomal, 16S/genetics ; Young Adult ; },
abstract = {Smoking, a risk factor for periodontitis and peri-implantitis, is associated with shifts in the oral microbiome (OM) composition. Although smoking habits are almost always established before adulthood, data on effects of smoking on the OM in adolescents is rare. The aim of this study was to investigate the early impact of smoking on the OM composition in pupils. The adolescent cohort, aged 14-20, comprised 98 smokers and 98 non-smokers matched for several physiological co-variates. Buccal swabs were analysed for OM composition using high-throughput sequencing of the full-length 16 S rRNA gene targeting species-level resolution. Parameters of bacterial diversity and abundance of individual bacterial taxa were related to information on smoking. The microbiome dataset contained 733 species-level taxa. Streptococcus, Rothia, and Haemophilus dominated both groups, smokers and non-smokers. Smoking exerted a discernible influence on the overall microbial composition as measured by weighted UniFrac distances. The number of species-level bacterial taxa was significantly higher in individual smokers compared to non-smokers. Furthermore, several taxa, including known pathogens, exhibited significant differences in abundance between the two groups. The genera Veillonella, and Actinomyces, as well as and multiple Actinomyces species, Dialister invisus, Atopobium parvulum, Streptococcus mutans and Prevotella melaninogenica were significantly more abundant in smokers. Our findings indicated an early onset of smoking-related changes already in the oral microbiome of adolescents.},
}

Humans
Adolescent
*Microbiota
Male
Female
*Mouth/microbiology
*Cigarette Smoking/adverse effects
*Bacteria/genetics/classification
RNA, Ribosomal, 16S/genetics
Young Adult

@article {pmid41519453,
year = {2026},
author = {Combs, MP and Shaver, CM},
title = {Emerging from the shadows: reading between the lines to illuminate the microbiome's role in CLAD.},
journal = {The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.healun.2026.01.001},
pmid = {41519453},
issn = {1557-3117},
}

@article {pmid41519378,
year = {2026},
author = {Jeong, H and Eppel, PS and Kaelber, DC and Singh, RP and Talcott, KE},
title = {Malabsorption Syndromes and Risk of Age-Related Macular Degeneration: Evidence from Real-World Data.},
journal = {Ophthalmology. Retina},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.oret.2026.01.002},
pmid = {41519378},
issn = {2468-6530},
abstract = {PURPOSE: Despite mechanistic links connecting malnutrition and gut microbiome with retinal health, clinical research exploring the relationship between malabsorption syndromes and age-related macular degeneration (AMD) remains limited. This study compared the risks of AMD diagnosis in patients with and without various malabsorption syndrome diagnoses.

DESIGN: Retrospective cohort study of aggregated, de-identified patient data from multiple healthcare organizations across the United States using the TriNetX U.S. Collaborative Research Network in 11/2025.

PARTICIPANTS: Adults with a cataract-related International Classification of Diseases (ICD) encounter diagnosis codes and no baseline AMD ICD encounter diagnosis codes were divided into groups based on the presence of ICD encounter diagnosis codes for celiac disease (CeD), ulcerative colitis (UC), Crohn's disease (CrD), chronic pancreatitis (CP), and short bowel syndrome (SBS). Within the CP cohort, patients with pancreatic enzyme replacement therapy (PERT) prescription orders were subanalysis. For each cohort, a corresponding control cohort of patients without the respective ICD encounter diagnosis codes was created.

METHODS: The study and control cohorts were propensity-matched 1:1 on demographic factors, comorbidities, and disease-related conditions and prescription orders. The matched cohorts were compared on the risk of having AMD ICD encounter diagnoses.

MAIN OUTCOME MEASURE: Risk ratios (RR) and 95% confidence intervals (CI) of having an AMD ICD encounter diagnosis code with an accompanying retinal optical coherence tomography Common Procedural Terminology code. Significance was defined as CI ≤0.9 or ≥1.1.

RESULTS: Compared to controls without IBD, the CrD cohort (n=9,537, RR=1.42, CI=1.16-1.74), but not the UC cohort (n=15,039, RR=1.28, CI=1.09-1.51), had a higher risk of having early/intermediate AMD. CP was associated with an increased risk of AMD (n=12,856, RR=1.82, CI=1.53-2.16), even in the PERT subset (n=3,812, RR=1.83, CI=1.35-2.48). SBS (n=3,747) was associated with an increased risk of advanced/exudative AMD (RR=1.98, CI=1.31-2.98), but not early/intermediate AMD (RR=1.28, CI=0.96-1.71). CeD was not associated with increased AMD risk (n=9,315, RR=1.09, CI=0.88-1.35).

CONCLUSIONS: Chronic non-infectious causes of malabsorption syndromes-CrD, CP, and SBS-may represent underrecognized risk factors of AMD. This explorative study adds clinical evidence for a potential role of the gut-retina axis in the pathogenesis of AMD.},
}

@article {pmid41519280,
year = {2026},
author = {Yan, T and Rong, L and Wang, S and Song, X and Hu, B and Wang, Z and Wang, X and Ding, X and Guan, R and Yu, H and Niu, D and Zhang, Y},
title = {Alterations in cardiovascular biomarkers and gut microbiome associated with night shift work: Insights from the Chinese Platform Workers Study.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123735},
doi = {10.1016/j.envres.2026.123735},
pmid = {41519280},
issn = {1096-0953},
abstract = {The expansion of the gig economy has been marked by an increase in platform workers, including ride-hailing drivers, who typically work non-standard schedules, with night shifts being common. Although night shift work was known to disrupt circadian rhythms and elevate cardiovascular risks, the interplay between early alteration in cardiovascular biomarkers and gut microbiome remain unclear. To investigate these associations in the platform worker groups, we conducted a cross-sectional study comparing 66 night shift and 175 day shift ride-hailing drivers in Beijing, China. All participants underwent health examinations, provided blood tests for the assessment of four key cardiovascular biomarkers (hs-cTnI, ET-1, NT-pro-BNP, and FABP-3), and submitted fecal samples for gut microbiome profiling via 16S rDNA sequencing. Bioinformatics, linear regression, and mediation analyses were conducted to evaluate the associations between night shift work, biomarkers, and microbial taxa, with adjustments for key sociodemographic and lifestyle factors. Night shift drivers exhibited significantly higher levels of NT-pro-BNP (median 49.8 vs. 41.3 pg/ml, P = 0.044), an association that remained significant after adjustment for covariates (β = 0.195, P = 0.004). Twenty differentially abundant taxa were identified, four of which were significantly associated with hs-cTnI. No significant mediation effect was observed. This study found that night shift work in ride-hailing drivers was significantly associated with adverse cardiovascular biomarker profiles and distinct gut microbiome alterations. Correlation analysis further suggested that gut microbial changes were linked to the observed cardiovascular risk. This study reported associations between night-shift work and alterations in early cardiovascular injury biomarkers as well as the gut microbiota, suggesting a potential link between gut microbiota and night-shift-related cardiovascular injury.},
}

@article {pmid41519271,
year = {2026},
author = {Nicholas, JC and Alkis, T and Bis, JC and Boerwinkle, E and Brody, JA and Clish, CB and de Vries, PS and Gao, Y and Gerzsten, RE and Guo, X and Johnson, AD and Larson, MG and Lemaitre, RN and Psaty, BM and Ramachandran, V and Reiner, AP and Rich, SS and Rodriguez, B and Rong, J and Rotter, JI and Simino, J and Smith, NL and Wilson, J and Yao, J and Morrison, AC and Yu, B and Raffield, LM},
title = {Fibrinogen-Associated Plasma Metabolites and Implications for Coagulation, Inflammation, and Vascular Diseases.},
journal = {Journal of thrombosis and haemostasis : JTH},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtha.2025.12.016},
pmid = {41519271},
issn = {1538-7836},
abstract = {BACKGROUND: Fibrinogen is a critical coagulation factor that plays an essential role in thrombosis and is elevated in individuals with chronic inflammation. Here, we used fibrinogen as a representative quantitative measure of pro-coagulant risk and evaluated metabolites associated with fibrinogen levels through non-targeted plasma metabolomic profiling (Broad and Metabolon platforms).

METHODS: Our analysis included 10,533 individuals across six U.S. based cohorts representing diverse population groups. The cross-sectional relationship between each of 789 tested metabolites and plasma fibrinogen concentration was assessed with adjustment for relevant covariates such as age, sex, body mass index, and circulating lipoprotein levels.

RESULTS: Meta-analysis of per-cohort results revealed 270 metabolites significantly associated with fibrinogen level (FDR adjusted p-value < 0.05). Lipid species such as glycerophospholipids, sphingolipids, and fatty acyls were prevalent among significantly associated metabolites; some of these may capture effects of inflammation, as supported by sensitivity analyses adjusted for C-reactive protein. Significant associations between fibrinogen levels and serotonin, thyroxine, and sex-hormone derivatives may capture endogenous influences on fibrinogen levels. Exogenous compounds and microbial co-metabolites significantly associated with fibrinogen also implicate lifestyle and microbiome risk-factors. Only a portion of fibrinogen-associated metabolites (30%) have been associated with a cardiovascular disease outcome in a prior study, suggesting the associations discovered here may provide insights on vascular biology which case-control studies may not yet be powered to detect.

CONCLUSIONS: These findings contribute to a growing list of metabolite biomarkers that may influence coagulation and inflammation pathways and may thereby contribute to vascular risk.},
}

@article {pmid41519234,
year = {2026},
author = {Holdaway, CM and Vo, A and Leonard, KA and Nelson, R and Thiesen, A and Fan, Y and Marcolla, CS and Clugston, RD and Willing, BP and Jacobs, RL},
title = {Dietary Ethanolamine Increases Hepatic Lipid Accumulation in Mice Fed a High Fat Diet.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101348},
doi = {10.1016/j.tjnut.2025.101348},
pmid = {41519234},
issn = {1541-6100},
abstract = {BACKGROUND: Ethanolamine (Etn), a precursor of phosphatidylethanolamine (PE), may alter hepatic lipid homeostasis and gut health; its dietary effects remain undefined.

OBJECTIVE: To determine the effects of dietary Etn on lipid and glucose metabolism and liver/gut health in high-fat diet (HFD)-fed mice, complemented by in vitro hepatocyte assays.

METHODS: Ten-week-old C57BL/6 mice (20 male, 18 female) were fed ad libitum HFD (45% energy from fat) with (ES) or without (CON) Etn (8 g/kg diet) for 10 weeks. Outcomes included body/liver weight, glucose tolerance (GTT), plasma PC/CE/TG, hepatic TG/PC/PE, hepatic ER-stress and inflammation markers, jejunal morphology/barrier/inflammation genes, and fecal microbiota (α/β diversity). HuH7 cells received 20 μM or 5 mM Etn to assess TG/PC/PE synthesis.

STATISTICS: repeated-measures ANOVA (GTT), t-test or Wilcoxon (other endpoints), PERMANOVA (β diversity); α=0.05.

RESULTS: ES increased hepatic TG in females by 230% vs CON (p = 0.001), and trended higher in males (p = 0.054); hepatic PC and PE masses were unchanged. In ES-males, GTT AUC decreased by 22.6% (p = 0.037), and plasma PC, CE, and TG were reduced by: PC - 16.6%, CE - 24.5%, TG - 25.9% (all p < 0.05). ES males showed higher hepatic Tnf and Cd68 and increased CHOP protein (all p < 0.05). In vitro, Etn did not alter hepatocellular TG, PC, or PE synthesis (all p > 0.05). Female ES mice exhibited altered fecal β-diversity (PERMANOVA p = 0.006) with early jejunal inflammatory signals (Tnf ↑; p = 0.055).

CONCLUSIONS: Dietary Etn modifies hepatic lipid storage and gut microbiota in a sex-dependent manner and improves glucose tolerance in males, whereas in vitro data indicate no direct effect on hepatocyte lipid synthesis.},
}

@article {pmid41519187,
year = {2026},
author = {Zhang, Z and Tao, H and Mao, K and Meng, F and Jiang, S and Chen, J and He, X and Tian, X},
title = {The Central Qi Theory in Traditional Chinese Medicine: Gut Microbiota Modulation as a Strategic Target for Hepatocellular Carcinoma Therapy.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121147},
doi = {10.1016/j.jep.2025.121147},
pmid = {41519187},
issn = {1872-7573},
abstract = {Patients with intermediate and advanced hepatocellular carcinoma (HCC) often derive limited benefit from systemic therapy and experience a substantial symptom burden with deterioration in quality of life. These challenges underscore the need for safe, effective adjunctive or alternative therapies. The traditional Chinese medicine concept of Central Qi shows conceptual contemporary with contemporary understanding of the gut-liver axis and microbiome biology. Chinese herbal medicines centered on tonifying the central and replenishing qi (Buzhong Yiqi) are considered adjunctive or alternative therapeutic options for alleviating symptoms, improving quality of life, and enhancing tolerance and adherence to standard treatments.

AIM OF THIS REVIEW: To delineate links among the interrelations among Central Qi, the gut microbiota, and HCC, to synthesize evidence on how Buzhong Yiqi medicines modulate the gut microbiota, and to elucidate the proposed mechanistic bases for their potential adjunctive effects in HCC. This review aims to provide a biologically plausible framework to inform microbiome-based mechanistic research and clinical translation.

METHODS: Databases including PubMed, Web of Science, Elsevier ScienceDirect, CNKI, and Google Scholar were searched using predefined terms related to hepatocellular carcinoma, gut microbiota, and the gut-liver axis, nutrient absorption, metabolic regulation, immune modulation, and Buzhong Yiqi medicines, as well as their representative herbs. In vivo, in vitro, and clinical studies published from 2000 to October 2025 were included.

RESULTS: Dysbiosis disrupts the metabolic pathways of bile acid, short-chain fatty acid, and tryptophan metabolic pathways, while compromising the intestinal barrier. This disruption can worsen appetite regulation and energy imbalance, as well as weaken antitumor immunity. Buzhong Yiqi medicines have been reported to enrich beneficial taxa, reduce pathogens and pathobionts, and improve microbial metabolite profiles, restoration of barrier integrity, improvements in nutrient intake and energy homeostasis. These findings are heterogeneous and largely derived from non-HCC models, but collectively suggest potential support of metabolic and immune homeostasis, with possible influence on the tumor immune microenvironment. Early exploratory data also indicate a potential interaction with immune checkpoint inhibitors, although its clinical significance remains uncertain.

CONCLUSION: Central Qi deficiency provides a biologically plausible conceptual framework linking impaired digestion, disrupted energy metabolism, microbial dysbiosis, and reduced immune responsiveness in HCC. Modulation of the GM through Buzhong Yiqi medicines may offer supportive metabolic and immunological benefits, but current evidence is preliminary, based mainly on associative findings, and requires cautious interpretation. Key uncertainties remain regarding causal relationships, HCC-specific mechanisms, and the consistency of clinical effects. Future research should prioritize standardized preparations, mechanistic validation, biomarker-guided stratification, and rigorously designed clinical trials to clarify the clinical relevance of these proposed pathways and to advance global acceptance of integrative therapy.},
}

@article {pmid41519162,
year = {2026},
author = {Olmstead, M and Van Nest, K and Swistek, S and Cohnstaedt, LW and Oppert, B and Shults, P},
title = {Microbial communities in filth flies collected from dairy and poultry farms for supplemental animal feed.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toaf283},
pmid = {41519162},
issn = {1938-291X},
support = {NP104- 3020-32000-20-00D//USDA/ ; },
abstract = {Alternative protein sources are needed due to the rising demand and increasing cost of protein ingredients in livestock diets. Mass collection of wild-caught flies from locations with high insect pressure may be an economical and environmentally sustainable approach to supplement livestock feed, but there may be feed safety issues from microbes found in field-caught insects. Therefore, we evaluated a sequencing-based approach to accurately identify potential pathogens in wild-caught flies captured on 2 different livestock farms. In this study, we combined whole-genome shotgun metagenomic sequencing with total RNA-seq to identify a broad range of microbial taxa present in and on wild-caught flies. We describe several databases tailored to the host insect, host animals, and pathogens associated with livestock and humans. Sequences were identified from potentially pathogenic bacteria including Escherichia coli, Gallibacterium anatis, Helicobacterium pullorum, Morganella morganii, Proteus mirabilis, and Providencia alcalifaciens. In addition, sequences from the pathogenic fungi Aspergillus fumigatus and viruses such as the fly pathogen Musca hytrosavirus were found. Despite the limitations of current database curation, a combination of metagenomics and total RNA-seq approaches to taxa identification can provide insight into a broad spectrum of potential pathogens in insects used as supplemental livestock feed.},
}

@article {pmid41519109,
year = {2026},
author = {Hoedt, EC and Talley, NJ},
title = {Toward a personalized diet-microbiome strategy in inflammatory bowel disease: Matching donor, diet, and patient.},
journal = {Med (New York, N.Y.)},
volume = {7},
number = {1},
pages = {100918},
doi = {10.1016/j.medj.2025.100918},
pmid = {41519109},
issn = {2666-6340},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology/therapy/diet therapy ; *Fecal Microbiota Transplantation/methods ; *Precision Medicine/methods ; *Gastrointestinal Microbiome ; *Diet ; },
abstract = {Fecal microbiota transplant plus dietary change to restore the imbalance of an individual's microbiome to relieve disorders such as inflammatory bowel disease has not been established but has promise. In this commentary, we suggest the need to embrace a more nuanced, personalized approach, one that considers microbial functionality, dietary context, and host compatibility.},
}

Humans
*Inflammatory Bowel Diseases/microbiology/therapy/diet therapy
*Fecal Microbiota Transplantation/methods
*Precision Medicine/methods
*Gastrointestinal Microbiome
*Diet

@article {pmid41518932,
year = {2026},
author = {Du, B and Yang, Y and He, L and Tang, Y},
title = {Microbiota and infertility: a translational review of mechanisms and clinical applications in assisted reproduction.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {318},
number = {},
pages = {114941},
doi = {10.1016/j.ejogrb.2026.114941},
pmid = {41518932},
issn = {1872-7654},
abstract = {Infertility constitutes a major global health concern, affecting approximately 17.5% of couples of reproductive age. Although advances in assisted reproductive technologies (ART) have expanded treatment options, success rates remain highly variable due to host-specific and biological determinants. This review synthesizes current evidence on the reproductive impact of the human microbiota and its translational relevance to ART outcomes. Vaginal microbial communities dominated by Lactobacillus, particularly L. crispatus, are associated with improved conception and implantation, whereas genital or intestinal dysbiosis correlates with infertility and suboptimal treatment responses. The microbiota modulates reproductive competence through intertwined immune, endocrine-metabolic, and mucosal barrier pathways that regulate inflammation, hormonal balance, and epithelial integrity. Emerging findings indicate that gut microbial alterations linked to polycystic ovary syndrome (PCOS) and endometriosis are accompanied by insulin resistance and chronic inflammation, impairing ovulation, endometrial receptivity, and embryo viability. Interventions such as probiotics and synbiotics yield heterogeneous efficacy; individualized antimicrobial strategies, metabolic modulation, and lifestyle optimization may offer complementary benefit, while microbiota reconstruction remains experimental. Methodological limitations, including contamination in low biomass samples, variations in sequencing workflows, and population heterogeneity, still hinder data comparability and mechanistic interpretation. Future research should prioritize adequately powered randomized controlled trials using standardized microbiome metrics and live birth as a primary endpoint. Integrating microbiome profiling into ART workflows may refine patient stratification and inform precision adjuvant therapies. However, clinical implementation requires stronger causal evidence, validated biomarkers, and harmonized methodological frameworks to translate microbiome discoveries into reproducible reproductive gains.},
}

@article {pmid41518832,
year = {2025},
author = {Hellwig, P and Seick, I and Meinusch, N and Benndorf, D and Wiese, J and Reichl, U and Heyer, R},
title = {Molecular community data meets anaerobic digestion Model 1 (ADM1) - a study about the correlation between metagenome-centric metaproteomics data of a two-step full-scale anaerobic digester and its corresponding mathematical model.},
journal = {Water research},
volume = {292},
number = {},
pages = {125272},
doi = {10.1016/j.watres.2025.125272},
pmid = {41518832},
issn = {1879-2448},
abstract = {Advanced models, such as the Anaerobic Digestion Model No 1 (ADM1), are essential for operating, planning, and optimizing renewable energy production in anaerobic digester plants (AD-P)s. In this study, the ADM1da model was employed to simulate a two-step AD-P in an industrial setting. The ADM1da model is an extended ADM1 model for mixed substrates, accounting for substrate-specific disintegration, temperature effects, biogas-related mass reduction, and mineral solids content. ADM1 models can represent the anaerobic digestion processes, although the biological assumptions are coarse and reflect the knowledge and available tools for microbial communities at the time of development. Meanwhile, metagenome-centric metaproteomics provides deeper insight into the metabolic activities of microbial communities in AD-Ps. Until now, this data has not been integrated with ADM1 models. The objective of this study is to assess the feasibility of incorporating metagenome-centric metaproteome data into the ADM1 model. In a novel approach, 49 high-quality metagenome-assembled genomes (MAGs) with associated protein abundances were systematically classified into the trophic groups defined by the ADM1 model using specifically developed grouping rules. Abundances of MAGs were more variable than the process parameter-dependent dynamics of ADM1. Depending on the grouping rules, 32%-78% of all high-quality MAGs were successfully categorized into ADM1 trophic groups. However, some MAGs, e.g., Methanotrix, were multifunctional (acetoclastic and hydrogenotrophic methanogenesis) and required assignment to multiple groups. Unfortunately, more precise grouping rules resulted in greater discrepancies between metaproteomics data and the model. Additionally, 22% of the MAGs could not be assigned. The metagenome-centric metaproteome data imply that ADM1 probably needs extension to cover the observed microbial function of syntrophic acetate oxidizers, hydrolytic bacteria, lactate- and ethanol-fermenting bacteria, and mortality by phages. It was also observed that changes in process parameters, such as those caused by seasonal feeding, led to significant changes in the protein abundance Integrating metagenome-centric metaproteomic data into ADM1 trophic groups was shown to be feasible.Some trophic groups detected in protein data but not implemented in ADM1 imply the need for data-driven model enhancement and approval. In the future, more accurate models considering molecular data could support a deeper understanding of microbial community dynamics in AD-Ps.},
}

@article {pmid41518828,
year = {2025},
author = {Wu, Z and Liang, F and Zhu, N and Han, C and Wang, Z and Wang, W and Wang, L and Guo, Y and Luo, W and Wang, Y},
title = {Codonopsis pilosula regulates pathogen defense mechanisms through collaboration of root volatile compounds and microbial interactions.},
journal = {Plant physiology and biochemistry : PPB},
volume = {231},
number = {},
pages = {110974},
doi = {10.1016/j.plaphy.2025.110974},
pmid = {41518828},
issn = {1873-2690},
abstract = {Codonopsis pilosula responds to pathogen infection by modulating root volatile organic compounds (VOCs) and reshaping the rhizosphere microbiome. GC-IMS analysis linked root VOCs with microbial community composition, showing positive correlations with Bradyrhizobium and beneficial fungi, and negative associations with Alternaria pathogens. Representative VOCs-benzothiazole, linalool, and (E,E)-2,4-heptadienal-showed significant antifungal activity against Fusarium oxysporum. Molecular docking and qPCR analyses indicate that these compounds may interact with stress-related proteins and potentially influence autophagy-associated pathways, suggesting stress responses that could contribute to fungal growth inhibition or cell death. Although autophagy was not directly demonstrated, these findings highlight VOCs as important mediators of plant defense signaling and may support the development of eco-friendly VOC-based antifungal strategies.},
}

@article {pmid41518802,
year = {2026},
author = {Yang, X and Ji, XH and Li, C and Lai, JL and Luo, XG},
title = {Multi-omics assessment of synthetic microbiome-mediated remediation of cyclotetramethylene tetranitroamine (HMX) contaminated water.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141026},
doi = {10.1016/j.jhazmat.2026.141026},
pmid = {41518802},
issn = {1873-3336},
abstract = {Cyclotetramethylene tetranitroamine (HMX) is a typical high-energy nitramine pollutant with an environmental persistence and toxic effects that pose serious ecological risks. In this study, a synthetic microbiome with complementary functions is built that enables the integration of multigroup technology to conduct a systematic analysis of the mechanism of remediation of HMX-contaminated water bodies. Four core bacterial strains (Bacillus altitudinis, B. cereus, B. subtilis, and Pseudomonas stutzeri) were directionally domesticated and screened from HMX-contaminated water. Through functional verification, they were confirmed to express key enzymes NfsA, YdhA, FdhA, and NirS, respectively, to form a complete HMX deep degradation-level connection path. The synthetic microbiome achieved 100 % removal of HMX and its intermediates within 60 days, and isotope tracing (δ[15]N enrichment +2.7 ‰) confirmed its complete mineralization ability. Multiomic analysis showed that the restoration process is accompanied by a systematic reshaping of the water microecology and chemical environment, so that the microbial community structure is optimized and the synthetic microbiome is successfully colonized and becomes the core node. Meanwhile, the energy metabolic network (glycolysis, TCA cycle, oxidative phosphorylation) is significantly enhanced; metagenomic data also revealed reduced viral abundance. Ionomics revealed that key nutrient elements, such as P and S, are efficiently assimilated and utilized. These findings identify an efficient HMX bioremediation strategy that utilizes the multiple dimensions of "community structure-metabolic function-environmental effects" through a multigroup integration framework. More importantly, this study provides a theoretical basis and practical paradigm for the rational design of functional microbial communities.},
}

@article {pmid41518158,
year = {2026},
author = {Barberá, A and Ortolá, R and Sotos-Prieto, M and Rodríguez-Artalejo, F and Moya, A and Ruiz-Ruiz, S},
title = {The Role of the Gut Microbiome in the Complex Network of Frailty Syndrome and Associated Comorbidities in Aging.},
journal = {Aging cell},
volume = {25},
number = {2},
pages = {e70365},
pmid = {41518158},
issn = {1474-9726},
support = {PID2019-105969GB-I00//Spanish Ministry of Science, Innovation and Universities/ ; PMPTA22/00107//Carlos III Health Institute (ISCIII)/ ; PMPTA22/00037//Carlos III Health Institute (ISCIII)/ ; PMPTA23/00001//Carlos III Health Institute (ISCIII)/ ; INVEST/2022/309//Next Generation-EU/ ; 22/1111//ISCIII/ ; //The Secretary of R + D + I/ ; //ERDF/ESF/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Frailty/microbiology ; Male ; Female ; Aged ; *Aging ; Comorbidity ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; },
abstract = {The gut microbiota changes throughout life, potentially influencing health and triggering physiological disorders. Frailty syndrome (FS) is an age-related condition that reduces quality of life and increases hospitalization and mortality risks, making early detection and prevention essential in older populations. This study analyzed 16S rRNA gene and metagenomics sequencing of fecal samples from 203 older adults (FS: n = 64, non-FS (NFS): n = 139) to assess the role of gut microbiota in FS and related comorbidities, such as sarcopenia and impaired lower extremity function (ILEF) or anthropometric variables. Consistent taxonomic patterns were observed: Eggerthella, Parabacteroides, and Erysipelatoclostridium were significantly abundant in FS, while Christensenellaceae R-7 group, Erysipelotrichaceae UCG-003, and Hungatella were enriched in NFS. Christensenellaceae R-7 group was also associated with better mobility. Metagenomics analysis identified 680 KEGG functions differing between groups, categorized into 28 metabolic pathways. FS individuals had overrepresented biotin metabolism, antimicrobial resistance, and energy production, but underrepresented ribosomal and protein synthesis and sporulation pathways. Resistome analysis found the tetM/tetO (K18220) gene most abundant, alongside tetracycline, β-lactam, and macrolide resistance, primarily mediated by antibiotic efflux and transporters. These findings highlight distinct microbial and functional signatures associated with FS, underscoring the complex interplay between the gut microbiota and host physiology in aging. Adjusting for covariates, age and diabetes acted as confounding factors in FS for both 16S gene and metagenomics sequencing. This study offers new insights into fundamental questions in the biology of aging and opens avenues for microbiota-targeted strategies to improve the quality of life in older adults.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Frailty/microbiology
Male
Female
Aged
*Aging
Comorbidity
Aged, 80 and over
RNA, Ribosomal, 16S/genetics
Metagenomics

@article {pmid41517910,
year = {2026},
author = {Gewirtzman, J},
title = {The Global Woody Surface: A Planetary Interface for Biodiversity, Ecosystem Function, and Climate.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70699},
doi = {10.1111/gcb.70699},
pmid = {41517910},
issn = {1365-2486},
support = {DGE-2139841//National Science Foundation/ ; //Institute for Biospheric Studies, Yale University/ ; 80NSSC25M7127//NASA CT Space Grant/ ; },
}

@article {pmid41517814,
year = {2026},
author = {Jacob, SM and Son, B and Bagheri, S and Lee, S and Leckie, J and Chohan, B and Belway, C and Mascarenhas, J and Mobach, T and Korngut, LW and Sharkey, KA and Park, J and Nguyen, MD and Kim, SH and Pfeffer, G},
title = {The Oral Microbiome in Amyotrophic Lateral Sclerosis Shows Differentially Abundant Organisms in Limb Versus Bulbar Onset Disease: A Binational Study.},
journal = {Journal of clinical neurology (Seoul, Korea)},
volume = {22},
number = {1},
pages = {66-75},
doi = {10.3988/jcn.2025.0219},
pmid = {41517814},
issn = {1738-6586},
support = {//ALS Canada Discovery Grant/Canada ; //Barry Barrett Foundation/Canada ; /CAPMC/CIHR/Canada ; //International Development Research Council/Canada ; //Rose Family Foundation/Canada ; //Fondation Brain Canada/Canada ; /MOHW/Ministry of Health and Welfare/Korea ; RS-2024-00348451/MSIT/Ministry of Science and ICT, South Korea/Korea ; },
abstract = {BACKGROUND AND PURPOSE: Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease of upper and lower motor neurons leading to progressive disability and death. Approximately 10% of cases are caused by single-gene disorders with the remaining 90% of cases presumed to be caused by a combination of environmental and genetic factors. The microbiome (the ensemble of microorganisms that colonize body surfaces and organs) was recently identified for its importance in the pathogenesis of ALS.

METHODS: In this study, we recruited 100 participants from two ethnically and geographically distinct sites (71 from Calgary, Canada, and 29 from Seoul, Republic of Korea) which included 59 ALS participants and 41 controls. All participants provided saliva samples for oral microbial analysis using 16S rRNA sequencing. Basic demographic information was collected from all participants, and ALS participants provided additional clinical information including site of disease onset, disease duration, and ALS Functional Rating Scale - Revised score.

RESULTS: Significant differences in beta diversity of the oral microbiomes were seen between limb- and bulbar-onset ALS participants. Two bacterial genera were differentially abundant between these groups, Bifidobacteriaceae Bifidobacterium was enriched in bulbar-onset cases, while Pasteurellaceae Haemophilus was enriched in limb-onset cases. No significant differences were found between ALS participants and controls, but there were significant differences when comparing participants from different sites of recruitment. Amongst household pairs (n=35 pairs), ALS participants differed from control participants at the Seoul site.

CONCLUSIONS: Despite the cohort and household effects, our study identified differentially abundant organisms that may be important to the phenotypic variability of ALS and should be considered for future study. Our study provides novel insights into design for future multi-site microbiome research in ALS.},
}

@article {pmid41517622,
year = {2026},
author = {Bicknell, B and Liebert, A and McLachlan, C and Kiat, H},
title = {Five-Year Follow-Up of Photobiomodulation in Parkinson's Disease: A Case Series Exploring Clinical Stability and Microbiome Modulation.},
journal = {Journal of clinical medicine},
volume = {15},
number = {1},
pages = {},
pmid = {41517622},
issn = {2077-0383},
support = {NA//private donor/ ; },
abstract = {Background: Parkinson's disease (PD) involves progressive neurodegeneration with clinical or subclinical disturbance of the gut-brain axis, including altered gastrointestinal motility and enteric nervous system involvement. Clinical studies have reported gut microbiome alterations in PD, with shifts in taxa associated with inflammatory signalling and short-chain fatty acid (SCFA) metabolism. Photobiomodulation (PBM), a non-invasive light therapy, has been investigated as a potential adjunctive treatment for PD, with proposed effects on neural, metabolic, and immune pathways. We previously reported the five-year clinical outcomes in a PBM-treated Parkinson's disease case series. Here we report the five-year gut microbiome outcomes based on longitudinal samples collected from the same participants. This was an exploratory, open-label longitudinal study without a control group. Objective: Our objective was to assess whether long-term PBM was associated with changes in gut microbiome diversity and composition in the same Parkinson's disease cohort as previously assessed for changes in Parkinson's symptoms. Methods: Six participants from the earlier PBM proof-of-concept study who had been diagnosed with idiopathic PD and who had continued treatment (transcranial light emitting diode [LED] plus abdominal and neck laser) for five years had their faecal samples analysed by 16S rDNA sequencing to assess microbiome diversity and taxonomic composition. Results: Microbiome analysis revealed significantly reduced evenness (α-diversity) and significant shifts in β-diversity over five years, as assessed by Permutational Multivariate Analysis of Variance (PERMANOVA). At the phylum level, Pseudomonadota and Methanobacteriota decreased in four of the six participants. Both of these phyla are often increased in the Parkinson's microbiome compared with the microbiomes of healthy controls. Family-level changes included increased acetate-producing Bifidobacteriaceae (five of the six participants); decreased pro-inflammatory, lipopolysaccharide (LPS)-producing Enterobacteriaceae (two of the three participants who have this bacterial family present); and decreased LPS- and H2S-producing Desulfovibrionaceae (five of six). At the genus level, Faecalibacterium, a key butyrate producer, increased in four of the six participants, potentially leading to more SCFA availability, although other SCFA-producing bacteria were decreased. This was accompanied by reductions in pro-inflammatory LPS and H2S-producing genera that are often increased in the Parkinson's microbiome. Conclusions: This five-year case series represents the longest follow-up of microbiome changes in Parkinson's disease, although the interpretation of results is limited by very small numbers, the lack of a control group, and the inability to control for lifestyle influences such as dietary changes. While causal relationships cannot be inferred, the parallel changes in improvements in mobility and non-motor Parkinson's symptoms observed in this cohort, raises the hypothesis that PBM may interact with the gut-brain axis via the microbiome. Controlled studies incorporating functional multi-omics are needed to clarify potential mechanistic links between microbial function, host metabolism, and clinical outcomes.},
}

@article {pmid41517479,
year = {2025},
author = {Wu, B and He, Z and Xu, T},
title = {A Vanished Association Between Proton Pump Inhibitors and Clostridioides Difficile Infection After Minimizing Bias.},
journal = {Journal of clinical medicine},
volume = {15},
number = {1},
pages = {},
pmid = {41517479},
issn = {2077-0383},
abstract = {Background: The gut microbiome might be affected by proton-pump inhibitors (PPIs), increasing the risk of Clostridioides difficile infection (CDI); however, the association between PPIs and Clostridioides difficile infection (CDI) remains controversial. Aim: The aim of this study is to reevaluate the association between PPIs and CDI based on pharmacovigilance data, taking competition bias into account. Methods: PPI-related CDI adverse event reports, based on the Food and Drug Administration adverse event reporting system database from 2004 to 2023, were analyzed. Included PPI cases were stratified into CDI and non-CDI groups. Disproportionality analysis was performed using the reporting odds ratio (ROR) and information component (IC). The effect of competition bias on signal detection was quantitatively investigated. Age-stratified analyses were conducted to assess residual confounding. Results: A total of 238,470 PPI reports were included, with 1268 cases in the CDI group and 237,202 cases in the non-CDI group. Initial analysis revealed a significant PPI-CDI association (ROR = 2.36, 95% confidence interval (95%CI) 2.19 to 2.53; IC = 1.21, 95%CI 0.97 to 1.45), with CDI signals detected for five PPI agents, including pantoprazole, omeprazole, lansoprazole, rabeprazole, and dexlansoprazole. After excluding competition from antibacterial drugs, CDI signal strength decreased substantially (ROR = 1.47, 95%CI 1.34 to 1.62; IC = 0.55, 95%CI 0.23 to 0.87), retaining a significant CDI signal only for rabeprazole and pantoprazole. Upon further exclusion of antibacterial or immunosuppressive drug users and renal injury event cases, CDI signal strength decreased (ROR = 1.48, 95%CI 1.32 to 1.66; IC = 0.56, 95%CI 0.18 to 0.94), with pantoprazole as the sole CDI signal drug. Age-stratified analyses demonstrated complete signal loss after antibacterial drug adjustment across all age groups. Conclusions: The current large-scale pharmacovigilance study indicated that the observed PPI-CDI association may be mediated predominantly by antibacterial drug co-exposure rather than PPI direct causation.},
}