@article {pmid42726613,
year = {2026},
author = {Chen, S and Guan, Q and Zhou, D and Duan, L and Hu, J},
title = {SPFuseRanker: A Multi-Importance Score Fusion Framework for Core Microbiome Identification in Metagenomic Data.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2026.3733474},
pmid = {42726613},
issn = {2998-4165},
abstract = {Clinical metagenomic data are typically high-dimensional, sparse, and zero-inflated, and are often characterized by limited sample sizes and measurement noise. In addition, different feature-importance methods may produce inconsistent taxon rankings, which limits the stability of single-method feature selection and complicates the identification of candidate core microbiome members. To address this issue, we propose SPFuseRanker, a score-fusion-based ranking framework for integrating multiple microbial importance measures in metagenomic data. The method constructs a consensus score vector by combining heterogeneous importance signals, including statistical tests, correlation analysis, univariate classification performance, and tree-based feature importance. A top-weighted distance function based on Softmax normalization is introduced to emphasize highly ranked taxa during the fusion process. The optimization of the fused score vector is formulated as a minimum-distance problem and solved using a genetic algorithm (GA). We evaluate the proposed method using both synthetic simulations and a real-world systemic lupus erythematosus (SLE) gut microbiome dataset. Experimental results show that SPFuseRanker achieves more stable ranking performance compared with several representative rank aggregation and score fusion methods, particularly in terms of ranking consistency and robustness under noise. In addition, the selected candidate microbial taxa demonstrate improved predictive performance in disease classification tasks, suggesting their potential relevance to SLE-associated microbial signatures. Overall, SPFuseRanker provides a practical framework for integrating multi-source importance information and may serve as a useful tool for candidate core microbiome identification in metagenomic studies.},
}

@article {pmid42727097,
year = {2026},
author = {Wangpraseurt, D and Valle-Pérez, AU},
title = {Translating Bioengineering Principles to Coral Reef Restoration Under Climate Change.},
journal = {Annual review of marine science},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-marine-040825-121115},
pmid = {42727097},
issn = {1941-0611},
abstract = {Coral reefs support immense biodiversity and human well-being, yet accelerating environmental change is driving unprecedented losses of habitat-forming hard corals in recent decades and demands new strategies to strengthen reef resilience. Advances in bioengineering are expanding the controllable parameter space of living systems, enabling intervention at genetic, cellular, and microenvironmental scales, thereby creating new possibilities for scalable coral reef restoration. In this review, we synthesize recent bioengineering advances applied to coral restoration, focusing on key bottlenecks such as recruitment limitation, outplant survivorship, bleaching susceptibility, and early mortality These approaches include controlled-release surfaces for inductive settlement signals, antifouling and growth-optimized substrates, modular biofabrication platforms, targeted microbiome manipulation, and nanomaterial-mediated mitigation of oxidative stress. We argue that, if successfully translated at scale, bioengineering approaches could prove transformative for sustaining reef ecosystem function under accelerating climate change.},
}

@article {pmid42727100,
year = {2026},
author = {de Goeij, JM and Hudspith, M and Achlatis, M and Easson, CG and Freeman, CJ and Fiore, CL and Mueller, B},
title = {The Sponge Loop: How an Ancient Animal-Microbe Engine Fuels Modern Ocean Ecosystems.},
journal = {Annual review of marine science},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-marine-040523-021051},
pmid = {42727100},
issn = {1941-0611},
abstract = {Sponges can be considered biological engines that fuel the ecology of shallow-water to deep-sea ecosystems through the sponge loop. Here, we discuss new insights on the role of the sponge holobiont in the uptake, transformation, and transfer of resources that fuel the many food webs in which sponge engines operate. The tightly coupled animal-microbe partnership consists of many intrinsic traits (e.g., growth form, tissue architecture, and number and diversity of microbial symbionts) that depend on a huge variety of environmental factors (e.g., temperature, light, and both organic and inorganic resources). The sponge loop mediates resource cycling at organismal, ecosystem, and potentially even global scales. Linking sponge physiology and microbiome function with ecosystem budgets and refined global biomass estimates to situate sponges within Earth's elemental cycles, including the biological carbon pump, is necessary to transition from illustrative case studies to predictive theory and to forecast the response of sponge engines to future ocean conditions.},
}

@article {pmid42727124,
year = {2026},
author = {Yang, H and Hoque, MM and Zhao, J and Dovom, HA and Hai, FI and Jiang, G},
title = {Wastewater-derived gut microbiome: global patterns and associations with population health.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126898},
doi = {10.1016/j.watres.2026.126898},
pmid = {42727124},
issn = {1879-2448},
abstract = {Urban wastewater systems aggregate gut microbiome signals from large populations, enabling exploration of their associations with population-level health patterns. However, it remains unclear whether wastewater-derived gut microbiome (WGM) simply represents a composite of individual gut microbes or whether it forms structured ecological patterns with potential relevance to population-level health-burden gradients. We analyzed 661 untreated wastewater metagenomes from 220 cities across 97 countries spanning all inhabited continents to characterize the global WGM. WGM exhibited broad phylogenetic diversity, with more than 95% of detected genera occurring in over 80% of samples worldwide. Co-occurrence network analysis revealed distinct, densely connected modules and structurally heterogeneous hub and bridging taxa, indicating organized network architecture that was not explained by abundance alone. Under the iCAMP framework, WGM turnover was predominantly classified as dispersal limitation across climate zones, continents, development levels, and sampling years. We then explored associations between WGM and population-level health indicators using a multi-model machine-learning framework. Across 21 health-burden indicators covering non-communicable diseases, infectious diseases, injuries, and mental health conditions, WGM-based classification of low- versus high-burden countries exceeded shuffled-label expectations for 19 indicators. Recurrently selected WGM taxa were identified across multiple feature-selection strategies. Together, these results show that operationally defined WGM profiles show reproducible structure and broad associations with country-level health-burden indicators.},
}

@article {pmid42727131,
year = {2026},
author = {Wang, T and Qian, JD and Hu, JT and Jiang, ZX and Qiu, LW and Yan, G and Xu, XY and Zhou, C and Ren, H},
title = {Building biofilms for saline hydrogenotrophic denitrification from contrasting origins: Convergent acclimation, divergent performance.},
journal = {Water research},
volume = {308},
number = {Pt B},
pages = {126879},
doi = {10.1016/j.watres.2026.126879},
pmid = {42727131},
issn = {1879-2448},
abstract = {Hydrogenotrophic denitrification is promising for deep nitrogen removal from saline, low-C/N wastewaters, but rapid establishment of stable biofilms at high salinity remains challenging. Here, two saline-adapted inocula from two representative, functionally contrasting habitats-a functionally-diversified inoculum from mangrove sediment and a functionally-focused inoculum from seabed sediment-were acclimated in parallel H2-based membrane biofilm reactors at constant 3.5% salinity. The Diverse-derived biofilm required 80 d to reach steady state and achieved only partial denitrification with 61.1% nitrate removal and considerable nitrite accumulation. In contrast, the Focus-derived biofilm rapidly established complete denitrification within ∼40 d, which was maintained for >50 d, with effluent NOx[-] below 1 mg-N·L[-1] and 98.7% nitrate removal. Microbiome analyses showed that identical operation promoted convergence in community structure and enriched similar community-level functional potentials. However, genome-resolved analysis revealed distinct source-dependent functional organization among dominant microbial populations. Complete denitrifiers co-encoding denitrifying, hydrogenotrophic, and autotrophic functions were preferentially enriched in the Focus-derived biofilm, whereas these functions remained partitioned among different dominant populations in the Diverse-derived biofilm, coinciding with less complete denitrification. These findings indicate that saline hydrogenotrophic denitrification performance depends not only on which functions are enriched at the community level, but also on how key functions become organized among microbial populations, providing a previously overlooked criterion for inoculum selection in saline biological nitrogen control.},
}

@article {pmid42727308,
year = {2026},
author = {Gautam, R and Das, A and Kumar, S and Ali, W and Pasha, SA},
title = {Artificial intelligence in postmortem interval estimation: emerging trends, predictive models, and forensic applications.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {86},
number = {},
pages = {102988},
doi = {10.1016/j.legalmed.2026.102988},
pmid = {42727308},
issn = {1873-4162},
abstract = {BACKGROUND AND OBJECTIVE: Accurate estimation of the postmortem interval (PMI) remains a critical yet challenging task in forensic science due to the inherent variability of biological and environmental factors. Conventional methods based on observable postmortem changes are often subjective and limited in temporal applicability. Recent advancements in artificial intelligence (AI), particularly machine learning (ML) and deep learning (DL), have provided promising approaches with the potential to improve the accuracy, objectivity, and reproducibility of PMI estimation. This systematic review aims to critically evaluate recent developments in AI-based approaches for PMI estimation, with emphasis on analytical techniques, biological matrices, and predictive performance.

METHODOLOGY: A systematic literature search was conducted following PRISMA 2020 guidelines across PubMed/MEDLINE, Scopus, Web of Science Core Collection, IEEE Xplore, and ScienceDirect databases for studies published between January 2021 and April 2026. Eligible studies included original research evaluating artificial intelligence, machine-learning, chemometric, statistical, and other data-driven computational approaches for PMI estimation using human or animal postmortem samples. Data extraction focused on study design, biological matrices, biomarkers, AI models, PMI range, and performance metrics such as accuracy, mean absolute error (MAE), and coefficient of determination (R[2]). Quality assessment was performed using the Prediction Model Risk of Bias Assessment Tool (PROBAST). Owing to substantial methodological heterogeneity across AI models, datasets, outcome measures, and validation strategies, a structured narrative synthesis with descriptive summaries of reported performance metrics was conducted instead of a quantitative meta-analysis.

RESULTS: A total of 29 studies were included, comprising animal (n = 14), human (n = 13), and combined human-animal datasets (n = 2). The evidence encompassed controlled animal experiments and human studies, with substantial variation in PMI windows, prediction tasks, computational approaches, and validation strategies. Machine learning and deep learning models, together with chemometric and conventional statistical approaches, demonstrated promising predictive performance across metabolomic, proteomic, microbiome, spectroscopic, and imaging datasets, with prediction errors as low as approximately 1-5 h reported in some controlled experimental settings. However, predictive performance was generally more promising in controlled experimental settings, whereas human evidence was more limited and heterogeneous. External validation was also limited, restricting assessment of model generalizability and routine forensic applicability.

CONCLUSION: Computational and predictive approaches demonstrate considerable potential to improve the objectivity and predictive performance of PMI estimation; however, substantial methodological heterogeneity, limited external validation, small human datasets, and reliance on experimental models currently constrain their translation into routine forensic practice.},
}

@article {pmid42727354,
year = {2026},
author = {Maréchal, S and Kümmerli, R},
title = {The role of siderophores for bacterial community building.},
journal = {Current opinion in microbiology},
volume = {94},
number = {},
pages = {102825},
doi = {10.1016/j.mib.2026.102825},
pmid = {42727354},
issn = {1879-0364},
abstract = {Iron is an essential trace element for most organisms on earth including bacteria. However, iron in the environment generally occurs in its ferric (Fe[3+]) form and is therefore not bioavailable. To capture ferric iron, many bacteria produce siderophores - a class of secreted secondary metabolites that scavenge iron from natural sources and allow iron uptake via specific transporters. As secreted molecules, siderophores inevitably affect other community members, and recent evidence suggests that siderophores play important roles in shaping interaction networks between strains and species in complex communities. In this review, we first explain how siderophores induce ecological interactions among bacteria ranging from mutualism to exploitation to competition. Subsequently, we elaborate on how physicochemical properties of siderophores, like production rates, diffusibility, stability, iron affinity, and chemical specificity, influence the type and strength of siderophore-mediated interactions. Finally, we introduce various scenarios to illustrate how siderophore interaction networks and community building can arise. We conclude our review by highlighting that our knowledge of siderophore interaction networks is restricted to a few taxa that were studied in detail, and that future work should break this limitation by studying the role of siderophore-mediated interactions at the microbiome scale.},
}

@article {pmid42727575,
year = {2026},
author = {Deng, ZL and Safaei, N and McHardy, AC},
title = {Metax enables accurate cross-domain taxonomic profiling of metagenomes.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.08.024},
pmid = {42727575},
issn = {1097-4172},
abstract = {Taxonomic profiling is fundamental to microbiome research, yet achieving high species-level accuracy remains challenging for complex communities that span bacteria, viruses, eukaryotes, and archaea, and these limitations are exacerbated in low-biomass, host-dominated samples. We introduce Metax, a cross-domain taxonomic profiler that integrates coverage-based probabilistic modeling with an expectation-maximization framework to distinguish true microbial signals from artifacts. Across >600 samples from host-associated, environmental, wastewater, and low-biomass clinical settings, including benchmarks with limited reference representation, Metax improved profiling accuracy, achieving on average 55% higher F1 scores and 45% lower Bray-Curtis dissimilarity than other methods. Moreover, this broad evaluation demonstrated that Metax resolved bacterial and viral signatures of peri-implantitis in oral microbiomes and revealed signals suggestive of reagent-borne contaminants and reference misassemblies in plasma-cell-free DNA. By leveraging genome-wide coverage evidence, Metax enables robust cross-domain profiling across diverse sample types and sequencing depths, including settings where reference databases are highly incomplete.},
}

@article {pmid42727634,
year = {2026},
author = {Narasimhamurthy, RK and N, RK and Rajendra, VKJ and Shetty, P},
title = {Microbiome Crosstalk Across Oral, Gut, and Breast Niches: Implications for Breast Cancer Diagnosis, Prevention, and Therapy.},
journal = {Translational research : the journal of laboratory and clinical medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.trsl.2026.09.007},
pmid = {42727634},
issn = {1878-1810},
abstract = {Breast cancer is a leading cause of morbidity and mortality in women worldwide. Breast tissue, oral and gut microbiota, are actively involved in regulating tumor onset, progression, and treatment response. Multiple factors, including ethnicity, sex, disease subtype, and stage, influence their signatures. The oral-gut-breast microbiome tripartite axis influences breast cancer by inducing DNA damage, altering the host immune response, and activating or suppressing cell-signaling processes through regulation of hormones, metabolites, and inflammatory markers. Modulating microbial homeostasis through diet, selective depletion of causative bacteria, and precise delivery techniques, such as nanotechnology, for delivering bioengineered microbes or microbial cargo, are among the recent therapeutic approaches with potential. However, generalizing findings and standardizing clinical regimens across diverse populations remains a persistent challenge. This review highlights the importance of microbiome-informed, integrated strategies for enhancing breast cancer prevention, diagnosis, and treatment by exploring the causal and mechanistic microbial trends.},
}

@article {pmid42727829,
year = {2026},
author = {Xu, P and Li, L and Wei, Y and Xu, Y and Zhang, Y and Ye, W and Peng, X},
title = {Divergent responses of the rhizosphere microbiome to organic amendments sustain cadmium immobilization and low crop Cd accumulation after remediation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135835},
doi = {10.1016/j.biortech.2026.135835},
pmid = {42727829},
issn = {1873-2976},
abstract = {This study integrated a two-stage immobilization-cultivation experiment to evaluate the effects of three immobilization strategies (inorganic, organic, and organo-mineral amendments) and two fertilization modes (mineral fertilizer alone and partial substitution with organic fertilizer) on soil cadmium (Cd) immobilization and plant Cd accumulation. During the immobilization phase, the organo-mineral strategy achieved the highest Cd immobilization efficiency of 69.5%. In the cultivation phase, the use of mineral fertilizer alone led to Cd remobilization, whereas organic substitution maintained or even enhanced immobilization, reducing shoot Cd accumulation in pak choi by up to 58.3%. Notably, the combined organic immobilization and organic substitution treatment (OP) was particularly effective: despite not having the lowest soil available Cd, it achieved the lowest plant Cd accumulation (2.83 mg·kg[-1]). Genomic analysis indicated that the OP treatment enriched core metagenome-assembled genomes (MAGs), including MAG8/Pelagerythrobacter, MAG13/Sphingomicrobium, and MAG30/VAYN01, which contained the highest abundances of genes related to extracellular polymeric substance (EPS) synthesis, phosphorus mobilization, and complexation-precipitation, suggesting the potential of these microbes to enhance EPS secretion and phosphate precipitation for rhizospheric Cd interception. This functional potential, along with the measured high EPS content (259.88 mg·kg[-1]) and low plant Cd accumulation in the OP group, provides coherent correlative evidence supporting the hypothesis that an "EPS barrier-chemical precipitation" mechanism synergistically reduces Cd migration to root surfaces. Collectively, continuous organic management can maintain soil fertility, enhance Cd immobilization, and promote low-Cd crop production, offering an efficient strategy for the safe utilization of remediated farmland.},
}

@article {pmid42727835,
year = {2026},
author = {Zwolińska, J and Olmo, R and Majo-Cuervo, M and Menéndez, E and Witek-Krowiak, A},
title = {From fibers to fields: electrospun nanofiber carriers at the soil-microbiome interface.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {109043},
doi = {10.1016/j.biotechadv.2026.109043},
pmid = {42727835},
issn = {1873-1899},
abstract = {Sustainable agriculture requires innovative technologies that improve crop productivity while reducing environmental impacts. Electrospun nanofibers (ESN) have emerged as promising materials due to their high surface area, tunable structure, and ability to incorporate and release bioactive compounds in a controlled manner. This review examines ESN as an integrative approach for delivering bioactive substances and beneficial microorganisms directly to soil and plants. Recent advances in the production, evaluation, and agricultural applications of ESNs are discussed, with particular attention given to the use of biodegradable polymers and the integration of live microorganisms into nanofibrous matrices. Beyond their role as delivery platforms, ESN may interact with soil microbial communities through their surface properties, degradation behavior, and effects on local resource availability. However, direct evidence linking ESN application to changes in soil microbiome structure and function remains limited. Nevertheless, critical limitations-such as scalability, high production costs, sterility challenges, and potential ecological risks-must be addressed. A thorough understanding of ESN-microbiome-soil dynamics, supported by standardized characterization, long-term field studies, and molecular tools, is crucial for their safe and effective deployment in sustainable agriculture.},
}

@article {pmid42727915,
year = {2026},
author = {Ma, Y and Li, Z and Zhu, Y and Li, J and Qu, Z and Zhou, X and Sun, J and Zhao, W and Dong, S},
title = {Nano-Enabled Agrochemicals as Ecological Technologies: Ecotoxicity, Non-Target Effects, and a Safe-and-Sustainable-by-Design Framework.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125660},
doi = {10.1016/j.envres.2026.125660},
pmid = {42727915},
issn = {1096-0953},
abstract = {Nanofertilizers and nanopesticides provide significant agricultural benefits through enhanced nutrient efficiency and reduced pesticide application; however, their nanoscale properties raise environmental safety concerns. As emerging ecological technologies designed to minimize environmental footprints, these nano-enabled agrochemicals require systematic safety evaluation. However, conventional ecotoxicity tests-designed for soluble chemicals-cannot adequately capture nanoparticle stability, aggregation, or time-dependent exposure, creating a 'measurement gap' in risk assessment. This review summarizes the historical development, primary application areas, and cutting-edge advancements of nanotechnology. A systematic analysis is conducted on the dose-dependent phytotoxicity of metal and metal oxide nanoparticles, including their impacts on chlorophyll content, microbial community structure, carbon and nitrogen cycling enzymes, arbuscular mycorrhizal colonization, soil respiration, and plant metabolic remodeling. Additionally, the review evaluates the effects on soil physicochemical properties, plant-microbe symbioses, and non-target organisms such as invertebrates, pollinators, and nematodes. Finally, we propose a Safe-and-Sustainable-by-Design framework that emphasizes low-hazard materials, predictable degradability, life-cycle thinking, carrier minimization, and AI-assisted risk prediction to guide responsible nano-agrochemical development.},
}

@article {pmid42727931,
year = {2026},
author = {Yang, J and Liu, H and Zhang, W and Cui, J and Xing, X and Dong, C},
title = {Urbanization-Associated Microbial Diversity Loss and Its Impact on Elderly Health: Integrating Environmental and Host Microbiome Dynamics.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70414},
doi = {10.1111/1462-2920.70414},
pmid = {42727931},
issn = {1462-2920},
support = {ZR2024QC264//Natural Science Foundation of Shandong Province/ ; },
mesh = {Humans ; *Urbanization ; *Bacteria/isolation & purification/classification/genetics ; *Microbiota ; China ; *Gastrointestinal Microbiome ; Biodiversity ; Feces/microbiology ; *Environmental Microbiology ; },
abstract = {Urbanization is strongly associated with microbial diversity loss in both built environments and elderly gut microbiomes, with significant health consequences. This study across 12 rural-to-urban care facilities in eastern China analysed 320 environmental and 120 faecal samples. Urbanization progressively reduced microbial alpha diversity in air, surfaces, and resident guts. Urban environments showed increased opportunistic pathogens and antibiotic resistance genes (ARGs), alongside decreased beneficial taxa and short-chain fatty acid pathways. Strong environment-host microbiome concordance was observed, with intensified microbial transmission in urban settings. Critically, environmental microbiome features mediated over 50% of urbanization's detrimental effects on resident frailty, inflammation, and cognitive decline. Models combining environmental and gut microbiome data accurately predicted frailty (AUC = 0.89). The findings highlight that urbanization-induced microbial alterations in care facilities are key mediators of elderly health decline, underscoring the need for microbiome-informed design to mitigate these risks.},
}

Humans
*Urbanization
*Bacteria/isolation & purification/classification/genetics
*Microbiota
China
*Gastrointestinal Microbiome
Biodiversity
Feces/microbiology
*Environmental Microbiology

@article {pmid42728218,
year = {2026},
author = {Qu, Y and Liu, X and Dong, L and Su, Z and Bouwmeester, H and Ma, P and Guo, Q},
title = {Spent mushroom substrate adsorbs fusaric acid to protect the cucumber rhizosphere microbiome and suppress fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71289},
pmid = {42728218},
issn = {1526-4998},
support = {//Outstanding Talent Project of the Yanzhao Golden Platform Program/ ; C2025301024//Natural Science Foundation of Hebei Province/ ; //HAAFS International Science and Technology Cooperation Project (2026KJCXZX-ZBS-GH01)/ ; //HAAFS Science and Technology Innovation Special Project (2026KJCXZX-ZBS-11)/ ; },
abstract = {BACKGROUND: Cucumber Fusarium wilt, caused by Fusarium oxysporum f. sp. cucumerinum, is aggravated by fusaric acid, a phytotoxic virulence factor that can disrupt rhizosphere microbial communities. Spent mushroom substrate can suppress Fusarium wilt, but whether this protection is linked to reduced fusaric acid stress in the rhizosphere remains unclear.

RESULTS: Spent mushroom substrate adsorbed fusaric acid in vitro and reduced its transfer through natural soil. Adsorption fitted the Langmuir-Freundlich isotherm, with a maximum adsorption capacity of 52.72 μg g[-1], and followed pseudo-second-order kinetics. Fourier transform infrared spectroscopy and chemical blocking assays implicated secondary amide groups as key binding sites. In a dual-chamber pot system, 1% spent mushroom substrate reduced fusaric acid transfer to the cucumber rhizosphere from 15.75, 31.50 and 62.29 μg g[-1] soil to 3.25, 8.31 and 15.49 μg g[-1] soil under low, medium and high fusaric acid inputs, respectively. In nonsterile soil, spent mushroom substrate reduced the disease index by 19-26%, whereas this suppressive effect was not observed in sterile soil. Bacterial 16S rRNA gene metabarcoding showed that medium and high fusaric acid inputs reduced bacterial richness and diversity and shifted community structure. Under high fusaric acid exposure, the relative abundance of Bacillus declined from 3.18 to 2.19%, but was maintained at 2.96% with spent mushroom substrate.

CONCLUSION: Spent mushroom substrate protects cucumber against Fusarium wilt partly by adsorbing fusaric acid and reducing its inhibitory effects on beneficial rhizobacteria. This adsorption-mediated mechanism supports spent mushroom substrate as a sustainable, microbiome-friendly amendment for managing soil-borne Fusarium diseases. © 2026 Society of Chemical Industry.},
}

@article {pmid42728275,
year = {2026},
author = {Charlier, P and Gebelin, M and Armengaud, J},
title = {A 12[th] century AD pathological oral microbiome: Saint Laurence O'Toole.},
journal = {British dental journal},
volume = {241},
number = {5},
pages = {288-289},
doi = {10.1038/s41415-026-0195-5},
pmid = {42728275},
issn = {1476-5373},
}

@article {pmid42728538,
year = {2026},
author = {Kumar, R and Maurya, R and Maity, A and Tiwari, RK and Lal, MK and Roy, A and Yadav, R and Rao, GP},
title = {Phytoplasma-plant interactions: effector-mediated host reprogramming, hormonal crosstalk, metabolic alterations and plant-mediated vector manipulation.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {9},
pages = {},
pmid = {42728538},
issn = {1573-0972},
mesh = {*Phytoplasma/genetics/pathogenicity/metabolism/physiology ; *Host-Pathogen Interactions ; *Plants/microbiology/metabolism ; Plant Growth Regulators/metabolism ; Plant Diseases/microbiology ; Animals ; Virulence Factors/metabolism/genetics ; *Phytoplasma Disease/microbiology ; Bacterial Proteins/metabolism/genetics ; Insect Vectors/microbiology ; },
abstract = {Phytoplasmas are wall-less, phloem-restricted bacterial pathogens that infect over 1,000 plant species, causing substantial losses in agriculture, horticulture, and forestry worldwide. Despite their reduced genomes and limited metabolic autonomy, these obligate parasites colonize diverse hosts through secreted effector proteins that extensively reprogram plant development, metabolism, immune signalling, and vector interactions. Advances in genomics, transcriptomics, proteomics, metabolomics, and functional studies have substantially clarified the molecular basis of phytoplasma pathogenicity and symptom development. This review synthesizes current understanding of phytoplasma-plant interactions, covering phytoplasma biology, genome evolution, and the infection cycle across plant and insect vector hosts. We examine the molecular functions of key effectors, SAP11, SAP54/PHYL1, SAP05, TENGU, SWP1, and recently identified virulence factors, focusing on how they target host transcription factors, phytohormone networks, protein degradation pathways, and immune responses to promote colonization and disease progression. We further discuss how phytoplasma infection disrupts phytohormone signalling, primary and secondary metabolism, and developmental programs to produce characteristic disease symptoms, with particular attention to pathogen-induced changes in host volatiles and nutritional quality that alter vector behaviour and enhance transmission. Finally, we summarize insights from multi-omics studies and emerging management strategies, including CRISPR-based genome editing, RNAi, rapid molecular diagnostics, resistant cultivars, microbiome-based approaches, and sustainable vector control, and highlight key knowledge gaps and priorities for developing effective, environmentally sustainable phytoplasma disease management.},
}

*Phytoplasma/genetics/pathogenicity/metabolism/physiology
*Host-Pathogen Interactions
*Plants/microbiology/metabolism
Plant Growth Regulators/metabolism
Plant Diseases/microbiology
Animals
Virulence Factors/metabolism/genetics
*Phytoplasma Disease/microbiology
Bacterial Proteins/metabolism/genetics
Insect Vectors/microbiology

@article {pmid42728625,
year = {2026},
author = {Schroeder, BG and Bhattacherjee, R and Bonatelli, ML and da Rocha, UN and Sträuber, H and Harms, H and Nikolausz, M},
title = {Anaerobic mono-digestion of wheat straw in a three-stage semi-continuous system inspired by a beetle larva gut.},
journal = {Biotechnology for biofuels and bioproducts},
volume = {19},
number = {1},
pages = {},
pmid = {42728625},
issn = {2731-3654},
support = {nº 88887.161417/2017-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {Based on the efficient digestive system of the larva of the sun beetle (Pachnoda marginata) in utilizing lignocellulose-rich biomass, a reactor system was designed to partially mimic processes that occur in the larval gut. We aimed developing a process with this system for anaerobic mono-digestion of wheat straw to produce volatile fatty acids (VFAs) and biogas. Three stirred tank reactors connected in series were customized with polyurethane foam and operated at 37 °C. The first two reactors were designed to mimic the midgut of the larva with enhanced VFA production and the third one to resemble the hindgut and optimized for methanogenesis. The system was fed in a semi-continuous regime with ground wheat straw in an alkaline medium. Enrichment cultures from midgut and hindgut of the larva were used as inocula and three conditions with increasing organic loading rate were tested. The highest biomass to methane conversion occurred at the lowest organic loading rate and highest retention time, when a methane yield of 148 mLNorm g[-1]VS was obtained and VS degradation reached 44%. The microbial community was enriched toward cellulose and hemicellulose degrading taxa, including Dysgonomonadaceae, Lachnospiraceae, Marinilabiliaceae and Ruminococcaceae. The methanogenic community shifted from predominance of Methanosarcina to Methanobacterium and Methanoculleus. A comparison with other studies investigating straw utilizing bioreactors confirmed that a core microbiome composed of the phyla Firmicutes, Bacteroidetes and Proteobacteria effectuates the anaerobic digestion of lignocellulose-rich materials, regardless of the source of the inoculum and the process conditions. The designed process was stable and capable to convert wheat straw into methane and carboxylates. Further adaptations are suggested to improve the anaerobic digestion and decrease assembly and operating costs.},
}

@article {pmid42728788,
year = {2026},
author = {Xu, F and Fan, Y and Guo, X and Lyu, J and He, Y},
title = {Microplastics and Nanoplastics in Food: Dietary Toxicology Beyond Particle Counts.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {5},
pages = {e70639},
doi = {10.1111/1541-4337.70639},
pmid = {42728788},
issn = {1541-4337},
support = {82474179//National Natural Science Foundation of China/ ; 2024A1515011705//Guangdong Basic Research Center of Excellence for Aggregate Science, Guangdong Basic and Applied Basic Research Foundation/ ; 2023A1515110677//Guangdong Basic Research Center of Excellence for Aggregate Science, Guangdong Basic and Applied Basic Research Foundation/ ; JCYJ20240813113552066//Foundation of Shenzhen Science and Technology Innovation Commission/ ; //Shenzhen Science and Technology Innovation Program/ ; //Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
mesh = {*Microplastics/toxicity/analysis ; Humans ; *Food Contamination/analysis ; Animals ; Dietary Exposure ; *Nanoparticles/toxicity/analysis ; },
abstract = {Microplastics (MPs) and nanoplastics (NPs) are ubiquitous contaminants in dietary sources, including seafood, table salt, infant formula, and drinking water. Recent stimulated Raman scattering microscopy has reported approximately 2.4 × 10[5] MPs and NPs per liter in selected bottled-water samples. While these estimates remain contested and should not be generalized across products, they highlight the extent to which conventional analytical methods may underestimate nanoscale exposure. Current risk frameworks remain anchored to particle-count and mass-based metrics that do not capture reactive surface area, food-matrix interactions, or chemical cargo. This review examines dietary MP/NP toxicology through three underexplored dimensions: food matrix-particle interactions that transform particle surfaces before intestinal contact; potential engagement of endogenous intestinal transport pathways; and diet-dependent modulation of epithelial permeability. It integrates evidence across molecular, cellular, organ-level, and microbiome-mediated pathways, with emphasis on immune-metabolic dysregulation, endocrine disruption, hepatic toxicity, and neurodevelopmental risk. Key uncertainties include NP absorption kinetics in lipid-rich matrices, particle-facilitated chemical transfer, progressive corona remodeling during digestion, and the lack of standardized methods for detecting NPs in complex foods. In vitro and rodent studies support mechanistic links between NP exposure and NLRP3-associated inflammation, hepatic steatosis, endocrine disruption, and gut dysbiosis, but most use concentrations exceeding estimated human tissue levels. We propose a surface-area-normalized hazard quotient for surface-mediated endpoints as a complement to mass-based metrics, while recognizing that additive-leaching toxicity may require a separate mass-based framework.},
}

*Microplastics/toxicity/analysis
Humans
*Food Contamination/analysis
Animals
Dietary Exposure
*Nanoparticles/toxicity/analysis

@article {pmid42728849,
year = {2026},
author = {Nabhan Homsi, M and von Bergen, M},
title = {GUTchetp: integrated prediction of gut microbial biotransformation profiles using ensemble monolingual and multilingual neural machine translation and enzyme class consistency-reaction similarity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2726639},
doi = {10.1080/19490976.2026.2726639},
pmid = {42728849},
issn = {1949-0984},
mesh = {Biotransformation ; Humans ; *Computational Biology/methods ; *Gastrointestinal Microbiome ; Neural Networks, Computer ; *Bacteria/metabolism/enzymology/classification/genetics ; Enzymes/metabolism ; },
abstract = {The analysis of the metabolic fate of chemical compounds in the human gut remains a fundamental challenge, as comprehensive experimental characterization across the vast chemical space is infeasible. Moreover, despite progress in computational biology, a comprehensive tool for predicting microbe-dependent metabolism of diverse chemicals is still lacking. To address these challenges, we introduce the GUTchetp framework, which comprises two components: one predicts gut biotransformation products and was tested on a benchmark of six compound categories, whereas the other identifies the associated microbial enzymes and species and was evaluated on a benchmark of 95 metabolism events. The first component employs an ensemble of monolingual and multilingual neural machine translation models, integrating transfer learning, mixed fine-tuning, multiple molecular representations, and adaptive data augmentation. The ensemble model outperformed previous approaches, achieving a Top-20 BLEU score and MaxFrag accuracy of 66.59% and 67.19%, respectively. The second component applies a re-ranking rule that combines the prediction consistency between two Enzyme Commission (EC) number classifiers with chemical reaction similarity, increasing accuracy by 34.38 percentage points over existing tools on the hidden dataset. Both components showed statistically significant improvements compared with existing tools, enabling the accurate prediction of 68.42% of known gut microbial biotransformation profiles, which is highly promising for anticipating gut microbial biotransformation outcomes. GUTchetp will thus pave the way for predicting the capacity of personalized gut microbiomes to metabolize intentional xenobiotics, such as pharmaceuticals and nutrients, and unintentional ones, such as environmental chemicals.},
}

Biotransformation
Humans
*Computational Biology/methods
*Gastrointestinal Microbiome
Neural Networks, Computer
*Bacteria/metabolism/enzymology/classification/genetics
Enzymes/metabolism

@article {pmid42728936,
year = {2026},
author = {La Porta, CAM and Marchi, E and Chiaffarelli, G and Vagge, I and Vaglia, V and De Marinis, P and Zapperi, S and Bocchi, S},
title = {Soil health and microbial diversity across land-use types: Evidence for agroecological management in peri-urban areas.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {29},
doi = {10.12688/openreseurope.22066.4},
pmid = {42728936},
issn = {2732-5121},
abstract = {BACKGROUND: Land-use change profoundly influences soil microbial communities, yet its impacts on richness and diversity remain incompletely resolved across taxa.

METHODS: Here, we characterized fungal and bacterial communities in soils from four contrasting land-use types-including crop, reforested, agroforestry, and uncultivated land-located in the same pedoclimatic conditions, using high-throughput amplicon sequencing of Internal Transcribed Spacer (ITS) and 16S ribosomal RNA (rRNA) genes. We quantified species richness and Shannon diversity and examined their relationships with key physicochemical parameters.

RESULTS: Our results reveal that fungal and bacterial communities responded differently to land-use management. Fungal richness was highest in reforested soils, whereas bacterial richness was more uniformly distributed across land uses. Shannon diversity showed greater sensitivity than richness, suggesting that differences in the distribution of relative abundances among taxa contributed substantially to the observed patterns. Multivariate ordinations and correlation analyses further demonstrated that soil properties such as pH, total nitrogen, and cation exchange capacity were significant drivers of microbial community composition and diversity patterns.

CONCLUSIONS: Our study provides new empirical evidence of how land management shapes biodiversity and informs strategies for enhancing soil health and ecosystem potential resilience.},
}

@article {pmid42729281,
year = {2026},
author = {Li, Y and Yang, J and Zhou, E and Geng, K and Lei, Z and Yao, X and Feng, F and Jin, Y and Kong, W and Hu, Y and Liang, H and Li, H and Yang, GP and Hong, T and Liu, D},
title = {A microdose cocktail and population pharmacokinetic study suggests potentially reduced CYP3A and P-gp activities in type 2 diabetes.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1924307},
doi = {10.3389/fphar.2026.1924307},
pmid = {42729281},
issn = {1663-9812},
abstract = {BACKGROUND: Diabetes patients often exhibit suboptimal efficacy and adverse reactions, accompanied by pharmacokinetic (PK) changes, indicating drug-metabolizing enzymes and transporters (DMET) activities may change. This study aimed to determine whether type 2 diabetes affects DMET activities and quantify impact magnitude. Furthermore, gut microbiome, pharmacogenetic and demographic characteristics were assessed to elucidate the sources of inter-individual variability (IIV) in DMET activities.

METHODS: The activities of CYP3A and transporters P-gp, OATP and BCRP were evaluated in type 2 diabetes patients and healthy volunteers (HVs) following a single oral dose of five probe drugs (midazolam, dabigatran etexilate, pitavastatin, rosuvastatin, and atorvastatin). Population pharmacokinetics (PopPK) and an exploratory machine learning (ML) analysis were employed to quantify the impact of type 2 diabetes on DMET activities.

RESULTS: Based on observed PK parameters, compared to HVs, type 2 diabetes patients exhibited increased exposure to midazolam (1.38-fold), dabigatran (1.40-fold), and atorvastatin (1.93-fold), whereas pitavastatin (0.931-fold) and rosuvastatin (1.25-fold) showed no change. PopPK analysis revealed that the mean activities of CYP3A and P-gp were potentially decreased by 23% and 27%, respectively, in type 2 diabetes patients, while no changes for OATP and BCRP. Notably, unlike the direct patient population covariate for P-gp, reduced CYP3A activity was indirectly estimated from lower Salmonella abundance. Additionally, factors such as sex, BCRP genotype, and Clostridium_XlVb partly explained the IIV in probe drugs exposure.

CONCLUSION: The findings regarding altered DMET activities and identified influence factors help to identify specific drug classes that may warrant closer clinical attention in type 2 diabetes patients.},
}

@article {pmid42729333,
year = {2026},
author = {Hu, W and Wang, X},
title = {Multi-omics approaches in idiopathic pulmonary fibrosis: from molecular mechanisms to therapeutic targets and precision medicine.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1899849},
doi = {10.3389/fphar.2026.1899849},
pmid = {42729333},
issn = {1663-9812},
abstract = {Idiopathic pulmonary fibrosis (IPF) is a progressive interstitial lung disease with limited therapeutic options and marked molecular heterogeneity. Despite available antifibrotic therapies, disease progression remains poorly predictable, highlighting the need for improved mechanistic understanding and therapeutic targeting. This review summarizes recent advances in multi-omics research to elucidate the molecular mechanisms underlying IPF and to identify potential biomarkers and pharmacological targets. Multi-omics studies, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiome profiling, and single-cell sequencing, have revealed key pathogenic mechanisms in IPF. Genetic susceptibility factors such as MUC5B promoter variants and telomere-related genes contribute to disease risk. Epigenetic regulation, including DNA methylation, histone modifications, and non-coding RNAs, plays a central role in fibrotic remodeling. Transcriptomic and proteomic analyses have identified dysregulated signaling pathways, including TGF-β, mTOR, cellular senescence, and extracellular matrix remodeling. Metabolomic alterations indicate disrupted lipid and amino acid metabolism. Importantly, integration of multi-omics datasets enables the identification of molecular endotypes, candidate biomarkers, and potential therapeutic targets. However, challenges including data integration, tissue heterogeneity, limited cohort size, and the need for functional validation remain important barriers to clinical translation. Continued development of multi-omics approaches may facilitate more accurate disease classification and support the development of personalized therapeutic strategies for IPF.},
}

@article {pmid42729411,
year = {2026},
author = {Du, H and Zhang, J and Xie, J and Chen, X},
title = {Optimal gut-brain equilibrium: moderate physical activity, microbiome, and the hormetic pathway to cognitive wellbeing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1778491},
doi = {10.3389/fmicb.2026.1778491},
pmid = {42729411},
issn = {1664-302X},
}

@article {pmid42729417,
year = {2026},
author = {Pierson, JT and Bond, AH and Cao, S and Zhang, S and Gold, A and Zhang, H and Zamary, KM and Gurer, A and Guo, C and Bhandari, M and Teegarden, MD and Peterson, DG and Mo, X and Zhu, J and Bruno, RS},
title = {Whole wheat bread improves postprandial glucose tolerance in adults with prediabetes: a controlled-feeding randomized crossover trial with microbiome-associated variation in response.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1907908},
doi = {10.3389/fnut.2026.1907908},
pmid = {42729417},
issn = {2296-861X},
abstract = {BACKGROUND/HYPOTHESIS: Whole grain intake is associated with reduced risk of type 2 diabetes, yet inconsistent findings from randomized trials and substantial interindividual variability suggest that gut microbiota may influence glycemic responses. We hypothesized that whole wheat bread would improve glucose tolerance compared with refined white bread under controlled feeding conditions in adults with prediabetes, and that gut microbial features would be associated with variability in glycemic response.

METHODS: In this randomized, controlled crossover trial, adults with prediabetes (n = 39; 34.7 ± 0.9 kg/m[2]) consumed fully controlled diets differing only in whole wheat (WHEAT) or refined white bread (WHITE) for 2-weeks each, separated by a 2-week washout. Fasting blood and stool samples were collected at baseline and post-intervention, and a 75 g oral glucose tolerance test was performed after each phase.

RESULTS: Compared with WHITE, WHEAT reduced postprandial glucose excursion by 27% (p = 0.04), independent of body weight, inflammation, carbonyl stress, and fecal short-chain fatty acids (SCFAs). Fasting glucose and insulin improved over time irrespective of treatment (PTime < 0.05), whereas inflammatory biomarkers, plasma methylglyoxal, and fecal SCFAs did not differ between interventions. Gut microbial α- and β-diversity were unchanged. However, compositional analyses identified directional shifts in selected taxa during WHEAT, including higher relative abundances of Agathobacter, Agathobaculum, and Lachnospiraceae NK4A136 group and lower Streptococcus, Lachnoclostridium, and Mediterraneibacter (nominal p < 0.05). Moderation analysis revealed that baseline abundances of Lachnoclostridium and Lachnospiraceae NK4A136 group predicted postprandial glycemic responses in a diet-dependent manner, identifying distinct microbial profiles associated with greater metabolic benefit from WHEAT relative to WHITE (PInteraction < 0.05).

CONCLUSION: Whole wheat bread improves postprandial glucose tolerance in adults with prediabetes while exhibiting microbiome-associated variation in glycemic response. These findings support whole wheat as an effective dietary strategy and highlight baseline gut microbial features as key contributors to inter-individual responses, advancing precision nutrition approaches to whole grain consumption.

CLINICAL TRIALS REGISTRATION: ClinicalTrials.gov: NCT05318183.},
}

@article {pmid42729475,
year = {2026},
author = {Zhang, M and He, L and Xin, H and Huang, T and Wang, F and Wang, L},
title = {Metagenomic profiling of blood-associated microbial DNA signatures in leukemia-associated febrile neutropenia.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1917043},
doi = {10.3389/fmicb.2026.1917043},
pmid = {42729475},
issn = {1664-302X},
abstract = {Febrile neutropenia (FN) is a life-threatening complication of chemotherapy, but the low microbial biomass of blood makes shotgun metagenomic profiles highly sensitive to technical background. We reanalyzed 47 publicly available patient sequencing runs representing 43 unique patient-timepoint samples from 19 SRA-labeled patients, together with 23 no-template-control (NTC) runs spanning 21 sequencing batches. To distinguish reference-catalogue content from progressively stronger evidence of patient-associated signal, we applied batch-matched NTC correction together with nested abundance thresholds and a feature-specific global NTC envelope. CheckM2 evaluated 1,013 bins; 13 met completeness ≥50% and contamination <10%, and dereplication yielded 11 draft MAG representatives. Ten representatives showed positive patient-to-control abundance excess, but only four showed recurrent support above both threefold matched-control abundance and the global NTC envelope. Functional annotations were therefore interpreted as reference-genome homologs rather than evidence of expression, phenotype, viability or bloodstream origin. Matched-control correction retained 19 read-level ARG types, but only seven subjects contributed complete longitudinal ARG-profile contrasts, limiting reliable temporal inference. The resulting run-resolved, nested evidence framework identified a subset of microbial DNA and ARG signals that remained detectable under increasingly stringent control criteria while distinguishing them from catalogue-level or background-sensitive signals. These findings support cautious reporting of patient-enriched microbial DNA and ARG signals rather than inference of a resident blood microbiome or clinical resistance phenotype.},
}

@article {pmid42729499,
year = {2026},
author = {Geiger, JT and Gill, AL and Matabele, M and Kruger, J and Kedwai, B and Lehane, D and Ford, B and Stoner, MC and Sohn, MB and Gill, SR and Mix, D},
title = {Streptococcus and related oral taxa are differentially abundant in patients with abdominal aortic aneurysms compared with atherosclerotic disease controls.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1884994},
doi = {10.3389/fcvm.2026.1884994},
pmid = {42729499},
issn = {2297-055X},
abstract = {OBJECTIVE: Bacterial DNA from oral microorganisms has been found in various cardiovascular tissues, including abdominal aortic aneurysm (AAA) tissue. In addition, experiments in murine models have shown that the oral pathogen Porphyromonas gingivalis can independently contribute to aneurysm formation. However, whether the oral microbial community differs between patients with AAA and those with advanced atherosclerotic disease remains unknown. This study tests the hypothesis that specific bacterial taxa are differentially abundant in patients with AAA compared to those with advanced atherosclerotic disease.

METHODS: A total of 73 oral wash samples were collected from 45 subjects with AAA and 28 with atherosclerotic disease. Bacterial DNA was isolated, and the V1-V3 segment of the bacterial 16S rRNA gene was amplified. Taxonomic profiles were constructed using DADA2, and statistical inferences on alpha diversity, beta diversity, and differential abundance were performed, adjusting for age, sex, smoking status, and cancer history. Sensitivity analyses additionally adjusted for cancer status, statin use, proton pump inhibitor use, and diabetes. Bacterial gene potential functions were predicted using PICRUSt2.

RESULTS: The oral microbial community composition differed in beta diversity (weighted UniFrac distance, R = 0.166, p < 0.001) and trended towards a difference in alpha diversity (Shannon index, p = 0.054) between patients with AAA and advanced isolated atherosclerotic disease. Ten bacterial taxa are overabundant in patients with AAA compared with those with atherosclerotic disease, most notably the genus Streptococcus (log2 fold change: 2.06, p = 0.002). PICRUSt2 predicted bacterial pathways related to protein synthesis and DNA replication that were likely to be less abundant, and pathways related to bacterial motility that were likely to be more abundant in oral cavity bacteria in subjects with AAA.

CONCLUSIONS: These findings demonstrate that the oral microbiome differs between patients with AAA and those with advanced atherosclerotic disease and support further investigation of oral microbial alterations and their relationship to vascular pathologies. The known link between Streptococcus and cardiovascular disease makes these results particularly intriguing. Further multi-omic studies with greater power may identify bacterial species and proteins that correlate with disease presence and progression.},
}

@article {pmid42729542,
year = {2026},
author = {Lu, Z and Tang, D},
title = {The dual roles of Prevotella in gastrointestinal tumorigenesis: from molecular mechanisms to therapeutic prospects.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1855577},
doi = {10.3389/fonc.2026.1855577},
pmid = {42729542},
issn = {2234-943X},
abstract = {Tumor microbiology is a prominent area of research that is reshaping cancer treatment paradigms. While most microbiological studies have focused on specific bacterial species such as Fusobacterium nucleatum, the genus Prevotella has emerged in recent years as a key research focus due to its notable functional duality in gastrointestinal tumorigenesis. The role of this genus is not unidirectional; specific strains of Prevotella have been associated with either pro-tumorigenic or anti-tumorigenic effects depending on the context. On one hand, pro-tumorigenic strains, exemplified by Prevotella intermedia, have been shown to correlate with malignant progression through various mechanisms, though direct causal evidence in humans remains limited. On the other hand, certain Prevotella strains may exert protective effects primarily through the production of short-chain fatty acids (SCFAs), particularly butyrate, as suggested by preclinical and correlational human studies. This functional duality is fundamentally shaped by strain-level heterogeneity, dietary patterns, microbial community context, and anatomical localization. Despite the critical importance of this genus in the gastrointestinal tract, a comprehensive synthesis of its strain-specific and context-dependent roles remains lacking. This narrative review is based on literature searched in PubMed and Web of Science up to March 2026 using keywords including "Prevotella", "gastrointestinal cancer", "short-chain fatty acids", and "gut microbiota". Additional references were identified from reference lists. No formal bias assessment was performed. Therefore, this review summarizes the current understanding of the underlying mechanisms of its dual roles-emphasizing where evidence is associative versus causal-and explores emerging translational strategies that leverage this duality for cancer prevention and therapy.},
}

@article {pmid42729560,
year = {2026},
author = {Selta, DRF and Abraham, L and Kavitha, R and Saikia, K and Rathankumar, AK and Mironescu, M and Mironescu, ID and Palanisamy, CP and Velliyur Kanniappan, G},
title = {Next-generation microbiome therapeutics: psychobiotics and fecal microbiota transplants for mental health treatment.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1719357},
doi = {10.3389/fcimb.2026.1719357},
pmid = {42729560},
issn = {2235-2988},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Mental Disorders/therapy ; Animals ; *Gastrointestinal Microbiome ; *Probiotics/therapeutic use ; Dysbiosis/therapy ; Mental Health ; },
abstract = {The human gastrointestinal tract (GIT) harbors a diverse microbial community, collectively referred to as gut microbiota, which plays an essential role in maintaining host physiology, metabolism, immune function, and neurobehavioral processes. Mounting evidence highlights the importance of the bidirectional Gut-brain (GB) axis, through which gut microbes influence neural signalling, stress response, and emotional regulation. Dysbiosis of this axis has been associated with psychiatric, neurodevelopmental, and neurodegenerative disorders, such as anxiety, autism spectrum disorder (ASD), major depressive disorder (MDD) and schizophrenia. A growing area of research has identified psychobiotics-live microorganisms with psychotropic potential-as promising therapeutic agents for mental health conditions. These microbes exert their effects through multiple mechanisms, including modulation of neurotransmitter production, short-chain fatty acid (SCFA) signalling, immune regulation, and hypothalamic-pituitary-adrenal (HPA) axis stabilization. Preclinical and clinical studies provide supportive evidence for their antidepressant and anxiolytic effects, although large-scale, long-term trials remain limited. In parallel, fecal microbiota transplantation (FMT) has emerged as a potential strategy to restore microbial balance and improve psychiatric symptoms. Early findings demonstrate its role in modulating immune pathways, such as NLRP3 inflammasome signalling, and neurotrophic factors via gut microbial reshaping. Together, psychobiotics and FMT represent next-generation microbiome therapeutics that may complement conventional psychiatric interventions. This review synthesizes current evidence and highlights the future potential of microbiome-based strategies in treating mental health disorders.},
}

Humans
*Fecal Microbiota Transplantation/methods
*Mental Disorders/therapy
Animals
*Gastrointestinal Microbiome
*Probiotics/therapeutic use
Dysbiosis/therapy
Mental Health

@article {pmid42729561,
year = {2026},
author = {Ji, F and Wang, S and Wang, L and Zhao, Y and Zhong, J and Wang, R and Qu, J and Lu, Y and Yuan, N and Zhang, Q},
title = {The impact of short-term intensive fasting on physical health and gut microbiota in obese individuals.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1873000},
doi = {10.3389/fnut.2026.1873000},
pmid = {42729561},
issn = {2296-861X},
abstract = {OBJECTIVES: This study aimed to characterize how a 7-day complete water-only fast followed by structured refeeding was associated with changes in body weight, hydration-dependent bioelectrical-impedance estimates, physical test performance, cardiovascular indicators, and gut microbial ecology in adults with obesity and normal-weight controls.

METHODS: Seventy-two eligible volunteers formed prespecified BMI sampling strata (normal weight, n = 36; obesity, n = 36), from which 14 participants were randomly selected within each stratum before the intervention and before outcome collection (N = 28). All selected participants completed a supervised 7-day water-only fast followed by a 7-day structured refeeding period. Physical indicators were assessed pre-fasting, post-fasting, and post-refeeding and analyzed using two-factor mixed-design repeated-measures models; gut microbiota (16S rRNA) was profiled pre- and post-fasting.

RESULTS: BMI-group-by-time interactions were significant for body weight and BMI (both p < 0.001) but not for BIA-derived fat mass, body-fat percentage, or muscle mass (all p > 0.05). Dynamometer-recorded grip, knee-flexion, and knee-extension scores increased over time (all time-effect p < 0.001), but none showed a BMI-group-by-time interaction (all p ≥ 0.340). Gut microbial alpha diversity remained largely stable apart from an FDR-significant ACE-index reduction in the normal-weight group (q = 0.021); most taxonomic findings did not survive FDR correction, and beta-diversity analysis showed no community-level convergence between groups.

CONCLUSION: Supervised seven-day water-only fasting followed by structured refeeding was associated with reduced body weight, particularly in participants with obesity. Changes in body composition were BIA-derived estimates, while higher dynamometer scores represented measured test performance that may have been influenced by familiarization. Gut-microbiota alpha diversity was largely stable, with exploratory compositional changes supporting further investigation in controlled studies.},
}

@article {pmid42729643,
year = {2026},
author = {Guo, T and Chen, Y and Yu, Y and Shao, Y and Wang, C and Li, X and Zhang, H and Xu, C and Cheung, Y and Chen, F and Xu, T and Li, X and Duan, C},
title = {Clinical translation of salivary MicroAge for understanding the oral-systemic connection in healthy longevity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1903972},
doi = {10.3389/fmicb.2026.1903972},
pmid = {42729643},
issn = {1664-302X},
abstract = {The oral-systemic connection, salivary microbiome, and healthy longevity are increasingly recognized as biologically interconnected. This review summarizes lifespan changes in the salivary microbiome, its links to age-related systemic diseases, and recent progress in salivary MicroAge modeling. It further highlights advances in data preprocessing, feature engineering, and artificial intelligence-based prediction, while emphasizing the importance of standardization, generalizability, and biological interpretability for clinical translation. Overall, salivary MicroAge may provide a noninvasive and interpretable framework for biological aging assessment and healthier aging.},
}

@article {pmid42729802,
year = {2026},
author = {Barry, N and Landreville, KD and Larson, JA and Kuzma, J},
title = {Exploring and defining concepts of microbiome stewardship for the indoor built environment.},
journal = {Sustainable microbiology},
volume = {3},
number = {3},
pages = {qvag035},
doi = {10.1093/sumbio/qvag035},
pmid = {42729802},
issn = {2755-1970},
abstract = {Microbiome stewardship (MS) aims to maintain microbiome diversity and functioning to support human and ecosystem health. However, the built environment presents a unique challenge, as human-made indoor spaces lack a native microbial baseline. This review addresses this challenge and proposes a framework for MS for the built environment that bridges indoor exposure science with socio-ecological, engineering, and policy insights. We consider indoor spaces as active exposure ecologies shaped by ventilation, filtration, and moisture control. While mitigating harmful pollutants, dampness-related microbiota, and pathogens is an ethical and practical prerequisite for MS of the built environment, it is insufficient for achieving MS. We must shift from traditional concepts of sterility toward a model of "healthy porosity" through intentional microbial cultivation. Synthesis of current evidence highlights the health benefits associated with taxonomically rich, environmentally sourced microbial consortia, such as outdoor-, soil-, dog-, and plant-associated taxa. Moreover, moisture control, dust-reservoir maintenance, appropriate filtration, and supportive occupant behaviors are needed to favor benign and beneficial microbial communities. To transition building operations from pathogen suppression to intentional cultivation of health-supportive indoor microbiomes, we outline actionable stewardship goals that prioritize human health, favor benign environmental inputs, and promote occupant behaviors that sustain resilient microbial communities.},
}

@article {pmid42729855,
year = {2026},
author = {Neginhal, R and George, RR},
title = {Microgravity- induced organ and system-level deconditioning: a network physiology perspective.},
journal = {Frontiers in network physiology},
volume = {6},
number = {},
pages = {1931834},
doi = {10.3389/fnetp.2026.1931834},
pmid = {42729855},
issn = {2674-0109},
abstract = {Microgravity removes the gravitational loading that anchors fluid distribution, mechanotransduction, vestibular calibration, and vascular homeostasis, exposing the human body to one of its most profound physiological challenges. Rather than producing isolated organ-specific changes, it induces a deeply interconnected, multi-system deconditioning response emerging from disrupted inter-organ communication. This narrative mini review synthesizes evidence from human spaceflight missions, ground-based analog models, and cellular studies to characterize organ- and system-level adaptations from a network physiology perspective. Skeletal muscle atrophy begins within days, with strength loss preceding structural loss due to early neural contributions. Bone mineral density falls 1%-2% per month at weight-bearing sites, with incomplete recovery after return to Earth. Cardiac remodeling, plasma volume contraction, and impaired baroreflex gain converge to produce post-flight orthostatic intolerance. Cephalad fluid redistribution elevates intracranial pressure and contributes to Spaceflight-Associated Neuro-Ocular Syndrome. Thymic involution and macrophage dysfunction impair immunity, while gut microbiome dysbiosis generates systemic inflammatory and metabolic consequences via the gut-brain axis. Endocrine shifts-including insulin resistance, cortisol dysrhythmia, and hypercalciuria-constitute an interrelated metabolic syndrome of spaceflight. These changes do not occur in isolation. Myokine-osteokine crosstalk, inflammatory amplification across the muscle-bone-gut axis, and gut-derived metabolites disrupting liver-brain metabolism represent proposed mechanisms of network-level deconditioning propagation. Critically, dynamic inter-organ coupling during spaceflight has not yet been directly measured-a fundamental research gap. Terrestrial Network Physiology studies of intermuscular and cardiorespiratory coupling networks serve as methodological precedents for future in-flight investigations. Any proposed network reconfiguration framework is explicitly hypothetical. Future research must prioritize integrated, sex-specific, network-aware countermeasure design and multi-omics biomarker development for long-duration exploration missions.},
}

@article {pmid42730242,
year = {2026},
author = {Alsaid, M and Ekambaram, M and Heng, NCK and Hasmun, NN},
title = {Mapping the oral microbiome in children with oral diseases using next-generation sequencing: a systematic review.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2723644},
doi = {10.1080/20002297.2026.2723644},
pmid = {42730242},
issn = {2000-2297},
abstract = {BACKGROUND: The oral microbiome is integral to paediatric oral health and disease. Next-generation DNA sequencing (NGS) technology enables culture-independent profiling of microbial communities, yet findings remain inconsistent due to methodological and population heterogeneity.

OBJECTIVE: This review synthesised NGS-based evidence comparing the oral microbiome of children/adolescents with oral diseases and healthy controls.

DESIGN: The protocol was registered in PROSPERO (CRD42025618407). PubMed, Medline, Embase, Scopus and Web of Science were searched for peer-reviewed studies (2015-2025). Eligible studies used 16S rRNA gene sequencing to compare children/adolescents (0-18 years) with oral diseases and healthy controls. Two reviewers independently screened studies, extracted data and assessed risk of bias using validated tools. Findings were synthesised narratively due to heterogeneity.

RESULTS: From 4,767 records, 61 studies were included. Most were cross-sectional designs conducted across diverse populations and conditions. Differences in community composition were more consistent than changes in alpha diversity, which varied by disease stage and sampling site. Shifts toward anaerobic, metabolically active communities were observed. Dental caries was consistently linked to acidogenic genera/species, whereas fluorosis, halitosis and gingivitis showed functional shifts involving proteolytic, sulphur-metabolising and anaerobic bacteria.

CONCLUSION: Paediatric oral diseases are more strongly associated with condition- and niche-specific compositional alterations than with uniform diversity changes.},
}

@article {pmid42730263,
year = {2026},
author = {Devarakonda, SLS and Hanlon, KD and Loinard-González, AP and Cummings, BP and Poole, AC},
title = {Effects of salivary amylase gene copy number on metabolic health.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1815044},
doi = {10.3389/fnut.2026.1815044},
pmid = {42730263},
issn = {2296-861X},
abstract = {Precision nutrition is the personalization of dietary recommendations based on characteristics such as genetics, the microbiome, lifestyle, environment, and baseline metabolic state. One potential basis for the development of guidelines is the characterization of gene-diet interactions. In this narrative review, we evaluate the published literature reporting associations between salivary amylase gene copy number and metabolic health. The salivary amylase enzyme facilitates starch digestion and is encoded by AMY1, a gene copy number (CN) variant. Humans have 2-20 copies, and AMY1 CN has been associated with metabolic health conditions such as obesity and insulin resistance. Studies of these associations have conflicting findings. The objectives of this review are to assess the findings from studies testing associations between AMY1 CN and adiposity, glucose metabolism, and gut microbiome composition; to explore possible mechanisms underlying the effects on metabolic health; and to identify knowledge gaps requiring additional research. To identify relevant articles, we searched PubMed, Web of Science, Cumulative Index to Nursing and Allied Health Literature, and Centre for Agricultural and Biosciences International for articles focused on AMY1 CN and one or more of the following: body mass index, glucose metabolism, and the microbiome. Key findings are that AMY1 CN has a positive association with postprandial glucose response and that a high AMY1 CN is protective against insulin resistance. AMY1 CN alone does not appear to be an accurate predictor of adiposity, and the relationship is likely convoluted by habitual starch intake, genetic background, and lifestyle factors. Future studies are required to determine how AMY1 CN could be used as a biomarker or to inform precision nutrition protocols to achieve metabolic health outcomes.},
}

@article {pmid42730307,
year = {2026},
author = {Yang, B and Zhang, H and Gou, Y and Ma, J and Wang, P and Li, J and Tong, Z},
title = {Bronchoalveolar Lavage Fluid Microbial and Metabolic Alterations Associated with Acute Respiratory Distress Syndrome in Hospitalized Patients with Community-Acquired Pneumonia.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {631648},
doi = {10.2147/JIR.S631648},
pmid = {42730307},
issn = {1178-7031},
abstract = {PURPOSE: To characterize bronchoalveolar lavage fluid (BALF) microbiome-metabolome alterations associated with acute respiratory distress syndrome (ARDS) in hospitalized patients with community-acquired pneumonia (CAP).

PATIENTS AND METHODS: Hospitalized patients with CAP were prospectively enrolled and stratified according to ARDS development during hospitalization. BALF was analyzed using 16S rRNA gene sequencing and untargeted metabolomics. Microbial diversity, community composition, and co-occurrence networks were evaluated alongside differential and network-based metabolomic analyses. Weighted co-expression network analysis and integrative multi-omics approaches were used to examine associations among microbiota, metabolites, and clinical traits. The cohort was randomly divided into training and internal validation sets at a 7:3 ratio. A LASSO-selected feature panel was used to develop and compare machine-learning models for distinguishing patients with and without ARDS.

RESULTS: Patients with ARDS exhibited greater disease severity and worse short-term clinical outcomes. BALF microbiomes demonstrated reduced alpha diversity, altered community structure, and diminished ecological network connectivity. Metabolomic profiling revealed intergroup separation and differential enrichment of amino acid and bile acid pathways. Integrated analyses identified coordinated microbiota-metabolite-clinical associations linked to ARDS status. A 10-feature signature showed promising discriminatory performance in the training and internal validation sets.

CONCLUSION: ARDS in hospitalized patients with CAP was associated with distinct microbial and metabolic alterations in BALF. Integrated BALF multi-omics profiling may help characterize airway-level pulmonary microenvironmental disturbances associated with CAP-related ARDS.},
}

@article {pmid42730360,
year = {2026},
author = {Hirkane, P and Verma, AK and Verma, UP and Singh, A},
title = {Does Periodontal Disease Influence Tuberculosis Outcomes? Insights from a Scoping Review.},
journal = {Annals of global health},
volume = {92},
number = {1},
pages = {89},
doi = {10.5334/aogh.5343},
pmid = {42730360},
issn = {2214-9996},
mesh = {Humans ; *Tuberculosis/epidemiology/complications ; Risk Factors ; *Periodontal Diseases/epidemiology ; *Periodontitis/epidemiology ; Disease Progression ; Prevalence ; },
abstract = {Background: Periodontitis and tuberculosis (TB) are common chronic infections disproportionately affecting disadvantaged groups. They share behavioural, environmental, and immunological risk factors. Emerging evidence suggests a bidirectional relationship, with TB patients often exhibiting poorer periodontal health and periodontal inflammation potentially exacerbating systemic TB. Objective: To comprehensively map and evaluate the existing evidence regarding the association between periodontal disease and TB outcomes, and to explore the potential influence of periodontal status on TB progression, treatment response, and overall disease outcomes through a scoping review. Methods: This scoping review examined human studies assessing periodontal status in TB patients, including observational studies, clinical trials, and reviews. Searches were conducted in PubMed, Scopus, and Google Scholar, complemented by reference screening. Two independent reviewers applied inclusion criteria, extracted data, and narratively synthesised the findings due to methodological diversity. Results: Out of 1,129 records screened, 8 studies met the inclusion criteria. The majority of observational studies demonstrated a significantly higher prevalence and severity of periodontitis in TB patients relative to controls, characterised by increased probing pocket depths and elevated bleeding on probing. Complementary evidence from recent reviews and microbiome analyses highlights shared inflammatory mediators, immune dysregulation, and alterations in oral microbial communities as potential mechanistic pathways underpinning the association between TB and periodontal tissue destruction. Conclusion: Current evidence supports a consistent but preliminary association between TB and deteriorated periodontal health, indicating complex bidirectional interactions rather than confirmed causality. Routine periodontal screening and oral health counselling integrated into TB management, along with heightened clinical vigilance for TB in unusual periodontal cases, may improve care. Further longitudinal and mechanistic studies are needed to clarify these relationships.},
}

Humans
*Tuberculosis/epidemiology/complications
Risk Factors
*Periodontal Diseases/epidemiology
*Periodontitis/epidemiology
Disease Progression
Prevalence

@article {pmid42730595,
year = {2026},
author = {Sileshi, RM and Mathes, K and Kosuri, S and Gupta, A and Phillips, N and Pimentel, R and Emert, M and Soma, S and Ramirez, R and Dendi, R and Reddy, M and Sheldon, SH and Atrouni, WE and Baddour, LM and Noheria, A},
title = {A Reassessment of Prophylactic Antibiotics in Low-Infection-Risk Electrophysiology Procedures.},
journal = {Pacing and clinical electrophysiology : PACE},
volume = {},
number = {},
pages = {},
doi = {10.1111/pace.70427},
pmid = {42730595},
issn = {1540-8159},
support = {//Department of Cardiovascular Medicine/ ; //University of Kansas Medical Center/ ; },
abstract = {Certain electrophysiology (EP) procedures are associated with minimal tissue disruption and do not involve permanent transvenous leads. As a result, these interventions carry a lower risk of device- or procedure-related infection. These procedures include placement of implantable cardiac monitors, leadless pacemakers, and left atrial appendage occlusion devices, as well as catheter ablation procedures in patients with preexisting cardiac implantable electronic device or prosthetic valve. Due to lack of clear guidelines regarding the use of prophylactic antibiotics in these procedures, clinical practice is variable. Therefore, we conducted a review of literature to evaluate the practice of prophylactic antibiotic administration and infection rates in low-infection-risk EP procedures. Available data indicate that periprocedural infection rates are low regardless of antibiotic use. Due to their observational design and limited power, existing studies are, however, insufficient to determine the benefit of routine antibiotic administration. At the same time, unnecessary antibiotic use may contribute to antimicrobial resistance and disrupt the patient's gut microbiome. Adequately powered randomized controlled trials are needed to determine whether routine prophylactic antibiotic administration is justified for low-infection-risk EP procedures.},
}

@article {pmid42730659,
year = {2026},
author = {Kumar, M and Narayanankutty, A and Nair, G and Kulkarni, R and Shouche, Y},
title = {Standardized Workflow for Human Fecal Sample Collection and Automated Deoxyribonucleic Acid Extraction Using a Magnetic Particle Processor.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {235},
pages = {},
doi = {10.3791/73312},
pmid = {42730659},
issn = {1940-087X},
mesh = {*Feces/microbiology/chemistry ; Humans ; Workflow ; *DNA/isolation & purification ; *DNA, Bacterial/isolation & purification/genetics ; RNA, Ribosomal, 16S/genetics ; Magnetics/methods ; *Specimen Handling/methods/standards ; },
abstract = {Gut microbiome sequencing has become an important approach for investigating microbial community dynamics in healthy and diseased states. Alterations in microbial composition have been associated with several lifestyle- and age-related disorders, including diabetes, leukemia, and neurodegenerative diseases. Because different microorganisms exhibit distinct physiological characteristics and environmental requirements, standardized fecal sample collection, transport, and processing are essential to preserve sample integrity and minimize technical variability. Variations introduced during pre-analytical handling and deoxyribonucleic acid (DNA) extraction can influence downstream microbiome analyses and affect data interpretation. The goal of this protocol is to provide a standardized workflow for human fecal sample collection and automated DNA extraction using the MagMAX Microbiome Ultra Nucleic Acid Isolation Kit (nucleic acid extraction kit) and the KingFisher Flex System (automated magnetic particle processor). The workflow integrates controlled sample handling with automated nucleic acid extraction to reduce manual variability and improve procedural consistency. The protocol includes standardized fecal sample collection, storage, preparation, automated extraction, and nucleic acid recovery from complex fecal matrices. Representative results demonstrate successful recovery of DNA suitable for downstream applications, including 16S ribosomal ribonucleic acid (rRNA) gene sequencing and shotgun metagenomic sequencing. The standardized workflow supports reproducible sample processing, facilitates scalability for microbiome studies, and promotes greater consistency across experiments. The visual demonstration provides practical guidance for implementing standardized fecal sample processing and automated nucleic acid extraction for gut microbiome research.},
}

*Feces/microbiology/chemistry
Humans
Workflow
*DNA/isolation & purification
*DNA, Bacterial/isolation & purification/genetics
RNA, Ribosomal, 16S/genetics
Magnetics/methods
*Specimen Handling/methods/standards

@article {pmid42730708,
year = {2026},
author = {Beacher, NG and Riggio, M and Khan, A and Butcher, MC and Delaney, C and Conway, DI},
title = {Associating the oral microbiome across the head and neck cancer continuum: a scoping review.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-27},
doi = {10.1080/1040841X.2026.2719594},
pmid = {42730708},
issn = {1549-7828},
abstract = {INTRODUCTION: Head and neck cancers (HNC) comprise oral cavity, oropharynx and larynx tumors. The role of the oral microbiome across the continuum from risk to diagnostic stage and outcomes is not well understood.

METHODS: Systematic searches were undertaken; Ovid MEDLINE and Embase, Web of Science and Open Grey (2011-2024), title/abstracts were screened in duplicate. Data were collected using an extraction template and subsequently descriptively analyzed.

RESULTS: There were 105 studies included, most from Asia (n = 64, 61%), focusing on oral cavity cancer (n = 58, 55%). Sample sizes were generally small (ranging n = 5-499), with age mainly >50-years (mean n = 102, 97%), and male (n = 4044, 75%). Stage was reported in 63 studies (60%) and survival in 18 (17%). Single clinical sample's were most frequently analyzed (n = 94, 90%). DNA extraction method and primers varied but Illumina technologies were most often employed (n = 73, 70%). Fusobacterium nucleatum most frequently increased in abundance (n = 7, 7%), while Haemophilus parainfluenzae (n = 9, 9%) most frequently decreased in abundance. Over half of studies (n = 58, 55%) provided accessible links to open data.

CONCLUSIONS: The abundance of microorganisms in relation to HNC is highly variable. Further large higher quality studies are required to assess the role of microbiome HNC stage, site, and prognosis.},
}

@article {pmid42720994,
year = {2026},
author = {Halle-Smith, JM and Fung, K and Efstathiou, E and Tovey, N and Stockton, J and Iqbal, TH and Moss, P and Beggs, AD and Roberts, KJ},
title = {The Effect of Pancreatic Exocrine Insufficiency and Pancreatic Enzyme Replacement Therapy on Gut Microbiome Composition in Pancreatic Disease: A Prospective Cohort Study.},
journal = {Pancreas},
volume = {},
number = {},
pages = {},
doi = {10.1097/MPA.0000000000002709},
pmid = {42720994},
issn = {1536-4828},
abstract = {OBJECTIVES: Increasing evidence demonstrates that pancreatic exocrine insufficiency (PEI) is associated with harmful changes to the gut microbiome. The mainstay of PEI treatment is with pancreatic enzyme replacement therapy (PERT), which has been shown to lead to significant survival benefit in pancreatic disease. The aim of this study was to determine how treatment of PEI with PERT affects gut microbiome composition.

METHODS: This is a prospective observational cohort study of patients being treated for pancreatic disease at a single centre. PEI status of patients was assessed at the time of recruitment using published diagnostic criteria. Pre-PERT samples were taken before treatment was started and post-PERT samples were taken after at least 4 weeks of treatment. To profile the gut microbiome composition, shotgun metagenomic sequencing was performed with DNA extracted from stool samples.

RESULTS: 25 patients with pancreatic disease were included. The abundance of pathogenic bacteria, such as Viridans group Streptococcus and Campylobacter species, was significantly increased in the gut microbiome of patients with PEI compared to those without PEI. Following PERT treatment, analysis of the gut microbiome of treated patients showed a significant reduction in the abundance of multiple pathogenic species, such as those from Viridans group Streptococci, compared to untreated PEI patients.

CONCLUSIONS: Treatment with PERT leads to significant changes in the gut microbiome composition of patients with pancreatic disease. Changes include a significant reduction in potentially pathogenic bacteria and so may contribute to the survival benefits seen with PERT treatment in pancreatic disease.},
}

@article {pmid42721036,
year = {2026},
author = {Zhang, Q and Wu, S and Xiao, Y and Chen, J and Zhou, H and Zhang, G and Shi, S},
title = {Genetic variation in glucosamine metabolism contributes to the colonization resistance of Bacteroides to Salmonella.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117998},
doi = {10.1016/j.celrep.2026.117998},
pmid = {42721036},
issn = {2211-1247},
abstract = {The gut microbiota contributes to variation in susceptibility to enteric infection, but the underlying mechanisms remain poorly defined. Here, we leverage a natural model of disease resistance comparing Salmonella-resistant indigenous Tibetan chickens with susceptible commercial broilers to uncover conserved mechanisms of colonization resistance relevant to human health. We find that enrichment of Bacteroides, particularly B. salanitronis, is associated with resistance, and supplementation with B. salanitronis significantly reduces S. Enteritidis colonization in susceptible hosts. Mechanistically, Bacteroides species competitively deplete N-acetyl-D-glucosamine (GlcNAc), a growth-limiting carbohydrate for S. Enteritidis, through highly efficient glucosamine-6-phosphate deaminase (GNPDA) activity. Enzymatic assays, structural modeling, and mutational analysis identify Ile138 as critical for the catalytic advantage of Bacteroides GNPDA over S. Enteritidis GNPDA. Replacing this residue abolishes the competitive advantage, confirming its role in nutrient-mediated colonization resistance. These findings show how genetic variation in microbial nutrient-metabolizing enzymes shapes interspecies competition and suggests microbiome-based strategies for controlling enteric pathogens.},
}

@article {pmid42721824,
year = {2026},
author = {He, Z and He, J and Zhang, C and Wang, H and Wang, F and Pei, T and Hu, R and Xian, Z and Li, J and Liu, D and Shi, C and Yu, C and Lin, J and Niu, W and Wang, M and Xiao, W},
title = {Shenshuai Yingyang Jiaonang attenuates CKD-induced muscle atrophy: a role for Faecalibacterium prausnitzii and the EGFR/PI3K/AKT signaling axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {161},
number = {},
pages = {158761},
doi = {10.1016/j.phymed.2026.158761},
pmid = {42721824},
issn = {1618-095X},
abstract = {BACKGROUND: The occurrence of muscle atrophy in chronic kidney disease (CKD) is a prevalent complication with serious consequences but lacks effective treatment. Modulating the gut microbiota offers a promising new therapeutic approach. Shenshuai Yingyang Jiaonang (SSYYJN) is a clinically validated prescription of traditional Chinese medicine for muscle atrophy in CKD, yet the molecular basis for its therapeutic action requires elucidation.

PURPOSE: To evaluate the therapeutic efficacy of SSYYJN against CKD-induced muscle atrophy, investigate the mechanism from the perspective of the gut microbiota, and explore potential strategies for enhancing the treatment efficacy of SSYYJN.

METHODS: A rat model of CKD with concomitant muscle atrophy was established by 5/6 nephrectomy. 16S rDNA sequencing and fecal microbiota transplantation (FMT) experiments were conducted to elucidate the gut microbiota's role in SSYYJN efficacy. Untargeted metabolomics profiling and the pharmacological network analysis were conducted to investigate the potential mechanism of Faecalibacterium prausnitzii (FP) probiotics on SSYYJN. The regulatory mechanism of SSYYJN in CKD-associated muscle atrophy was validated through in vitro C2C12 cell experiments.

RESULTS: In patients with CKD-associated protein-energy wasting (PEW), effective SSYYJN treatment improved mid-arm muscle circumference, hand grip strength, mid-arm circumference, and serum albumin. Moreover, post-hoc microbiome analysis revealed that the abundance of FP was higher in treatment-responsive patients. In a CKD rat model, SSYYJN conferred protection against renal injury, malnutrition, and muscle atrophy, this therapeutic effect was related to the gut microbiota modulation. Of note, a higher abundance of FP was also observed in SSYYJN-treated CKD rats. Further analyses suggested that FP was associated with increased levels of carnosol and may enhance EGFR/PI3K/AKT signaling, thereby potentiating the therapeutic effect of SSYYJN against CKD-induced muscle atrophy.

CONCLUSION: These findings suggest a gut microbiota-dependent mechanism underlying the action of SSYYJN against muscle atrophy in CKD. FP may be linked to the effects of SSYYJN, potentially involving the generation of carnosol and the upregulation of the EGFR/PI3K/AKT pathway, representing a targeted therapeutic strategy.},
}

@article {pmid42721830,
year = {2026},
author = {Męcik, M and Stefaniak, K and Harnisz, M and Czatzkowska, M and Felis, E and Bajkacz, S and Sawicki, J and Krawczyk, K and Paukszto, Ł and Korzeniewska, E},
title = {From regionalization to homogenization: Nationwide metagenomic assessment of priority pathogens and the resistome in Polish hospital wastewater.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143526},
doi = {10.1016/j.jhazmat.2026.143526},
pmid = {42721830},
issn = {1873-3336},
abstract = {Hospital wastewater (HWW) is a critical hotspot for the dissemination of antibiotic resistance genes (ARGs) and pathogens. This study provides the first comprehensive metagenomic characterization of HWW across Poland, analyzing 64 medical facilities across two seasons via Nanopore long-read sequencing (total of 128 HWW samples). The HWW microbiome was mostly dominated by Proteobacteria, Bacteroidota, and Firmicutes. Multivariate analysis confirmed a significant seasonal shift in the resistome. Winter samples exhibited geographic regionalization, with localized hotspots of specific ARGs, including vancomycin resistance (operon van) and carbapenemase genes (blaOXA, blaNDM). Conversely, summer samples showed a significant trend toward nationwide homogenization, characterized by a uniform distribution of ESBL genes (blaTEM, blaCTX-M) and multidrug resistance (MDR) determinants, alongside the persistence of localized clinical hotspots. Klebsiella pneumoniae emerged as a central network hub, particularly in summer, showing strong correlations with ESBLs. Quantitative genomic co-occurrence analysis revealed a functional division within dominant taxa: while environmental species like Acinetobacter johnsonii comprised the general background microbiome, clinical pathogens such as Acinetobacter baumannii served as primary vectors, showing frequent associations with high-risk ARGs. Environmental and opportunistic bacteria, such as Aeromonas spp. and Citrobacter spp., were identified as putative 'bridge hosts' associated with mobile resistance determinants and potentially contributing to HGT. The findings indicate that seasonal factors, such as increased temperature and sub-inhibitory antibiotic concentrations, may contribute to the transition from regionalized to homogenized resistance profiles, demonstrating that background resistome convergence can coexist with point-source clinical outbreaks. This seasonal "blurring" of regional boundaries positions HWW as an active vector for large-scale antimicrobial resistance (AMR) dissemination. These results underscore the urgent need for nationwide metagenomic surveillance and advanced wastewater treatment strategies within the "One Health" framework to mitigate the environmental spread of WHO priority pathogens.},
}

@article {pmid42721838,
year = {2026},
author = {Han, X and Pei, J and Wang, Y and Sun, Y and Zheng, F},
title = {Trophic decoupling of soil-nematode microbiomes induced by co‑contamination of silver nanoparticle and oxytetracycline.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143539},
doi = {10.1016/j.jhazmat.2026.143539},
pmid = {42721838},
issn = {1873-3336},
abstract = {Due to excellent antibacterial properties, silver nanoparticles (AgNPs) have been widely used as a potential alternative to antibiotics in livestock farming, agricultural disinfection, and medical materials. Consequently, excess AgNPs are released into the soil, co-occurring with other antibiotics, and forming a combined contamination. However, effects of combined contamination with AgNPs and oxytetracycline (OTC) on microbial communities across different trophic levels within the soil micro-food web remain poorly understood. In this study, we systematically compared the differential responses of soil and nematode gut microbiomes using high-throughput sequencing under single and combined contamination (Control, AgNPs, OTC, and combined AgNPs+OTC). The results revealed systematic trophic-level differentiation between soil and nematode gut bacterial community in terms of diversity, community structure, assembly mechanisms, and functional phenotypes. Both communities were dominated by stochastic processes, but nematode gut bacterial community was more strongly influenced by deterministic processes and exhibited higher stability. Pollutant exposure induced pronounced trophic decoupling: soil bacterial community remained structurally stable, whereas nematode gut community underwent significant compositional reassembly (p = 0.031) without a change in alpha diversity, indicating a species replacement pattern. AgNPs treatment enriched Escherichia-Shigella, while OTC and co-contamination enriched the potential degrader genera Pontibacter, Sphingomonas, and Sphingobium. Cross-kingdom network analysis showed that co-contamination strengthened network modularity (clustering coefficient 0.84, modularity 53), highlighting the role of shared ASVs as cross-kingdom bridges. This study introduces the concept of pollution-induced trophic decoupling, demonstrating that the impact of co-contamination on adjacent trophic levels is not a simple transmission of effects but rather a systematic decoupling of structure, function, and assembly mechanisms, thereby providing new perspectives for multi-trophic ecological risk assessment of combined pollution.},
}

@article {pmid42722013,
year = {2026},
author = {Blake, S and Cannon, H and Shantikumar, S},
title = {The Association Between Attention-Deficit Hyperactivity Disorder and Gastrointestinal Symptoms: A Systematic Review and Meta-Analysis.},
journal = {Journal of attention disorders},
volume = {},
number = {},
pages = {10870547261469626},
doi = {10.1177/10870547261469626},
pmid = {42722013},
issn = {1557-1246},
abstract = {INTRODUCTION: Attention-Deficit/Hyperactivity Disorder (ADHD) is a neurodevelopmental condition with rising prevalence worldwide. Although alterations in the gut-brain axis have been implicated in its pathophysiology, underlying mechanisms remain unclear. An increase of gastrointestinal (GI) symptoms is well documented in autism spectrum disorder, but the extent of GI involvement in ADHD has not yet been systematically evaluated.

AIM: To determine whether individuals with ADHD exhibit a higher prevalence of GI symptoms compared with neurotypical controls.

METHODS: Following PRISMA 2020 guidelines (PROSPERO: CRD42024602363) (Blake et al., 2024), we searched MEDLINE, Embase and APA PsycInfo (all via Ovid) up to 12 May 2026. We included primary studies involving participants of any age with a DSM- or ICD-defined ADHD diagnosis and reporting GI symptoms. Studies involving formally diagnosed organic GI disease (e.g., IBD) were excluded. Two independent reviewers conducted screening and quality appraisal using Joanna Briggs Institute (JBI) tools. Where appropriate, random-effects meta-analyses were performed for individual and composite GI symptoms.

RESULTS: From 9,613 records, 23 studies met inclusion criteria, representing over 1.9 million participants. ADHD was associated with increased odds of every GI symptom investigated, including total GI symptoms (OR 1.48, 95% CI [1.35, 1.62]), irritable bowel syndrome (OR 1.58, 95% CI [1.39, 1.78]), constipation (OR 1.97, 95% CI [1.49, 2.61]) and encopresis (OR 4.32, 95% CI [2.50, 7.47]).

CONCLUSION: ADHD is associated with a substantial increase in functional GI symptoms, distinct from organic gastrointestinal disease. Possible mechanisms include gut microbiome dysbiosis, vagal dysregulation and behavioural contributors. Future research should differentiate intrinsic biological pathways from medication-related effects to improve clinical management.},
}

@article {pmid42722053,
year = {2026},
author = {Zhang, Y and Yan, R and Wang, K and Wang, H and Gui, H and Man, J and Yang, L},
title = {Gut Microbiota in Kidney Transplantation: Mechanistic Insights and Implications for Precision Immunosuppression.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {179336},
doi = {10.1016/j.ejphar.2026.179336},
pmid = {42722053},
issn = {1879-0712},
abstract = {Kidney transplantation represents the optimal treatment for eligible patients with end-stage renal disease (ESRD), yet long-term graft survival remains threatened by rejection, infection, and immunosuppressant-related toxicity. Increasing evidence identifies the gut microbiome as an important modulator of these outcomes through the bidirectional gut-kidney axis. After kidney transplantation, microbial dysbiosis is commonly characterized by reduced diversity, enrichment of pathobionts such as Escherichia-Shigella and Enterococcus, and depletion of short-chain fatty acid (SCFA)-producing bacteria, including Faecalibacterium prausnitzii and members of the Lachnospiraceae family. These alterations are driven by the combined effects of pre-existing uremia, surgical and ischemia-reperfusion stress, immunosuppressive therapy, and antimicrobial exposure. Mechanistically, impaired barrier integrity and reduced SCFA production promote systemic inflammation and disrupt the regulatory T-cell (Treg)/T helper 17-cell (Th17) balance, whereas tryptophan metabolites and aryl hydrocarbon receptor signaling further influence alloimmune responses. The microbiota also contributes to variability in immunosuppressant efficacy and toxicity. Bacterial metabolism of tacrolimus and microbiota-mediated regulation of intestinal ABCB1 expression may account for a clinically relevant proportion of tacrolimus pharmacokinetic variability, while bacterial beta-glucuronidase reactivates mycophenolic acid in the intestine and contributes to mycophenolate mofetil-associated gastrointestinal toxicity. Microbiota-derived uremic toxins may additionally reinforce oxidative stress and graft fibrosis. Although fecal microbiota transplantation, precision nutrition, probiotics, and postbiotics show therapeutic potential, current evidence remains largely observational or exploratory. Multicenter randomized controlled trials are therefore required before microbiome-based strategies can be incorporated into routine precision immunosuppression.},
}

@article {pmid42722099,
year = {2026},
author = {Yan, W and Qing, Q and Wang, Y and Li, S and Shen, H and Xing, B and Guo, W and Ma, Q and Li, H and Zhang, J and Zhang, T and Huang, H},
title = {Chronic Exposure to Areca Alkaloids at Environmentally Relevant Concentrations Alters Neurobehavior, Gut Microbiota and Brain Metabolism in Adult Zebrafish.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125657},
doi = {10.1016/j.envres.2026.125657},
pmid = {42722099},
issn = {1096-0953},
abstract = {Trace-level neuroactive contaminants in aquatic environments are increasingly recognized as ecological hazards, yet the neurotoxic potential of areca alkaloids remains largely unexplored. In this study, adult zebrafish were chronically exposed to arecoline or arecaidine for 90 days to investigate long-term neurobehavioral toxicity and associated biological alterations. Behavioral assessments revealed persistent impairments in social interaction, reduced aggression, and altered exploratory activity following alkaloid exposure. Concomitantly, areca alkaloids induced intestinal injury characterized by villus atrophy, goblet cell depletion, epithelial alterations, and increased macrophage infiltration. Gut microbiota profiling revealed compositional shifts, with significant enrichment of inflammation-associated genera, including Acinetobacter, Pseudomonas and Rhodococcus, and depletion of several commensal taxa. At the central level, brain histopathology revealed neuronal damage and increased expression of apoptosis-associated markers. Brain metabolomic analysis further revealed extensive alterations in amino acid- and neurotransmitter-related metabolism, highlighted by alterations in glutamate, glycine, serine, N-acetyl-L-aspartic acid, and citrate, as well as enrichment of pathways related to alanine, aspartate and glutamate metabolism and aminoacyl-tRNA biosynthesis. Integrated correlation analyses revealed associations among altered gut bacterial genera, brain metabolic pathways, and behavioral endpoints, suggesting potential links among gut microbial alterations, brain metabolic changes, and behavioral outcomes following areca alkaloid exposure. In summary, these findings reveal that long-term exposure to areca alkaloids at environmental concentrations elicits neurobehavioral and neurotoxic effects in adult zebrafish accompanied by alterations in gut microbiota and brain metabolism, highlighting the potential of areca alkaloids as environmental neurotoxicants relevant to aquatic health risk assessment.},
}

@article {pmid42722156,
year = {2026},
author = {Kaundal, S and Patil, AN and Khatri, P and Jana, P and Talukdar, D and Singh, C and Jandial, A and Jain, A and Prakash, G and Khadwal, A and Sharma, V and Dutta, U and Arora, A and Das, B and Malhotra, P and Lad, DP},
title = {Early gut microbiome metabolites and diversity predict GVHD-free survival after allogeneic hematopoietic cell transplantation.},
journal = {Transplantation and cellular therapy},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jtct.2026.09.012},
pmid = {42722156},
issn = {2666-6367},
abstract = {BACKGROUND: Disruption of the gut microbiome has been implicated in graft‑versus‑host disease (GVHD) and mortality after allogeneic hematopoietic cell transplantation (HCT). However, prior studies have focused on GVHD‑specific or mortality endpoints in isolation rather than integrated measures of transplant success. We evaluated whether early gut microbial metabolic injury and impaired ecological recovery are associated with GVHD‑free survival (GFS), a composite endpoint incorporating clinically significant GVHD and death.

METHODS: We conducted a prospective observational cohort study of 62 patients undergoing allogeneic HCT at a single center. Stool samples were collected before conditioning and at weeks 2 and 4 after HCT. Fecal short‑chain fatty acids (SCFAs) were quantified using liquid chromatography-tandem mass spectrometry, and microbial diversity was assessed using 16S rRNA gene sequencing. Prespecified landmark analyses were performed at day +15 (week‑2 biomarkers) and day +28 (week‑4 biomarkers). The primary endpoint was GFS at 24‑months, defined as survival without grade II-IV acute GVHD, moderate-severe chronic GVHD, or death. Multivariable Cox regression models adjusted for key clinical covariates were used, with biomarkers modeled as log₂‑transformed continuous variables.

RESULTS: During follow‑up, 43 patients (69%) experienced GFS failure, due to acute GVHD (n=18), chronic GVHD (n=18), or death without prior GVHD (n=7). In day +15 landmark analyses, higher week‑2 concentrations of all three SCFAs were independently associated with improved GFS: butyrate (adjusted hazard ratio [aHR] per doubling 0.81, 95% CI 0.71-0.93; p=0.002), propionate (aHR 0.83, 95% CI 0.75-0.93; p<0.001), and acetate (aHR 0.85, 95% CI 0.74-0.97; p=0.018). In day +28 landmark analyses, recovery of microbial diversity at week 4 was independently associated with GFS, with each doubling of the Simpson diversity index associated with a lower hazard of GFS failure (aHR 0.53, 95% CI 0.34-0.83; p=0.005). Similar associations were observed for Shannon diversity (aHR 0.51, 95% CI 0.30-0.84; p=0.009), whereas Chao1 richness showed a concordant but borderline association (aHR 0.64, 95% CI 0.41-1.02; p=0.061).

CONCLUSIONS: Early post‑transplant depletion of microbiome‑derived metabolites and impaired recovery of gut microbial diversity are independently associated with inferior GVHD‑free survival after allogeneic HCT. These findings are consistent with temporally distinct associations between early metabolic injury and subsequent ecological recovery and support further investigation of microbiome‑directed strategies to improve transplant outcomes.},
}

@article {pmid42722268,
year = {2026},
author = {Zhou, J and Ma, J and Wang, H and Meng, F and Li, Q and Cui, S and Zou, N},
title = {T-2 toxin-induced neurotoxicity in juvenile rats involves hippocampal oxidative stress-ER stress-mediated neuronal apoptosis and potential gut-brain axis involvement.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {112341},
doi = {10.1016/j.cbi.2026.112341},
pmid = {42722268},
issn = {1872-7786},
abstract = {T-2 toxin, a common Fusarium-derived mycotoxin, poses severe threats to livestock production and public health and exhibits potent neurotoxicity by disrupting blood-brain barrier integrity and neuronal function. However, the detailed mechanisms responsible for its developmental neurotoxicity remain poorly elucidated. This study investigated cognitive impairment and associated central and peripheral alterations in juvenile rats following subchronic T-2 toxin exposure. Juvenile male Wistar rats were orally exposed to T-2 toxin for 28 days. Behavioral, histopathological, microbiome, biochemical, and molecular analyses were performed to evaluate cognitive function, hippocampal injury, intestinal barrier integrity, and gut microbial alterations. T-2 toxin exposure significantly impaired learning, memory, recognition ability, and exploratory behavior. Hippocampal neuronal loss, Nissl body reduction, and endoplasmic reticulum dilation were observed following exposure. T-2 toxin disrupted hippocampal redox homeostasis, as evidenced by increased ROS and MDA levels and decreased SOD activity and GSH content. These changes were accompanied by activation of the PERK-eIF2α-ATF4-CHOP signaling pathway and enhanced neuronal apoptosis. In parallel, T-2 toxin altered gut microbial composition, induced colonic injury, reduced ZO-1 and Occludin expression, and triggered systemic inflammatory imbalance. Collectively, these findings indicate that T-2 toxin-induced cognitive impairment in juvenile rats is associated with oxidative stress-triggered ER stress and neuronal apoptosis in the hippocampus. Concurrent gut microbiota dysbiosis, intestinal barrier dysfunction, and inflammatory alterations suggest a potential contribution of gut-brain interactions to developmental T-2 toxin neurotoxicity. These findings expand current understanding of developmental T-2 toxin neurotoxicity by integrating hippocampal oxidative stress-ER stress signaling with gut microbial and intestinal alterations.},
}

@article {pmid42722277,
year = {2026},
author = {Xue, X and Ge, Y and Meng, T and Chen, Y and Zhou, L and Xu, D},
title = {Anthropogenic disturbance enhances bacteria-mediated resistome transmission across the sediment-benthos-demersal fish trophic continuum.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129137},
doi = {10.1016/j.envpol.2026.129137},
pmid = {42722277},
issn = {1873-6424},
abstract = {Aquatic ecosystems are important environmental reservoirs of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), yet how anthropogenic disturbance influences their distribution and cross-niche transmission through benthic food webs remains poorly understood. Here, we systematically characterized resistome and virulome profiles across trophic niches, including sediments, benthic invertebrates and demersal fishes, along a gradient of anthropogenic disturbance in Gehu Lake, China. Metagenomic analysis identified 1,645 ARG and 1,939 VFG subtypes, with both gene pools exhibiting pronounced niche differentiation. Sediments harbored the highest abundance and diversity of both gene pools, whereas animal-associated niches exhibited substantial but host-dependent attenuation. Notably, anthropogenic disturbance significantly altered ARG and VFG profiles across all ecological niches, with stronger effects in sediments and benthic organisms than in fish guts, and was generally associated with higher ARG and VFG abundance and diversity. Integrative source-tracking and bacteria-gene association network analyses further demonstrated that bacterial transmission was the primary vector mediating the cross-trophic dissemination of both gene pools. Anthropogenic disturbance reshaped bacterial community structure across niches and enhanced bacterial migration along the food chain, as reflected by the increased contribution of bacteria derived from upstream trophic compartments. KEGG functional profiling suggested that these transmitted bacterial assemblages processed enhanced metabolic and adaptive capacities functions such as xenobiotic degradation. Among the enriched bacterial lineages, Pseudomonadota, Actinomycetota and Bacillota were dominant and showed a higher propensity to harbor ARGs and VFGs, thereby facilitating their persistence, amplification and trophic transfer. Collectively, our findings reveal a disturbance-driven, microbiome-mediated mechanism underlying the co-dissemination of ARGs and VFGs across aquatic food webs, highlighting the critical role of host-associated microbial selection in amplifying environmental health risk.},
}

@article {pmid42722294,
year = {2026},
author = {Vimonpatranon, S and Mika, SK and Pang, APS and Machmach, K and Lima, NS and Godbole, S and Sajjaweerawan, C and Longtine, ER and Henry, AR and Laboune, F and Metz, E and Ratnaratorn, N and Phuang-Ngern, Y and Sacdalan, C and Ake, JA and Shacklett, BL and Sandberg, JK and Rerknimitr, R and Phanuphak, N and Vasan, S and Douek, DC and Corley, MJ and Schuetz, A and Paquin-Proulx, D},
title = {Mucosal-associated invariant T cells respond to colonic microbiome alterations during acute HIV infection.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {100403},
doi = {10.1016/j.mucimm.2026.100403},
pmid = {42722294},
issn = {1935-3456},
abstract = {Mucosal-associated invariant T (MAIT) cells are an unconventional subset of T cells that respond to vitamin B2 metabolites from a range of bacteria and fungi. We have previously reported that peripheral MAIT cells are activated during acute HIV infection (AHI) in a manner associated with markers of microbial translocation. Here, we characterized peripheral and colonic MAIT cells from people with HIV (PWH) during AHI and after ART initiated during AHI or chronic HIV infection (CHI) and investigated their interplay with the colonic microbiome. During AHI, both peripheral and colonic MAIT cells were activated and showed evidence of proliferation. MAIT cell activation in blood and colon were unrelated to viral load and to each other, suggesting compartmentalized responses. Colonic CD4 MAIT cells were reduced and their reduction was associated with viral load, suggesting a direct viral effect. In vitro experiments confirmed that CD4 MAIT cells are susceptible to HIV-1 infection. Finally, changes in colonic microbiome composition were evident already during AHI and were associated with peripheral blood MAIT cell activation and effector maturation. Thus, these findings indicate that viral replication and colonic microbiome perturbation are associated with distinct, compartment-specific components of the MAIT cell response during AHI.},
}

@article {pmid42722527,
year = {2026},
author = {Yang, F and Cheng, J},
title = {From promising signatures to clinically credible prediction: Strengthening microbiome-metabolome prognostic research.},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.09.007},
pmid = {42722527},
issn = {0929-6646},
}

@article {pmid42722574,
year = {2026},
author = {Diaz-Olea, X and Ramer-Tait, AE and Cohen, JE and Osterman, A and Ronai, ZA},
title = {Molecular pathways linking the gut microbiome to antitumor immunity.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.08.013},
pmid = {42722574},
issn = {1878-4380},
abstract = {Accumulating evidence supports the important role played by the gut microbiota in controlling antitumor immune responses that impact tumor development. Extensive studies of bacterial species known to impact tumor growth have identified metabolites, produced by either bacteria or the host, that may alter efficacy of chemo- and/or immune-based therapies. Here, we summarize our current knowledge of those metabolites and the related bacterial species that influence activities linked with antitumor immunity, including epigenetic changes, the aryl hydrocarbon receptor signaling, cytokine and chemokine production, Janus kinase/signal transducer and activator of transcription signaling, and toll-like receptor signaling. We focus on specific metabolites, produced in the gut microbiome, which can alter molecular pathways associated with antitumor immunity, findings that warrant further evaluation in preclinical or clinical settings.},
}

@article {pmid42722645,
year = {2026},
author = {Frene, JP and Custódio, V and Rouco, H and Martinez-Jarquin, S and Gao, YQ and di Bari, V and Bakhoum, N and Northen, TR and Bowen, BP and Louie, KB and Velchova, K and Ware, A and Bishopp, A and Mata, A and Castrillo, G},
title = {The metabolic and anatomical complexity of root microhabitats modulate their interaction with the microbiota.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42722645},
issn = {2041-1723},
support = {RGP005/2024//Human Frontier Science Program (HFSP)/ ; RGP005/2024//Human Frontier Science Program (HFSP)/ ; UKRI755//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {*Plant Roots/anatomy & histology/microbiology/metabolism ; *Microbiota/physiology ; Ecosystem ; Lysine/analogs & derivatives/metabolism ; Stress, Physiological ; },
abstract = {Plant roots constantly communicate with their microbiota, adapting their anatomy to facilitate microbial colonisation under abiotic stresses. Microbes, in turn, can reshape root anatomy once they establish. However, the mechanisms that coordinate this interplay remain largely unknown. Working with the aquatic plant family Lemnaceae, we reveal that the inherent complexity of root anatomy determines root plasticity in response to microbial colonisation. This microbiota-driven anatomical plasticity enhances plant survival in nutrient-competitive environments. By combining synthetic root models with real roots, we also find that anatomical plasticity is associated with metabolic reprogramming during microbial establishment. Moreover, we identify a plant metabolite, N[6],N[6],N[6]-Trimethyl-L-lysine, that regulates anatomical plasticity in response to microbial colonisation. Our work generalizes the importance of microhabitat complexity for microbiome recruitment under challenging environmental conditions.},
}

*Plant Roots/anatomy & histology/microbiology/metabolism
*Microbiota/physiology
Ecosystem
Lysine/analogs & derivatives/metabolism
Stress, Physiological

@article {pmid42722700,
year = {2026},
author = {Kim, NE and Cho, B and Kim, Y and Kim, G and Yie, GE and Kim, H and Park, J and Kim, H and Jeong, C and Lee, M and Joo, Y and Lim, S and Park, S and Hong, Y and Min, K and Cho, B and Yun, JM and Jung, ES and Ji, Y and Cho, S and Seong, JK and Park, H and Park, JH and Won, S},
title = {Linking visceral fat accumulation to gut microbiota: key bacterial taxa and their roles in the glycogen synthesis pathway.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42722700},
issn = {2092-6413},
support = {2022R1A2C2008976//Ministry of Science, ICT and Future Planning (MSIP)/ ; RS-2023-00228315//Ministry of Science, ICT and Future Planning (MSIP)/ ; 2024-ER2108-00//Ministry of Health, Welfare and Family Affairs | Korea National Institute of Health (KNIH)/ ; RS-2021-NR060088//National Research Foundation of Korea (NRF)/ ; KSC-2024-CRE-0514//National Research Foundation of Korea (NRF)/ ; },
abstract = {Obesity, marked by visceral fat accumulation, has a complex relationship with the gut microbiome that impacts body weight and fat accumulation. However, previous studies did not account for fat distribution, reflecting only overall fat mass, leaving specifics of this relationship partially understood. Here we analyzed the mechanistic links between visceral fat and the microbiome in a large cohort of healthy Koreans. Using permutational multivariate analysis of variance and prediction modeling, we examined associations between microbial profiles and metabolic variables including insulin, triglycerides, waist circumference and visceral fat. The strongest correlations were noted with specific enterotypes. Shotgun sequencing revealed that visceral fat is linked to the glycogen synthesis pathway influenced by Dorea longicatena and Bifidobacterium adolescentis. This suggests that these specific microbial signatures and their associated functional potential play a role in visceral fat-related obesity. To validate these findings, we conducted an in vivo study using diet-induced obesity mouse model. Oral administration of D. longicatena or B. adolescentis significantly promoted body weight gain and fat mass expansion and induced hepatic lipogenic gene upregulation. The prevalence of these strains in Korean and American populations highlights their global relevance, contributing to the development of personalized treatments and advanced health strategies.},
}

@article {pmid42722760,
year = {2026},
author = {Rath, S and Dash, R and Pattanayak, M and Varshni, K and Sohal, P and Mishra, P and Dash, OMP and Bhuniya, S and Mitra, JK and Ramadass, B},
title = {Effects of ResB supplementation on gut microbiome composition in elderly pneumonia: a randomized pilot trial.},
journal = {European journal of clinical nutrition},
volume = {},
number = {},
pages = {},
pmid = {42722760},
issn = {1476-5640},
abstract = {RATIONALE: Pneumonia remains a leading cause of morbidity and mortality in older adults, often exacerbated by immune dysregulation and prolonged hospitalization. The gut-lung axis is increasingly recognized as a modulator of respiratory immunity, yet the therapeutic potential of targeted probiotic interventions in elderly pneumonia patients remains underexplored.

OBJECTIVES: To characterize gut microbial compositional changes, temporal shifts, and microbial interaction network dynamics associated with ResB® Lung Support probiotic supplementation in elderly patients hospitalized with pneumonia in this exploratory, hypothesis-generating pilot trial.

METHODS: In a randomized, double-blind, placebo-controlled trial, patients aged ≥60 years admitted with Pneumonia received either resB® probiotic capsules or placebo for 14 days alongside standard care. Stool samples were collected at baseline, day 15, and day 30 (or discharge). Microbiome profiling was performed using 16S rRNA gene sequencing. Statistical analyses included linear mixed-effects Modeling, Wilcoxon rank-sum tests, and trajectory and network assessments.

RESULTS: Sixteen patients completed the study. The probiotic group exhibited increased abundance of several beneficial taxa, including Bifidobacterium longum (p = 0.08, FDR = 0.16) and Blautia_A_141781 (p = 0.05, FDR = 0.1), along with positive temporal shifts in Prevotella copri and CAG_83. Pathogenic genera such as Corynebacterium (p = 0.06, FDR = 0.3) and Streptococcus (p = 0.07, FDR = 0.3) declined in the treatment arm. Log-fold change analysis showed significant increases in CAG_83 (p = 0.02, FDR = 0.09) and P. copri (p = 0.027, FDR = 0.09), with an upward trend for B. longum (p = 0.09, FDR = 0.18). Microbiome trajectory analysis indicated temporal shifts in gut microbial composition in the treatment group, and network analysis demonstrated enhanced connectivity among commensal taxa with reduced pathogenic interactions.

CONCLUSIONS: Probiotic supplementation with resB® Lung Support was associated with changes in gut microbiome composition in elderly pneumonia patients, including shifts in several commensal and potentially pathogenic taxa. Given the exploratory nature of this pilot trial, these findings should be interpreted cautiously. The results suggest that microbiome-targeted nutritional interventions may influence gut microbial dynamics during acute respiratory illness and warrant further investigation in larger, multicenter studies.

TRIAL REGISTRATION NUMBER: CTRI/2022/04/041687 (URL: https://ctri.nic.in/Clinicaltrials/pmaindet2.php?EncHid=NjY5MjI) .},
}

@article {pmid42722802,
year = {2026},
author = {Packi, K and Świerczewski, D and Klimczak, S and Ochab, D and Gałęziewska, J and Gromek, P and Kruczkowska, W and Płuciennik, E and Kałuzińska-Kołat, Ż and Kołat, D},
title = {Parasites and allergies: a complex bidirectional relationship from evolutionary origins to modern therapeutics.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {10},
pages = {},
pmid = {42722802},
issn = {1572-9699},
mesh = {Humans ; Animals ; *Hypersensitivity/immunology/therapy/parasitology ; *Host-Parasite Interactions/immunology ; *Parasites/immunology ; Immunoglobulin E/immunology ; Biological Evolution ; Helminths/immunology ; *Parasitic Diseases/immunology ; },
abstract = {Parasites and allergic diseases are linked by a complex, bidirectional relationship shaped by long-term host-parasite coevolution. This review discusses how different parasites may either promote or attenuate allergic responses through immunological, epithelial, and microbiome-mediated mechanisms. IgE-mediated immunity, mast cell activation, eosinophilia, and pruritus may have evolved as protective responses against helminths and blood-feeding ectoparasites. In contrast, modern allergies may partly reflect misdirected responses to harmless environmental antigens. The effects of parasites on allergy are not uniform and depend on parasite type, infection site, exposure intensity and chronicity, host immune status, and the degree of host-parasite adaptation. Protozoa such as Giardia intestinalis may contribute to food allergy-related manifestations by disrupting the intestinal barrier, altering gut microbiota composition, and modifying mucosal immune responses, particularly in atopic individuals. In contrast, selected helminths may attenuate allergic inflammation by inducing regulatory T and B cells, anti-inflammatory cytokines, antigen-presenting cell modulation, and IgG4-associated mechanisms that can limit IgE-mediated effector responses. Molecular similarities between parasite-derived antigens and environmental allergens, including conserved protein families and carbohydrate epitopes, may contribute to cross-reactive IgE responses and complicate allergy diagnostics. Therefore, current research is shifting from live helminth therapy toward defined parasite-derived molecules and immunomodulatory pathways that may inspire safer and more controlled therapeutic strategies. A clearer understanding of parasite-allergy interactions may improve diagnostic interpretation and support the development of new approaches to the management of allergic disease.},
}

Humans
Animals
*Hypersensitivity/immunology/therapy/parasitology
*Host-Parasite Interactions/immunology
*Parasites/immunology
Immunoglobulin E/immunology
Biological Evolution
Helminths/immunology
*Parasitic Diseases/immunology

@article {pmid42722995,
year = {2026},
author = {Brandt, L and Abrahão, A and Wicht, AC and Schulz, S and Schloter, M and Schweizer, S and Marhan, S and Kandeler, E},
title = {Reciprocal transport of carbon and nitrogen between plants and the hyphosphere microbiome in a temperate grassland.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71576},
pmid = {42722995},
issn = {1469-8137},
support = {119111086//Deutsche Forschungsgemeinschaft/ ; 512307488//Deutsche Forschungsgemeinschaft/ ; 512359828//Deutsche Forschungsgemeinschaft/ ; 60986592//Deutsche Forschungsgemeinschaft/ ; },
abstract = {Despite its relevance for plant nutrient acquisition, the role of the hyphosphere in structuring fungal-bacterial networks and mediating carbon-nitrogen (C-N) exchange under field conditions remains unclear. We therefore examined reciprocal C-N fluxes along the plant-fungi-bacteria continuum and their link to microbial community assembly across grassland soil microhabitats. Sterilized compartmentalized ingrowth cores were exposed to soil in the field for 3 months. Plants were pulse-labeled with [13]CO2 and [13]C was traced into microbial biomarkers over 7 d. [15]N-labeled urea was supplied to a hyphal compartment and isotope recovery in plants was quantified. We reconstructed microbial networks and visualized microscale isotope distributions. Plant-derived [13]C was rapidly incorporated into fungi within 1 d and into hyphosphere bacteria after 7 d. Conversely, 16.9% of the initially added 150 μg [15]N was transferred from the hyphal compartment to plants. Microbial diversity declined from the rooted toward the hyphal-dominated compartments, while networks reorganized with relatively more positive fungal-bacterial associations. Arbuscular mycorrhizal fungi act as primary channels of reciprocal C-N exchange, rapidly transporting newly fixed plant C into root-distant soil zones. More broadly, soil fungi act as ecological filters shaping bacterial assembly and may foster increasingly positive associations with bacteria in hyphal-dominated habitats.},
}

@article {pmid42723054,
year = {2026},
author = {Zhao, J and Chen, X and Wang, X and Cui, Y and Zhuge, J and Zhang, Y and Zhang, L and Yan, Y and Fang, H and Hua, Z and Li, G},
title = {Metagenomic-based quantification of Pseudomonas aeruginosa burden links microbiome collapse to mortality in severe community-acquired pneumonia.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {25},
number = {1},
pages = {},
pmid = {42723054},
issn = {1476-0711},
support = {2024KY1761//2024 Science and Technology Program for Medicine and Health in Zhejiang Province/ ; 2023K112//Quzhou Science and Technology Program/ ; },
mesh = {Humans ; *Community-Acquired Pneumonia/mortality/microbiology ; *Pseudomonas aeruginosa/genetics/isolation & purification ; Female ; *Microbiota ; Retrospective Studies ; *Pseudomonas Infections/mortality/microbiology ; Metagenomics ; Male ; Aged ; Middle Aged ; Lung/microbiology ; *Community-Acquired Infections/microbiology/mortality ; ROC Curve ; Metagenome ; High-Throughput Nucleotide Sequencing ; Prognosis ; },
abstract = {BACKGROUND: Severe community-acquired pneumonia (sCAP) remains a major cause of mortality in critically ill patients, Pseudomonas aeruginosa (P. aeruginosa) is a frequent pathogen associated with poor prognosis in this population. While metagenomic next-generation sequencing (mNGS) is widely used for pathogen detection, its value in quantifying pathogen abundance and linking it to lung microbiome alterations remains unclear.

OBJECTIVES: This study investigated the association between P. aeruginosa abundance quantified by mNGS and lung microbiome alterations and clinical outcomes in sCAP patients.

METHODS: This multicenter retrospective study included 130 patients with sCAP caused by P. aeruginosa from five hospitals (September 2021-June 2025). Patients were stratified into low, medium, and high abundance groups according to mNGS-derived reads per ten million (RPTM) values of P. aeruginosa. Lung microbiome diversity and community structure were analyzed, and differences between groups were assessed using appropriate statistical methods. The association between P. aeruginosa abundance and clinical outcomes was evaluated using correlation analysis, sankey diagram, receiver operating characteristic curve, grey zone analysis and logistic regression.

RESULTS: A total of 130 patients with sCAP due to P. aeruginosa were stratified into low, medium, and high abundance groups based on mNGS-derived RPTM value. Microbial diversity decreased progressively with increasing abundance, and community structures differed significantly among groups (all P < 0.05). P. aeruginosa became increasingly dominant, accounting for up to 95.99% of the microbiota in the high abundance group. Higher P. aeruginosa abundance was associated with increased disease severity, including longer mechanical ventilation, prolonged hospital stay, and higher 28-day mortality. Sankey diagram showed a progressive decline in treatment effectiveness and an increase in mortality with increasing P. aeruginosa abundance. P. aeruginosa_RPTM showed moderate predictive value for mortality (AUC = 0.761, Sens = 69.40%, Spec = 75.30%, cutoff: 41122, grey zone: 2287-220339) and remained independently associated with 28-day mortality in multivariable analysis [2.219 (1.509 to 3.262), P < 0.001].

CONCLUSION: In patients with sCAP, higher P. aeruginosa_RPTM measured by mNGS was associated with reduced lung microbiome diversity and unfavorable clinical outcomes. RPTM-based risk stratification may help identify patients at increased risk of poor prognosis.},
}

Humans
*Community-Acquired Pneumonia/mortality/microbiology
*Pseudomonas aeruginosa/genetics/isolation & purification
Female
*Microbiota
Retrospective Studies
*Pseudomonas Infections/mortality/microbiology
Metagenomics
Male
Aged
Middle Aged
Lung/microbiology
*Community-Acquired Infections/microbiology/mortality
ROC Curve
Metagenome
High-Throughput Nucleotide Sequencing
Prognosis

@article {pmid42723085,
year = {2026},
author = {Orth, N and Siefen, N and Staudt, J and Mahmoud, FM and Benning, S and Gschwendtner, S and Pielhop, TP and Hauschild, K and Schloter, M and Schmitz, M and Winkelmann, T},
title = {Linking microbial community composition of three rootstock genotypes to apple replant disease susceptibility.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42723085},
issn = {2524-6372},
abstract = {BACKGROUND: Apple replant disease (ARD) is a worldwide issue of complex biotic origin. The exact aetiology has yet to be fully elucidated and environmentally friendly and economically feasible countermeasures are sparse. The breeding of tolerant apple rootstock genotypes shows some promise as reduced sensitivity on selected ARD-affected soils has been shown for some rootstock genotypes. By adding insights into the root-associated microbiome, we aimed to complement previously published results, examining the response in growth, gene expression and production of phenolic compounds in roots of seven Malus genotypes in ARD soil. We selected the two least susceptible rootstock genotypes of the previous study, EMR.2 and G.935, in addition to the susceptible rootstock genotype M.26. The objective of this study was to gain insights into the bacterial community composition of the rhizosphere and root endosphere of less susceptible rootstock genotypes in comparison to the susceptible one.

RESULTS: In an Illumina-based sequencing approach, the composition of rhizosphere as well as endophytic bacterial communities was investigated for apple plants in ARD soil and disinfected ARD soil. ARD impacted the rhizosphere stronger than the endosphere, where rootstock genotype influence was stronger. G.935 generally showed a more distinct and diverse microbiome than the other two rootstock genotypes. In bacterial communities, the relative abundance of Pseudomonadota decreased in ARD samples, while Actinomycetota increased. In the endosphere, this was mostly accounted for by Streptomyces. A qPCR approach confirmed the high abundance of Streptomyces. Interestingly, another qPCR approach did not indicate a high abundance of plant pathogenic Streptomyces in the same samples.

CONCLUSIONS: ARD strongly influenced the bacterial microbiome in the rhizosphere and, to a lesser extent, the root endophytic microbiome. The distinct and more diverse bacterial microbiome of G.935 might help against biotic stress, such as ARD. However, EMR.2 was previously found to be less susceptible to ARD, too, suggesting additional factors must play a role and additional research is necessary. Pathogenicity of Streptomyces could not be proven but repeatedly high abundance of root endophytic Streptomyces under ARD conditions indicate an important role.},
}

@article {pmid42723086,
year = {2026},
author = {Afkhamian, A and Saffari Natanzi, A and Jafaridarabjerdi, M and Aghaei, S and Haghjou, A and Shafiei, M and Bashkandi, AH and Shahraki, S and Reiter, RJ and Haddad Kashani, H and Yang, Y},
title = {Virobiome-mediated regulation of microbiota-gut-brain axis signaling and neuroimmune homeostasis.},
journal = {Cell communication and signaling : CCS},
volume = {24},
number = {1},
pages = {},
pmid = {42723086},
issn = {1478-811X},
mesh = {Humans ; *Homeostasis ; Animals ; *Signal Transduction ; *Brain/immunology/metabolism ; *Gastrointestinal Microbiome ; *Virome ; },
abstract = {The human gut-brain axis (GBA) is increasingly recognized as a complex bidirectional communication system integrating microbial, neural, endocrine, and immune networks that shape neurological health. While bacterial contributions to this dialogue have been extensively characterized, the viral component of the gut ecosystem, the virome, has emerged as an important component associated with host physiological regulation. This review synthesizes evidence suggesting that bacteriophages and eukaryotic viruses may contribute to microbial and immune homeostasis and may influence signaling along the microbiota-gut-brain axis. In experimental studies, Bacteriophages have been shown to influence microbial community structure through lytic and lysogenic cycles, horizontal gene transfer, and metabolic modulation, indirectly regulating production of neuroactive metabolites such as short-chain fatty acids and tryptophan derivatives which in turn have been linked to blood brain barrier integrity and modulate microglial activation. In observational human studies and experimental models, eukaryotic viruses including Epstein Barr virus and cytomegalovirus have been associated with systemic inflammation, molecular mimicry, and cytokine dysregulation, amplifying neuroimmune cascades implicated in Alzheimer's disease (AD), multiple sclerosis (MS), autism spectrum disorder (ASD), and major depressive disorder (MDD). The convergence of viral-bacterial interactions highlights a transkingdom signaling network shaping neuroinflammatory tone and influencing disease susceptibility. Emerging experimental strategies, including precision phage therapy, engineered probiotics incorporating CRISPR-based antiviral systems, and fecal virome transplantation (FVT), are being explored as potential approaches to modulate virome-microbiome interactions. Integration of multiomics platforms with artificial intelligence-driven modeling will be critical for clarifying the temporal and mechanistic relationships between virome dynamics and neurological function. Collectively, these insights highlight the gut virobiome as a potentially important contributor to neuroimmune equilibrium and illuminate avenues for microbiome-informed diagnostics and interventions in neurodegenerative and neuropsychiatric disorders. This review therefore highlights the often underappreciated role of the gut virobiome and proposes an integrative conceptual model linking virome dynamics with microbiota-gut-brain axis signaling.},
}

Humans
*Homeostasis
Animals
*Signal Transduction
*Brain/immunology/metabolism
*Gastrointestinal Microbiome
*Virome

@article {pmid42723101,
year = {2026},
author = {Liu, X and Yang, Z and Zhang, X and Tang, W and Wang, Y and Cao, Z and Yang, H and Wang, W and Hao, Y and Li, S},
title = {Gut microbiota-driven indole-3-propionic acid and kynurenine production is associated with improved metabolic adaptation in periparturient dairy cows.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42723101},
issn = {1674-9782},
abstract = {BACKGROUND: Gastrointestinal microbes convert tryptophan into various bioactive metabolites that influence host energy metabolism; however, these mechanisms are not well understood in periparturient dairy cows, which experience marked metabolic challenges during this period.

RESULTS: In this study, we used periparturient dairy cows with rumen and ileal cannulas as in vivo models. Blood, rumen fluid, ileal digesta, and fecal samples were collected at four time points during the periparturient period. By combining metagenome-assembled genomes (MAGs) and targeted metabolite quantification, we characterized microbial tryptophan metabolism and associated metabolite profiles during the periparturient period. The results showed that postpartum cows exhibited significantly increased serum concentrations of triglyceride (TG), aspartate aminotransferase (AST), β-hydroxybutyrate (BHBA), and total bilirubin (T-Bil) compared with prepartum cows, together with decreased levels of several tryptophan metabolites, including indole-3-propionic acid (IPA) and kynurenine (KYN), indicating that tryptophan deficiency might aggravate metabolic disturbances. Metagenomic analysis identified 578 high-quality MAGs, of which 461 contained genes involved in microbial tryptophan metabolic pathways. Among these, the ruminal taxon CAG-791 harbors acdA and contributes to IPA production, whereas the hindgut taxon Treponema_D harbors kynB and promotes KYN formation. Decreases in both taxa were consistent with the reduced levels of these metabolites observed above. In a follow-up in vivo trial with tryptophan supplementation, the abundance of CAG-791 and Treponema_D increased, along with tryptophan-derived metabolites (IPA and KYN), which further partially mitigated metabolic disturbances.

CONCLUSIONS: These findings characterize spatial and temporal changes in tryptophan metabolites and gut microbial features in periparturient dairy cows, and provide integrated evidence that alterations in tryptophan metabolism are associated with postpartum metabolic adaptation, thereby supporting the potential of tryptophan-targeted nutritional strategies to improve metabolic health in dairy cows.},
}

@article {pmid42723210,
year = {2026},
author = {Achterberg, P and Lekkerkerker, M and Koelemeijer, L and Illidge, S and Vroom, J and Hertzberger, RY and Vreede, J and van Loosdrecht, MCM and Kort, R},
title = {A Mobile Glycosylation Locus Modulates Cell Wall Architecture in Lactobacillus crispatus.},
journal = {Molecular microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/mmi.70112},
pmid = {42723210},
issn = {1365-2958},
support = {//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; //Vrije Universiteit Amsterdam/ ; },
abstract = {Lactobacillus crispatus dominance in the vaginal microbiome is associated with beneficial health outcomes, yet strain-level variation and its implications remain poorly understood. Here, we resolve the genomic context of three glycosyltransferase gene fragments (GT1-3) previously linked with dysbiotic states. Long-read resequencing revealed that GT1-3 are part of a ~18.7 kb Wzx/Wzy-dependent cell wall polysaccharide (CWPS) locus, containing several IS256-family transposases. Serial propagation in vitro produced isolates with 4.1 kb excised via a composite transposon encompassing the GT3, UDP-galactopyranose mutase, flippase, and hypothetical protein, demonstrating structural plasticity. Transmission electron microscopy showed a ~20%-25% thinner peptidoglycan layer in the derived strains, while FT-IR and monosaccharide analysis indicated no gross changes. Molecular dynamics simulations suggest that GT3 contributes to the structural stability of the glycosyltransferase complex, without compromising catalytic function. Together, these findings establish the CWPS locus as a mobile, structurally plastic element that directly influences cell wall architecture in L. crispatus.},
}

@article {pmid42723264,
year = {2026},
author = {Aware, C and Neher, CM and Woods, C and Khegai, O and Dwivedi, AK and Govindarajan, M and Ivanich, K and Kurt, M and Beversdorf, D and Cheng, J and Bresette, N and Cui, T and Balchandani, P and Gonzales, MM and Ericsson, AC and Altes, T and Lin, AL},
title = {EXPRESS: Rapamycin increases cerebral blood flow and modulates metabolic, inflammatory, and microbiome profiles in healthy middle-aged APOE4 carriers: a pilot single-arm trial.},
journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism},
volume = {},
number = {},
pages = {271678X261490342},
doi = {10.1177/0271678X261490342},
pmid = {42723264},
issn = {1559-7016},
abstract = {Carriers of the apolipoprotein E4 (APOE4) allele often develop cerebrovascular dysfunction and broader systemic alterations decades before the onset of Alzheimer's disease (AD) pathology or clinical symptoms. Early interventions that can improve these functions may help delay or slow AD progression. In this study, we repurposed rapamycin (sirolimus), an FDA-approved medication with anti-aging properties, to target APOE4 associated multisystem dysfunction. We conducted a single arm trial of low dose rapamycin (1 mg/day for 4 weeks) in cognitively normal adults aged 45 to 65 years, prior to detectable AD pathology, stratified by APOE genotype. The primary outcome was cerebral blood flow (CBF), while secondary outcomes included plasma metabolomics, inflammatory cytokines, AD biomarkers, and gut microbiome composition. Twenty-three participants completed the study, including nine APOE4 carriers and fourteen non-carriers. Rapamycin significantly increased CBF in APOE4 carriers, with increases exceeding 15% across multiple brain regions, and improved metabolic and inflammatory profiles with minimal adverse effects. In contrast, non-carriers showed no significant change in CBF and exhibited distinct physiological responses, highlighting genotype dependent effects. These findings suggest that rapamycin may mitigate early cerebrovascular and systemic dysfunction in APOE4 carriers and support a precision medicine approach in which therapeutic response is influenced by genotype.},
}

@article {pmid42723314,
year = {2026},
author = {Hong, DK and Jeon, S and Woo, S and Shin, S and Lee, DY and Park, SD and Choi, ID and Shim, JJ and Lee, JH},
title = {Effects of Lactiplantibacillus plantarum HY7715 Supplementation on Lower Limb Muscle Strength and Power in Older Adults: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Journal of medicinal food},
volume = {},
number = {},
pages = {1096620X261486094},
doi = {10.1177/1096620X261486094},
pmid = {42723314},
issn = {1557-7600},
abstract = {Age-associated reductions in muscle strength and physical function have become an important public health concern among older adults, and gut microbiome-targeted interventions have emerged as a potential strategy to mitigate these declines. We evaluated the effects of Lactiplantibacillus plantarum HY7715 (L. plantarum HY7715) on lower-limb muscle function, serum vitamin B2, and gut microbiome profiles in older adults exhibiting reduced muscle strength. In this 12-week, randomized, double-blind, placebo-controlled trial, 100 adults aged 50-85 years were assigned to receive HY7715 (5.0 × 10[9] CFU/day) or placebo. Compared with placebo, HY7715 supplementation was associated with greater increases in multiple measures of quadriceps strength, with the left and bilateral mean measures remaining significant after baseline adjustment. Selected hamstring strength and quadriceps muscle power outcomes also showed significant improvements in the unadjusted analyses. Overall, the most consistent findings were observed for quadriceps strength, whereas the hamstring strength and quadriceps muscle power findings were less consistent after baseline adjustment. Serum vitamin B2 concentration increased significantly following HY7715 supplementation, and the between-group difference remained significant after adjustment for baseline dietary riboflavin intake. Microbiome analyses demonstrated increased Chao1 alpha diversity, significant within-group shifts in beta diversity, and increased relative abundances of Lactiplantibacillus and L. plantarum. HY7715 supplementation was associated with greater increases in selected quadriceps strength measures and serum vitamin B2 concentrations in adults with reduced muscle strength.},
}

@article {pmid42723362,
year = {2026},
author = {Madej, M and Rodríguez-Banqueri, A and Mizgalska, D and Szmigielski, B and Nowakowska, Z and Benedyk-Machaczka, M and Bzowska, M and Mikruta, K and Ramírez-Larrota, JS and Agunanne, C and Julien, O and O'Donoghue, AJ and Scavenius, C and López-Martín, M and Marcos, E and Koziej, Ł and Glatt, S and Guerra, P and Eckhard, U and Potempa, J and Gomis-Rüth, FX},
title = {Structure and Function of a Multi-Megadalton Virus-Like Proteolytic Dodecahedron.},
journal = {Angewandte Chemie (International ed. in English)},
volume = {},
number = {},
pages = {e5597279},
doi = {10.1002/anie.5597279},
pmid = {42723362},
issn = {1521-3773},
support = {MCIN/AEI/10.13039/501100011033//Polish (National Science Centre and Ministry of Science and Higher Education), Spanish (State Agency for Research [AEI]/ ; PID2022-137827OB-I00//Catalan (AGAUR, Government of Catalonia)/ ; PID2025-171123OB-I00//Catalan (AGAUR, Government of Catalonia)/ ; RYC2020-029773-I//CONEXIÓN TRIGO/ ; PID2021-128682OA-I00//CONEXIÓN TRIGO/ ; PID2024-159901OB-I00//CONEXIÓN TRIGO/ ; CNS2024-154537//CONEXIÓN TRIGO/ ; PID2023-153085NB-I00//CONEXIÓN TRIGO/ ; MMT24-IBMB-01//CONEXIÓN TRIGO/ ; 2021SGR00423//CONEXIÓN TRIGO/ ; PRE2020-096731//CONEXIÓN TRIGO/ ; IU16-014045//CONEXIÓN TRIGO/ ; UMO-2023/51/D/NZ1/02675//CONEXIÓN TRIGO/ ; UMO-2024/53/B/NZ1/03079//CONEXIÓN TRIGO/ ; 233068//Support for research and development with the use of research infrastructure of the National Synchrotron Radiation Centre SOLARIS/ ; },
abstract = {Natural pentamer dodecahedra (Ddhs) span six orders of magnitude in diameter. Among proteins, only two catalytic Ddhs have been structurally characterized: lumazine synthase (LS) and the core of pyruvate dehydrogenase (PDH). Zuzalysin (ZUZ) is a ≈95-kDa metallopeptidase secreted for virulence by Porphyromonas gingivalis. Calcium converts latent flexible monomers into active ≈0.5-MDa pentamers that further assemble hierarchically into bipentamers, tripentamers, and a ≈5.6-MDa, ≈355-Å virus-like dodecahedron (DdhZUZ). Experimental structures (1.8-3.6 Å) across these states reveal the molecular basis of activation, association, and catalysis, culminating in DdhZUZ, which is physiologic, exceeds small viral capsids, and has 20 main entry pores and 60 lumen-facing active sites. ZUZ represents the largest catalytic protein assembly resolved at high resolution, exceeding LS, PDH, and major peptidase complexes in size and/or resolution.},
}

@article {pmid42723559,
year = {2026},
author = {Ranzani, FA and Montrucchio, C and Ferrrocino, I and Penoncelli, D and Cavecchia, I and Tettoni, C and Ferrara, M and Pezzana, A and Palermiti, A and Lazzaro, A and Bonora, S and DiPerri, G and Calcagno, A},
title = {The effect of a tailored dietary intervention on serum biomarkers and faecal microbiome composition in people with HIV at risk of cardiovascular disease.},
journal = {HIV medicine},
volume = {},
number = {},
pages = {},
doi = {10.1111/hiv.70291},
pmid = {42723559},
issn = {1468-1293},
abstract = {BACKGROUND: People with HIV (PWH) are at higher risk of cardiovascular disease (CVD) despite spontaneous or antiretroviral therapy-induced long-lasting suppressed viremia. Traditional and HIV-specific factors have been identified, but CVD incidence and mortality remain high. A microbiome is a community of germs living close to their human host, and bacterial dysbiosis is associated with atherosclerosis and chronic non-communicable disease development.

METHODS: We conducted a pilot study designed to analyze the effect of tailored diet intervention on body mass index (BMI), metabolic features and microbiota composition in PWH with suppressed HIV viremia (HIV RNA <50 copies/mL) under combination antiretroviral treatment. Biomarkers and parameters were measured at baseline and 6 months (M6) after.

RESULTS: Ten male participants were enrolled. The median age was 60.5 years (54-69) and the 10-year CV risk was 11.7% (7.2-21.2). CD4+ T lymphocyte count was 568 cells/mm[3] (398-625). Approximately 75% of participants declared to be adherent to the given dietary recommendations. Participants showed reduced amounts of food intake (p = 0.022) and, specifically, of saturated fat (p = 0.007) and cholesterol (p = 0.011). At M6, most metabolic and inflammatory parameters remained stable. TMAO concentrations were higher at M6 than at baseline (157 vs. 129 ng/mL, p = 0.050). Microbiota alpha and beta diversity did not change over time: yet we observed a significant reduction of Firmicutes (p = 0.047) and an increase in Proteobacteria (p = 0.028) relative abundance at M6.

CONCLUSIONS: In this pilot study assessing a tailored dietary intervention in high CV-risk PWH, we observed stable metabolic and inflammatory parameters and an unexpected increase in TMAO levels at 6 months. Microbiome composition was marginally affected, and active interventions are probably needed to elicit significant changes over time.},
}

@article {pmid42723725,
year = {2026},
author = {Peng, YL and Huang, QL and Zhu, HY and Chen, ZH and Deng, Y and Lu, C and Xu, CR and Xiao, FM and Zhou, Q},
title = {Association between antibiotic exposure and outcomes of chemoimmunotherapy in extensive-stage small cell lung cancer: a single-center retrospective cohort study.},
journal = {Translational lung cancer research},
volume = {15},
number = {8},
pages = {233},
pmid = {42723725},
issn = {2218-6751},
abstract = {BACKGROUND: Lung cancer remains a leading cause of cancer incidence and mortality worldwide. Small cell lung cancer (SCLC), though only 15% of cases, shows aggressive biological behavior and poor prognosis. Chemoimmunotherapy is the standard first-line treatment for extensive-stage SCLC (ES-SCLC). Gut microbiota affects immunotherapy in other cancers, but its role in ES-SCLC is unclear. This study examined the association of antibiotics, cathartics, and probiotics with the efficacy of chemoimmunotherapy in ES-SCLC.

METHODS: This retrospective study enrolled patients with ES-SCLC receiving chemoimmunotherapy at the Guangdong Lung Cancer Institute (GLCI). Kaplan-Meier curves and Cox regression were used to evaluate associations of antibiotic, cathartic, and probiotic use with progression-free survival (PFS) and overall survival (OS). Multivariable Cox regression models, including an Akaike information criterion (AIC)-based model and a clinically guided model with prespecified covariates, were used to evaluate the association between antibiotic exposure and survival outcomes. Propensity score-based weighting and matching, together with additional sensitivity analyses, were performed to assess the robustness of antibiotic-related associations.

RESULTS: Antibiotic exposure was associated with shorter PFS in univariable Cox regression [hazard ratio (HR): 2.71, 95% confidence interval (CI): 1.41-5.22; P=0.003] and multivariable Cox regression (AIC model: HR: 2.63, 95% CI: 1.28-5.41; P=0.008; clinical model: HR: 2.16, 95% CI: 1.06-4.39; P=0.03). Antibiotic exposure was also associated with shorter OS in univariable analysis (HR: 6.02, 95% CI: 3.06-11.84; P<0.001) and multivariable analysis (AIC model: HR: 6.88, 95% CI: 3.26-14.54; P<0.001; clinical model: HR: 5.34, 95% CI: 2.62-10.87; P<0.001). Propensity score-weighted and sensitivity analyses showed generally consistent directions of association, whereas propensity score-matched analyses showed a consistent adverse direction without reaching statistical significance. Cathartic and probiotic use were not significantly associated with PFS or OS in exploratory analyses.

CONCLUSIONS: Antibiotic exposure was associated with shorter PFS in ES-SCLC patients receiving chemoimmunotherapy, with generally consistent findings across multiple analyses. The OS association was also observed. However, these results should be interpreted cautiously given the small exposed cohort, residual confounding, and possible proportional hazards violations. Prospective multicenter validation with detailed antibiotic, infection, and microbiome data is warranted.},
}

@article {pmid42723730,
year = {2026},
author = {Wei, Y and Yin, H and Hou, D and Chen, H and Xu, G and Zheng, B and Chen, C and Yang, Z},
title = {Emotional distress and clinical response to neoadjuvant chemoimmunotherapy in resectable non-small-cell lung cancer: a protocol for the prospective observational NeoFUSE-Lung cohort study.},
journal = {Translational lung cancer research},
volume = {15},
number = {8},
pages = {255},
pmid = {42723730},
issn = {2218-6751},
abstract = {BACKGROUND: Neoadjuvant chemoimmunotherapy (NACI) has improved pathological and survival outcomes in patients with resectable non-small-cell lung cancer (NSCLC), yet marked heterogeneity in treatment response persists. Emotional distress (ED) may modulate antitumor immunity through neuroendocrine and immune-related mechanisms, but its association with response to NACI in patients with resectable NSCLC remains insufficiently explored. This study aims to prospectively evaluate the relationship between ED and clinical outcomes in patients with resectable NSCLC receiving NACI, with exploratory analyses of stress-related biomarkers and gut microbiome profiles.

METHODS: This single-center, prospective observational cohort study will enroll patients with treatment-naïve, resectable stage II-IIIB NSCLC scheduled to receive first-line NACI at Fujian Medical University Union Hospital. All participants will receive NACI as part of routine clinical care, and no experimental intervention will be assigned. ED will be assessed using the Hospital Anxiety and Depression Scale (HADS) at baseline and after two cycles of NACI, and participants will be classified according to baseline ED status and longitudinal ED trajectories. Clinical, psychological, quality-of-life, biochemical, and fecal microbiome data will be collected at prespecified time points. The primary outcomes are overall survival (OS) and progression-free survival (PFS). Secondary outcomes include objective response rate (ORR), pathological complete response (pCR), major pathological response (MPR), and quality of life (QoL). Associations between ED and clinical outcomes will be analyzed using appropriate regression and survival models, with exploratory analyses of stress-related biomarkers and gut microbiome profiles.

DISCUSSION: This trial aims to provide prospective data on the association between ED and response to NACI in patients with resectable NSCLC, while exploring potential neuroimmune-microbiome pathways underlying this association.

TRIAL REGISTRATION: Chinese Clinical Trial Registry (ChiCTR) identifier: ChiCTR2600119872.},
}

@article {pmid42723739,
year = {2026},
author = {Melipil-Millán, D and Izquierdo, M and Ovalle, R and Espinoza-Cavieres, FA and Gallardo, P and Valenzuela, R and Farfan, MJ},
title = {Dynamics of the gut microbiome and metabolome in children during and after an infectious diarrheal episode.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1905670},
pmid = {42723739},
issn = {2235-2988},
mesh = {Humans ; *Diarrhea/microbiology ; Child, Preschool ; *Metabolome ; Feces/microbiology/chemistry ; Fatty Acids, Volatile/analysis/metabolism ; Infant ; Histamine/analysis/metabolism ; *Gastrointestinal Microbiome ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {INTRODUCTION: Acute diarrhea is associated with significant alterations in the gut microbiota and metabolome. Despite several studies documenting increased levels of histamine and short-chain fatty acids (SCFAs) during diarrheal episodes, the dynamics of these metabolites and microbiota following clinical recovery remain poorly understood, especially in children.

METHODS: We evaluated the composition of the intestinal microbiota and the levels of histamine and SCFAs in stool samples from children under five years old with acute diarrhea and after clinical recovery. Additionally, a comparison with a sample of healthy children was included.

RESULTS: Our results revealed significant differences in the community structure of the intestinal microbiota among the three conditions. The recovery samples exhibited a greater abundance of genera associated with diarrhea, such as Escherichia-Shigella, Streptococcus, Veillonella, and Akkermansia, as well as genera associated with healthy microbiota, such as Bifidobacterium. Regarding metabolites, butyrate levels decreased following clinical recovery, reaching values comparable to those found in the healthy samples, whereas histamine levels did not differ significantly among the conditions.

DISCUSSION: Our findings suggest that, after clinical resolution of diarrhea, the gut microbiota and its metabolites remain significantly different from those observed in healthy children, possibly representing an intermediate stage between diarrhea and a healthy condition. These findings suggest that recovery of the gut microbiota to a healthy condition may take longer and does not necessarily coincide with clinical recovery from diarrhea.},
}

Humans
*Diarrhea/microbiology
Child, Preschool
*Metabolome
Feces/microbiology/chemistry
Fatty Acids, Volatile/analysis/metabolism
Infant
Histamine/analysis/metabolism
*Gastrointestinal Microbiome
Female
Male
*Bacteria/classification/genetics/isolation & purification

@article {pmid42723779,
year = {2026},
author = {Xiong, J and Lu, C},
title = {Clarifying the nutritional and functional context of gut microbiome signals during chemotherapy for advanced non-small cell lung cancer.},
journal = {Translational lung cancer research},
volume = {15},
number = {8},
pages = {267},
pmid = {42723779},
issn = {2218-6751},
}

@article {pmid42723799,
year = {2026},
author = {Ruiz-Roca, JA and Pecci-Lloret, MP and Romano, A and Carinci, F and Lauritano, D and Pérez-Guzmán, N and Lucchese, A},
title = {Oral dysbiosis in children with renal failure: a systematic review.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1832651},
pmid = {42723799},
issn = {2673-4915},
abstract = {INTRODUCTION: The oral microbiome plays an important role in maintaining host homeostasis and may interact with systemic diseases through the oral-systemic axis. Chronic kidney disease (CKD) in childhood is associated with chronic inflammation, metabolic alterations, and immune dysfunction, which may influence microbial ecosystems. While intestinal dysbiosis has been widely studied in paediatric CKD, alterations in the oral microbiome remain less well understood. The aim of this study was to qualitatively synthesize evidence on oral microbiome alterations in children and adolescents with CKD compared with systemically healthy controls.

METHODS: A systematic review was conducted according to PRISMA 2020 and registered in PROSPERO (CRD420261334000). PubMed, Scopus, Web of Science, Cochrane, and SciELO were searched (February 24, 2026). Eligible studies included participants aged 0-18 years with CKD (any stage), dialysis, or kidney transplantation and a healthy control group. Risk of bias was assessed using JBI and ROBINS-I v2 tools.

RESULTS: From 109 records, 7 studies were included. Most used saliva, tongue/oral swabs, or dental plaque, and 16S rRNA sequencing was the most frequent method. Five studies reported oral dysbiosis in CKD, including severe dysbiosis grades in adolescents with end-stage disease, while two studies reported no significant differences versus controls.

CONCLUSION: Findings on individual taxa were inconsistent across studies, likely due to heterogeneity in renal phenotype, oral niche sampled, and analytical methods. Evidence suggests that salivary biochemical alterations (notably urea and pH) and inflammatory burden may influence microbial composition, whereas the tongue microbiome may show relative ecological stability in some paediatric cohorts. Children and adolescents with CKD may present oral microbiome alterations, but current evidence is limited by methodological heterogeneity and moderate-to-high risk of bias. Standardized sampling and longitudinal multicentre studies are needed to determine robust microbial signatures and their value as non-invasive biomarkers in paediatric nephrology.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420261334000.},
}

@article {pmid42723994,
year = {2026},
author = {Ni, H and Gong, QL and Li, JM and Liu, F and Leng, X and Song, YH and Jiang, J and Li, ZY and Li, Y and Sun, YZ},
title = {Genome-resolved analysis of colonization factor repertoires reveals ecological stratification in cervid gut microbiomes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1929306},
pmid = {42723994},
issn = {1664-302X},
abstract = {INTRODUCTION: Colonization factors (CFs) are important microbial traits associated with persistence and host adaptation in the gut, yet their large-scale organization in cervid gut microbiomes remains unclear.

METHODS: A total of 3,311 non-redundant high-quality metagenome-assembled genomes (MAGs), derived from 688 cervid gut metagenomic samples across 15 publicly available projects and one in-house dataset, were analyzed. CF-associated genes were identified by comparison against the GHA CF database, and CF repertoires were characterized at genome, host-species, and gastrointestinal-segment levels.

RESULTS: A total of 138,729 CF-associated genes spanning 71 CF families were identified. MAGs from Cervinae contained richer CF repertoires than those from Caprinae, and CF47 (Peptidase_C69), CF24_29 (QueH), and CF18 (Glycos_transf_2) were among the most prevalent families. CF repertoires were strongly structured by taxonomy, showed a moderate association with bacterial phylogenetic distance, and formed two recurrent genome-level configurations with distinct KEGG functional profiles. Integration of sample metadata further revealed differentiation of CF repertoires across host species and gastrointestinal segments, representing the major ecological dimensions examined in this study. Segment-associated CF variation was accompanied by redistribution of broader functional profiles, including enrichment of carbohydrate and lipid metabolism in the jejunum, membrane transport in the ileum, xenobiotics biodegradation in the cecum, and environmental adaptation in the rumen.

DISCUSSION: These findings provide a genome-resolved view of CF repertoire organization in cervid gut microbiomes and demonstrate that colonization-associated functions are structured across microbial lineages and ecological contexts. This study highlights the importance of considering microbial taxonomy and host-associated environments when interpreting the distribution of CF repertoires in mammalian gut ecosystems.},
}

@article {pmid42724134,
year = {2026},
author = {Wang, Z and Ji, X and Wang, Z and Zheng, S and Liu, F and Lu, J and Chang, H},
title = {The metastatic spectrum in functional and non-functional NENs: mechanistic insights from multi-omics.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1782791},
pmid = {42724134},
issn = {1664-2392},
mesh = {Humans ; *Neuroendocrine Tumors/pathology/genetics/metabolism ; Multiomics ; Neoplasm Metastasis ; Animals ; Biomarkers, Tumor/metabolism ; Pancreatic Neoplasms/pathology/genetics ; },
abstract = {Neuroendocrine neoplasms (NENs) are biologically heterogeneous tumors in which differentiation/grade and hormonal functionality are intersecting but non-equivalent axes. This review focuses on functional and non-functional well-differentiated neuroendocrine tumors (NETs), principally gastroenteropancreatic and pancreatic NETs, and critically evaluates how site, lineage, stage, tumor burden, genomic and epigenetic alterations, immune-stromal remodeling, metabolic adaptation, microbiome-associated signals, and treatment pressure converge on metastasis and recurrence. Apparent outcome differences by functionality are inconsistent after clinicopathological adjustment: non-functional presentation is often enriched for delayed diagnosis and adverse features, whereas functional subtypes range from typically indolent insulinomas to clinically aggressive hormone-producing tumors. We reconcile these observations through a layered model in which lineage-defining alterations and chromatin/telomere programs establish cellular state; signaling and metabolic plasticity enable stress adaptation; and hypoxia, angiogenesis, immune cells, fibroblasts, extracellular matrix, and therapy create selective niches for dissemination and relapse. We also define computational strategies for heterogeneous multi-omics integration and a staged biomarker-validation pathway. Evidence remains dominated by pancreatic NETs, and causal support is weakest for microbiome-functionality relationships and several proposed cross-omic links. A spectrum-based framework is therefore most useful when it generates testable, site- and grade-specific hypotheses rather than treating functionality as an isolated prognostic variable.},
}

Humans
*Neuroendocrine Tumors/pathology/genetics/metabolism
Multiomics
Neoplasm Metastasis
Animals
Biomarkers, Tumor/metabolism
Pancreatic Neoplasms/pathology/genetics

@article {pmid42724150,
year = {2026},
author = {Brokemond, AJ and Amamoo, R and Alexandre, FJ and Ajisegiri, SB and Thounaojam, MC and Martin, PM and Jadeja, RN},
title = {Short-Chain Fatty Acids: Microbial Metabolites Driving Gut-Eye Axis Signaling.},
journal = {Comprehensive physiology},
volume = {16},
number = {5},
pages = {e70251},
pmid = {42724150},
issn = {2040-4603},
abstract = {Short-chain fatty acids (SCFAs) have emerged as key molecular mediators of gut-eye communication, linking microbial metabolism to ocular physiology and disease. Produced through microbial fermentation of dietary fiber, SCFAs function as systemic signaling molecules that regulate immune homeostasis, metabolic function, vascular integrity, and neuroinflammatory pathways through activation of SCFA-responsive receptors and epigenetic mechanisms. Growing evidence indicates that SCFAs influence biological processes central to ocular health, including inflammation, oxidative stress, neurodegeneration, and pathological angiogenesis. Experimental, metabolomic, and emerging clinical studies suggest that disruptions in SCFA signaling may contribute to the pathogenesis of retinal and ocular surface diseases; however, the mechanisms governing ocular exposure, target engagement, and therapeutic efficacy remain incompletely understood, highlighting a critical gap between mechanistic insight and clinical translation. In this review, we integrate current evidence into a mechanistic and translational framework that positions SCFAs as central effectors of the gut-eye axis. We further evaluate the therapeutic potential of SCFA modulation and identify key barriers to clinical implementation, including bioavailability, pharmacokinetics, dosing, and long-term safety, thereby delineating a roadmap for the development of microbiome-derived precision therapeutics in ophthalmology.},
}

@article {pmid42724165,
year = {2026},
author = {Alauddin, W and Srivastava, C and Goyal, P and Shukla, M and Garg, DK and Prajesh, BR and Singh, S and Shaikh, FI and Khairnar, S},
title = {Gut Microbiota, Neuroinflammation, and Autonomic Dysfunction in Neurodegenerative Diseases: A Systematic Review of Mechanistic and Translational Evidence.},
journal = {Cureus},
volume = {18},
number = {8},
pages = {e114312},
pmid = {42724165},
issn = {2168-8184},
abstract = {Neurodegenerative disorders, including Parkinson's disease, Alzheimer's disease, multiple system atrophy, and amyotrophic lateral sclerosis, are increasingly recognized as complex conditions arising from interactions among the gut microbiota, immune system, and autonomic nervous system. Growing evidence indicates that disruption of the intestinal microbial ecosystem may contribute to neuroinflammatory processes, autonomic impairment, and progressive neurodegeneration through the microbiota-gut-brain axis, although the underlying mechanisms and their translational implications remain incompletely understood. This systematic review was conducted in accordance with the PRISMA 2020 guidelines to comprehensively evaluate the evidence linking gut microbiota dysbiosis with neuroinflammation and autonomic dysfunction across neurodegenerative diseases. A systematic search of PubMed/MEDLINE, Scopus, Web of Science, EMBASE, EBSCOhost, CINAHL, PsycINFO, CENTRAL, Google Scholar, and major grey literature sources yielded 2,769 records. After duplicate removal and eligibility screening, 62 full-text reports underwent detailed assessment, of which 11 studies met the predefined eligibility criteria and were included in the qualitative synthesis. The evidence encompassed human observational, animal experimental, and in vitro approaches, with several studies integrating complementary clinical, microbiome, and experimental methodologies. Most included studies focused on Parkinson's disease and multiple system atrophy. Across studies, microbial dysbiosis was characterized by reduced abundance of short-chain fatty acid (SCFA)-producing bacteria alongside increased representation of pro-inflammatory microbial taxa. These microbial alterations were associated with disruption of intestinal barrier integrity, activation of inflammatory signaling pathways, microglial activation, elevated pro-inflammatory cytokine production, α-synuclein aggregation, and autonomic manifestations such as gastrointestinal dysmotility and cardiovascular autonomic dysfunction. Experimental studies provided biological support for the microbiota-gut-brain axis, whereas clinical investigations consistently demonstrated associations without establishing causality. Overall, current evidence suggests that gut microbial dysbiosis is closely associated with neuroinflammation and autonomic dysfunction in neurodegenerative diseases and may represent a promising avenue for biomarker discovery and therapeutic intervention. Nevertheless, the available literature is constrained by methodological heterogeneity, limited sample sizes, and the predominance of observational and preclinical studies. Future large-scale longitudinal investigations and rigorously designed randomized controlled trials are required to determine causal relationships and define the clinical utility of microbiome-targeted strategies.},
}

@article {pmid42724200,
year = {2026},
author = {Kusamoto, A and Osuga, Y and Hirota, Y and Harada, M},
title = {Gut Microbiome-Targeted Preventive Strategies for Polyendocrine Metabolic Ovarian Syndrome: Insights From the Prenatal and Early-Life Environment.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70097},
pmid = {42724200},
issn = {1445-5781},
abstract = {BACKGROUND: Polyendocrine metabolic ovarian syndrome (PMOS), the proposed new name for polycystic ovary syndrome (PCOS), is a complex endocrine and metabolic disorder influenced by genetic and environmental factors. Despite its high prevalence and familial aggregation, no effective preventive strategy is available. Prenatal androgen exposure is considered a key factor in PMOS pathogenesis, with studies indicating a significant role for the gut microbiome.

METHODS: This review summarizes evidence from human and animal studies exploring the association between PMOS and the gut microbiome, spotlighting the impact of the intrauterine environment, including prenatal androgen exposure and maternal gut microbiome, in PMOS development.

MAIN FINDINGS: Gut microbiota dysbiosis is associated with features of PMOS pathophysiology, including hyperandrogenism, insulin resistance, neuroendocrine dysfunction, and ovarian dysfunction. Emerging evidence suggests that prenatal and early postnatal environments shape gut microbiota establishment and maturation, which may interact with multiple developmental pathways and potentially modify susceptibility to PMOS later in life.

CONCLUSION: The gut microbiome may be involved in the developmental origins and pathophysiology of PMOS, although its precise role remains unclear. Understanding early-life host-microbiome interaction may provide a foundation for future preventive and personalized management strategies for PMOS, but further mechanistic studies and clinical validation are required.},
}

@article {pmid42724277,
year = {2026},
author = {Jenkinson, A and Ahmed, S and Gupta, A and Greenough, A},
title = {Chronic respiratory morbidity and wheeze after preterm birth: a narrative review.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1880728},
pmid = {42724277},
issn = {2296-2360},
abstract = {Preterm birth, defined as birth before 37 weeks of gestation, affects approximately 10% of pregnancies worldwide. Premature birth disrupts normal lung development with those born at earlier gestations most affected. Individuals born preterm are at increased risk of lifelong respiratory morbidity, including recurrent wheeze. As a consequence, affected individuals are often given an incorrect diagnosis of asthma. Asthma is considered a clinical description and is defined as a clinical syndrome characterised by wheeze, breathlessness, and chest tightness, sometimes accompanied by excess cough. This narrative review reports wheeze following preterm birth, considers prematurity-associated lung disease as an alternative diagnosis to asthma and discusses early life exposures as modifiable factors. Furthermore, whether prediction of those at highest risk is possible and what is the optimum management and follow up for affected individuals is discussed. Preterm birth is associated with an approximately double the risk of wheezing in childhood and is particularly common in those born extremely prematurely. While type two (T2) asthma is the predominant asthma phenotype in the general paediatric population, non-T2 mechanisms may be more relevant in those born preterm and hence why they are often unresponsive to standard asthma regimens. Potentially modifiable risk factors are antenatal corticosteroids, in utero growth retardation, chorioamnionitis, maternal antenatal smoking, breast feeding, neonatal antibiotic exposure, aspiration lung disease, viral infections, pollution, the microbiome and socio-economic factors. Prematurely born individuals have a lower lung function trajectory than those born at term, predictors of those at higher risk may be possible using either a definition of BPD that emphasises the respiratory support needed at 36 weeks PMA or cluster analysis using clinical data. The heavy burden of chronic respiratory morbidity in this population warrants their lifelong follow-up and a personalised approach to their management.},
}

@article {pmid42724339,
year = {2026},
author = {Miller, BC and Hoover, JH and Yadav, H and Jain, S},
title = {The potential of microbiome modulators to improve quality of life in cancer survivors through gut microbiome-immune interactions.},
journal = {Frontiers in molecular neuroscience},
volume = {19},
number = {},
pages = {1815079},
pmid = {42724339},
issn = {1662-5099},
abstract = {Advancements in oncology research have led to the development of highly effective and safe cancer treatments, resulting in increased survival rates from cancer. However, treatments including chemotherapy, radiation, immunotherapy, and combination regimens suppress or modulate the immune system, contributing to the development of multi-organ dysfunctions in cancer survivors. Cognitive impairment (CI) and bowel dysfunctions are adverse outcomes commonly reported in cancer survivors and collectively hamper quality of life (QoL). Therefore, it is critical to develop strategies to improve or protect from these side effects and improve QoL in cancer survivors. The gut microbiome is a superlative regulator of human health and abnormalities in its composition and function (gut dysbiosis) contribute to many disease pathologies. Emerging studies suggest that cancer treatments significantly perturb the gut microbiota composition, impacting several peripheral organs, including the gut and brain. Gut dysbiosis also impacts the immune system, suggesting that cancer treatment-mediated gut microbiome alterations can alter brain health through the gut microbiome-immune axis. Thus, beneficial modulation of the microbiome through probiotics, prebiotics, and other interventions may be a feasible approach for improving cognitive function, gut health, and/or QoL in cancer survivors via gut microbiome-immune interactions. The purpose of this review is to report the prevalence of and mechanisms contributing to CI and gut dysfunctions in cancer survivors as well as provide a comprehensive review of the potential of microbiome modulators for improving gut and brain health and QoL in these cohorts, through the gut microbiome-immune axis. Additional studies are warranted to fully elucidate the effects and mechanisms of microbiome modulators in cancer survivors.},
}

@article {pmid42724341,
year = {2026},
author = {Alharthi, NS},
title = {Metabolic reprogramming in diabetes and cancer: the role of PI3K/AKT/mTOR and beyond.},
journal = {American journal of cancer research},
volume = {16},
number = {8},
pages = {3294-3318},
pmid = {42724341},
issn = {2156-6976},
abstract = {Diabetes mellitus and cancer are among the most prevalent chronic diseases worldwide, and accumulating evidence suggests a significant association between these conditions. The metabolic disturbances characteristic of diabetes, including hyperglycemia, hyperinsulinemia, insulin resistance, and chronic inflammation, create a favorable environment for tumor initiation and progression. These alterations contribute to cellular metabolic reprogramming, enhanced proliferative signaling, and resistance to apoptosis. Key molecular pathways such as PI3K/AKT/mTOR, along with dysregulated glucose, lipid, and amino acid metabolism, play central roles in linking diabetic and oncogenic processes. In addition to metabolic alterations, genetic and epigenetic modifications, including mutations in oncogenes and tumor suppressor genes, as well as the involvement of non-coding RNAs, further strengthen this association. Emerging evidence also highlights the gut microbiome's role in modulating inflammation, metabolic homeostasis, and cancer susceptibility in diabetic conditions. Therapeutically, antidiabetic agents such as metformin, GLP-1 receptor agonists, and SGLT2 inhibitors have shown potential in modulating cancer-related pathways, although clinical evidence remains variable and requires further validation. This review provides a comprehensive overview of the shared metabolic and molecular mechanisms underlying the diabetes-cancer link, emphasizing the interplay between metabolic dysregulation, genetic alterations, and microbiome dynamics. A better understanding of these interconnected pathways may support the development of targeted therapeutic strategies and improve clinical outcomes. However, further well-designed studies are necessary to establish causal relationships and translate these findings into effective clinical interventions.},
}

@article {pmid42724447,
year = {2026},
author = {Hu, Y and Hendi, M and Du, L and Chen, X},
title = {Global research trends in fecal microbiota transplantation combined with immune checkpoint inhibitors for cancer immunotherapy: a bibliometric analysis.},
journal = {Translational cancer research},
volume = {15},
number = {8},
pages = {602},
pmid = {42724447},
issn = {2219-6803},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have revolutionized cancer treatment by restoring antitumor immune responses. However, heterogeneous efficacy, primary or acquired resistance, and immune-related adverse events (irAEs) remain major clinical challenges. There is evidence that gut microbiota critically regulate ICI efficacy, and fecal microbiota transplantation (FMT) has emerged as a promising intervention to improve therapeutic outcomes. Here, we performed a bibliometric analysis to map global research trends, hotspots, and frontiers in FMT combined with ICIs for cancer immunotherapy.

METHODS: A range of scientometric tools, including CiteSpace, VOSviewer, Bibliometrix R package, and Tableau, were employed to retrieve and analyze the literature on FMT combined with ICIs for cancer immunotherapy from the Web of Science Core Collection for the period from 2015 to 2026. The analyses covered national and institutional collaboration networks, the identification of highly productive authors, journal impact and publication trends, co-cited reference analysis, as well as keyword co-occurrence, clustering, and burst detection.

RESULTS: A total of 345 relevant publications were identified, with annual output rising rapidly since 2019 and reaching a peak in 2025. China ranked first in publication volume, while the United States showed the highest centrality in international collaboration. The leading research institutions were the University of Texas MD Anderson Cancer Center, Shanghai Jiao Tong University, and Université Paris-Saclay. Routy, Bertrand and Wang, Yinghong were prominent high-impact authors. Co-citation and keyword analyses revealed a shift in research focus from gut microbiota-mediated regulation of ICI efficacy to clinical translation of FMT for reversing resistance, and further to mechanistic insights into microbial metabolites and the tumor microenvironment (TME). Further keyword analysis demonstrated that FMT research has expanded to digestive system malignancies, including colorectal, gastric, and hepatocellular carcinomas (HCCs). Current research hotspots include "dysbiosis", "dietary fiber", "chain fatty acids", "tumor microenvironment", "consensus statement", and "international scientific association".

CONCLUSIONS: This bibliometric analysis reveals that the research field of FMT combined with ICIs has evolved from descriptive correlations to mechanism-driven research, with an expanding focus on digestive system tumors. Future research should prioritize large-scale randomized controlled trials (RCTs) and standardized clinical protocols, underpinned by in-depth mechanistic studies, to advance microbiome-based precision cancer immunotherapy.},
}

@article {pmid42724514,
year = {2026},
author = {He, X and Gan, H and Wu, F and Wang, Y and Zhang, H},
title = {Akkermansia muciniphila attenuates apatinib resistance in hepatocellular carcinoma through NF-κB-mediated reprogramming of tumor-associated macrophages.},
journal = {Translational cancer research},
volume = {15},
number = {8},
pages = {615},
pmid = {42724514},
issn = {2219-6803},
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) remains among the most lethal malignancies worldwide, and acquired resistance to targeted therapy limits durable clinical benefit. Apatinib, a selective vascular endothelial growth factor receptor-2 inhibitor, is used in advanced HCC, but the contribution of the gut microbiota to Apatinib resistance remains incompletely defined. This study aimed to determine whether gut microbiota dysbiosis, particularly loss of Akkermansia muciniphila (Akk), contributes to an Apatinib-resistant HCC phenotype and to evaluate whether Akk-derived factors modulate macrophage NF-κB signaling.

METHODS: A Hepa1-6 syngeneic subcutaneous HCC model was established in C57BL/6 mice. The apatinib-resistant phenotype was operationally defined by continued tumor growth under apatinib pressure together with an ex vivo right shift in the half-maximal inhibitory concentration (IC50) determined using the Cell Counting Kit-8 (CCK-8) assay. Fecal microbiota were analyzed by 16S ribosomal RNA (16S rRNA) gene sequencing, Akk abundance was validated by quantitative polymerase chain reaction, and inferred microbial functional potential was explored using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2. Macrophage polarization, tumor-level NF-κB signaling, live Akk oral supplementation, and bone marrow-derived macrophage (BMDM) responses to Akk supernatant or pasteurized Akk were assessed.

RESULTS: Apatinib-resistant mice showed gut dysbiosis characterized by reduced microbial diversity, distinct beta-diversity clustering, and marked depletion of Akk. Resistant tumors exhibited reduced M1-like and increased M2-like macrophage fractions, together with lower phosphorylation of p65 and IκBα in whole-tumor lysates. Oral live Akk administration restored intestinal Akk abundance, reduced tumor volume and weight, re-established M1-like macrophage polarization, and reactivated tumor-level NF-κB signaling. In BMDMs exposed to apatinib-resistant Hepa1-6-conditioned medium, Akk supernatant and pasteurized Akk partially restored NF-κB phosphorylation and attenuated M2-like transcriptional skewing.

CONCLUSIONS: Akk depletion accompanies an apatinib-resistant HCC phenotype and Akk-centered microbial modulation may help counteract resistance by reshaping macrophage-associated antitumor immunity. These findings support further validation of Akk-derived signals in community-level microbiome models and clinically relevant HCC settings.},
}

@article {pmid42724580,
year = {2026},
author = {Yang, L and Han, J and Li, S and Wang, X and Jia, Y and Bao, Z and Ge, T and He, G and Zhou, J and Cui, J and Tian, Y and Xie, Y and Liu, L and Du, J and Li, W and Yu, J},
title = {Gut dysbiosis, metabolic signals, and pulmonary immune reprogramming: decoding the gut microbiota -immune axis in stroke-associated pneumonia.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1812306},
pmid = {42724580},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/metabolism ; *Stroke/complications/immunology ; *Gastrointestinal Microbiome/immunology ; Animals ; *Pneumonia/immunology/etiology/metabolism/therapy/microbiology ; *Lung/immunology/metabolism ; Fecal Microbiota Transplantation ; },
abstract = {Stroke-associated pneumonia (SAP) is the most common infectious complication following acute stroke. The limited efficacy of conventional antimicrobial therapy suggests that SAP may be fundamentally a syndrome driven by dysregulated cross-system interactions. This review proposes the "gut microbiota-immune axis" (GMIA) as a comprehensive framework for the development of SAP and systematically discusses the potential mechanisms by which post-stroke microbial-derived metabolic signals-including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, and endotoxins-drive systemic immune reprogramming, predisposing patients to SAP. Based on the GMIA, we highlight several promising intervention strategies, including dietary modulation, precision antibiotic use, probiotics, fecal microbiota transplantation (FMT), supplementation with microbial metabolites, and receptor-targeted therapies, and summarize the current clinical translation related to the GMIA. Future research directions require high-quality clinical trials that integrate multi-omics data from the microbiome with immune biomarkers and clinical parameters. Such an approach is essential for constructing validated risk stratification models and advancing the management of SAP from empirical anti-infective treatment toward a precision medicine model centered on GMIA-based immune modulation.},
}

Humans
*Dysbiosis/immunology/metabolism
*Stroke/complications/immunology
*Gastrointestinal Microbiome/immunology
Animals
*Pneumonia/immunology/etiology/metabolism/therapy/microbiology
*Lung/immunology/metabolism
Fecal Microbiota Transplantation

@article {pmid42724614,
year = {2026},
author = {Wang, Y and Wang, R and Wang, T and Zhao, Y and Ju, X},
title = {Evolution of proton pump inhibitor research in reflux esophagitis: a Web of Science-based global bibliometric assessment [1990-2026].},
journal = {Journal of thoracic disease},
volume = {18},
number = {8},
pages = {850},
pmid = {42724614},
issn = {2072-1439},
abstract = {BACKGROUND: Reflux esophagitis remains a prevalent acid-related disorder with an increasing global burden, yet the growing challenges of refractory disease and the transition toward newer acid-suppressing agents highlight critical knowledge gaps. This study aimed to analyze the global research trends and identify emerging hotspots in proton pump inhibitors (PPIs) treatment for reflux esophagitis through a Web of Science-based bibliometric analysis [1990-2026].

METHODS: A systematic search was conducted in the Web of Science Core Collection (WoSCC) on June 18, 2026, using MeSH-derived terms. Only English-language original research articles were included. Two independent researchers manually screened all records for relevance. The analysis was performed using VOSviewer, CiteSpace, and the "bibliometrix" package of R.

RESULTS: A total of 338 articles were included. Publications showed an overall upward trend with an annual growth rate of 2%. Japan emerged as the leading country (111 publications), followed by the United States [59] and China [38]. The American Journal of Gastroenterology and the Journal of Gastroenterology were the most influential journals. Keyword co-occurrence analysis identified five major research clusters spanning clinical assessment, pathophysiological mechanisms, disease classification, pharmacological evaluation, and comparative clinical trials, with research evolving from early PPI efficacy studies [1991-2005] to disease mechanisms [2005-2015] and to patient-centered outcomes [2015-2026].

CONCLUSIONS: Three distinct research phases were identified in PPI treatment for reflux esophagitis. Current research insufficiently addresses the long-term impact of PPIs on gut microbiome and the comparative effectiveness of emerging potassium-competitive acid blockers (P-CABs). Future research should prioritize pharmacogenetic optimization, real-world evidence generation for novel therapeutic agents, and enhanced international collaboration.},
}

@article {pmid42724691,
year = {2016},
author = {Roeselers, G and Bouwman, J and Levin, E},
title = {The human gut microbiome, diet, and health: "Post hoc non ergo propter hoc".},
journal = {Trends in food science & technology},
volume = {57},
number = {Pt B},
pages = {302-305},
pmid = {42724691},
issn = {0924-2244},
abstract = {The gastro-intestinal microbiome has become the subject of intensive research, which is beginning to elucidate its roles in human health. It is becoming increasingly recognised that gut microbiota plays a part in regulating human immune homeostasis and metabolism, which gives rise to novel opportunities for preventative and treatment strategies. The key challenge in this field is the ability to define causality in the relationship between nutrition, microbiota and host health. In this commentary we argue for an increased focus on cause-and-effect relationships within studies that relate to the human microbiome in health and predispositions to disease. With the right experimental models, data accessibility infra-structure and advanced machine learning tools, causal relationships among components of complex host-microbiome systems can be elucidated.},
}

@article {pmid42724718,
year = {2026},
author = {Xing, Y and Song, J and Shang, B and Yang, G and Zhao, Y and Li, M and Hou, B},
title = {Research advances on postbiotics in promoting skin wound healing: mechanisms, formulations, and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1912496},
pmid = {42724718},
issn = {1664-3224},
mesh = {Humans ; *Wound Healing/drug effects ; Skin Microbiome ; Animals ; *Skin/microbiology/immunology ; Translational Research, Biomedical ; Microbiota ; Re-Epithelialization ; },
abstract = {Wound healing is a complex process involving different cell types, molecules and stages in the dermis, epidermis and associated microbiome. Chronic wounds caused by pressure, diabetes, or immunodeficiency often have huge economic and therapeutic costs. Postbiotics, in particular inactivated bacteria, cell components and metabolites, are emerging as novel treatments targeting the skin microbiome and provide precise treatment options for wound healing, inflammation, angiogenesis and re-epithelialization. We review the positive regulatory role of different microbial communities in skin healing; evaluate evidence and mechanisms of various postbiotics, in vitro and in vivo models as well as preliminary clinical studies; and summarize progress in the translation of postbiotics for skin wound repair.},
}

Humans
*Wound Healing/drug effects
Skin Microbiome
Animals
*Skin/microbiology/immunology
Translational Research, Biomedical
Microbiota
Re-Epithelialization

@article {pmid42724737,
year = {2026},
author = {Raval, R and Hejmadi, S and Hettiarachchi, M and Chandna, S and Mehta, AC},
title = {Gut-lung axis in chronic respiratory diseases: a narrative review of emerging insights.},
journal = {Journal of thoracic disease},
volume = {18},
number = {8},
pages = {967},
pmid = {42724737},
issn = {2072-1439},
abstract = {BACKGROUND AND OBJECTIVE: The gut-lung axis is a bidirectional network through which intestinal microbial ecology, mucosal immunity, epithelial barrier function, microbial metabolites, and neurohumoral signalling influence pulmonary inflammation. This narrative review summarizes the mechanistic basis of gut-lung communication, compares the strength of evidence across major chronic respiratory diseases (CRDs), and evaluates emerging microbiome-targeted interventions.

METHODS: PubMed, Embase, and Google Scholar were searched for peer-reviewed English-language literature published from January 2010 through June 2024 using combinations of terms related to the gut-lung axis, microbiome, asthma, chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), short-chain fatty acids (SCFAs), intestinal permeability, bile acids, tryptophan metabolites, vagal signalling, and glucagon-like peptide-1 (GLP-1). Human and animal original studies, randomized trials, cohort studies, mechanistic studies, and relevant narrative or systematic reviews were considered; case reports, non-English articles, and studies without respiratory outcomes were excluded. Reference lists of key papers were also hand-searched.

KEY CONTENT AND FINDINGS: Evidence is strongest for biologically plausible immune and metabolic pathways linking intestinal dysbiosis to pulmonary disease. In asthma, early-life depletion of SCFA-producing taxa may impair regulatory T-cell development and promote allergic sensitization. In COPD, gut dysbiosis, increased intestinal permeability, and systemic endotoxin exposure are more consistently associated with inflammatory phenotype and exacerbation burden. Evidence in ILD remains preliminary but supports a possible role for gut-derived pathogen-associated molecular patterns in profibrotic signalling. After lung transplantation (LT), antibiotic exposure, immunosuppression, and microbial loss may interact with allograft inflammation and chronic lung allograft dysfunction (CLAD). Dietary modulation, probiotics, prebiotics/synbiotics, post-biotics, and fecal microbiota transplantation (FMT) remain investigational, with heterogeneous and generally limited clinical evidence.

CONCLUSIONS: Current data support mechanistic plausibility but do not justify routine microbiome-directed treatment of CRDs. Future trials should standardize microbiome profiling, incorporate metabolomic and disease-specific clinical endpoints, and stratify responders to define where gut-lung axis interventions can add clinically meaningful benefit.},
}

@article {pmid42725163,
year = {2026},
author = {Kaddoura, MJ and Amaya-Quiroz, L and Samsatly, J and Meglouli, H and George, S},
title = {Greenhouse and field evaluation of bacterial endophytes from Cannabis sativa and Chelidonium majus reveals beneficial stage-dependent growth and yield responses in common bean.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1922467},
doi = {10.3389/fpls.2026.1922467},
pmid = {42725163},
issn = {1664-462X},
abstract = {Bacterial endophytes are increasingly recognized for their ability to enhance plant growth and productivity through multiple physiological and biochemical mechanisms. However, how these responses are coordinated across plant developmental stages and translate into final crop performance remains unclear. This study evaluated previously characterized bacterial endophytes belonging to Bacillus subtilis (BS-114, BS-120) and Pseudomonas wadenswilerensis (PPW-26) as plant growth-promoting agents in yellow bean under in vitro, greenhouse, and field conditions. Bacterial treatments enhanced early developmental responses relative to the non-inoculated control (NC), with BS-114 increasing germination (+19.1%) and seedling total root length (+71.3%), while PPW-26 increased root biomass (+61.7%). Under greenhouse conditions, BS-114 improved reproductive development, increasing bud count (+47.4%), immature pod count (+60.2%), and pod fresh mass (+42.1%). Cell-free extracts reproduced several of these beneficial effects, with the BS-114 cell-free extract (BS-114E) producing the highest cumulative pod fresh mass (+94.2%), suggesting the contribution of extracellular components to reproductive performance. Physiological and gene-expression analyses further indicated that treatment responses were not attributable to a single pathway. Among the measured gas-exchange parameters, photosynthetic rate increased (+175.8%) and stomatal conductance increased (+306.9%). Gene expression analyses showed treatment-specific upregulation of selected genes, with N-fixation-related expression (nifH) reaching +5.62 log2FC (49.31×) with the BS-114 live-cell treatment (BS-114L), while hormone-related responses were characterized by coordinated upregulation of auxin signaling-related expression +5.24 log2FC (37.89×) and cytokinin-related expression patterns consistent with increased biosynthesis and reduced degradation. Field validation showed that all treatments increased yield relative to NC, with the BS-114+BS-120 consortium achieving a +32.65% increase, which was comparable to NPK (+37.76%), despite limited shifts in soil microbial diversity and moderate variation in soil nutrients. Together, these findings indicate that the evaluated bacterial treatments improved plant performance through coordinated responses across multiple biological levels and plant developmental stages, supporting their application as plant growth-promoting agents under controlled and field conditions.},
}

@article {pmid42725339,
year = {2026},
author = {Cadoná, FC and Pelosof, AG and Bartelli, TF and In, H and Wu, L and da Silva, IT and Pasqualini, R and Arap, W and Nunes, DN and Dias-Neto, E},
title = {Endoscopic Collection and Analysis of Gastric Fluid DNA: A Liquid Biopsy Methodology for Tumor Biomarker Discovery.},
journal = {Bio-protocol},
volume = {16},
number = {17},
pages = {e5809},
doi = {10.21769/BioProtoc.5809},
pmid = {42725339},
issn = {2331-8325},
abstract = {Gastric cancer remains a major global health challenge, and reliable prognostic biomarkers are urgently needed to guide treatment decisions. Here, we present a simple and efficient protocol for a novel liquid biopsy approach based on quantifying gastric fluid DNA (gfDNA) collected during routine esophagogastroduodenoscopy (EGD). We have previously shown that gfDNA carries gastric cancer-derived mutations; moreover, its concentration increases with tumor progression and varies according to cancer prognosis. This empirically observed increase in gfDNA may mechanistically stem from enhanced cellular turnover, tissue disorganization, dysbiosis of the local microbiota, and/or fluctuations in immune cell infiltrates. Surprisingly, however, in patients diagnosed with gastric cancer, elevated gfDNA levels were also associated with improved survival. This paradoxical finding may be reconciled by an increased anti-tumor immune cell response in treatment-responsive gastric cancers, as well as by the contribution of non-tumoral DNA from inflammatory processes within the microenvironment of the stomach. Here, we detail a standardized protocol for gastric fluid collection and processing, designed to support downstream gfDNA quantification among other potential molecular applications. Key features • A novel liquid biopsy approach for discovering potential biomarkers in human gastric cancer. • Translation of simple gfDNA concentration analysis for the diagnosis and prognosis of gastric cancer. • gfDNA cutoff metrics that discriminate between groups and enable tumor prognostic classification. • gfDNA as a source for downstream profiling of genetic mutations and microbiome-related studies.},
}

@article {pmid42725392,
year = {2026},
author = {Meng, Y and Liu, Q and Zou, H and Zhu, X and Mi, X and Li, S and Xia, Y and Ma, Y and Yang, Q and Peng, J and Li, J and Liu, X and Chen, J},
title = {Research advances in the microbiota‑gut‑brain axis and Parkinson's disease (Review).},
journal = {Molecular medicine reports},
volume = {34},
number = {5},
pages = {},
doi = {10.3892/mmr.2026.14016},
pmid = {42725392},
issn = {1791-3004},
mesh = {Humans ; *Parkinson Disease/microbiology/therapy/metabolism ; *Gastrointestinal Microbiome ; *Brain/metabolism ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Prebiotics ; *Brain-Gut Axis ; },
abstract = {Parkinson's disease (PD) is a common neurodegenerative disease with diverse pathogenic mechanisms. The microbiota‑gut‑brain axis is closely related to the development of PD, in which non‑motor symptoms are considered to be the early manifestation and exacerbation of the disease. Nevertheless, reliable diagnostic criteria or biomarkers for PD have not been fully developed. The gut microbiota as a key transmitter of the gut‑brain axis, can affect disease progression through a variety of pathways, and may be a potential therapeutic target for PD. Therefore, new strategies have been developed with the aim to prevent and control PD by modulating the intestinal microflora, using tools such as antibiotics, probiotics, prebiotics, dietary interventions, fecal microbiota transplantation and vagus nerve stimulation; however, these interventions also face certain issues and challenges. The present article reviewed the latest research on PD through the microbiome‑gut‑brain axis, offering new angles for understanding and treating the condition.},
}

Humans
*Parkinson Disease/microbiology/therapy/metabolism
*Gastrointestinal Microbiome
*Brain/metabolism
Animals
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Prebiotics
*Brain-Gut Axis

@article {pmid42725602,
year = {2026},
author = {Fatima, J and Siddique, YH},
title = {The Gut-Brain Axis: Exploring the Role of Gut Microbiota in Alzheimer's Disease Pathogenesis and Therapeutics.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273460507260827112721},
pmid = {42725602},
issn = {1996-3181},
abstract = {INTRODUCTION: Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by amyloid-β (Aβ) accumulation, tau hyperphosphorylation, and cognitive decline. Increasing evidence implicates the gut-brain axis as a key regulator of AD pathogenesis through immune, metabolic, and neuroendocrine pathways.

METHODS: This review systematically synthesizes recent preclinical and clinical studies investigating the role of gut microbiota in AD, focusing on microbial composition, mechanistic communication pathways, and microbiota-targeted therapeutic strategies.

RESULTS: Gut microbiota dysbiosis contributes to AD progression through multiple mechanisms, including activation of TLR4/NF-κB-mediated neuroinflammation, disruption of blood-brain barrier integrity, and altered microbial metabolite production, particularly short-chain fatty acids (SCFAs) and tryptophan-derived compounds. These changes influence amyloid deposition, tau phosphorylation, and synaptic dysfunction.

DISCUSSION: Gut microbiota dysbiosis plays a significant role in AD progression by promoting neuroinflammation, BBB dysfunction, and altered microbial metabolite production. Microbiota-targeted interventions, such as probiotics, prebiotics, synbiotics, and fecal microbiota transplantation, have the potential to modulate these pathways and improve cognitive outcomes, although results vary across studies.

CONCLUSIONS: The gut microbiota acts as an upstream regulator of AD pathology through interconnected molecular mechanisms. However, variability in study design, limited clinical validation, and lack of standardized protocols remain major challenges. Future research should focus on mechanistic validation using multi-omics approaches and the development of personalized microbiome-based therapeutic strategies.},
}

@article {pmid42725723,
year = {2026},
author = {Jensen, IC and Nazipi Bushi, S and Mogensen, AL and Braad Lund, M and Offenberg, J and Schramm, A},
title = {Bacterial microbiomes and antifungal effect of Danish wood ant (Formica polyctena) populations.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0076326},
doi = {10.1128/aem.00763-26},
pmid = {42725723},
issn = {1098-5336},
abstract = {UNLABELLED: Ants, including wood ants (Formica polyctena), can control arthropod pests, and recent research has highlighted their potential against plant pathogens. The latter effect is likely aided by antimicrobial ant-associated microbes. Here, we investigated the bacterial microbiome of wood ants (F. polyctena), and their nests across five sites in Denmark. We assessed the ants' deposition of antimicrobial microbes with inhibitory effects against the economically important plant-pathogenic fungi, Monilinia fructigena, Botrytis cinerea, and Fusarium graminearum, and hypothesized that deposited microbes are part of a specific, ant-surface-associated microbiome. To assess this, we sampled ant legs and bodies separately, assuming that the bacterial communities of the legs would be distinct from the body and nest microbiomes. Ants deposited antimicrobial microorganisms within 10 s of walking on agar plates, and a 24-h exposure to ants led to dense microbial growth on the agar plates. We isolated seven bacterial and seven fungal antimicrobial strains, with six bacterial isolates matching 16S rRNA amplicon sequences from ant microbiomes across all sites. These sequences were more abundant and prevalent on ant bodies and legs than on nests, suggesting that isolates originated from the ant-surface microbiome. Ant bacterial microbiomes were similar across the five sites, heavily dominated by the endosymbiont Wolbachia, and differed significantly between bodies, legs, and nests, indicating selective acquisition of the surface microbiome instead of random acquisition from the environment. These findings suggest that wood ants have a distinct leg microbiome and are consistently associated with antifungal microorganisms with potential against plant-pathogenic fungi.

IMPORTANCE: This study constitutes the first comprehensive study of the bacterial microbiomes of wood ants (Formica polyctena) and their nests, providing valuable insights into the ants' association with antimicrobial microbes and the composition and compartmentalization of their microbiomes. Our results highlight that wood ants are generally associated with antimicrobial microbes that are effective against commercially important plant-pathogenic fungi, emphasizing their potential as biocontrol agents in agriculture. Additionally, the results show that the bacterial microbiome of wood ants is highly dominated by the endosymbiont Wolbachia, while bacterial microbiomes of wood ant legs, bodies, and nests were all significantly different. These results suggest that the wood ant microbiome is selectively acquired, rather than randomly acquired from the ants' environment. In conclusion, the findings of this study provide new insights into the wood ant microbiome and emphasize the potential of using ants and their associated microbes as biocontrol agents against plant-pathogenic fungi.},
}

@article {pmid42725726,
year = {2026},
author = {Holm, JB and Maros, A and Williams, A and France, M and Ravel, J},
title = {VISTA: a classifier for metagenomic subspecies and community state typing of the vaginal microbiome.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0061226},
doi = {10.1128/mra.00612-26},
pmid = {42725726},
issn = {2576-098X},
abstract = {Metagenomic community state types (mgCSTs) capture within-species genetic and functional diversity and community structure of the vaginal microbiome, enabling precise links between microbiome composition, function, and health-related risk. VISTA, the Vaginal Inference of Subspecies and Typing Algorithm, is a two-step classifier that assigns mgCSTs to vaginal metagenomes, providing standardized, scalable classifications.},
}

@article {pmid42725738,
year = {2026},
author = {Beals, DG and Crockett, Z and Phan, DA and Nguyen, A and Schadt, CW and Cottingham, RW and Pelletier, DA},
title = {Genome sequences of five phylogenetically diverse bacterial isolates from the Populus root microbiome.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0085126},
doi = {10.1128/mra.00851-26},
pmid = {42725738},
issn = {2576-098X},
abstract = {Five bacterial genomes were sequenced from isolates obtained from Populus deltoides and Populus trichocarpa roots collected in Tennessee and Oregon. These genomes expand the representation of underrepresented bacterial genera within the Populus root microbiome and provide new reference resources for studies of plant-associated bacteria.},
}

@article {pmid42725769,
year = {2026},
author = {Van Rossum, U and Heyndrickx, M and Demaître, N and Sadiq, FA and Boon, N and Rasschaert, G and Cools, A and De Reu, K},
title = {Biofilm formation and multispecies interactions of bacteria recovered from drinking water systems in broiler houses and piglet nursery units.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0108426},
doi = {10.1128/spectrum.01084-26},
pmid = {42725769},
issn = {2165-0497},
abstract = {The presence of biofilms on the surfaces of drinking water systems in livestock housing can compromise the microbiological quality of drinking water. Understanding the biofilm microbiome and the biofilm-forming capacity of its dominant species is therefore essential, particularly for identifying species that coexist and enhance biofilm formation through interactions. This study investigated 248 bacterial isolates representing the dominant microbiota of biofilm samples collected from drinking water systems in broiler houses and pig nursery units. Biofilm formation was assessed in both single-species cultures and 341 multispecies combinations. Of the tested isolates, 80% formed biofilms in single culture; however, only 25% were classified as strong biofilm formers. In multispecies combinations with up to four species or isolates, antagonistic or competitive interactions were dominant, whereas biofilm mass enhancement was observed in only a limited number of combinations. These included opportunistic pathogens, with Citrobacter freundii and Staphylococcus nepalensis identified as key species driving the interactions. Our research highlights the importance of specific microbial interactions in biofilm development and provides a potentially practice relevant four-species model to guide future research aimed at improving strategies for controlling biofilms in livestock drinking water systems.IMPORTANCEEnsuring the quality of drinking water on livestock production farms benefits animal production and health. Persistent biofilms on water line surfaces can lead to microbial contamination, resulting in lower-quality drinking water. This study examines bacteria commonly found in biofilms within livestock drinking water systems in pig nursery units and broiler houses. Most bacterial isolates can form biofilms in monoculture. Specific interactions among certain species primarily mediate bacterial interactions that enhance biofilm biomass in multispecies communities. Identifying these key interactions enables the development of a synthetic model to guide research on controlling biofilms in livestock drinking water systems.},
}

@article {pmid42725788,
year = {2026},
author = {Liu, F and Streett, H and Solano-Aguilar, G and Smith, AD and Carbaugh, D and Urban, JF and Li, RW},
title = {In vivo porcine multi-omics integration identifies microbiome-driven histamine elevation and lasting gut perturbations following Ascaris suum infection and fenbendazole treatment.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2728766},
doi = {10.1080/21505594.2026.2728766},
pmid = {42725788},
issn = {2150-5608},
mesh = {Animals ; *Fenbendazole/therapeutic use ; *Ascaris suum/drug effects ; *Ascariasis/drug therapy/veterinary/parasitology/microbiology ; *Swine Diseases/drug therapy/parasitology/microbiology ; Swine ; *Histamine/blood/metabolism ; Multiomics ; *Gastrointestinal Microbiome/drug effects ; Feces/chemistry ; Cresols ; },
abstract = {Ascaris roundworms impair human and swine health. While treatments using anthelmintic drugs are generally effective in eliminating worms, their effects on the gut microenvironment remain poorly understood. Here we applied integrated multi-omics to characterize infection- and treatment-associated alterations in the pig-Ascaris system. In vitro anaerobic cultures were conducted as supportive validation of selected observations. Ascaris suum infection altered microbial composition and dysregulated 182 serum and fecal metabolites, including histamine and p-cresol sulfate. Compared with time-matched uninfected controls, infected pigs treated with fenbendazole showed marked differences in gut microbial composition 13 days after confirmed worm clearance. Eleven microbial pathways were enriched in successfully treated pigs, including peptidoglycan biosynthesis and histidine metabolism, indicating that infection-associated alterations may persist after treatment. In vitro co-exposure of Lactobacillus reuteri to fenbendazole and A. suum proteins increased histamine production by approximately 79% at 48 h (p < 0.05), serving as supportive evidence of a microbiome contribution. Collectively, our in vivo findings support that host-microbiota-parasite interactions are multifaceted. Microbiota-derived metabolites were associated with regulation of host gene expression, such as TFF2 and IL8. Microbiota plasticity allows the exploitation of the niche differentiated upon infection, resulting in the proliferation of certain Lactobacillus strains in treated animals. Nevertheless, interpretations of treatment effects are made cautiously given the absence of an uninfected drug-only group and the cross-sectional design. Understanding these complex interactions will be important for the design of next-generation functional anthelmintics.},
}

Animals
*Fenbendazole/therapeutic use
*Ascaris suum/drug effects
*Ascariasis/drug therapy/veterinary/parasitology/microbiology
*Swine Diseases/drug therapy/parasitology/microbiology
Swine
*Histamine/blood/metabolism
Multiomics
*Gastrointestinal Microbiome/drug effects
Feces/chemistry
Cresols

@article {pmid42725967,
year = {2026},
author = {Talbert, JA and Kalmer, TL and Walker, AS and Gaddy, JA and Townsend, SD},
title = {Human Milk Oligosaccharides Modulate Nitrogen Utilization in Lactobacillus crispatus in a Glucose-Dependent Manner.},
journal = {ACS infectious diseases},
volume = {12},
number = {9},
pages = {3080-3091},
doi = {10.1021/acsinfecdis.6c00250},
pmid = {42725967},
issn = {2373-8227},
support = {1R24OD037694//National Institutes of Health (NIH)/ ; 1S10MH137068//National Institutes of Health (NIH)/ ; 1S10OD034315//National Institutes of Health (NIH)/ ; CA68485//National Institutes of Health (NIH)/ ; DK20593//National Institutes of Health (NIH)/ ; DK58404//National Institutes of Health (NIH)/ ; DK59637//National Institutes of Health (NIH)/ ; EY08126//National Institutes of Health (NIH)/ ; R01HD113674//National Institutes of Health (NIH)/ ; R35GM133602//National Institutes of Health (NIH)/ ; R35GM146987//National Institutes of Health (NIH)/ ; },
mesh = {Humans ; *Milk, Human/chemistry/metabolism ; *Oligosaccharides/metabolism/pharmacology ; *Glucose/metabolism ; Female ; Vagina/microbiology ; *Lactobacillus crispatus/metabolism/growth & development/drug effects ; *Nitrogen/metabolism ; Lactobacillus/metabolism/growth & development ; },
abstract = {The vaginal microbiome's transition to a dysbiotic state increases susceptibility to pathogens like group B Streptococcus. While human milk oligosaccharides are established prebiotics in the neonatal gut, their impact on the vaginal niche remains largely unexplored. This study investigated the effects of pooled human milk oligosaccharides on the growth and physiology of vaginal (Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners) and gut-derived (Lactobacillus reuteri, Lactobacillus rhamnosus) commensals. Growth analyses revealed that human milk oligosaccharides significantly and selectively stimulated growth across all vaginal strains tested, whereas gut commensals exhibited variable or inhibited growth. Carbohydrate utilization assays and comparative genomics against Bifidobacterium infantis showed that Lactobacillus crispatus and Lactobacillus reuteri lack the canonical metabolic machinery to catabolize human milk oligosaccharides. Instead, nitrogen utilization assays identified a glucose-dependent pathway where human milk oligosaccharides are associated with the depletion of primary amines and amino acids in Lactobacillus crispatus supernatants. These results suggest that human milk oligosaccharides act as noncatabolic modulators of vaginal lactobacilli. Collectively, these in vitro findings may warrant investigation of human milk oligosaccharides as modulators of vaginal commensal physiology in more complex experimental systems.},
}

Humans
*Milk, Human/chemistry/metabolism
*Oligosaccharides/metabolism/pharmacology
*Glucose/metabolism
Female
Vagina/microbiology
*Lactobacillus crispatus/metabolism/growth & development/drug effects
*Nitrogen/metabolism
Lactobacillus/metabolism/growth & development

@article {pmid42726296,
year = {2026},
author = {Jilo, DD and Abebe, BK and Ullah, W and Guo, J and Wang, J and Ma, H and Yiheng, L and Cheng, G and Cui, H and Zan, L},
title = {Pan-genomics and multi-omics for deciphering genetic variation and accelerating genetic improvement in ruminant livestock.},
journal = {Functional & integrative genomics},
volume = {26},
number = {1},
pages = {},
pmid = {42726296},
issn = {1438-7948},
mesh = {Animals ; Multiomics ; *Genomics ; *Genetic Variation ; *Livestock/genetics ; *Ruminants/genetics ; Breeding ; },
abstract = {Livestock reference genomes have transformed the discovery of variants associated with production, reproduction, health, and environmental adaptation. Nevertheless, a single linear reference represents only one mosaic haplotype and incompletely captures sequence diversity within a species, particularly structural variants, copy-number changes, repeat-rich regions, and breed-specific sequences. Pangenomes address this limitation by integrating multiple high-quality assemblies or population-scale variants into a unified sequence or graph representation. Concurrently, multi-omics approaches connect genomic variation with transcriptomic, epigenomic, manuscriptproteomic, metabolomic, and microbiome responses, thereby improving biological interpretation of genotype-phenotype relationships. This review synthesizes recent progress in livestock pangenomics and multi-omics, with emphasis on cattle, goats, sheep, water buffalo, and chickens. It describes advances in long-read and haplotype-resolved sequencing, graph construction, structural-variant discovery and genotyping, functional annotation, and integrative analysis. Recent pangenome studies have uncovered substantial non-reference sequence, reduced reference bias, identified breed- and population-specific structural variants, and resolved candidate variants underlying pigmentation, body size, tail morphology, cashmere production, altitude adaptation, and other economically relevant traits. However, translation into routine breeding remains constrained by uneven population representation, inconsistent structural-variant definitions, limited functional annotation, computational demands, and insufficient validation across environments. Future progress will depend on diverse near-complete assemblies, graph-aware imputation and genomic prediction, long-read transcriptomics, single-cell and spatial omics, rigorous causal validation, and open, interoperable resources. Together, these developments can support more accurate, resilient, and biologically informed livestock improvement. Importantly, current dairy-cattle evidence indicates that pangenome-derived structural variants can substantially improve variant discovery and functional interpretation while yielding only marginal average gains in routine genomic prediction, favoring targeted augmentation rather than wholesale replacement of established SNP-based evaluations.},
}

Animals
Multiomics
*Genomics
*Genetic Variation
*Livestock/genetics
*Ruminants/genetics
Breeding

@article {pmid42726321,
year = {2026},
author = {Duan, DY and Ran, J and Guo, XL and Liu, L and Liu, GH and Asada, M and Cheng, TY},
title = {Metagenomic analysis of the midgut microbiome in Dermacentor abaensis ticks at different feeding states.},
journal = {Experimental & applied acarology},
volume = {97},
number = {3},
pages = {},
pmid = {42726321},
issn = {1572-9702},
support = {No. 2025JJ50143//Natural Science Foundation of Hunan Province, China/ ; No. kq2502005//Natural Science Foundation of Changsha City, China/ ; No. 31902294//National Science Foundation of China/ ; 2024YFD1800103//National Key Research and Development Program of China/ ; },
mesh = {Animals ; *Dermacentor/microbiology/physiology ; Female ; Bacteria/classification/isolation & purification/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; Feeding Behavior ; China ; *Metagenome ; },
abstract = {Ticks are blood-sucking ectoparasites of humans and animals, ranking second only to mosquitoes as vectors of diseases. Dermacentor abaensis is distributed in Sichuan, Qinghai, and Gansu, China. Because D. abaensis harbors several pathogens, it poses a threat to public health and livestock production. However, the midgut microbiota of D. abaensis at distinct feeding states remains poorly characterized. Adult D. abaensis ticks at various feeding states were collected from yaks in Gansu Province, China. Genomic DNA was extracted from midguts and midgut contents of unfed, partially fed, and fully engorged female D. abaensis. A metagenomic sequencing approach was employed to profile the midgut microflora among three groups. A total of 83 phyla, 908 genera, and 1857 species were annotated across the three groups. At the phylum level, Pseudomonadota, Mucoromycota, and Ascomycota were the most abundant. At the species level, common bacterial species such as Klebsiella pneumoniae and Anaplasma phagocytophilum, alongside viruses and eukaryotes, were detected in all three groups. Unique microorganisms were also observed in each group: unfed (n = 305), partially fed (n = 59), and fully engorged (n = 20). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis suggested that the D. abaensis microbiome contains a relatively high abundance of functional genes involved in lipid and amino acid metabolism across the three different feeding states. These findings indicate that while core microbial taxa are shared in the midgut of female D. abaensis, observable trends suggest variations in microbial diversity and composition as blood-feeding progresses. The present study provides a descriptive baseline of the midgut microbial composition of D. abaensis, which may inform future studies on tick biology and the ecology of tick-borne pathogens.},
}

Animals
*Dermacentor/microbiology/physiology
Female
Bacteria/classification/isolation & purification/genetics
Metagenomics
*Gastrointestinal Microbiome
Feeding Behavior
China
*Metagenome

@article {pmid42726367,
year = {2026},
author = {Wayal, V and Lee, MF and Wang, JY and Chen, YH},
title = {Gram-Positive and Gram-Negative Probiotic Extracellular Vesicles: Mechanisms of Immune Modulation and Therapeutic Opportunities in Atopic Dermatitis.},
journal = {Clinical reviews in allergy & immunology},
volume = {69},
number = {1},
pages = {},
pmid = {42726367},
issn = {1559-0267},
mesh = {Humans ; *Dermatitis, Atopic/therapy/immunology/metabolism/etiology ; Animals ; *Probiotics/therapeutic use ; *Extracellular Vesicles/immunology/metabolism ; Immunomodulation ; *Gram-Negative Bacteria/immunology ; *Gram-Positive Bacteria/immunology ; Immunity, Innate ; },
abstract = {Atopic dermatitis (AD) is a prevalent chronic inflammatory skin disease characterized by epidermal barrier dysfunction, type 2 immune skewing, and microbiome dysbiosis. Although live probiotics can modulate the gut-skin axis, their clinical use is limited by variable efficacy and safety concerns. Probiotic extracellular vesicles (PEVs) have emerged as cell-free nanotherapeutics that retain microbial bioactivity while circumventing the risks associated with live bacteria. However, the comparative immunological roles of vesicles from Gram-positive and Gram-negative probiotics remain incompletely understood. This review systematically compares Gram-negative outer membrane vesicles (OMVs) and Gram-positive membrane vesicles (MVs) in the context of AD. OMVs, enriched with lipopolysaccharide (LPS) and other bioactive cargo, mainly signal through toll-like receptor 4 (TLR4) to regulate innate immunity, strengthen antimicrobial defense, and modulate inflammation. In contrast, Gram-positive MVs, containing lipoteichoic acid (LTA), peptidoglycan (PG), proteins, and small RNAs, preferentially activate TLR2-linked pathways that support immune tolerance, regulatory T cell (Treg) responses, and barrier repair. Both PEV classes demonstrate significant potential in preclinical models by attenuating inflammation, improving epithelial integrity, and restoring microbiome balance. Despite this potential, clinical translation requires standardized isolation protocols, scalable manufacturing, rigorous safety testing, and regulatory alignment. Advances in microbial engineering and EV design may enable targeted, microbiota-directed therapies for AD.},
}

Humans
*Dermatitis, Atopic/therapy/immunology/metabolism/etiology
Animals
*Probiotics/therapeutic use
*Extracellular Vesicles/immunology/metabolism
Immunomodulation
*Gram-Negative Bacteria/immunology
*Gram-Positive Bacteria/immunology
Immunity, Innate