@article {pmid40555926,
year = {2025},
author = {Wiele, N and de Melo Pereira, GV and da Silva Vale, A and de Mello Sampaio, V and Ribeiro-Barros, AI and Diniz de Souza, AF and Dos Santos, DVN and Góes-Neto, A and Soccol, CR},
title = {Comparative microbiomes reveal microbial signatures in coffee fermentation and flavor development across distinct Brazilian biomes.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {207},
pmid = {40555926},
issn = {1573-0972},
support = {440343/2022-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; UIDB/00239/2020//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {Recent studies underscore the pivotal role of microbial terroir in shaping coffee fermentation and quality. However, the specific influence of regional microbiomes on flavor development remains underexplored. This study explored the link between the coffee farm microbiome and the resulting spontaneous fermentation process in Brazil’s Atlantic Forest and Semi-arid Cerrado biomes. Using Illumina-based amplicon sequencing, 972 prokaryotes and 435 eukaryotes were identified from coffee fruits, leaves, depulped coffee beans, over-ripe beans, soil, and temporal fermentation samples. During the fermentation process, microorganisms present in the pulped fruit (viz., Leuconostoc and Kazachstania) were the main microbial groups driving fermentation process across the two biomes, leading to the accumulation of primary (ethanol and lactic acid) and secondary (esters, aldehydes, higher alcohols, and ketones) metabolites. However, Leuconostoc and Kazachstania communities were significantly higher in the pulped fruit samples from the Atlantic Forest compared to the Cerrado biome. Therefore, the Atlantic Forest farm showed more stable microbial dynamics during the fermentation process and the formation of key flavor metabolites, such as methyl salicylate, linalool, ethyl linoleate, benzeneacetic acid ethyl ester, and phenylethyl alcohol. In contrast, the Cerrado samples exhibited higher microbial richness, leading to the emergence of co-dominant species such as Pantoea, Cutaneotrichosporon, Hyphopichia, Wickerhamomyces, and Cladosporium. Sensory evaluation revealed higher overall scores for the Atlantic Forest coffee, characterized by fruity, floral, and caramel notes, compared to earthy and herbal characteristics of Cerrado coffee. The findings demonstrate the influence of terroir-driven microbial communities on coffee fermentation and coffee quality, providing insights into optimizing fermentation for enhanced coffee flavor development and contributing to the growing field of microbial-assisted coffee production.},
}

@article {pmid41182402,
year = {2025},
author = {Tekgül, ZB and Adıgüzel, A},
title = {Microbial viability assessment with PMA-qPCR: challenges, opportunities, and future directions.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {343},
pmid = {41182402},
issn = {1432-072X},
abstract = {Since molecular analyzes are insufficient to distinguish living and non-living cells, lead to misleading results, and dead cells also multiply their DNA/RNA, a method that can give more sensitive results was needed. PMA (propidium monoazide), which is used to prevent the DNA of dead cells from negatively affecting the experimental results, is a viability indicator that binds only to the DNA of damaged cells and prevents them from being multiplied by PCR, and was first introduced in 2006. Recently the interest in the use of PMA in many fields such as microbiome and metagenomic studies, environmental microbiology, food microbiology, antibiotic and disinfectant effectiveness tests, clinical microbiology and diagnosis, and cell culture and biotechnology has increased considerably. Therefore, the purposes of use, principles, applications in various fields and limitations of PMA have been investigated. The current review of this vitality marker, which has a history of less than 20 years, will lead to its use of many new scientific studies and will provide convenience to scientists by bringing together studies on the use of this dye.},
}

@article {pmid41329407,
year = {2025},
author = {Wang, W and Liang, Y and Cheng, T and Du, J and Zhang, Y and Jiang, L and Luo, X and Wang, Y},
title = {Gut Microbiota-Driven Modulation of Intestinal Barrier Function, Antioxidant Capacity, and Immune Response in Green-Footed Chicken by Dietary Fermented Chinese Herbal Compounds.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41329407},
issn = {1867-1314},
support = {16ZG6103//National Defense Basic Research Program/ ; },
abstract = {After the ban on antibiotics, fermented herbs have become an alternative. In the experiment, 960 one - day - old green - footed chickens were divided into four groups: T1 (basal ration), T2 (1% fermented herbs), T3 (3% fermented herbs), and T4 (5% fermented herbs). The experiment was conducted over a 69-day period. The health and growth of the chickens were assessed by evaluating growth performance, serum biochemistry, and gut microbiota. The results showed that during days 22–42 and 43–69, the average daily weight gain of T4 group chickens was significantly higher than that of T1 group (P < 0. 05). Serum biochemistry analysis showed that the IgA and IgG levels of T2, T3 and T4 group chickens were significantly higher than those of T1 group (P < 0. 05), while ALT activity was significantly lower than that of T1 group (P < 0. 05). In addition, the CD4+/CD8 + cell content in the blood of T2, T3 and T4 groups also increased (P < 0. 05). Notably, the Bursa of Fabricius Index in the T4 group was significantly enlarged (P < 0. 05). Gut immune and sequencing analyses showed that the villus height of the jejunum and duodenum increased significantly (P < 0. 05). 16s microbiome sequencing results showed that the gut markers of the test groups were Coriobacteriia, Subdoligranulum, and unidentified Actinobacteria. This study shows that fermentation of astragalus, cypress, dandelion, Scutellaria baicalensis, and honeysuckle herbs can modulate the intestinal microbial community structure through multiple pathways, promote gut health in broiler chickens, and thereby enhance growth performance.},
}

@article {pmid41372737,
year = {2025},
author = {Shah, A and Doshi, G},
title = {Stress and neurodegeneration: mechanistic insights and therapeutic opportunities for preserving brain resilience.},
journal = {Acta neurologica Belgica},
volume = {},
number = {},
pages = {},
pmid = {41372737},
issn = {2240-2993},
abstract = {Neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and Amyotrophic Lateral Sclerosis are strongly influenced by persistent stress, which accelerates both their onset and progression. This review explores the intricate interplay between chronic stressors, oxidative and metabolic imbalances, protein misfolding, inflammatory responses, and psychosocial adversity, and their cumulative impact on the aging brain’s capacity for homeostasis. The loss of cellular resilience due to prolonged stress leads to maladaptive outcomes, including mitochondrial dysfunction, sustained neuroinflammation, breakdown in proteostasis, and disruption of hypothalamic-pituitary-adrenal axis signaling, all of which amplify neuronal vulnerability. The detailed molecular pathways that underlie these phenomena, the article identifies key mediators such as Reactive Oxygen species, mitochondrial regulators, heat shock proteins, and proinflammatory cytokines that drive neurodegeneration. A comprehensive literature search was conducted using PubMed, Scopus, Web of Science, and Google Scholar up to 2025. Eligible publications included original research articles, clinical studies, and systematic reviews focusing on stress-related molecular pathways, oxidative metabolism, proteostasis, neuroinflammation, and therapeutic interventions in aging and neurodegenerative diseases. A qualitative synthesis of these studies was performed to identify key mechanisms, biomarkers, and emerging treatment strategies relevant to stress-induced neurodegeneration. Further, the review evaluates both established and emerging interventions aimed at mitigating these stress-driven processes. Lifestyle modifications such as aerobic exercise, calorie restriction, and cognitive behavioural therapies complement pharmacological agents like antioxidants, chaperone modulators, and anti-inflammatory drugs to enhance brain resilience and delay disease onset. Recent advances in the field, including integrated multi-omics profiling, biomarker discovery, and medicine approaches, promise to refine our ability to satisfy patients and deliver targeted therapies based on individual stress profiles. Additionally, the article discusses the neuroimmune-gut axis and the potential for interventions targeting microbiome-related inflammation. Early detection of stress-related biomarkers and personalized strategies holds considerable promise for improving clinical outcomes, enabling earlier diagnosis, and fostering tailored therapies that preserve cognitive function and independence in aging populations.},
}

@article {pmid41417288,
year = {2025},
author = {Deng, J and Ji, J and Khan, A and Wang, Z and Xiang, W and Qiao, H and Salama, ES and Gu, J and Mao, C and Liu, P and Li, X},
title = {Antimicrobial Proteins from Limosilactobacillus fermentum GR-9 Inhibit Pathogens and Alleviate Salmonella Paratyphi B Infection in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41417288},
issn = {1867-1314},
support = {24ZDWA005//Natural Science Foundation of Gansu Province/ ; },
abstract = {Probiotics employ defense molecules that include antimicrobial peptides (AMPs) and lytic enzymes to inhibit pathogens; however, translating these mechanisms into applications remains challenging. In this study, Limosilactobacillus fermentum GR-9, isolated from “Jiangshui”, secretes AMPs and NlpC/p60 hydrolase, exhibiting 64%-77% of inhibition against both Gram-positive and Gram-negative pathogens. In mice model, GR-9 treatment reduced 93% of Salmonella Paratyphi B intestinal pathogen colonization effectively, similar to the antimicrobial norfloxacin. Moreover, GR-9 promoted beneficial microbiota, including Ligilactobacillus spp. and Bifidobacterium, highlighting its dual role in pathogen clearance and microbiome restoration. GR-9 further alleviated inflammation by modulating the immune response, significantly reducing the levels of pro-inflammatory cytokine (both TNF-α and IL-6) by 16% in both serum and intestinal tissues. Ultimately, this treatment highlights that probiotic-producing therapeutic compounds in situ offer a viable alternative to synthetic AMP production, addressing its critical challenges while providing a sustainable tool against antimicrobial-resistant pathogens.},
}

@article {pmid41432892,
year = {2026},
author = {Seenivasan, SN and Vasudevan, SA and Raghupathy, AK and Rajan, F and Selvan, E and Sharma, SM and Muthusamy, RK and Paramasivam, L and Seethalakshmi, SP and Yogeswaran, S and Velmurugan, G},
title = {Intratumoural microbial metabolites in breast cancer: a longitudinal study on association with metastatic progression.},
journal = {Molecular and cellular biochemistry},
volume = {481},
number = {2},
pages = {1045-1057},
pmid = {41432892},
issn = {1573-4919},
support = {SRG/2020/001867//Science and Engineering Research Board/ ; },
abstract = {Delayed diagnosis and metastasis remain major challenges in breast cancer. While the gut microbiome’s influence on tumour progression is established, the presence and role of intratumoural microbial metabolites in breast cancer and their association with metastasis remain unexplored. Paired tumour and adjacent tissues were collected from 50 breast cancer patients at baseline. Patients were followed for five years; 10 who developed distant metastasis were classified as pre-metastatic, and 10 who remained disease-free formed the non-metastatic group. Untargeted LC–MS/MS-based metabolomics was performed to profile host and microbial metabolites. Multivariate analysis and pathway enrichment were used to identify discriminatory signatures. Elevated levels of carnitine, indole, tryptophan-derived metabolites, ceramides and polyamines were observed in tumour tissues on comparison with adjacent tissues. Interestingly, these metabolites were downregulated in tumour tissues of patients who progressed for metastasis (pre-metastatic) with increase in N-methylhistamine and taurolithocholic acid sulfate, suggesting metabolic reprogramming during metastatic priming. Baseline host–microbial metabolic disruptions in breast tumours are linked to future metastasis, with metabolites like indoles, bile acids, and polyamines showing promise as early biomarkers and therapeutic targets in precision oncology.},
}

@article {pmid41452511,
year = {2025},
author = {Al-Adham, ISI and Ali Agha, ASA and Al-Remawi, M and Al-Akayleh, F and Al-Sheikh, A and Aburub, F and Collier, PJ},
title = {Probiotics, Psychobiotics, Paraprobiotics, and Postbiotics in Gut-Brain Axis Modulation: Multi-Omics and AI-Driven Precision Nutrition for Cognitive Health.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41452511},
issn = {1867-1314},
abstract = {The gut-brain axis has emerged as a key regulatory interface in cognitive function and neurological health, influenced by diet-driven microbial metabolism and host-microbiome interactions. Integrating multi-omics approaches with AI-driven precision nutrition offers novel insights into how diet modulates neuroimmune, neuroendocrine, and metabolic pathways. This article explores recent advances in microbiome research, highlighting the role of microbiota-derived extracellular vesicles (MEVs) as bioactive carriers that facilitate gut-brain communication by transporting neuroactive metabolites and immune modulators. These findings reveal an underexplored mechanism by which dietary interventions can reshape brain function at the molecular level. Additionally, synthetic biology and CRISPR-mediated microbiome engineering are advancing targeted interventions, allowing precise modulation of microbial gene expression to enhance neuroprotective pathways and mitigate neuroinflammation. Emerging strategies such as psychobiotics, paraprobiotics, and postbiotics further expand this therapeutic landscape, offering novel microbiome-based tools to influence neurotransmission, neuroimmune regulation, and cognitive resilience. Artificial intelligence (AI)-driven multi-omics integration further enables predictive modeling of microbiome-neurotransmitter interactions, hence refining personalized nutritional strategies for cognitive resilience and neuroprotection. However, challenges such as inter-individual variability, algorithmic biases, and ethical considerations in AI-driven dietary recommendations must be addressed to ensure the suitability of potential therapies. Future research should focus on in vivo validation of AI-guided dietary interventions through multi-modal neuroimaging, metabolomics, and transcriptomics. These advances position precision nutrition as a transformative tool in neuroscience, bridging microbiome science, AI, and personalized medicine to optimize brain health and mitigate neurodegenerative risks.},
}

@article {pmid41455009,
year = {2025},
author = {Safari, F and Golafshan, F and Malekpour, E and Mirzaei, SA and Rouzbahani, H and Hajarzadeh, MO and Nasir Harandi, S and Nasirharandi, S and Noursina, A},
title = {Functional Proteins of Akkermansia Muciniphila: Impacts on Host Health and Metabolism.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41455009},
issn = {1867-1314},
abstract = {Akkermansia muciniphila, a mucin-degrading bacterium endemic to the human gut microbiome, plays a crucial role in modulating host physiology through the action of its functional proteins. This review compiles the latest insights into these proteins, elucidating their molecular mechanisms and their influence on host health. Notable proteins include Amuc_1100, Amuc_1631 (P9), Amuc_2109, and Amuc_1434, each of which is involved in key physiological processes. Amuc_1100 functions as an immune rheostat, engaging TLR2 and TLR4 pathways to modulate immune responses. Amuc_1631 enhances glucose homeostasis by promoting GLP-1 secretion, thereby linking gut microbiota to metabolic regulation. Amuc_2109 is implicated in the reinforcement of tight junctions, contributing to intestinal barrier integrity. In contrast, Amuc_1434 has demonstrated anti-tumor effects through the induction of apoptosis in colorectal cancer cells. Beyond these functions, these proteins also facilitate mucin degradation, support microbial cross-feeding, and promote resilience to gastrointestinal stressors. The review emphasizes their therapeutic potential for a range of conditions, including metabolic disorders, inflammatory bowel disease, cancer, and neuropsychiatric disorders. However, it also identifies translational hurdles such as the need for robust human clinical trials and the development of optimized delivery systems to harness their benefits fully. These findings position the proteins of A. muciniphila as promising targets for microbiota-centric therapeutic interventions.},
}

@article {pmid41483122,
year = {2026},
author = {Aghdam, MM and Rezagholizadeh, L and Fazaeli, A and Moradi, A and Ojarudi, M},
title = {Nutritional modulation of metabolic signaling within the tumor microenvironment for cancer therapy.},
journal = {Molecular and cellular biochemistry},
volume = {481},
number = {3},
pages = {1155-1182},
pmid = {41483122},
issn = {1573-4919},
abstract = {The tumor microenvironment (TME) constitutes a complex ecosystem of cellular and non-cellular components. Together, these constituents exert a critical influence on cancer progression. A principal mechanism underlying this influence is metabolic reprogramming, in which tumor cells alter glucose, amino acid, and lipid metabolism to promote growth, survival, and immune evasion. Metabolic adaptation is further regulated by nutrient-sensing pathways, including mammalian target of rapamycin (mTOR), AMP-activated protein kinase (AMPK), and hypoxia-inducible factor (HIF), which often exhibit context-dependent and sometimes opposing functions in tumor and immune cells within the TME. Given this complexity, targeting metabolic vulnerabilities has become a promising therapeutic approach. In this context, nutritional interventions, such as caloric restriction, ketogenic diets, fasting-mimicking diets, protein or amino acid modulation, and lipid metabolism adjustments, aim to deprive tumors of essential nutrients, remodel the immunosuppressive TME, and increase cancer cell sensitivity to chemotherapy, radiotherapy, and immunotherapy. However, the efficacy of these interventions varies according to cancer type, oncogenic drivers, and immune contexture, and there is a risk of impairing anti-tumor immune function. Addressing these challenges will require personalized nutrition strategies that integrate tumor genetics, metabolic profiling, and the gut microbiome, together with technological advances for real-time monitoring. Progress in this area depends on a deeper mechanistic understanding of nutrient-immune interactions and the optimization of combination approaches for improved metabolic targeting in precision oncology. Accordingly, this review addresses a critical gap by synthesizing mechanistic and translational literature and outlining actionable priorities to advance nutritional modulation from preclinical research to clinical application.},
}

@article {pmid41493541,
year = {2026},
author = {Dhiman, I and Nandni, and Poria, V and Kumar, S and Yadav, R and Shaik, T and Bedwal, S and Wati, L},
title = {Plant growth promoting rhizobacteria (PGPR) mediated amelioration of plant tolerance to abiotic stresses: Drought, salinity, and heavy metals.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {100},
pmid = {41493541},
issn = {1432-072X},
abstract = {Plants, being sessile organisms, are perpetually subjected to a spectrum of escalating abiotic stresses, which have detrimental repercussions on agriculture worldwide. In the forthcoming era of climate change and ecosystem degradation, fostering the use of beneficial microbiota in agroecosystems represents a major challenge towards sustainability. Some plant-associated bacteria, called Plant Growth Promoting Rhizobacteria (PGPR), may confer growth-promoting advantages to the host plant through enhancing nutrient uptake, altering hormone homeostasis, and/or improving tolerance to abiotic stress factors (drought, heavy metal, and salinity stress) in plants. These include promoting plant growth through the activation of antioxidant enzymes to detoxify reactive oxygen species, accumulation of compatible solutes to maintain osmotic homeostasis, suppression of lipid peroxidation to conserve membrane integrity, and emission of volatile organic compounds to induce systemic resistance. Additionally, PGPR synthesize phytohormones and exopolysaccharides that reinforce their persistence in soil, improve plant-water relations, and optimize nutrient uptake efficiency. In this regard, exploring the key ecological and evolutionary interactions between plants and their microbiomes is a prerequisite to developing innovative approaches and novel natural products that will complement conventional farming techniques. Collectively, these interactions fortify plant defense mechanisms, enhance physiological homeostasis, and promote adaptive plasticity in adverse environments. Herein, we describe the role of plant-microbe interactions in mitigating abiotic stress and fostering sustainable crop production. Leveraging multifactorial PGPR in agroecosystems strengthens the adaptive resilience of plants, reduces dependency on synthetic fertilizers, maintains soil microbiome integrity, cellular homeostasis, nutrient cycling, improves water retention, and ensures sustainable productivity in stress-prone and resource-limited regions.},
}

@article {pmid41524778,
year = {2026},
author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK},
title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {105},
pmid = {41524778},
issn = {1432-072X},
support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; },
abstract = {Microorganisms play pivotal roles in maintaining host physiology and ecosystem balance, with fish-associated microbiomes offering unique insights due to the diverse habitats and feeding behaviours of their hosts. This review comprehensively explores the diversity, composition, and functional roles of gut and skin-associated microbial communities in fish across freshwater, brackish, and marine environments, with emphasis on recent advancements in metagenomic methodologies. Culture-independent techniques, particularly high-throughput and third-generation sequencing technologies, have revolutionized our ability to uncover microbial diversity, gene functions, and interspecies interactions. The fish gut microbiome, heavily influenced by factors such as diet, habitat, and host species, contributes significantly to nutrient metabolism, immune modulation, and physiological adaptation. Similarly, the skin microbiota provides a critical first line of defence, offering protection through competitive exclusion and antimicrobial activity. Functional metagenomics reveals microbial contributions to host metabolism, energy homeostasis, xenobiotic degradation, and environmental adaptation via the gut-brain axis and metabolic pathways. Emerging evidence highlights the bidirectional relationships between microbiota and host phenotypic plasticity. This review underscores the importance of integrative metagenomic approaches to decode complex microbial functions and their ecological relevance in aquaculture, with implications for sustainable fish health management, disease prevention, and improved productivity.},
}

@article {pmid41642480,
year = {2026},
author = {Chriaa, O and Gdoura-Ben Amor, M and Mathlouthi, NEH and Slima, AB and Mhalhel, K and Turki, M and Kacem, FH and Germanà, A and Ben Ali, M and Gdoura, R},
title = {Probiotic intervention attenuates hypercholesterolemia and modulates gut microbiota in high-fat diet-fed rats.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {74},
pmid = {41642480},
issn = {1573-0972},
abstract = {Hypercholesterolemia is a major risk factor for cardiovascular diseases and is often associated with lipid metabolism disturbances, liver dysfunction, and gut microbiota imbalances. Probiotics have emerged as promising agents to improve cholesterol management through gut microbiome modulation and anti-inflammatory effects. This study investigated the impact of probiotics on weight, lipid profiles, liver function, and gut microbiota composition in high-fat diet (HFD)-induced hypercholesterolemic rats. Rats were divided into five groups: normal diet (NG), HFD, HFD + Rosuvastatin (SG), HFD + probiotics (Lactobacillus spp.) (PG), and HFD + Rosuvastatin + probiotics (PSG). Probiotic supplementation significantly attenuated weight gain, reduced triglycerides (TG), total cholesterol (TCH), and LDL-C levels, and improved liver enzyme profiles (ALT, AST) compared to the HFD group. Histological analysis revealed that probiotics mitigated HFD-induced hepatocellular degeneration and decreased pro-inflammatory cytokine expression (IL-1β, TNF-α) in liver tissues. Gut microbiota analysis showed that probiotics modulated the relative abundance of key bacterial phyla and families, increasing beneficial taxa such as Lachnospiraceae and Lactobacillaceae. These findings suggest that probiotics can serve as a potential therapeutic strategy for managing hypercholesterolemia by improving lipid metabolism, protecting hepatic health, and reshaping the gut microbiome.Trial registration: CEREASFS4625/4022 (https//www.medecinesfax.org/fra/pages/518/projetscereas).},
}

@article {pmid41697296,
year = {2026},
author = {Chengcheng, L and Yanduo, Z and Zhebin, W and Jianzhang, L and Yangtao, Z and Jun, L and Yu, L and Felemban, HR and Alyahyawy, OY and Alhomodi, AF and Hadadi, F and Shaibah, A and Bingzhi, L and Xianwei, W},
title = {Metagenomic analysis of fecal microbial communities in dairy goats from different farms.},
journal = {Protoplasma},
volume = {263},
number = {3},
pages = {1031-1045},
pmid = {41697296},
issn = {1615-6102},
abstract = {This study aims to investigate the differences in the microbial community structure of goat manure under various breeding environments, providing scientific evidence and theoretical support for healthy breeding practices. Gut microbiota is a key determinant of feed conversion, disease resistance and overall productivity in ruminants. The gut microbiome is an integral part of the digestive system. Its composition and functional traits markedly influence digestive efficiency, immune development, gut homeostasis and reproductive performance. Using four goat dairy farms in the Yangling, Shaanxi Province as study subjects, fecal samples were collected and analyzed using 16S rRNA sequencing technology, combined with α-diversity indices and β-diversity analysis. The results revealed significant differences in the microbial community structure of goat feces across different farms, with each farm exhibiting unique microbial communities. Each farm harboured distinct microbial signatures and functional profiles, providing microbiota-based targets for precision management of Guanzhong dairy goats.},
}

@article {pmid41731166,
year = {2026},
author = {Zhang, X and Su, Q and Chen, X and Wang, S and Du, J and Chen, L and Xu, Q and Liu, C and Zhao, J},
title = {Inference of drowning sites of cases in the Pearl river based on microbial community profiling and random forest algorithm.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {41731166},
issn = {1437-1596},
support = {82371901//National Natural Science Foundation of China/ ; 2024B04J0022//Funding by Science and Technology Projects in Guangzhou/ ; 2022JC35//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; 2022JC26//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; },
abstract = {Accurate inference of drowning sites remains a critical challenge in forensic investigations, particularly for corpses recovered from dynamic aquatic environments. Conventional methods, such as diatom testing, are limited by the absence or scarcity of diatoms in certain water bodies, labor-intensive morphological identification, and challenges in distinguishing morphologically similar species. In this study, we explored the feasibility of inferring drowning sites in human cases by integrating pulmonary microbial community profiling with machine learning. A total of 56 lung tissue samples from confirmed drowning victims were collected from four regions of the Pearl River’s Guangzhou section, including the central urban waterfront (site1), mid-reach brackish transition zone (site2), southern estuarine outflow zone (site3), and eastern tributary confluence (site4). High-throughput sequencing of the 16 S rRNA gene (V3 – V4 region) was performed to characterize microbial community composition. Significant spatial heterogeneity in pulmonary microbiota was observed across drowning sites, as demonstrated by alpha diversity analysis, unweighted UniFrac-based principal coordinates analysis, and differential abundance testing. Linear discriminant analysis effect size (LEfSe) further identified 111 differentially abundant microbial taxa, providing biological interpretation of spatial microbial variation among groups. To enable drowning site inference, microbial features at the genus level were subjected to feature engineering using a hybrid strategy combining variance thresholding and the Boruta algorithm. Through this process, 32 genera—including Ralstonia, Sphingomonas, Akkermansia, and Faecalibacterium—were selected as key microbial markers for geolocation. Multiple classification models, including Random Forest (RF), Decision Tree (DT), Support Vector Machine (SVM), and Logistic Regression (LR), were constructed and compared. The RF model exhibited the superior predictive performance, achieving a test set accuracy of 92.3% and a macro-average area under the receiver operating characteristic curve (AUC) of 0.949. External validation using five independent cases further confirmed the model’s practical utility, correctly predicting the drowning sites for four of the victims. Overall, This study preliminarily demonstrates the feasibility of inferring drowning locations through pulmonary microbiome analysis combined with machine learning in human samples, demonstrating the novel application of this approach to human cases. Future efforts should expand geographic sampling and integrate environmental metadata to enhance methodological robustness.},
}

@article {pmid41733709,
year = {2026},
author = {Sahariah, P and Saikia, L and Bharali, A and Law, D and Sen, S and Dutta, PP},
title = {Modulation of mitochondrial biogenesis by flavonoids via SIRT1 signalling in metabolic syndrome: a systematic review.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41733709},
issn = {1573-4978},
abstract = {Metabolic syndrome (MetS) is a complex cluster of metabolic abnormalities, including insulin resistance, central obesity, dyslipidemia, and hypertension. Dysregulated mitochondrial biogenesis has emerged as a key pathogenic feature of MetS, while flavonoids are increasingly recognised for their ability to modulate mitochondrial function through SIRT1-dependent pathways. This review aims to critically evaluate the role of flavonoids in modulating mitochondrial biogenesis via SIRT1 signalling in MetS, with emphasis on mechanistic evidence. A systematic review was conducted with a mechanistic focus, integrating preclinical and translational evidence to assess the role of flavonoids in MetS through SIRT1. A comprehensive literature search was performed in PubMed, Scopus, and Web of Science up to 2025 using the keywords “flavonoids,” “flavonols,” “SIRT1,” “AMPK,” “GLUT4,” and “metabolic syndrome.” Flavonols have emerged as the most extensively studied subclass of flavonoids in MetS models, with compounds such as quercetin, myricetin, and luteolin demonstrating consistent protective effects. These effects were mediated by AMPK activation, GLUT4 translocation, and mitochondrial biogenesis via SIRT1 signalling, thereby improving insulin resistance, dyslipidemia, and mitochondrial dysfunction. Despite robust mechanistic evidence, no clinical trials to date have evaluated flavonols in the context of MetS. Limitations, such as poor bioavailability, pharmacokinetic variability, and the absence of standardised formulations, continue to hinder their clinical translation. To overcome translational barriers, future research should prioritise randomised controlled trials, alongside innovative strategies such as nanoformulations, microbiome-targeted interventions, and flavonoid-inspired therapeutics. Addressing these gaps could establish the flavonoid–SIRT1 axis as a novel therapeutic avenue for MetS.},
}

@article {pmid41746458,
year = {2026},
author = {Almeida, LF and Li, L and de Vries, RP and Sun, P and Maitan-Alfenas, GP},
title = {Enzymatic production of prebiotic xylooligosaccharides.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41746458},
issn = {1573-0972},
abstract = {Xylooligosaccharides (XOS) have been shown to have prebiotic activities and therefore have beneficial effects on human and animal health. Production of these oligosaccharides from xylan often results in diverse mixtures, largely due to the variation in the xylan structure and the substrate specificities of the enzymes used to generate them. In this review, we will shortly describe the xylan structure and its variations, and the enzymes that are involved in its degradation. The use of these enzymes for the production of XOS and how this affects the variation in XOS structures will be addressed, which will then be linked to their prebiotic effects, especially related to modulation of the gut microbiome. The resulting health benefits will be summarized and finally the remaining challenges will be highlighted and suggestions for further improvement of their production will be provided.},
}

@article {pmid41779114,
year = {2026},
author = {Medeiros, EB and Lidio, AV and Zabot, GC and Fenilli, GP and de Bem Silveira, G and Keller, GS and Carrion, FRA and De Felice, FG and Kluwe-Schiavon, B and Walls-Bass, C and Barichello, T and Budni, J},
title = {Exploring the Gut-Brain Connection: Are Probiotics the Next Frontier in Alzheimer's Disease Treatment?.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12602-026-10927-w},
pmid = {41779114},
issn = {1867-1314},
abstract = {Alzheimer’s disease (AD) is the most common form of dementia, historically considered exclusively as a neurological condition treated primarily with cholinergic and glutamatergic inhibitors. Recent evidence highlights the significant influence of peripheral systems, particularly the gut-brain axis, on AD pathology. The gut microbiota plays a critical role in both physiological and psychological functions, and its interactions may impact the integrity of the blood-brain barrier, potentially contributing to neurodegenerative processes. Emerging therapeutic strategies targeting the gut microbiome, including both pharmacological and non-pharmacological approaches such as probiotics and prebiotics, offer promising avenues for intervention. This review synthesizes current literature and illustrative data to elucidate the connections among the gut-brain axis, neuroinflammation, and neuroprotection, and their implications for the pathogenesis and potential treatment of AD.},
}

@article {pmid41793457,
year = {2026},
author = {Hussain, B and Haouala, F and Fariduddin, Q},
title = {From night hormone to green signal: The journey of melatonin.},
journal = {Protoplasma},
volume = {},
number = {},
pages = {},
pmid = {41793457},
issn = {1615-6102},
support = {grant number IMSIU-DDRSP-RP25).//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Melatonin (MT), once considered exclusive to animals, is now recognized as a universal and multifunctional molecule in plants, playing pivotal roles in growth regulation, stress tolerance, and antioxidant defense. Since its discovery in plants in the mid-1990s, the presence of MT has been reported to be prevalent across diverse plant taxa. MT modulates plant responses to abiotic stresses such as heat, cold, salinity, drought, heavy metals, and UV radiation, as well as biotic stresses including pathogen attack and herbivory, primarily by regulating antioxidant enzymes, stress-responsive genes, hormone signaling pathways, and production of secondary metabolites. Advanced analytical techniques such as HPLC, LC-MS, and NMR have facilitated sensitive detection and structural characterization of MT in various plant species. Molecular studies have identified receptors of MT and its roles in regulating different processes, highlighting its integration with other phytohormones and signaling molecules. Genetic engineering tools have been proven effective in raising the level of endogenous MT levels, which has immense potential for enhancing crop resilience. Emerging evidence points to the role of MT in modulating the plant microbiome and systemic signaling, offering new avenues for research. Despite significant advances, key challenges remain in understanding the structure of receptors, signaling crosstalk, and the regulation of its biosynthesis under stress. This review discusses the methods for detecting MT in plants and evaluates its physiological, molecular, and functional aspects. Tracing the evolution of MT research in plants, from its initial discovery to the present day, key milestones, cross-talk, and signaling pathways of MT in plants have been discussed.},
}

@article {pmid41807782,
year = {2026},
author = {Stevanoska, M and Cremona, M and Beekmann, K and Sturla, SJ and Aichinger, G},
title = {Interindividual variability in gut microbial formation of the hop phytoestrogen 8-prenylnaringenin results in elevated but sub-toxic internal exposures.},
journal = {Archives of toxicology},
volume = {100},
number = {6},
pages = {2397-2409},
pmid = {41807782},
issn = {1432-0738},
support = {SCAHT-AP_22_02//Swiss Centre for Applied Human Toxicology/ ; },
abstract = {The gut microbiome converts the prenylated polyphenol isoxanthohumol (iXN), a natural constituent of hops found in beer, into 8-prenylnaringenin (8-PN), a potent phytoestrogen associated with endocrine-disrupting effects. Following oral exposure, interindividual differences in microbiome composition may lead to variable systemic 8-PN concentrations and consequently to differences in susceptibility to toxicity. To characterize the contribution of gut microbiota to health effects of hop polyphenols, a human physiologically based kinetic (PBK) model that includes microbial 8-PN formation was developed. Ex vivo fecal fermentation coupled to LC–MS/MS revealed substantial interindividual variation in biotransformation capacity. Derived kinetic parameters were incorporated into the PBK model, which was subsequently used to predict systemic 8-PN exposure while accounting for interindividual variability. Model simulations indicated that high iXN metabolizers experience approximately two-fold more internal 8-PN exposure than low metabolizers. Estrogenicity of the predicted uterine 8-PN concentrations was assessed via alkaline phosphatase induction in Ishikawa cells. Even in high metabolizers, systemic 8-PN concentrations appeared to remain below levels of concern regarding endocrine disruption. These findings highlight the importance of accounting for interindividual variability in gut microbial biotransformation when predicting xenobiotic toxicokinetics and illustrate the applicability of microbiome-competent PBK modeling for predicting the systemic fate of gut microbial metabolites.},
}

@article {pmid41831055,
year = {2026},
author = {Longoria, CR and DeSio, DD and Oydanich, M and Su, X and Chiles, EN and Kerkhof, LJ and Ibironke, O and Häggblom, MM and Wages, NP and Guers, JJ and Vatner, DE and Vatner, SF and Campbell, SC},
title = {Disruption of the gut microbiota in regulator of G protein signaling 14 knockout (RGS14 KO) mice alters the metabolome and reduces enhanced exercise capacity.},
journal = {European journal of applied physiology},
volume = {},
number = {},
pages = {},
pmid = {41831055},
issn = {1439-6327},
support = {826640//Office of Naval Research/ ; R01HL37368//NHLBI Division of Intramural Research/ ; R01HL106511//NHLBI Division of Intramural Research/ ; P30CA072720-6852//Division of Cancer Prevention, National Cancer Institute/ ; },
abstract = {Regulator of G-protein Signaling 14 Knockout (RGS14 KO) mice exhibit enhanced exercise capacity and health span, however the contribution of the gut microbiota to this phenotype remains unclear. This study integrated long-read rRNA operon amplicon sequencing and metabolomics to first determine how microbial composition and tissue metabolite profiles differ between RGS14 KO and their wild-type littermates. Next, we investigated how administration of antibiotics to perturb the gut microbiota may affect the RGS14 KO phenotype. Prior to antibiotic treatment (ABX), RGS14 KO mice outperformed WT littermates in maximal running distance and work performed, accompanied by elevated skeletal muscle citrate synthase, complex IV activity, and nitric oxide production. One week of ABX significantly reduced exercise capacity in both genotypes and markedly suppressed mitochondrial activity in RGS14 KO skeletal muscle. Gut microbiota profiling revealed similar phylum-level structure between genotypes but distinct species- and strain-level signatures. Metabolomics of brown adipose tissue (BAT) and quadriceps identified genotype-specific metabolic programs that were disrupted by ABX, including pathways related to amino acid metabolism, nucleotide turnover, and mitochondrial energetics. Collectively, these findings demonstrate that RGS14 KO mice harbor unique microbial and metabolic networks that support enhanced thermogenesis and exercise performance, and that microbiota depletion eliminates these advantages. This work establishes a mechanistic foundation connecting the gut microbiota to BAT and skeletal muscle metabolism, highlighting potential microbiome-targeted strategies to improve metabolic health and physical performance.},
}

@article {pmid41872932,
year = {2026},
author = {Imtiaz, H and Liu, R and Li, QH and Zhou, CZ and Ying, YT and Tan, X},
title = {Reduction in microbiota-derived short-chain fatty acids contributes to the pathogenesis of pulmonary arterial hypertension.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03591-9},
pmid = {41872932},
issn = {1465-993X},
support = {31872444//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Pulmonary arterial hypertension (PAH) is a progressive and fatal cardiopulmonary disorder, with growing evidence implicating proinflammatory gut dysbiosis in its pathogenesis. Fast growing broiler chickens (Gallus gallus) spontaneously develop PAH with histopathological features that closely resemble those of the human disease, providing a robust translational model. METHODS: Gut microbiota composition in PAH-afflicted broilers was compared to that of healthy controls to identify disease-associated microbial alterations. Microbiota depletion was achieved using a broad-spectrum antibiotic cocktail, and oral supplementation with calcium acetate, a short-chain fatty acid (SCFA) salt, was administered to assess therapeutic potential. Pulmonary cytokine expression was measured to evaluate inflammation. RESULTS: PAH-afflicted broilers exhibited gut microbial alterations similar to those observed in human patients, characterized by a reduction in bacterial genera involved in the production of anti-inflammatory metabolites, particularly SCFAs, and an increase in arginine- and tryptophan-producing taxa. Microbiota depletion selectively enriched SCFA-producing bacteria and prevented the onset of PAH. Calcium acetate supplementation significantly mitigated disease progression and reduced pulmonary expression of proinflammatory cytokines. CONCLUSIONS: These findings establish a causal relationship between microbiome-derived metabolites and pulmonary vascular remodeling, supporting SCFA-based interventions as a promising therapeutic strategy for PAH.},
}

@article {pmid41885972,
year = {2026},
author = {Peng, B and Feng, Q and Wang, S and Zhao, X and Sheng, T and Wang, S and Liu, W and Liu, W and Huang, W and Meng, S and Zeng, S and Lin, R},
title = {Salivary microbiota composition and caries status in children with hearing impairment: a cross-sectional comparative study.},
journal = {Clinical oral investigations},
volume = {30},
number = {4},
pages = {},
pmid = {41885972},
issn = {1436-3771},
support = {201904010085//the Science and Technology Planning Project of Guangzhou/ ; 2025-2027-12//the Key Project of Medicine Discipline of Guangzhou/ ; },
abstract = {OBJECTIVES: To characterize the salivary microbiota structure in children with hearing impairment using 16 S rRNA gene sequencing and explore its potential association with caries burden. METHODS: A total of 114 hearing-impaired children aged 6–16 years underwent oral clinical examination and completed a questionnaire. From this cohort, 20 children (HI group) and 20 age- and sex-matched healthy children (HS group) were randomly selected for salivary microbiome sequencing. Analyses included alpha and beta diversity, LEfSe, and caries-stratified subgroup comparisons. RESULTS: Hearing-impaired children carried a heavy caries burden (overall prevalence: 93.9%; mean DMFT/dmft: 6.4 ± 3.9). Oral hygiene practices were generally suboptimal, with only 54.5% brushing twice daily and 41.6% using fluoride toothpaste. Beta diversity analysis significantly differed between groups (ANOSIM, R[2] = 0.057, P < 0.05). The HI group exhibited trends of increased Proteobacteria, Neisseria, and Gemella and decreased Veillonella and Capnocytophaga (all P > 0.05). LEFSe analysis revealed richer signature taxa in controls (e.g., Selenomonas, Tannerella), whereas hearing-impaired children showed limited enriched taxa, especially in the low-caries subgroup, indicating microbiota simplification. CONCLUSIONS: The oral microbiome of hearing-impaired children displays alterations in overall community structure, characterized by reduced diversity of signature microbial taxa and a trend toward ecological simplification. CLINICAL RELEVANCE: These findings identify oral microbial trends associated with hearing impairment, providing potential insights for early caries risk assessment and tailored preventive interventions in this vulnerable population.},
}

@article {pmid41915144,
year = {2026},
author = {Liu, S and Zhang, H and Jin, C and Geng, X and Li, R and Wu, N and Wang, Y},
title = {Pediococcus pentosaceus JNL0053 Mitigates DSS-induced Colitis in Mice Via the IL-22-Gut Barrier Pathway.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41915144},
issn = {1867-1314},
support = {2023YFC2506000//National Key R&D Program of China/ ; ZR2024QH412//Natural Science Foundation of Shandong Province/ ; JNL-2023010Q//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; },
abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease that imposes a growing socioeconomic burden worldwide. Among emerging live biotherapeutics, the probiotic Pediococcus pentosaceus has shown therapeutic promise against UC, yet its molecular mode of action remains poorly understood. In this study, we isolated a novel strain P. pentosaceus JNL0053 from traditional Inner Mongolian cheese. By integrating transcriptomics, untargeted metabolomics, and 16 S rRNA gene profiling, we elucidated its protective efficacy in the dextran sulfate sodium (DSS)-induced murine colitis model. Mice receiving P. pentosaceus JNL0053 exhibited reduced body-weight loss, lower disease activity index scores and attenuated histopathological damage. This treatment reshaped the gut microbiota and was accompanied by a more balanced immune microenvironment, as evidenced by markedly decreased serum levels of pro-inflammatory cytokines interleukin (IL)-6 and IL-1β, alongside significantly elevated anti-inflammatory IL-10. N-acetylmuramate, identified as a key differential metabolite, potently promoted Th17 cell differentiation, leading to the secretion of IL-22 and IL-17 F. This, in turn, increased the expression of mucin 2 and occludin, thereby protecting the intestinal barrier against pathogens. Collectively, P. pentosaceus JNL0053 orchestrated multi-level crosstalk between host immunity and the gut microbiome to alleviate DSS-induced colitis. By activating the IL-22–MUC axis and restoring epithelial integrity, this food-derived P. pentosaceus JNL0053 represents a compelling therapeutic strategy for UC.},
}

@article {pmid41917507,
year = {2026},
author = {Suparmin, A and Cahyani, LE and Ngadiman, and Sudibyo, H and Handayani, DP and Kirana, RP},
title = {First genomic report of Enterobacter mori strain Pna8 from Pandanus conoideus with antagonistic activity against plant wilt pathogen Fusarium odoratissimum and Ralstonia solanacearum.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41917507},
issn = {1573-0972},
support = {Academic Excellence Program C of Universitas Gadjah Mada 431/UN1.P1/KPT/HUKOR/2024//Universitas Gadjah Mada/ ; },
abstract = {Plant wilt diseases are among the most destructive threats to global agriculture, largely due to the rapid adaptive capacity and treatment resistance of their causal pathogens. Endophytic bacteria represent a promising, sustainable alternative for disease management. Here, we report the first isolation and characterization of an endophytic bacterium, Enterobacter mori strain Pna8, from Pandanus conoideus, a tropical plant whose microbiome has remained unexplored. Strain Pna8 displayed strong antagonistic activity, inhibiting the fungal pathogen Fusarium odoratissimum by 55.9% and suppressing the growth of the bacterial wilt pathogen Ralstonia solanacearum, demonstrating dual biocontrol potential against both fungal and bacterial wilt diseases. Whole-genome sequencing revealed a 4.81 Mb genome comprising 4,433 coding sequences enriched in functions related to carbohydrate metabolism, phytohormone biosynthesis, phosphate solubilization, and stress tolerance. Importantly, Pna8 lacks pectinolytic CAZymes commonly associated with pathogenic E. mori, supporting its non-destructive, endophytic lifestyle. The genome also encodes unique biosynthetic gene clusters, including a lassopeptide absent from pathogenic relatives and siderophore variants related to frederiksenibactin. Comparative genomic analysis identified 119 singleton genes involved in transcriptional regulation, ion transport, and biofilm formation, indicating niche-driven evolution and ecological specialization. Collectively, these results highlight E. mori Pna8 as a novel and promising biocontrol resource for sustainable agriculture and tropical crop protection.},
}

@article {pmid41998320,
year = {2026},
author = {Chaitra, HS and Pandiyan, K and Singh, J and Kalia, VK},
title = {Influence of sex and geographical location on culturable midgut bacterial diversity of pink bollworm, Pectinophora gossypiella larvae and their enzyme production potential.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998320},
issn = {1573-0972},
abstract = {Gut microbes play a dynamic role in many metabolic and physiological activities in insects. Recent studies have shown the difference in the gut microbiota associated with both sex and geographical locations. Deciphering the gut microbiota hosted with respect to their function in an economic pest like pink bollworm, Pectinophora gossypiella, is essential to understand the relationship between insect and its gut microbiome. In the present study, culturable midgut bacteria were isolated from Bt cotton resistant P. gossypiella larvae (male and female) collected from different cotton growing regions across India. A total of 37 bacterial isolates, 21 from male and 16 from female were obtained and identified based on 16S rRNA gene sequence. All the isolates belonged to two major phyla, Proteobacteria and Firmicutes. Only three isolates, Enterococcus casseliflavus, Enterobacter hormaechei subsp. xiangfangensis and Bacillus cereus were common to both the sexes, while the rest were specific to each sex. The study also indicated a higher bacterial diversity in populations collected from two locations, Adilabad and Khandwa. All the isolates were screened for extracellular hydrolytic enzyme production, protease, amylase, cellulase, xylanase and chitinase. The results revealed that, among 37 bacterial isolates, 33, 7, 6 and 4 isolates exhibited protease, cellulase, chitinase and amylase activity, respectively. Maximum production of protease was noticed in Pantoea dispersa GM2 (0.39 ± 0.02 U/ml), amylase from B. cereus RF2 (0.17 ± 0.04 U/ml), cellulase from Burkholderia contaminans KhF1 (endoglucanase – 8.29 ± 1.60 U/ml; exoglucanase – 12.77 ± 1.5 U/ml; β-glucosidase – 10.01 ± 0.7 U/ml) and chitinase from E. hormaechei subsp. xiangfangensis AuF (87 ± 0.02 U/ml). The findings suggest that the gut bacterial community is influenced by both sex and geographical locations and the enzyme production are confined to specific locations. Further molecular studies would reveal the factors responsible for microbial community diversity and enzyme production.},
}

@article {pmid42020671,
year = {2026},
author = {Cruz, D and Saati-Santamaria, Z and Achury-Arrubla, L and Garcia-Fraile, P},
title = {From Wild to Farm: Gut Bacteriome Differences and Probiotic Potential of Pantoea Agglomerans in Two-Spotted Cricket (Gryllus Bimaculatus) Rearing.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42020671},
issn = {1867-1314},
abstract = {The gut microbiome plays a crucial role in insect nutrition and performance, yet its targeted exploitation in cricket farming remains underexplored. Here, we combined gut microbiota profiling of wild and farmed Gryllus bimaculatus with probiotic testing of host-derived bacterial isolates to explore microbiome-informed strategies for sustainable cricket farming. Wild crickets exhibited higher Shannon diversity but lower phylogenetic diversity than farmed counterparts. Wild populations were enriched in Oscillospiraceae and Christensenellaceae families, while farmed crickets showed higher abundance of Parabacteroides. From 199 bacterial isolates, wild populations showed higher frequencies of uricolytic capabilities (44% vs. 31%), related to nitrogen recycling, while farmed crickets had more pectinolytic isolates (70% vs. 50%), linked to plant fiber degradation. Pantoea agglomerans I53BLB, which demonstrated broad enzymatic capabilities, was selected for probiotic evaluation; we further provide its genome sequence and analysis to contextualize its metabolic and probiotic potential. A feeding experiment with a 2 × 3 factorial design (two diets × three probiotic treatments, n = 10 replicates per group) compared control chicken feed versus a high-fiber diet formulated with agricultural by-products, each supplemented with water, live or heat-inactivated P. agglomerans. A significant diet × probiotic interaction was observed for weight gain (χ[2] = 18.8, p = 0.0021) and adult emergence (χ[2] = 17.7, p = 0.0033). Live P. agglomerans enhanced performance only when combined with the high-fiber diet, with individuals reaching a mean wet weight of 0.602 g compared to 0.451 g (heat-inactivated, p = 0.035) and 0.427 g (water control, p = 0.003), and a significantly higher adult emergence rate (37%) compared to all other treatment combinations (13%, p < 0.05), suggesting a symbiotic effect likely related with carbohydrate digestion. No effects were observed on survival or reproductive output. Notably, the high-fiber diet alone performed comparably to commercial feed, suggesting potential for sustainable cricket production using agricultural by-products. These findings demonstrate the feasibility of microbiome informed probiotic strategies to enhance cricket farming efficiency while reducing feed costs.},
}

@article {pmid42020676,
year = {2026},
author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR},
title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42020676},
issn = {1867-1314},
abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.},
}

@article {pmid42020691,
year = {2026},
author = {Vávrová, P and Janďourek, O and Coraça-Huber, DC and Spiegel, C and Nachtigal, P and Krátký, M and Konečná, K},
title = {Host soluble plasma factors increase dual-species Staphylococcus epidermidis and Candida albicans biofilm biomass without enhancing stress tolerance.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49557-1},
pmid = {42020691},
issn = {2045-2322},
support = {SVV 260 664//Univerzita Karlova v Praze, Czechia/ ; NW24-05-00539//Ministerstvo Zdravotnictví Ceské Republiky/ ; },
abstract = {Staphylococcus epidermidis (S. epidermidis) and Candida albicans (C. albicans) are common members of the human microbiome and opportunistic pathogens, forming mixed biofilms, leading to catheter-associated bloodstream infections or wound infections. They are increasingly difficult to treat, highlighting the urgent need for new antibiofilm strategies. Understanding how host environmental factors affect microbial communities is crucial for their development. Based on our previous findings, we investigated whether higher levels of host soluble factors in human plasma (HP) and freeze-thaw lysed sheep red blood cells (FT-RBC) support the formation of S. epidermidis-C. albicans dual-species biofilm and increase resilience. Tryptic soy broth, RPMI 1640, and Lubbock media with HP or FT-RBC supplementation were used for in vitro biofilm formation. Total biomass, individual microorganisms, key matrix components (carbohydrates, proteins, eDNA), and antimicrobial tolerance were evaluated. Our results showed that although higher concentrations of HP in Lubbock medium support the formation of complex dual-species biofilm biomass, this does not correlate with enhanced antimicrobial tolerance. In contrast, higher adaptive resistance was detected in less heterogeneous biofilms formed under nitrogen-limited conditions in RPMI 1640-supplemented medium. These findings indicate that biofilm resilience is not solely dependent on biomass amount and complexity, underscoring the need to better understand host-biofilm interactions.},
}

@article {pmid42020874,
year = {2026},
author = {Xia, Y and Chen, S and Deng, Z and Ye, C and Wu, H and Wang, Y and Guo, S and Guo, N and Yang, J and Tao, Z and Xiong, X and Guo, Y and Shang, Y},
title = {Soil microbial succession for forensic estimation of postmortem interval and decomposition site identification.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {42020874},
issn = {1437-1596},
support = {82402196//Natural Science Foundation of China/ ; 82572150//Natural Science Foundation of China/ ; 2024JJ6546//Natural Science Foundation of Hunan Province/ ; },
abstract = {Estimating the postmortem interval (PMI) and identifying decomposition sites are important challenges in forensic science. The soil microbiome has shown potential in both applications. This study used pig models to simulate human decomposition and analyzed soil microbial succession over both short (0–11 days) and mid-to-long-term (up to 10 months) intervals to develop a PMI estimation model, while simultaneously comparing control and decomposition soils to assist in identifying potential corpse deposition sites. We built KNN (K-nearest neighbors) models at the genus level, which achieved high performance in short-term PMI estimation. Furthermore, a Linear Discriminant Analysis (LDA) model demonstrated robust performance in long-term PMI estimation, relying primarily on animal-associated microbial genera. Additionally, the KNN machine learning model effectively distinguished soils impacted by cadavers. This study provides a promising tool for estimating PMI and identifying potential body deposition sites.},
}

@article {pmid42031861,
year = {2026},
author = {Kamyab, M and Motamedi, H},
title = {Introducing silica-solubilizing and plant growth-promoting bacteria from sugarcane as inducers of drought stress tolerance.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48745-3},
pmid = {42031861},
issn = {2045-2322},
abstract = {Today’s sugarcane cultivation is faced with abiotic stresses including drought, salinity, heat and water limitation leading to, its reduced growth, yield, and economic productivity. Given the significant role of silica in alleviating these negative effects as well as pathogens, silica solubilizing bacteria opens an eco-friendly and sustainable approach to overcome these challenges. The aim was to find native silicate solubilizing bacteria from sugarcane and assessment their plant growth-promoting potential. Extensive screening was done from five sugarcane fields and symbiont bacterial species were qualitatively and quantitatively selected with regard to silicate solubilization. The isolates were explored for plant growth-promoting traits. As a result, Pantoea ananatis ASEna, Pantoea dispersa E345Se, and Pseudomonas migulae DSb were identified as high silica solubilizers. These also exhibited antifungal activity; phosphorus and potassium solubilization; sulfur oxidation; protease and cellulose production; auxin, hydrogen cyanide, and ammonia synthesis; nitrogen fixation; tolerance to heat, salinity (10%), drought, and pH stresses. The identified genera are part of the core sugarcane microbiome, and this is for the first time that these species have been documented as possessing growth-promoting traits for sugarcane and silicate-solubilizing capabilities. Currently, sugarcane producers are seeking for solutions to mitigate biotic and abiotic stresses and enhance crop yield in sugarcane fields. The strategic selection of bacteria that not only solubilize silica but also possess growth-promoting traits and can supply other essential nutrients to stimulating plant growth through various mechanisms, can enhance the effectiveness of silicate-solubilizing bacteria and make them suitable candidates for development of biofertilizers.},
}

@article {pmid42032090,
year = {2026},
author = {Wang, R and Li, W and Yin, Y and Jiang, S and Yang, B and Yu, R},
title = {Human milk-derived Bifidobacterium longum subsp. infantis CCFM1269 alleviates food allergy by modulating gut microbiota and restoring intestinal barrier.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50287-7},
pmid = {42032090},
issn = {2045-2322},
abstract = {Food allergy (FA) is an immune-mediated disorder increasingly linked to intestinal dysbiosis and epithelial barrier dysfunction. This study evaluated the protective effects of Bifidobacterium longum subsp. infantis CCFM1269, a human milk-derived probiotic, using a β-lactoglobulin-induced FA mouse model. Oral administration of CCFM1269 significantly reduced allergic symptoms, including poor weight gain, diarrhea, and elevated allergy scores. The probiotic restored immune balance by downregulating IL-4 and IL-17 A and upregulating IL-10 and IFN-γ in both serum and jejunal tissues. It also alleviated oxidative stress by increasing superoxide dismutase activity and decreasing malondialdehyde levels. CCFM1269 enhanced intestinal barrier integrity through the upregulation of tight junction proteins Occludin, Claudin-1, and ZO-1. Microbiome analysis showed that CCFM1269 reshaped the gut microbial structure by increasing Helicobacter and reducing Alloprevotella and Bacteroides, taxa strongly associated with FA severity. Correlation analysis confirmed that these microbial changes were linked to improvements in immune and barrier function. Collectively, these findings indicate that human milk-derived CCFM1269 alleviates FA through microbiota modulation and epithelial restoration, supporting its potential as a probiotic strategy for preventing and treating FA.},
}

@article {pmid42032553,
year = {2026},
author = {Somarathna, MT and Leuke Bandara, D and Gunasekare, SKV and Nawarathna, LS and Wijetunge, S and Paranagama, MP and Gunawardhana, ND},
title = {Molecular detection of Helicobacter pylori in saliva of Sri Lankan adults with periodontitis, gastritis or both conditions.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08421-4},
pmid = {42032553},
issn = {1472-6831},
support = {Multidisciplinary Research Grant -2024 (MRG) 500//University Research Council, University of Peradeniya, Peradeniya, Sri Lanka/ ; },
abstract = {BACKGROUND: Periodontitis is an immuno-inflammatory disease affecting the tooth-supporting structures, primarily caused by dysbiosis of the oral microbiome. The involvement of one of the gastric pathogens, Helicobacter pylori, has been reported among individuals with periodontitis. However, the evidence regarding the association between oral H. pylori, periodontitis, and gastritis remains inconsistent and has not been investigated in Sri Lanka. Therefore, this study aimed to detect the oral H. pylori in a cohort of Sri Lankan adults and to evaluate its association with periodontitis and gastritis. METHODS: This cross-sectional study recruited 214 adults from two tertiary care institutes in Sri Lanka. Participants were categorized into four groups: (A) periodontitis only (n = 60), (B) gastritis only (n = 51), (C) both periodontitis and gastritis (n = 48), and (D) healthy controls without periodontitis or gastritis (n = 55). Unstimulated saliva samples were collected, DNA was extracted, and H. pylori was detected using PCR targeting the 16S rRNA gene. Positive samples were confirmed by ureA gene amplification. Detection rates were compared using Fisher’s exact test with Holm correction for multiple comparisons (p < 0.05). RESULTS: H. pylori was detected in 44 of 214 participants (20.6%; 95% CI 15.4–26.5%): periodontitis only 20.0%, gastritis only 21.6%, both conditions 31.3%, and controls 10.9%. The highest detection rate was observed in individuals with both periodontitis and gastritis (31.3%; OR 3.71, 95% CI 1.31–10.55). Although this difference did not reach statistical significance after Holm correction (adjusted p = 0.084), it represents a biologically meaningful trend warranting further investigation with larger sample sizes. No significant associations were found with age or sex (p > 0.05). CONCLUSION: H. pylori DNA is detectable in the saliva of Sri Lankan adults, with the highest detection rate observed in individuals with both periodontitis and gastritis (31.3%). This clinically relevant trend suggests that the inflamed periodontium may provide a favorable niche for the pathogen, although larger studies are needed to confirm statistical significance. This study represents the first investigation in Sri Lanka to identify the oral cavity as a potential extragastric niche for H. pylori using salivary detection. However, PCR-based detection cannot distinguish viable colonization from transient contamination. Longitudinal studies with culture-based methods and viability testing are required to clarify whether the oral cavity serves as an active reservoir for H. pylori transmission and reinfection.},
}

@article {pmid42043454,
year = {2026},
author = {Oyedokun, PA and Alade, TA and Olawale, IJ and Laoke, TS and Adeyemi, MO and Oyedokun, MD and Olaolu, OA and A S, LS and Olayemi, SB and Ndako, JA},
title = {Translating microbial dysbiosis into brain health interventions: a focus on the oral-gut-reproductive inflammatory pathways.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043454},
issn = {1432-072X},
abstract = {Alterations in the microbial communities along the oral, gut, and reproductive (OGR) axis are increasingly recognized as major contributors to systemic inflammation, endocrine dysregulation, and neuroimmune pathophysiology. Scientific evidence has demonstrated that OGR dysbiosis is associated with neuroimmune signaling potentially by the leakage of lipopolysaccharides and cytokine cascades, with associated disruption of blood-brain barrier integrity, degeneration of the neurovascular unit, dysregulation of the hypothalamic-pituitary-adrenal axis, and disruption of neurotransmitter balance via abnormal tryptophan metabolism. The mechanisms have been implicated in the development of several neuropsychiatric and neurodegenerative disorders across preclinical and human observational models. Novel microbiome-targeted approaches, including antimicrobial therapy, prebiotics, probiotics, dietary modifications, and hormone-microbiota-targeting treatment, demonstrate potential to restore microbial balance and reduce neuroinflammation, with mechanistic effects on neurotransmitter production, barrier protection, and immune tolerance. However, these effects have been demonstrated predominantly in preclinical and animal models; robust evidence from well-powered human clinical trials is currently limited. Accordingly, these approaches should be considered exploratory and hypothesis-generating rather than established clinical strategies, and their translation to patient care requires rigorous evaluation in controlled human trials. This review addresses the gap in understanding how dysbiosis in these interdependent microbial ecosystems transmits inflammatory and metabolic signals that impair neurophysiology. This review presents a translational perspective on OGR-axis modulation as a frontier for the prevention and management of brain disorders, integrating microbial, immune, endocrine, and neural perspectives. Exploring these insights would birth a paradigm shift from symptom-management-based brain health interventions to microbiota-specific interventions.},
}

@article {pmid42043591,
year = {2026},
author = {Hu, Y and Lin, H and Jiang, M and Lin, C and Li, H and Sun, J and Chen, K and Yu, Y and Liu, C},
title = {Host-derived Bacillus velezensis enhances intestinal structure, antioxidant capacity, and pathogen resistance in the American bullfrog (Aquarana catesbeiana).},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043591},
issn = {1432-072X},
support = {KB23Y1101//Application Research and Extension of Fermented Chinese Herbal Medicine in Bullfrog Farming under the 2023 Rural Revitalization Strategy/ ; },
abstract = {The development of host-derived probiotics presents a forward-looking nutritional component strategy for sustainable aquaculture. However, research on host-associated probiotics for the globally farmed American bullfrog (Aquarana catesbeiana) is limited. The research put Bacillus velezensis (BLS) isolated from bullfrog guts determine its probiotic potential. Bullfrogs were divided into two groups: one fed a control diet and the other fed a diet enriched with 1 × 10[8] CFU/g BLS for 7 weeks. BLS supplementation significantly enhanced growth performance and markedly decreased mortality after challenge with Streptococcus agalactiae. Relative to controls, the BLS cohort demonstrated heightened activity of essential antioxidant enzymes (CAT, GSH-Px, and SOD) and lower malondialdehyde levels in liver and intestinal tissues. Moreover, BLS supplementation enhanced intestinal structure, demonstrated by markedly increased villus height and goblet cell count, alongside enhanced hepatocyte arrangement and tissue integrity. Gut microbiome analysis revealed that BLS elevated the proportion of Firmicutes while decreasing the proportion of harmful genera such as Elizabethkingia. These findings suggest that the probiotic effects are mediated through the modulation of gut barrier function and microbial community. In conclusion, dietary supplementation with B. velezensis BLS enhanced growth, pathogen resistance, antioxidant capacity, and bowel health in bullfrogs through enhanced intestinal morphology and microbiome regulation. Consequently, supplementation holds significant promise as a probiotic in bullfrog farming.},
}

@article {pmid42050727,
year = {2026},
author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S},
title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00577-2},
pmid = {42050727},
issn = {2524-4671},
abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of pathogen diversity, virulence and antimicrobial resistance. Here, we evaluated Oxford Nanopore Technologies (ONT) metagenomic sequencing as a diagnostic tool for direct detection of pathogens, virulence factors and antimicrobial resistance genes (ARGs) from diarrhoeal pig faeces. RESULTS: Twenty-six diarrhoeal and six healthy pig faecal samples were analysed using culture, qPCR and ONT metagenomics with both high-output and rapid workflows. Culturing recovered 26 haemolytic E. coli and nine Clostridium perfringens isolates. PromethION metagenomics detected a significantly higher diversity of bacterial species, virulence factors and ARGs compared with GridION. Direct read mapping achieved 71–96% genome coverage for six E. coli isolates. Fourteen high- and medium-quality E. coli metagenome-assembled genomes (MAGs) were reconstructed, of which seven clustered closely with corresponding cultured isolates. All virulence factors detected in isolates were captured by metagenomics, while metagenomics identified additional fimbrial and enterotoxin genes not recovered by culture. Metagenomic ARG profiling identified resistance to 16 antibiotic classes, compared to eight classes in cultured isolates. No ESBL, carbapenemase or mcr genes were detected. CONCLUSIONS: Long-read ONT metagenomics enables culture-independent, strain-resolved characterisation of the pig gut microbiome during PWD, capturing pathogen diversity together with virulence and antimicrobial resistance profiles. This approach reveals within-sample strain heterogeneity and functional potential that are not resolved by conventional culturing, supporting its value for studying microbial ecology and dysbiosis in diseased animal microbiomes.},
}

@article {pmid42280338,
year = {2026},
author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ},
title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280338},
issn = {2072-6643},
support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; },
mesh = {Humans ; *Synbiotics/administration & dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; },
abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.

METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.

RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.

CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.},
}

Humans
*Synbiotics/administration & dosage
*Metagenomics/methods
Child, Preschool
*Autism Spectrum Disorder/microbiology/therapy
Male
Child
Female
Pilot Projects
Feces/microbiology
*Gastrointestinal Microbiome
Treatment Outcome
*Precision Medicine/methods

@article {pmid42280343,
year = {2026},
author = {Biagioli, V},
title = {Probiotics, Maternal Microbiome, and Early-Life Programming: A One Health Perspective on Perinatal and Infant Health.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280343},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/physiology ; *Infant Health ; Female ; Pregnancy ; Infant ; Infant, Newborn ; Developmental Origins of Health and Disease ; Maternal Nutritional Physiological Phenomena ; },
abstract = {In recent years, the role of the gut microbiota in regulating human health has gained increasing scientific attention, particularly during early life [...].},
}

Humans
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/physiology
*Infant Health
Female
Pregnancy
Infant
Infant, Newborn
Developmental Origins of Health and Disease
Maternal Nutritional Physiological Phenomena

@article {pmid42280356,
year = {2026},
author = {Kim, EJ and Hong, DK and Choi, ID and Shim, JJ and Lee, JH and Jung, WK},
title = {Effect of Latilactobacillus curvatus HY7601 and Lactiplantibacillus plantarum KY1032 on Serum Triglyceride Levels and the Gut-Metabolic Axis: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280356},
issn = {2072-6643},
mesh = {Humans ; Double-Blind Method ; *Triglycerides/blood ; *Probiotics/administration & dosage/therapeutic use ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; *Hypertriglyceridemia/blood/therapy/microbiology ; Adult ; Cholesterol, LDL/blood ; Biomarkers/blood ; *Lactobacillaceae ; *Lactiplantibacillus plantarum ; Overweight/blood ; },
abstract = {Background/Objectives: Hypertriglyceridemia is a critical cardiovascular risk factor, and the probiotic combination of Latilactobacillus curvatus HY7601 and Lactiplantibacillus plantarum KY1032 (HY+KY) has emerged as a potential therapeutic strategy, though clinical validation in adults with mild hypertriglyceridemia (HTG) is needed. Methods: In this randomized, double-blind, placebo-controlled, 12-week trial, a total of 100 overweight participants with mild HTG were randomized (n = 50 per group). Ultimately, 80 participants completed the study without major protocol violations and were evaluated in the Per-Protocol Set (probiotics group: n = 41; placebo group: n = 39). Primary outcomes included changes in serum lipid profiles such as triglycerides (TG) and LDL cholesterol (LDL), metabolic biomarkers, and gut microbiota composition analyzed via 16S rRNA gene sequencing. Results: HY+KY supplementation led to significant reductions in serum TG (158.61 ± 23.17 to 139.54 ± 54.31 mg/dL, p = 0.009) and LDL (129.22 ± 28.45 to 111.34 ± 21.03 mg/dL, p = 0.005) compared to baseline, while the placebo group showed no significant changes. Furthermore, the HY+KY group exhibited a significant increase in Apolipoprotein CII (ApoC2, p = 0.034) and a reduction in fasting glucose levels (p = 0.021). Microbiome analysis revealed that HY+KY significantly increased alpha diversity (Shannon index, p = 0.012) and significantly altered the microbial community structure (beta diversity, p = 0.015). Co-occurrence network analysis identified Lactiplantibacillus as a highly connected central node that is strongly associated with the favorable shifts in clinical biomarkers. Conclusions: HY+KY supplementation was associated with improved fasting TG and LDL profiles in adults with mild HTG, alongside coordinated changes in ApoC2, fasting glucose, and gut microbiota structure. These findings support the potential of probiotic supplementation as a preventive nutritional approach in borderline HTG.},
}

Humans
Double-Blind Method
*Triglycerides/blood
*Probiotics/administration & dosage/therapeutic use
Female
Male
*Gastrointestinal Microbiome
Middle Aged
*Hypertriglyceridemia/blood/therapy/microbiology
Adult
Cholesterol, LDL/blood
Biomarkers/blood
*Lactobacillaceae
*Lactiplantibacillus plantarum
Overweight/blood

@article {pmid42280361,
year = {2026},
author = {Chiesa, A and Generali, L and Butera, A and Filippini, T and Lanteri, V and Veneri, F},
title = {Oral Microbiota Characteristics in Relation to Different Dietary Patterns: A Systematic Review.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280361},
issn = {2072-6643},
mesh = {Humans ; *Microbiota/physiology ; *Mouth/microbiology ; *Diet/methods ; Diet, Mediterranean ; Oral Health ; Female ; Diet, Vegetarian ; *Feeding Behavior/physiology ; Male ; Adult ; Diet, Vegan ; },
abstract = {Background: Diet is a key modifiable factor influencing oral health and may shape the oral microbiota. While individual nutrients, especially free sugars, have been widely studied, the role of overall dietary patterns remains unclear. This systematic review aimed to evaluate the association between dietary patterns and oral microbiota in humans. Methods: PubMed/MEDLINE, Embase, and Web of Science were searched up to 18 March 2026. Studies assessing defined dietary patterns (Mediterranean, vegan, vegetarian, omnivorous) and oral microbiota using sequencing-based methods in healthy individuals were included. Due to heterogeneity in study design, dietary assessment, and microbiome analysis, a narrative synthesis was conducted. Results: Six studies (n = 448 participants) were included. Dietary patterns showed limited impact on overall microbiota structure, with no consistent changes in alpha and beta diversity. However, differences were observed at the taxonomic level. The Mediterranean diet was generally associated with a lower abundance of periodontopathogenic taxa. Plant-based and omnivorous diets showed distinct microbial profiles, particularly involving Neisseria, Haemophilus, Prevotella, and Streptococcus. Functional activity and metabolomic profiles appeared more sensitive to dietary variation than taxonomic composition alone. Conclusions: The oral microbiota appears relatively stable across dietary patterns, although diet may influence specific taxa and functional pathways relevant to oral health. The Mediterranean diet shows the most consistent association with beneficial microbial shifts. However, evidence is limited by heterogeneity and cross-sectional designs, highlighting the need for longitudinal and interventional studies.},
}

Humans
*Microbiota/physiology
*Mouth/microbiology
*Diet/methods
Diet, Mediterranean
Oral Health
Female
Diet, Vegetarian
*Feeding Behavior/physiology
Male
Adult
Diet, Vegan

@article {pmid42280378,
year = {2026},
author = {Cabri, G and Bhatti, SFM and Hemeryck, LY and Boon, P and Volk, HA and Hesta, M and Verdoodt, F},
title = {Canine Idiopathic Epilepsy as a Natural Animal Model for Human Epilepsy: A Scoping Review Highlighting Metabolic Perspectives Beyond the Brain.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280378},
issn = {2072-6643},
support = {1297623N//Research Foundation - Flanders/ ; },
mesh = {Animals ; Dogs ; Humans ; *Disease Models, Animal ; *Epilepsy/metabolism/veterinary ; *Dog Diseases/metabolism ; Brain/metabolism ; },
abstract = {Background: Emerging evidence indicates that epilepsy extends beyond the brain, involving systemic metabolic, immune, and microbiome perturbations that shape neuronal excitability and treatment response. Canine idiopathic epilepsy (CE) offers a naturally occurring model with strong electrophysiological, pharmacological, and clinical homology to human epilepsies. Methods: This scoping review was conducted according to the PRISMA-ScR guidelines. A systematic literature search was performed in Web of Science and MEDLINE (PubMed) to identify original studies reporting metabolic, immunometabolic, or neurochemical alterations in CE compared with healthy controls. Eligible studies included peer-reviewed original research involving client-owned dogs diagnosed with CE according to international consensus criteria (IVETF guidelines). Studies focusing exclusively on genetics or neuroimaging without metabolic outcomes were excluded. Titles, abstracts, and full texts were screened for eligibility, and data were extracted from included studies using a standardized approach. Identified metabolic domains were synthesized narratively and grouped into functional systems, including amino acid and lipid metabolism, micronutrients, neurotransmission, oxidative stress, inflammation and immunology, endocannabinoid signalling, microRNAs, and gut-brain axis-related pathways. In a second step, the identified metabolic domains were evaluated for translational relevance through a targeted, non-systematic narrative synthesis of the human epilepsy literature. This approach aimed to assess cross-species parallels and to provide a conceptual framework to guide future research, rather than to perform a comprehensive systematic review of metabolic alterations in human epilepsy. Results: Across CE studies, consistent alterations were observed in multiple interconnected functional systems, including metabolic, immune, and gut-brain axis pathways, in agreement with findings reported for human epilepsy. These data support a model of epileptogenesis involving systemic dysfunction beyond the central nervous system. Translationally, these findings suggest opportunities for biomarker development, patient stratification, and mechanism-based interventions, including dietary and metabolic approaches (e.g., medium-chain triglyceride supplementation), microbiome modulation, and immunometabolic targeting. The current evidence is limited by small and heterogeneous cohorts, potential confounding effects of antiseizure medications, variability in dietary and fasting conditions, breed-related effects, and a predominance of associative over causal relationships. Conclusions: This review positions CE as a reference framework for future research into epilepsy metabolism, integrating current evidence and its translational relevance to human disease. The findings support a shift toward a systems-level view of epileptogenesis, involving interconnected metabolic, immune, and gut-brain axis pathways beyond the brain. CE represents a valuable translational model to identify shared mechanisms, inform biomarker discovery, and guide the development of mechanism-based therapeutic strategies across veterinary and human epilepsy.},
}

Animals
Dogs
Humans
*Disease Models, Animal
*Epilepsy/metabolism/veterinary
*Dog Diseases/metabolism
Brain/metabolism

@article {pmid42280379,
year = {2026},
author = {Xie, A and Yuan, L and Yang, B},
title = {Immune Responses Against Allergic Asthma Following Intervention with Lacticaseibacillus paracasei DMLA16017 and Vitamin D in Rats.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280379},
issn = {2072-6643},
mesh = {Animals ; *Asthma/immunology/therapy ; *Vitamin D/pharmacology/administration & dosage ; Rats ; Cytokines/blood ; Disease Models, Animal ; Male ; Gastrointestinal Microbiome/drug effects ; Lung/pathology/immunology ; Ovalbumin ; Immunoglobulin E/blood ; Rats, Sprague-Dawley ; },
abstract = {OBJECTIVES: Allergic asthma (AA) is an increasing public health concern. The aim of this study was to investigate the potential effects of immune responses against AA in rats following intervention with Lacticaseibacillus paracasei DMLA16017 and vitamin D (VD).

METHODS: L. paracasei DMLA16017 was identified using 16S rDNA sequencing, while a rat model of AA was established via ovalbumin (OVA) induction. Subsequently, samples were collected for biomarker analysis in peripheral blood and lung tissue (including serum OVA-immunoglobulin E (IgE) and cytokines) using enzyme-linked immunosorbent assays and assessment of the composition of the intestinal microbiota and species diversity using 16S rRNA sequencing.

RESULTS: In the rat model, OVA-induced sensitization induced significant physiological alterations, including pulmonary tissue damage, elevated white cell counts, increased serum levels of OVA-IgE and cytokines interleukin (IL)-4 and IL-17, and reduced levels of IFN-γ and TGF-β. These changes were accompanied by dysbiosis of the gut microbiota and decreased species diversity. Co-administration of VD and DMLA16017 effectively ameliorated the physiological disturbances and histopathological abnormalities in rats with AA, restored the balance between cellular and immune responses, and improved the composition of the gut microbiota and species diversity.

CONCLUSIONS: Combined intervention with VD and DMLA16017 can be used to treat AA disorders, with potential long-term modulation of the immune system.},
}

Animals
*Asthma/immunology/therapy
*Vitamin D/pharmacology/administration & dosage
Rats
Cytokines/blood
Disease Models, Animal
Male
Gastrointestinal Microbiome/drug effects
Lung/pathology/immunology
Ovalbumin
Immunoglobulin E/blood
Rats, Sprague-Dawley

@article {pmid42280407,
year = {2026},
author = {Acierno, C and Caturano, A and Barletta, F and Rinaldi, L and Sasso, FC and Adinolfi, LE and Nevola, R},
title = {Nutritional Interventions Targeting the Gut Microbiome in MASLD: From Prebiotics and Probiotics to Postbiotics and Fecal Microbiota Transplantation.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280407},
issn = {2072-6643},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Fecal Microbiota Transplantation ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome ; *Fatty Liver/therapy/microbiology ; Synbiotics/administration & dosage ; Dysbiosis ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a highly prevalent liver-centred manifestation of systemic metabolic dysfunction. The gut-liver axis provides a biologically credible therapeutic rationale because intestinal dysbiosis, impaired barrier integrity, microbial metabolites, bile acid signalling, short-chain fatty acids, and trimethylamine N-oxide may influence hepatic steatosis, inflammation, and fibrogenesis. This narrative review critically evaluates dietary patterns, prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation (FMT) as microbiome-directed strategies in MASLD. The comparative framework prioritises disease-specific human evidence, clinically meaningful endpoints, trial duration and sample size, reproducibility, safety, and feasibility. Dietary optimisation remains the most clinically grounded intervention, whereas probiotics and synbiotics show modest and heterogeneous signals on biochemical or metabolic surrogate endpoints. Prebiotics are mechanistically coherent but supported by limited liver-centred trials. Postbiotics and microbiome-mediated bioactives remain early-stage and require stricter definitional boundaries. FMT is investigational and should not be extrapolated from its established role in recurrent Clostridioides difficile infection. Most available evidence across all intervention categories relies principally on surrogate endpoints-including aminotransferases, insulin resistance indices, lipid parameters, and microbiome compositional shifts-rather than on validated liver-centred outcomes such as histological improvement or quantitative liver fat assessment; this constrains the strength of conclusions that can currently be drawn. Across all categories, microbiome modulation does not by itself establish liver disease modification, and no microbiome-targeted nutritional intervention has yet demonstrated histological benefit in MASLD. Future trials in this field should prioritise validated hepatic endpoints, phenotype-stratified patient enrolment, adequate follow-up duration, and direct comparisons between intervention categories to determine which microbiome-directed strategies, if any, deliver measurable and reproducible hepatic benefit beyond surrogate markers.},
}

Humans
*Prebiotics/administration & dosage
*Fecal Microbiota Transplantation
*Probiotics/administration & dosage
*Gastrointestinal Microbiome
*Fatty Liver/therapy/microbiology
Synbiotics/administration & dosage
Dysbiosis

@article {pmid42280409,
year = {2026},
author = {Ostrowska, M and Komoń-Janczara, E and Mikołuć, B and Iłowiecka, K and Jarczak, J and Zagórska, J and Zambrzycka, P and Turroni, S and Szczerba, H},
title = {Oral Mycobiome Alterations in Children with Phenylketonuria: Associations with Dietary Intake and Metabolic Context-A Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280409},
issn = {2072-6643},
support = {2022/06/X/NZ9/00519//National Science Centre/ ; },
mesh = {Humans ; *Phenylketonurias/microbiology/metabolism ; Pilot Projects ; Male ; Female ; Child ; *Diet ; *Saliva/microbiology ; *Mycobiome ; Child, Preschool ; Case-Control Studies ; *Mouth/microbiology ; *Fungi/classification ; },
abstract = {BACKGROUND: Phenylketonuria (PKU) is a metabolic disorder requiring a strict low-phenylalanine diet. Oral health impairment, including bacteriome dysbiosis, is common in PKU, yet the mycobiome remains poorly defined. This pilot study aimed to characterise the salivary oral mycobiome of children with PKU compared with controls and to explore associations with dietary intake.

METHODS: Saliva samples from 18 children, including 8 patients with PKU and 10 age-matched controls, were profiled using internal transcribed spacer (ITS) amplicon sequencing. Alpha/beta diversity, taxonomic composition, diet-fungi correlations, discriminative taxa and LEfSe were analysed.

RESULTS: Alpha diversity did not differ significantly between groups after correction for multiple comparisons, although exploratory subgroup analyses suggested lower evenness in PKU children aged <10 years compared with older controls. Beta diversity differed by diagnosis (PERMANOVA: F = 1.7251, p = 0.0062) and in the age-diagnosis model (F = 1.8502, p = 0.0004). Taxonomic analyses identified nominal differences in several fungal taxa, including Candida (p = 0.011), Saccharomycetales_fam_Incertae_sedis (p = 0.011), Naganishia (p = 0.020), and Aspergillaceae (p = 0.036) in PKU samples; however, these findings should be interpreted as exploratory because many did not remain significant after FDR correction. Diet-mycobiome analyses identified selected FDR-supported associations, including an inverse relationship between phenylalanine intake and Naganishia in PKU.

CONCLUSIONS: This pilot study suggests preliminary compositional differences in the oral mycobiome of children with PKU that may be related to dietary therapy and metabolic context. These exploratory findings require validation in larger cohorts with detailed oral health assessment and control of confounders.},
}

Humans
*Phenylketonurias/microbiology/metabolism
Pilot Projects
Male
Female
Child
*Diet
*Saliva/microbiology
*Mycobiome
Child, Preschool
Case-Control Studies
*Mouth/microbiology
*Fungi/classification

@article {pmid42280416,
year = {2026},
author = {Kim, J and Lee, J},
title = {Nutritional Regulation of Ovarian Bioenergetics: Implications for Reproductive Aging and Female Infertility.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280416},
issn = {2072-6643},
support = {RS-2025-00513071//National Research Foundation of Korea/ ; },
mesh = {Female ; Humans ; *Energy Metabolism/physiology ; *Infertility, Female/metabolism/physiopathology ; *Aging/metabolism/physiology ; *Ovary/metabolism ; Animals ; *Reproduction/physiology ; Mitochondria/metabolism ; },
abstract = {Ovarian function is critically dependent on tightly coordinated cellular energy metabolism, which governs follicular development, oocyte competence, and reproductive longevity. Increasing evidence indicates that metabolic dysregulation, including mitochondrial dysfunction, oxidative imbalance, and impaired NAD[+] metabolism, contributes to the pathophysiology of major ovarian disorders such as PCOS, ovarian aging, and DOR. In parallel, emerging studies suggest that nutritional factors influence ovarian function by modulating mitochondrial bioenergetics, redox homeostasis, and nutrient-sensing signaling pathways. This review summarizes current knowledge on the molecular basis of ovarian energy metabolism and its disruption in female reproductive disorders. We further discuss nutritional strategies targeting ovarian bioenergetics, including antioxidants, NAD[+] precursors, mitochondrial cofactors, and dietary metabolic interventions. In addition, we highlight recent advances in metabolomics, microbiome research, epigenomics, and multi-omics integration that are shaping emerging nutrition-based approaches in reproductive medicine. Collectively, positioning ovarian metabolism at the center of nutritional reproductive research may provide a conceptual framework for understanding metabolic regulation in ovarian function and for guiding future research on reproductive health.},
}

Female
Humans
*Energy Metabolism/physiology
*Infertility, Female/metabolism/physiopathology
*Aging/metabolism/physiology
*Ovary/metabolism
Animals
*Reproduction/physiology
Mitochondria/metabolism

@article {pmid42280426,
year = {2026},
author = {Arshad, F and Akbar, A and Chinnappan, R and Khan, MI and Yaqinuddin, A and Arora, I},
title = {Dietary Polyphenols and Selected Nutraceuticals in Hepatocellular Carcinoma: Mechanistic Insights, Translational Evidence, and Clinical Prospects.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280426},
issn = {2072-6643},
mesh = {Humans ; *Dietary Supplements ; *Liver Neoplasms/prevention & control ; *Carcinoma, Hepatocellular/prevention & control ; *Polyphenols/pharmacology/administration & dosage ; Animals ; Signal Transduction/drug effects ; Diet ; },
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) develops predominantly from chronic liver injury, with diet representing a clinically actionable yet mechanistically complex modulator of hepatic carcinogenesis. Despite advances in immunotherapy, long-term survival remains poor, underscoring the need for complementary preventive and adjunctive strategies.

METHODS: We conducted a narrative review of epidemiological, experimental, and clinical literature on dietary patterns, polyphenols, and non-polyphenol nutraceuticals for HCC prevention and management, with a focus on underlying molecular and cellular mechanisms.

RESULTS: Dietary polyphenols and selected nutraceuticals exert pleiotropic effects on signaling pathways implicated in HCC, including NF-κB, STAT3, TGF-β/SMAD, PI3K/AKT, and Wnt/β-catenin, while modulating hepatic stellate cell activation, immune cell polarization, and microbiome-derived metabolites. Preclinical studies suggest that some compounds may enhance antitumor immunity and sensitize tumors to systemic therapies; however, clinical translation is constrained by limited bioavailability, pharmacokinetic variability, formulation heterogeneity, and a lack of high-quality trials.

CONCLUSIONS: This review highlights the potential of dietary patterns and nutraceuticals in HCC prevention and as adjunctive therapies. It outlines key translational priorities, including etiologic stratification, biomarker-driven trial design, and rigorous safety evaluation.},
}

Humans
*Dietary Supplements
*Liver Neoplasms/prevention & control
*Carcinoma, Hepatocellular/prevention & control
*Polyphenols/pharmacology/administration & dosage
Animals
Signal Transduction/drug effects
Diet

@article {pmid42280436,
year = {2026},
author = {Hwang, JH and Choi, YK},
title = {Effects of Herbal and Natural Product Interventions on Gut Microbiota and Clinical Outcomes in Patients Receiving PPI-Containing Therapy: A Systematic Review and Meta-Analysis.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280436},
issn = {2072-6643},
support = {NRF-2022R1A2C1013518//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Proton Pump Inhibitors/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Biological Products/pharmacology/therapeutic use ; Helicobacter Infections/drug therapy/microbiology ; Treatment Outcome ; *Plant Preparations/pharmacology ; Helicobacter pylori/drug effects ; Female ; *Phytotherapy ; Male ; Middle Aged ; },
abstract = {Proton pump inhibitor (PPI)-containing regimens, including bismuth quadruple therapy, may perturb gut microbiota through combined exposure to acid suppression, antibiotics, bismuth, and underlying disease context. Herbal medicines and natural products have been proposed as adjunctive interventions to mitigate treatment-related microbiota perturbations; however, systematic synthesis of the clinical evidence remains limited. This systematic review and meta-analysis evaluated the effects of herbal and natural product interventions on gut microbiota and clinical outcomes in patients receiving PPI-containing therapy. Six databases (PubMed, EMBASE, Web of Science, Scopus, CENTRAL, and CNKI) were searched from their inception to March 2026. Risk of bias was assessed using RoB 2.0 and ROBINS-I. This review was prospectively registered in PROSPERO (CRD420261346672). Eighteen studies (17 randomized controlled trials, 1 observational study; n = 1984 participants) were included in the final analysis. Meta-analysis demonstrated significantly higher Helicobacter pylori eradication rates (pooled relative risk (RR) = 1.20, 95% confidence interval (CI) 1.14-1.27; I[2] = 33%). Chinese-style total effective rate was also higher in the herbal groups (RR = 1.19, 95% CI 1.14-1.25; I[2] = 0%), but this non-standardized outcome should be interpreted cautiously. Exploratory microbiome meta-analyses suggested higher post-treatment Bifidobacterium and Lactobacillus levels; however, substantial heterogeneity limited interpretability. Narrative synthesis revealed potential preservation of α-diversity and attenuation of pathobiont proliferation in herbal groups. Overall, herbal and natural product interventions may be associated with favorable clinical outcomes and potential microbiota-modulating effects in patients receiving PPI-containing therapy, but certainty remains limited due to methodological concerns, outcome indirectness, and heterogeneity. High-quality trials stratified by antibiotic exposure are warranted.},
}

Humans
*Proton Pump Inhibitors/adverse effects/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Biological Products/pharmacology/therapeutic use
Helicobacter Infections/drug therapy/microbiology
Treatment Outcome
*Plant Preparations/pharmacology
Helicobacter pylori/drug effects
Female
*Phytotherapy
Male
Middle Aged

@article {pmid42280437,
year = {2026},
author = {Samiksha, F and Singh, D and Harbool, SS and Di Martino, L and Kruithoff, C and S McCormick, T and Ghannoum, M},
title = {Fungal β-1,3-glucans: Cell Wall Constituents That Promote Gut Health Through Innate Immune Modulation.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280437},
issn = {2072-6643},
mesh = {Humans ; *beta-Glucans/pharmacology/immunology ; *Immunity, Innate/drug effects ; *Cell Wall/chemistry/immunology ; Animals ; *Gastrointestinal Microbiome/drug effects/immunology ; *Fungi/chemistry ; Innate Immunity Recognition ; Prebiotics ; Intestinal Barrier Function ; },
abstract = {Fungal β-1,3-glucans are structurally conserved polysaccharide components of the fungal cell wall that exhibit potent immunomodulatory activity. These molecules are recognized by pattern recognition receptors, Toll-like receptors, complement receptor 3, lactosylceramide, scavenger receptors, and EphA2. Binding of β-1,3-glucans through these receptors triggers coordinated innate and adaptive immune responses such as cytokine production, phagocytosis, and trained immunity. In addition to receptor-mediated immune activation, dietary β-1,3-glucans function as fermentable prebiotic fibers that modulate gut microbiota composition, increase short-chain fatty acid production, and strengthen epithelial barrier integrity. These combined immunological and microbiome-mediated effects position β-1,3-glucans as key regulators of gut homeostasis. Preclinical and emerging clinical evidence supports broad therapeutic potential across multiple disease domains, including inflammatory bowel disease, metabolic disorders, respiratory infections, and cancer. In oncology, β-1,3-glucans enhance anti-tumor immunity, improve responses to monoclonal antibodies and chemotherapy, and serve as promising adjuvants in vaccine-based strategies. Additionally, β-1,3-glucan is widely used as a biomarker for invasive fungal infections and represents a validated target of antifungal therapies such as echinocandins. Despite these advances, clinical translation remains limited by heterogeneity in glucan source, structure, and formulation, as well as a lack of appropriately powered, standardized human clinical trials. Future efforts should focus on clarifying mechanisms of action, as well as rigorous clinical evaluation, to fully define the therapeutic utility of fungal β-1,3-glucans.},
}

Humans
*beta-Glucans/pharmacology/immunology
*Immunity, Innate/drug effects
*Cell Wall/chemistry/immunology
Animals
*Gastrointestinal Microbiome/drug effects/immunology
*Fungi/chemistry
Innate Immunity Recognition
Prebiotics
Intestinal Barrier Function

@article {pmid42280469,
year = {2026},
author = {Ang, MY and Choo, SW},
title = {The Nutri-Exposome Intelligence Framework: Integrating Multi-Omics, Machine Learning, and Digital Nutrition for Precision Chronic Disease Prevention.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280469},
issn = {2072-6643},
support = {Reference Number: 5000105//High-Level Talent Recruitment Program for Academic and Research Platform Construction/ ; Grant Number: KY20250604000448//IFIRI Talents Program/ ; },
mesh = {Humans ; Multiomics ; *Machine Learning ; Chronic Disease/prevention & control ; *Precision Medicine/methods ; Digital Health ; *Exposome ; Nutrigenomics/methods ; Data Analytics ; Diet ; },
abstract = {Background/Objectives: Precision nutrition is moving beyond population-based guidance and isolated gene-diet interactions toward integrative models of dietary response. However, current approaches remain fragmented across nutrigenomics, microbiome research, multi-omics profiling, digital health, and machine learning. This review proposes the Nutri-Exposome Intelligence Framework as a conceptual, data science-driven model for integrating cumulative dietary, environmental, microbial, molecular, clinical, and digital exposures for precision chronic disease prevention. Methods: This conceptual review synthesizes the literature on precision nutrition, nutrigenetics, nutrigenomics, exposomics, gut microbiome research, multi-omics integration, wearable and biomarker-based monitoring, and machine learning in nutrition studies. Evidence was organized into a framework linking exposure assessment, host susceptibility, microbiome-mediated biotransformation, molecular response profiling, computational modelling, personalized intervention, and longitudinal feedback. Results: The proposed framework consists of seven interconnected layers: diet, environment, and lifestyle exposures; host genome and microbiome; multi-omics molecular responses; machine learning-based integration; risk prediction and responder stratification; personalized dietary intervention; and wearable and biomarker-based feedback. It positions the nutri-exposome as a cumulative exposure-response system and highlights how machine learning can support data harmonization, feature engineering, predictive modelling, responder classification, explainable interpretation, and adaptive refinement of dietary recommendations. Key applications include obesity, type 2 diabetes, cardiovascular disease, metabolic dysfunction-associated steatotic liver disease, cardiovascular-kidney-metabolic syndrome, and broader cardiometabolic prevention. Conclusions: Nutri-exposome intelligence offers a structured pathway for transforming complex nutrition data into predictive, explainable, and adaptive precision nutrition strategies. Implementation will require longitudinal and multi-ethnic cohorts, standardized metadata, causal validation, interpretable machine learning, ethical governance, and equitable access to support responsible clinical and public health translation globally.},
}

Humans
Multiomics
*Machine Learning
Chronic Disease/prevention & control
*Precision Medicine/methods
Digital Health
*Exposome
Nutrigenomics/methods
Data Analytics
Diet

@article {pmid42280542,
year = {2026},
author = {Zhou, T and He, Y and Liew, A and Wang, M and Cheong, KL},
title = {Polysaccharides from the Peel of Hylocereus undatus Promote Wound Healing by Reshaping the Skin Microbiome and Regulating Immune Balance.},
journal = {Polymers},
volume = {18},
number = {11},
pages = {},
pmid = {42280542},
issn = {2073-4360},
support = {2025A1515010078//Natural Science Foundation of Guangdong Province/ ; 2024ZDZX2084//Key Research Project of High Education of Guangdong Province/ ; },
abstract = {Polysaccharides isolated from the peel of Hylocereus undatus exhibit promising anti-inflammatory activity; however, the underlying mechanisms-particularly their modulatory effects on cutaneous microbiota composition and host immune responses-remain incompletely characterized. This study investigates the therapeutic potential of polysaccharides isolated from the peel of Hylocereus undatus in the management of inflammatory cutaneous wounds. The polysaccharide extracted from the peel of Hylocereus undatus via ultrasound-assisted extraction is an acidic heteropolysaccharide, with galacturonic acid and rhamnose as its dominant monosaccharide components. It exhibits low crystallinity, a porous structure, and good thermal stability. In a mouse wound model, treatment with the polysaccharide extracted from the peel of Hylocereus undatus significantly accelerated wound closure as early as day 3 (** p < 0.01). By day 9, the wound closure rate approached that of the positive control group and remained significantly higher than that of the untreated group (** p < 0.01), exceeding 90%. Treatment with the polysaccharide advanced the inflammatory peak, as evidenced by elevated anti-inflammatory cytokines (IL-10 and TGF-β) and suppression of the pro-inflammatory cytokine IL-6. Immunofluorescence staining confirmed that polysaccharide promoted cell proliferation and neovascularization at the wound site. In conclusion, polysaccharides isolated from the peel of Hylocereus undatus accelerate skin wound healing by modulating the skin microbiota, enhancing the anti-inflammatory response, and promoting tissue regeneration, highlighting its potential as a natural wound dressing.},
}

@article {pmid42280664,
year = {2026},
author = {Hashemi, SM and Graeff, M and Nai, EA and Savidov, N},
title = {Cultivation System Dominates Cucumber Performance and Root-Zone Microbiomes Across Biochar Particle Sizes.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280664},
issn = {2223-7747},
abstract = {Hydroponic (HP) and aquaponic (AQ) systems are widely known in greenhouse production; however, the combined effects of nutrient delivery system and substrate physical structure on crop performance and root-zone microbiomes remain insufficiently understood. Substrate physical properties influence water retention and aeration, which can affect root-associated microorganisms, plant growth, and yield. This study evaluated cucumber (Cucumis sativus L.) growth, yield, nutrient dynamics, physiological stress responses, and bacterial community composition under HP and AQ systems using bamboo-derived biochar substrates and coconut coir as a control. Vegetative growth was enhanced under AQ, with the greatest plant elongation (1102 ± 40.1 cm) and stem diameter (15.1 ± 1.0 mm) observed in biochar-grown plants. Total yield was consistently higher under AQ than HP, with the highest yield recorded in the coarse biochar treatment (28.6 kg m[-2]). Aquaponic systems were associated with greater nutrient availability under the conditions evaluated during mid to late season production, including nitrate concentrations of up to 226 mg L[-1]. Physiological stress monitoring indicated lower stress exposure under aquaponic conditions in plants grown in medium and coarse biochar substrates across both systems, with 78 to 81% of the growing season classified within low to balanced stress conditions. Bacterial community composition was primarily shaped by cultivation system, which explained 19.3% of the observed variation, whereas substrate treatment did not significantly alter overall bacterial community structure. Overall, cultivation system was the dominant factor associated with variation in cucumber performance and root-zone bacterial communities, while biochar substrates supported improved plant growth, yield, and reduced physiological stress.},
}

@article {pmid42280669,
year = {2026},
author = {Zhang, L and Dong, J and Zhao, J and Jiang, H and Zhang, W},
title = {Rhizosphere Functional Plasticity and the Keystone Taxon Sphingomonas Facilitate Sweet Cherry Adaptation to Semi-Arid Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280669},
issn = {2223-7747},
support = {2023LHMS03007//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; },
abstract = {Translocation of elite cultivars across distinct climatic regions often induces transplantation shock. Although the rhizosphere microbiome can facilitate host acclimation, the underlying functional mechanisms remain unclear. Here, we investigated microbiome-mediated adaptation in "Hongdeng" sweet cherry (Prunus avium L.) moved from a humid coastal region (Dalian, DL) to a semi-arid inland habitat (Hohhot, HS). We integrated plant physiological assays, metagenomic sequencing, and structural equation modeling (SEM) to compare the source population (DL), the introduced population (HS), and a locally acclimated reference cultivar ("Summit", HSY). The introduced trees adjusted physiologically to the semi-arid environment by elevating proline levels and antioxidant enzyme activities. Although environmental stress reduced microbial alpha diversity, the core taxonomic framework persisted. Community assembly analysis indicated that the semi-arid climate intensified environmental filtering. Network analysis identified Sphingomonas as a keystone taxon; notably, it maintained a highly connected topological role despite a stable relative abundance. Furthermore, structural equation modeling showed that the environmental stress index positively correlated with the upregulation of microbial DNA repair pathways (R = 0.81, p < 0.001). Ultimately, the SEM demonstrated that environmental stress primarily shapes microbial functional profiles rather than driving species turnover, thereby contributing to host adaptation. The successful establishment of introduced sweet cherry in semi-arid regions is tied more closely to rhizosphere functional plasticity than to taxonomic restructuring. These findings highlight the role of the keystone taxon Sphingomonas in maintaining rhizosphere homeostasis, offering a theoretical framework for targeted microbiome engineering to mitigate transplant shock and enhance crop resilience.},
}

@article {pmid42280740,
year = {2026},
author = {Ding, Y and Zhao, Y and Xie, Y and Sun, C and Yang, L and Sun, Z and Yang, L and Wang, Y and Zhang, J and Han, Z},
title = {Aspergillus neoalliaceus MR-86 Promotes the Growth of Saposhnikovia divaricata by Regulating the Rhizosphere Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280740},
issn = {2223-7747},
support = {20260204099YY, 20260204045YY//Jilin Province Science and Technology Department/ ; JLAUHLRG20102006//Jilin Agricultural University high-level researcher grant/ ; D23007//The 111 Project, Northeast Advantageous Characteristic Resources and Health Food Discipline Innovation Introduction Base/ ; },
abstract = {Plant growth-promoting fungi (PGPF) have shown broad potential to improve soil conditions and enhance root growth and development. However, few studies have examined the effects of exogenous PGPF inoculation on the growth of the medicinal plant Saposhnikovia divaricata and the associated changes in the rhizosphere microbiome. In this study, Aspergillus neoalliaceus MR-86 exhibited phosphate solubilization, growth in nitrogen-free medium, potassium solubilization, IAA production, and siderophore production. PCR assays did not detect the aflatoxin biosynthesis-related genes aflR, aflS, and omtA in strain MR-86. Pot trials demonstrated that inoculation with MR-86 significantly increased the plant height and root dry weight of S. divaricata by 10.32% and 21.05%, respectively (p < 0.05). In the rhizosphere, soil pH decreased, whereas soil alkaline-hydrolyzable nitrogen and available phosphorus levels, as well as the activities of protease, urease, and cellulase, increased significantly. Illumina NovaSeq sequencing revealed that MR-86 inoculation altered the soil microbial community structure and specifically enriched several microbial taxa, including Talaromyces, Subulicystidium, and Aspergillus. Moreover, MR-86 inoculation did not alter the composition of dominant bacterial and fungal phyla, but significantly modified microbial interactions and the topology of microbial networks. Correlation analysis indicated that the specific microbial taxa Subulicystidium, Aspergillus, and Talaromyces were positively associated with soil nutrient indices, enzyme activities, and plant growth parameters. Functional prediction analysis indicated that MR-86 treatment was predicted to be enriched bacterial metabolic pathways, including flavone and flavonol biosynthesis and ether lipid metabolism, and was predicted to increase the relative abundance of functional fungal groups such as ectomycorrhizal and wood-decomposing fungi. In summary, A. neoalliaceus MR-86 may contribute to improved growth of S. divaricata by enhancing nutrient availability and transformation and by modulating the structure and function of the rhizosphere microbiome.},
}

@article {pmid42280750,
year = {2026},
author = {Liu, J and Haider, FU and Liu, Y and Zhang, P and Liu, T and Li, X and Li, S},
title = {Reframing Partial Root-Zone Irrigation: A Spatial Stress-Priming Mechanism for Crop Adaptation to Abiotic Stresses.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280750},
issn = {2223-7747},
support = {2024YFD1501500//The National Key R&D Program of China/ ; 20240101010JJ//Jilin Province Science and Technology Department/ ; },
abstract = {Abiotic stresses limit crop productivity by disrupting water relations, carbon assimilation, nutrient acquisition, membrane stability, and redox homeostasis. Partial root-zone irrigation (PRI), commonly implemented as partial root-zone drying (PRD), is often viewed as a deficit-irrigation strategy to improve water-use efficiency; however, this view underestimates the biological consequences of spatial root-zone heterogeneity. This review evaluates PRI as a spatially structured, priming-like framework for crop adaptation to abiotic stress. Available evidence indicates that localized drying and wet-side water uptake can coordinate root sensing, hydraulic-chemical signaling, abscisic acid delivery, hormone crosstalk, xylem-mediated regulation, and stomatal control. Beyond gas exchange, PRI is associated with photosynthetic maintenance, osmotic adjustment, antioxidant and redox regulation, root architectural plasticity, nutrient acquisition, and metabolic reprogramming. Evidence is strongest for drought, whereas responses to low temperature, salinity, heat-associated evaporative demand, and combined stresses remain more context-dependent. Emerging work also links PRI to rhizosphere restructuring and microbiome shifts, but the causal mechanisms and field reproducibility remain unresolved. We argue that future progress requires matched PRI-deficit-irrigation comparisons, standardized switching thresholds, shared physiological and molecular readouts across crops, high-resolution root biology, and commercially realistic field validation. This framing distinguishes conserved physiological outcomes from mechanisms that may differ among crops, genotypes, and irrigation designs.},
}

@article {pmid42280785,
year = {2026},
author = {Nunes, A and Minello, LVP and Oliveira, ER and Schneider, AR and Dutra, FS and Guizolfi, T and Santos, LRB and Gelli, VC and Granada, CE and Sperotto, RA and Moura, S and Maraschin, M and Lima, GPP},
title = {Impact of Kappaphycus alvarezii Biostimulant on Growth, Biochemistry, Essential Oil, and Rhizosphere of Basil (Ocimum basilicum) Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280785},
issn = {2223-7747},
support = {2023/03886-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 25/2551-0002537-0//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; 22/2551-0001641-3//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; 88887.696139/2022-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 405949/2022-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 306495/2023-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303956/2023-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 405779/2022-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 305135/2021-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 314977/2025-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 311719/2023-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 24/2551-0001302-4//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; 2024TR002499//Fundação de Amparo à Pesquisa e Inovação do Estado de Santa Catarina/ ; 408526/2024-6//Institutos Nacionais de Ciência e Tecnologia/ ; },
abstract = {Seaweed-derived biostimulants are a promising strategy for improving crop performance in sustainable agriculture. In this context, this study evaluated the effects of foliar application of Kappaphycus alvarezii extracts, obtained from two Brazilian regions (São Paulo: Kal-SP and Santa Catarina: Kal-SC), at different concentrations (1%, 3%, 5%, and 7%) on the growth, biochemical profile, essential oil yield, and rhizosphere microbiome of Ocimum basilicum under field conditions. Morphological analysis indicated that the 5% and 7% concentrations increased plant height, biomass, root development, and inflorescence production, with biomass gains of up to 51% and essential oil production increases of up to 142% compared to the control. Biochemical responses varied by extract origin, with Kal-SC promoting greater increases in photosynthetic pigments, antioxidant activity, and carbon-related metabolites, whereas Kal-SP induced only minor metabolic changes. The algal biostimulant modulated essential oil yield and composition, promoting treatment-dependent shifts in major terpenoid compounds. Microbiome analysis showed no significant changes in alpha diversity, but significant shifts in beta diversity and functional groups, such as Bacillaceae, indicating rhizosphere reorganization. Overall, the effectiveness of K. alvarezii-based biostimulants depends on concentration and biomass source, highlighting their potential as sustainable agricultural bioproducts and the importance of standardized extraction for consistent outcomes.},
}

@article {pmid42280795,
year = {2026},
author = {Geng, H and Xin, Y and Jin, H and Zheng, Z and Pan, T and Zeng, Z},
title = {Physiological Responses, Molecular Basis, and Integrated Regulation of Heat Tolerance in Soybean.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280795},
issn = {2223-7747},
support = {LQ24C130001//Zhejiang Provincial Natural Science Foundation/ ; CARS-04-CES33//China Agriculture Research System-Soybean/ ; 2022LFR109//Program for Research and Development of Zhejiang A&F University/ ; },
abstract = {Global warming has led to frequent occurrences of extreme heat, posing a huge threat to soybean (Glycine max L.) yield. As a major source of plant protein and oil, soybean is particularly sensitive to heat stress during its growth and development, especially in critical stages such as flowering and seed filling. Heat tolerance in crops is a complex trait governed by polygenic networks and environmental interactions; although existing studies have identified several heat-tolerance-related genes, the molecular regulatory networks regulating crop responses to heat stress remain elusive. This review synthesizes recent advances in soybean heat tolerance research, with a particular emphasis on physiological responses and molecular regulatory mechanisms under heat stress. We further evaluate the potential of modern technologies, including gene editing, marker-assisted selection, and pan-genomics, for the precise improvement of heat tolerance in soybean. Additionally, we outline sustainable agronomic practices and field management strategies to mitigate heat stress. The development of heat-tolerant soybean varieties depends not only on the identification of superior alleles but also requires a shift from gene-centric genetic improvement toward a system-wide solution that integrates "Genotype × Environment × Management".},
}

@article {pmid42281243,
year = {2026},
author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE},
title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2685381},
doi = {10.1080/19490976.2026.2685381},
pmid = {42281243},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; },
abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.},
}

Humans
*Gastrointestinal Microbiome/physiology
Multiomics
Feces/microbiology
Biomarkers/urine/blood
Female
Adult
Male
*Diet
Australia
*Bacteria/classification/genetics/isolation & purification/metabolism
Cross-Over Studies
Middle Aged
Metabolome
Metabolomics
Blood Pressure

@article {pmid42281266,
year = {2026},
author = {Hu, M and Li, Y and Zhao, L and Cha, S and Xue, Y and Han, Y and Xue, C and Dong, N},
title = {Engineered Lactococcus lactis for Oral Delivery of an Antimicrobial Peptide against Enterotoxigenic Escherichia coli in Weaned Piglets.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17784},
pmid = {42281266},
issn = {1520-5118},
abstract = {Food-grade strategies against foodborne pathogens while preserving intestinal health are gaining attention. Here, we developed a regulated delivery platform using Lactococcus lactis engineered to secrete a tandem dimeric antimicrobial peptide (SD). The engineered strain (SDLactis) exhibited stable growth, genetic stability, and tolerance to simulated gastrointestinal conditions. Chloride-responsive SD secretion enabled effective antibacterial activity against enterotoxigenic Escherichia coli (ETEC) K88 in vitro. In ETEC-challenged piglets, oral SDLactis alleviated diarrhea, improved growth, and reduced intestinal injury and inflammation. It strengthened intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Claudin-1,Occludin) and downregulating CFTR. Microbiome analysis revealed that SDLactis partially restored gut microbial diversity, reducing Escherichia-Shigella while enriching Lactobacillus and short-chain fatty acid-producing genera. Overall, food-grade engineered lactic acid bacteria serve as controllable delivery vehicles for antimicrobial peptides, offering a nonantibiotic strategy for pathogen control and gut health management in food and feed applications.},
}

@article {pmid42281376,
year = {2026},
author = {Zhang, R and Li, X and Chen, X and Shen, A and Zhang, X and Peng, C and Qiu, J},
title = {Charge-Competition AIEgens Induce Mitochondrial Dysfunction for Selective Eradication of Candida albicans while Restoring Vaginal Microbiota.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2601074},
doi = {10.4014/jmb.2601.01074},
pmid = {42281376},
issn = {1738-8872},
mesh = {Female ; *Candida albicans/drug effects ; Animals ; *Antifungal Agents/pharmacology/chemistry ; *Candidiasis, Vulvovaginal/drug therapy/microbiology ; *Vagina/microbiology ; *Mitochondria/drug effects ; Biofilms/drug effects ; Lactobacillus/drug effects/growth & development ; Mice ; *Microbiota/drug effects ; Humans ; Disease Models, Animal ; },
abstract = {The principal therapeutic challenge in vulvovaginal candidiasis (VVC) is that the non-selective nature of conventional antifungal drugs, which frequently perturb vaginal microecological homeostasis and disrupt Lactobacillus barrier, lead to the emergence of recurrent infection and drug resistance. This study aims to develop novel antifungal agents capable of efficiently and selectively eradicating pathogenic fungi while protecting and promoting the growth of Lactobacilli, with real-time monitoring capabilities and significant potential for clinical application. Harnessing the principle of charge-competition, we engineered a cationic amphiphilic aggregation-induced emission luminogens (AIEgens, named as TPE-ET), where hydrophobic chain length served as a key determinant governing membrane affinity, aggregation propensity, and antimicrobial selectivity. This design empowered potent eradication of Candida albicans (C. albicans) while concomitantly favoring the proliferation of beneficial Lactobacilli. Moreover, TPE-ET disrupted C. albicans biofilms and suppressed virulence genes related to adhesion, invasion, and drug resistance. In a murine VVC model, TPE-ET reduced fungal burden by over 90%, facilitating the repair of damaged vaginal epithelium and the reconstitution of a Lactobacillus-dominat vaginal microbiome. Remarkably, TPE-ET outperformed clotrimazole in restoring healthy microecological balance, as manifested by diminished Proteobacteria abundance alongside increased Firmicutes (notably Lactobacillus) and Bacteroidetes. Mechanistic studies revealed that TPE-ET exerted its remarkable antifungal activity by targeting the mitochondrial inner membrane, disrupting the metabolism-inflammation axis and eliciting mitochondrial dysfunction. Collectively, this dual merits of membrane charge-selective targeting and AIEgens-mediated visualization established an innovative therapeutic strategy for VVC, featuring superior efficacy, exquisite selectivity, and real-time monitoring capability with significant clinical potential.},
}

Female
*Candida albicans/drug effects
Animals
*Antifungal Agents/pharmacology/chemistry
*Candidiasis, Vulvovaginal/drug therapy/microbiology
*Vagina/microbiology
*Mitochondria/drug effects
Biofilms/drug effects
Lactobacillus/drug effects/growth & development
Mice
*Microbiota/drug effects
Humans
Disease Models, Animal

@article {pmid42281379,
year = {2026},
author = {Bae, Y and Kim, DJ and Seo, Y and Noh, Y and Lee, S and Kwon, SK},
title = {Large-Scale Microbiome Profiling of Brown Algae Identifies a Specific Vibrio aphrogenes Clade Strain That Promotes Gametophyte Settlement.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604061},
doi = {10.4014/jmb.2604.04061},
pmid = {42281379},
issn = {1738-8872},
mesh = {Biofilms/growth & development ; *Microbiota ; *Vibrio/classification/physiology/isolation & purification/genetics ; *Phaeophyceae/microbiology/physiology ; Symbiosis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {Marine macroalgae are foundation species of coastal ecosystems, maintaining close interactions with their microbiome for development and environmental adaptation. Although secure attachment to substrates is essential for both morphological development and survival, the potential causal link between microbial symbionts and this fundamental attachment process remains poorly understood. To address this gap, we integrated large-scale field sampling with functional validation to identify bacteria that influence the attachment of brown algae, specifically comparing attached and drifted individuals of Undaria pinnatifida and Ecklonia cava. Notably, Vibrio was consistently enriched in attached algae, whereas Marinomonas dominated drifted individuals. Translating these field observations into lab-scale validation, we isolated and evaluated their biofilm-formation capacity and impact on gametophyte settlement. A specific isolate belonging to the Vibrio aphrogenes clade exhibited superior biofilm formation and significantly enhanced algal abundance 2.57-fold in co-culture with U. pinnatifida gametophytes. These findings provide a scientific basis for developing bacterial inocula for seaweed seedling production and support broader macroalgae restoration strategies under changing environmental conditions.},
}

Biofilms/growth & development
*Microbiota
*Vibrio/classification/physiology/isolation & purification/genetics
*Phaeophyceae/microbiology/physiology
Symbiosis
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid42281420,
year = {2026},
author = {Góngora, E and Altshuler, I and Ellis, M and Okshevsky, M and Greer, CW and Whyte, LG},
title = {In Situ Mesocosm Experiment Shows the Capability of the Microbial Community of a Canadian High Arctic Shoreline to Degrade the New Generation of Ship Fuels.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c10583},
pmid = {42281420},
issn = {1520-5851},
abstract = {The warming effects of climate change are leading to a reduction in sea ice, which could open new shipping routes across the Arctic, leading to the possibility of hydrocarbon spills washing onto a shoreline. The behavior and biodegradability of new low-sulfur fuels (LSFs), currently being used by vessels worldwide, has not been assessed on Arctic beaches. We deployed mesocosm experiments on a remote Canadian high Arctic beach for 33 days using two LSFs (marine diesel and ultra-low-sulfur fuel oil, ULSFO) and Bunker C fuel oil (currently being phased out). Bunker C was mostly removed from beach sediments by natural attenuation (14.6% biodegradation, 62.8% nonbiological removal), while the LSFs were more easily biodegraded (37.6-72.8% biodegradation, 2.9-10.0% nonbiological removal). Native beach sediment microorganisms, including putatively novel taxa, adapted to the presence of fuel by expressing multiple aliphatic hydrocarbon biodegradation genes, but only few aromatic hydrocarbon degradation genes. Our results suggest that, while not as biodegradable as marine diesel, ULSFO appears to be a more environmentally friendly alternative to Bunker C due to its higher biodegradability under in situ Arctic environmental conditions. However, limited aromatic hydrocarbon biodegradation under cold and nutrient-poor environmental conditions could negatively affect the efficacy of natural attenuation.},
}

@article {pmid42281424,
year = {2026},
author = {Garland, S and Orr, VT and Hall, JPJ and Harrison, E},
title = {Invasive plasmids as ecosystem engineers-from mechanism to application.},
journal = {Essays in biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1042/EBC20250040},
pmid = {42281424},
issn = {1744-1358},
support = {APP37189//UKRI | Biotechnology and Biological Sciences Research Council (AFRC)/ ; NE/X009971/1//UKRI | Natural Environment Research Council (NERC)/ ; MR/W02666X/1//UKRI | Medical Research Council (MRC)/ ; },
abstract = {Horizontal gene transfer, mediated by mobile genetic elements such as conjugative plasmids, is recognised as a major driver of bacterial innovation. While predominantly explored in the context of change within individual strains and species, the broad host ranges of many plasmids mean that they can invade not just lineages but communities. This has far-reaching implications for both the fate of the plasmid and our understanding of bacterial adaptation, as well as applications for the functional engineering of microbial communities. In comparison to single-strain systems, in which plasmid invasion is largely determined by a now well-defined set of parameters-conjugation rate, fitness cost of carriage, and segregation loss-the spread of plasmids into communities is vastly more complex: governed by the wide range of dynamics within strains, but also by community dynamics, spatial heterogeneity, and the interactions between strain- and community-level selection. Here, we review the processes by which plasmids can invade communities and discuss how community complexity both constrains and facilitates plasmid spread. We further explore how this mechanistic understanding can be harnessed to enhance microbial community function.},
}

@article {pmid42281763,
year = {2024},
author = {Winston, JA and Suchodolski, JS and Gaschen, F and Busch, K and Marsilio, S and Costa, MC and Chaitman, J and Coffey, EL and Dandrieux, JRS and Gal, A and Hill, T and Pilla, R and Procoli, F and Schmitz, SS and Tolbert, MK and Toresson, L and Unterer, S and Valverde-Altamirano, É and Verocai, GG and Werner, M and Ziese, AL},
title = {Clinical Guidelines for Fecal Microbiota Transplantation in Companion Animals.},
journal = {Advances in small animal care},
volume = {5},
number = {1},
pages = {79-107},
pmid = {42281763},
issn = {2666-450X},
}

@article {pmid42282017,
year = {2026},
author = {Chaulagain, D and Paul, B and Leslie, S and Artigues-Lleixà, M and Cros, MP and Toloza, L and Tang, Z and Hoover, A and Güell, M and Karig, D},
title = {Rational assembly of synthetic marine biofilm community with chitinase production.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9419003/v1},
pmid = {42282017},
issn = {2693-5015},
abstract = {Highly diverse multispecies biofilms are ubiquitous in microbial ecosystems; however, our current understanding of biofilm dynamics is limited to single species or low richness studies. We aimed to design a multispecies biofilm with a targeted function, chitinase production, using natural marine bacteria. We present a top-down assembly approach to design functional biofilm communities. Using our method, we found that final community membership was established within 24 hours, regardless of nutrient availability. However, cultivation in nutrient-rich media enabled rapid identification of the competitive dominant taxon, Pseudoalteromonas , among the 17 initial isolates used in the assembly. By repeating community assembly in a low-nutrient medium without these highly competitive taxa, we achieved the highest species diversity in the biofilm. The resulting multispecies biofilm exhibited chitinase production and maintained ~ 50% persistence during peak invasion. By comparison, a single species chitinase-producing biofilm formed lower biomass and suffered higher displacement during invasion. Importantly, one member that withstood invasion challenge in the multispecies community was completely undetectable at seven days post-invasion as a single species biofilm, indicating collective invasion resilience in the multispecies community. Further evidence of cooperation for coexistence is supported by increased β-N-acetylglucosaminidase, enzyme that hydrolyzes chitin oligomers, in the 14-member community at later timepoints, while the detected exochitinase activity remained stable. Our findings present a streamlined strategy to assemble diverse and functional biofilm communities for targeted biofilm engineering in marine and applied microbiome contexts, and our achievement of engineered function using natural bacteria offers a powerful complement to synthetic biology.},
}

@article {pmid42282041,
year = {2026},
author = {Schutz, C and Queiroz, A and Mota, T and Ward, A and Barr, D and Janssen, S and Shey, M and Wilkinson, R and Wilkinson, K and Burton, R and Lelouvier, B and Andrade, B and Meintjes, G},
title = {Microbial product translocation and mortality in adults hospitalised with HIV-associated tuberculosis: a prospective observational cohort study.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9856875/v1},
pmid = {42282041},
issn = {2693-5015},
abstract = {Background: HIV-associated tuberculosis (HIV-TB) results in unacceptably high mortality rates despite appropriate treatment. Patients hospitalized with HIV-TB often have disseminated tuberculosis and sepsis syndrome which may result in gastro-intestinal barrier dysfunction and facilitate microbial product translocation. Microbial product translocation may contribute to HIV-TB deaths by driving systemic inflammation. Objectives: To assess microbial product translocation and gastrointestinal epithelial damage in patients hospitalized with HIV-TB and the association with 12-week mortality and biomarkers of tuberculosis dissemination. To describe the bacterial blood microbiome (abundance and diversity) in patients with HIV-TB, its association with mortality and tuberculosis dissemination and compare to outpatient controls. Methods: Patients hospitalized with a new diagnosis of HIV-TB were enrolled and prospectively followed for 12 weeks. Markers of microbial product translocation and gastrointestinal damage were measured in a subset (n=373) and bacterial 16s rDNA was quantitated and metagenomic sequencing performed in 235 patients. Microbial product translocation and gastrointestinal epithelial damage marker concentrations were compared between hospitalized patients who died and survivors and inpatients compared to HIVpositive outpatient controls. Logistic regression analysis was performed to determine associations with mortality. Bacterial abundance, diversity and immune perturbation was measured and analysed across patient outcome groups and in patients with tuberculosis dissemination. Results: Patients hospitalized with HIV-TB had significantly higher concentrations of bacterial 16s rDNA, soluble CD14 (sCD14), lipopolysaccharide binding protein (LBP), trefoil factor 3 (TFF3) and lower endotoxin core antibody IgM (EndoCAB), compared to outpatient controls. Soluble CD14 and TFF3 were significantly higher and EndoCAB lower in inpatients who died versus survivors. TFF3 was independently associated with mortality. LPS, sCD14, LBP, EndoCAB and TFF3 showed significant trends in patients with positive biomarkers of tuberculosis dissemination. Metagenomic sequencing showed higher diversity in hospitalised HIV-TB patients compared to controls, but diversity was not different between outcome groups. Mycobacterium genus proportions were increased in hospitalised patients who died compared to survivors. Conclusion: We found evidence of increased gastrointestinal epithelial damage and microbial product translocation in patients hospitalized with HIV-TB and in patients with positive biomarkers for tuberculosis dissemination, however, only TTF3 (a marker of gastrointestinal epithelial damage), was independently associated with mortality.},
}

@article {pmid42282125,
year = {2026},
author = {Zhang, S and Chen, J and Lai, Y and Wang, C},
title = {Migrasomes program tissue microenvironment: from physiology to oncology, future perspectives in clinical advances.},
journal = {Journal of the National Cancer Center},
volume = {6},
number = {3},
pages = {219-233},
pmid = {42282125},
issn = {2667-0054},
abstract = {Cancer remains a critical global health challenge, necessitating an in-depth investigation into spatiotemporal dimensions. Migrasomes, a class of migration-dependent organelles that sequester spatiotemporal and biochemical cues, offer a previously overlooked pathway for microenvironmental programming during tumor evolution. At the cellular level, migrasomes mediate extensive intercellular communication and material transfer, while facilitating cellular quality control via the extrusion of damaged organelles. Within tissue microenvironments, these organelles exert context-dependent, bidirectional effects, modulating homeostasis in processes such as wound healing, senescence, inflammation, and microbial infection, while being exploited in cancer to drive proliferation, angiogenesis, immunomodulation, and metastasis. This review elucidates the intricate role of migrasomes within tumor microenvironments and other tissue settings, discusses their potential involvement in the transition from tissue homeostasis to malignancy, and evaluates their potential implications for clinical therapeutic strategies, as well as diagnostic and prognostic biomarkers.},
}

@article {pmid42282175,
year = {2026},
author = {Dedon, LR and Lee, DJ and Lin, Q and Yuan, H and Chi, J and Li, L and Gu, H and Tennen, H and Covault, JM and Zhou, Y},
title = {Baseline Gut Microbiome-Metabolome Signatures Are Associated with Drinking Severity and Reduction Following Dutasteride Treatment in Alcohol Use Disorder.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.26.26354041},
pmid = {42282175},
abstract = {The gut microbiome has been implicated in alcohol use disorder (AUD), but its relationship to drinking intensity and treatment response remains poorly understood. We conducted a longitudinal multi-omics analysis of stool samples collected at baseline and endpoint (after 12 weeks) from 122 participants enrolled in a double-blind, placebo-controlled trial of dutasteride for AUD. Gut microbiome composition was characterized using 16S rRNA gene sequencing, and fecal metabolites were measured by LC-MS-based metabolomics. At baseline, drinking intensity was associated with increasingly lower microbial richness. Genera in the class Clostridia emerged as key microbial hubs associated with drinking intensity in an age- and sex-dependent manner. Drinking intensity promoted co-enrichment of [ Ruminococcus ] gnavus group and [ Clostridium ] inocuum group with amino acid catabolites, as well as the co-depletion of diverse Clostridia taxa and lipid metabolites. Dutasteride treatment and drinking reduction had minimal impact on gut microbiome composition. Random forest models integrating baseline clinical, microbiome, and metabolome data improved the classification of clinically meaningful drinking reduction compared to models using clinical data alone. These findings show that a coupled baseline gut microbiome-metabolome signature is associated with drinking intensity and future treatment response in AUD, highlighting the potential for multi-omics integration to inform precision treatment approaches.},
}

@article {pmid42282268,
year = {2026},
author = {Frame, LA and Warren, A and Al Qalam, A and Corr, PG and Farah, M and Karam, M and Rangoussis, K and Fahim Devin, M and Celikkol, Z and Gordon, L and Villarreal, D and Catto, E and Udam, Y and Thompson, K and Lubinski, O and Samman, A and Badawi, A and Hack, H and Hunter, M and Hines, I and Servetas, S and Jackson, SA and Hasan, NA and Kogan, M},
title = {Brain health and the gut microbiome (bMicrobiome Study): a proof-of-concept, feasibility study integrating shotgun metagenomics, metrology, and multidimensional phenotyping across the cognitive aging spectrum.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2679810},
pmid = {42282268},
issn = {2993-3935},
abstract = {BACKGROUND: Associations between the gut microbiome and cognitive decline remain inconsistent, reflecting methodological variability, small cohorts, and limited integration of behavioral and lifestyle factors. The microbiota-gut-brain axis may influence cognition through metabolic, immune, and neuroendocrine pathways affecting mood, decision-making, and health behaviors.

METHODS: This prospective, proof-of-concept study integrated multidimensional phenotyping with metagenomic sequencing (shotgun) in adults (50-90 y) around Washington, DC. Participants were classified as healthy controls (HC) or mild cognitive impairment (MCI) by clinical history; early Alzheimer's disease (eAD) participants were unable to complete study requirements. Longitudinal assessment used Boston Cognitive Assessment (BoCA), patient-reported outcomes (PROMIS-29), dietary intake and quality (DietID™), readiness-for-change (adapted URICA), at-home stool sample collection.

RESULTS: Seventeen participants completed sufficient assessments (HC n = 11; MCI n = 6). Substantial overlap in gut microbiome composition was observed between HC and MCI. Poorly characterized or uncommon taxa drove trends; unassigned taxa were common. Assessment revealed high diet quality and variability in dietary patterns and key components (vegetables, whole grains, fat, fish). Participants demonstrated high readiness to engage in nutritional behavior change, with individuals with MCI reporting greater concern about maintaining changes and a stronger desire for external support.

CONCLUSIONS: Integrating multidimensional phenotyping with metagenomics is feasible in cognitive decline. Findings highlight biological and behavioral heterogeneity, limitations of species-level inference, and diet and behavioral readiness as modifiable contextual factors.},
}

@article {pmid42282286,
year = {2026},
author = {Jain, M and Jain, T and Nayak, R and Saad, T and Karale, AW and Ilyas, M and Arjariya, R},
title = {Estimation of gut microbiome motif associated with active tuberculosis - A case control study.},
journal = {Bioinformation},
volume = {22},
number = {4},
pages = {2083-2086},
pmid = {42282286},
issn = {0973-2063},
abstract = {Tuberculosis (TB) is the most tenacious health issue affecting individuals globally. Therefore, it is of interest to estimate gut microbiota motifs associated with the outbreak of active TB by incorporating the insights from human case-control data. 106 respondents were categorised into 2 groups: group A with TB and group B controls with 53 respondents in each category. The Shannon diversity index was substantially diminished in affected individuals. The active TB cases exhibited substantially decreased micro-biomes (P < 0.001). Thus, we show the need to develop microbiome-targeted strategies to reduce the incidence of active TB cases and improve their effective management.},
}

@article {pmid42282445,
year = {2026},
author = {Zhu, L and Wen, X and Zhu, W and Hu, X and Xu, Y and Peng, X},
title = {Enteromorpha prolifera Polysaccharide Alleviates Type 2 Diabetes via the Gut Microbiota-Liver Axis to Modulate Cholesterol Metabolism.},
journal = {Food science & nutrition},
volume = {14},
number = {6},
pages = {e71998},
pmid = {42282445},
issn = {2048-7177},
abstract = {Enteromorpha prolifera polysaccharide (EPP), a major bioactive sulfated polysaccharide derived from green algae, possesses potent hypoglycemic and hypolipidemic properties. This study aimed to evaluate the therapeutic efficacy of EPP in a murine model of type 2 diabetes mellitus (T2DM) and elucidate its underlying molecular mechanisms through an integrated multi-omics approach-comprising 16S rRNA microbiomics, untargeted metabolomics, and transcriptomics. Our findings demonstrate that EPP intervention significantly suppressed fasting blood glucose (FBG) levels, attenuated dyslipidemia, and enhanced systemic insulin sensitivity. At the microbiome level, EPP restored intestinal homeostasis by enriching beneficial taxa, specifically Lactobacillus, Ligilactobacillus, and Dubosiella, while depleting the T2DM-associated genus Blautia. These microbial shifts correlated with significantly elevated fecal concentrations of short-chain fatty acids (SCFAs), including acetate, propionate, and branched-chain fatty acids (isobutyrate and isovalerate). Integrated pathway analysis revealed that EPP significantly modulates steroid hormone biosynthesis; integrated pathway analysis suggested that EPP potentially modulates pathways related to steroid hormone biosynthesis, cholesterol metabolism, and primary bile acid synthesis. Quantitative RT-PCR validation confirmed that EPP treatment was accompanied by the upregulation of critical genes involved in bile acid and steroidogenesis (Cyp17a1, Cyp11a1, Hsd3b7, and Stard1) and the downregulation of Srebf2 and Hnf4α, the master transcriptional regulators of cholesterol biosynthesis and hepatic gluconeogenesis, respectively. Correlation analyses further indicated potential links between gut microbiota alterations, SCFA production, and glycemic control. Collectively, these results suggest that EPP may alleviate T2DM symptoms, which is associated with the modulation of the gut microbiota-hepatic cholesterol metabolism axis, positioning it as a promising functional food ingredient or therapeutic candidate for metabolic disorders.},
}

@article {pmid42282557,
year = {2026},
author = {Adelfio, M and Bonzanni, M and Callen, GE and Diaz, AR and Paster, BJ and He, X and Hasturk, H and Ghezzi, CE},
title = {Profiling Gingival Inflammation in a 3D Oral Tissue Model Reveals Early Features of Disease Progression.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.05.730462},
pmid = {42282557},
issn = {2692-8205},
abstract = {Gingival health depends on a balanced interplay among the gingival epithelium, immune system, and oral microbiome. Disruption of this equilibrium through sustained biofilm accumulation and host inflammatory responses leads to gingivitis, a highly prevalent yet reversible condition which if left untreated could progress into more severe and irreversible condition called periodontitis. The early onset of gingivitis remains poorly defined due to subtle clinical presentation and pronounced interindividual variability. Current diagnostic approaches rely largely on clinical assessment and endpoint biomarkers, limiting insight into the early host-microbiome interactions that drive disease initiation. Here, we employ a previously validated, physiologically relevant oral tissue model (OTM) to longitudinally investigate epithelial-microbiome interactions following inoculation with patient-derived dysbiotic microbiomes from early-stage gingivitis. The OTM maintained host tissue integrity and microbial viability over a seven-day period, preserving epithelial barrier function, dynamic inflammatory responses, and disease-associated microbial signatures. Notably, we establish, for the first time in an in vitro platform, clinical calibration against gingival crevicular fluid (GCF), demonstrating that OTM responses recapitulate inoculum-dependent inflammatory signatures, increased microbial dissimilarity under dysbiotic conditions, and coordinated host-microbiome metabolic interactions. While pro-inflammatory responses were most pronounced at early time points, subsequent modulation toward anti-inflammatory states highlights the temporal complexity of host responses and suggests that longer culture durations may further resolve disease trajectories. Collectively, these findings validate the OTM as a robust, physiologically relevant platform that captures key features of periodontal health and inflammation. By integrating host viability, microbial ecology, and clinical benchmarking, this system enables mechanistic interrogation of early disease-driving processes and provides a translational framework for advancing predictive diagnostics and preventive therapeutic strategies in periodontal disease.},
}

@article {pmid42282600,
year = {2026},
author = {Corbett, CM and O'Shall, AE and Niedringhaus, M and West, EA},
title = {Behavioral flexibility and gut microbiome as potential predictors of oral oxycodone self-administration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.02.729613},
pmid = {42282600},
issn = {2692-8205},
abstract = {Prescription opioids such as oxycodone have been widely used in the United States and have contributed to the ongoing opioid epidemic. While many individuals limit use to prescribed contexts, a subset transitions to misuse and, in some cases, to illicit opioid use. Identifying behavioral and biological factors that predict this vulnerability is critical for improving prevention and intervention strategies. Here, we investigated whether individual differences in behavioral flexibility and gut microbiome composition are associated with future oxycodone intake using a translationally relevant model of oral oxycodone self-administration in male and female Long-Evans rats. We established a model in which distinct intake phenotypes emerged, characterized by animals with high versus low oxycodone consumption. Behavioral flexibility, assessed using a contingency degradation task, was associated with oxycodone intake, identifying it as a potential behavioral biomarker of vulnerability. In parallel, oral oxycodone exposure altered gut microbiome composition, and microbiome features were associated with both behavioral flexibility and drug-taking behavior. These findings support a framework in which individual differences in opioid intake arise from the interaction of pre-existing behavioral traits and biological states, including gut microbiome composition which provides a foundation for identifying predictive biomarkers and developing individualized strategies to mitigate risk for opioid misuse.},
}

@article {pmid42282663,
year = {2026},
author = {Torres-Morales, J and Dewhirst, F and Kauffman, KM and Mark Welch, J and Borisy, G},
title = {Site-specialization of human oral Porphyromonas species.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.02.729646},
pmid = {42282663},
issn = {2692-8205},
abstract = {Site-specificity within the human oral cavity reflects adaptation mechanisms such as genome divergence and metabolic specialization. Members of the genus Porphyromonas are distributed across oral sites in health and disease, yet the specific distribution of taxa and the functional basis of their site-specificity remain poorly understood. We analyzed 1,242 metagenomes from nine oral sites in healthy individuals and 24 subgingival plaque samples from individuals with periodontitis. Competitive mapping to a dereplicated genus-level pangenome of 84 reference genomes, combined with phylogenomic, gene-level detection, and functional profiling, revealed distinct site-specific distribution patterns, ecotype differentiation, and metabolic specialization across Porphyromonas taxa. Porphyromonas pasteri was the most abundant and widespread taxon in healthy subjects, comprising two ecotypes--one mucosal, one plaque-associated. Porphyromonas gingivalis was rare in healthy subjects but present in periodontal disease, although detected in only half of periodontitis samples. P. gingivalis exhibited the broadest metabolic repertoire, suggestive of a survival strategy adaptive to disparate conditions. In contrast, Porphyromonas catoniae, restricted to healthy dental plaque, lacked biosynthetic pathways for cobalamin, biotin, and serine, implying nutritional dependency on other taxa or the host. Porphyromonas endodontalis, detected in subgingival plaque across both health and disease, also lacked several metabolic pathways. A 44 kb conjugative element identified in P. gingivalis was detected across healthy and periodontitis subgingival plaque microbiomes independently of the P. gingivalis chromosome, indicating horizontal transfer. These findings reveal genomic divergence and complex metabolic specialization among Porphyromonas taxa, refining our understanding of their role in the ecological structure of the human oral microbiome.},
}

@article {pmid42282679,
year = {2026},
author = {Laurin, PJ and Garud, NR},
title = {Complex adaptive architectures constrain the pace of adaptations sweeping across human gut microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.01.729358},
pmid = {42282679},
issn = {2692-8205},
abstract = {Recent work has shown that commensal gut bacteria can evolve rapidly within hosts on short timescales of days to months, fueled by the enormous mutational input generated daily in the microbiome. Yet how rapidly adaptations spread across gut microbiomes of different hosts remains unclear. We address this question by estimating the number of independent origins of gene-specific sweeps spreading via recombination across bacterial populations. Multiple origins (soft sweeps) indicate that adaptive mutations arise rapidly whereas one origin (hard sweeps) indicate slower mutational input. Contrary to expectations of rapid adaptation, we find that many gene-specific sweeps have only one or a few origins. We show that this requires that sweeps arise from adaptive mutation rates orders of magnitude lower than single base pair mutation rates. This implies that gene-specific sweeps bear difficult-to-mutate complex adaptations such as structural or epistatic variants. Consistent with this interpretation, we find that identified sweep regions exhibit patterns of nucleotide diversity and linkage disequilibrium inconsistent with a single adaptive mutation rising to high frequency. We conclude that recombination across human gut microbiomes enables the spread of adaptations with complex genetic architectures that otherwise would require a long waiting time to generate de novo within an individual host.},
}

@article {pmid42282687,
year = {2026},
author = {Woods, E and Jones, D and Gorden, O and Nusbacher, N and Kofonow, J and Dumont, G and Frank, DN and Friedman, NR and Herrmann, BW and Lozupone, C and Verneris, MR},
title = {Altered Tonsillar Microbiome in Children with Down Syndrome and Obstructive Sleep Apnea.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.29.728812},
pmid = {42282687},
issn = {2692-8205},
abstract = {BACKGROUND AND OBJECTIVES: Children with Down syndrome (DS) have a high prevalence of obstructive sleep apnea (OSA) due to anatomic, neuromuscular, immunological and metabolic factors, yet the contribution of the tonsillar microbiome to airway obstruction in this population remains unexplored. We hypothesized that DS-associated OSA would be associated with a distinct tonsillar microbiome compared to non-DS OSA.

METHODS: Tonsillar tissue from 22 DS and 18 NDS participants were analyzed by 16S rRNA sequencing. Alpha and beta diversity were assessed using Faith's phylogenetic diversity and UniFrac distances, respectively, and significantly different taxa were identified with ANCOM-BC and Mann-Whitney testing.

RESULTS: Although overall microbial richness and community structure were similar between groups, overweight DS participants demonstrated increased phylogenetic diversity compared to normal-weight DS peers. Taxonomic profiling of the entire patient cohort revealed that in DS tonsils there were selective alterations in key genera with selective depletion of Haemophilus and enrichment of Staphylococcus , Rothia , and Lactobacillales . Haemophilus abundance correlated positively with tonsil weight in both cohorts.

CONCLUSIONS: These findings suggest that while global diversity is preserved, specific microbial shifts distinguish the DS tonsillar niche, potentially reflecting altered immune and metabolic environments associated with trisomy 21. Understanding these microbial differences may reveal mechanisms underlying the higher incidence and persistence of OSA in DS and inform targeted therapeutic strategies.},
}

@article {pmid42282707,
year = {2026},
author = {Blumstein, DM and Patel, A and Schiro, G and Suzuki, TA},
title = {Beyond distance-decay: The Mississippi River shapes gut microbiome communities in the Peromyscus maniculatus species complex.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.03.729934},
pmid = {42282707},
issn = {2692-8205},
abstract = {Biogeographic barriers are fundamental in shaping the distribution of animals and plants, yet the role of discrete landscape features in constraining microbial dispersal remains poorly understood. Identifying the barriers that partition gut microbial communities is essential for modeling the distribution of hosts and their symbionts across physical space and evolutionary time. The deer mouse (Peromyscus maniculatus species complex), which inhabits nearly all terrestrial environments in North America, provides an ideal model for testing these biogeographic drivers of the mammalian gut microbiome. Using NSF NEON biorepository samples, we characterized the gut microbiomes of 13 populations across the contiguous United States using full-length 16S rRNA long-read sequencing. While we observed a consistent distance-decay relationship across the continent, our results reveal that the Mississippi River acts as a major biogeographic break, significantly increasing microbial dissimilarity beyond the levels predicted by geographic distance alone. This "river effect" suggests that large fluvial systems impose a discrete barrier to microbial transmission, likely due to restricted host dispersal. Furthermore, we identified specific microbial lineages that exhibit differential sensitivity to this barrier, suggesting a gradient in microbial acquisition patterns ranging from the environment to host-host transmission. Together, these findings demonstrate that the gut microbiome may act as a sensitive bio-indicator of landscape-level ecological connectivity, revealing that large-scale landscape barriers disrupt microbial transmission even among closely related host populations that lack reproductive barriers.},
}

@article {pmid42282751,
year = {2026},
author = {Duchamp-Smith, C and Burchat, N and Pantula, LG and Mitchell, SB and Aydemir, TB and Sampath, H},
title = {Hepatic stearoyl-CoA desaturase-1 is specifically suppressed by dextran sodium sulfate but does not influence colitis sensitivity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.29.728832},
pmid = {42282751},
issn = {2692-8205},
abstract = {UNLABELLED: The delta-9 desaturase stearoyl-CoA desaturase-1 (SCD1) catalyzes the conversion of saturated fatty acids to monounsaturated fatty acids (MUFA) and is highly expressed in liver and adipocytes. Previous studies have demonstrated that treating mice with dextran sulfate sodium (DSS), a chemical inducer of ulcerative colitis, results in severe downregulation of SCD1 in the liver. However, the specific role of hepatic SCD1 in modulating colitis severity, as well as the impact of DSS on SCD1 and other lipogenic factors in other tissues has not been investigated. Here we show that downregulation of hepatic SCD1 following DSS treatment is not accompanied by changes to other lipogenic genes in the liver. In contrast, adipose tissue demonstrates coordinated reductions in lipogenic genes, including SCD1 and SCD2, while the colon does not display any perturbation of these targets. Furthermore, we demonstrate that the downregulation of hepatic SCD1 occurs independently of sterol regulatory element binding protein-1c (SREBP-1c) and does not require an intact gut microbiome. Interestingly, a distinct model of colitis induced by IL-10 deficiency does not result in downregulation of hepatic SCD1. Concomitant with transcriptional changes, DSS treatment is associated with significant remodeling of the hepatic lipidome, including reductions in total phospholipids (PLs) and reduced MUFA-containing PLs and triacyglycerols (TAGs), consistent with the observed reduction in SCD1. Interestingly, hepatic cholesterol esters and plasma lipids including free cholesterol and glycerophospholipids were significantly elevated following DSS treatment. Given the significant reduction in hepatic SCD1 following DSS treatment, we tested a role for liver SCD1 in modulating colitis sensitivity. Mice with a targeted deletion of hepatic SCD1 were not more prone to colitis, indicating that the loss of hepatic SCD1, while a consequence of DSS-induced colitis, does not mediate colitis sensitivity in vivo.

SYNOPSIS: Hepatic SCD1 does not modulate colitis severity upon DSS exposure. However, DSS-induced colitis elicits significant lipid metabolism dysfunction, demonstrated by elevated plasma and liver lipids, particularly plasma cholesterol and hepatic cholesterol esters, highlighting a role for gutliver crosstalk following colonic inflammation.},
}

@article {pmid42282818,
year = {2026},
author = {Richmond, GR and Cunha, E and Kelly, L and Dias, Ó and Chang, RL},
title = {Nutrient control enables metabolic reconstruction of L. rhamnosus GG and analysis of secretions.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.02.729517},
pmid = {42282818},
issn = {2692-8205},
abstract = {Lacticaseibacillus rhamnosus GG (LGG) is an important gut commensal bacterial strain that has been extensively studied in both industrial and health settings. Despite its long history of study, a high-quality genome-scale metabolic network model (GEM) for LGG has yet to be reconstructed. Only automatically-generated draft models have been published, which have notoriously limited functional accuracy. Furthermore, comprehensive nutrient requirements have not been established for well-controlled in vitro study. Here we present the first curated GEM for LGG using a new approach for reconstruction and validation that leverages multiple automatically-generated draft models, applied study literature, and high-throughput defined media experiments. In addition, our results include a series of chemically defined media, extensive single-component nutrient dropout growth data, insights from in silico and in vitro experiments into major secretion products lactate and indole-3-carboxaldehyde, a minimal medium and in silico characterization of LGG's nutrient requirements. Our approach for developing interdisciplinary research tools for LGG metabolism comprises a new framework that could be applied to many understudied microorganisms, particularly useful in studying bacteria within the human microbiome.},
}

@article {pmid42282998,
year = {2026},
author = {Zeng, B and Maitikuerban, M and Chen, L and Wang, DK and Li, J and Yang, L and Lao, XM and Zhang, SE and Liao, GQ and Liang, YJ},
title = {Microbiome dynamics and early microbial signatures predict bone regeneration in marsupialized jaw lesions: a longitudinal 16S sequencing cohort study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2684137},
pmid = {42282998},
issn = {2000-2297},
abstract = {BACKGROUND: Marsupialization is a conservative treatment for odontogenic jaw lesions but is hampered by protracted, unpredictable bone regeneration, lacking early biomarkers. Furthermore, whether these intraosseous lesions harbour a unique microbiome remains unknown. We aimed to characterize microbial dynamics during treatment and develop a prognostic model to address clinical unpredictability.

METHODS: A prospective longitudinal study was conducted with multi-site sampling (saliva, tissue, luminal fluid and swabs) across three phases: primary surgery, 3-month follow-up and secondary surgery. Bacterial 16S rRNA gene sequencing was subsequently performed. Microbial dynamics were analyzed using diversity analysis and source tracking. A prognostic model was constructed using a hybrid feature selection strategy to predict 12-month bone regeneration using 3-month post-operative swabs.

RESULTS: Baseline analysis revealed that odontogenic jaw lesions harbour a unique, biologically selected microbiome enriched in Fusobacterium and Clostridia, which are distinct from saliva. Marsupialization induced a profound microbial remodelling, transforming this closed niche into an open, stochastic ecosystem dominated by salivary commensals. Long-term analysis indicated a secondary succession, where primary pathogens were replaced by a Bacteroidia-enriched community. Crucially, after a rigorous feature selection process, a streamlined microbial signature accurately predicted 12-month bone regeneration (AUC = 0.937). Poor bone regeneration was associated with the persistence of the primary Clostridia core, whereas favourable regeneration was linked to a shift towards Bacteroidia and Proteobacteria.

CONCLUSION: Marsupialization drives the lesion microbiome from a pathogenic niche toward a stochastic, commensal-like state. This succession trajectory is associated with clinical outcome. Our prognostic model offers a novel precision tool to optimize lesion management.},
}

@article {pmid42283379,
year = {2026},
author = {Eleftherianos, I and Zhang, W and Mohamed, A and Al-Akeel, RK and Alkhaibari, AM and Keyhani, N and Smagghe, G},
title = {Microbiome-mediated chemical communication in insects: Implications for pest management.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71015},
pmid = {42283379},
issn = {1526-4998},
support = {32472644//National Natural Science Foundation of China/ ; QiankehePingtaiCXPTXM[2025]-026//Guizhou Provincial S&T Innovation Platform Research Project/ ; },
abstract = {Insects rely on semiochemicals to regulate aggregation, mating, foraging, and host selection. This review synthesizes evidence that insect-associated microbiota shape these chemical signals and evaluates their potential for pest management. The literature supports four principal routes by which microbes influence insect chemical communication: (i) direct production of volatile organic compounds; (ii) microbial provision or modification of pheromone precursors; (iii) microbiome-mediated effects on sensory and neural function; and (iv) context dependence driven by diet, development, quorum sensing, and environmental microbiomes. The strongest evidence comes from loss-gain-rescue studies, including German cockroach fecal volatiles and Wolbachia-linked effects on Drosophila paulistorum mating chemistry. Translationally, fermentation-based lures for fruit flies and microbial deterrents such as Xenorhabdus-derived metabolites show clear promise, whereas most other systems remain correlative because gene-to-metabolite-to-behavior chains are incomplete and field validation is limited. Microbiome-semiochemical interactions offer a credible platform for next-generation attractants, repellents, and symbiont-based pest control. Progress will depend on rigorous mechanistic validation, standardized behavioral assays, and biosafety-aware field testing to convert promising discoveries into scalable integrated pest management tools. © 2026 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid42283450,
year = {2026},
author = {Pishchany, G and Fryling, KE and Vasukuttan, V and Shin, YH and Mortimer, TD and Grad, YH and Clardy, J},
title = {Aerocavin Is an Antibiotic with Potent and Specific Anti-Neisserial Activity.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.6c00197},
pmid = {42283450},
issn = {2373-8227},
abstract = {Gonorrhea, caused by Neisseria gonorrhoeae, is a widespread sexually transmitted disease that is becoming resistant to all currently used antibiotics. Therefore, new therapeutics for gonorrhea are desperately needed. Here, we show that a natural product, aerocavin, is highly potent and specific against Neisseria. Aerocavin accumulates in N. gonorrhoeae at high levels and inhibits bacterial RNA polymerase (RNAP) by binding the switch region. Aerocavin resistance mutations evolve in N. gonorrhoeae at a low rate and are absent in clinical isolates. Previously overlooked narrow-spectrum antimicrobials like aerocavin may enable microbiome-sparing treatments of gonorrhea.},
}

@article {pmid42283564,
year = {2026},
author = {Ardizzone, CM and Lammons, JW and Lan, RS and Elnaggar, JH and Lillis, RA and Toh, E and Pack, LM and Mott, PD and Jacobs, CD and Yeruva, L and Taylor, CM and Quayle, AJ},
title = {Integrated multi-omics analysis uncovers cervicovaginal ecological networks and their association with Chlamydia trachomatis load.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0068125},
doi = {10.1128/iai.00681-25},
pmid = {42283564},
issn = {1098-5522},
abstract = {Chlamydia trachomatis (Ct) is a causal agent of upper reproductive tract pathology. There is a broad spectrum of cervical Ct load in infected women, and upper tract infection is associated with higher cervical Ct load. Recent studies indicate that bacterial vaginosis (BV) can modulate host-Ct outcomes. To identify features associated with BV status and Ct load, we performed an integrated multi-omics analysis of the cervicovaginal microbiome, tryptophan metabolome, and cytokines. Samples were analyzed using 16S rRNA gene sequencing, targeted UPLC-MS/MS quantification of tryptophan metabolites, and multiplex cytokine profiling. Ordination analyses showed that BV status was separated by the microbiome, metabolome, and cytokines, whereas Ct load was separated only by cytokines. K-means clustering of tryptophan metabolites defined three metabolome state types (MSTs). MST I, associated primarily with Lactobacillus crispatus-dominated community state type (CST) I, exhibited high tryptophan availability, indole-3-lactic acid, and complete kynurenine-pathway activity. Both MST II and MST III were associated with BV-associated CST IV and showed marked tryptophan depletion. MST II was broadly depleted of most tryptophan metabolites, while MST III was enriched in downstream microbially derived indole pathway metabolites and kynurenic acid. Hierarchical all-against-all association testing revealed coordinated relationships linking clusters of bacterial taxa, metabolites, and cytokines. Importantly, multi-omics network analyses identified integrated microbial-metabolic-immune modules that predicted high versus low Ct load, highlighting CXCL9, CXCL10, IL-17, BV-associated taxa, and indole pathway metabolites as key discriminative features. Results demonstrate that cervical Ct load reflects coordinated microbial-metabolic-immune ecological states rather than microbiome composition alone and refine current models of Ct-BV interactions.},
}

@article {pmid42283770,
year = {2026},
author = {Liu, H and Tian, J and Sun, X and Li, R and Gao, W and Zhang, D and Dong, G},
title = {Divergent Colorectal Cancer Risks Following Metabolic Bariatric Surgery: Anatomical Remodeling and the Genotoxic Microenvironment.},
journal = {Obesity surgery},
volume = {},
number = {},
pages = {},
pmid = {42283770},
issn = {1708-0428},
abstract = {Metabolic bariatric surgery (MBS) reduces overall cancer incidence, yet colorectal cancer (CRC) risk diverges by procedure. Roux-en-Y gastric bypass (RYGB) has been associated with increased long-term CRC risk (HR 1.55 at 10-14 years), whereas sleeve gastrectomy (SG) shows no equivalent elevation, though shorter follow-up (mean 4.5 vs. 8.5 years) precludes definitive conclusions. This review develops a biologically plausible mechanistic framework for these divergent outcomes. RYGB-induced anatomical bypass and accelerated transit are proposed to drive distal substrate overload, with an associated shift of the colonic microbiome toward proteolytic fermentation. The proposed genotoxic luminal environment is characterized by convergent actions of secondary bile acids, tyramine, and hydrogen sulfide, compounded by butyrate depletion. By preserving gastrointestinal continuity, SG is hypothesized to avoid these alterations. These considerations support integrating baseline CRC risk into surgical selection and procedure-specific surveillance after RYGB.},
}

@article {pmid42283822,
year = {2026},
author = {Santos, ACC and Corrêa, JL and de Lima, DS and Andrade, ACAS and Junqueira, CN and Dos Santos, AR and Augusto, SC and Bonetti, AM and Ueira-Vieira, C},
title = {Gut microbiome composition and cellulolytic bacteria associated with the carpenter bee Xylocopa frontalis.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13911-0},
pmid = {42283822},
issn = {1432-0614},
abstract = {Carpenter bees of the genus Xylocopa interact extensively with woody substrates during nest construction, suggesting that associated microorganisms may contribute to the degradation of plant-derived polymers. Despite their ecological relevance, the gut microbiome and functional potential of Xylocopa species remain poorly characterized. In this study, we investigated the bacterial and fungal gut microbiome of Xylocopa frontalis using 16S rRNA and ITS amplicon sequencing, complemented by culture-dependent approaches. The gut microbiome was dominated by bacterial taxa commonly associated with bees, including Bombiscardovia, Bifidobacterium, and Frischella, whereas fungal communities were more variable and included genera such as Aspergillus and Cladosporium. Several taxa were consistently detected across samples, indicating recurrent community members; however, a consistent core microbiome was not clearly observed. We established a collection of cultivable microorganisms, including a bacterial isolate capable of utilizing cellulose as a carbon source, as demonstrated by plate assays. Phylogenetic and genomic analyses identified this isolate as Bacillus velezensis strain Xf, which harbors genes associated with cellulose and hemicellulose degradation. These findings suggest the potential for lignocellulose-related metabolism in the gut microbiome. Together, our results provide a combined culture-independent and culture-dependent characterization of the X. frontalis gut microbiome and identify microorganisms with relevant functional traits. Although based on a limited sample size, this study expands current knowledge of microbial associations in carpenter bees and establishes a foundation for future investigations into their functional roles. KEY POINTS: • Gut microbiome of Xylocopa frontalis was characterized by amplicon sequencing • Bacillus velezensis strain Xf showed cellulolytic activity in vitro • Gut-associated microbes showed genes linked to lignocellulose degradation.},
}

@article {pmid42283827,
year = {2026},
author = {Wiśniewski, P and Maździarz, M and Kwietniewska, K and Krawczyk, K},
title = {Shifts in Rhizosphere Bacterial Community Composition and Predicted Functional Potential Associated with Impatiens parviflora Invasion in Temperate Forest.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02807-1},
pmid = {42283827},
issn = {1432-184X},
support = {No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; No. 12.610.002-110//Uniwersytet Warmińsko-Mazurski w Olsztynie/ ; },
abstract = {Impatiens parviflora is a widespread invasive plant in temperate European forests, yet its influence on rhizosphere microbial communities remains poorly understood. This study provides initial metagenomic insights into taxonomic shifts and predicted functional potential of bacterial communities associated with this invader. Rhizosphere soils were collected from eight I. parviflora-invaded and eight non-invaded control plots in a mixed coniferous forest in northern Poland and analysed using Oxford Nanopore shotgun sequencing, with functional inference performed using the taxonomy-dependent FAPROTAX database. Bacterial richness was significantly higher in invaded soils, whereas Shannon and Simpson diversity indices did not differ between treatments, indicating an expansion of rare taxa without changes in overall diversity structure. The invaded rhizosphere was characterised by a uniform depletion of dominant bacterial orders, with no significantly enriched taxa detected, contrasting with the selective enrichment of microbial groups often reported for other invasive plant species. FAPROTAX-based predictions indicated consistently lower inferred abundances of 37 metabolic processes in invaded plots, including those related to nitrogen cycling and degradation of complex plant polymers. Because these functional predictions are derived from taxonomic composition, they represent inferred ecological potential rather than measured activity. Overall, these results generate testable hypotheses regarding plant-soil feedbacks and highlight the utility of long-read metagenomics for exploring microbial dynamics potentially contributing to the ecological success of I. parviflora in temperate forests.},
}

@article {pmid42283898,
year = {2026},
author = {Hu, T and Li, Y and Li, A and Liu, M and Li, S and Zheng, L and Zhang, J and Liu, R and Zhong, W},
title = {Application of a native Weissella starter to modulate the microbiome, metabolome, and quality characteristics of fermented Ma bamboo shoots.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {7},
pages = {},
pmid = {42283898},
issn = {1573-0972},
support = {32402036//National Natural Science Foundation of China/ ; LQ23C010004//Natural Science Foundation of Zhejiang Province/ ; },
mesh = {*Weissella/metabolism/isolation & purification/classification/genetics ; Fermentation ; *Microbiota ; *Metabolome ; *Fermented Foods/microbiology/analysis ; Food Microbiology ; *Plant Shoots/microbiology/chemistry ; Bacteria/classification/genetics/isolation & purification ; Metabolomics ; Food, Processed ; *Bambusa/microbiology ; },
abstract = {Spontaneous fermentation of bamboo shoots often leads to unstable quality and safety risks, such as nitrite accumulation. To solve this problem, two native Weissella strains (N2-1 and N2-2) with fast acid-producing and nitrite-degrading abilities were isolated from traditionally fermented Ma bamboo shoots. This study evaluated their use as a starter culture. High-throughput sequencing showed that inoculation quickly changed the microbial community. Weissella became the dominant genus, while the diversity of other bacteria and fungi decreased. In addition, metabolomics analysis revealed major changes in the metabolites. The Weissella fermentation increased umami-related nucleotides (adenine and adenosine) and flavor volatiles, while speeding up the breakdown of bitter phenolics and dipeptides. These chemical changes improved the texture: both raw and cooked bamboo shoots showed higher chewiness and cohesiveness, and lower hardness. Correlation analysis confirmed that the dominance of Weissella was closely linked to these positive changes. In conclusion, using this native Weissella starter is a practical way to standardize the safety, microbial stability, and sensory quality of fermented bamboo shoots.},
}

*Weissella/metabolism/isolation & purification/classification/genetics
Fermentation
*Microbiota
*Metabolome
*Fermented Foods/microbiology/analysis
Food Microbiology
*Plant Shoots/microbiology/chemistry
Bacteria/classification/genetics/isolation & purification
Metabolomics
Food, Processed
*Bambusa/microbiology

@article {pmid42283913,
year = {2026},
author = {Zhang, Y and Yu, X and Shi, L and Qi, C and Wang, H},
title = {The role of the microbiome in uterine cancer: insights into tumorigenesis, therapeutic implications, and clinical prospects.},
journal = {Journal of the Egyptian National Cancer Institute},
volume = {38},
number = {1},
pages = {},
pmid = {42283913},
issn = {2589-0409},
mesh = {Humans ; Female ; *Microbiota/immunology ; Tumor Microenvironment/immunology ; *Uterine Neoplasms/therapy/microbiology/etiology/pathology/diagnosis ; Prognosis ; *Carcinogenesis ; },
abstract = {Malignant tumors of the uterine cavity are a leading cause of cancer-related mortality in women worldwide. In recent years, the tumor microenvironment, as a novel biological concept, has garnered increasing attention. The microenvironment plays a crucial role in the initiation, progression, and response to treatment of tumors. Although research on the microenvironment of malignant uterine tumors is in its early stages, preliminary findings suggest that alterations in the microbial communities of cervical and endometrial cancers are closely associated with tumorigenesis, immune evasion, metastasis, and treatment resistance. Notably, specific microbial community changes have potential diagnostic and prognostic implications, offering novel insights into the management of these cancers.This review aims to summarize and analyze the current state of research on the microenvironment of malignant uterine tumors, particularly its role in cervical and endometrial cancers. We first overview the epidemiological landscape and microenvironmental features of these tumors, emphasizing how microbial communities influence tumor initiation and progression. This influence occurs through immune modulation, metabolic changes, and alterations within the tumor microenvironment. Second, the potential role of the microenvironment in tumor therapy is explored, particularly its application prospects in chemotherapy, radiotherapy, and immunotherapy. In addition, the application potential of microbial communities in early tumor diagnosis, efficacy monitoring, and prognosis assessment is discussed.},
}

Humans
Female
*Microbiota/immunology
Tumor Microenvironment/immunology
*Uterine Neoplasms/therapy/microbiology/etiology/pathology/diagnosis
Prognosis
*Carcinogenesis

@article {pmid42284092,
year = {2026},
author = {Astolfi, A and Potenza, M and Ciavarella, C and Moramarco, A and Bonci, P and Zaghi, A and Foschi, C and D'Eliseo, LA and D'Eliseo, D and Lazzarotto, T and Fontana, L and Versura, P},
title = {Distinct Ocular Surface Microbial Profiles in Corneal Transplant Candidates.},
journal = {Cornea},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICO.0000000000004088},
pmid = {42284092},
issn = {1536-4798},
support = {RC-2022/51//Ministero della Salute/ ; },
abstract = {PURPOSE: To characterize the ocular surface microbiome in patients undergoing corneal transplantation and to evaluate microbial shifts associated with corneal endothelial decompensation and surgical history.

METHODS: In this single-center case-control study, conjunctival swabs were collected from 54 adults scheduled for lamellar or penetrating keratoplasty and from 16 healthy controls. Sampling was performed under sterile conditions immediately before surgery. Bacterial DNA was analyzed by 16S rRNA gene sequencing targeting the V3-V4 regions. Alpha and beta diversity indices were calculated using the Shannon index and Bray-Curtis dissimilarity. Taxonomic composition was compared across groups stratified by clinical status and prior ocular surgery.

RESULTS: Pretransplant patients showed significantly higher alpha diversity than healthy controls (P = 0.04), and beta diversity analysis confirmed distinct microbial community structures between groups (P = 0.002). The patient group exhibited enrichment of Enterobacteriaceae, Pseudomonas, and Escherichia-Shigella, whereas Bacteroidota and Bacteroidia predominated in healthy subjects. No significant differences in diversity or composition were observed between decompensated and nondecompensated cases. Patients with prior penetrating keratoplasty displayed higher microbial diversity than those with previous phacoemulsification (P = 0.03).

CONCLUSIONS: Corneal transplant candidates exhibit distinct ocular surface microbial profiles characterized by increased diversity and enrichment of opportunistic taxa. Although endothelial decompensation did not significantly alter microbial composition, prior surgical history appeared to influence diversity patterns. These exploratory findings provide preliminary evidence that the ocular surface microbiome may play a role in the preoperative assessment and postoperative outcomes of corneal transplantation.},
}

@article {pmid42284364,
year = {2026},
author = {Li, M and Sun, P and Zhou, X and Yang, X and Li, W},
title = {Microbial modulation of CNS remyelination in multiple sclerosis: the missing link in gut-brain axis research.},
journal = {Nutritional neuroscience},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/1028415X.2026.2686736},
pmid = {42284364},
issn = {1476-8305},
abstract = {Multiple sclerosis (MS) is a chronic, immune-mediated disorder of the central nervous system (CNS) marked by demyelination and neurodegeneration. While much attention has focused on immune dysregulation and neuroinflammation, the failure of effective remyelination is a key driver of disease progression, especially in progressive MS. Recently, the gut microbiome has emerged as a potent modulator of systemic immunity and CNS function, influencing processes such as neuroinflammation and neurogenesis. This review examines current evidence on microbiota-derived metabolites, including short-chain fatty acids (SCFAs), indole derivatives, and bile acids, and their potential roles in pathways associated with oligodendrocyte precursor cell (OPC) biology and remyelination. Evidence from preclinical models, including germ-free systems, fecal microbiota transplantation (FMT), and probiotic interventions, suggests that microbial signals can modulate immune responses and CNS environments that may indirectly affect demyelination and repair processes. However, direct causal effects on OPC differentiation and functional remyelination remain incompletely established. We critically evaluate the strengths and limitations of existing studies, highlighting inconsistencies across experimental models and the context-dependent nature of microbiota-host interactions. Clinical evidence remains limited, with current studies primarily assessing inflammatory or metabolic outcomes rather than direct measures of remyelination. Key translational challenges include uncertainties regarding metabolite bioavailability in the CNS, cell-specific mechanisms of action, and reproducibility of microbiome-targeted interventions.},
}

@article {pmid42284458,
year = {2026},
author = {Palayyan, SR and Siddiqui, AH and Jiang, P and Margolskee, RF and Sukumaran, SK},
title = {Expression of Calca gene-derived peptides in the murine taste system.},
journal = {Chemical senses},
volume = {},
number = {},
pages = {},
doi = {10.1093/chemse/bjag014},
pmid = {42284458},
issn = {1464-3553},
abstract = {Taste cell regeneration and taste signaling are regulated by myriad growth factors and signaling molecules secreted by neurons and taste papillae-resident cells. The Calcitonin Related Polypeptide Alpha (Calca) gene is a source of four biologically active peptides with varied physiological roles. Alternative splicing of the Calca messenger RNA generates either prepro calcitonin gene related peptide (CGRP) or preprocalcitonin encoding transcripts. Proteolytic processing of preprocalcitonin generates procalcitonin, calcitonin and katacalcin. Calcitonin is a ligand for the G-protein coupled receptor calcitonin receptor (CALCR) while CGRP is a ligand for the CGRP receptor (CGRP1R) formed by the calcitonin receptor like receptor (CALCRL)-receptor activity modifying protein 1 (RAMP1) complex. Interestingly, procalcitonin too, is a ligand for the CGRP1R where it can antagonize CGRP. CGRP expression in taste and trigeminal neurons has been documented and is posited to regulate taste signaling. Single cell and bulk RNASeq of taste papillae revealed that the preprocalcitonin but not the Cgrp transcript is expressed in Tas1r3- expressing type II taste cells, while CGRP1R subunits are expressed in taste stem/progenitor cells and by subsets of fibroblasts and immune cells in the lingual mesenchyme. We confirmed this expression pattern using quantitative polymerase chain reaction (qPCR) and histological techniques. qPCR of geniculate and nodose-petrosal-jugular ganglia revealed that both express Cgrp and CGRP1R subunit mRNAs, but not preprocalcitonin and Calcr. This interesting expression patterns suggests that procalcitonin and CGRP might reciprocally regulate the CGRP1R in the taste papillae and potentially influence taste signaling, taste cell regeneration and the taste microbiome.},
}

@article {pmid42284780,
year = {2026},
author = {Gu, D and Cao, X and Wang, D and Chen, D and Yao, J and Song, M},
title = {Respiration-coupled redox metabolism supports Cr(VI) reduction by an indigenous Bacillus in soil-groundwater systems.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142691},
doi = {10.1016/j.jhazmat.2026.142691},
pmid = {42284780},
issn = {1873-3336},
abstract = {Reliable in situ remediation of Cr(VI)-contaminated soil-groundwater systems remains challenging because introduced microorganisms often show poor persistence, competitiveness, and functional stability under site-specific subsurface conditions. Indigenous microorganisms may provide a more adaptable alternative, yet how their respiratory metabolism, ecological fitness, and community interactions support sustained Cr(VI) reduction and immobilization under field-relevant conditions remains insufficiently understood. Here, an indigenous Cr(VI)-reducing strain GS was isolated and evaluated in aqueous batch cultures, soil microcosms, and a pilot-scale in situ trial, supported by multi-omics and microbiome analyses. Strain GS maintained high Cr(VI) reduction across wide temperature and pH ranges in aqueous cultures. In soil microcosms (100-1000 mg kg[-1] Cr(VI)), strain GS bioaugmentation achieved 66-77% Cr(VI) reduction and shifted chromium from labile pools to more stable solid-phase fractions, indicating effective immobilization. Transcriptomic and metabolomic profiling indicated that Cr(VI) stress activated a respiration-coupled redox response, characterized by enhanced heme/porphyrin metabolism, increased respiration-associated redox activity, and strengthened carbon/redox metabolism. Community analyses identified Bacillus as a key taxon associated with Cr(VI) reduction. A 180-day field trial achieved rapid Cr(VI) depletion in soil and groundwater within 30-120 days and showed no rebound over 180 days. These findings support indigenous Bacillus-based in situ bioremediation as a sustainable strategy for Cr(VI)-contaminated soil-groundwater systems.},
}

@article {pmid42284849,
year = {2026},
author = {Salia, S and Swift-Gallant, A},
title = {Hormones, sex differences, and autism: From single-cause theories to integrated developmental systems.},
journal = {Hormones and behavior},
volume = {183},
number = {},
pages = {105964},
doi = {10.1016/j.yhbeh.2026.105964},
pmid = {42284849},
issn = {1095-6867},
}

@article {pmid42284942,
year = {2026},
author = {Yang, X and Peng, AD and Huang, YH and Cheng, JH and Zhong, HT and Zhou, HT and Liu, PQ and Ji, XH and Li, C and Zhang, SR and Lai, JL and Luo, XG},
title = {Ecological risk assessment of 1,4-thioxane and its remediation by a synthetic microbiome based on a sulfur transformation system: From multi-omics to water application.},
journal = {Water research},
volume = {303},
number = {},
pages = {126258},
doi = {10.1016/j.watres.2026.126258},
pmid = {42284942},
issn = {1879-2448},
abstract = {Among the chemicals in weapons abandoned by Japan in China during World War II, 1,4-thioxane, a typical degradation product of mustard gas, has environmental persistence and potential ecological risks. However, its toxicity mechanism and efficient remediation strategy remain unclear. This study first employed multi-omics technologies (16S sequencing, metagenomics, and metabolomics) to analyze the toxic effects of 1,4-thioxane (0-100 mg·L[-1], 120 days) on water microecology. Subsequently, an efficient degrader, Pseudomonas sp. M1, was screened, and transcriptome analysis revealed significant upregulation of Fe-S cluster assembly-related genes (sufB, sufU, sufS), which are key components of the SUF sulfur conversion system. These three genes were heterologously expressed in Escherichia coli to construct three engineered strains, each capable of degrading 1,4-thioxane via the SUF system. When mixed in equal proportions to form a synthetic microbiome, they completely degraded 100 mg·L[-1] 1,4-thioxane in culture medium within 16 h and achieved 100% removal in simulated polluted water within 15 days. Integrated multi-omics analysis demonstrated that 1,4-thioxane is highly persistent (residual rate > 98%) but significantly inhibits nitrogen cycling, manifested by NH4[+] accumulation (1.5-3.1-fold increase) and NO3[-] depletion (24.9-87.6% decrease), along with reduced ammonia monooxygenase, nitrite oxidoreductase, and nitrate reductase activities (67.8-91.0%, 53.2-90.1%, and 42.8-80.9% reductions, respectively). Ionome analysis showed K and P accumulation and Mo depletion; 16S sequencing revealed reduced microbial diversity, suppression of nitrogen-cycling genera, and enrichment of Pseudomonas; metagenomics uncovered widespread suppression of nitrogen metabolism pathways, dysregulation of antibiotic resistance genes, and decreased viral abundance; and metabolomics confirmed global inhibition of the alanine-aspartate-glutamate pathway. This is the first study to combine multi-omics toxicity analysis with synthetic microbiome remediation based on the SUF sulfur conversion system. The findings provide a theoretical basis and technical support for ecological risk assessment and bioremediation of sites contaminated by relic Japanese chemical weapons.},
}

@article {pmid42285364,
year = {2026},
author = {Bieber, T and Bochner, BS and Boyce, JA and Kabashima, K and Barrett, N and Holloway, JW and Izuhara, K and Jenmalm, M and Kraft, M and Sagi-Eisenberg, R and Sehmi, R and Wenzel, SE and Vercelli, D and , },
title = {Highlights from the 2025 Symposium of the Collegium Internationale Allergologicum.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.05.028},
pmid = {42285364},
issn = {1097-6825},
}

@article {pmid42285653,
year = {2026},
author = {Manikandan, C and Devi V K, A and Manivasagam, G and Pereira, A and Mano, JF and Borges, J and Jaiswal, AK and Udduttula, A},
title = {Nature's blueprint: Exopolysaccharides linking microbiome dynamics to advanced bone tissue engineering.},
journal = {Carbohydrate polymers},
volume = {387},
number = {},
pages = {125447},
doi = {10.1016/j.carbpol.2026.125447},
pmid = {42285653},
issn = {1879-1344},
mesh = {*Tissue Engineering/methods ; Humans ; *Bone and Bones/metabolism ; Animals ; *Polysaccharides, Bacterial/chemistry ; Tissue Scaffolds/chemistry ; Bone Regeneration ; *Microbiota ; *Gastrointestinal Microbiome ; Osteoarthritis/therapy ; Osteogenesis ; },
abstract = {Emerging evidence increasingly suggests a strong correlation linking the human gut microbiome and bone health, particularly in its ability to modulate bone metabolism and the genesis of bone disorders. It is essential to properly understand the mechanisms of the human microbiome to prevent and treat such bone complications. While several therapeutic and analytical techniques have been explored in the past, tissue engineering has recently gained prominence as a strategy that can take advantage of the microbiome's potential. Within this context, microbial exopolysaccharides represent a promising yet largely overlooked source of functional and structural polysaccharides. These natural polymers have significant potential offering meaningful advancements in creating effective materials for bone repair and regeneration. Their potential roles span from enhancing scaffold architecture and mechanical integrity to modulating immune response and promoting osteogenic activity. This review investigates the dynamic interplay between microbiome and bone health through exopolysaccharide-driven tissue engineering. The use of both gut-derived and non-gut microbial EPS in bone tissue engineering has been emphasized. Further EPS driven strategies and their potential for treating bone dysbiosis and contributing to the development of cell-free scaffolds for bone disorders like osteoporosis and osteoarthritis have been discussed.},
}

*Tissue Engineering/methods
Humans
*Bone and Bones/metabolism
Animals
*Polysaccharides, Bacterial/chemistry
Tissue Scaffolds/chemistry
Bone Regeneration
*Microbiota
*Gastrointestinal Microbiome
Osteoarthritis/therapy
Osteogenesis

@article {pmid42285833,
year = {2026},
author = {Zyzynska, K and Rodziewicz, M and Grycner, K and Tretiakow, D and Lipska-Zietkiewicz, BS and Skorek, A},
title = {Early childhood asthma and adenotonsillectomy: From upper airway microbiota to type 2 biomarkers and clinical outcomes.},
journal = {Paediatric respiratory reviews},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.prrv.2026.05.008},
pmid = {42285833},
issn = {1526-0550},
abstract = {Early childhood asthma is one of the most common chronic diseases in children, and its course may be modified by coexisting upper airway obstruction. It remains uncertain whether adenoidectomy or adenotonsillectomy can improve asthma control or reduce exacerbations in children with asthma and obstructive symptoms. Emerging evidence links asthma phenotype, type 2 inflammatory biomarkers (fractional exhaled nitric oxide, blood eosinophilia, periostin, chitinase) and changes in upper airway microbiota with variable clinical responses to surgery. This narrative review summarises studies evaluating the impact of adenoidectomy and adenotonsillectomy on asthma outcomes in paediatric populations, including secondary analyses of major randomised controlled trials (CHAT, PATS). Across heterogeneous cohort and database studies, surgery is associated with improved symptom control and reductions in hospitalisations and emergency visits in selected children, particularly younger patients with severe obstruction and poorly controlled disease despite pharmacotherapy. A post-hoc analysis of the CHAT trial demonstrated a significant reduction in wheezing after adenotonsillectomy, and a secondary analysis of the PATS trial showed a trend toward improved asthma symptom burden, although neither trial was designed with asthma as a primary endpoint. Conversely, some large population-based analyses suggest a neutral effect or even an increased long-term risk of asthma in specific subgroups, underscoring substantial uncertainty. Critically, no randomised controlled trial has evaluated asthma control or exacerbation rate as a primary outcome after adenotonsillectomy, and overall evidence quality is low to very low. Adenotonsillectomy should therefore be considered a targeted option for a carefully selected subgroup of young children with documented upper airway obstruction and poorly controlled asthma, rather than a routine intervention. Well-designed multicentre prospective studies with standardised asthma endpoints, detailed phenotyping and microbiome and biomarker assessment are needed to clarify which patients derive durable benefit and to define the role of surgery within personalised asthma management.},
}

@article {pmid42285959,
year = {2026},
author = {Lyu, C and Wang, Z and Zhao, R and Zhao, H and Liu, S and Lian, H and Wang, X},
title = {Preoperative gut microbial network alterations and BCAA-Related metabolic disturbance in postoperative delirium after cardiac surgery: a prospective matched multi-omic study.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04161-9},
pmid = {42285959},
issn = {2158-3188},
abstract = {Postoperative delirium (POD) is a frequent neuropsychiatric complication after cardiac surgery, yet the biological basis of individual susceptibility remains unclear. In this prospective cohort study, 317 adults undergoing elective on-pump cardiac surgery were enrolled and followed for POD during the first 7 postoperative days. Thirty patients who developed POD were then matched 1:1 with 30 non-POD controls by age, sex, and primary diagnosis for multi-omic analyses. Preoperative fecal samples were collected from the first bowel movement after admission and before prophylactic antibiotic administration, and postoperative fecal samples were collected from the first postoperative bowel movement. Paired fecal samples underwent shotgun metagenomic sequencing, and perioperative serum samples underwent untargeted metabolomic profiling. Preoperatively, α- and β-diversity were comparable between groups, but patients who subsequently developed POD exhibited a less connected and less integrated microbial network structure. Postoperatively, gut microbial composition differed significantly between groups (PERMANOVA R[2] = 0.053, P < 0.001). Metagenomic profiling identified 35 differentially abundant species and 16 differentially enriched KEGG level 3 pathways, with POD-associated features showing inferred functional shifts toward amino-acid catabolism, including branched-chain amino acid (BCAA)-related pathways. Untargeted metabolomics demonstrated marked perioperative remodeling in both groups, but POD was associated with a 27-metabolite panel characterized predominantly by lower postoperative levels or impaired recovery, with pathway enrichment converging on valine, leucine, and isoleucine metabolism. Integrative analyses further linked POD-associated microbial taxa with amino-acid catabolic pathways and lower levels of BCAA-related serum metabolites. These findings suggest that POD is associated with preoperative alterations in microbial network organization and a postoperative microbiome-metabolome disturbance pattern centered on amino-acid metabolism, particularly the BCAA axis.},
}

@article {pmid42286232,
year = {2026},
author = {Byrd, DA and Zouiouich, S and Wahl, D and Pardini, B and Gomez Morales, MF and Tarallo, S and Bulfamante, S and Francavilla, A and Francescato, G and Hogue, SR and Armaroli, P and Bellisario, C and Ferrante, G and Vogtmann, E and Wan, Y and Hua, X and Shi, J and Gunter, M and Naccarati, A and Senore, C and Sinha, R},
title = {Fecal immunochemical tests from population-based colorectal cancer screening programs support prospective microbiome cohorts.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {42286232},
issn = {1532-1827},
abstract = {BACKGROUND: Large, prospective cohorts are needed to research the gut microbiome's role in colorectal cancer (CRC) risk. We evaluated the gut microbiome leveraging residual fecal immunochemical tests (FIT) from a CRC screening program in Turin, Italy, and conducted one of the largest population-based case-control studies across the adenoma-carcinoma sequence to date.

METHODS: We extracted DNA from residual FIT stool, used whole-genome shotgun sequencing, and included those with CRC (N = 44), advanced adenomas (N = 269), early adenomas (N = 134), and FIT-negative controls (N = 478). Alpha diversity, beta diversity, and species, gene, and pathway relative abundances were estimated. Multivariable logistic regression models were used to estimate associations of these metrics with colorectal neoplasms.

RESULTS: Alpha diversity was mostly inversely associated with colorectal neoplasms, particularly early adenomas (OR: 0.45, 95% CI: 0.25-0.80; P = 0.01). Presence of oral pathogens, including Parvimonas micra, was associated with higher odds of CRC. Furthermore, Escherichia coli and Bacteroides fragilis were strongly associated with higher odds of all colorectal neoplasms. Several genes and pathways were associated with colorectal neoplasms.

CONCLUSIONS: Our findings align with smaller studies of the gut microbiome and colorectal neoplasms, supporting that CRC screening programs provide opportunities to prospectively study the gut microbiome's association with cancer risk in large populations.},
}

@article {pmid42286247,
year = {2026},
author = {Glass, EM and Kolling, GL and Papin, JA},
title = {Genome-scale metabolic modelling identifies vaginal microbiome members as potential probiotics.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42286247},
issn = {2058-5276},
support = {R01-AI154242//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; R01-AT010253//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; 1 T 32 GM 145443-1//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; GRFP award number 1842490//National Science Foundation (NSF)/ ; },
abstract = {Probiotic supplements are marketed for diverse health benefits, yet species inclusion often lacks functional rationale. Our survey of 352 over-the-counter probiotic products available in the USA revealed 36 unique microbial species. However, there is no clear link between species inclusion and the intended health benefit. Here, to address this gap, we developed HaPaPro, a collection of 1,012 genome-scale metabolic models spanning pathogenic, probiotic and host-associated bacteria, constructed from publicly available genome sequences. Flux balance analysis revealed that probiotic species fail to capture the metabolic diversity of host-associated microbes. Focusing on vaginal health, we computationally identified vaginal microbes with metabolic profiles overlapping Gardnerella vaginalis. In vitro spent media assays using 11 vaginal isolates showed variable inhibition of G. vaginalis, primarily driven by D-lactic acid production, which was also produced by non-Lactobacillus species. These findings highlight the need for function-based probiotic design and demonstrate a scalable framework integrating metabolic modelling with experimental validation.},
}

@article {pmid42286383,
year = {2026},
author = {Feng, Y and Zhou, Y and Wang, Y and Wang, Y and Liu, X and Sun, T and Xu, J},
title = {The gut-liver axis: exploring microbial dysbiosis and specific biomarkers in hepatocellular carcinoma.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-026-02082-w},
pmid = {42286383},
issn = {2191-0855},
support = {2020-48-3-1//Shenyang Breast Cancer Clinical Medical Research Center/ ; 22-321-31-04//Shenyang Public Health R&D Special Project/ ; 82373113//National Natural Science Foundation of China/ ; 2025-MSLH-421//Natural Science Foundation of Liaoning Province/ ; XLYC1907160//LiaoNing Revitalization Talents Program/ ; },
abstract = {Hepatocellular carcinoma represents a major global health challenge, with its link to the commensal microbiota being clearly established. However, developing reproducible microbial biomarkers for early-stage hepatocellular carcinoma diagnosis across diverse populations remains challenging. We conducted an integrative analysis of 13 studies, examining 16S rRNA sequencing data from 607 fecal samples and 263 liver tissue samples. Data processing utilized VSEARCH, QIIME, and R packages (vegan, phyloseq, cooccur, random forest), with PICRUSt for functional prediction. Alpha diversity analysis revealed significant differences in liver microbiota but not in gut microbiota between hepatocellular carcinoma patients and non-cancer individuals. Linear Discriminant Analysis Effect Size identified Blautia and Streptococcus as biomarker shared across the gut and liver micro-niches. Based on the internal data, the models constructed using gut and liver microbiome characteristics demonstrated high discriminative ability (gut model AUC = 0.8064; liver model AUC = 0.9645). Mendelian randomization analysis revealed a potential association between Streptococcus and the development of hepatocellular carcinoma. KEGG enrichment analysis further indicated marked functional differences in microbiota, primarily linked to metabolic irregularities, between cancer patients and controls. Therefore, this study reveals unique gut-liver microbial community features in patients with hepatocellular carcinoma, identifies potential cross-site diagnostic biomarkers, and constructs gut and liver predictive model with good performance, providing preliminary evidence for the application of microbial biomarkers in the early diagnosis and screening of hepatocellular carcinoma.},
}

@article {pmid42286462,
year = {2026},
author = {Dai, W and Jahangir, M and Li, T and Guo, WJ},
title = {Early-life stress and adolescent circadian dysrhythmia drives unique behavioral and microbial profiles in rats.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05287-y},
pmid = {42286462},
issn = {1471-2180},
support = {82171487//National Natural Science Foundation of China/ ; 2024C03006//"Pioneer" and "Leading Goose" R&D Program of Zhejiang/ ; TD2024003//Leading innovation and entrepreneurship team of Hangzhou/ ; },
abstract = {OBJECTIVES: Early life adversity and circadian disruptions are known to impact neurodevelopment and physiology. This study investigated the effects of maternal separation (MS), adolescent circadian dysrhythmia, and their combination (double hit) on anxiety-like behavior and gut microbiota composition in rats.

METHODS: Rats were divided into four groups: CL (control group: normal early-life conditions with a standard light/dark cycle during adolescence), MS + N (maternal separation (MS) with a standard light/dark cycle (N=normal)) during adolescence), N + ALD (normal early-life conditions (N) with an altered light/dark cycle (ALD) during adolescence), and MS + ALD (combined exposure: MS with an altered light/dark cycle (ALD) during adolescence). Anxiety-like behavior and locomotor activity were assessed using the Open Field Test. Gut microbial diversity and taxonomic composition were analysed to identify microbial shifts across groups.

RESULTS: Behavioral analysis indicated that the combined stress group (MSLD) spent significantly (p < 0.05) more time in the center of the arena compared to the CL, MS + N, and N + ALD groups, suggesting a compromise in risk assessment ability due to dual stress exposure. Microbiome profiling revealed that while a core microbiome was conserved, each stressor generated a unique taxonomic signature. The N + ALD group appeared as the most distinct outlier, characterized by the lowest number of unique features and a specific enrichment of the viral species of phylum Uroviricota. Conversely, the MS + ALD group was distinguished by an enrichment of Bacteroidota species, including Muribaculum intestinale and Phocaeicola vulgatus, while the MS + N group showed enrichment in Bacteroides acidifaciens. Mycobiome analysis showed that early-life stress was the primary driver of fungal restructuring, distinguishing maternal separation groups by the loss of Neocallimastix species and the competitive expansion of Piromyces finnis. While adolescent circadian disruption alone largely preserved the baseline mycobiome, the cumulative dual-hit stress (MS + ALD) generated a distinct dysbiotic profile evident by the unique proliferation of Anaeromyces robustus.

CONCLUSIONS: In conclusion, the developmental timing of stress exposure drives distinct dysbiotic shifts. Specifically, adolescent circadian disruption selectively targets the virome, whereas early-life stress causes shift in the microbiome which endures a long-term foundation for adolescent psychiatric vulnerability. Notably, the cumulative effect of early life and adolescence stressors results in a unique microbial and behavioral profile, highlighting that the specific developmental window of exposure is a decisive factor in gut-brain axis dysfunction.},
}