@article {pmid40945908,
year = {2025},
author = {Gao, H and Wang, H and Li, X and Zhang, F and Ba, Y and Zhao, J and He, C and Xin, S and Liu, X and Liang, G},
title = {From Theory to Practice: A Comprehensive Review of Pseudomyxoma peritonei Research and its Implications for Future Treatment.},
journal = {The American journal of pathology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajpath.2025.08.005},
pmid = {40945908},
issn = {1525-2191},
abstract = {Pseudomyxoma peritonei (PMP) is a rare disease characterized by symptoms such as mucinous ascites and omental cake, typically arising from a perforated epithelial tumour of appendix. Due to its rarity, non-specific histological characteristics, and slow progression, its pathogenesis and optimal treatment remain subjects of debate. PMP is still a challenging and enigmatic condition. Increasing global attention is being directed toward understanding its pathogenesis and establishing standard treatment approaches. PMP and mucin are inextricably linked. This article highlighted the important role of mucin in the disease's pathogenesis. It also discussed several potential therapeutic strategies for eliminating mucin in PMP. Tumor development and metastasis involve a series of steps that include the interaction between the tumor and the host-derived stromal environment, which promotes angiogenesis and activation of inflammatory cells. Inflammatory cytokines and chemokines play a crucial role in the progression and development of PMP. The microbiome and specific microorganisms may directly influence tumor development, progression, and responses to certain therapies in PMP. Thus, the paper summarized the interactions among bacteria, the immune system, and mucin interact in PMP, focusing on the mechanisms that related to abnormal mucin and tumor growth. This review critically examined the existing literature on the clinical features, pathological processes, and treatment options in PMP, aiming to guide future research towards identifying novel therapeutic targets and gut-related disease biomarkers.},
}

@article {pmid40945867,
year = {2025},
author = {He, X and Dennis, KK and Jarrell, ZR and Ly, VT and Go, YM and Jones, DP},
title = {Vanadyl sulfate supplementation alters the intestinal microbiome and bile acid metabolism.},
journal = {Toxicology and applied pharmacology},
volume = {},
number = {},
pages = {117548},
doi = {10.1016/j.taap.2025.117548},
pmid = {40945867},
issn = {1096-0333},
abstract = {Less than 10 μg/kg body weight (BW) vanadium (V) is consumed daily by humans in their diet and drinking water. V in the form of vanadyl sulfate (V[+4]) is promoted as an over-the-counter supplement with anti-diabetic effects and is consumed by some individuals at up to 200 μg/kg BW per day in dietary supplements. The impact of long-term consumption of high-dose V supplements on intestinal microbial communities and intestinal metabolomics is not known. This project tested the hypothesis that long-term intake of high-dose supplemental vanadyl sulfate alters the intestinal microbiome and metabolome in mice. In this study, four-week-old C57BL/6 J female mice were fed standard mouse food and provided V[+4] (0.02, 0.2, 2 mg/L in drinking water) or control drinking water (0 μg V[+4]/d) for 6 months. Cecal contents were analyzed with 16S rRNA microbiome sequencing and liquid chromatography-high-resolution mass spectrometry. Biostatistics, bioinformatics, community detection, and metabolic pathway enrichment analysis were used to characterize vanadyl sulfate-dependent changes to the cecal microbiome and metabolome. Pathway analysis of metabolomics data identified alterations to bile acid metabolism, likely by altering reabsorption, and inflammatory pathways including arachidonic acid and linoleate metabolism. Bile acids including cholic acid, chenodeoxycholic acid/deoxycholic acid, and lithocholic acid were decreased in V[+4]-treated animals. In addition, altered arachidonic acid levels associated with inflammatory pathways were observed. Integrated microbiome-metabolome analysis identified unique communities with inflammation-related metabolites as well as metabolites and microbes linked to bile acid metabolism. In summary, chronic high-dose V[+4] exposure at levels similar to human dietary supplement use altered bile acid metabolism and inflammatory pathways and resulted in compositional changes to the microbiome.},
}

@article {pmid40945782,
year = {2025},
author = {Castillo-Lopez, E and Hartinger, T and Ricci, S and Xu, K and Schwartz-Zimmermann, HE and Berthiller, F and Reisinger, N and Zebeli, Q},
title = {Association between the severity of subacute ruminal acidosis and the microbiome of the rumen, and the metabolome of the rumen, blood, and milk in primiparous cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27008},
pmid = {40945782},
issn = {1525-3198},
abstract = {Cows have been shown to develop different severities of SARA when fed the same diet. In the present study, we used 24 Holstein dairy cows to investigate the association between SARA severity and the ruminal microbiome as well as the metabolomes of the rumen, blood, and milk from 21 d before parturition until 70 DIM. The dietary concentrate was increased from 32% to 60% (DM basis) during the first week of lactation. Based on the severity of SARA, 3 groups were compared: high, moderate, and low severity. Relative to parturition, the rumen microbiome and metabolome were analyzed on d -21, 14, 28, and 56; blood metabolome was analyzed on d -21, -7, 1, 3, 7, 10, 14, 21, 28, 42, 56, and 70, and milk metabolome was analyzed on d 1, 3, 7, 14, 21, 56, and 70. Statistical analysis of the metabolome was performed with MetaboAnalyst v. 6.0; and statistical analyses for microbial abundance data were conducted in R using Maaslin2 package. Rumen microbial abundance profile was not associated with the SARA severity, but several amylolytic acid tolerant genera (i.e., Acidobacteria and Lactobacillus) were found only within the high SARA group. In addition, the transition to the lactation diet decreased fibrolytic bacteria and increased amylolytic and proteolytic bacteria (P < 0.05). In the ruminal metabolome, High SARA was associated with greater levels of nucleotides, nitrogen compounds, and pyrimidine derivatives as well as enrichment of metabolic pathways for nitrogen and AA metabolism (P < 0.05). In the blood metabolome, High SARA was associated with greater levels of cholesterol esters, phosphatidylcholines, and enrichment of metabolic pathways for steroid and bile acid biosynthesis (P < 0.05). In the milk metabolome, moderate SARA was associated with greater levels of triglycerides as well as enrichment of metabolic pathways for fatty acid biosynthesis (P < 0.05). The change from pre- to postpartum increased ruminal triglycerides, amino acids, carbohydrates and their derivatives in the rumen, and increased sugars and lipid derivatives in the blood. Milk showed a decrease mainly in triglycerides with increased DIM compared with first day of lactation. Overall, findings from this study reveal differential metabolomic response of dairy cows when fed the same diet. The greatest differences in the cow metabolome among SARA severity groups were observed either around calving or at peak of lactation, likely due to increased nutrient metabolism. High severity of SARA was associated with enriched metabolic pathways for nitrogen and AA metabolism in the rumen, as well as greater steroid biosynthesis, cholesterol esters and phosphatidylcholines in blood. Moderate SARA severity was associated with enrichment of metabolic pathways for fatty acid biosynthesis and triglycerides in milk.},
}

@article {pmid40945509,
year = {2025},
author = {Louw, NL and Eagan, JL and Larlee, J and Kehler, M and Keller, NP and Wolfe, BE},
title = {Long-term monitoring of a North American cheese cave reveals mechanisms and consequences of fungal adaptation.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.08.053},
pmid = {40945509},
issn = {1879-0445},
abstract = {Previous comparative and experimental evolution studies have suggested how fungi may rapidly adapt to new environments, but direct observation of in situ selection in fungal populations is rare due to challenges with tracking populations over human time scales. We monitored a population of Penicillium solitum over eight years in a cheese cave and documented a phenotypic shift from predominantly green to white strains. Diverse mutations in the alb1 gene, which encodes the first protein in the dihydroxynaphthalene (DHN)-melanin biosynthesis pathway, explained the green-to-white shift. A similar phenotypic shift was recapitulated with an alb1 knockout and experimental evolution in laboratory populations. The most common genetic disruption of the alb1 genomic region was caused by putative transposable element insertions upstream of the gene. White strains had substantial downregulation in global transcription, with genetically distinct white strains possessing divergent shifts in the expression of different biological processes. White strains outcompeted green strains in co-culture, but this competitive advantage was only observed in the absence of light. Our results illustrate how fermented food production by humans provides opportunities for relaxed selection of key fungal traits over short time scales. The local adaptation we observed may be part of a domestication process that could provide opportunities to generate new strains for innovation in fermented food production.},
}

@article {pmid40945381,
year = {2025},
author = {Pathak, VA and Kshirsagar, SJ and Deokar, GS},
title = {Linking altered gut microbiome to polycystic ovarian syndrome through immune mediated pathway.},
journal = {Journal of reproductive immunology},
volume = {172},
number = {},
pages = {104648},
doi = {10.1016/j.jri.2025.104648},
pmid = {40945381},
issn = {1872-7603},
abstract = {Polycystic ovarian syndrome (PCOS) is an endocrine disorder characterized by hyperandrogenism, ovulatory dysfunction, and metabolic disturbances. A balanced gut microbiome plays an important role in managing homeostatic signalling pathways in the body. These pathways regulate normal bodily functions but can become dysregulated under dysbiotic conditions. Recent research has highlighted the role of gut microbiota in the pathogenesis of polycystic ovarian syndrome. Key Bacterial taxa such as Akkermansia, Prevotella, Lactobacillus, Escherichia coli, Bacteroides and Ruminococcaceae (family-level) whose abundance is correlated with disease severity. At dysbiotic conditions, the pathobionts bypass the tight gut junction, enters the systemic circulation and trigger an immunomodulatory response subsequently releasing proinflammatory cytokines. Initially, first line and second line defence mechanisms are generated through immune responses such as IgG-mediated mechanisms. The immunological responses and inflammation cause macrophage pyroptosis, hormonal imbalance, and polycystic ovaries, followed by insulin resistance and hyperinsulinemia. Also, neuroendocrine alterations including dysregulation of GnRH secretion is influenced by gut-derived metabolites. The current review aids in understanding the mechanism pathway between gut microbiota and polycystic ovaries. Understanding 'The Gut-PCOS axis' explores various ways for targeting gut microbiota through prebiotics, probiotics and synbiotics as a potential therapeutic approach for polycystic ovarian syndrome management.},
}

@article {pmid40945353,
year = {2025},
author = {Liu, Q and Kong, X and Yu, T and Jiao, Y and Wu, W and Yue, S and Shen, Y},
title = {Rhizosphere microbial community and function activation in rain-fed agricultural areas confer growth advantages to spring maize.},
journal = {Journal of environmental management},
volume = {393},
number = {},
pages = {127251},
doi = {10.1016/j.jenvman.2025.127251},
pmid = {40945353},
issn = {1095-8630},
abstract = {The integration of maize stover return and organic alternative cropping under mulching (MSO) represents an efficacious production strategy in the rain-fed agricultural landscapes. In this study, we employed a two-year field experiment coupled with high-throughput sequencing technology to delineate the mechanisms by which rhizosphere microbes facilitate spring maize growth under the MSO strategy, thereby elucidating the microbial contributions to crop productivity. Our findings indicate that MSO serves as a potent conduit for soil carbon sequestration, with a 3.48 % increase in soil organic carbon relative to conventional chemical fertilizer applications. The concentrations of microbial biomass carbon, dissolved organic carbon and readily oxidizable carbon reached their zenith under MSO conditions. Soil carbon components emerged as crucial determinants of both bacterial and fungal communities, influencing their composition and potential functionalities. The alteration of the rhizosphere microbiome mediated by stover return reshaped the carbon and nitrogen cycling pathways within the rhizosphere. In the functional prediction of the rhizosphere, stover incorporation reinforced the two-component system process while mitigating the quorum sensing pathway. Within the elemental cycle prediction model, the processes of methane and CO2 generation from organic carbon in the rhizosphere carbon cycle, as well as the nitrification and ammonia oxidation processes in the nitrogen cycle, exhibited divergent trends with the introduction of stover. The co-occurrence network analysis revealed a more robust cooperative network among rhizosphere bacteria under the MSO mode compared to fungi. This study offers a novel perspective on the MSO strategy in rain-fed agricultural regions and underscores the pivotal role of key ecological clusters within the rhizosphere in the plant-microbial interaction process.},
}

@article {pmid40945100,
year = {2025},
author = {Caley, A and Marzinelli, EM and Mayer-Pinto, M},
title = {Limited microbial community responses of marine macroalgae to artificial light at night and moderate warming conditions.},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107536},
doi = {10.1016/j.marenvres.2025.107536},
pmid = {40945100},
issn = {1879-0291},
abstract = {Multiple stressors such as Artificial Light at Night (ALAN) and warming are increasingly common in marine systems and can interact in complex ways. Microbial communities play critical roles in the functioning of coastal habitat-forming species such as seaweeds, however the effects of ALAN on seaweed-associated microbial communities remain unknown. We tested the independent and combined effects of ALAN and warming on microbial communities associated with the habitat-forming seaweeds Ecklonia radiata and Sargassum sp. In Ecklonia, ALAN increased the relative abundance of two potentially light-responsive taxa: Dokdonia sp000212355 and an unidentified ASV from Pseudomonadales, whereas warming had the opposite effect. Warming increased microbial community dispersion in Ecklonia and resulted in non-significant increases in relative abundance of putative pathogenic and agarolytic taxa (microbes capable of degrading algal polysaccharides). However, further analyses using metagenomics are needed to confirm functional roles. In contrast, neither ALAN nor warming affected dominant taxa associated with Sargassum. Contrary to expectations, cyanobacteria relative abundance was unaffected by ALAN in either seaweed host, despite their photosynthetic capacity. We found limited evidence for interactive effects of ALAN and warming, and community composition remained unchanged in both seaweed species. Our findings highlight the importance of considering species-specific microbial responses to ALAN and warming, with implications for coastal management.},
}

@article {pmid40945095,
year = {2025},
author = {Li, Y and Ma, J and Shen, X and Li, X and Zhang, R and Ling, T and Cui, B},
title = {Enhancing cadmium resistance in Kandelia obovata seedlings via Sonneratia apetala: Rhizosphere microbial restructuring as a key mechanism.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {119047},
doi = {10.1016/j.ecoenv.2025.119047},
pmid = {40945095},
issn = {1090-2414},
abstract = {As critical blue carbon ecosystems, the mangrove forests in China's Pearl River Delta (PRD) are under severe pressure from cadmium (Cd) pollution and habitat degradation. The introduction of exotic mangrove species, such as Sonneratia apetala, has been adopted as a restoration strategy, yet it may compromise the ecological niche of native species. However, the physiological responses and rhizosphere microbial dynamics of native mangroves under these dual pressures, particularly during the critical seedling stage, are still largely unknown. In this study, pot experiments were conducted to evaluate how co-planting with S. apetala enhances Cd resistance in seedlings of the native species Kandelia obovata. Results showed that co-planting significantly improved the biomass of K. obovata seedlings (roots: +25.0 %; shoots: +23.0 %) and photosynthetic efficiency under high Cd stress (20 mg·kg[-1]), while reducing Cd translocation to shoots (translocation factor: 0.293 vs. 0.359 in monocultures). Furthermore, co-planting and Cd pollution jointly reshaped the rhizosphere bacterial community, with microbial network analysis identifying three environmentally sensitive modules (Modules 1, 3, and 4) among five. Key bacterial families (Pseudomonadaceae, Comamonadaceae, Moraxellaceae, and Sphingomonadaceae) within these modules presented strong correlations with ammonium nitrogen, nitrate nitrogen, and Cd levels, simultaneously functioning as biomarkers in co-planting systems under high Cd pollution. Partial least squares path modeling demonstrated that the enhancement of Cd resistance in K. obovata seedlings was driven by both rhizosphere microbiome restructuring (total effect = 0.891) and synergistic improvements in photosynthetic performance and nutrient acquisition. These findings demonstrate that interspecific facilitation via S. apetala introduction alleviates Cd toxicity in native mangrove seedlings through multilevel mechanisms, suggesting a potential strategy for improving mangrove seedling establishment and restoration in Cd-polluted environments.},
}

@article {pmid40945093,
year = {2025},
author = {Niu, Y and Zhang, X and Jiao, M and Storey, KB and Shekhovtsov, SV},
title = {Metabolic plasticity and gut microbiome synergy underlie high-altitude adaptation in the plateau frog Rana kukunoris: A multi-omics perspective.},
journal = {Ecotoxicology and environmental safety},
volume = {303},
number = {},
pages = {119050},
doi = {10.1016/j.ecoenv.2025.119050},
pmid = {40945093},
issn = {1090-2414},
abstract = {Life on the Qinghai-Tibet Plateau is exposed to extreme abiotic stressors, yet endemic frog species such as Rana kukunoris thrive due to specialized adaptations. However, the metabolic and gut microbial mechanisms that enable survival at high altitude remain unclear. Here, we used metabolomic analysis and metagenomic sequencing to compare metabolic profiles of liver and skeletal muscle, as well as gut microbial composition and function, between high- (3730 m) and low-altitude (1990 m) populations. Metabolomic profiling revealed significant altitude-driven shifts, including the down-regulation of glycolysis (fructose-1,6-bisphosphate and glyceraldehyde 3-phosphate decreased by 44.2 % and 40.7 %, respectively) and tricarboxylic acid (TCA) cycle intermediates (fumaric acid and malic acid reduced by 37.7 % and 35.9 %, respectively) in the liver, and enhanced oxidative phosphorylation efficiency via elevated flavins (flavin mononucleotide and flavin adenine dinucleotide increased 1.43- and 1.28-fold, respectively) in skeletal muscle. These findings suggest a conserved strategy of metabolic rate depression and tissue-specific metabolic regulation. Significantly differential metabolites were enriched in glycerophospholipid metabolism and glycosylphosphatidylinositol (GPI)-anchor biosynthesis, highlighting membrane remodeling as a key adaptive response to cold stress at high altitudes. Moreover, gut microbiomes of high-altitude frogs exhibited increased α-diversity and functional enrichment in the biosynthesis of secondary metabolites, cofactors, amino acids, and carbohydrate-active enzymes (GHs/GTs), all likely improving tolerance to stressful environments and maintaining homeostasis. Key microbial taxa, including Candidatus Udaeobacter, Desulfovibrio, Bradyrhizobium, and Akkermansia, showed a specific dominance in high-altitude frogs, which may support host energy homeostasis and fortify gut barrier function. Multi-omics data highlighted the convergence of protective mechanisms in high-altitude frogs, including autophagy and two-component/quorum sensing systems. This study reveals significant adaptive remodeling of metabolism and gut microbiota in high-altitude R. kukunoris, providing novel insights into host-microbe synergistic interactions under extreme environments.},
}

@article {pmid40945060,
year = {2025},
author = {Zhang, M and Zhao, C and Zhang, W and Guo, Y and Han, F and Li, Y and Zhou, W},
title = {Stable ammonium assimilation mediates the metabolic adaptation of halophilic microbiome to hypo-osmotic stress in wastewater treatment.},
journal = {Water research},
volume = {288},
number = {Pt A},
pages = {124572},
doi = {10.1016/j.watres.2025.124572},
pmid = {40945060},
issn = {1879-2448},
abstract = {Salinity barrier shapes distinct microbial ecology on earth, and applications of microbiomes are frequently hindered by trans-osmotic challenges. As a central nutrient metabolism, nitrogen transformations may contribute to conquering osmotic perturbations in microbiomes, and thus understanding the nitrogen metabolic responses to non-isosmotic exposure is crucial. Here we uncover that ammonium assimilation mediates the maintenance of physicochemical properties in a marine-derived halophilic microbiome when adapting to hypo-osmotic stress from salinity of 3 % to 0.5 %. An adaptive threshold at salinity approximately around 1 % is observed that reducing osmotic gradients disrupt ammonium assimilation and microbial community stability with decreasing specific ammonium assimilation rates from 2.34 to 0.62 mg-N/(g MLSS h). Multi-omics analysis demonstrates that enhancing ammonium-assimilating function prevents nitrogen metabolic differentiation and promotes production of amino acids and their derivatives recognized as osmoprotectants. Genes coding for transporter systems and mechanosensitive channels are also up-regulated. The results of this study suggest that maintaining stable ammonium assimilation could enhance the amino acid metabolism and subsequent osmoprotectant production, thus improving the metabolic adaptation of the halophilic microbiome to hypotonic conditions. Our findings provide insights into the adaptation of microbiomes to osmotic alterations, and highlight the importance of enhancing ammonium assimilation in engineering microbiomes under environmental stress.},
}

@article {pmid40944778,
year = {2025},
author = {Zhao, J and Liu, H and Badehnoosh, B},
title = {Microbial modulators of the mind: probiotic interventions in hippocampal neurogenesis and cognitive flexibility.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {10},
pages = {151},
pmid = {40944778},
issn = {1572-9699},
abstract = {The gut-brain axis serves as a foundational communication channel between the intestinal microbiome and the brain, facilitating microbial impact on neural functions. Probiotics, defined as health-promoting live microorganisms, are being increasingly investigated for their regulatory effects on neuroplasticity and mental acuity. Recent evidence suggests that probiotics modulate hippocampal neurogenesis, a crucial process underlying learning, memory, and cognitive flexibility. Through the suppression of pro-inflammatory mechanisms, enhancement of neurotrophic factor biosynthesis, alleviation of oxidative burden, and stabilization of HPA axis function, probiotics contribute to sustaining hippocampal neural resilience and promoting synaptic adaptability. Evidence from both preclinical experiments and clinical evaluations suggests that strains like Lactobacillus rhamnosus, Bifidobacterium longum, and Lactobacillus plantarum may play a beneficial role in promoting adaptive cognitive functioning. These benefits are thought to be mediated via increased expression of brain-derived neurotrophic factor, modulation of microglial activation, and alteration of neurotransmitter metabolism including serotonin, dopamine, and GABA. This review synthesizes current findings on the molecular and cellular pathways through which probiotics support hippocampal neurogenesis and cognitive flexibility, and discusses their potential as a non-invasive, adjuvant strategy for cognitive enhancement in neurological disorders and age-related cognitive decline.},
}

@article {pmid40944761,
year = {2025},
author = {Gundogdu, A and Nalbantoglu, OU and Ulgen, M and Sav, MA and Ekinci, G and Kelestimur, F and Türe, U},
title = {Unveiling gut microbiome divergence in sellar-parasellar masses and brain tumors: A link beyond the skull.},
journal = {Neurosurgical review},
volume = {48},
number = {1},
pages = {641},
pmid = {40944761},
issn = {1437-2320},
abstract = {The gut microbiome is increasingly linked to systemic health and central nervous system disorders, including brain tumors. This study investigated gut microbiome composition and metabolic profiles in patients with sellar-parasellar tumors (SPTs), other brain tumor types (OBTs) and healthy controls (HCs) to identify microbial and metabolic biomarkers for brain tumor phenotypes. A cross-sectional study involving 56 participants (17 SPTs, 11 OBTs, 28 HCs) was conducted. Gut microbiota composition was analyzed with 16 S rRNA sequencing, and metabolic activity was inferred via metagenome-scale metabolic models. Multivariable regression and machine learning were used to evaluate microbial and metabolic differences across groups. Taxonomic and metabolic analyses revealed distinct profiles across these groups. The result showed that HCs exhibited higher levels of Lachnospira and Comamonadaceae, while tumor patients had an over-representation of Bacilli. OBT patients showed elevated metabolic exchange scores (MES) for amino acids (D-alanine, L-glutamic acid), carbohydrates (mucin-type O-glycans, alpha-lactose), and lipids (stearic acid, choline), most likely reflecting tumor-associated metabolic demands. Conversely, SPT patients had profiles closer to HCs, with lower MES and reduced systemic disruption. Key taxa such as Akkermansia, Faecalibacterium, and Lachnospira demonstrated tumor-specific adaptive metabolic outputs, emphasizing functional microbial contributions over purely taxonomic roles. These findings highlight the role of gut microbiota in brain tumor progression through altered metabolic pathways, suggesting potential biomarkers and therapeutic targets for neuro- oncology. The study integrates genome-scale metabolic modeling with 16 S profiling to show that functional metabolic divergence can exist even when taxonomic differences are subtle, revealing overlooked biomarkers of the gut-brain axis in neuro-oncology.},
}

@article {pmid40944668,
year = {2025},
author = {Huh, E and Kim, JM and Kim, SH and Choi, Y and Park, MG and Oh, MS},
title = {Methylglyoxal Aggregates α-Synuclein by Inhibiting SIRT1-Hif-1α in Intestinal Enteroendocrine Cells.},
journal = {International journal of toxicology},
volume = {},
number = {},
pages = {10915818251378724},
doi = {10.1177/10915818251378724},
pmid = {40944668},
issn = {1092-874X},
abstract = {Parkinson's disease (PD) is characterized by the abnormal aggregation of α-synuclein, which can originate in the gut and propagate to the brain. Recent evidence suggests a correlation between metabolic disorders, particularly diabetes, and PD pathogenesis through the gut-brain axis. Methylglyoxal (MGO), a glucose-derived metabolite produced by gut bacteria such as Proteus mirabilis, is implicated in protein misfolding and glycation. This study investigated whether MGO induced α-synuclein aggregation in intestinal enteroendocrine cells and explored the underlying mechanisms. Mouse enteroendocrine STC-1 cells were treated with MGO (0.01-1 mM) for 36 h, and changes in α-synuclein aggregation, neuronal markers, and relevant signaling pathways were assessed. MGO at 1 mM significantly reduced cell viability and neuronal marker expression, and concentrations of 0.1 and 1 mM increased α-synuclein aggregation. MGO also inhibited SIRT1 expression, leading to increased Hif-1α transcription and reduced expression of autophagy-related proteins Beclin1 and LC3B. These changes were accompanied by mitochondrial dysfunction, as evidenced by decreased Bcl2, increased cytochrome C expression, and reduced levels of the antioxidant factor HO-1. Our findings provide the first evidence that MGO directly induces α-synuclein aggregation in enteroendocrine cells via the SIRT1-Hif-1α-autophagy pathway dysregulation, establishing a potential mechanistic link between gut microbiome-derived metabolites and PD pathogenesis. These results suggest that intestinal glycation may be a critical target for preventing α-synuclein pathology originating in the gut.},
}

@article {pmid40944450,
year = {2025},
author = {Lock, C and Miller, TC and Anthony, CJ and Rouzé, H and Fifer, J and McDermott, G and Tramonte, CA and Paulino, L and Davies, SW and Raymundo, L and Bentlage, B},
title = {Symbiodiniaceae and Bacterial Microbiome Dynamics Differentially Impact the Survival of Dominant Reef-Flat Porites Corals.},
journal = {Environmental microbiology},
volume = {27},
number = {9},
pages = {e70175},
doi = {10.1111/1462-2920.70175},
pmid = {40944450},
issn = {1462-2920},
support = {OIA-1946352//National Science Foundation/ ; },
abstract = {Coral reefs face significant threats across the globe, prompting a surge in restoration efforts aimed at mitigating their global decline. The health, resilience, and adaptability of corals are greatly influenced by their microbial communities, and while the response of coral microbiomes to many environmental stressors has been extensively studied, less is known about their natural dynamics following transplantation, which is an essential process for restoring degraded reef habitats. In this study, we integrated DNA metabarcoding (16S & ITS2) with ecological monitoring to investigate the dynamics of Symbiodiniaceae and bacterial communities in two dominant coral spp., Porites lobata and Porites cylindrica, and their different colour morphs, as they underwent transplantation and an 18-week acclimatisation period. We saw significant differences in microbial communities between the two Porites spp., outplanting sites, and individual coral colonies, as well as a colour morph-related difference in P. lobata bacterial communities. We saw reduced relative abundances of Endozoicomonadaceae, specifically from the genus Parendozoicomonas, following transplantation. P. lobata colonies with later Symbiodiniaceae shifts (18 weeks) had lower long-term survival. Changes in Symbiodiniaceae and bacterial communities have implications for holobiont function and colony survival, which should be considered when designing and implementing coral reef rehabilitation projects.},
}

@article {pmid40944292,
year = {2025},
author = {Szrejder, M and Piwkowska, A},
title = {Gut Microbiome-Derived Short-Chain Fatty Acids in Glomerular Protection and Modulation of Chronic Kidney Disease Progression.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172904},
pmid = {40944292},
issn = {2072-6643},
abstract = {Chronic kidney disease (CKD) is a progressive disorder that is characterized by the gradual loss of kidney function, often leading to end-stage renal failure. Recent research has highlighted the role of gut dysbiosis and its metabolic byproducts in the pathogenesis of CKD, with a particular focus on short-chain fatty acids (SCFAs). SCFAs, including acetate, propionate, and butyrate, are primarily produced by the fermentation of dietary fibers by the gut microbiota and are known for their systemic anti-inflammatory and immunomodulatory properties. In CKD, gut dysbiosis results in a reduction in SCFA-producing bacteria and an increase in uremic toxin-producing microorganisms, contributing to systemic inflammation, oxidative stress, and renal fibrosis. The depletion of SCFAs has been shown to exacerbate glomerular injury, whereas their presence supports integrity of the glomerular barrier and confers protection against damage. These protective effects are mediated by several mechanisms, including the modulation of immune responses, preservation of epithelial barrier function, and activation of specific receptors, such as G protein-coupled receptor 41 (GPR41), GPR43, and GPR109A. The present review provides a comprehensive overview of current understanding of SCFA-mediated pathways in glomerular protection during CKD progression. It highlights the therapeutic potential of targeting the gut-kidney axis to mitigate CKD progression by examining the complex interplay between gut microbiota and disease development, with a particular focus on strategies to protect the glomerular structure and function.},
}

@article {pmid40944290,
year = {2025},
author = {Li, X and Liu, B and Sekar, D and Sur, M and Reddy, J and Natarajan, SK and Lund, PJ and Yu, J},
title = {Shiitake Mushroom-Derived Vesicle-like Nanoparticles Improve Cognitive Function and Reshape Gut Microbiota and Fecal Metabolome in Aged Mice.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172902},
pmid = {40944290},
issn = {2072-6643},
support = {DK124590//National Institute of Health/ ; 2021-67017-34206//United States Department of Agriculture/ ; },
abstract = {BACKGROUND/OBJECTIVES: Population aging and its associated chronic conditions have become an unprecedented challenge in the United States and worldwide. Many aged individuals experience certain forms of cognitive decline, which increases their risk of developing a pre-dementia condition called mild cognitive impairment and even dementia. No effective pharmacological treatments are available to treat normal age-associated cognitive decline or mild cognitive impairment. Our previous study has shown the potent anti-inflammatory effects of shiitake mushroom-derived vesicle-like nanoparticles (S-VLNs) in vitro and in an acute inflammatory disease model. In this study, we aimed to investigate the potential benefits of orally administered S-VLNs in aged mice.

METHODS: S-VLNs were extracted from fresh shiitake mushrooms. S-VLNs in phosphate-buffered saline (PBS) or vehicle only was orally administered to 13-month-old male C57BL/6J mice weekly for 9 months. These mice were subjected to a series of physiological tests, followed by euthanasia at 22 months of age. Their fecal samples were subjected to 16S rRNA and untargeted metabolomics analyses, followed by comprehensive bioinformatics analyses.

RESULTS: The long-term oral administration of S-VLNs significantly improved the cognitive function of aged mice. Orally administered S-VLNs did not travel to the brain. Instead, they impacted the composition of the gut microbiota and reshaped the fecal metabolome. Functional predictions of the gut microbiota and fecal metabolome suggested that S-VLNs regulated tryptophan metabolism. Specifically, S-VLNs markedly decreased the tryptophan-related metabolite kynurenic acid (KYNA). The integrative analyses of omics data identified a strong correlation between 18 gut bacterial genera and 66 fecal metabolites. KYNA was found to highly correlate with five genera positively and twelve genera negatively.

CONCLUSIONS: The oral intake of S-VLNs represents a new and superior dietary approach with the ability to modulate the gut microbiota and fecal metabolome and to improve cognitive function during aging.},
}

@article {pmid40944282,
year = {2025},
author = {Grasa-Ciria, D and Couto, S and Samatán, E and Martínez-Jarreta, B and Cenit, MDC and Iguacel, I},
title = {Disrupted Rhythms, Disrupted Microbes: A Systematic Review of Shift Work and Gut Microbiota Alterations.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172894},
pmid = {40944282},
issn = {2072-6643},
abstract = {Background: Shift work, especially during nighttime hours, disrupts the circadian system and is linked to higher rates of metabolic, gastrointestinal, cardiovascular, and neurocognitive disorders. Emerging evidence suggests that gut microbiota may mediate these associations. This systematic review assessed whether shift work alters gut microbiota composition and explored potential health consequences. Methods: A systematic search was conducted in PubMed, Scopus, and ScienceDirect from inception to March 2025. Studies reporting gut microbiota alterations in adult shift workers were included. Two reviewers independently screened articles and extracted data. Risk of bias was assessed using the NIH Quality Assessment Tool and the ROBINS-E framework. Five studies met the eligibility criteria and were included in the final synthesis. Results: The selected studies comprised four observational investigations with small sample sizes and one Mendelian randomization study leveraging large-scale genetic datasets. Observational studies reported reduced α-diversity and increased relative abundance of pro-inflammatory genera-including Escherichia/Shigella, Blautia, and Dialister-in night shift workers. These microbiota alterations were associated with gastrointestinal complaints and indicators of cardiometabolic dysfunction. The Mendelian randomization study provided preliminary evidence supporting a causal relationship between circadian misalignment, gut dysbiosis, and increased cardiovascular risk. Conclusions: Shift work is associated with significant alterations in gut microbiota composition that may contribute to adverse health outcomes. However, current evidence is limited and heterogeneous, preventing firm causal conclusions. Further high-quality longitudinal and interventional research is needed to clarify underlying mechanisms and inform preventive strategies.},
}

@article {pmid40944274,
year = {2025},
author = {Qu, Z and Wu, Y and Jiang, Y and Fan, J and Cao, L and Dong, Y and Fang, S and Gu, S},
title = {Effects of Two Compound Probiotic Formulations on Gastrointestinal Symptoms and Gut Microbiota: A 4-Week Randomized, Double-Blind Intervention Trial.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172886},
pmid = {40944274},
issn = {2072-6643},
support = {231100310200//Major Science and Technology Special Projects in Henan Province/ ; },
abstract = {Background/Objectives: Probiotic interventions can alleviate gastrointestinal (GI) discomfort, but evidence comparing multi-strain combinations at different doses remains limited. We evaluated whether formulation potency influences clinical and microbiome outcomes. Methods: In a 4-week, randomized, double-blind trial, 100 eligible adults received one of two higher-dose multi-strain probiotic formulations at different dosages (Wec120B vs Wec300B). Weekly Gastrointestinal Symptom Rating Scale (GSRS) scores tracked symptom trajectories. Gut microbiota composition and diversity were profiled by 16S rRNA gene sequencing. Biomarkers included lipopolysaccharide (LPS), fecal calprotectin (FC), and immunoglobulin A (IgA). Results: Results indicated that the Wec120B group showed more significant improvement in abdominal pain during the early phase of intervention, while the Wec300B group was more effective in relieving reflux symptoms. In terms of biomarkers, Wec120B was more effective in reducing lipopolysaccharide (LPS) levels, whereas Wec300B showed a greater increase in immunoglobulin A (IgA) and a more pronounced reduction in fecal calprotectin (FC) levels. Both formulations significantly increased the abundance of beneficial genera such as Bifidobacterium, Blautia, [Eubacterium]_hallii_group, and Anaerostipes, while suppressing the growth of potential pathogens including Prevotella and Escherichia-Shigella. Conclusions: These findings suggest that both compound probiotic products can significantly improve GI symptoms and modulate gut microbiota structure, with Wec300B showing a superior performance in microbial regulation, likely due to its higher dosage of probiotics. This study provides reference evidence for the rational application of probiotic products in gut health management.},
}

@article {pmid40944264,
year = {2025},
author = {Hayden, M and Stewart, EC and Almatani, MF and Case, J and Rice, S and Rompato, G and Hintze, KJ and Benninghoff, A},
title = {Cocoa Polyphenols Modulate the Mouse Gut Microbiome in a Site-Specific Manner.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172876},
pmid = {40944264},
issn = {2072-6643},
support = {UTA-01456//Utah Agricultural Experiment Station/ ; 2018-67017-27516//U.S. Department of Agriculture/ ; },
abstract = {Background/Objectives: The dietary modulation of the gut microbiome is a promising strategy for mitigating gastrointestinal diseases, such as inflammatory bowel disease (IBD) and colitis-associated colorectal cancer (CAC). Cocoa powder is rich in polyphenols, including (-)-epicatechin and (+)-catechin, which have been associated with beneficial effects on gut health and microbiome modulation. Importantly, changes in the bacterial populations associated with the gut mucosal layer may have different health impacts compared to changes in cecal or fecal microbiomes. This study investigated the effects of cocoa polyphenol supplementation on microbiome composition across the cecal, fecal, and mucosal compartments in a mouse model of colitis. Methods: Mice were fed either a healthy AIN93G diet (AIN) or a total Western diet (TWD), with or without 2.6% (w/w) CocoaVia™ Cardio Health Powder. Gut microbiomes from the cecum, feces, and colon mucosa were profiled using 16S rRNA sequencing at three time points: pre-, during, and post-colitis. Results: Microbiome composition varied substantially by site, with reduced richness and distinct taxa in the mucosal layer compared to cecal and fecal communities. The TWD significantly altered microbial composition, decreasing species evenness and shifting beta diversity. Cocoa polyphenol supplementation modulated microbial communities in a site-specific manner, increasing diversity and promoting rare taxa (e.g., Monoglobaceae, Eggerthellaceae, and RF39) primarily in cecal and fecal samples. Mucosa-associated communities were less responsive. Conclusions: These findings underscore the importance of the sampling site in gut microbiome research. Cocoa polyphenols exert site-selective effects, particularly in the gut lumen, highlighting the importance of considering anatomical context in dietary intervention studies aimed at improving gastrointestinal health.},
}

@article {pmid40944251,
year = {2025},
author = {Page, L and McCain, E and Freemark, M},
title = {Adaptive Responses in Severe Acute Malnutrition: Endocrinology, Metabolomics, Mortality, and Growth.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172864},
pmid = {40944251},
issn = {2072-6643},
abstract = {Malnutrition afflicts millions of the world's children and predisposes to death from diarrhea and infectious diseases. Children with severe acute malnutrition (SAM) are at highest risk. Our review of the endocrinology and metabolomics of SAM implicates critical roles for white adipose tissue and its regulatory hormones and growth factors in the adaptation to nutritional deprivation and the restoration of metabolic homeostasis: white adipose provides substrates and energy for hepatic glucose production and cardiopulmonary and central nervous system function, and products of fat metabolism inhibit muscle glucose uptake and utilization and spare muscle protein. Collectively, these effects maintain glucose availability for the brain, red blood cells, and renal medulla and conserve muscle mass. White adipose tissue also secretes leptin, which facilitates the immune response and may protect against mortality from infection. Euglycemia and survival in SAM are thereby prioritized over linear growth, which is suppressed owing to inhibition of insulin-like growth factor 1 production and action. Diversion of energy from growth serves to maintain essential bodily functions in critically ill malnourished children, who have limited energy reserves. Thus, short-term reductions in growth rate have adaptive benefits in SAM. Under favorable conditions, clinical and metabolic recovery are accompanied by catch-up growth, which can mitigate, and in many cases reverse, the stunting of growth in childhood. Nevertheless, clinical recovery can be complicated by preferential accrual of central fat and a relative deficiency of lean/skeletal mass, with potential long-term complications including insulin resistance, glucose intolerance, and metabolic syndrome.},
}

@article {pmid40944193,
year = {2025},
author = {Fayyaz, K and Din, MSU and Bashir, H and Ahmad, F and Barrow, CJ and Khalid, N},
title = {Personalized Nutrition Biomarkers and Dietary Strategies for Atherosclerosis Risk Management: A Systematic Review.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172804},
pmid = {40944193},
issn = {2072-6643},
support = {PSF/Res/P-UMT/Agr (502)//Pakistan Science Foundation/ ; },
abstract = {Background/Objectives: Atherosclerosis is a major contributor to ischemic cardiovascular diseases (CVDs) such as myocardial infarction and stroke, which are leading causes of mortality and morbidity. The management of atherosclerosis through personalized nutrition has gained importance in recent years due to advancements in nutrigenomics, gut microbiome evaluation, and metabolomics. However, no systematic review has comprehensively evaluated the impact of personalized nutrition interventions on atherosclerotic plaque progression and clinical outcomes in humans. Methods: We adopted a systematic approach based on Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Key databases like PubMed, Cochrane, Google Scholar, and MEDLINE via EBSCOhost were searched using predefined terms related to personalized nutrition, atherosclerosis, nutrigenomics, and clinical outcomes. Results: Evidence evaluation using the framework of Boffetta et al. for cumulative evidence on the joint effects of genes and environments strongly suggested significant diet-gene interactions. Polymorphisms in the apolipoprotein A-II (APOA2) gene have been shown to influence body mass index and lipid levels. Furthermore, studies have demonstrated that omega-3 polyunsaturated fatty acids (PUFAs) can modulate microRNA expression, thereby impacting lipid metabolism. Epigenetic studies showed that dietary components can modify histone acetylation and non-coding RNA activity, which ultimately influence gene expression related to inflammation and lipid metabolism, improving clinical outcomes in atherosclerosis management. Conclusions: Integrating personalized nutrition into clinical practice promises to enhance atherosclerosis outcomes through targeted dietary interventions. Advancements in personalized nutrition offer a promising pathway toward more effective and personalized approaches to cardiovascular health.},
}

@article {pmid40944192,
year = {2025},
author = {Nie, H and Li, Q and Zhao, K and Li, W and Zhang, C and Jiang, X},
title = {Potential Efficacy of Propolis in Treating Helicobacter pylori Infection and Its Mechanisms of Action.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172803},
pmid = {40944192},
issn = {2072-6643},
support = {32302812//the National Natural Science Foundation of China/ ; 31972627//the National Natural Science Foundation of China/ ; r Anhui Education Secretary Department [2023]13//Biological and Medical Sciences of Applied Summit Nurturing Disciplines in Anhui Province/ ; },
abstract = {BACKGROUND: Helicobacter pylori (H. pylori) is a major pathogen associated with a variety of gastrointestinal disorders, including gastritis, peptic ulcers, and gastric cancer. As a natural bioactive product, propolis exhibits multifaceted and multi-mechanistic effects. Due to its immunomodulatory, anti-inflammatory, and antioxidant properties, propolis has emerged as a promising therapeutic alternative, offering an innovative approach to managing H. pylori infections and providing new insights into addressing antibiotic resistance.

METHODS: This comprehensive review, synthesizing data from PubMed, ScienceDirect, and SciFinder, examines the mechanisms by which propolis combats H. pylori.

RESULTS: Propolis has demonstrated significant antibacterial efficacy against H. pylori in both in vitro and in vivo models. Its multitargeted mechanisms of action include direct inhibition of bacterial growth, interference with the expression of virulence factors, suppression of virulence-associated enzymes and toxin activity, immunomodulation, and anti-inflammatory effects. These combined actions alleviate gastric mucosal inflammation and damage, reduce bacterial colonization, and promote mucosal healing through antioxidant and repair-promoting effects. Furthermore, propolis disrupts oral biofilms, restores the balance of the oral microbiome, and exerts bactericidal effects in the oral cavity. Synergistic interactions between propolis and conventional medications or other natural agents highlight its potential as an adjunctive therapy.

CONCLUSIONS: Propolis demonstrates dual functionality by inhibiting the release of inflammatory mediators and suppressing H. pylori growth, highlighting its potential as an adjuvant therapeutic agent. However, clinical translation requires standardized quality control and higher-level clinical evidence. Future research should focus on validating its clinical efficacy and determining optimal dosing regimens, and exploring its role in reducing H. pylori recurrence.},
}

@article {pmid40944184,
year = {2025},
author = {Venter, C and Boden, S and Pickett-Nairne, K and O'Mahony, L and Glime, GNE and Matzeller, KL and Frank, DN and Kotter, C and Kofonow, JM and Robertson, CE and Campbell, WW and Krebs, NF and Tang, M},
title = {Blueberry Consumption in Early Life and Its Effects on Allergy, Immune Biomarkers, and Their Association with the Gut Microbiome.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172795},
pmid = {40944184},
issn = {2072-6643},
support = {UM1 TR004399/TR/NCATS NIH HHS/United States ; 1R01DK126710//NIH/NIDDK/ ; NA//Section of Allergy and Immunology, Children's Hospital Colorado/ ; NA//US Highbush Blueberry Council/ ; },
abstract = {Background/Objectives: The complementary feeding period is a critical window for shaping infant diet, gut microbiota, and immune development. While allergic symptoms often emerge in the first year of life, the effects of specific foods, such fruits, on infant allergy symptoms, inflammation, immunity and associated microbiota remain unclear. This study aimed to assess the impact of daily blueberry consumption during the complementary feeding period on allergy-related symptoms, immune biomarkers, and gut microbiota in breastfed U.S. infants. Methods: In a double-blind, randomized, placebo-controlled trial, infants from the Denver metro area were assigned to receive up to 10 g/day of freeze-dried blueberry powder or an isocaloric placebo from 5 to 12 months of age. Stool, blood, and caregiver-reported allergy-related symptom data were collected at baseline and study end. Results: Of the 76 infants enrolled, 61 completed the study (Blueberry: n = 30; Placebo: n = 31). While more infants in the blueberry group had allergy-related symptoms at baseline, they had significantly different longitudinal symptom trajectories than the placebo (p = 0.05), showing a greater resolution rate of symptoms by study end. Pro-inflammatory serum IL-13 levels were significantly reduced (p = 0.035) and anti-inflammatory IL-10 levels borderline increased (p = 0.052) in the blueberry group. However, changes in allergy symptoms were not significantly associated with IL-10 or IL-13. The relative abundances of Lacticaseibacillus, Blautia, and Peptostreptococcaceae at 12 months were negatively correlated with IL-10, while Lactobacillus, Clostridiaceae, and Megasphaera were positively associated. IL-13 was positively associated with Citrobacter and negatively associated with Anaerostipes and Blautia. Conclusions: The consumptio9n of blueberries as an early complementary food may improve resolution of allergy symptoms, modulate immune biomarkers, and promote beneficial shifts in gut microbiota during infancy. Future research should aim to identify the specific bioactive components of blueberries responsible for these effects and explore the potential of other complementary foods to favorably influence developing biological systems involved in microbiota and immune development.},
}

@article {pmid40944183,
year = {2025},
author = {Mahdi, L and Graziani, A and Baffy, G and Mitten, EK and Portincasa, P and Khalil, M},
title = {Unlocking Polyphenol Efficacy: The Role of Gut Microbiota in Modulating Bioavailability and Health Effects.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172793},
pmid = {40944183},
issn = {2072-6643},
abstract = {In humans, the bioactivity of polyphenols is highly dependent on dose intake and their interactions with the gastrointestinal tract and gut microbiota, which metabolize polyphenols into bioactive or inactive derivatives. Polyphenols are only partially absorbed in the small intestine, where enzymatic hydrolysis releases aglycone forms that may cross the gut barrier. A significant proportion of polyphenols escapes absorption and reaches the colon, where resident microbes convert them into simpler phenolic metabolites. Such molecules are often more bioavailable than the parent compounds and can enter systemic circulation, leading to distant effects. Although higher polyphenol consumption has been associated with preventive and therapeutic outcomes, even low intake or poor intestinal absorption may still confer benefits, as polyphenols in the colon can positively modulate gut microbiota composition and function, contributing to favorable shifts in the microbial metabolome. These interactions can influence host metabolic, immune, and neurological pathways, particularly through the gut-liver-brain axis. To provide a comprehensive understanding of these relationships, this review examines the dose-related activity of polyphenols, their microbiota-mediated biotransformation, their bioavailability, and the health effects of their metabolites, while also presenting a comparative overview of key studies in the field. We underscore the importance of integrating microbiome and polyphenol research to recapitulate and contextualize the health benefits of dietary polyphenols.},
}

@article {pmid40944126,
year = {2025},
author = {Napier, BA and Allegretti, JR and Feuerstadt, P and Kelly, CR and Van Hise, NW and Jäger, R and Kassam, Z and Reid, G},
title = {Multi-Species Synbiotic Supplementation Enhances Gut Microbial Diversity, Increases Urolithin A and Butyrate Production, and Reduces Inflammation in Healthy Adults: A Randomized, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172734},
pmid = {40944126},
issn = {2072-6643},
support = {N/A//Seed Health, Inc./ ; },
abstract = {Background: In healthy adults, probiotic supplementation alone does not increase Urolithin A (UroA) and rarely increases butyrate, both microbiome-derived metabolites that influence key biological functions involved in regulating gastrointestinal symptoms. Accordingly, this clinical trial evaluated key biological functions of a multi-species synbiotic with 24 probiotic strains and a polyphenol-based prebiotic using capsule-in-capsule delivery technology. Methods: We conducted a randomized, placebo-controlled trial among healthy participants (n = 32). Participants were administered a daily synbiotic (53.6 billion AFU multi-species probiotic and 400 mg Indian pomegranate extract; DS-01) or matching placebo for 91 days. Samples were obtained at baseline Day 0, and Days 7, 14, 49, and 91. Endpoints included changes in fecal microbiome composition, urinary UroA, fecal butyrate, serum CRP, and safety. Results: The synbiotic significantly increased alpha-diversity of Bifidobacterium and Lactobacillus spp. at all timepoints, including at end-of-study (Day 91, p < 0.0001) and increased native beneficial microbes. UroA production was significantly increased in the synbiotic arm at short-term (Day 7, 12-fold, p < 0.02) and long-term (Day 91, 49-fold, p < 0.001) timepoints. A higher proportion of synbiotic participants were capable of converting polyphenols into UroA (Day 91, 100% vs. 44.4%; p < 0.01). Mechanistically, synbiotic participants showed an increased abundance of Lactobacillus species involved in UroA precursor metabolism and UroA-producing Gordonibacter species. The synbiotic also significantly increased fecal butyrate levels (p < 0.03), and butyrate-producing species, in low-baseline butyrate producers, through Day 91, and was associated with reduced systemic inflammation. Conclusions: This multi-species synbiotic significantly increases diversity and abundance of key beneficial bacteria, enhances UroA production and butyrate levels, and is associated with lowered systemic inflammation. This is the first synbiotic to increase both UroA and butyrate.},
}

@article {pmid40944120,
year = {2025},
author = {Sala-Climent, M and Bu, K and Coras, R and Cedeno, M and Zuffa, S and Murillo-Saich, J and Mannochio-Russo, H and Allaband, C and Hose, MK and Quan, A and Choi, SI and Nguyen, K and Golshan, S and Blank, RB and Holt, T and Lane, NE and Knight, R and Scher, J and Dorrestein, P and Clemente, J and Guma, M},
title = {Targeted Microbial Shifts and Metabolite Profiles Were Associated with Clinical Response to an Anti-Inflammatory Diet in Osteoarthritis.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172729},
pmid = {40944120},
issn = {2072-6643},
support = {NA//Krupp Endowed Fund/ ; },
abstract = {Introduction: Osteoarthritis (OA) is a chronic degenerative joint disease with limited treatment options focused primarily on symptom management. Emerging evidence suggests that dietary interventions may influence inflammation and pain through modulation of the gut microbiome and metabolome. Methods: We conducted a 4-week open-label pilot trial evaluating the effects of an anti-inflammatory dietary intervention (ITIS diet) in 20 patients with knee OA (ClinicalTrials.gov ID: NCT05559463, registered prior to enrollment; sponsor: University of California, San Diego; responsible party: Monica Guma; study start date: 1 October 2021). The following were assessed before and after the intervention: (1) clinical outcomes; (2) gut and salivary microbiomes; and (3) salivary, stool, and plasma metabolomes. Responders were defined as patients achieving ≥30% reduction in Western Ontario and McMaster Universities Arthritis Index (WOMAC) pain scores. Results: The ITIS diet was well-tolerated, with good adherence (66.2%) and a significant improvement in clinical outcomes, including reduced pain and improved overall health measured with the visual analog scale (VAS). Responders (n = 8) showed distinct gut microbiome and metabolome profiles compared to non-responders (n = 12). Notably, taxa within the Lachnospiraceae family exhibited dynamic, bidirectional shifts post-intervention: Anaerostipes and Limivivens were enriched among responders and negatively correlated with pain scores, while Oliverpabstia and Fusicatenibacter were depleted following dietary intervention. These taxa also showed strong correlations with anti-inflammatory metabolites, including hydroxydecanoic acid derivatives and pyridoxine. Furthermore, subsequent network analysis revealed more structured and selective microbiome-metabolome interactions in responders, specifically post-intervention. Conclusions: This pilot study shows that a short-term anti-inflammatory dietary intervention was associated with meaningful changes in the gut microbiome and metabolome. Members of the Lachnospiraceae family emerged as key taxa associated with pain reduction and anti-inflammatory metabolite production. Our findings suggest that specific microbial responses-rather than global diversity changes-may underlie dietary responsiveness in OA. Although exploratory and limited by sample size, our results support further investigation into personalized, microbiome-informed nutritional strategies for OA management.},
}

@article {pmid40944110,
year = {2025},
author = {López-Carrasquillo, J and Ramos-Plaza, VY and Cruz, ML and Rodriguez-Morales, BM and Sánchez, R and López, P and Chompré, G and Appleyard, CB},
title = {Probiotic and Vitamin D Ameliorate TNBS-Induced Colitis by Targeting Mucosal Barrier and Neutrophil Infiltration.},
journal = {Nutrients},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/nu17172719},
pmid = {40944110},
issn = {2072-6643},
support = {1R25GM082406-19/NH/NIH HHS/United States ; 1T32GM144896-22/NH/NIH HHS/United States ; 1U54MD007579-19/NH/NIH HHS/United States ; Porter Physiology Development Fellowship//American Physiological Society/ ; },
abstract = {BACKGROUND/OBJECTIVE: Probiotic and vitamin D supplements are widely studied in clinical and animal studies as potential treatments for inflammatory bowel disease. However, their potential synergistic or additive effect in ameliorating colitis development is still poorly understood. The aim of this study was to investigate the potential beneficial enhancement of combining a mixed-strain probiotic with vitamin D supplementation in a colitis animal model.

METHOD: After 5 days of acclimation, C57BL/6 mice received Vivomixx probiotic (at least 1 × 10[9] Colony-Forming Units) and/or vitamin D (5 IU/g) in drinking water and chow, respectively, for 7 days prior to intracolonic TNBS-induced colitis and until sacrifice. On day 10, animals were sacrificed, and colons were collected to assess colonic damage, cytokine and chemokine expression, total M1 macrophage phenotype, and neutrophil recruitment. Serum and fecal samples were collected to assess vitamin D levels and microbiome composition.

RESULTS: Administration of probiotic and vitamin D alone or combined decreased colonic damage and neutrophil recruitment and activity. This effect was associated with an increase in the active form of vitamin D in serum and mucosal barrier integrity. However, administration of probiotics and/or vitamin D did not modulate macrophage infiltration or the M1 pro-inflammatory phenotype.

CONCLUSIONS: These results suggest that combined probiotic and vitamin D supplementation attenuates TNBS-induced colitis by targeting neutrophil infiltration while enhancing the mucosal barrier. This alternative approach may offer protective potential for IBD management.},
}

@article {pmid40943897,
year = {2025},
author = {Lee, CH and Min, M and Jin, SS and Sivamani, RK},
title = {Skin Microbiome Shifts in Various Dermatological Conditions.},
journal = {Journal of clinical medicine},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/jcm14176137},
pmid = {40943897},
issn = {2077-0383},
abstract = {Background/Objectives: The human skin provides a protective barrier composed of bacteria, fungi, viruses, and archaea that prevents the invasion of harmful organisms. Recent advancements in genomic sequencing have allowed for greater accuracy of species detection. This review aims to summarize the most up-to-date skin microbiome shifts in various dermatological diseases. Methods: A systematic search was conducted to examine microbiome shifts comparing lesional and nonlesional or diseased and healthy skin across various dermatological conditions. A literature search was conducted on PubMed, Web of Science, and Embase Databases from inception through April 2024, yielding 38 studies. Results: Staphylococcus aureus was reported unanimously in all skin conditions. Most studies in this review, except those investigating acne vulgaris, showed a decreased microbiome diversity in diseased skin. Finally, there was a greater shift in the proportion of pro-inflammatory bacterial and fungal strains. Conclusions: The skin microbiome is significantly altered in the progression of numerous dermatological diseases. Diversity of the skin microbiome is decreased, and there is an increased proportion of pro-inflammatory bacterial and fungal strains. The skin microbiome also provides a more comprehensive understanding of the development and progression of many inflammatory skin diseases. Prebiotic treatments may propose a much safer and cheaper alternative to antibiotics, which can have highly toxic side effects and negative implications for public health regarding antibiotic resistance. More research is required to fully understand both the microbiome changes and efficacy and viability of using probiotic treatments to restore the skin microbiome, thereby improving patient outcomes in all dermatological conditions.},
}

@article {pmid40943878,
year = {2025},
author = {Appiah, JK and Hayat, U and Garg, N and Asante, R and Donneyong, E and Haider, MU and Patel, P and Khan, Z and Siddiqui, AA},
title = {Emerging Therapies in Inflammatory Bowel Disease: A Comprehensive Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/jcm14176119},
pmid = {40943878},
issn = {2077-0383},
abstract = {Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), represents a significant challenge in gastroenterology due to its chronic nature, unpredictable course, and impact on patients' quality of life. The therapeutic landscape for IBD has evolved significantly with the advent of biologic agents targeting specific immune pathways. However, limitations, including partial efficacy, side effects, and development of resistance, highlight the ongoing need for innovative treatment approaches. This review explores emerging therapies in IBD, including novel biologics, small molecules, microbiome-based therapies, and gene and stem cell therapies. The article summarizes their mechanisms of action, clinical efficacy, safety profiles, and potential future directions in IBD management. Methods: This comprehensive narrative review synthesizes current knowledge and emerging developments in inflammatory bowel disease (IBD) therapeutics. Literature was identified through targeted selection of high-quality sources, including pivotal randomized controlled trials, systematic reviews and meta-analyses, regulatory approval documents, and clinical practice guidelines from major gastroenterology societies. Emphasis was placed on recent publications (2020-2024) to capture the rapidly evolving therapeutic landscape, with particular attention to FDA/EMA-approved therapies and promising late-stage investigational agents. Sources were prioritized based on clinical relevance, study quality, and regulatory status. This narrative approach was selected to provide comprehensive coverage of diverse therapeutic modalities spanning conventional treatments to cutting-edge techniques, including biologics, small molecules, microbiome-based therapies, gene therapy, and stem cell treatments. The review acknowledges the inherent limitations of non-systematic literature selection while prioritizing clinical utility and educational value for healthcare providers managing IBD patients in contemporary practice.},
}

@article {pmid40943798,
year = {2025},
author = {Roszkiewicz, J and Lach, J and Baranowska, M and Strapagiel, D and Wyka, K and Smolewska, E},
title = {The Intestinal Microbiome in Juvenile Idiopathic Arthritis-Results of a Single-Center Pilot Study from Poland.},
journal = {Journal of clinical medicine},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/jcm14176038},
pmid = {40943798},
issn = {2077-0383},
support = {503/1-000-01/503-81-002-19-00.//Medical University of Lodz/ ; },
abstract = {Background: Altered microbiome structures are perceived as one of the factors triggering the rise of autoimmune diseases, including juvenile idiopathic arthritis (JIA). Despite the extensive research conducted on rheumatoid arthritis (RA), data on microbiome compositions in pediatric populations are scarce and inconclusive. Moreover, no study has addressed this issue in Polish patients with rheumatic diseases. Objectives: The aim of our study was to compare diversity in the fecal microbiome and concentration of the intestinal permeability marker zonulin in patients with new-onset JIA and healthy subjects. Materials and Methods: 15 treatment- naive patients with JIA and 15 age- and sex-matched controls qualified for the study. Analyses of fecal microbiome structure were performed using 16SrRNA gene sequencing, while concentration of serum zonulin was established using the ELISA method. Results: We found no statistically significant difference in alpha (p = 0.92) and beta diversity (p = 0.57)in the fecal microbiome between JIA patents and healthy children. Additionally, analyses of relative abundances of phyla, families, and genera identified no differences. Zonulin concentration did not vary (p = 0.88) between the study and control groups. Conclusions: There is no statistically significant difference in fecal microbiome structure between new-onset JIA patients and healthy controls.},
}

@article {pmid40943665,
year = {2025},
author = {Regvar, M and Bočaj, V and Mravlje, J and Pelko, T and Likar, M and Pongrac, P and Vogel-Mikuš, K},
title = {Towards Understanding the Factors Shaping the Composition and Function of the Noccaea Microbiome in Metal-Contaminated Environments.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178748},
pmid = {40943665},
issn = {1422-0067},
support = {P10212//The Slovenian Research and Innovation Agency/ ; J1-3014//The Slovenian Research and Innovation Agency/ ; J1-50014//The Slovenian Research and Innovation Agency/ ; J7-60126//The Slovenian Research and Innovation Agency/ ; J43091//The Slovenian Research and Innovation Agency/ ; N4-0346//he Slovenian Research and Innovation Agency/ ; },
abstract = {Noccaea species (formerly Thlaspi) are Brassicaceae plants renowned for their capacity to hyperaccumulate zinc (Zn), cadmium (Cd), and nickel (Ni), which has made them model systems in studies of metal tolerance, phytoremediation, and plant adaptation to extreme environments. While their physiological and genetic responses to metal stress are relatively well characterised, the extent to which these traits influence microbiome composition and function remains largely unexplored. These species possess compact genomes shaped by ancient whole-genome duplications and rearrangements, and such genomic traits may influence microbial recruitment through changes in secondary metabolism, elemental composition, and tissue architecture. Here, we synthesise the current findings on how genome size, metal hyperaccumulation, structural adaptations, and glucosinolate diversity affect microbial communities in Noccaea roots and leaves. We review evidence from bioimaging, molecular profiling, and physiological studies, highlighting interactions with bacteria and fungi adapted to metalliferous soils. At present, the leaf microbiome of Noccaea species remains underexplored. Analyses of root microbiome, however, reveal a consistent taxonomic core dominated by Actinobacteria and Proteobacteria among bacterial communities and Ascomycetes, predominantly Dothideomycetes and Leotiomycetes among fungi. Collectively, these findings suggest that metal-adapted microbes provide several plant-beneficial functions, including metal detoxification, nutrient cycling, growth promotion, and enhanced metal extraction in association with dark septate endophytes. By contrast, the status of mycorrhizal associations in Noccaea remains debated and unresolved, although evidence points to functional colonisation by selected fungal taxa. These insights indicate that multiple plant traits interact to shape microbiome assembly and activity in Noccaea species. Understanding these dynamics offers new perspectives on plant-microbe co-adaptation, ecological resilience, and the optimisation of microbiome-assisted strategies for sustainable phytoremediation.},
}

@article {pmid40943646,
year = {2025},
author = {Kovenskiy, A and Katkenov, N and Ramazanova, A and Vinogradova, E and Jarmukhanov, Z and Mukhatayev, Z and Kushugulova, A},
title = {Bacteroides fragilis and Microbacterium as Microbial Signatures in Hashimoto's Thyroiditis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178724},
pmid = {40943646},
issn = {1422-0067},
support = {AP19675503//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Hashimoto's thyroiditis (HT) and alopecia areata (AA) are organ-specific autoimmune diseases that frequently co-occur, suggesting shared immunological and microbial pathways. The gut microbiome has emerged as a key modulator of immune function, yet disease-specific microbial signatures remain poorly defined. Fecal samples from 51 participants (HT: n = 16, AA: n = 17, healthy controls: n = 18) aged 18-65 years were analyzed using shotgun metagenomic sequencing followed by multivariate statistical analyses. While alpha and beta diversity did not differ significantly across groups, taxonomic profiling revealed disease-specific microbial patterns. Bacteroides fragilis was significantly enriched in HT, suggesting a potential role in immune modulation; although mechanisms such as polysaccharide A production and molecular mimicry have been proposed in previous studies, their involvement in HT remains to be confirmed. Microbacterium sp. T32 was elevated in both HT and AA, indicating its potential as a shared autoimmune marker. Functional analysis showed increased fermentation and amino acid biosynthesis in AA, contrasting with reduced metabolic activity and elevated carbohydrate biosynthesis in HT. HT and AA exhibit distinct gut microbial and metabolic signatures. Bacteroides fragilis and Microbacterium sp. T32 may serve as potential microbial correlates for autoimmune activity, offering new insights into disease pathogenesis and targets for microbiome-based interventions.},
}

@article {pmid40943606,
year = {2025},
author = {Garaci, E and Russo, MA and Pariano, M and Puccetti, M and Fabi, C and Balucchi, S and Bellet, MM and Ricci, M and Fini, M and Romani, L},
title = {Innovative Approaches to Medical Rehabilitation: Regeneration, Immune Training, Homeostasis, and Microbiome Synergy.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178687},
pmid = {40943606},
issn = {1422-0067},
support = {847507//HDM-FUN/ ; },
abstract = {This article explores an integrative framework for medical rehabilitation that combines regenerative medicine, systemic homeostasis, and microbiome modulation to optimize recovery and long-term health. Moving beyond conventional rehabilitation approaches focused on symptomatic recovery, this multidimensional paradigm emphasizes cellular repair, physiological balance, and microbial health as interdependent pillars of effective recovery. The framework leverages advancements in stem cell therapy, immune system modulation, and microbiota-targeted interventions to address both immediate functional restoration and long-term systemic resilience. By highlighting the synergistic interplay between these components, this article provides actionable insights into transforming medical rehabilitation into a proactive and holistic endeavor, paving the way for enhanced therapeutic outcomes and sustained patient well-being.},
}

@article {pmid40943581,
year = {2025},
author = {Gałęcki, R and Nowak, A and Szulc, J},
title = {Tenebrio molitor Meal-Induced Changes in Rat Gut Microbiota: Microbiological and Metagenomic Findings.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178663},
pmid = {40943581},
issn = {1422-0067},
support = {LIDER/5/0029/ L-12/20/NCBR/2021//National Centre for Research and Development/ ; },
abstract = {As demand for sustainable protein sources grows, edible insects like Tenebrio molitor (yellow mealworm) are gaining attention as functional feed ingredients. This study investigated how dietary inclusion of T. molitor meal affects gut microbiota composition and diversity in laboratory rats. Wistar rats were divided into three diet groups: standard feed, 35% chicken meal, and 35% T. molitor meal. Fecal samples were collected at weeks 4, 6, and 8. Microbial populations were assessed using culture-based methods, and community structure was analyzed at week 9 via Illumina MiSeq 16S rRNA sequencing. Bioinformatic analyses evaluated microbial diversity and predicted functions. Rats fed T. molitor meal showed significantly reduced counts of total aerobic/anaerobic bacteria, fungi, and coagulase-positive staphylococci. Metagenomics revealed a Firmicutes-dominated microbiota, with enrichment of protein- and cholesterol-metabolizing taxa (e.g., Eubacterium coprostanoligenes, Oscillospiraceae, Ruminococcaceae), and a decline in fiber- and mucin-degrading bacteria like Akkermansia and Muribaculaceae. Functional predictions indicated upregulated amino acid metabolism and chitin degradation. Despite compositional shifts, microbial diversity remained stable, with no signs of dysbiosis. These findings suggest that T. molitor meal supports a safe, functional adaptation of gut microbiota to high-protein, chitin-rich diets, supporting its potential use in monogastric animal nutrition.},
}

@article {pmid40943575,
year = {2025},
author = {Rubas, NC and Torres, A and Maunakea, AK},
title = {The Gut Microbiome and Epigenomic Reprogramming: Mechanisms, Interactions, and Implications for Human Health and Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178658},
pmid = {40943575},
issn = {1422-0067},
support = {R01MD016593//National Institute on Minority Health and 510 Health Disparities/ ; R56MD014630//National Institute on Minority Health and 510 Health Disparities/ ; },
abstract = {The human gut microbiome is a metabolically active and ecologically dynamic consortium that profoundly influences host physiology, in part by modulating epigenetic mechanisms such as DNA and RNA methylation. These modifications regulate gene expression and phenotypic plasticity and are shaped by a combination of environmental factors, such as diet, stress, xenobiotics, and bioactive microbial metabolites. Despite growing evidence linking microbial signals to host epigenetic reprogramming, the underlying molecular pathways remain incompletely understood. This review highlights recent mechanistic discoveries and conceptual advances in understanding microbiome-host epigenome interactions. We discuss evolutionarily conserved pathways through which gut microbiota regulate host methylation patterns, including one-carbon metabolism, polyamine biosynthesis, short-chain fatty acid signaling, and extracellular vesicle-mediated communication. We also examine how host factors such as aging, diet, immune activity, and sociocultural context reciprocally influence microbial composition and function. Beyond basic mechanisms, we outline translational frontiers-including biomarker discovery, live biotherapeutic interventions, fecal microbiota transplantation, and adaptive clinical trial designs-that may enable microbiome-informed approaches to disease prevention and treatment. Advances in high-throughput methylation mapping, artificial intelligence, and single-cell multi-omics are accelerating our ability to model these complex interactions at high resolution. Finally, we emphasize the importance of rigorous standardization and ethical data governance through frameworks such as the FAIR and CARE principles. Deepening our understanding of how the gut microbiome modulates host epigenetic programs offers novel opportunities for precision health strategies and equitable clinical translation.},
}

@article {pmid40943542,
year = {2025},
author = {Farràs Solé, N and Wydh, S and Alizadeh Bahmani, AH and Bui, TPN and Nieuwdorp, M},
title = {Endogenous Ethanol Metabolism and Development of MASLD-MASH.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178609},
pmid = {40943542},
issn = {1422-0067},
support = {101141346/ERC_/European Research Council/International ; 2022 [09150162210057]//ZonMw, The Dutch Organisation for knowledge and innovation in health, healthcare and well-being/ ; 2020 (09150182010020)/NWO_/Dutch Research Council/Netherlands ; HORIZON-WIDERA-2023-ACCESS-02-01//STRIMHealth/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is an increasingly prevalent liver disorder driven by metabolic dysregulation and inflammation. Recent studies highlight the importance of the gut microbiome as a key contributor to this pathology through its ability to ferment dietary sugars into ethanol, a metabolite previously overlooked in MASLD. In this review, we discuss the role of the gut microbiome in MASLD, covering functional and compositional shifts observed in the disease; we dive into the different microbial pathways of ethanol synthesis, hepatic mechanisms of ethanol clearance, and pathological consequences. We also discuss the role of a healthy microbiome in the clearance of ethanol in the gut and how microbiome-based strategies could be beneficial in targeting endogenous production of ethanol, going from the traditional probiotic-prebiotic combination to discussing new approaches.},
}

@article {pmid40943539,
year = {2025},
author = {Sadegh, H and Choi, JP},
title = {The Emerging Role of the Gut Microbiome in Cerebral Cavernous Malformation: A New Novel Therapeutic Strategy?.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178622},
pmid = {40943539},
issn = {1422-0067},
abstract = {Cerebral cavernous malformation (CCM) is a cluster of abnormal blood vessels in the brain that leads to severe neurological deficits, seizures, and fatal hemorrhagic stroke. Currently, there is no available drug treatment for CCM. Most CCMs are conservatively managed by observing change in appearance (MRI), recent hemorrhage, or any clinical symptoms. Neurosurgery is the only current treatment option, but it is only effective in a few cases. Since most CCM lesions are surgically inaccessible, when left untreated they lead to severe neurological deficits, seizures, and fatal hemorrhagic stroke. Hence, new non-invasive, safe, and effective treatment strategies are urgently needed. Recent research has identified gut microbiome dysbiosis and its innate immune response as the critical stimulus in experimental CCM pathogenesis, demonstrating the importance of the gut-brain axis in CCM. Importantly, CCM patients also manifest gut microbiome dysbiosis and gut barrier health can impact CCM disease course. This review highlights the emerging involvement of the gut microbiome in CCM pathogenesis and its potential as a therapeutic target. While preclinical data suggest mechanistic links, the lack of clinical intervention studies limits current applicability and underscores the need for translational research.},
}

@article {pmid40943536,
year = {2025},
author = {Çirkin, G and Aydemir, S and Açıkgöz, B and Çelik, A and Güler, Y and Kiray, M and Baykara, B and Dinleyici, EÇ and Öztürk, Y},
title = {Hepatic Histopathological Benefit, Microbial Cost: Oral Vancomycin Mitigates Non-Alcoholic Fatty Liver Disease While Disrupting the Cecal Microbiota.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178616},
pmid = {40943536},
issn = {1422-0067},
abstract = {Non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH) encompasses a spectrum of liver conditions and involves gut-liver axis crosstalk. We aimed to evaluate whether oral vancomycin modifies liver injury and the cecal microbiota in a methionine-choline-deficient (MCD) diet model of NASH. Male C57BL/6J mice (n = 28) were block-randomized to four groups (n = 7 each) for 10 weeks: standard diet (STD); MCD diet; STD + vancomycin (VANC); and MCD + VANC (2 mg/mouse ≈ 50 mg/kg, every 72 h). After 10 weeks, liver tissues were analyzed for histological changes, cytokine levels [interleukin-6 (IL-6), interleukin-8 (IL-8), transforming growth factor beta 1 (TGF-β1)], and immunohistochemical markers [ubiquitin and cytokeratin 18 (CK18)]. Cecal microbiota composition was evaluated with 16S ribosomal RNA (rRNA) sequencing. The MCD reproduced key NASH features (macrovesicular steatosis, lobular inflammation). Vancomycin shifted steatosis toward a microvesicular pattern and reduced hepatocyte injury: CK18 and ubiquitin immunoreactivity were decreased in MCD + VANC vs. MCD, and hepatic IL-8 and TGF-β1 levels were lower in MCD + VANC vs. STD. Taxonomically, STD mice had Lactobacillus-rich microbiota. The MCD diet alone reduced alpha diversity (α-diversity), modestly lowered Firmicutes and increased Desulfobacterota/Fusobacteriota. Vancomycin alone caused a much larger collapse in richness, depleting Gram-positive commensals and promoting blooms of Escherichia-Shigella, Klebsiella, Parabacteroides, and Akkermansia. In the MCD + VANC group, vancomycin profoundly remodeled the microbiota, eliminating key commensals (e.g., Lactobacillus) and enriching Desulfobacterota, Fusobacteriota, and Campylobacterota. Oral vancomycin in the MCD model of NASH improved liver injury markers and altered steatosis morphology, but concurrently reprogrammed the gut into a low-diversity, pathobiont-enriched ecosystem with near-loss of Lactobacillus. These findings highlight a therapeutic trade-off-hepatic benefit accompanied by microbiome cost-that should guide microbiota-targeted strategies for NAFLD/NASH.},
}

@article {pmid40943494,
year = {2025},
author = {Barraza-Ortega, E and Gómez-Gil, B and García-Gasca, T and Lizárraga, D and Díaz, N and García-Gasca, A},
title = {The Impact of Lifestyle on Reproductive Health: Microbial Complexity, Hormonal Dysfunction, and Pregnancy Outcomes.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178574},
pmid = {40943494},
issn = {1422-0067},
abstract = {Endocrine dysfunctions refer to alterations in hormone production, release, or regulation that can significantly impact health. In pregnant women or those planning pregnancy, these conditions may manifest as disorders such as polycystic ovary syndrome, hypothyroidism, endometriosis, gestational diabetes mellitus, and other metabolic issues, which could potentially cause infertility or pregnancy complications. Research and clinical experience indicate that hormones play a crucial role in basic physiology and are essential for overall health and well-being. At the same time, lifestyle-defined as daily habits related to nutrition, exercise, sleep, stress management, and other factors-directly influences microbial composition and hormonal regulation. The human microbiome, a diverse community of microorganisms residing within the human body, plays essential roles in supporting overall health. The increasing prevalence of hormonal disorders, especially in urban populations, has heightened interest in how modern lifestyles-characterised by sedentary habits, chronic stress, imbalanced diets, and inadequate sleep-may contribute to the development or aggravation of these conditions, leading to higher infertility rates or pregnancy complications if untreated. This review investigates the interaction between hormonal dysfunction, the human microbiome, and lifestyle factors, with a focus on their effects on pregnant women and those seeking to conceive. Its purpose is to provide a comprehensive overview of the underlying pathophysiological mechanisms and to examine preventative and therapeutic approaches that could alter these patterns.},
}

@article {pmid40943460,
year = {2025},
author = {Del Rio, EA and Valenzano, MC and DiGuilio, KM and Rybakovsky, E and Kjelstrom, S and Montone, G and Mercogliano, G and Newman, G and Wong, P and Albert, N and Burris, V and Szymanski, K and Rodriguez, A and Hollis, E and Kossenkov, A and Mullin, JM},
title = {Orally Administered Zinc Gluconate Induces Tight Junctional Remodeling and Reduces Passive Transmucosal Permeability Across Human Intestine in a Patient-Based Study.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178540},
pmid = {40943460},
issn = {1422-0067},
support = {2023-02//Sharpe-Strumia Research Foundation of the Bryn Mawr Hospital/ ; },
abstract = {This study focuses on the issue of whether orally administered zinc (gluconate) (26 mg BID) can induce the remodeling of gastrointestinal barrier function and reduce passive leak across the human intestinal mucosal barrier in situ. Increased transmucosal leak has been implicated in diseases as diverse and seemingly unconnected as Inflammatory Bowel Disease (IBD), Celiac Disease, Autism Spectrum Disorders and Alzheimer's Dementia. Our current investigation represents the first patient-based study to examine the effect of zinc on gastrointestinal epithelial tight junctions and gastrointestinal barrier leak in otherwise healthy test subjects. Using independent test subject groups for each endpoint, three separate molecular analyses indicated that zinc treatment can achieve a positive outcome: (1) RNA-seq analyses of intestinal biopsies showed salutary patterns of gene transcription changes dealing with not only transcripts of junctional proteins but also transcripts mitigating the proinflammatory state, as well as dedifferentiation (both modulators of tight junction permeability); (2) Western immunoblot analyses of intestinal tissue indicated that tight junctional protein expression was being modified by the administered zinc, most notably Claudin-2 and Tricellulin; (3) zinc treatment induced a reduction in serum levels of a functional marker of passive intestinal leak, namely the GI microbiome metabolite D-Lactate. The data collectively suggest that orally administered zinc can induce remodeling of the intestinal epithelial barrier, resulting in the reduction in GI barrier leak. The overall safety and economy of supplement levels of zinc suggest that this micronutrient could be efficacious as an adjuvant therapy to reduce the condition known as leaky gut, and possibly therefore be protective regarding diseases postulated to involve leaky gut.},
}

@article {pmid40943440,
year = {2025},
author = {Grieco, T and Paolino, G and Moliterni, E and Chello, C and Sernicola, A and Brandi, ML and Egan, CG and Morelli, M and Nannipieri, F and Battaglia, S and Accoto, M and Tirotta, E and Trasciatti, S and Bonaretti, S and Calvieri, C and Pellacani, G and Calvieri, S},
title = {Non-Skeletal Roles of Vitamin D in Skin, Gut, and Cardiovascular Disease: Focus on Epithelial Barrier Function and Immune Regulation in Chronic Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178520},
pmid = {40943440},
issn = {1422-0067},
support = {N/A//Abiogen Pharma S.p.A/ ; },
abstract = {Vitamin D is increasingly recognized as a key regulator of epithelial barrier integrity and mucosal immune homeostasis, with implications extending far beyond skeletal health. Through the vitamin D receptor (VDR), vitamin D regulates epithelial cohesion, innate immune responses, and tight-junction gene expression. This review explores the multifactorial role of vitamin D in modulating inflammation and preserving tissue barriers, with particular emphasis on its effects on tight junction (TJ) regulation and disease states characterized by barrier dysfunction, namely atopic dermatitis, psoriasis, inflammatory bowel disease (IBD), and celiac disease. In these settings, vitamin D/VDR signaling exerts protective actions by enhancing barrier structure, suppressing Th1/Th17-driven inflammation, modulating the gut and skin microbiome, and promoting epithelial repair. Animal studies and clinical data suggest that vitamin D supplementation can restore TJ expression, reduce disease activity, and improve clinical outcomes in both intestinal and dermatologic diseases. In the cardiovascular system, the role of vitamin D remains complex. While vitamin D influences endothelial function, insulin sensitivity, and systemic inflammation, supplementation trials yield mixed results, indicating a need for individualized approaches. Overall, this review synthesizes mechanistic, translational, and clinical data supporting vitamin D as a crucial modulator of barrier integrity and inflammation. These findings highlight its therapeutic relevance in chronic diseases characterized by immune dysregulation and epithelial disruption.},
}

@article {pmid40943341,
year = {2025},
author = {Yang, EJ},
title = {The Emerging Role of the Brain-Gut Axis in Amyotrophic Lateral Sclerosis: Pathogenesis, Mechanisms, and Therapeutic Perspectives.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178419},
pmid = {40943341},
issn = {1422-0067},
support = {(KIOM) KSN2224011//KIOM/ ; },
abstract = {Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease characterized by progressive loss of motor neurons. Although genetic and environmental factors are established contributors, recent research has highlighted the critical role of the gut-brain axis (GBA) in ALS pathogenesis. The GBA is a bidirectional communication network involving neural, immune, and endocrine pathways that connect the gut microbiota with the central nervous system. Dysbiosis in ALS disrupts this axis, leading to increased intestinal permeability, neuroinflammation, and excitotoxicity. Notably, reductions in butyrate-producing bacteria, alterations in microbial metabolites, and enhanced NLRP3 inflammasome activation have been observed in patients with ALS. These changes may precede motor symptoms, suggesting a potential causative role. Interventions targeting the microbiome, such as dietary modulation, have shown promise in delaying disease onset and reducing inflammation. However, the clinical evidence remains limited. Given that gut dysbiosis may precede neurological symptoms, microbiota-targeted therapies offer a novel and potentially modifiable approach to ALS treatment. Understanding the role of GBA in ALS will open new avenues for early diagnosis and intervention. Further clinical trials are required to clarify the causal links and evaluate the efficacy of microbiome-based interventions. Understanding the brain-gut-microbiota axis in ALS could lead to new diagnostic biomarkers and therapeutic strategies.},
}

@article {pmid40943331,
year = {2025},
author = {Skenderidou, I and Leontopoulos, S and Skenderidis, P},
title = {Functional Food Ingredients Enhancing Immune Health.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178408},
pmid = {40943331},
issn = {1422-0067},
abstract = {Functional foods enriched with bioactive compounds-including vitamins, minerals, polyphenols, probiotics, fatty acids, and amino acids-have gained growing attention due to their ability to modulate immune responses. This review aims to summarize and critically evaluate evidence from both preclinical and clinical studies on the immunomodulatory effects of these compounds. A structured literature search was performed across major scientific databases in accordance with PRISMA 2020 guidelines. Seventy studies met the predefined eligibility criteria and were included. Evidence indicates that functional ingredients support immune function via antioxidant, anti-inflammatory, and microbiome-mediated pathways. Clinical trials further report benefits including a reduced risk of respiratory infections and enhanced vaccine responses. Nonetheless, important challenges remain regarding bioavailability, inter-individual variability, and the long-term safety of supplementation. Emerging research on precision nutrition and innovative delivery systems may further enhance the efficacy of these bioactive compounds. Overall, functional foods and nutraceuticals show strong potential as adjunct strategies for maintaining immune health; however, further well-designed clinical studies are required to confirm their translational applicability.},
}

@article {pmid40943196,
year = {2025},
author = {Dicks, LMT},
title = {Are an Aging Gut and a Decrease in Butyrate Production the Reasons for Atherosclerosis?.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178276},
pmid = {40943196},
issn = {1422-0067},
abstract = {Atherosclerosis (AS) is directly linked to the aging and damage of endothelial cells (ECs). As ECs and vascular smooth muscle cells (VSMCs) age, more autocrine and paracrine signals are released, extending a vicious cycle of tissue aging and physiological dysfunction. The recruitment of immune cells to inflamed arteries, including coronary arteries, and an increase in the uptake of oxidised low-density lipoprotein (ox-LDL) by macrophages (foam cells) onto the tunica intima (intima) of coronary arteries restrict blood flow. The inability of aging and damaged ECs to accommodate vast changes in signalling molecules, many produced by gut microbiota, leads to a range of anatomical and physiological arterial anomalies. These include degradation of cardiovascular membranes, fibrosis, calcification, plaque formation, and an increasingly dysfunctional immune system. Changes in the gut microbiome of the elderly have a direct effect on the immune response, as the signalling molecules produced by gut microbiota target specific receptors on inflamed arteries. This review summarizes the anatomical and physiological changes associated with the aging of coronary arteries and emphasizes the conditions leading to AS. The importance of butyrate-producing gut microbiota in preventing AS, especially in the elderly, is discussed.},
}

@article {pmid40943103,
year = {2025},
author = {Deethai, P and Siriwathanakul, C and Pitchakarn, P and Imsumran, A and Wongnoppavich, A and Dissook, S and Chewonarin, T},
title = {Perilla frutescens Seed Residue Extract Restores Gut Microbial Balance and Enhances Insulin Function in High-Fat Diet and Streptozotocin-Induced Diabetic Rats.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178176},
pmid = {40943103},
issn = {1422-0067},
support = {FF67/024//Chiang Mai University/ ; },
abstract = {The seed residue of Perilla frutescens possesses diverse biological properties and is rich in bioactive phytochemicals, including luteolin, rosmarinic acid, and apigenin. The aim of this study was to investigate the anti-diabetic effects of perilla seed residue crude extract (PCE) and its impact on the composition of the gut microbiome in rats with diabetes induced by a high-fat diet (HFD) and streptozotocin (STZ). Forty male Wistar rats were fed on an HFD for six weeks before receiving an injection of STZ injection to induce diabetes. These rats were then treated for four weeks with metformin (100 mg/kg bw) or PCE (100 and 1000 mg/kg bw) alongside a control group maintained on a normal diet. The results showed that PCE treatment improved metabolic parameters in diabetic rats, as evidenced by reduced water and food intake, increased body weight gain, lower blood glucose levels, and enhanced insulin secretion effects, especially at the 100 mg/kg bw dosage. PCE also promoted the regeneration of pancreatic β-cells and improved utilization of glucose. PCE also suppressed inflammation and oxidative stress, enhanced antioxidant capacity, and reduced circulating triglyceride levels. Most notably, PCE administration increased gut microbial diversity and shifted the microbiome closer to that of healthy controls, demonstrating its prebiotic effect. It promoted the abundance of beneficial bacteria that are linked to improved glucose metabolism and reduced inflammation-specifically, Bacteroides fragilis, Lactobacillus, Clostridium, and Akkermansia. Harmful bacteria associated with inflammation and poor glycemic control were reduced. Collectively, these results suggest that PCE not only helps restore a balanced gut microbiome but also offers metabolic benefits that could improve diabetic outcomes. These findings position PCE as a promising supplement for the management of diabetes and encourage further exploration of the mechanisms associated with its actions.},
}

@article {pmid40943094,
year = {2025},
author = {Righetti, R and Cinque, F and Lebouché, B and Ramos Ballesteros, L and Routy, JP and Klein, MB and Szabo, J and Cox, J and Falutz, J and Haraoui, LP and Costiniuk, CT and De Pokomandy, A and Pembroke, T and Constante, M and Santos, M and Sebastiani, G},
title = {Distinct Gut Microbiota Signatures Are Associated with Severity of Metabolic Dysfunction-Associated Steatotic Liver Disease in People with HIV.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178165},
pmid = {40943094},
issn = {1422-0067},
abstract = {The progression of metabolic dysfunction-associated steatotic liver disease (MASLD) to severe forms, including metabolic dysfunction-associated steatohepatitis (MASH) and liver fibrosis, involves metabolic dysfunction, genetics, and gut dysbiosis. People with HIV (PWH) represent a high-risk group for MASLD, but the role of gut microbiota alterations in disease severity within this population remains poorly understood. We prospectively recruited PWH with MASLD, defined as the controlled attenuation parameter (CAP) ≥ 238 dB/m, and excluded those with viral hepatitis coinfection or alcohol abuse. Severe MASLD was defined as the presence of MASH (cytokeratin-18 ≥ 130.5 U/L) and/or significant liver fibrosis (liver stiffness ≥ 7.1 kPa). Stool samples were collected for 16S rRNA gene sequencing to characterize gut microbiota composition. Functional predictions were generated using PICRUSt. The differential abundance of bacterial taxa and predicted functions were analyzed using a generalized linear model with a negative binomial distribution. Among 34 PWH with MASLD, 18 (53%) met the criteria for severe MASLD. Microbiota profiling revealed significant differences in bacterial genera between the PWH with and without severe MASLD. Enrichment was observed in the Ruminococcus gnavus group, Negativibacillus, Holdemanella, Subdoligranulum, the Eubacterium hallii group, and Butyricicoccus, while depletion was seen in Prevotella, Alloprevotella, Dialister, Catenibacterium, the Christensenellaceae R 7 group, Clostridium sensu stricto, Olsenella, Oscillospiraceae UCG-005, Libanicoccus, and the Eubacterium siraeum group. Predicted functional pathways related to fatty acid degradation, folate biosynthesis, and amino acids metabolism did not differ between groups. MASLD severity in PWH is associated with a distinct gut microbiota signature, though not with functional pathway alterations. Microbial profiling may complement existing non-invasive biomarkers for risk stratification in this high-risk population.},
}

@article {pmid40943051,
year = {2025},
author = {Joura, MI and Nemes-Nikodém, É and Jobbágy, A and Dunai, ZA and Makra, N and Bánvölgyi, A and Kiss, N and Sárdy, M and Sándor, SE and Holló, P and Ostorházi, E},
title = {Integrative Analysis of Fungal and Bacterial Microbiomes Across Skin, Blood, and Stool in Rosacea Patients.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178127},
pmid = {40943051},
issn = {1422-0067},
abstract = {Rosacea is a chronic inflammatory skin disorder with multifactorial pathogenesis involving immune dysregulation and microbial alterations. This study compared the mycobiomes of skin, blood, and stool samples in rosacea patients and healthy controls to assess fungal diversity, abundance, and possible translocation, as well as associations with bacterial microbiomes. Internal transcribed spacer (ITS) region sequencing was performed on samples from 14 rosacea patients and 8 controls. While distinct fungal community compositions were observed across sample types, no significant differences in fungal diversity or genus abundance were found between the patient and control groups in any compartment. Malassezia dominated the skin mycobiome, while stool samples showed higher abundances of Candida and Saccharomyces, which were inversely correlated. Patients with high skin and blood Malassezia also exhibited increased Cutibacterium abundance, suggesting a potential role in impaired skin barrier integrity. Stool samples with elevated Saccharomyces correlated with higher levels of anti-inflammatory bacteria Prevotella and Agathobacter, whereas Candida dominance showed the opposite. These findings suggest that fungal dysbiosis, in the interplay with bacterial communities, may influence rosacea pathogenesis through the gut-skin axis. This work underscores the significance of integrated microbiome research across multiple biological compartments in order to enhance our understanding and potential targeting of microbial factors in rosacea.},
}

@article {pmid40943045,
year = {2025},
author = {Hatch, K and Horseman, TS and Parajuli, B and Murphy, EK and Cole, RN and O'Meally, RN and Perl, DP and Burmeister, DM and Iacono, D},
title = {Abscopal Brain Proteomic Changes Associated with Microbiome Alterations Induced by Gastrointestinal Acute Radiation Syndrome in Swine.},
journal = {International journal of molecular sciences},
volume = {26},
number = {17},
pages = {},
doi = {10.3390/ijms26178121},
pmid = {40943045},
issn = {1422-0067},
support = {PAT-74-10982//Uniformed Services University of the Health Sciences/ ; MED-11233//Uniformed Services University of the Health Sciences/ ; },
abstract = {Emerging research highlights the gut microbiota's critical role in modulating brain activity via the gut-brain axis. This study explores whether targeted gastrointestinal irradiation induces abscopal effects on the brain proteome, revealing microbiota-mediated neurobiological changes. Male Sinclair minipigs were randomized to receive either sham treatment (n = 6) or 8 Gy lower hemibody (gut-targeted) irradiation (n = 5). Over 14 days, rectal swabs were collected to monitor microbiota dynamics, followed by frontal cortex proteomic analysis. Irradiation altered gut microbiota composition, notably reducing Chlamydiae and Firmicutes phyla, while increasing Coriobacteriaceae and Acinetobacter. Proteomic analysis identified 75 differentially abundant proteins in the frontal cortex, including a significant decrease in pannexin-1 (PANX1), suggesting modulation of the NLRP3 inflammasome pathway. Functional enrichment analysis revealed immune and neurotransmission-related changes linked to microbial shifts. These results demonstrate that gut-targeted radiation can remotely affect brain protein expression, emphasizing the microbiota's role in neuroimmune regulation and pointing to novel therapeutic opportunities in gut-brain axis disorders.},
}

@article {pmid40942152,
year = {2025},
author = {Owe-Larsson, M and Drobek, D and Iwaniak, P and Kloc, R and Urbanska, EM and Chwil, M},
title = {Microbiota-Derived Tryptophan Metabolite Indole-3-Propionic Acid-Emerging Role in Neuroprotection.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {17},
pages = {},
doi = {10.3390/molecules30173628},
pmid = {40942152},
issn = {1420-3049},
abstract = {In recent years, gut-brain axis signaling has been recognized as an essential factor modifying behavior, mood, cognition, and cellular viability under physiological and pathological conditions. Consequently, the intestinal microbiome has become a potential therapeutic target in neurological and psychiatric disorders. The microbiota-derived metabolite of tryptophan (Trp), indole-3-propionic acid (IPA), was discovered to target a number of molecular processes and to impact brain function. In this review, we outline the key mechanisms by which IPA may affect neuronal activity and survival and provide an update on the evidence supporting the neuroprotective action of the compound in various experimental paradigms. Accumulating data indicates that IPA is a free radical scavenger, a ligand of aryl hydrocarbon receptors (AhR) and pregnane X receptors (PXR), and an anti-inflammatory molecule. IPA decreases the synthesis of the proinflammatory nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), tumor necrosis factor-α (TNF-α), and other cytokines, reduces the generation of the NLR family pyrin domain containing 3 (NLRP3) inflammasome, and enhances the synthesis of neurotrophic factors. Furthermore, produced in the gut, or administered orally, IPA boosts the central levels of kynurenic acid (KYNA), a neuroprotective metabolite of Trp. IPA reduces the release of proinflammatory molecules in the gut, breaking the gut-inflammation-brain vicious cycle, which otherwise leads to neuronal loss. Moreover, as a molecule that easily enters central compartment, IPA may directly impact brain function and cellular survival. Overall, the gathered data confirms neuroprotective features of IPA, and supports its potential use in high-risk populations, in order to delay the onset and ameliorate the course of neurodegenerative disorders and cognitive impairment. Clinical trials evaluating IPA as a promising therapeutic add-on, able to slow down the progress of neurodegenerative disorders such as Alzheimer's or Parkinson's disease and to limit the morphological and behavioral consequences of ischemic stroke, are urgently needed.},
}

@article {pmid40941864,
year = {2025},
author = {Thingujam, D and Gouli, S and Cooray, SP and Chandran, KB and Givens, SB and Gandhimeyyan, RV and Tan, Z and Wang, Y and Patam, K and Greer, SA and Acharya, R and Moseley, DO and Osman, N and Zhang, X and Brooker, ME and Tagert, ML and Schafer, MJ and Jeong, C and Hoffseth, KF and Bheemanahalli, R and Wyss, JM and Wijewardane, NK and Ham, JH and Mukhtar, MS},
title = {Climate-Resilient Crops: Integrating AI, Multi-Omics, and Advanced Phenotyping to Address Global Agricultural and Societal Challenges.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/plants14172699},
pmid = {40941864},
issn = {2223-7747},
support = {IOS-2038872//National Science Foundation/ ; OIA-2418230//National Science Foundation/ ; OIA-2418230//National Science Foundation/ ; DUE 1758292//National Science Foundation/ ; R25132976/GF/NIH HHS/United States ; R25CA244092/GF/NIH HHS/United States ; NRCS-CIG NR213A750013G014//USDA/ ; 2023-67019-39722//USDA_AFRI/ ; OIA-2418231//National Science Foundation/ ; MSPB//NIFA/ ; MIS-430030//NIFA/ ; LAB#94588//USDA/ ; OIA-2418232//National Science Foundation/ ; 2022-6701-3036140//USDA-NIFA/ ; 2023-68012-39002//USDA-NIFA/ ; LAB94575//USDA-NIFA/ ; OIA-2418231//National Science Foundation/ ; },
abstract = {Drought and excess ambient temperature intensify abiotic and biotic stresses on agriculture, threatening food security and economic stability. The development of climate-resilient crops is crucial for sustainable, efficient farming. This review highlights the role of multi-omics encompassing genomics, transcriptomics, proteomics, metabolomics, and epigenomics in identifying genetic pathways for stress resilience. Advanced phenomics, using drones and hyperspectral imaging, can accelerate breeding programs by enabling high-throughput trait monitoring. Artificial intelligence (AI) and machine learning (ML) enhance these efforts by analyzing large-scale omics and phenotypic data, predicting stress tolerance traits, and optimizing breeding strategies. Additionally, plant-associated microbiomes contribute to stress tolerance and soil health through bioinoculants and synthetic microbial communities. Beyond agriculture, these advancements have broad societal, economic, and educational impacts. Climate-resilient crops can enhance food security, reduce hunger, and support vulnerable regions. AI-driven tools and precision agriculture empower farmers, improving livelihoods and equitable technology access. Educating teachers, students, and future generations fosters awareness and equips them to address climate challenges. Economically, these innovations reduce financial risks, stabilize markets, and promote long-term agricultural sustainability. These cutting-edge approaches can transform agriculture by integrating AI, multi-omics, and advanced phenotyping, ensuring a resilient and sustainable global food system amid climate change.},
}

@article {pmid40941714,
year = {2025},
author = {Lee, KS and Kim, ES},
title = {Genetic Artificial Intelligence in Gastrointestinal Disease: A Systematic Review.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172227},
pmid = {40941714},
issn = {2075-4418},
support = {K2209721//Korea University College of Medicine grant/ ; HI21C156001//Korea Health Industry Development Institute grant/ ; HI22C1302//Korea Health Industry Development Institute grant/ ; 20001533//Technology Innovation Program/ ; },
abstract = {Background/Objectives: The application of predictive and explainable artificial intelligence to bioinformatics data such as single nucleotide polymorphism (SNP) information is attracting rising attention in the diagnosis of various diseases. However, there are few reviews available on the recent progress of genetic artificial intelligence for the early diagnosis of gastrointestinal disease (GID). The purpose of this study is to complete a systematic review on the recent progress of genetic artificial intelligence in GID. Methods: The source of data was ten original studies from PubMed. The ten original studies were eligible according to the following criteria: (participants) the dependent variable of GID or associated disease; (interventions/comparisons) artificial intelligence; (outcomes) accuracy, the area under the curve (AUC), and/or variable importance; a publication year of 2010 or later; and the publication language of English. Results: The performance outcomes reported varied within 79-100 for accuracy (%) and 63-98 for the AUC (%). Random forest was the best approach (AUC 98%) for the classification of inflammatory bowel disease with 13 single nucleotide polymorphisms (SNPs). Similarly, random forest was the best method (R-square 99%) for the regression of the gut microbiome SNP saturation number. The following SNPs were discovered to be major variables for the prediction of GID or associated disease: rs2295778, rs13337626, rs2296188, rs2114039 (esophageal adenocarcinoma); rs28785174, rs60532570, rs13056955, rs7660164 (Crohn's disease early intestinal resection); rs4945943 (Crohn's disease); rs316115020, rs316420452 (calcium metabolism); rs738409_G, rs2642438_A, rs58542926_T, rs72613567_TA (steatotic liver disease); rs148710154, rs75146099 (esophageal squamous cell carcinoma). The following demographic and health-related variables were found to be important predictors of GID or associated disease besides SNPs: age, body mass index, disease behavior, immune cell type, intestinal microbiome, MARCKS protein, smoking, and SNP density/number. No deep learning study was found even though deep learning was used as a search term together with machine learning. Conclusions: Genetic artificial intelligence is effective and non-invasive as a decision support system for GID.},
}

@article {pmid40941635,
year = {2025},
author = {Ahmet, RAM and Nascu, AG and Camen, GC and Obleaga, CV and Popa, DG and Mirea, CS},
title = {Unveiling the Microbiota: A New Frontier in Breast Cancer Pathogenesis-A Single-Center Preliminary Study.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/diagnostics15172147},
pmid = {40941635},
issn = {2075-4418},
abstract = {Background: Breast cancer is the most common malignancy affecting women worldwide and continues to pose significant challenges despite progress in early detection and personalized therapies. While its pathogenesis has traditionally been associated with genetic, hormonal, and environmental factors, recent studies have highlighted the potential role of dysbiosis-an imbalance in gut and systemic microbiota-in breast cancer development and progression. This article aims to examine the mechanisms through which systemic dysbiosis may contribute to breast cancer risk and explore its therapeutic implications. Methods: This study seeks to analyze and compare the fecal microbiota profiles of breast cancer patients and healthy individuals from a single center in Craiova, Romania, in order to identify microbial signatures linked to breast cancer and BRCA mutation status. Special attention is given to the gut-liver axis and its influence on estrogen circulation, a key factor in hormone-sensitive breast cancers. Results: Evidence suggests that dysbiosis can influence breast cancer progression by promoting chronic inflammation, impairing immune regulation, and altering estrogen metabolism through the gut-liver axis. These effects may contribute to tumor development, immune evasion, and therapeutic resistance. Interventions aimed at restoring microbial balance show promise in preclinical studies for mitigating these effects. Conclusions: Systemic dysbiosis represents a potentially modifiable risk factor in breast cancer. Microbiota profiling may serve as a useful biomarker for risk stratification and therapeutic response. Future research into microbiome-based interventions could offer novel approaches for prevention and treatment in breast cancer care.},
}

@article {pmid40941485,
year = {2025},
author = {Wright, SL and Slusanschi, O and Giura, AC and Părlătescu, I and Funieru, C and Gaidula, SM and Moore, NE and Weyrich, LS},
title = {SANA-Biome: A Protocol for a Cross-Sectional Study on Oral Health, Diet, and the Oral Microbiome in Romania.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {17},
pages = {},
doi = {10.3390/healthcare13172133},
pmid = {40941485},
issn = {2227-9032},
abstract = {Periodontal disease is a widespread chronic condition linked to systemic illnesses such as cardiovascular disease, diabetes, and adverse pregnancy outcomes. Despite its global burden, population-specific studies on its risk factors remain limited, particularly in Central and Eastern Europe. The SANA-biome Project is a cross-sectional, community-based study designed to investigate the biological and social determinants of periodontal disease in Romania, a country with disproportionately high oral disease rates and minimal microbiome data. This protocol will integrate metagenomic, proteomic, and metabolomic data of the oral microbiome from saliva and dental calculus samples with detailed sociodemographic and lifestyle data collected through a structured 44-question survey. This study is grounded in two complementary frameworks: the IMPEDE model, which conceptualizes inflammation as both a driver and a consequence of microbial dysbiosis, and Ecosocial Theory, which situates disease within social and structural contexts. Our aims are as follows: (1) to identify lifestyle and behavioral predictors of periodontal disease; (2) to characterize the oral microbiome in individuals with and without periodontal disease; and (3) to evaluate the predictive value of combined microbial and sociodemographic features using statistical and machine learning approaches. Power calculations based on pilot data indicate a target enrollment of 120 participants. This integrative approach will help disentangle the complex interplay between microbiological and structural determinants of periodontal disease and inform culturally relevant prevention strategies. By focusing on an underrepresented population, this work contributes to a more equitable and interdisciplinary model of oral health research and supports the development of future precision public health interventions.},
}

@article {pmid40941386,
year = {2025},
author = {Tian, S and Chen, C and Yang, L and Abulaiti, A and Hua, J},
title = {Comprehensive Evaluation of the Immune Response of Angus Cattle to Live Attenuated and Inactivated Goatpox Virus Vaccines.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/ani15172592},
pmid = {40941386},
issn = {2076-2615},
support = {[2021]1146//Joint Research on Improved Beef Cattle Breeds in Anhui Province/ ; },
abstract = {Lumpy skin disease (LSD) is a contagious animal disease caused by the lumpy skin disease virus (LSDV). LSD can be transmitted through direct, indirect and insect vectors, severely impacting global cattle production. To evaluate difference in immune response and gut microbiota of 30 healthy 16-18 months old Angus cattle, treated with live attenuated or inactivated goatpox vaccine virus strains. The cattle were randomly divided into three groups (10 animals per group): Group A-goatpox live attenuated vaccine; Group B-goatpox inactivated vaccine; Group C-control (saline). Blood samples were collected on days 14, 28, 42, and 56 post-vaccination to assess hematological parameters, serum biochemical indices, and antibody levels; rectal feces were collected on day 28 for 16S rRNA analysis of gut microbiota. Results showed that, on day 28, both Group A and Group B reached their peak antibody levels (the log10 value of Group A was 2.6, and that of Group B was 2.7), with about 90% of the cattle in each vaccinated group testing antibody-positive. On day 42, Group B retained 90% seropositivity, whereas Group A declined to 80%. Significantly altered in vaccinated Groups (A and B) compared to controls on days 14 and 28 (p < 0.05). Hematological parameters (PLT, NEUT, and LYM) and serum biochemical indices (AST, TP, and GGT) were elevated early after vaccination but returned to baseline by days 42 and 56.Which returned to control levels by days 42 and 56. On day 28 post-vaccination, Vaccinated cattle showed significantly higher gut microbiome richness and diversity than unvaccinated controls (p < 0.05). At the phylum level, the dominance was observed in Firmicutes and Bacteroidetes: the relative abundances were 62.90% and 29.65% in Group A, 60.84% and 30.13% in Group B, and 49.99% and 39.73% in Group C, respectively. These findings indicate that the inactivated goatpox vaccine elicits a more durable and stable antibody response, maintaining higher specific antibody titers, and induces more pronounced shifts in the gut microbiota community structure at the phylum level compared with the live attenuated vaccine.},
}

@article {pmid40941346,
year = {2025},
author = {Ishii, PE and Teixeira, FA and Lin, CY and Naqvi, SA and Sardi, MI and Norton, SA and Jarett, JK and Khafipour, E and Frantz, N and Chakrabarti, A and Suchodolski, JS},
title = {Effects of a Saccharomyces cerevisiae Fermentation Product on Diet Palatability and Feline Intestinal Health, Immunity, and Microbiome.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/ani15172551},
pmid = {40941346},
issn = {2076-2615},
abstract = {This study evaluated the effects of adding a Saccharomyces cerevisiae fermentation product (SCFP) to adult cat diets on palatability, intestinal health, nutrient digestibility, immune parameters, and the fecal microbiome over 42 days. Sixty-three healthy Domestic Short-hair cats were randomized to three diets: a control diet (CD) without SCFP, or the same diet containing 1.0% or 2.0% SCFP, targeting daily intakes of 150 or 300 mg/kg body weight, respectively. Body weight and blood parameters remained within reference ranges across all groups. Stool quality was largely not affected, although compared with controls, SCFP-supplemented cats had slightly firmer stools at day 21, and increased fecal pH. Shotgun metagenomic sequencing revealed that microbiome diversity remained steady in SCFP-fed cats, whereas diversity in the control group declined over time. Fecal immunoglobulin A concentrations were lower in cats supplemented with SCFP at 150 mg/kg BW by the end of the study, and positive shifts in the circulatory leukocyte profile were observed at both inclusion levels. Apparent total tract macronutrient digestibility did not differ among groups. Palatability tests showed diets with SCFP were generally preferred, indicating a potential benefit for commercial feline feeds, particularly at the 150 mg/kg BW level, which was preferred over 300 mg/kg BW. Overall, these findings suggest that SCFP can act as a functional ingredient in feline nutrition to maintain microbial diversity and enhance diet acceptance without compromising digestibility.},
}

@article {pmid40941342,
year = {2025},
author = {Lacerenza, MD and Arantes, JA and Reginato, GM and Finardi, GLF and Marchi, PH and Vendramini, THA and Corrêa, RR and Pereira, PAM and Valadão, CAA and Dória, RGS},
title = {Microbiome and Dental Changes in Horses Fed a High Soluble Carbohydrate Diet.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {17},
pages = {},
doi = {10.3390/ani15172547},
pmid = {40941342},
issn = {2076-2615},
support = {2020/09633-0//São Paulo Research Foundation (FAPESP)/ ; 309701/2022-8//National Council for Scientific and Technological Development (CNPQ)/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES)/ ; },
abstract = {This study investigated the oral microbiome of horses maintained on a high soluble carbohydrate diet based on sugarcane, in comparison to those fed a pasture-based diet composed of Cynodon spp., aiming to identify associations between dietary intake, the composition of oral microbial communities, and the occurrence of dental caries and diastemata. A total of 20 healthy horses, both male and female, with an average age of 9 ± 3 years and weight of 400 ± 100 kg, without a defined breed, were selected. They were divided into two groups: the High Soluble Carbohydrate Group (HSCCG), consisting of 10 horses fed sugarcane for at least 3 years, and the Low Soluble Carbohydrate Group (LSCCG), consisting of 10 horses fed pasture with Cynodon spp. Dental examinations were performed using an adapted oral endoscope to assess caries and diastemata, and saliva samples were collected for microbiota analysis. Statistical analyses included a Student's t-test and Mann-Whitney test, with significance set at p < 0.05. Horses in the HSCCG had a higher presence of peripheral caries (p = 0.001), as well as differences in the degree (p = 0.010), class (p = 0.05), and presence of diastemata. Microbial diversity indices (Chao, inverse Simpson, and Shannon) showed no significant differences, but the relative abundance differed (p = 0.003). Linear Discriminant Analysis revealed distinct microbial profiles: Candidatus Saccharibacteria and Bacteroidetes were more abundant in the HSCCG, while Cyanobacteria_Chloroplast and Proteobacteria dominated in the LSCCG. Over 35 genera differed significantly between groups. The study concludes that diet plays a significant role in shaping oral microbiota and influencing the development of dental caries in horses.},
}

@article {pmid40941257,
year = {2025},
author = {Zhao, L and Ju, WM and Wang, LL and Ye, YB and Liu, ZY and Cavender, G and Sun, YJ and Sun, SQ},
title = {Functional Ingredients: From Molecule to Market-AI-Enabled Design, Bioavailability, Consumer Impact, and Clinical Evidence.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173141},
pmid = {40941257},
issn = {2304-8158},
support = {No. 2024MK078//The Science and Technology Project of the State Administration for Market Regulation of China/ ; 2022XDRH034//Yantai Science and Technology Bureau Support Grant/Science and Technology Innovation Development Project/ ; 22097155283227//The Industry-Academia Collaborative Program of the Ministry of Education/ ; RC20SP001//Yantai Institute of Technology Scientific Research and Innovation Fund for High-level Talents/ ; 2023YYK20//Yantai Institute of Technology Scientific Applied Curriculum Development Project/ ; },
abstract = {Functional ingredients such as dietary fibers, probiotics and prebiotics, polyphenols, omega-3 fatty acids, and bioactive peptides are increasingly central to food systems that aim to deliver health benefits beyond basic nutrition. This review explores how molecular structure, physicochemical properties, metabolism, and microbiome interactions affect bioactivity and bioavailability. We highlight advances in green extraction, encapsulation technologies, and 3D/4D printing that enhance the stability and targeted delivery of bioactives. AI-enabled tools for ingredient discovery, structure-activity modeling, and personalized formulation are also discussed. Sensory research and market insights inform strategies to improve consumer acceptance, while clinical studies provide evidence for cardiometabolic, immune, and cognitive benefits. Safety and regulatory aspects are addressed, particularly for emerging proteins and delivery systems. By integrating scientific and technological developments across disciplines, this review provides a comprehensive foundation for future research and commercialization of safe, effective, and personalized functional food products.},
}

@article {pmid40941186,
year = {2025},
author = {Dissook, S and Thongkumkoon, P and Noisagul, P and Sriaporn, C and Suwannapat, S and Pramoonchakko, W and Suksawat, M and Kulthawatsiri, T and Phetcharaburanin, J and Chewonarin, T and Ruangsuriya, J},
title = {Insights into Microbial and Metabolite Profiles in Traditional Northern Thai Fermented Soybean (Tuanao) Fermentation Through Metagenomics and Metabolomics.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173070},
pmid = {40941186},
issn = {2304-8158},
support = {FF66/023//Fundamental Fund 2023, Chiang Mai University/ ; },
abstract = {Tuanao, a traditional Northern Thai fermented soybean product, was profiled with an integrated multi-omics workflow to clarify how microbes and metabolites co-evolve during household fermentation. Soybeans were fermented spontaneously for three days; samples from four time points were analyzed by shotgun metagenomics alongside 1H-NMR and UHPLC-ESI-QTOF-MS/MS metabolomics. Bacillus spp. (phylum Bacilliota) quickly supplanted early Enterobacterales and dominated the mature microbiome. The rise of Bacillus coincided with genes for peptide and carbohydrate utilization and with the accumulation of acetate, free amino acids (glutamine, leucine, alanine, valine) and diverse oligopeptides, whereas citrate and glucose-1-phosphate were depleted. This Bacillus-linked metabolic shift indicates that Tuanao is a promising source of probiotics and bioactive compounds. Our study provides the first system-level view of Tuanao fermentation and offers molecular markers to guide starter-culture design and quality control.},
}

@article {pmid40941154,
year = {2025},
author = {Zhang, J and Wei, ZJ and Fan, G},
title = {Emerging Understanding of Gut Microbiome in Colorectal Cancer and Food-Related Intervention Strategies.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14173040},
pmid = {40941154},
issn = {2304-8158},
support = {2022YFF1100306//National Key Research & Development Program of China/ ; 2023AAC03272//the Natural Science Foundation of Ningxia Hui Autonomous Region/ ; },
abstract = {Colorectal cancer (CRC) is one of the most common cancers, accounting for approximately 10% of all new cancer cases globally. An increasing number of studies have revealed that the gut microbiome is strongly associated with the pathogenesis and progression of CRC. Based on these advances, this review delineates the mechanistic links between specific microbes and CRC, as well as emerging food-related nutritional intervention strategies. In vivo and in vitro studies have pinpointed the implications of key microbes such as Fusobacterium nucleatum, certain strains of Escherichia coli, enterotoxigenic Bacteroides fragilis, and Enterococcus faecalis, among others, and metabolite involvement and immune responses. Particular attention is paid to the roles of intratumoral microbiota in the development and treatment of CRC, given their direct interaction with tumor cells. Various food-related nutritional intervention strategies have been developed to mitigate CRC risk, including probiotics, antibiotics, or the administration of bioactive compounds such as luteoloside. Finally, we outline critical research directions regarding the influence of animal lineage, carcinoma location, population demographics, the application of advanced in vitro models, and the mediatory roles of gut-associated epithelial cells. In summary, this review might consolidate our current knowledge on the contribution of gut microbiota to CRC and highlights the microbe-based strategies to enhance nutritional interventions for this disease.},
}

@article {pmid40941111,
year = {2025},
author = {Zhadyra, S and Tao, F and Xu, P},
title = {Two-Dimensional GC-ToFMS Analysis of Volatile Organic Compounds in Fermented Camel Milk (Shubat).},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14172995},
pmid = {40941111},
issn = {2304-8158},
support = {AP25793809//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Shubat, a traditional fermented camel milk from Kazakhstan, is renowned for its unique flavor and nutritional properties, though its volatile compound profile remains poorly characterized. In this study, headspace solid-phase microextraction coupled with comprehensive two-dimensional gas chromatography-time-of-flight mass spectrometry (HS-SPME-GC×GC-ToFMS) was employed to qualitatively identify and semi-quantitatively analyze volatile metabolites in seven Shubat samples collected from four regions of Kazakhstan. Of the 372 volatile organic compounds initially detected, 202 were retained after screening, predominantly comprising esters, acids, alcohols, ketones, and aldehydes. Esters, acids, and alcohol were found to be the most abundant categories. Diversity analyses (α and β) revealed substantial variation across regions, likely influenced by Shubat's rich and region-specific microbiome. An UpSet analysis demonstrated that 75 volatile compounds were shared among all samples, accounting for over 87% of the total volatile content, indicating a chemically stable core. These findings underscore the chemical complexity of Shubat and provide novel insights into its metabolite composition, thereby establishing a foundation for future sensory, microbial, and quality-related research.},
}

@article {pmid40941096,
year = {2025},
author = {Nguyen, DHH and El-Ramady, H and Törős, G and Muthu, A and Elsakhawy, T and Abdalla, N and Alibrahem, W and Kharrat Helu, N and Prokisch, J},
title = {Food-Derived Carbon Dots: Formation, Detection, and Impact on Gut Microbiota.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14172980},
pmid = {40941096},
issn = {2304-8158},
abstract = {Food-derived carbon dots (F-CDs) are a novel class of carbon-based nanomaterials unintentionally generated during common thermal food processing techniques, such as baking, roasting, frying, and caramelization. These nanostructures exhibit unique optical and chemical properties, including photoluminescence, high aqueous solubility, and tunable surface functionality, making them increasingly relevant to both food science and biomedical research. Recent studies have highlighted their ability to interact with biological systems, particularly the gut microbiota, a critical determinant of host metabolism, immunity, and overall health. This review critically summarizes the current understanding of F-CDs, including their mechanisms of formation, analytical detection methods, and physicochemical properties. It explores their biological fate in the gastrointestinal tract, encompassing absorption, distribution, metabolism, and excretion, with a focus on their stability and cellular uptake. Special attention is given to the interaction between F-CDs and the gut microbiota, where evidence suggests both beneficial (e.g., anti-inflammatory, antioxidant) and detrimental (e.g., dysbiosis, inflammatory signaling) effects, depending on the CD type, dose, and exposure context. Additionally, this review addresses toxicological concerns, highlighting gaps in long-term safety data, standardized detection methods, and regulatory oversight. The dual role of F-CDs-as potential modulators of the microbiota and as emerging dietary nanomaterials with uncharted risks-underscores the need for further interdisciplinary research. Future efforts should aim to refine detection protocols, assess chronic exposure outcomes, and clarify structure-function relationships to enable the safe and responsible application of these nanomaterials in food and health contexts.},
}

@article {pmid40941077,
year = {2025},
author = {Sang, X and Xing, Z and Zhou, B and Wang, Y and Guan, X and Wang, F and Li, Y and Zhao, Q and Li, Z},
title = {Sea Cucumber Polysaccharides Promote Gut-Liver Axis Health by Modulating Microbiota, Metabolism, and Gene Expression in Mice.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14172962},
pmid = {40941077},
issn = {2304-8158},
support = {32302093//National Natural Science Foundation of China/ ; 2024-MSLH-049//Liaoning Provincial Natural Science Foundation Program Project/ ; 2024JH2/102600074//Liaoning Provincial Natural Science Foundation Program Project/ ; 2024JH2/102400002//Key Science and Technology Program of Liaoning Province/ ; },
abstract = {This study investigated the beneficial effect of sea cucumber polysaccharides (SCP) on gut microbiota composition, metabolic profiles, and liver gene expression in mice. Using an integrative approach combining microbiome, metabolome, and transcriptome analyses, we demonstrated that SCP supplementation led to a marked rise in norank_f_Muribaculaceae levels and reduced the Firmicutes-to-Bacteroidota ratio. Metabolomic analysis revealed key alterations in amino acid and lipid metabolism, with L-arginine and 7-dehydrocholesterol identified as potential mediators of SCP's beneficial effects. Transcriptomics revealed genes expression across nine metabolic pathways, with genes involved in steroid biosynthesis being upregulated, while those related to protein digestion and absorption were downregulated. Spearman's correlation analysis highlighted strong associations between gut microbiota, lipid metabolism-related genes, and corresponding metabolites. Integration omics data further suggested that SCP primarily supports arginine biosynthesis through gut-liver axis crosstalk. These results provide an important basis for developing SCP-based functional food with prebiotic properties to support metabolic and liver health.},
}

@article {pmid40941064,
year = {2025},
author = {Lemons, JMS and Firrman, J and Mahalak, KK and Liu, L and Narrowe, AB and Higgins, S and Moustafa, AM and Baudot, A and Deyaert, S and Van den Abbeele, P},
title = {The Effect of Sodium Benzoate on the Gut Microbiome Across Age Groups.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/foods14172949},
pmid = {40941064},
issn = {2304-8158},
support = {8072-41000-108-00-D//USDA In-House Project/ ; },
abstract = {The food additive sodium benzoate (SB) has been used for decades as an antimicrobial to prevent food spoilage. SB has been deemed to pose no risk to human health when consumed at levels under 5 mg/kg body weight per day; however, when many of the supporting studies were conducted, the importance of the gut microbiome to human health was not yet appreciated. Given SB's known antimicrobial qualities, it is important to assess the effect of this food additive on the human gut microbiome. The ex vivo SIFR[®] (Systemic Intestinal Fermentation Research) technology was used to test the effect of SB on microbial communities from 24 donors, aged infants to older adults. A dose of 3.5 g/L SB elicited a drop in the Pseudomonadota phylum for multiple age groups but did not alter the alpha or beta diversity within any of these groups. This was accompanied by changes in the functional outputs that included an overall rise in butyrate and a drop in propionate production. This higher butyrate correlates with an increase in the abundance of several known butyrate producers in the presence of SB, although the genetic potential for its production in the community did not change. Overall, despite using a dose ten times higher than the accepted daily intake limit, the effect on the gut microbiome was minimal.},
}

@article {pmid40940924,
year = {2025},
author = {Ratajczak-Pawłowska, AE and Jezierska, K and Szymczak-Tomczak, A and Zawada, A and Rychter, AM and Skoracka, K and Dobrowolska, A and Krela-Kaźmierczak, I},
title = {Lifestyle and Breast Cancer: Prevention and Treatment Support.},
journal = {Cancers},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/cancers17172830},
pmid = {40940924},
issn = {2072-6694},
abstract = {Breast cancer is the most common malignant tumor among women. It is a significant health and social issue affecting 2.3 million women worldwide. Breast cancer is caused by various factors, including gender, age, race, genetics, hormonal balance, obesity, alcohol and many others. A crucial issue related to breast cancer is the impact of diet on the development of the disease. Dietary fats play a key role. Saturated fatty acids and trans fatty acids increase the risk of breast cancer, while polyunsaturated fatty acids have a protective effect. A high-protein diet reduces the risk of breast cancer and improves prognosis among patients. The role of carbohydrates remains unclear, but women may benefit from reducing their intake of high glycemic index foods. Among the macronutrients influencing the development and progression of breast cancer are calcium and magnesium. Adopting a Mediterranean diet may offer benefits. Among the factors influencing the development of breast cancer, the gastrointestinal microbiota is also noteworthy. Regular physical activity can reduce the risk of developing breast cancer, support treatment, reduce side effects and improve patients' quality of life. Chronic stress also contributes to the development of breast cancer by affecting the nervous, hormonal and immune systems, disrupting the body's homeostasis.},
}

@article {pmid40940892,
year = {2025},
author = {Mohamed, AS and Bhuju, R and Martinez, E and Basta, M and Deyab, A and Mansour, C and Tejada, D and Deshpande, V and Elias, S and Nagesh, VK},
title = {The Gut Microbiome's Impact on the Pathogenesis and Treatment of Gastric Cancer-An Updated Literature Review.},
journal = {Cancers},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/cancers17172795},
pmid = {40940892},
issn = {2072-6694},
abstract = {The gut microbiota plays a critical role in maintaining gastrointestinal homeostasis, immune regulation, and metabolic processes. Recent evidence has highlighted its significant influence on gastric carcinogenesis. Helicobacter pylori, a well-established class I carcinogen, remains the most prominent microbial risk factor for gastric cancer. However, emerging studies indicate that alterations in the broader gastric and intestinal microbial communities, referred to as dysbiosis, may also contribute to tumor initiation, progression, and immune evasion. These microbial shifts can lead to chronic inflammation, genotoxic metabolite production, and modulation of signaling pathways such as NF-κB and Wnt/β-catenin. This review explores the current understanding of the gut microbiome's contribution to gastric cancer pathogenesis, including microbial signatures associated with precancerous lesions and the tumor microenvironment. Furthermore, the potential of microbiota-based biomarkers and therapeutic interventions, including probiotics, prebiotics, and fecal microbiota transplantation, is discussed as part of emerging precision medicine strategies.},
}

@article {pmid40940890,
year = {2025},
author = {Hilliard, AL and Russell, TD and Mendonca, P and Soliman, KFA},
title = {Targeting the Tumor Immune Microenvironment in Triple-Negative Breast Cancer: The Promise of Polyphenols.},
journal = {Cancers},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/cancers17172794},
pmid = {40940890},
issn = {2072-6694},
abstract = {Breast cancer remains a formidable global health challenge, with triple-negative breast cancer (TNBC) posing unique clinical complexities. Characterized by its aggressive nature and limited number of specific therapeutic targets, this breast cancer subtype disproportionately affects African American women, highlighting critical disparities in care. The tumor immune microenvironment (TIME) plays a critical role in breast cancer development and response to immunotherapy, and it is essential in fostering an immunosuppressive and pro-inflammatory niche. Inflammation, primarily mediated by the NF-κB signaling pathway and chemokine signaling, particularly involving CCL2, plays a pivotal role in TNBC progression and therapy resistance. This review describes some of the molecular mechanisms of polyphenols, which are naturally occurring compounds abundant in various dietary sources, and their potential use as therapeutic agents in the management of TNBC. Polyphenolic compounds have been described as modulating the TIME through the inhibition of tumor progression, immune evasion, and therapy resistance, due to their diverse bioactivities, including anti-inflammatory, antioxidant, and anticancer properties, making them attractive candidates for combating the aggressiveness of TNBC and addressing treatment disparities. Polyphenols, such as curcumin, gossypol, butein, epigallocatechin gallate, cardamonin, and resveratrol, have demonstrated efficacy in modulating several signaling pathways within the TIME, which are implicated in the progression of TNBC. This review highlights the potential effects of polyphenols on inflammatory cytokine release, programmed cell death ligand 1 (PD-L1) expression, which is associated with immune evasion by the host cell, and various intracellular signaling cascades, demonstrating their potential use in personalized therapeutic interventions for TNBC. This study also describes differential responses of TNBC cell lines to polyphenol treatment, highlighting the importance of considering genetic variability in therapeutic strategies, as well as the importance of the interaction of polyphenols with the gut microbiome, which may establish the bioavailability and effectiveness of these compounds toward therapeutic outcomes. Further preclinical and clinical studies are warranted to fully elucidate the therapeutic potential of polyphenols and translate these findings into clinical practice, thereby improving outcomes for patients with TNBC worldwide.},
}

@article {pmid40940833,
year = {2025},
author = {Golusińska-Kardach, E and Yadav, H and Jain, S and Masternak, MM and Golusiński, W},
title = {The Oral Microbiome and Head and Neck Cancer: A Narrative Review.},
journal = {Cancers},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/cancers17172736},
pmid = {40940833},
issn = {2072-6694},
abstract = {In recent years, a growing body of evidence points to a link between alterations in the oral microbiome and the development and progression of head and neck cancer (HNC). At present, however, this highly complex relationship is only partially understood. In this context, there is a clear need to characterise and differentiate microbial profiles in patients with and without HNC to identify risk factors, prognostic biomarkers, and potential therapeutic targets. In the present narrative review, we synthesize the current evidence on the role of oral dysbiosis in HNC, with a particular focus on potential biomarkers and novel treatment and prevention strategies.},
}

@article {pmid40940828,
year = {2025},
author = {Saito, R and Shigematsu, Y and Amori, M and Amori, G and Takamatsu, M and Nishida, K and Kanda, H and Takahashi, Y and Miura, Y and Takeuchi, K and Takahashi, S and Inamura, K},
title = {Association of Enterotoxigenic Bacteroides fragilis with Immune Modulation in Colorectal Cancer Liver Metastasis.},
journal = {Cancers},
volume = {17},
number = {17},
pages = {},
doi = {10.3390/cancers17172733},
pmid = {40940828},
issn = {2072-6694},
support = {na//JSPS KAKENHI/ ; },
abstract = {Background: Enterotoxigenic Bacteroides fragilis (ETBF) carries the bft toxin gene, which influences the host immune response and inflammatory pathways and promotes colorectal cancer (CRC). This study investigated the potential role of ETBF in CRC liver metastasis. Methods: We reviewed the records of 226 consecutive patients who underwent curative-intent (R0) resection of CRC liver metastases. ETBF DNA in fresh-frozen metastasis specimens was quantified using droplet digital PCR (ddPCR). Patients were grouped into very-low (≤80%; N = 178), low (80-90%; N = 24), and high (>90%; N = 24) ETBF-DNA groups. Three tissue cores per specimen were stained for CD8, CD4, CD20, FOXP3, CD68, and CD163, and immune-cell densities were measured digitally (cells/mm[2]). Results: ETBF DNA was detected in 219 of 226 lesions (96.9%). The densities of cytotoxic CD8[+] T-cells, effector CD4[+] T-cells, CD20[+] B-cells, and CD163[+] macrophages did not differ significantly by ETBF-DNA group (Ptrend all > 0.12). FOXP3[+] regulatory T-cells (Tregs) decreased (Ptrend = 0.010), and CD68[+] macrophages increased (Ptrend = 0.020) as ETBF-DNA levels increased. ETBF-DNA levels in CRC liver metastases were not associated with disease-free survival or overall survival or serum C-reactive protein levels. Conclusions: ETBF was present in almost all CRC liver metastases. Higher ETBF levels were associated with a tumor-immune microenvironment enriched in CD68[+] macrophages and deficient in FOXP3[+] Tregs, suggesting that ETBF facilitates immune evasion without loss of effector lymphocytes. Although ETBF-DNA levels did not predict survival in this single-center cohort, the potential role of ETBF in immune remodeling and as a candidate biomarker and therapeutic target in metastatic CRC warrants further study.},
}

@article {pmid40940774,
year = {2025},
author = {Rzeczycki, P and Pęciak, O and Plust, M and Droździk, M},
title = {Molecular Aspects of Geriatric Pharmacotherapy.},
journal = {Cells},
volume = {14},
number = {17},
pages = {},
doi = {10.3390/cells14171363},
pmid = {40940774},
issn = {2073-4409},
abstract = {Pharmacotherapy in the geriatric population is one of the greatest challenges in modern medicine. Elderly patients, characterized by multimorbidity and the resulting polypharmacy, are significantly more exposed to adverse drug reactions (ADRs), which often lead to hospitalization and a decline in quality of life. Understanding the reasons for this difference requires an analysis of the physiological changes that occur during the aging process at the molecular level. This article presents a perspective on the molecular aspects of geriatric pharmacotherapy, focusing on the fundamental mechanisms that are modified with age. The analysis covers changes in pharmacokinetics, including the role and regulation of cytochrome P450 (CYP) enzymes, whose activity, especially in phase I reactions, is significantly reduced. The age-dependent dysfunction of drug transporters from the ABC (ATP-binding cassette) and SLC (solute carrier) families in key organs such as the intestines, liver and kidneys is discussed, which affects the absorption, distribution and elimination of xenobiotic compounds, including drugs. The article also provides a comprehensive analysis of the blood-brain barrier (BBB), describing changes in neurovascular integrity, including the dysfunction of tight junctions and a decrease in the activity of P-glycoprotein, sometimes referred to as multidrug resistance protein (MDR). This increases the susceptibility of the central nervous system to the penetration and action of drugs. In the realm of pharmacodynamics, changes in the density and sensitivity of key receptors (serotonergic, dopaminergic, adrenergic) are described based on neuroimaging data, explaining the molecular basis for increased sensitivity to certain drug classes, such as anticholinergics. The paper also explores new research perspectives, such as the role of the gut microbiome in modulating pharmacokinetics by influencing gene expression and the importance of pharmacoepigenetics, which dynamically regulates drug response throughout life via changes in DNA methylation and histone modifications. The clinical implications of these molecular changes are also discussed, emphasizing the potential of personalized medicine, including pharmacogenomics, in optimizing therapy and minimizing the risk of adverse reactions. Such an integrated approach, incorporating data from multiple fields (genomics, epigenomics, microbiomics) combined with a comprehensive geriatric assessment, appears to be the future of safe and effective pharmacotherapy in the aging population.},
}

@article {pmid40940504,
year = {2025},
author = {Ruiz-Malagón, AJ and Rodríguez-Sojo, MJ and García-García, J and Ho-Plagaro, A and García, F and Vezza, T and Redondo-Cerezo, E and Griñán-Lisón, C and Marchal, JA and Rodríguez-Cabezas, ME and Rodríguez-Nogales, A and Gálvez, J},
title = {Tigecycline suppresses colon cancer stem cells and impairs tumor engraftment by targeting SNAI1-regulated epithelial-mesenchymal transition.},
journal = {Acta pharmacologica Sinica},
volume = {},
number = {},
pages = {},
pmid = {40940504},
issn = {1745-7254},
abstract = {Cancer stem cells (CSCs) play a key role in the progression of colorectal cancer (CRC). The high heterogeneity of CSCs has hindered the clinical application of CSC-targeting therapies. Tetracyclines are drugs with therapeutic potentials beyond their antibiotic activity. We previously demonstrated the efficacy of tigecycline, a third-generation tetracycline, against a model of colitis-associated colorectal cancer, primarily focusing on its immunomodulatory role with a preliminary assessment of its impact on stemness. In this study we characterize the effects of tigecycline on colon CSCs in vitro and in a CRC xenograft model, with special attention on the signaling pathways involved and the modulation of the gut microbiota. We generated secondary colonospheres from two colon tumor cell lines HCT116 and CMT93, and evaluated the effect of tigecycline on CSCs properties. We showed that tigecycline (25, 50 μM) effectively reduced colon CD133[+]CD44[+]LGR5[+]ALDH[+] subpopulations and their viability, self-renewal and migratory capacity. Moreover, tigecycline treatment hindered epithelial-mesenchymal transition (EMT) process through targeting SNAI1 and β-catenin, resulting in an upregulation of epithelial markers (E-cadherin) and a downregulation of pluripotency and mesenchymal ones (Vimentin, N-cadherin, SOX2, NANOG, MIR155, MIR146). This effect was confirmed in two independent CRC-xenograft murine models in which tigecycline administration led to a reduction in tumor volume. Finally, CRC samples were taken from HCT116 xenograft model mice for analysis of CSCs-related signaling pathways and stools were collected for gut microbiome metagenomic analysis. We found that the antibiotic modulated gut dysbiosis by increasing the abundance of beneficial bacterial species such as Parabacteroides sp., which were involved in metabolic pathways that hindered SNAI1-Wnt-β-catenin signaling. These results reinforce the new role of tigecycline in the therapy of CRC and demonstrate for the first time the effect of tigecycline on colon CSCs and their malignancies.},
}

@article {pmid40940474,
year = {2025},
author = {Brookes, Z and Bescos, R and Witton, R and Bishop, MC and Whawell, S and McColl, E},
title = {An update on mouthwashes: advice for dental practitioners.},
journal = {British dental journal},
volume = {239},
number = {5},
pages = {312-315},
doi = {10.1038/s41415-025-9115-3},
pmid = {40940474},
issn = {1476-5373},
abstract = {Due to their antimicrobial constituents, mouthwashes are well-known to be clinically effective for reducing plaque biofilms containing bacteria and reducing gingival inflammation. However, with a variety of products now available (often containing more than one active ingredient), it is important to consider which chemical constituents are most suitable for different types of oral disease and how mouthwashes should be best used. This article thus updates professionals on techniques for use and which agent to select, using current professional guidelines and the highest level of evidence available. As examples, clinicians need to be aware of adjunctive approaches for mouthwash use and 'spit don't rinse with water' instructions. However, there is currently insufficient evidence on mouthwashes and the oral microbiome (including systemic health) to support microbiome testing to guide a choice. After consulting the literature, this article reiterates that adjunctive fluoride mouthwashes, alongside effective toothbrushing and interdental cleaning, are effective for preventing dental caries. Adjunctive chlorhexidine, essential oils and/or cetylpyridinium chloride mouthwashes may also be effective for managing plaque-induced periodontal diseases at early stages. Some possible risks to mouthwash use are highlighted, including allergies, tooth staining and oral microbiome dysbiosis. Until more evidence is available, clinicians should ensure that benefits outweigh risks and refer to current mouthwash guidelines to support personalised preventive care advice.},
}

@article {pmid40940422,
year = {2025},
author = {Kumar Nath, A and da Silva, RR and Gauvin, CC and Akpoto, E and Dlakić, M and Lawrence, CM and DuBois, JL},
title = {Commensal gut bacteria employ de-chelatase HmuS to harvest iron from heme.},
journal = {The EMBO journal},
volume = {},
number = {},
pages = {},
pmid = {40940422},
issn = {1460-2075},
support = {P30GM140963//HHS | National Institutes of Health (NIH)/ ; R35GM136390//HHS | National Institutes of Health (NIH)/ ; DBI-1828765//National Science Foundation (NSF)/ ; },
abstract = {Iron is essential for almost all organisms, which have evolved different strategies for ensuring a sufficient supply from their environment and using it in different forms, including heme. The hmu operon, primarily found in Bacteroidota and ubiquitous in gastrointestinal tract metagenomes of healthy humans, encodes proteins involved in heme acquisition. Here, we provide direct physiological, biochemical, and structural evidence for the anaerobic removal of iron from heme by HmuS, a membrane-bound, NADH-dependent de-chelatase that deconstructs heme to protoporphyrin IX (PPIX) and Fe(II). Heme can serve as the sole iron source for the model gastrointestinal bacterium Bacteroidetes thetaiotaomicron, when active HmuS is present. Heterologously expressed HmuS was isolated with bound heme molecules under saturating conditions. Its cryo-EM structure at 2.6 Å resolution revealed binding of heme and a pair of cations at distant sites. These sites are conserved across the HmuS family and chelatase superfamily, respectively. The proposed structure-based mechanism for iron removal by HmuS is chemically analogous to the chelatases in both unrelated heme biosynthetic pathways and homologous enzymes in the biosynthetic pathways for chlorophyll and vitamin B12, although the reaction proceeds in the opposite direction. Taken together, our study identifies a widespread mechanism via which anaerobic bacteria can extract nutritional iron from heme.},
}

@article {pmid40940406,
year = {2025},
author = {Zina, HA and Kalaba, MH and Shaban, AS and Elrefaey, AA and Mahdy, HM and Haikal, A},
title = {Honeybee associated Aspergillus niger AW17 as a source of selective anticancer compounds with cytotoxicity evaluation in human cancer cell lines.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {32472},
pmid = {40940406},
issn = {2045-2322},
abstract = {Cancer remains a leading cause of death worldwide, necessitating the discovery of novel therapeutic agents with improved efficacy and selectivity. This study investigated the anticancer potential of Aspergillus niger strain AW17 isolated from honeybees, a previously unexplored ecological niche for anticancer drug discovery. The fungal isolate was characterized through morphological, microscopic, and molecular methods, confirming its identity as Aspergillus niger. Chemical profiling using GC-MS and UPLC-MS/MS revealed a complex composition including high oleic acid content (28.88%) and unique compounds like pachymic acid (18.93%), rarely associated with A. niger. The extract's anticancer activity was evaluated against colorectal (Caco-2), liver (HepG2), breast (MCF-7), and lung (A549) cancer cell lines using MTT assay, confocal microscopy with AO/PI staining, cell cycle analysis, and apoptosis detection. Results demonstrated remarkable selective cytotoxicity of the Aspergillus niger extract against cancer cell lines, following the sensitivity hierarchy HepG2 (IC50 = 5.22 µg/ml) > Caco-2 (26.78 µg/ml) > A549 (34.18 µg/ml) > MCF-7 (55.91 µg/ml), while sparing normal cell lines significantly, with IC50 values of 1454.7 µg/ml for WI-38 and 668.3 µg/ml for HFB-4, indicating high cancer cell selectivity. Confocal microscopy confirmed membrane integrity loss as a primary cytotoxic mechanism. Cell cycle analysis revealed cell-type specific arrest patterns, with Caco-2 and HepG2 exhibiting G1 arrest, while MCF-7 and A549 showed S phase accumulation. Flow cytometry indicated distinct death mechanisms, with Caco-2 undergoing early apoptosis and substantial necrosis, HepG2 showing predominant late apoptosis, and A549 displaying primary necrotic death. These findings highlight the potential of honeybee-associated fungi as sources of novel anticancer compounds with remarkable selectivity, providing new avenues for targeted cancer therapy development and demonstrating the value of exploring specialized ecological niches in natural product discovery.},
}

@article {pmid40940205,
year = {2025},
author = {Gattuso, JJ and Kong, G and Bezcioglu, B and Lu, D and Ekwudo, MN and Wilson, C and Gubert, C and Hannan, AJ and Renoir, T},
title = {Corrigendum to "Chronic psilocybin administration increases sociability and alters the gut microbiome in male wild-type mice but not in a preclinical model of obsessive-compulsive disorder" [Neuropharmacology 279 (2025) 110648].},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {110679},
doi = {10.1016/j.neuropharm.2025.110679},
pmid = {40940205},
issn = {1873-7064},
}

@article {pmid40939787,
year = {2025},
author = {Zhao, Z and Chua, LW and Feng, S and Kang, X and Wong, SH and Loo, SCJ},
title = {Levan-like exopolysaccharide EPS-SOM8 produced by Bacillus subtilis SOM8 isolated from sesame oil meal as potential prebiotic and Synbiotic formulations for altering human gut microbiome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {147391},
doi = {10.1016/j.ijbiomac.2025.147391},
pmid = {40939787},
issn = {1879-0003},
abstract = {Bacillus subtilis SOM8, isolated from sesame oil meal processing residues, produces a levan-like exopolysaccharide EPS-SOM8 with promising prebiotic properties. Structural characterization using NMR, FTIR, and GPC revealed it as a branched fructan polymer with β-2,6 glycosidic linkages, β-2,1 branches, and an average molecular weight of 171.3 kDa. EPS-SOM8 exhibited stability throughout simulated gastrointestinal conditions and demonstrated selective growth stimulation of beneficial bacteria, most notably Bifidobacterium longum. Using human stool-derived in vitro communities models, EPS-SOM8 treatment significantly enriched Firmicutes populations, particularly Enterococcus and Lactobacillus species, while reducing Fusobacteriota abundance. Synbiotic formulations combining EPS-SOM8 with B. longum DSM20219 synergistically amplified metabolic benefits including short-chain fatty acids production, particularly propionate biosynthesis. These results establish EPS-SOM8 as a promising naturally derived prebiotic for targeted gut microbiome modulation and metabolic health enhancement.},
}

@article {pmid40939728,
year = {2025},
author = {de Souza, MA and Pereira, DE and da Silva, ECA and Medeiros, RG and Duarte, AM and Dutra, LMG and Araújo, DFS and de Araújo, WJ and de Oliveira, CJB and Guerra, GCB and Alves, AF and Viera, VB and Soares, JKB},
title = {Consumption of Brazilian palm fruit (Acrocomia intumescens drude) improves biochemical and gut microbiome parameters, reducing cardiovascular risk in exercised rats.},
journal = {Physiology & behavior},
volume = {},
number = {},
pages = {115102},
doi = {10.1016/j.physbeh.2025.115102},
pmid = {40939728},
issn = {1873-507X},
abstract = {OBJECTIVE: This study aimed to evaluate the effects of macaiba pulp on physical, biochemical, intestinal health, and oxidative stress parameters in exercised rats.

METHODOLOGY: Forty-four male rats were divided into four groups (n = 11): sedentary control (CT), exercised control (CT-EX), sedentary macaiba (MC), and exercised macaiba (MC-EX). MC and MC-EX groups received 1000 mg/kg/day of macaiba pulp, while CT and CT-EX received distilled water for eight weeks. Exercised animals underwent swimming for five days a week, beginning with 10 minutes and progressing to 60 minutes. Blood was collected to measure cholesterol (TC, HDL, LDL, VLDL), glucose, urea, liver enzymes (AST, ALT), and cardiovascular risk factors. Liver samples were analyzed for malonaldehyde (MDA), total fat, and cholesterol, while feces were collected for metagenome analysis. Body fat and adiposity index were also measured.

RESULTS: Macaiba-treated groups showed improved gut microbiome balance, reduced TC, LDL, VLDL, glucose, urea, liver enzymes, cardiovascular risks, body fat, MDA, and liver fat, with an increase in HDL.

CONCLUSION: Macaiba pulp effectively improved biochemical parameters, reduced lipid peroxidation from exercise, and lowered adipose tissue and cardiovascular risks.},
}

@article {pmid40939656,
year = {2025},
author = {Ren, Z and Sun, P and Li, H and Wei, Y and Kraslawski, A and An, X and Sun, L},
title = {Novel photocatalytic bacteria-algae coupling system mediated by g-C3N4 nanoparticles: Effects of microbial ratio on performance and microbiome.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133301},
doi = {10.1016/j.biortech.2025.133301},
pmid = {40939656},
issn = {1873-2976},
abstract = {This study explored symbiotic interactions within a graphitic carbon nitride (g-C3N4)-enhanced bacterial-algal system for advanced wastewater treatment by examining the effects of varying bacterial-algal ratios (10:1, 5:1, and 1:1) on nutrient removal, microbial aggregation, and community dynamics in sequencing batch reactors. The 1:1 ratio (R3) exhibited optimal performance, achieving highest chemical oxygen demand removal (98.7 %) and ammonium nitrogen removal (92.4 %), alongside increased algal biomass. R3 enhanced microbial aggregation via elevated extracellular polymeric substances (EPS, 80.2 mg/g SS), reduced electrostatic repulsion. Microbial profiling revealed higher abundances of Proteobacteria (37.6 %) and Cyanobacteria (9.1 %), synergistically enabling nitrogen assimilation and integration of photocatalytic and biological degradation pathways. The balanced ratio improved dissolved oxygen regulation via algal photosynthesis, while EPS helped mitigate g-C3N4-induced oxidative stress. These findings provide mechanistic insights for the strategic optimization of bacterial-algal consortia in photocatalytically enhanced wastewater treatment systems, with implications for the development of sustainable and energy-efficient water remediation technologies.},
}

@article {pmid40939563,
year = {2025},
author = {Rath, S and Das, R and Misra, SR},
title = {Oral microbiome and oral squamous cell carcinoma: Expanding perspectives on mechanisms, methodology, and translation.},
journal = {Oral oncology},
volume = {169},
number = {},
pages = {107684},
doi = {10.1016/j.oraloncology.2025.107684},
pmid = {40939563},
issn = {1879-0593},
}

@article {pmid40939545,
year = {2025},
author = {Li, R and Qian, W and Li, C and Yao, B and Wang, A and Guan, T and Liu, Z and Gao, L and Qin, D},
title = {Exposure of crayfish (Procambarus clarkii) to pinoxaden disrupts hepatic transcriptome, gut microbiome, and redox homeostasis.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {56},
number = {},
pages = {101627},
doi = {10.1016/j.cbd.2025.101627},
pmid = {40939545},
issn = {1878-0407},
abstract = {With the widespread use of pesticides, pinoxaden has become a commonly used herbicide in rice-crayfish co-culture fields. However, the mechanism of toxicity to aquatic organisms is unclear. This study investigated the acute toxicity effects of pinoxaden on crayfish. Biochemical analysis revealed significant alterations in malondialdehyde content, as well as glutathione peroxidase, superoxide dismutase and catalase activities in hepatopancreas tissues following pinoxaden exposure. Histological examination revealed pinoxaden-induced impairment in the hepatopancreas and gut tissues of crayfish. Transcriptomic profiling detected genes with differential expression following pinoxaden treatment, significant enrichment of pathways including lysosome, antigen processing presentation, phagosome. Furthermore, pinoxaden exposure altered the abundance of bacterial families such as Actinobacteriota and Erysipelatoclostridium in the gut microbiota of exposed groups. This study provides important insights into the toxicity of pinoxaden to crayfish, offering practical guidance for the scientifically based and rational use of pesticides in rice-crayfish co-culture systems.},
}

@article {pmid40939247,
year = {2025},
author = {Suteau, L and Colaert-Sentenac, L and Law, SR and Simonin, M},
title = {Transient microbial architects: tracing the legacy effects of ephemeral taxa during plant microbiome assembly.},
journal = {Current opinion in microbiology},
volume = {88},
number = {},
pages = {102664},
doi = {10.1016/j.mib.2025.102664},
pmid = {40939247},
issn = {1879-0364},
abstract = {Plant microbiota assembly is a dynamic process shaped by a succession of microbial dispersal events, interactions, and environmental fluctuations. While most research emphasizes the roles of resident and core taxa in driving microbiome structure and plant health, the ecological significance of transient microbial members (taxa temporarily present in plant tissue and then disappearing from microbiota) remains underexplored. In this opinion article, we propose that these ephemeral microorganisms may act as 'transient microbial architects', capable of generating legacy effects that influence the trajectory of microbiota assembly and long-term plant fitness. By reviewing the available temporal studies, we show that transient taxa often collectively represent the most diverse and abundant plant microbiota members compared to core taxa. We highlight how priority effects, niche modification, and microbe-microbe interactions mediated by transient taxa, can alter community composition, modulate the recruitment of symbionts, and shape plant responses to biotic and abiotic stressors. We identify outstanding questions and propose methodological advances to address them, including high-resolution longitudinal sampling and integrative omics approaches, that will enable the detection and functional characterization of these elusive taxa. Finally, we discuss the potential for harnessing transient microbial architects in microbiome engineering strategies for sustainable agriculture, emphasizing the need for targeted interventions during critical plant developmental windows. By recognizing and harnessing the legacy effects of these transient members, we gain access to previously overlooked ecological levers for shaping plant-microbe interactions.},
}

@article {pmid40939227,
year = {2025},
author = {Gan, RH and Qu, J and Lan, LQ and Zheng, DL and Lu, YG and Zhang, M},
title = {Supragingival Plaque Microbial Signatures Between Radiation Related Caries and Common Caries.},
journal = {International dental journal},
volume = {75},
number = {6},
pages = {103898},
doi = {10.1016/j.identj.2025.103898},
pmid = {40939227},
issn = {1875-595X},
abstract = {OBJECTIVES: The clinical manifestations of radiation-related caries (RRC) differ considerably from those of common caries. This study aims to investigate potential differences in the microbial compositions of supragingival plaque between RRC and common caries.

METHODS: Supragingival plaque samples from 10 RRC and 10 patients with common caries were analyzed using Type IIB Restriction-site Associated DNA sequencing for Microbiome (2bRAD-M). Analyses of microbial diversity, relative abundance and composition were performed. LEfSe analysis was employed to identify differentially abundant species between the 2 groups. Additionally, 24 RRC and 33 common caries samples were examined using qRT-PCR. Species indicators of RRC were identified through random forest analysis. KEGG and COG functional prediction analyses were conducted to assess microbial functional pathways.

RESULTS: 2bRAD-M sequencing revealed a significant enrichment of Prevotella conceptionensis, Treponema vincentii, and 4 Nanoperiomorbus species in the RRC group. These findings were further validated by LEfSe and qRT-PCR analyses, which confirmed the dominance of P. conceptionensis in RRC. Random forest analysis identified P. conceptionensis as a potential biomarker for RRC. The bacterial abundance in RRC samples was higher than in common caries, particularly in pathways related to glucose metabolism, including 6-phosphofructokinase activity and sugar transferases involved in LPS biosynthesis.

CONCLUSIONS: This study uniquely identifies distinct microbial signatures in supragingival plaque associated with RRC compared to common caries. Prevotella conceptionensis was identified as a specific pathogenic bacterium linked to RRC. The underlying mechanisms may involve enhanced microbial glucose metabolism and an inflammatory response mediated by ferroptosis.},
}

@article {pmid40938872,
year = {2025},
author = {Ghouri, YA and Ericsson, AC and Anderson, JM and George, JG and Parks, EJ and Anguah, KOB},
title = {Repopulation of the gut microbiota after a screening colonoscopy.},
journal = {PloS one},
volume = {20},
number = {9},
pages = {e0320712},
doi = {10.1371/journal.pone.0320712},
pmid = {40938872},
issn = {1932-6203},
abstract = {OBJECTIVE: Role of microbiome has been highly studied for its association with various medical conditions. After a colonoscopy, repopulation of colonic microbial load is known to occur, however the quality and timing of natural repopulation has not been investigated after a bowel preparation. Further, no study has documented detailed free-living dietary intakes concurrently with gut microbiome repopulation post-colonoscopy. Here we sought to determine the early pattern of repopulation relative to dietary intake.

METHODS: Healthy adults (n = 15 [4 female/11 male], BMI = 27.2 ± 3.9 kg/m2, age 51.4 ± 7.2 y) who were scheduled to undergo a screening colonoscopy were recruited from the Gastroenterology Clinic at the University of Missouri. Within two weeks before the colonoscopy (baseline), subjects completed detailed food records for 3 days. Post-colonoscopy, subjects ate their free-living diets and detailed food records were collected on Days 0, 1, 2, 4, 7, 10, and 13. Fecal samples were obtained pre-colonoscopy and on post-colonoscopy Days 3, 5, 8, 11, and 14. Gut microbiome composition was assessed by 16S rRNA amplicon sequencing.

RESULTS: Within 5 days after the procedure, subjects reported consuming more total daily energy relative to baseline, presumably to make up for the low energy intake that occurred during the bowel-prep. At baseline, fiber intake (21.0 ± 9.1 g/d) was higher than on the day of the colonoscopy, Day 0 (16.1 ± 11.2, P = 0.0159). Thereafter, daily fiber intake was the same as baseline. Marked intersubject microbiome beta diversity was observed by principal coordinate analysis using weighted and unweighted dissimilarities (P = 0.0001, F = 15.23, one-way PERMANOVA). Select taxa were depleted acutely post-colonoscopy (e.g., within the phylum Bacillota). Specifically, significant effects of time were observed between baseline and Day 3 fecal samples (pairwise P = 0.0013, F = 2.9). These changes tended to return to baseline by Day 5 and with subsequent samples, taxa remained similar to baseline when tested using a weighted dissimilarity analysis (Bray-Curtis).

CONCLUSIONS: These results quantitatively demonstrate the magnitude of the significant changes in microbial relative abundance and diversity immediately post-colonoscopy. The timing of repopulation aligned with changes in fiber intake after the procedure. These data highlight the importance of nutrition after a screening colonoscopy in reestablishing a healthy microbiome.},
}

@article {pmid40938736,
year = {2025},
author = {Choi, H and Richardson, H and Hennayake, C and Shuttleworth, M and Cant, E and Bottier, M and Spinou, A and Robertson, K and Long, M and De Soyza, A and Ringshausen, FC and Goeminne, P and Lorent, N and Haworth, C and Altenburg, J and Loebinger, MR and Alferes de Lima Headley, D and Dicker, AJ and Blasi, F and Shteinberg, M and Aliberti, S and Polverino, E and Sibila, O and Shoemark, A and Chalmers, JD},
title = {Upper Airway Microbiome, Mucociliary Function, and Clinical Outcomes in Bronchiectasis: Data from the EMBARC-BRIDGE Study.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202504-0875OC},
pmid = {40938736},
issn = {1535-4970},
abstract = {RATIONALE: Infection is a key disease driver in bronchiectasis, and the upper airway microbiome has been known to shape the lower airway microbiome.

OBJECTIVES: To evaluate the relationship between the upper airway microbiome, mucociliary function, and clinical outcomes in bronchiectasis.

METHODS: Nasopharyngeal swabs were collected from 344 bronchiectasis patients enrolled across five European centers. A total of 104 patients had nasopharyngeal samples obtained at the 1-year follow-up. Microbiome composition was assessed according to BSI and severe exacerbations. The α- and β-diversity were measured using the Chao1 and Bray-Curtis indices, respectively. Random forest analysis was performed. Dysbiosis was defined as >10% relative abundance of pathogenic taxa comprising Pseudomonas, Haemophilus, and Staphylococcus.

MEASUREMENTS AND MAIN RESULTS: Of the 344 patients, 200 (58.1%) were female (median age, 68 years; interquartile range, 59-75 years). α-diversity significantly differed according to disease severity (P=0.002), and β-diversity analysis revealed distinct microbiome profiles associated with disease severity and severe exacerbation (PERMANOVA, P=0.021 and 0.001, respectively). Random forest analysis identified Pseudomonas as being associated with severe bronchiectasis (BSI≥9) and severe exacerbations. The genus-level relative taxon abundance of Pseudomonas was well correlated with Pseudomonas aeruginosa growth in the sputum culture. Patients with nasopharyngeal dysbiosis had more severe respiratory symptoms, showed epithelial disruption on nasal epithelial biopsy, and experienced more severe exacerbation over a 1-year follow-up period than those in the non-dysbiosis group. The microbiome profiles were relatively stable between baseline and 1-year follow-up (P=0.95).

CONCLUSION: The upper airway microbiome is associated with disease severity and severe exacerbation of bronchiectasis.},
}

@article {pmid40938671,
year = {2025},
author = {Song, Z and Tsou, S and Martin, F and Kayumov, M and Xiao, Y and Zhou, H and Abdi, R and Tullius, SG},
title = {Kidney Disease as a Driver of Immunosenescence: Mechanisms and Potential Interventions.},
journal = {Journal of the American Society of Nephrology : JASN},
volume = {},
number = {},
pages = {},
doi = {10.1681/ASN.0000000896},
pmid = {40938671},
issn = {1533-3450},
abstract = {Immunosenescence, a state marked by immune dysfunction, chronic low-grade inflammation, and impaired pathogen defense, is accelerated in chronic kidney disease (CKD). CKD promotes systemic inflammation through the accumulation of uremic toxins, oxidative stress, and dysregulated immune signaling, all driving premature aging of both innate and adaptive immune cells. These mechanisms result in dysregulated immune activation and impaired surveillance, thereby aggravating kidney damage and increasing the risk for co-morbidities. Despite removing uremic toxins, dialysis may further accelerate immunosenescence by exposing immune cells to oxidative and antigenic stress, inducing telomere shortening and T cell exhaustion. Kidney transplantation can partially reverse CKD-induced immunosenescence by restoring renal function. Commonly used immunosuppressive agents, however, may further promote immunosenescence by impairing thymic function, depleting naïve T cells, and suppressing NK cell activity. However, mTOR inhibitors have shown anti-aging effects by promoting autophagy and inhibiting pro-inflammatory pathways. Therapeutic strategies targeting immunosenescence in CKD have been gaining momentum. Senotherapeutics can eliminate senescent cells and reduce SASP-mediated inflammation. SGLT2 inhibitors, caloric restriction, microbiome modulation, mesenchymal stem cell therapies and renal replacement therapies also offer the potential to slow accelerated immunosenescence as a consequence of CKD. Here, we provide a comprehensive overview of the mechanisms linking CKD and immunosenescence, along with emerging therapeutic strategies that have the potential to target premature aging.},
}

@article {pmid40938657,
year = {2025},
author = {Troci, A and Haas, J and Weiß, A and Heinzel, S and Franke, A and Berg, D and Bang, C and Schaeffer, E},
title = {Differences in intestinal microbiota in Parkinson's disease and isolated REM sleep behavior disorder.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X251354931},
doi = {10.1177/1877718X251354931},
pmid = {40938657},
issn = {1877-718X},
abstract = {Previous studies have shown differences in the microbiota of patients with Parkinson's disease (PD) compared to healthy controls (HC). To deduce a possible causality, it is highly relevant to examine changes in the prodromal phase. This study investigated the microbiome in stool samples of individuals with isolated REM sleep behavior disorder (iRBD, n = 32) compared to clinical PD (n = 23) and HC (n = 34) and showed significant changes of beta-diversity in PD and iRBD patients compared to HC (p = 0.025; p = 0.003), with an increase in proinflammatory species in iRBD and PD and decrease in SCFA-producing bacteria in PD.},
}

@article {pmid40938637,
year = {2025},
author = {Fuentes, JJ and Singh, S and Pudlo, NA and Heaver, SL and Ley, RE and Martens, EC},
title = {Carbohydrates and the oxidative branch of the pentose phosphate pathway modify Bacteroides thetaiotaomicron phage resistance by phase-variable S-layers.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0017825},
doi = {10.1128/jb.00178-25},
pmid = {40938637},
issn = {1098-5530},
abstract = {The human gut microbiota consists of hundreds of bacterial species, some of which persist in the presence of lytic phage that infect them. Bacteroides employ numerous phase-variable strategies to survive in the presence of phage, including capsular polysaccharides (CPS) and S-layer lipoproteins. We previously reported that a Bacteroides thetaiotaomicron strain lacking CPS exhibits almost complete resistance to multiple phages when forced to express the S-layer protein BT1927. However, this strain was only resistant after certain growth conditions, suggesting nutritional variables alter infection and resistance. We grew this strain on various simple sugars and polysaccharides, finding that some substrates (fructose, glucose) promote strong resistance to a single phage (ARB25), while others like N-acetylgalactosamine (GalNAc) and mucin O-glycans increase susceptibility. Mixing fructose and GalNAc indicates the effects of GalNAc are dominant. Despite increasing ARB25 susceptibility, GalNAc did not reduce BT1927 transcript or protein levels. Instead, GalNAc reduced the amount of BT1927 displayed on the cell surface and increased outer membrane vesiculation. Mutants in any of the three steps of the oxidative branch of the pentose phosphate pathway-grown in fructose-behaved similarly to wild-type cells grown in GalNAc, illuminating this pathway in the regulation of sugar-mediated phage resistance. Despite promoting strong resistance, cells grown in glucose/fructose sometimes displayed sub-populations that appeared to completely lack surface BT1927, suggesting another checkpoint exists to control whether this phage defense is deployed. Finally, we show the mucin sugar GalNAc increases susceptibility to several other phage, which has implications for B. thetaiotaomicron persistence in niches like the mucus layer.IMPORTANCEThe persistence of viruses that infect bacteria (bacteriophages or phages) in the human gut microbiome and their effects on bacterial physiology and host health are active areas of investigation. Our study investigates how various sugars and polysaccharides alter the susceptibility of the model gut symbiont Bacteroides thetaiotaomicron to lytic phages that are capable of infecting it. Our finding that the mucin sugar, N-acetylgalactosamine, and mucin O-glycans that contain this sugar reduce B. thetaiotaomicron resistance to multiple phages has implications for how this symbiont persists in different gut microhabitats, such as the mucus layer, and which defense mechanisms it can deploy to survive in these niches.},
}

@article {pmid40938338,
year = {2025},
author = {Feckler, A and Bollinger, E and Katzenmeier, S and Adamovsky, O and Vespalcova, H and Budinska, E and Stoeck, T and Bundschuh, M},
title = {Antimicrobials Shape the Gut Microbiome Structure and Digestive Profile of Invertebrates.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c04159},
pmid = {40938338},
issn = {1520-5851},
abstract = {The gut microbiome is crucial for host well-being but is vulnerable to external stressors, such as antimicrobials. This study examined how an antibiotic, a fungicide, and their mixture affect the prokaryotic and fungal gut microbiome in Gammarus fossarum via dietary, waterborne, and combined exposure. Antimicrobial exposure altered the relative abundance of bacterial classes, including Verrucomicrobiae, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria, with effect directions depending on the antimicrobial. These structural shifts were predicted to enhance lipid and energy metabolism, particularly under dietary and combined exposure, potentially influencing host physiology. Previous studies on the same species reported up to 25% higher biomass gain under these exposure routes, whereas waterborne exposure had negligible effects. As this study primarily relies on predictive models linking microbiome shifts to physiological changes, experimental validation is required to substantiate these findings. Likewise, several fungal classes were affected, but limited knowledge of the mycobiome hinders functional interpretation. Overall, dietary uptake emerged as a key driver of gut microbiome changes, while waterborne exposure played a minor role in the metabolic and physiological responses. Future research should investigate the mycobiome alongside its prokaryotic counterpart for a more comprehensive understanding of the gut digestive profile of invertebrates as a whole and its role in host health.},
}

@article {pmid40938123,
year = {2025},
author = {Zhu, Z and Guan, J and Xie, X and Zhang, C and Liao, Z and Li, Z and Lin, B and Chen, H and Zhuang, Z and Meng, S and Zou, Y and Li, W and Luo, M and Dai, D},
title = {Genome sequence of Mediterraneibacter faecis SZCH001, isolated from an autistic child.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0070125},
doi = {10.1128/mra.00701-25},
pmid = {40938123},
issn = {2576-098X},
abstract = {Here, we report the draft genome sequence of Mediterraneibacter faecis SZCH001, isolated from a fecal sample of an autistic child. The bacterial genome was sequenced using Illumina technology on a Novaseq 6000 platform. The assembled genome of M. faecis comprises 3,423,666 base pairs with a G+C content of 40.27%.},
}

@article {pmid40938109,
year = {2025},
author = {Deng, Q and Zheng, Y and Gao, H and Wu, H and Shi, E and Cheng, M and Wang, H and Liao, L},
title = {The role of MorI/MorR quorum sensing in Methylobacterium oryzae CBMB20: modulating bacterial functions for enhanced adaptability.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0211725},
doi = {10.1128/spectrum.02117-25},
pmid = {40938109},
issn = {2165-0497},
abstract = {UNLABELLED: The quorum-sensing (QS) system in Methylobacterium oryzae CBMB20, an endophytic bacterium associated with rice (Oryza sativa L.), plays a critical role in regulating bacterial behaviors essential for plant growth promotion and adaptation. This study aimed to elucidate the functional role of the MorI/MorR QS system in M. oryzae CBMB20 and its potential application as a bioinoculant. We identified and characterized two QS signals, 3-OH-C12-HSL and 3-oxo-C12-HSL, synthesized by the MorI enzyme. The MorR receptor was found to preferentially respond to 3-OH-C12-HSL, indicating a high degree of specificity in QS signaling. The deletion mutants of morI and morR exhibited significant changes in exopolysaccharides (EPS), motility, and methanol utilization, suggesting that the MorI/MorR system is crucial for bacterial survival and adaptation. Transcriptome analysis revealed that MorR acts as a repressor, controlling the expression of numerous genes, many of which are upregulated upon its deletion. Our findings highlight the multifaceted role of the MorI/MorR QS system in M. oryzae CBMB20, influencing key biological functions such as EPS production, motility, and methanol utilization. The modulation of these traits through QS could enhance the bacterium's effectiveness as a bioinoculant for promoting plant growth. This study contributes to the understanding of how QS systems can be harnessed to improve the efficacy of plant growth-promoting bacteria in agricultural settings, offering insights into the potential for genetic manipulation to optimize bioinoculant performance.

IMPORTANCE: This study provides critical insights into microbial communication by functionally characterizing the MorI/MorR quorum-sensing (QS) system in Methylobacterium oryzae CBMB20, a plant-beneficial methylotroph. We identify 3-OH-C12-AHL as a key long-chain signal governing exopolysaccharides biosynthesis, swimming motility, and methanol metabolism traits pivotal for host colonization. These findings not only elucidate novel regulatory mechanisms in plant-associated bacteria but also pave the way for engineering QS-driven strategies, such as synthetic consortia or targeted microbiome interventions, to enhance sustainable agricultural practices.},
}

@article {pmid40938107,
year = {2025},
author = {Stinson, LF and Pang, WW and Rea, A and Fok, D and Chua, MC and Tan, KH and Yap, F and Godfrey, KM and Shek, LP and Eriksson, JG and Chong, Y-S and Chan, S-Y and Wlodek, M and Geddes, DT},
title = {Composition of the human milk microbiome in the GUSTO cohort is shaped by intrapartum antibiotic prophylaxis and breastfeeding exclusivity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0067725},
doi = {10.1128/msystems.00677-25},
pmid = {40938107},
issn = {2379-5077},
abstract = {Human milk contains a low biomass microbiome, which is thought to contribute to mammary and infant health. However, the determinants of the human milk microbiome across populations are poorly understood. Here, we characterized the microbiome of 266 milk samples collected from 208 mothers at 3 weeks and 3 months postpartum from the Growing Up in Singapore Toward healthy Outcomes (GUSTO) study, a multi-ethnic Asian cohort. Full-length 16S rRNA gene sequencing showed a substantial level of inter-individual variation, as well as temporal variation, highlighting the need for broad-scale longitudinal sampling in this field. Milk microbiome composition and diversity were associated with maternal, socioeconomic, and breastfeeding factors. In particular, intrapartum antibiotic prophylaxis and breastfeeding exclusivity modulated milk bacterial composition and diversity, even at 3 months postpartum. These results highlight the dynamic nature of the human milk microbiome and its relationship with clinical and breastfeeding factors, with potential implications for infant health.IMPORTANCEHuman milk exposes infants to a constant source of maternal bacteria that may influence the development of the infant immune system and gut microbiome. However, compared to other body niches, the human milk microbiome is relatively under-studied, and there is limited consensus on the factors driving variance in these bacterial communities. In this study, we performed in-depth microbiome profiling of milk samples from 208 mothers in a diverse Asian population, finding a high level of variation between individuals and over time. We found that factors such as delivery-related antibiotics, breastfeeding practices, and maternal lifestyle can influence which bacteria are present in milk. These findings suggest that the milk microbiome is not static, but dynamic and shaped by both medical and social factors. Understanding what drives variance in the milk microbiome could help inform strategies to support maternal and infant health, especially in the critical early months of life when microbial exposures can have long-term effects.},
}

@article {pmid40938096,
year = {2025},
author = {Alexandre, G},
title = {Movement of bacteria in the soil and the rhizosphere.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0024625},
doi = {10.1128/aem.00246-25},
pmid = {40938096},
issn = {1098-5336},
abstract = {The soil and the rhizosphere are physicochemically heterogeneous environments that host diverse macro- and micro-organisms that together influence soil productivity. The ability of organisms to disperse in these environments allows them to exploit resources and to occupy niches that support growth and protect them from predation and stressful conditions. The dispersal of soil macroorganisms has been much better characterized than that of bacteria because of the complexity and physicochemical heterogeneity of the soil and the rhizosphere, and challenges in quantifying the dispersion of bacteria in these environments. However, even limited bacterial dispersal in soils and the rhizosphere could have the potential to alter the local microbiome composition and its function. Active bacterial movement includes swimming and swarming using flagella, twitching motility using pili, as well as emerging forms of motility that result from microbe-microbe interactions. Passive transport of bacteria throughout the soil may be mediated by passive physical factors such as rainfalls, as well as through transport mediated by protists, nematodes, or hitchhiking using other microbes' appendages. This minireview focuses on the modes of bacterial movement in the soil and the rhizosphere that do not depend on passive physical factors (e.g., rainfalls) and identifies areas of future research.},
}

@article {pmid40937939,
year = {2025},
author = {Zaletova, TS and Feofanova, TB and Zainudinov, ZM and Zavistyaeva, TY and Korotkova, TN and Solovyeva, SY},
title = {[Evaluation of the effect of dietary soluble corn fiber on metabolic activity and colonic microbiota composition in patients with dysbiosis and obesity].},
journal = {Voprosy pitaniia},
volume = {94},
number = {3},
pages = {91-100},
doi = {10.33029/0042-8833-2025-94-3-91-100},
pmid = {40937939},
issn = {0042-8833},
support = {//This article was prepared based on exploratory analytical work conducted on a contractual basis/ ; },
abstract = {The gut microbiome is critically important for human health. Intestinal bacteria are involved in nutrient metabolism, immune modulation, maintaining intestinal barrier integrity, and protecting against pathogenic bacteria. Soluble corn fiber (SCF) has been shown to possess prebiotic properties, improve intestinal peristalsis, affect blood glucose and insulin levels, improve calcium absorption and reabsorption in bone tissue. The aim of the research was to evaluate the effectiveness of incorporating soluble corn fiber into a low-calorie diet (LCD) in obese patients with dysbiosis, and its effect on the metabolic activity and composition of the colonic microbiota. Material and methods. 48 patients with reduced amounts of Bifidobacterium and/ or Lactobacillus in their stool, who were included in the study, were divided into 2 groups - the main group and the control group. They followed LCD for 28 days. Patients in the main group, in addition to the LCD, received soluble corn fiber (1.8%) at the dose 7 g 3 times daily (dissolved in 200 ml of liquid). Drug therapy was administered according to standard regimens for therapeutic diseases and was not adjusted during the study. The groups were compared using clinical and functional methods (assessment of actual nutrition, determination of body composition, a stool change assessment scale, a scale for assessing the organoleptic properties of dishes), and laboratory methods (biochemical blood serum analysis, microbiological stool diagnostics by cultural method). Results. After the course of diet therapy, all patients showed a statistically significant decrease in body weight, but in patients of the main group it occurred due to skeletal muscles and lean mass decrease (p<0.005), while against the background of the SCF intake, a statistically significant decrease in body fat mass (p=0.015) was noted with a tendency to decrease skeletal muscle mass and lean mass (p<0.10). After the course of diet therapy, the number of Bifidobacterium in the feces of patients in the main group statistically significantly increased from 8.75±0.61 to 9.04±0.20 lg CFU/g (p=0.035), while in patients from the control group, on the contrary, the number of these bacteria was significantly lower upon repeated examination (7.96±1.12 versus 8.46±0.78 lg CFU/g, p=0.046). The inclusion of SCF in the LCD was accompanied by a significant decrease in the number of individuals with reduced levels of Bifidobacterium and Lactobacillus, a positive effect on the populations of commensal and transient (opportunistic) representatives of the microbiota and an improvement in stool characteristics. Upon repeated examination, patients in both groups showed a statistically significant decrease in the levels of total cholesterol, low- and high-density lipoprotein cholesterol. Conclusion. Therefore, SCF can be used in dietary therapeutic and preventive nutrition as a source of soluble dietary fiber. It can be used as part of a diet for direct consumption after pre-dissolving in water, juice, or fermented milk drinks, and can be used as an ingredient in the production of foods enriched with soluble dietary fiber.},
}

@article {pmid40937858,
year = {2025},
author = {Lee, JM and Yang, HO and Tanizawa, H and Noma, K-i and Lee, TK and Jung, WH and Cho, Y-J and Kim, K-D},
title = {Acetic acid produced by Staphylococcus epidermidis remodels chromatin architecture and suppresses gene expression in Malassezia restricta.},
journal = {mBio},
volume = {},
number = {},
pages = {e0159225},
doi = {10.1128/mbio.01592-25},
pmid = {40937858},
issn = {2150-7511},
abstract = {The skin microbiome is composed of diverse microbial communities that engage in interkingdom interactions, influencing host physiology and microbial balance. Although Malassezia restricta and Staphylococcus epidermidis are codominant members of the human skin microbiome, the molecular mechanisms underlying their interactions remain poorly understood. We aimed to investigate the mechanism by which S. epidermidis-derived acetic acid affects chromatin organization and gene expression in M. restricta. S. epidermidis modulated chromatin structure and transcriptional activity in M. restricta by secreting acetic acid (AcOH), a common skin-associated organic acid. Using in situ Hi-C, we established the first three-dimensional genome architecture map of M. restricta and identified putative centromeric loci based on inter-chromosomal association scores. Co-culture with S. epidermidis or direct treatment with AcOH induced large-scale chromatin decompaction and enhanced centromeric clustering, indicating significant reorganization of the nuclear architecture. Through chromatin immunoprecipitation (ChIP)-seq analysis, we observed that AcOH exposure led to a redistribution of histone acetylation from promoter regions to gene bodies. This chromatin remodeling was further associated with extensive transcriptional repression, particularly of genes involved in translation, metabolism, and virulence, as revealed by RNA-seq analysis. Of note, these changes were specific to AcOH and were not replicated under inorganic acid stress (HCl), indicating a metabolite-specific epigenetic response. This study reveals a novel form of interkingdom communication in the skin microbiome, in which S. epidermidis-derived AcOH acts as an epigenetic modulator in M. restricta. Our findings provide key mechanistic insights into how bacterial metabolites influence fungal chromatin architecture and transcription, with implications for microbial community dynamics and skin health.IMPORTANCEThis study provides essential insights into interkingdom interactions within the human skin microbiome, highlighting how microbial metabolites influence fungal biology at the chromatin level. Specifically, we identify acetic acid (AcOH), secreted by Staphylococcus epidermidis, as a key regulator that induces significant chromatin remodeling and transcriptional changes in Malassezia restricta. By presenting the first three-dimensional genome architecture map of M. restricta, our findings uncover metabolite-specific chromatin dynamics that cannot be replicated by inorganic acid stress. Additionally, the conservation of this chromatin response in other Malassezia species suggests broader implications for understanding microbial adaptation mechanisms in the skin environment. This work underscores the critical role of bacterial metabolites as modulators of microbial interactions and provides new avenues for investigating microbial community balance and potential therapeutic strategies for skin health.},
}

@article {pmid40937800,
year = {2025},
author = {Khotko D, N and Khotko A, I and Bucharskaya A, B and Polukonova N, V and Popkov V, M and Tarasenko A, I and Altynbaev R, R and Al-Jazaeri M, IM and Kozlov D, A},
title = {[The relationship between bacteria and kidney stones of different compositions in patients with urolithiasis].},
journal = {Urologiia (Moscow, Russia : 1999)},
volume = {},
number = {4},
pages = {80-84},
pmid = {40937800},
issn = {1728-2985},
abstract = {Urolithiasis is one of the most prevalent urological disorders and remains among the leading urinary tract diseases worldwide. The risk of developing urolithiasis is influenced by a wide range of factors, and its global prevalence continues to rise, particularly in both developed and developing countries. A deeper understanding of its etiology, including the contribution of bacteria, is of paramount importance, as microorganisms may contribute to recurrent stone formation. This review summarizes current evidence supporting bacterial involvement in urolithiasis. Particular attention is given to the potential role of microorganisms in the pathogenesis of so-called non-infectious stones, as well as to the complex interplay between stone formation and urinary tract infection. The aim of this article is to integrate available data on the association between bacteria and urinary stones, with a focus on the pathophysiology of stone formation and the urinary microbiome in calculi of different chemical compositions.},
}

@article {pmid40937767,
year = {2025},
author = {Jablonska, S and Nelson, L and Finger, G and Kula, A and Putonti, C},
title = {Draft genome sequence of Staphylococcus aureus N208 isolated from a nasal swab of a healthy female.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0081125},
doi = {10.1128/mra.00811-25},
pmid = {40937767},
issn = {2576-098X},
abstract = {Staphylococcus aureus, a common member of the healthy human microbiota, is an opportunistic pathogen. To investigate the genomic features of this species in healthy individuals, we present the draft genome sequence of S. aureus N208, isolated from a nasal swab collected from a healthy female participant.},
}

@article {pmid40937720,
year = {2025},
author = {Xian, Y and Chen, Z and Lan, Z and Zhang, C and Sun, H and Liu, Z and Kong, P and Liang, Y and Zhao, Y and Liu, SM and Zhou, Y and Gan, L and Li, B and Su, X and Huang, B and Xiao, C and Zhu, R and Zhao, G and Lao, C and Lin, CS and Zhang, D and Jiang, X},
title = {Live biotherapeutic enterococcus lactis MNC-168 promotes the efficacy of immune checkpoint blockade in cancer therapy by activating STING pathway via bacterial membrane vesicles.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2557978},
doi = {10.1080/19490976.2025.2557978},
pmid = {40937720},
issn = {1949-0984},
abstract = {The gut microbiome has the potential to influence tumor development and affect the efficacy of cancer therapeutics, particularly immunotherapy. However, the specific species and strains rather than all microbes that promote antitumor immunity by modulating the function of systemic immunity or tumor-infiltrating lymphocytes (TILs) in tumor environments remain to be elucidated. In this study, we analyzed the microbiome composition of responders and non-responders to PD-1 blockade therapy from a clinical cohort and found that Enterococcus spp. were abundant in the responders. Through in vitro screening, we identified Enterococcus lactis MNC-168, a commensal bacterium isolated from a healthy individual, which significantly inhibited tumor growth and enhanced the efficacy of anti-PD-1 treatment by promoting antitumor immunity. Mechanistically, MNC-168 activates innate immunity through a STING-IFN-I (stimulator of interferon genes-type I interferons) dependent pathway by releasing bacterial membrane vesicles (MVs), and targeting tumor tissue, thereby augmenting the antitumor immune response. Furthermore, we have confirmed the safety profile of MNC-168 and its enhancing effect on Anti-PD-1 activity across multiple preclinical models, as well as its potential clinical relevance to Anti-PD-1 therapy. These findings suggest that MNC-168 could represent a promising strategy for cancer therapy and has the potential to improve the efficacy of current immunotherapies.},
}

@article {pmid40937701,
year = {2025},
author = {Ćwiek, M and Gimenez, JB and Izdebska, J},
title = {Etiopathogenesis of Keratoconus: A Contemporary Overview.},
journal = {Seminars in ophthalmology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/08820538.2025.2557985},
pmid = {40937701},
issn = {1744-5205},
abstract = {INTRODUCTION: Keratoconus (KC) is a progressive corneal disorder characterized by thinning and conical protrusion, leading to visual impairment. Whereas traditionally viewed as non-inflammatory, recent evidence highlights the role of chronic inflammation, oxidative stress, and genetic susceptibility in its pathogenesis.

METHODS: A literature review was conducted using PubMed, Embase, and Scopus databases focusing on keratoconus etiology and risk factors.

RESULTS: The most significant factors include eye rubbing, male sex, time spent using computers after work or school, and exposure to dust or particulates in the workplace. Additionally contributors include environmental factors (UV exposure, air pollution) and systemic conditions (connective tissue disorders, autoimmune diseases). Developing research also ensnares lifestyle factors such as poor nutrition, sleep disruption, and psychological stress in disease progression. Advances in genetic and epigenetic studies uncover dysregulation in corneal structure and repair mechanisms, while microbiome imbalances may further exacerbate inflammation.

DISCUSSION: This review synthesizes current knowledge on KC's multifactorial etiology, emphasizing the shift toward holistic management strategies that address both ocular and systemic factors. Environmental exposures, daily habits, and systemic health converge to influence keratoconus onset and progression for understanding this enigmatic disease. Future directions include personalized therapies focusing on fundamental molecular pathways and public health measures to moderate environmental risks.},
}

@article {pmid40937639,
year = {2025},
author = {Byrd, DA and Gomez, MF and Hogue, SR and Burns, JR and Smith, N and Sampson, J and Loftfield, E and Wolf, PG and Wan, Y and Warner, A and Hicks, B and Dagnall, C and Jones, K and Kim, Y and Xu, J and Shi, J and Sinha, R and Vogtmann, E},
title = {Associations of the Colon Tissue Microbiome and Circulating Bile Acids With Colorectal Adenoma Among Average-Risk Women.},
journal = {Cancer medicine},
volume = {14},
number = {18},
pages = {e71048},
doi = {10.1002/cam4.71048},
pmid = {40937639},
issn = {2045-7634},
support = {P30 CA 076292//Moffitt Cancer Center/ ; /CA/NCI NIH HHS/United States ; },
abstract = {OBJECTIVE: The gut microbiome and bile acids (BAs) likely influence colorectal cancer (CRC) development and disparities. We conducted a nested case-control study of the associations of the colon tissue microbiome and circulating BAs with colorectal adenoma prevalence in the previously conducted multi-center Colorectal Neoplasia Screening with Colonoscopy in Average-Risk Women Regional Navy/Army Medical Centers study (CONCeRN).

METHODS: We individually matched 143 women with adenoma to 279 without adenoma. Using 16S rRNA gene sequencing, we assessed alpha and beta diversity, taxonomic abundance, and co-abundance groups (CAGs). Fasting serum was analyzed for 13 primary and secondary BAs.

RESULTS: The presence of oral-originating Porphyromonas was positively associated with adenomas (odds ratio [OR] and 95% confidence interval [CI] = 2.50 [1.18, 5.30]; p = 0.02). Race and study center explained statistically significant percentages of variation in the beta diversity matrices. BAs were generally positively associated with adenomas, though these results were not statistically significant.

DISCUSSION: Overall, our findings suggest the colon tissue microbiome may differ by race and geography, and that certain oral-originating bacteria may be positively associated with adenomas.},
}

@article {pmid40937477,
year = {2025},
author = {Zhong, W and Lin, Z and Schmidt, EW and Agarwal, V},
title = {Discovery, biosynthesis, and bioactivities of peptidic natural products from marine sponges and sponge-associated bacteria.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5np00048c},
pmid = {40937477},
issn = {1460-4752},
abstract = {Covering 2010 to 2025Sponges are benthic, sessile invertebrate metazoans that are some of the most prolific sources of natural products in the marine environment. Sponge-derived natural products are often endowed with favorable pharmaceutical bioactivities, and paired with their structural complexity, have long served as title compounds for chemical syntheses. Sponges are holobionts, in that the sponge host is associated with symbiotic and commensal microbiome. Natural products isolated from sponges can be produced by the sponge host, or the associated microbiome. Recent genomic studies have shed light on the sponge eukaryotic host as the true producer of several classes of sponge-derived peptidic natural products. In this review spanning years 2010-2025, we describe peptidic natural products isolated from the sponge hosts and the associated microbiome, detail their biosynthetic processes where known, and offer forward looking insights into future innovation in discovery and biosynthesis of peptidic natural products from marine sponges.},
}

@article {pmid40937471,
year = {2025},
author = {Wang, D and Hunt, KA and Abrahamson, B and Flinkstrom, Z and Tao, X and Tanner, RS and DeLeόn, KB and Zhou, A and Zhou, J and McInerney, MJ and Winkler, MH and Stahl, DA and Candry, P and Pan, C},
title = {Higher-order microbial interactions revealed by comparative metabolic modeling of synthetic communities with varying species composition.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf142},
pmid = {40937471},
issn = {2730-6151},
abstract = {Understanding how microbial interactions scale with community complexity is key to microbiome engineering and ecological theory. This study investigates emergent metabolic behaviors in controlled in vitro synthetic anaerobic communities of two, three, or four species: cellulolytic bacterium (Ruminiclostridium cellulolyticum), a hydrogenotrophic methanogen (Methanospirillum hungatei), an acetoclastic methanogen (Methanosaeta concilii), and a sulfate-reducing bacterium (Desulfovibrio vulgaris), representing core metabolic guilds in cellulose degradation and carbon conversion. We applied a systems biology framework combining proteogenomics, stoichiometric flux modeling, and SMETANA (Species Metabolic Coupling Analysis) to quantify syntrophic cooperation and competition across configurations. Cooperation peaked in tri-cultures and declined nonlinearly in more complex assemblies. Species roles shifted contextually. Ruminiclostridium cellulolyticum was the dominant donor, adjusting cellulase and hydrogenase expression by partner. Methanosaeta concilii became fully metabolite-dependent while enhancing methanogenesis. Desulfovibrio vulgaris improved syntrophic efficiency via redox and hydrogen turnover. In contrast, Methanospirillum hungatei's metabolic centrality declined despite higher CH4 output, suggesting interaction strength depends more on compatibility than richness. Reduced interactions in the four-species community stemmed from a single configuration and need further validation. This study moves beyond descriptive work by quantitatively resolving how metabolic networks rewire across defined communities. By characterizing context-dependent flux shifts at multiple layers, we provide a framework for interpreting and engineering stable, functionally interdependent microbial ecosystems.},
}