@article {pmid41045571,
year = {2025},
author = {Chang, C and Gupta, R and Sedighian, F and Louie, A and Gonzalez, DM and Le, C and Cho, JM and Park, SK and Castellanos, J and Ting, TW and Dong, TS and Arias-Jayo, N and Lagishetty, V and Navab, M and Reddy, S and Sioutas, C and Hsiai, T and Jacobs, JP and Araujo, JA},
title = {Corrigendum to "Subchronic inhalation exposure to ultrafine particulate matter alters the intestinal microbiome in various mouse models" [Environ. Res. 248 (2024) 118242].},
journal = {Environmental research},
volume = {286},
number = {Pt 3},
pages = {122855},
doi = {10.1016/j.envres.2025.122855},
pmid = {41045571},
issn = {1096-0953},
}

@article {pmid41045547,
year = {2025},
author = {Yang, X and Li, Y and Wang, T and Li, Z and Zhuang, Q and Liang, C and Wang, X and Tian, J},
title = {GmSPX5 regulates arbuscular mycorrhizal colonization and phosphate acquisition through modifying transcription profile and microbiome in soybean.},
journal = {The Plant journal : for cell and molecular biology},
volume = {124},
number = {1},
pages = {e70511},
doi = {10.1111/tpj.70511},
pmid = {41045547},
issn = {1365-313X},
support = {2021YFF1000500//National Key Research and Development Program of China/ ; 2024A1515013054//Guangdong Basic and Applied Basic Research Foundation/ ; 2023ZD04072//STI 2030-Major Project/ ; 2022B0202060005//Key Areas Research and Development Programs of Guangdong Province/ ; 2022SDZG07//the Open Competition Program of Ten Major Directions of Agricultural Science and Technology Innovation for the 14th Five-Year Plan of Guangdong Province/ ; 32172658//National Natural Science Foundation of China/ ; 32172659//National Natural Science Foundation of China/ ; 32302662//National Natural Science Foundation of China/ ; },
mesh = {*Glycine max/microbiology/genetics/metabolism ; *Mycorrhizae/physiology ; *Phosphates/metabolism ; Symbiosis ; *Plant Proteins/genetics/metabolism ; Plants, Genetically Modified ; Gene Expression Regulation, Plant ; Plant Roots/microbiology/metabolism ; *Microbiota/genetics ; },
abstract = {Symbiosis with arbuscular mycorrhizal (AM) fungi is a crucial strategy for plant adaptation to low phosphorus (P) stress. However, the mechanisms underlying how phosphate (Pi) signaling regulators participate in AM colonization remain largely unknown in soybean (Glycine max). In this study, the expression of GmSPX5, one member of the SPX (SYG1/Pho81/XPR1) family, was induced by AM fungal inoculation in soybean roots. Furthermore, the expression of GmSPX5 seems to overlap with AM infection structures through analyzing GUS activity of transgenic soybean plants harboring ProGmSPX5:GUS. Four transgenic lines with GmSPX5 overexpression (OX8 and OX12) and suppression (Ri9 and Ri11) were subsequently used to examine the functions of GmSPX5 on AM symbiosis and Pi acquisition. Despite no difference between Ri and wild-type (WT), the overexpression of GmSPX5 significantly increased AM colonization as reflected by 8.4% in OX8 and 8.7% in OX12, respectively. Consistently, the dry weight and total P content of OX8 and OX12 were higher than WT. Furthermore, a total of 3483 genes were found to exhibit differential expression patterns in roots between OX12 and WT, including genes related to linolenic acid metabolism and flavonoid metabolism. Meanwhile, the composition of the bacterial community in the roots of OX12 was distinct from that in WT through β-diversity analysis. Particularly, an ASV19 (Sphingomonadales) was enriched in OX12 roots, which was positively related to total P content and AM fungi colonization. Taken together, these results highlight that GmSPX5 can regulate AM symbiosis, as well as Pi acquisition in soybean. Our findings advance the understanding of SPX functions in plant-microbe interaction.},
}

*Glycine max/microbiology/genetics/metabolism
*Mycorrhizae/physiology
*Phosphates/metabolism
Symbiosis
*Plant Proteins/genetics/metabolism
Plants, Genetically Modified
Gene Expression Regulation, Plant
Plant Roots/microbiology/metabolism
*Microbiota/genetics

@article {pmid41045399,
year = {2025},
author = {Moon, J and Liu, Z and Park, T},
title = {PSM-SMOTE: propensity score matching and synthetic minority oversampling for handling unbalanced microbiome data.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41045399},
issn = {2092-9293},
support = {NRF-2022R1A2C1092497//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Predictive models using microbiome data often suffer from covariate imbalance and class imbalance, biasing results. Propensity Score Matching (PSM) balances covariates but reduces sample size, while borderline synthetic minority oversampling technique (borderline-SMOTE) oversamples minority classes but can generate uninformative examples.

OBJECTIVE: To develop and evaluate PSM-SMOTE, a novel hybrid sampling method that integrates PSM and borderline-SMOTE to handle both covariate and class imbalance in microbiome data.

METHODS: We developed PSM-SMOTE, a three-step hybrid sampling algorithm for microbiome data: (1) PSM at four caliper levels to balance covariates, (2) selection of at least ten robust differential markers via seven statistical tests with false discovery rate correction, and (3) application of borderline-SMOTE on the marker-based distance matrix to oversample minority classes. We evaluated PSM-SMOTE on three publicly available microbiome case-control datasets: pancreatic ductal adenocarcinoma (PDAC), colorectal cancer (CRC), and obesity, using logistic regression (LR), random forest (RF), and support vector machine (SVM) classifiers. Performance was assessed via area under the ROC curve (AUC).

RESULTS: PSM-SMOTE improved test AUCs in multiple model-dataset combinations compared with using PSM alone. Notably, for the RF model, PSM-SMOTE consistently enhanced AUC across nearly all oversampling settings in the PDAC and obesity cohorts. For the SVM model, PSM-SMOTE also achieved a significant AUC increase in the CRC cohort. For the LR model, PSM-SMOTE showed modest improvement under strict matching.

CONCLUSION: PSM-SMOTE effectively addresses dual imbalance in microbiome data and consistently enhances performance, providing a practical solution for imbalanced data analyses.},
}

@article {pmid41045195,
year = {2025},
author = {Green Buzhor, M and Longobardi, G and Kandli, O and Krinsky, A and Avramoff, O and Katyal, A and Salomon, K and Miari, A and Venkert, D and Barnatan, TT and García Alvarado, A and Greenberg, S and Satchi-Fainaro, R},
title = {Harnessing Next-Generation 3D Cancer Models to Elucidate Tumor-Microbiome Crosstalk.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e03198},
doi = {10.1002/adhm.202503198},
pmid = {41045195},
issn = {2192-2659},
support = {835227//European Research Council (ERC) Advanced/ ; 3DBrainStrom//European Research Council (ERC) Advanced/ ; 862580//ERC PoC/ ; 3DCanPredict//ERC PoC/ ; 101113390//ERC PoC/ ; ImmuNovation//ERC PoC/ ; 101214384//The European Innovation Council (EIC)/ ; TIMNano//The European Innovation Council (EIC)/ ; ISF 3706/24//Israel Science Foundation/ ; PROF-18-602//Israel Cancer Research Fund (ICRF)/ ; LCF/PR/HR19/52 160 021//"La Caixa" Foundation/ ; LCF/PR/HR22/52 420 016//"La Caixa" Foundation/ ; LCF/PR/HR24/00968//"La Caixa" Foundation/ ; //Morris Kahn Foundation/ ; },
abstract = {The tumor microenvironment (TME) is a complex and dynamic ecosystem increasingly recognized for its interplay with the microbiome. In colorectal, breast, lung, liver, and brain cancers, bacterial communities and their metabolites are shown to influence tumor progression, immune responses, and therapeutic outcomes. To study these interactions in physiologically relevant contexts, advanced 3D in vitro models have emerged, including spheroids, organoids, microfluidic organ-on-a-chip platforms, and 3D-bioprinted constructs. These systems provide spatial organization, mechanical cues, and co-culture capabilities that facilitate investigation of host-microbiome-tumor cross-talk. Incorporation of live bacteria, their metabolites, and immune components into these platforms has yielded new insights into how the microbiome shapes cancer behavior, inflammation, and drug resistance. This review outlines recent advances in 3D model development for studying tumor-microbiome interactions, highlighting organ-specific applications, extracellular matrix-mimicking hydrogels, and biofabrication strategies. It also addresses key challenges, including maintaining microbiome viability, modeling temporal dynamics, and integrating immune complexity. Overcoming these limitations requires interdisciplinary approaches that merge bioengineering, microbiology, and oncology. Evolving 3D platforms offer powerful tools for microbiome-informed cancer modeling and hold significant promise for advancing therapeutic screening and precision oncology.},
}

@article {pmid41045140,
year = {2025},
author = {Pongpamorn, P and Zwart, M and Bouwmeester, HJ},
title = {The Role of Soil Microbiota in the Control of Parasitic Weeds.},
journal = {Plant & cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/pcp/pcaf125},
pmid = {41045140},
issn = {1471-9053},
abstract = {Parasitic weeds from the Orobanchaceae family, particularly Striga, Orobanche and Phelipanche spp., are responsible for substantial agricultural losses worldwide. A better understanding of the intricate chemical interaction between parasitic plants and their host crops, and the effect the rhizosphere microbiome may have on this, offers potential for developing sustainable and effective biocontrol strategies. We review the biology of parasitic plants, with a focus on host-derived signaling molecules such as strigolactones (SLs) and haustorium inducing factors (HIFs) that coordinate key stages of their lifecycle, and hence are potential targets for control through microorganisms. We highlight several examples of pathogenic microorganisms, and plant growth-promoting rhizobacteria (PGPR) and fungi (PGPF) that have been shown to suppress parasitic weeds. These microbes act through multiple mechanisms: direct antagonism of the parasite, enhancement of the host's defense responses, and interference with chemical signaling between host and parasite. Both laboratory and field studies are reviewed to evaluate the efficacy and future potential of these biological control agents.},
}

@article {pmid41045128,
year = {2025},
author = {Xia, S and Huang, S and Wu, J and Lin, H and Duan, J and Ye, W and Xie, T and Cai, J and Sun, Y and Luo, X and Song, Y},
title = {Molecular Pathogenesis of Ovarian Endometrioma: Mechanistic Insights and Therapeutic Implications.},
journal = {Biology of reproduction},
volume = {},
number = {},
pages = {},
doi = {10.1093/biolre/ioaf219},
pmid = {41045128},
issn = {1529-7268},
abstract = {Ovarian endometrioma (OMA), the most prevalent and clinically consequential subtype of endometriosis, represents a chronic inflammatory disorder characterized by ectopic endometrial-like lesions. This condition manifests as progressive dysmenorrhea, ovarian reserve depletion, and subfertility, imposing substantial physical and psychosocial burdens. Current diagnostic modalities remain constrained by the absence of reliable biomarkers, while surgical interventions often yield suboptimal outcomes marked by incomplete lesion resolution and elevated recurrence rates. Despite growing recognition of endometriosis as a systemic disease, the distinct pathogenic mechanisms underlying OMA formation-particularly the interplay between immune dysregulation, steroid hormone hypersensitivity, and microenvironmental reprogramming-remain insufficiently characterized. Emerging evidence implicates multifaceted pathophysiological cascades involving chronic peritoneal inflammation, T-cell polarization anomalies, vascular endothelial growth factor (VEGF)-mediated neoangiogenesis, progesterone resistance, and reactive oxygen species accumulation. Notably, microbiome-derived metabolites and multi-omics integration have redefined paradigms of disease progression by elucidating mechanisms sustaining lesion viability. This review consolidates recent advances in OMA pathogenesis, dissecting molecular drivers of cellular survival, adhesive interactions, and inflammatory cascades within the ovarian microenvironment.},
}

@article {pmid41044998,
year = {2025},
author = {Modin, O and Zheng, D and Schnürer, A and Lundwall, T and Bolanos, SE and Olsson, J},
title = {From Low-Loaded Mesophilic to High-Loaded Thermophilic Anaerobic Digestion: Changes in Reactor Performance and Microbiome.},
journal = {Microbial biotechnology},
volume = {18},
number = {10},
pages = {e70238},
doi = {10.1111/1751-7915.70238},
pmid = {41044998},
issn = {1751-7915},
support = {//Käppalaförbundet/ ; //The Swedish Research Council (VR)/ ; },
mesh = {*Bioreactors/microbiology ; Anaerobiosis ; *Sewage/microbiology ; Methane/metabolism ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Temperature ; *Microbiota ; *Archaea/classification/genetics/metabolism ; Metagenomics ; },
abstract = {This study investigated temporal dynamics in reactor performance and microbial community structure during anaerobic digestion of sewage sludge when the temperature was changed from 37°C to 55°C, followed by an increase in organic loading rate (OLR). Performance instability was observed immediately following the temperature increase and in the end of the study when the OLR was 11.1 ± 0.3 kgVS m[-3]d[-1]. The specific methane production peaked at 0.31 ± 0.06 Nm[3] kg[-1] volatile solids (VS) during thermophilic operation and when the OLR was 3.5 ± 0.9 kgVS m[-3]d[-1]. Using metagenomic sequencing, 304 species-representative genome bins (SGB) were assembled. Network analysis revealed that 186 SGB were associated with thermophilic conditions and several new species putatively involved in key reactor functions were identified. When reactor function initially stabilised, two hydrogenotrophic and one aceticlastic methanogen (Methanothermobacter spp. and Methanosarcina thermophila), the hydrolytic Coprothermobacter proteolyticus, and putative syntrophic propionate oxidisers (e.g., Pelotomaculaceae) had high relative abundance. During the peak in specific gas production, the community was dominated by one hydrogenotrophic Methanothermobacter species coexisting with syntrophic acetate oxidising bacteria (Thermacetogenium phaeum and other species). Finally, when the reaction function deteriorated due to high OLR, new hydrolytic taxa emerged and the same aceticlastic methanogen as seen during the initial acclimatisation phase returned.},
}

*Bioreactors/microbiology
Anaerobiosis
*Sewage/microbiology
Methane/metabolism
*Bacteria/classification/genetics/metabolism/isolation & purification
Temperature
*Microbiota
*Archaea/classification/genetics/metabolism
Metagenomics

@article {pmid41044986,
year = {2025},
author = {Chen, R and Wu, X and Yin, N and Xie, E and Sun, S and Shen, J and Chen, Y and Zhou, F and Li, T and Li, Q and Su, D and Fu, F and Li, G and Li, X and Shan, Y},
title = {Mechanisms of flavonoid-mediated amelioration of MASLD: flavonoids, their metabolites or impact on gut microbes?.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-24},
doi = {10.1080/10408398.2025.2566391},
pmid = {41044986},
issn = {1549-7852},
abstract = {Metabolic syndrome (MetS), characterized by symptoms like hyperlipidemia, abdominal obesity, and insulin resistance, is closely associated with metabolic dysfunction-associated steatotic liver disease (MASLD), an established disease burden worldwide. Health-promoting, side-effect-free preventative, and treatment strategies for MetS are required. Flavonoids, which are active phytochemicals easily obtained from dietary sources, have been shown in animal and population studies to improve lipid metabolism disorders and offer protective support against MASLD. However, it remains unclear which among flavonoids, their metabolites, or indirect mechanisms such as impact on gut microbiota most significantly ameliorates MASLD. This review first explores the diverse mechanisms through which flavonoids attenuate the onset and progression of MASLD. It then summarizes the flavonoid metabolites that have enhanced MASLD protection. Additionally, certain flavonoids can mitigate MASLD by reshaping the specific or entire gut microbiome. Finally, the review outlines the potential for developing prebiotic-probiotic systems with flavonoids and discusses potential directions for identifying causal relationship between flavonoids and MASLD amelioration.},
}

@article {pmid41044807,
year = {2025},
author = {Kim, H and Kim, A and Kim, H and Seo, D and Son, S and Kim, D and Shin, JU},
title = {Differential Modulation of Skin Barrier Proteins and Lipid Synthesis by Staphylococcus aureus, Staphylococcus hominis, and Cutibacterium acnes.},
journal = {Annals of dermatology},
volume = {37},
number = {5},
pages = {276-285},
doi = {10.5021/ad.25.020},
pmid = {41044807},
issn = {2005-3894},
support = {RS-2023-KH140992/MOHW/Ministry of Health and Welfare/Korea ; RND2023-103//Aekyung Co., Ltd./Korea ; },
abstract = {BACKGROUND: The skin microbiome plays a critical role in regulating epidermal differentiation and immune responses. Understanding of how individual microbial species influence the expression of barrier proteins and lipid synthesis pathways is essential for elucidating their contributions to skin barrier function.

OBJECTIVE: This study aimed to investigate the distinct effects of Staphylococcus aureus (S. aureus), Staphylococcus hominis (S. hominis), and Cutibacterium acnes (C. acnes) on the skin barrier protein expression and lipid synthesis, thereby clarifying their roles in maintaining skin barrier integrity and homeostasis.

METHODS: Keratinocyte 2-dimensional monolayer cultures and self-assembled 3-dimensional skin models were treated with S. aureus, S. hominis, or C. acnes. Alterations in skin barrier proteins and lipid synthesis were assessed using quantitative real-time polymerase chain reaction, immunofluorescence staining, and Oil Red O staining.

RESULTS: S. aureus significantly downregulated the messenger ribonucleic acid expression of skin barrier proteins and lipid synthesis enzymes, resulting in reduced lipid accumulation. In contrast, S. hominis upregulated barrier protein expression and enhanced lipid accumulation. Similarly, C. acnes increased the expression of both skin barrier proteins and lipid synthesis enzymes, leading to a marked increase in lipid accumulation.

CONCLUSION: Collectively, these findings suggest that S. aureus compromises the skin barrier function by downregulating the expression of barrier-associated proteins and lipid synthesis enzymes, whereas S. hominis and C. acnes enhance barrier integrity by upregulating these components. These differential microbial effects elucidate potential mechanisms by which the skin microbiome contributes to barrier homeostasis.},
}

@article {pmid41044805,
year = {2025},
author = {Hong, JY and Kwon, D and Park, KY},
title = {Microbiome-Based Interventions for Skin Aging and Barrier Function: A Comprehensive Review.},
journal = {Annals of dermatology},
volume = {37},
number = {5},
pages = {259-268},
doi = {10.5021/ad.25.009},
pmid = {41044805},
issn = {2005-3894},
support = {H12300860/MOHW/Ministry of Health and Welfare/Korea ; },
abstract = {The skin microbiome, a dynamic ecosystem of microorganisms, is essential for maintaining skin health by protecting against pathogens, modulating immunity, and enhancing barrier function. External factors such as pollutants, harsh skincare products, and aging disrupt microbial balance, leading to compromised skin health and accelerated aging. Aging-related changes, including reduced microbial diversity, loss of beneficial metabolites, and increased oxidative stress, contribute to inflammaging. Microbiome-supportive skincare, incorporating probiotics, prebiotics, and postbiotics, offers promising solutions to restore microbial balance, strengthen the skin barrier, and delay aging. These formulations work by reducing inflammation, enhancing antioxidant defenses, and regulating skin pH. However, challenges in microbiome research and product development persist, including individual variability in microbial composition, formulation complexities, and a limited understanding of microbe-skin interactions. Future innovations such as personalized microbiome skincare, genetically engineered probiotics, and advanced diagnostic tools could enable more targeted and effective interventions. Long-term clinical trials and detailed mechanistic studies are crucial to validate the efficacy of microbiome-focused skincare and optimize formulations for diverse populations. By addressing these challenges and advancing research, microbiome-supportive skincare has the potential to revolutionize approaches to skin health, preserving resilience and combating aging through tailored microbial interventions.},
}

@article {pmid41044758,
year = {2025},
author = {Pérez-Pérez, L and Galisteo, C and Sanjuán, JMO and Cobo-Díaz, JF and Puente, H and Rubio, P and Carvajal, A and Arguello, H},
title = {Severity of Brachyspira hyodysenteriae colitis correlates to the changes observed in the microbiota composition and its associated functionality in the large intestine.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {105},
pmid = {41044758},
issn = {2524-4671},
support = {PRE2020-093762//Ministerio de Ciencia, Innovación y Universidades/ ; JDC2023-051122-I//Ministerio de Ciencia, Innovación y Universidades/ ; LE088P23//Junta de Castilla y León/ ; },
abstract = {BACKGROUND: The gut microbiota is essential for maintaining nutritional, physiological and immunological processes, but colonic infections such as swine dysentery, caused by Brachyspira hyodysenteriae (B. hyo) disrupt this homeostasis. This study uses shotgun and full-length 16S rRNA sequencing in faeces, colonic contents and mucosa from pigs challenged with B. hyo to provide a high-resolution characterisation of the taxa, functions and metagenome-assembled genomes (MAGs) of interest, disclose their association with the primary pathogen and how they are affected by the pathological changes of the infection.

RESULTS: Changes in the microbiota were associated with disease severity. In early infection, no major findings were observed in diversity or abundance analyses, whereas in acute infection, B. hyo load, mucosal neutrophil infiltration, epithelial ulceration and mucosal thickness were clearly associated with changes in microbiota ordination, which were also associated with a decrease in species richness. Changes included a significant increase in Acetivibrio ethanolgignens, Campylobacter hyointestinalis and Roseburia inulinivorans, which, with the exception of C. hyointestinalis, established themselves as part of the core microbiota and shifted the colonic enterotype in acutely infected animals. MAGs analyses revealed that no major virulence genes were detected in the genomes of the species co-interacting with B. hyo in acute infection. Similarly, functional changes were observed only after the onset of clinical signs, with an increase in functions related to inflammation and toxic effects on the colonic epithelium.

CONCLUSIONS: Our study shows that in colitis caused by B. hyo, changes in the microbiota are mainly a consequence of the lesions that occur in the intestine, with no differences observed in early infection. Similarly, the bacterial species that are increased at the onset of clinical signs may promote intestinal inflammation caused by B. hyo infection, but the analysis of their genomes rule out their participation in the primary infection.},
}

@article {pmid41044750,
year = {2025},
author = {Kang, L and Li, Y and Wang, J and Fu, J and Li, Q and Jiang, Q and Zhou, H and Xiao, H and Zhang, Z and Hong, M},
title = {Seasonal dynamics, dietary patterns, and bamboo leaf nutrition shape the phyllosphere-associated gut microbiota of red pandas.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {104},
pmid = {41044750},
issn = {2524-4671},
support = {grant no. 32470516//National Natural Science Foundation of China/ ; grant no. KCXTD2022-7//Innovation Team Funds of China West Normal University/ ; grant no. 2024NSFSC2082//Sichuan Natural Science Foundation/ ; },
abstract = {BACKGROUND: The gut microbiota of bamboo-eating red pandas (Ailurus fulgens) comprises a intricate and multifaceted ecosystem influenced by numerous factors. Despite considerable research dedicated to captive red pandas, the microbial dynamics observed in wild populations are still not well understood. To address this research gap, our study employed advanced techniques such as high-throughput sequencing and metagenomic analysis to characterize the microbial communities and their functional profiles in fresh fecal samples from wild red pandas and in samples of their primary food source. Our objective was to conduct a thorough examination of how seasonality, diet, bamboo leaf nutrition, and phyllosphere-associated microorganisms affect the gut microbiota of red pandas.

RESULTS: Our findings reveal that seasonal variations have a notable impact on the composition, structure, and functionalities of red pandas' gut microbiota. Specifically, autumn and winter exhibit heightened microbial diversity and richness. Moreover, during different feeding phases (leaf-feeding, shoot-feeding, and mixed-feeding), the gut microbiota displays varied cellulose-digesting abilities, marked by increased expression of key enzymes during high-fiber dietary phases. Our analysis reveals robust correlations between bamboo nutrients and microbial communities in both bamboo and red panda guts. Notably, bamboo's crude protein and phosphorus content are pivotal in shaping the phyllosphere and gut microbial communities, while crude fat, crude protein, and phosphorus emerge as key drivers of microbial structure. Seasonal fluctuations in microbial populations of both bamboo and red panda guts with shared genera, underscore their tight linkage and interconnected seasonal adaptations.

CONCLUSIONS: In conclusion, our study provides a comprehensive understanding of how seasonality, diet, and bamboo leaf nutrition shape the gut microbiota of red panda connected to bamboo microbiome. It underscores the gut microbes' indispensable role in facilitating red pandas' adaptation to their bamboo-based diet, crucial for their survival in natural habitats.},
}

@article {pmid41044695,
year = {2025},
author = {Cun, H and He, P and Ahmed, A and He, P and Wu, Y and Jiang, Y and Zhang, H and Tang, G and Kong, B and Youssef, SA and Munir, S and He, Y},
title = {Intercropping between persimmon and apple enriched the leaf endophytes and rhizosphere communities against apple root rot.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1307},
pmid = {41044695},
issn = {1471-2229},
support = {202202AE090025//Technology Special Project of Yunnan Province/ ; 2022YFD140070//National Key Research and Development Program of China/ ; },
mesh = {*Malus/microbiology/growth & development ; *Rhizosphere ; *Endophytes/physiology ; Plant Leaves/microbiology ; Plant Roots/microbiology ; *Plant Diseases/microbiology/prevention & control ; Soil Microbiology ; *Diospyros/microbiology/growth & development ; Microbiota ; },
abstract = {BACKGROUND: Root rot disease has seriously restricted the development of the apple industry Worldwide. After being infected by pathogens, the microbial communities of rhizosphere soil and leaves may change. We found that apple and persimmon intercropping can reduce the occurrence of apple root rot achieving a relative control efficacy of 80.3% following persimmon intercropping.

RESULTS: Here, we investigate the effect of intercropping with persimmon tree on rhizosphere microbiome and leaf endophytes. For this, we tested the rhizosphere soil and leaves of healthy and infected apple trees during intercropping. The soil and leaves of healthy and infected root rot apple trees, persimmon trees, and intercropping were collected (during sampling time, apple trees were 5 years old, and persimmon trees were 3 years old). The high-throughput sequencing was performed on the Illumina Miseq platform to analyze the leaf endophytic bacterial and soil microbial communities. We further revealed that infection by root rot pathogens severely impacts the synergistic effects between endophytes and the composition of rhizosphere microbial communities. The intercropping between apple and persimmon trees can modulate apple leaf endophytes and rhizosphere microbial communities. Importantly, the relative abundance of Pantoea and Serratia increased significantly in the leaves of apple trees affected by root rot. We argue that bacteria such as Pantoea and Serratia are conducive to the occurrence of root rot. Notably, Bacillus and Trichoderma were significantly reduced in the rhizosphere of apples with root rot trees; however, persimmon trees and apple trees can maintain the relative abundance of beneficial species or improve the abundance compared with healthy apple trees.

CONCLUSIONS: The overall study concludes that intercropping apples and persimmons maintains the beneficial microbial balance and plant growth and helps to prevent dysbiosis caused by pathogens. Based on this shift in microbiome balance, a management strategy for apple root rot is discussed.},
}

*Malus/microbiology/growth & development
*Rhizosphere
*Endophytes/physiology
Plant Leaves/microbiology
Plant Roots/microbiology
*Plant Diseases/microbiology/prevention & control
Soil Microbiology
*Diospyros/microbiology/growth & development
Microbiota

@article {pmid41044678,
year = {2025},
author = {Ren, C and Meng, Y and Liu, Y and Wang, Y and Wang, H and Liu, Y and Liu, C and Fan, X and Zhang, S},
title = {Probiotic Bacillus subtilis enhances silkworm (Bombyx mori) growth performance and silk production via modulating gut microbiota and amino acid metabolism.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {103},
pmid = {41044678},
issn = {2524-4671},
support = {No. SDAIT-18//Modern Agricultural Technology System of Shandong Province/ ; No. CARS-18//China Agriculture Research System of MOF and MARA/ ; },
abstract = {BACKGROUND: Artificial diet-reared silkworms (Bombyx mori) exhibit reduced gut microbial diversity and impaired growth performance compared to mulberry-fed counterparts. While Bacillus subtilis is widely used as a probiotic in livestock and aquaculture, its impact on silkworms remains unexplored. This study investigates whether dietary supplementation with B. subtilis enhances larval development and elucidates the underlying mechanisms involving gut microbiota and metabolic pathways.

RESULTS: Supplementing artificial diets with B. subtilis (6 × 10[5] CFU/g) significantly increased larval body weight by 9.1-22.1% during instar stages and improved feed utilization efficiency (FUE) by 4.09%-6.80% compared to controls. Cocoon quality metrics, including cocoon shell weight (+ 9.77% in females) and cocoon shell ratio (+ 6.56%), also improved. Mechanistically, B. subtilis did not colonize the midgut but transiently modulated gut physiology: it elevated midgut fluid pH and enhanced α-amylase, trypsin, and lipase activities. 16 S rRNA sequencing revealed reduced gut microbial diversity (Shannon index, P < 0.01) and shifts in community structure, with decreased abundances of potential pathogens (e.g., Pseudomonas) and commensals (e.g., Lactobacillus). Targeted metabolomics identified a 3.1-fold increase in phenylalanine levels in hemolymph, linked to upregulated aromatic amino acid metabolism pathways (KEGG). Dietary phenylalanine supplementation (0.4%) replicated B. subtilis-induced growth promotion, confirming its pivotal role in host-microbe interactions.

CONCLUSIONS: B. subtilis enhances silkworm growth and silk production through multi-faceted mechanisms: reshaping gut microbiota composition, improving digestive enzyme activity, and elevating phenylalanine biosynthesis. These findings establish B. subtilis as a promising probiotic for optimizing artificial diet systems in Lepidoptera and highlight the central role of amino acid metabolism in insect-microbiome symbiosis.},
}

@article {pmid41044628,
year = {2025},
author = {Chun, SJ and Cui, Y and Kim, J and Lee, JW and Nam, KH},
title = {Multidimensional sampling framework reveals plant-driven effects on microbial spatial heterogeneity and niche differentiation in a natural ecosystem.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {125},
pmid = {41044628},
issn = {2524-6372},
support = {NIE-A-2025-10; NIE-A-2025-04; NIE-A-2025-11//The Ministry of Environment (MOE) of the South Korea/ ; },
abstract = {BACKGROUND: The identification of complex spatial patterns of microbial communities in relation to their ecological niches is fundamental to understanding the mechanisms of ecological interactions among diverse organisms. This study introduces a novel three-dimensional (3D) sampling approach to examine the spatial dynamics of microbial populations and niche differentiation influenced by plant-mediated effects in natural ecosystem.

RESULTS: Microbial communities across horizontal and vertical dimensions were systematically mapped, and we found that the total microbial diversity, particularly among eukaryotes, increased more than ten-fold compared to that obtained via single-grid sampling, emphasizing the importance of spatial heterogeneity in shaping microbial dynamics. Moreover, the 3D framework enabled us to identify taxa specifically associated with particular plants, offering insights into plant-microbe interactions, pathogen prevalence, and ecological consequences of plant-driven effects on local communities.

CONCLUSIONS: Collectively, these findings demonstrate that 3D sampling approach provides a reproducible and scalable methodology for investigating microbial spatial heterogeneity, pathogen ecology, and niche differentiation in natural environments.},
}

@article {pmid41044486,
year = {2025},
author = {Huang, P and Liu, Y and Li, N and Zhang, Q and Luo, Y and Zhang, Y and Zhou, Y and Mu, W and Yuan, M and Liu, Y and Xin, Y and Li, H and Peng, Y and Wang, X and Zhao, M and Yu, K and Wang, C},
title = {Causal relationship between gut microbiota and pneumonia: a Mendelian randomization and retrospective case-control study.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {449},
pmid = {41044486},
issn = {1471-2466},
support = {U20A20366//the National Natural Science Foundation of China-Regional Innovation and Development Joint Fund/ ; No.82430069//the National Natural Science Foundation of China/ ; No.82472198//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; Mendelian Randomization Analysis ; *Gastrointestinal Microbiome/genetics ; Retrospective Studies ; Case-Control Studies ; *Pneumonia/microbiology/genetics ; Male ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Aged ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: The relationship between microbiota and the gut-lung axis has been extensively studied in both experimental and epidemiological contexts. However, it is still unclear whether the gut microbiome plays a causal role in the development of pneumonia.

METHODS: Our study initially identified the genetic instruments in the gut microbiota GWAS across phylum, class, order, family, and genus levels. Pneumonia data were sourced from the open GWAS project of the Integrated Epidemiology Group (IEU). Mendelian randomization (MR) analysis employed several methods such as inverse variance weighting (IVW), weighted median, and MR-Egger, with Cochran's Q were calculated to assess heterogeneity via IVW and MR-Egger. Additionally, MR-PRESSO and MR-Egger intercepts were utilized to mitigate horizontal pleiotropy. A retrospective case-control study collected anal swab samples from severe pneumonia patients on the 1st and 3rd days after ICU admission. Samples were analyzed using 16S ribosomal ribonucleic acid (16S rRNA) and PERMANOVA analysis.

RESULTS: Eleven potential causal relationships between the gut microbiome and pneumonia (critical care), as well as nine potential causal relationships between the gut microbiome and pneumonia (28-day death in critical care) were identified. By integrating the results of PERMANOVA analysis with Mendelian randomization analysis, we were able to determine a negative correlation between genus Akkermansia and lactate levels, as well as length of ICU days in patients with septic acute respiratory distress syndrome (ARDS). Moreover, we found a potential negative causal relationship between the genus Akkermansia and pneumonia (28-day death in critical care) (OR 0.42, 95% CI 0.22-0.79, P = 0.007).

CONCLUSIONS: Our Mendelian randomization analysis has provided evidence for a potential causal relationship between gut microbiota and pneumonia. Furthermore, we observed that the genus Akkermansia may decrease the risk of pneumonia (28-day death in critical care), as observed in septic ARDS patients which Akkermansia could reduce ICU days and lactate levels. These findings provide valuable insights into the gut-lung axis and have the latent to inform future research in this field.

TRIAL REGISTRATION: The study was registered at the Chinese Clinical Trial Registry (https://www.chictr.org.cn/index.html , ChiCTR2300075450).},
}

Humans
Mendelian Randomization Analysis
*Gastrointestinal Microbiome/genetics
Retrospective Studies
Case-Control Studies
*Pneumonia/microbiology/genetics
Male
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Aged
Genome-Wide Association Study

@article {pmid41044437,
year = {2025},
author = {Kwa, M and Hussey, G and Novik, Y and Franke, AA and Volkova, A and Flores, K and Blaser, MJ and Speyer, J and Oratz, R and Meyers, M and Jhaveri, K and Fadel, E and Heguy, A and Schluter, J and Ruggles, KV and Adams, S},
title = {Evaluation of the gut microbiome and sex hormones in postmenopausal women with newly diagnosed hormone receptor-positive breast cancer versus healthy women: a prospective case-control study.},
journal = {Journal of cancer research and clinical oncology},
volume = {151},
number = {10},
pages = {275},
pmid = {41044437},
issn = {1432-1335},
support = {P30CA71789/NH/NIH HHS/United States ; 5P30CA16087-40/NH/NIH HHS/United States ; },
mesh = {Humans ; Female ; *Breast Neoplasms/microbiology/metabolism/pathology/blood ; *Postmenopause ; Case-Control Studies ; Prospective Studies ; *Gastrointestinal Microbiome ; Middle Aged ; Aged ; Receptors, Progesterone/metabolism ; Receptors, Estrogen/metabolism ; *Gonadal Steroid Hormones/blood/urine/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {PURPOSE: The functional composition and diversity of the gut microbiome may affect breast cancer risk by modulation of systemic sex hormones. Gut bacteria with β-glucuronidase enzymatic activity may deconjugate estrogens, leading to increased estrogen reabsorption into the circulation thereby increasing breast cancer risk. We investigated the relationship between the gut bacterial microbiome and endogenous estrogens and related sex hormones in women with hormone receptor-positive breast cancer compared to healthy control women. The goal was to determine if the estrobolome (i.e., bacteria capable of modulating the body's circulated estrogen levels) was altered in those with breast cancer compared with controls.

METHODS: In this prospective case-control study, postmenopausal women (n = 46) with newly diagnosed stage I-III estrogen and/or progesterone receptor-positive breast cancer were compared with healthy postmenopausal female controls (n = 22). Bacterial composition of the gut microbiome was analyzed by 16S rRNA gene sequencing from fecal specimens. Plasma and urine sex hormones were quantified using high-performance liquid chromatography/mass spectrometry.

RESULTS: We found evidence that some β-glucuronidase positive bacteria were enriched in the breast cancer patients compared to healthy controls, whereas abundances of some β-glucuronidase negative bacteria were reduced. There was also a wide distribution of prevalence of β-glucuronidase positive taxa in both breast cancer subjects and healthy controls, as well as higher probability of breast cancer subjects having higher average β-glucuronidase levels. Significant differences were found in endogenous progesterone levels between the breast cancer patients and healthy controls.

CONCLUSION: This pilot study showed differences in the gut microbiome and endogenous progesterone levels among postmenopausal women with hormone receptor-positive breast cancer compared with healthy controls. These interesting findings may have implications for breast cancer risk and prevention and warrant further exploration.},
}

Humans
Female
*Breast Neoplasms/microbiology/metabolism/pathology/blood
*Postmenopause
Case-Control Studies
Prospective Studies
*Gastrointestinal Microbiome
Middle Aged
Aged
Receptors, Progesterone/metabolism
Receptors, Estrogen/metabolism
*Gonadal Steroid Hormones/blood/urine/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid41044363,
year = {2025},
author = {Catacutan, DB and Tran, V and Arnold, A and Alexander, J and Corso, G and Yousefi, Y and Tu, MM and McLellan, S and Tertigas, D and Magolan, J and Surette, MG and Brown, ED and Coombes, BK and Barzilay, R and Stokes, JM},
title = {Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41044363},
issn = {2058-5276},
abstract = {Current clinical antibiotics are largely broad-spectrum agents that can alter the gut microbiome and promote colonization by Enterobacteriaceae, which are often drug resistant. This includes adherent-invasive Escherichia coli (AIEC), particularly in patients with inflammatory bowel disease, in which dysbiosis creates a niche for this pathogen to colonize. There is an urgent and unmet need for novel narrow-spectrum and microbiome-sparing antibiotics. Here we screened 10,747 bioactive small molecules for antibacterial activity against AIEC and discovered enterololin, an antibacterial compound with targeted activity against Enterobacteriaceae species. Enterololin could overcome intrinsic and acquired resistance mechanisms in clinical isolates when combined with a subinhibitory concentration of SPR741, a polymyxin B analogue used here to increase outer membrane permeability in Gram-negative bacteria. Molecular substructure- and deep learning-guided mechanism-of-action investigations revealed that enterololin perturbs lipoprotein trafficking through a mechanism involving the LolCDE complex, laboratory-evolved resistant mutants predominantly mapped to lolC and lolE, with an in vitro frequency of resistance of ~10[-8] to 10[-7]. Enterololin showed low mammalian cytotoxicity (HEK293 half-maximal inhibitory concentration ~100 µg ml[-1]) and suppressed AIEC infection in mouse models when administered in combination with SPR741, while largely preserving the overall microbiome composition. This study highlights the utility of deep learning methods for predicting molecular interactions and identifies a promising Enterobacteriaceae-specific antibacterial candidate for further development.},
}

@article {pmid41044104,
year = {2025},
author = {Hafeez, SH and Khalid, A and Ahmed, S and Umrani, F and Qureshi, AK and Ahmed, K and Shaheen, F and Hotwani, A and Kabir, F and Moore, SR and Ali, SA and Iqbal, J and Iqbal, NT},
title = {Fermented pickles improve gut microbiota and immune profile in women in a community trial in rural Pakistan.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34522},
pmid = {41044104},
issn = {2045-2322},
support = {5D43TW007585-13//National Institute of Health's Fogarty International Center/ ; 5D43TW007585-13//National Institute of Health's Fogarty International Center/ ; 5D43TW007585-13//National Institute of Health's Fogarty International Center/ ; 5D43TW007585-13//National Institute of Health's Fogarty International Center/ ; INV- 033567//Bill & Melinda Gates Foundation/ ; INV- 033567//Bill & Melinda Gates Foundation/ ; INV- 033567//Bill & Melinda Gates Foundation/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Adult ; Rural Population ; Pakistan ; Biomarkers ; Feces/microbiology ; *Fermented Foods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Peroxidase ; Prospective Studies ; Lipocalin-2 ; },
abstract = {A gut microbiome-targeted diet can potentially mitigate chronic diseases, including malnutrition. In a prospective 12-week intervention trial, we evaluated the effects of six different plant-based fermented pickles (~ 50 g/day) on clinical, inflammatory, and gut microbiota parameters in a cohort of women (n = 230) in a rural setting with a high prevalence of undernutrition. Blood was collected at two, whereas stool was collected at three timepoints. Among fecal biomarkers, myeloperoxidase (MPO), Lipocalin-2 (LCN2), and 16S rRNA gene sequencing were measured at baseline, 8[th,] and 12[th] weeks. Overall, the compliance rate was > 70%. Among radish group, WBCs (p = 0.002, two-tailed paired T-test) decreased, whereas neutrophils and platelets decreased among both radish (p = 0.016, p = 0.017, two-tailed paired T-test) and carrot (p = 0.005, p = 0.006, two-tailed paired T-test) groups after intervention. Similarly, in lemon-chilli group, platelets decreased while mean corpuscular hemoglobin (MCH) increased (p < 0.001, p = 0.022, two-tailed paired T-test). In onion and lemon-chilli groups, α- (р =0.001 and p = 0.0005, Kruskal-Wallis Test, respectively) and β-diversity indices (p = 9e-04 and p = 0.022, pairwise PERMANOVA, respectively) were significantly increased, post-intervention. Linear discriminant analysis (LDA) of lemon-chilli group identified 25 bacterial taxa markers in 8[th] and 12[th] week, which included Eggerthellaceae and Oscillospiraceae, Erysipelatoclostridiaceae and Subdoligranulum. Correlation analysis revealed six taxa negatively associated with inflammatory markers such as C-reactive protein (CRP), LCN2, and platelets. Our study provides preliminary evidence that the consumption of traditional fermented pickles leads to beneficial changes in women's hematological and gut microbiota profiles.},
}

Humans
Female
*Gastrointestinal Microbiome
Adult
Rural Population
Pakistan
Biomarkers
Feces/microbiology
*Fermented Foods
RNA, Ribosomal, 16S/genetics
Middle Aged
Peroxidase
Prospective Studies
Lipocalin-2

@article {pmid41044018,
year = {2025},
author = {Araujo, ASF and Pereira, APA and de Medeiros, EV and Mendes, LW},
title = {Soil microbes: below-ground defenders against desertification.},
journal = {Trends in ecology & evolution},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tree.2025.09.014},
pmid = {41044018},
issn = {1872-8383},
abstract = {Soil microbes act as below-ground defenders against desertification by several mechanisms, such as rhizosheath formation, necromass accumulation, biological soil crusts, exopolysaccharide (EPS) production, hyphal networks, and calcium carbonate precipitation. Here, we discuss how soil microbes drive ecosystem recovery in drylands, offering promising, nature-based strategies for restoring soils in the face of desertification.},
}

@article {pmid41039216,
year = {2025},
author = {Ma, Y and Wang, D and Yu, X and Fan, Y and Yang, Z and Gao, X and Huang, X and Meng, J and Cheng, P and Liu, X and Liu, Z and Li, X},
title = {Moderate altitude exposure induced gut microbiota enterotype shifts impacting host serum metabolome and phenome.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {591},
pmid = {41039216},
issn = {1471-2180},
support = {2023YFE0114300//National key research and development program intergovernmental key projects/ ; No.2024A1515012697//Guangdong Provincial Basic and Applied Basic Research Fund Project/ ; No. 202206010044//Science and Technology Program of Guangzhou, China/ ; No. U24A20652//The Joint Funds of the Natural Science Foundation of China/ ; No. 82272246//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Consistent patterns of gut microbiota variations, particularly in relative abundance, have been identified in the adult human gut. Enterotype, another general measure of the gut microbiota, is a valuable approach for categorizing the human gut microbiota into distinct clusters. The impact of different enterotypes on human health varies, and the changes induced by moderate altitude exposure remain unclear. This study aimed to conduct a comprehensive investigation of the cascade effects triggered by enterotype shifts following moderate altitude exposure.

RESULTS: Using shotgun metagenome sequencing, participants before and after moderate-altitude exposure were classified into cluster BL (dominated by Blautia) and cluster BA (dominated by Bacteroides). Relative to cluster BL, cluster BA consisted predominantly of individuals exposed to moderate altitude. Compared to cluster BL, Cluster BA exhibited rewired metabolism of serum metabolites (i.e., amino acids, fatty acids and bile acids) and gut microbiota, lower inflammatory factor levels (i.e., tumor necrosis factor-α (TNF-α)), and sparser correlations among these parameters. Individuals with baseline BL enterotype who transitioned to the BA enterotype following moderate-altitude exposure showed prominent improvement in fasting blood glucose (FBG) levels, with higher abundance of Bacteroidetes species (e.g., Bacteroides thetaiotaomicron, and Bacteroides uniformis), but lower Proteobacteria species abundance (e.g., Escherichia coli) and decreased L-Glutamic acid levels. Furthermore, fecal microbiota transplantation (FMT) from moderate-altitude exposed individuals to high-fat diet (HFD) fed mice confirmed increased Bacteroides abundance shifts associated with improvements in glucose homeostasis regulation and rewired amino acid metabolism. In addition, significant increases in alanine aminotransferase (ALT) levels but decreased serum creatinine (Scr), arterial oxygen saturation (SaO2), 4-Hydroxyproline, L-Glutamic acid, L-Asparagine, L-Threonine, L-Citrulline, L-Lysine and Isovaleric acid levels were identified as potentially important signals for individuals upon moderate altitude exposure, regardless of the gut microbiota enterotype.

CONCLUSIONS: Moderate altitude exposure could induce enterotype switching, and a Bacteroides-dominant enterotype may be a beneficial pattern of the gut microbiome related to host metabolism. Moderate-altitude exposure has potential implications for glycemic control, suggesting new avenues for managing FBG levels in future.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-025-04245-4.},
}

@article {pmid41043862,
year = {2025},
author = {Jeong, SH and Kim, YJ and Shin, JY and Oh, KW and Lee, JW and Lee, PH},
title = {DPP-4 inhibitor alleviates gut-brain axis pathology in Parkinson's disease.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-334988},
pmid = {41043862},
issn = {1468-3288},
abstract = {BACKGROUND: Dipeptidyl peptidase-4 inhibitors (DPP-4is) have been reported to exhibit therapeutic effects in Parkinson's disease (PD), increasing their potential for drug repurposing. One aspect of PD pathogenesis is thought to be associated with the gut-brain axis, where α-synuclein from the gut is transmitted to the brain via the vagus nerve (VN).

OBJECTIVE: We explored whether sitagliptin, a DPP-4i, exhibits a protective effect in a low-dose rotenone-treated gut-brain axis-associated PD model.

DESIGN: To explore the effect of sitagliptin, we used the oral rotenone-treated mouse model, which showed spreading of pathological α-synuclein from the intestine in a stereotypic manner via the VN into the midbrain with motor deficits.

RESULTS: Sitagliptin mitigated rotenone-induced gut inflammation and toll-like receptor 2 (TLR2) expression, reduced α-synuclein accumulation in the gut, VN and brain and lessened neuronal loss in the medulla and midbrain with recovery of motor performance. In addition, sitagliptin suppressed inflammation in response to a TLR2 agonist and rotenone in macrophages, enteric glial cells and enteroendocrine cell lines in vitro. In secretin tumour cell 1, an enteroendocrine cell line, sitagliptin also decreased rotenone-induced endogenous α-synuclein levels. The beneficial effects of sitagliptin were maintained even under glucagon-like peptide-1 receptor blockade. Notably, sitagliptin significantly altered the gut microbiome, shifting towards a profile that may counteract PD pathology.

CONCLUSION: These findings demonstrated that sitagliptin alleviated α-synuclein deposition in the gut and brain through modulation of TLR2-mediated inflammation and altered the gut microbiome composition towards a more favourable profile, which indicates that DPP-4is can offer a novel therapeutic avenue for managing PD.},
}

@article {pmid41043686,
year = {2025},
author = {Biruete, A and Buobu, PS and Considine, R and Hoxha, EM and Eicher-Miller, HA and Kinzig, KP and Panjwani, AA and Running, CA and Rutigliani, G and Savaiano, DA and Veile, AJ and Wolf, PM and Mattes, R},
title = {Ingestive Behavior and Precision Nutrition: Part of the Puzzle.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100531},
doi = {10.1016/j.advnut.2025.100531},
pmid = {41043686},
issn = {2156-5376},
abstract = {The marked individual variability in response to common dietary exposures necessitates tailoring of dietary guidance to individuals, or small groups of individuals with similar needs, to optimize health. This is a complex task requiring integration of environmental, cultural, psychological and biological contributions. Work in the area of precision nutrition is an effort to translate science into practice. A research roadmap developed through an National Institutes of Health (NIH) conference identified many of the inputs that require quantification. Better characterization of ingestive behaviors is one key area. The aim of this narrative review is to summarize current understanding of the influences of age, sex, Body Mass Index (BMI), ethnicity and genetics on ingestive behaviors, including culture, sensory function, appetite, dietary intake, the gut-brain axis and microbiome. To do so, the extant literature was accessed through search engines relevant to the various topics covered. Outcomes assessed varied topically. In addition to compiling evidence on the nature and magnitude of these relationships, this review highlights the degree of individual variability in attributes or responses to an intervention. More broadly, it: a) documents that cause and effect relationships are difficult to establish as most are dynamic and interactive; b) there are inherent and learned contributions to both behavior and biology that will require different considerations and offer different opportunities for manipulation; c) a focus on intuitive approaches may not be as successful as desired; d) that external influences can, and often do, override internal influences of biology; and e) there are multiple ways to construct healthful diets. At the same time, it is vital that improved methods to characterize the multiple relevant inputs to ingestive behavior be developed. It is hoped the evidence compiled here will inform efforts to develop precision nutrition guidance.},
}

@article {pmid41043678,
year = {2025},
author = {Kumar, P and Gulati, M and Kapoor, B and Yadav, AK and Hussain, MS and Kumar, R},
title = {Beyond the HCG test: Microbiome-based diagnosis of pregnancy.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {120639},
doi = {10.1016/j.cca.2025.120639},
pmid = {41043678},
issn = {1873-3492},
abstract = {The complex but definitive relationship between pregnancy and the body microbiota offers a significant opportunity for novel diagnostic techniques. This work proposes a new diagnostic method that correlates the significant changes in the gut, vaginal, and oral microbiota composition that occur in the early stages of pregnancy. The main premise is identification of those microbial indicators that are strongly linked to early pregnancy by describing the periodic shifts in these microbial ecosystems. Early and precise pregnancy identification may be made possible by these biomarkers' potential as highly sensitive and precise indicators. More importantly, understanding of the fundamental processes by which the microbiota in various organs affects pregnancy outcomes, tailored therapies to enhance the health of both the mother and the foetus may be considered as a long-term goal. Analysis of vaginal swabs or saliva is proposed as a non-invasive method that might transform prenatal care. Healthcare professionals might monitor pregnancy progress, understand and mitigate the expected problems, and initiate prompt measures by identifying early pregnancy indicators. Finding microbiome-based indicators of pregnancy complications may also make it possible to identify at-risk patients early and implement individualised treatment plans. We may get fresh understanding of the intricacies of pregnancy and create creative methods to enhance the health of both mothers and children by utilizing the potential of the human microbiome.},
}

@article {pmid41043575,
year = {2025},
author = {Ahmed, LA and Al-Massri, KF},
title = {Insights into the Role of Gut Microbiota Modulation in the Management of Various Cardiovascular Diseases: A New Approach for Improving the Efficacy of Current Cardiovascular Medications.},
journal = {European journal of pharmacology},
volume = {},
number = {},
pages = {178210},
doi = {10.1016/j.ejphar.2025.178210},
pmid = {41043575},
issn = {1879-0712},
abstract = {Gut microbiome is an emerging contributor to various cardiovascular diseases (CVDs) where gut dysbiosis increases the risk of development and progression of atherosclerosis, coronary artery diseases, hypertension, and heart failure. Microbiota can also affect the metabolism of medications including cardiovascular drugs, resulting in alteration of their pharmacokinetics and pharmacodynamics or producing metabolites which can interfere with response of these drugs. Importantly, CVDs require prolonged pharmacological interventions with medications which may have impacts on the diversity and composition of gut microbiota. Gut microbiota modulation using diets, prebiotics, probiotics, fecal microbiota transplantation, and microbial trimethylamine-lyase inhibitors, has also shown benefits in the management of CVDs where gut microbiota and their metabolites have recently been studied as potential targets for the management of these diseases. Specifically, using innovative microbiota therapies in combination with traditional pharmacological agents have been evaluated for additional benefits in various CVDs. However, assessing the interactions among host factors, gut microbiome, and drug response will be essential for the development of new therapeutic targets for cardiovascular disorders, ultimately hoping better prognosis and patient's quality of life for those affected with CVDs.},
}

@article {pmid41043335,
year = {2025},
author = {He, B and Ma, Y and Wang, K and Bing, P and Ji, L and Tian, G and Liu, H and He, P and Yang, J},
title = {Microbiome-transcriptome-histology triad enhances survival risk stratification in multiple cancers.},
journal = {Computational biology and chemistry},
volume = {120},
number = {Pt 2},
pages = {108703},
doi = {10.1016/j.compbiolchem.2025.108703},
pmid = {41043335},
issn = {1476-928X},
abstract = {Accurate prognostic stratification is essential for optimizing postoperative therapeutic strategies in oncology. While deep learning approaches have shown promise for survival prediction through unimodal analyses of histopathological images, transcriptomic profiles, and microbial signatures, their clinical utility remains limited due to fragmented biological insights. In this study, we introduce HMTsurv, a multimodal survival prediction framework that integrates digital histopathology, host transcriptomics, and tumor-associated microbiome features. Utilizing multi-omics datasets from four major malignancies-colorectal, gastric, hepatocellular, and breast cancers-our model exhibited superior prognostic accuracy (c-index: 0.68-0.72) when compared to single-modality benchmarks, as validated through rigorous cross-validation methods. Notably, our model achieved robust risk stratification (log-rank p < 0.001 across all cohorts) as demonstrated by Kaplan-Meier analysis, effectively distinguishing patients into distinct survival trajectories. Systematic examination of multimodal signatures identified 14 pan-cancer survival biomarkers, including MAGE family genes, which were consistently upregulated in high-risk subgroups. Additionally, we elucidated distinct histopathological patterns, dysregulated microbial communities, and altered gene-microbiota co-expression networks that were predictive of adverse outcomes. This study not only establishes a generalizable multimodal architecture for cancer prognosis but also elucidates the intricate interactions among histological, molecular, and ecological determinants of survival, providing a clinically actionable framework for precision oncology.},
}

@article {pmid41043307,
year = {2025},
author = {Ji, Z and Liu, S and Tian, Z and Guo, N and Wei, W and Jiang, Q},
title = {Tooth Loss-Induced Gut Dysbiosis Promotes Neuroinflammation via L-Asparagine-Mediated Neuronal Toxicity.},
journal = {International dental journal},
volume = {75},
number = {6},
pages = {103929},
doi = {10.1016/j.identj.2025.103929},
pmid = {41043307},
issn = {1875-595X},
abstract = {INTRODUCTION AND AIMS: Tooth loss is not only a dental issue but also affects gut microbial composition and downstream physiological responses. This study investigates how tooth loss-induced alterations in the gut microbiota influence metabolic and neural function. This study aimed to elucidate the mechanistic links between microbiota dysbiosis, metabolic imbalance, and neuroinflammation following tooth loss.

METHODS: Using a murine model, the first molars of C57BL/6 mice were extracted, followed by the collection of fecal samples, serum, and brain tissue for subsequent metagenomic sequencing, metabolomics, and transcriptomics. Pro-inflammatory markers (IL-6, TNF-α) and PSD95 expression were assessed. The neurotoxic effects of key metabolite L-Asparagine were validated using HT22 neuronal cell models.

RESULTS: Tooth loss induced gut microbiota dysbiosis, which subsequently mediated pathological alterations in brain tissue, characterised by a reduction in beneficial Butyribacter and an increase in pathogenic taxa. Corresponding shifts in systemic metabolism were observed, along with changes in brain gene expression, particularly in genes related to neuroinflammation. In vitro experiments further demonstrated that L-Asparagine directly induced neurotoxicity in HT22 hippocampal neurons through ROS overproduction, apoptosis, and inflammatory activation.

CONCLUSION: Tooth loss induced gut microbiota dysbiosis, systemic metabolic disruptions, and neuroinflammatory responses. Our findings demonstrated that tooth loss exacerbated neuroinflammation via gut-derived L-Asparagine, providing a mechanistic link in the oral-gut-brain axis.

CLINICAL RELEVANCE: This study demonstrated that molar extraction in mice disrupted gut microbiota and promoted neuroinflammation via L-Asparagine, suggesting that maintaining oral integrity might help preserve neurological health. This could open new avenues for microbiota-targeted interventions in neurodegenerative disease prevention.},
}

@article {pmid41043233,
year = {2025},
author = {Sun, C and Liu, X and Wang, M and Zhang, Q and Geng, H and Ji, X and Wang, H and Li, S and Jin, E and Zhang, F},
title = {Metagenome-metabolome responses to linarin alleviate hepatic inflammatory response, oxidative damage, and apoptosis in an ETEC-challenged weaned piglet model.},
journal = {Ecotoxicology and environmental safety},
volume = {304},
number = {},
pages = {119145},
doi = {10.1016/j.ecoenv.2025.119145},
pmid = {41043233},
issn = {1090-2414},
abstract = {Enterotoxigenic Escherichia coli (ETEC), present in contaminated food, water, and environments, can induce hepatic injury via the gut-liver axis, posing a serious threat to ecological systems and public health. Linarin, a flavonoid extracted from Chrysanthemum indicum, exhibits anti-inflammatory and antioxidant properties, but its protective effects against ETEC-induced hepatic injury remain unclear. In this study, 24 weaned piglets were randomly assigned to four groups: BD+NB (basal diet + nutrient broth), LN+NB (basal diet + 150 mg/kg linarin + nutrient broth), BD+ETEC (basal diet + ETEC challenge), and LN+ETEC (basal diet + 150 mg/kg linarin + ETEC challenge). Dietary linarin significantly increased ADFI and the genes related to oxidative damage and bile acid metabolism, while decreasing F:G ratio, liver index, serum liver function-related parameters, and the genes related to inflammatory response and apoptosis. It also significantly altered the relative abundances of gut microbiota, which were closely associated with key hepatic metabolic pathways, including nicotinate and nicotinamide metabolism and fatty acid biosynthesis. Our study suggests that linarin alleviated ETEC-induced hepatic inflammation and apoptosis, enhanced antioxidant capacity, and regulated bile acid metabolism. The potential mechanism involves linarin modulating gut microbiota-mediated key hepatic metabolic pathways to exert protective effects. In contrast to previous flavonoid-ETEC studies that primarily focused on the gut, this study, based on the gut-liver axis, investigates the potential mechanisms by which linarin is associated with the alleviation of ETEC-induced hepatic injury through integrated analysis of gut microbiome metagenomics and liver metabolomics.},
}

@article {pmid41043219,
year = {2025},
author = {Gugescu, L and Yang, Y and Kool, JF and Fyhrquist, N and Wincent, E and Alenius, H},
title = {Microbiota modulates compound-specific toxicity of environmental chemicals: A multi-omics analysis in zebrafish embryos.},
journal = {Environment international},
volume = {204},
number = {},
pages = {109828},
doi = {10.1016/j.envint.2025.109828},
pmid = {41043219},
issn = {1873-6750},
abstract = {Interactions between gut microbiota and environmental chemicals critically influence toxicological outcomes, yet mechanistic insights remain limited. Here, we combine developmental toxicity with full-length 16S rRNA gene sequencing, transcriptomic, and metabolomic analyses in germ-free (GF) and conventionally colonized wild-type (WT) zebrafish embryos to elucidate the microbiota's role in modulating chemical toxicity. Using representative compounds from major classes of environmental contaminants, we show that microbial presence significantly alters toxicity profiles in a compound-specific manner. The perfluorinated contaminant PFOS (perfluorooctanesulfonic acid) induced the strongest microbiota-dependent effects, with a greater number of differentially expressed genes in WT embryos and pronounced changes in immune and stress-related pathways. The pesticide boscalid and bisphenol F elicited distinct microbiota-modulated transcriptional and metabolic responses. Gene network analysis identified baseline microbial regulation of immune and metabolic programs, while metabolomics showed PFOS-dependent changes in L-tryptophan and its microbe-associated metabolites, including inosine, indoxyl sulfate and indole acetaldehyde, exclusively in WT embryos. These findings establish a mechanistically grounded framework for microbiota-chemical interactions and highlight the importance of integrating microbiome context into environmental health assessments.},
}

@article {pmid41043062,
year = {2025},
author = {Malogan, J and Hallowell, HA and Francis, B and Suez, J},
title = {Supplementation and Elimination of Microbiome-Produced Metabolites in the Treatment of Human Disease.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.70103},
pmid = {41043062},
issn = {1749-6632},
abstract = {The human gut microbiome has a complex and influential relationship with host physiology that is governed through commensal-derived metabolites, small molecules, and endogenous microbial patterns. Indeed, microbial metabolites from the gut microbiome have been implicated in promoting health as well as contributing to the pathogenesis of microbiome-associated diseases. Live microbial therapeutics, such as probiotics and fecal microbiota transplantations, have been extensively utilized to establish health-promoting assemblages of bacteria and their associated beneficial metabolites. However, broad clinical use of live microbial therapeutics is limited by efficacy, specificity, and safety concerns. To circumvent this, a postbiotic approach can be taken, in which a beneficial effect may be achieved by direct administration of bacterially derived bioactive molecules. Alternatively, in cases where microbiome-derived metabolites drive disease, specific oral inhibitors can be used to restrict compound production. In this review, we examine the use of postbiotics to alleviate disease and highlight recent translational successes. Additionally, we discuss emerging approaches for precision elimination of disease-causing metabolites, as well as the exciting possibility of utilizing bacteriophages to modulate the production of metabolites in the microbiome.},
}

@article {pmid41042689,
year = {2025},
author = {Gao, S and Li, L and Wang, J and Wang, Y and Dong, Y},
title = {MicroSTNet: a spatio-temporal graph-based framework for time-series microbiome analysis.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001519},
pmid = {41042689},
issn = {2057-5858},
mesh = {Humans ; *Microbiota/genetics ; Mouth/microbiology ; Spatio-Temporal Analysis ; *Gastrointestinal Microbiome ; Algorithms ; Machine Learning ; },
abstract = {The structure and function of microbial communities are profoundly influenced by spatio-temporal dynamics. While existing machine learning algorithms are extensively used for phenotype prediction based on microbial communities, particularly for disease forecasting, they fail to fully utilize the spatio-temporal dynamics embedded in microbial data. Moreover, data collected at a single time point often proves inadequate for the accurate prediction of host or environmental phenotypes. This study investigates the interaction dynamics of microbial communities in closed environments using data from two independent research projects. We introduce the microbial spatio-temporal network model, which combines two-stream spatio-temporal graph convolutional networks with long short-term memory to predict dynamic microbial abundance in the human oral cavity and gut. The model captures the temporal trajectories of microbes together with spatial features embedded in network structures, enabling accurate prediction of future community trends. Experimental validation confirmed its ability to track temporal patterns with high accuracy, even for micro-organisms exhibiting significant fluctuations. Ablation experiments demonstrated that the integrated model outperforms individual components, harnessing the strengths of both approaches. This technology presents a promising strategy for low-cost, non-invasive early diagnosis of human diseases, offering valuable insights into future health risks.},
}

Humans
*Microbiota/genetics
Mouth/microbiology
Spatio-Temporal Analysis
*Gastrointestinal Microbiome
Algorithms
Machine Learning

@article {pmid41042595,
year = {2025},
author = {Bywater-Brenna, KK and Unnikrishnan, M},
title = {Unravelling three-way interactions between Clostridioides difficile, microbiota and the host.},
journal = {Journal of medical microbiology},
volume = {74},
number = {10},
pages = {},
doi = {10.1099/jmm.0.002067},
pmid = {41042595},
issn = {1473-5644},
mesh = {*Clostridioides difficile/physiology ; Humans ; *Clostridium Infections/microbiology/immunology ; *Gastrointestinal Microbiome ; Animals ; Dysbiosis/microbiology ; *Host-Pathogen Interactions ; },
abstract = {Clostridioides difficile infection is a global issue, representing a huge financial burden on healthcare systems worldwide which is further exacerbated by high recurrence rates. Infection is closely linked with the gut microbiome status, with successful C. difficile colonization usually occurring when there is dysbiosis. Our understanding of the molecular mechanisms underlying microbiota-mediated colonization resistance has advanced significantly in recent years, although the nuanced crosstalk occurring between C. difficile, the gut microbiota and host mucosa has yet to be fully elucidated. Deciphering these three-way interactions is critical for the development of effective therapeutic and prophylactic strategies. This review will discuss known interactions between this pathogen, the microbiota and the host in addition to the tools available to dissect complex microbial interchanges.},
}

*Clostridioides difficile/physiology
Humans
*Clostridium Infections/microbiology/immunology
*Gastrointestinal Microbiome
Animals
Dysbiosis/microbiology
*Host-Pathogen Interactions

@article {pmid41042593,
year = {2025},
author = {Varliero, G and Bauder, A and Stierli, B and Qi, W and Frey, B},
title = {Host-virome associations in the weathering crust of a rapidly retreating temperate Alpine glacier.},
journal = {Microbial genomics},
volume = {11},
number = {10},
pages = {},
doi = {10.1099/mgen.0.001524},
pmid = {41042593},
issn = {2057-5858},
mesh = {*Ice Cover/microbiology/virology ; *Bacteria/genetics/virology/classification ; *Microbiota/genetics ; *Viruses/genetics/classification/isolation & purification ; Switzerland ; Metagenomics/methods ; Ecosystem ; Host Specificity ; },
abstract = {Glaciers are retreating rapidly, altering ecosystem dynamics and increasing meltwater outflow into populated areas. Understanding microbial-virome interactions is crucial for predicting the consequences of this release. We sampled ice from four shallow pits in the weathering crust of the Rhonegletscher, Swiss Alps, and found a microbiome dominated by bacteria and microeukaryotes, alongside a metavirome infecting both groups. Viruses exhibited variable host specificity, with some targeting particular taxa and others showing a broader infectivity range. Variable genomic regions, including metagenomic and metaviromic islands, were enriched in genes related to replication, recombination, repair and transposable elements. Detected auxiliary metabolic genes were primarily involved in host coenzyme biosynthesis, uptake or utilization and in altering bacterial methylation patterns to evade detection. These findings underscore the major role of viruses in regulating microbial dynamics in glaciers and their potential downstream environmental impacts.},
}

*Ice Cover/microbiology/virology
*Bacteria/genetics/virology/classification
*Microbiota/genetics
*Viruses/genetics/classification/isolation & purification
Switzerland
Metagenomics/methods
Ecosystem
Host Specificity

@article {pmid41042542,
year = {2025},
author = {Torrez Lamberti, MF and Thompson, S and Harrison, NA and Gardner, CL and da Silva, DR and Teixeira, LD and Kondepudi, KK and Gonzalez, CF and Chukkapalli, SS and Lorca, GL},
title = {Lactobacillus johnsonii N6.2 Improves Glycemia, and Reduces Diabetes-induced Organ Injury in the db/db Mice Model.},
journal = {The Journal of endocrinology},
volume = {},
number = {},
pages = {},
doi = {10.1530/JOE-25-0184},
pmid = {41042542},
issn = {1479-6805},
abstract = {Diabetes mellitus is a complex metabolic disorder characterized by hyperglycemia as well as the associated comorbidities. Type 2 diabetes is also associated with dysfunction of liver, kidney and nervous system. In addition, an altered microbiota is frequently observed in subjects with Type 2 diabetes. In this study a db/db (diabetic) mouse model of Type 2 diabetes was used to elucidate the beneficial effects of the probiotic Lactobacillus johnsonii N6.2. To evaluate metabolic effects, we performed metabolomics on liver samples, and RNA-seq from liver and visceral adipose tissue, followed by qRT-PCR validation. Using L. johnsonii N6.2 extracellular vesicles we evaluated lipid accumulation in hepatocytes. Finally, the gut microbiome of db/db mice was profiled using 16S rRNA sequencing. We observed that administration of the probiotic improved glycemic levels and decreased diabetes scores, as well as Type 2 diabetes-associated injury to the pancreas, liver and kidneys. Liver metabolomic and transcriptome analyses identified biomarkers of L. johnsonii N6.2 activity, including modulation of the vitamin K pathway, upregulation of FGF21-, a key regulator of glucose and lipid metabolism, and alternations in selected circadian genes. This study elucidates the beneficial effects of L. johnsonii N6.2, against the common symptoms of type 2 diabetes, highlighting its potential as an adjuvant therapeutic agent.},
}

@article {pmid41042396,
year = {2025},
author = {Wu, J and Zhou, J and Zhao, Q and Yang, C and Bai, Y},
title = {Metagenomic analysis of microbial community dynamics in konjac rhizosphere during soft rot disease progression.},
journal = {Applied microbiology and biotechnology},
volume = {109},
number = {1},
pages = {212},
pmid = {41042396},
issn = {1432-0614},
support = {32072558//the Nature Science Foundation of China/ ; 2024-620-000-001-007//Hubei Agricultural Science and Technology Innovation Center Innovation Team Project/ ; },
mesh = {*Rhizosphere ; *Plant Diseases/microbiology ; *Soil Microbiology ; Metagenomics ; *Amorphophallus/microbiology ; *Microbiota/genetics ; Bacteria/classification/genetics/isolation & purification ; Fungi/genetics/classification ; },
abstract = {Amorphophallus konjac, the sole glucomannan-rich species in the Araceae family, faces significant yield and quality losses due to soft rot disease. Understanding the relationship between soil microbial communities and soft rot incidence is critical for sustainable konjac production. Metagenomic profiling was employed to systematically characterize the spatiotemporal dynamics of rhizosphere microbiomes during disease progression. Microbial alpha diversity (Chao1 index) exhibited a significant peak in the rhizosphere of diseased plants at the mature stage, contrasting with stable diversity patterns in healthy and latently infected groups, indicating dysbiosis-associated richness inflation during disease progression. Principal coordinate analysis (PCoA) revealed significant divergence in rhizosphere microbial structures between diseased and healthy/latently infected groups, with higher compositional variability observed in diseased samples. At the phylum level, Chloroflexi and Acidobacteria abundances in healthy mature plants exceeded those in diseased plants by 11.54% and 4.6%, respectively, while pathogenic Rhizopus arrhizus and Rhizopus microsporus were significantly enriched in diseased mature plants. Correlation analyses demonstrated predominantly negative associations between bacterial species and soil factors, contrasting with positive fungal correlations. KEGG pathway annotation identified carbohydrate metabolism and amino acid synthesis as core microbial functions in the konjac rhizosphere. Collectively, Chloroflexi and Acidobacteria were validated as putative biocontrol agents, while Rhizopus spp. emerged as key drivers of soft rot development. These findings provide mechanistic insights for designing microbiome-based biocontrol strategies to mitigate konjac soft rot, offering a sustainable alternative to conventional agrochemical reliance. KEY POINTS: • Diseased konjac microbial richness peaks; healthy plants enrich Chloroflexi/Acidobacteria. • Rhizopus pathogens drive soft rot; bacteria and fungi show opposing soil factor links. • Lays groundwork for microbiome approaches to cut agrochemicals in konjac rot control.},
}

*Rhizosphere
*Plant Diseases/microbiology
*Soil Microbiology
Metagenomics
*Amorphophallus/microbiology
*Microbiota/genetics
Bacteria/classification/genetics/isolation & purification
Fungi/genetics/classification

@article {pmid41042380,
year = {2025},
author = {Wang, S and Jiang, H and Yao, T},
title = {Integrative genomics and functional immunology reveal Clostridia species as modulators of neuroinflammation in amyotrophic lateral sclerosis.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {74},
number = {1},
pages = {136},
pmid = {41042380},
issn = {1420-908X},
support = {2020B22//Doctoral Fund of the First Affiliated Hospital of Harbin Medical University/ ; 2023ZX07D06//The key research and development project of Heilongjiang Province/ ; 2022-KYYWF-0301//Innovative Scientific Research Funding Project of Harbin Medical University/ ; PL2024H140//Natural Science Foundation of Heilongjiang Province,China/ ; },
mesh = {Humans ; *Amyotrophic Lateral Sclerosis/immunology/microbiology/genetics ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Cytokines/immunology ; Genomics ; *Neuroinflammatory Diseases/immunology/microbiology/genetics ; Aged ; Myeloid-Derived Suppressor Cells/immunology ; Mendelian Randomization Analysis ; },
abstract = {OBJECTIVE: This multiomics study investigated causal relationships between the gut microbiota (GM), immune dysregulation, and amyotrophic lateral sclerosis (ALS) pathogenesis using Mendelian randomization (MR) with experimental validation.

MATERIALS: Analyses incorporated genome-wide data from 87,347 participants (GM: n = 7738; ALS: 20,806 patients, 59,804 controls; immune phenotypes: n = 3757), transcriptomic data from 71 subjects (56 ALS patients, 15 controls), and experimental validation in matched cohorts (n = 6 subjects per group).

METHODS: Two-sample bidirectional MR and mediation analysis were used to evaluate associations. Experimental validation employed flow cytometry for myeloid-derived suppressor cell quantification, enzyme-linked immunosorbent assay for cytokines, and real-time polymerase chain reaction for bacterial validation. Statistical analyses included inverse variance weighted methods with Cohen's d calculations.

RESULTS: Sixteen bacterial taxa, including p_Firmicutes.c_Clostridia, displayed protective associations with the risk of ALS, whereas sixteen showed harmful associations. Mediation analysis suggested that p_Firmicutes.c_Clostridia may confer protection through CD33+HLA-DR-myeloid-derived suppressor cell upregulation (23.8% mediation effect). Experimental validation confirmed fewer myeloid-derived suppressor cells in ALS patients (4.0 ± 0.8% vs. 7.5 ± 1.0%, p < 0.001, Cohen's d = 1.4) and lower levels of anti-inflammatory cytokines (TGF-β1: Cohen's d = 1.8, p < 0.001).

CONCLUSIONS: These findings support causal associations between gut microbial taxa and the ALS risk, which are mediated through immunoregulatory mechanisms, highlighting therapeutic targets within the gut‒immune‒brain axis.},
}

Humans
*Amyotrophic Lateral Sclerosis/immunology/microbiology/genetics
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Cytokines/immunology
Genomics
*Neuroinflammatory Diseases/immunology/microbiology/genetics
Aged
Myeloid-Derived Suppressor Cells/immunology
Mendelian Randomization Analysis

@article {pmid41042228,
year = {2025},
author = {Paccou, J and Gagnon, C and Yu, EW and Rosen, CJ},
title = {Effects of weight-loss interventions on bone health in people living with obesity.},
journal = {Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research},
volume = {},
number = {},
pages = {},
doi = {10.1093/jbmr/zjaf135},
pmid = {41042228},
issn = {1523-4681},
abstract = {Strategies to reduce weight in people living with obesity (PwO) include calorie restriction, metabolic and bariatric surgery (MBS), and anti-obesity drugs including glucagon-like peptide-1 receptor agonists (GLP-1Ra), such as liraglutide and semaglutide. Although weight loss in PwO has many health benefits, it can result in increased bone loss and fracture risk. Indeed, the consequences of weight loss interventions are well known: (i) significant weight loss induced by caloric restriction and MBS results in high turnover bone loss and (ii) unlike calorie restriction, PwO experience a substantial deterioration in bone microarchitecture and strength associated with an increased risk of fracture after MBS, especially malabsorptive procedures. GLP-1 may enhance bone metabolism and improve bone quality, and liraglutide appears to have a positive effect on bone health despite significant weight loss in several rodent models. However, most of the positive effects on bone have been observed at concentrations much higher than those approved for obesity care in humans. The effects of GLP-1Ra on bone health in PwO are still limited; however, significant weight loss induced by GLP-1Ra may also result in accelerated bone turnover and bone loss, and semaglutide could lead to an increased risk of fractures in the at-risk population. The mechanisms responsible for the adverse skeletal effects of MBS are not yet fully understood, and there are insufficient human studies supporting pathophysiological hypotheses. However, data suggest that multiple mechanisms are involved, including nutritional factors, mechanical unloading, hormonal factors, adipokines, and alterations in the gut microbiome. Recommendations for the prevention and treatment of osteoporosis secondary to MBS are now available, and the efficacy of anti-osteoporosis medications in preventing bone loss has been evaluated in two randomized controlled trials. Priorities for future research include the development of effective approaches to reduce fracture risk in PwO following MBS and investigation of the effects of anti-obesity drugs on bone health.},
}

@article {pmid41041974,
year = {2025},
author = {Najafpour, B and Canario, AVM and Power, DM},
title = {Bacterial 16S Ribosomal Gene Fingerprints as a Tool to Diagnose and Mitigate Fish Larvae Gut Dysbiosis.},
journal = {Environmental microbiology reports},
volume = {17},
number = {5},
pages = {e70187},
doi = {10.1111/1758-2229.70187},
pmid = {41041974},
issn = {1758-2229},
support = {UIDP/04326/2020//Portuguese national funds from FCT-Foundation for Science and Technology/ ; LA/P/0101/2020//Portuguese national funds from FCT-Foundation for Science and Technology/ ; 727610//European Unions Horizon 2020 research and innovation programme, PerformFISH/ ; 871108//European Unions Horizon 2020 research and innovation programme (AQUAEXCEL3.0)/ ; EMBRC.PT ALG-01-0145-FEDER-022121//The operational programmes CRESC Algarve 2020 and COMPETE 2020/ ; BIODATA.PT ALG-01-0145-FEDER-022231//The operational programmes CRESC Algarve 2020 and COMPETE 2020/ ; },
mesh = {Animals ; *Dysbiosis/microbiology/diagnosis/veterinary ; Larva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Bacteria/genetics/classification/isolation & purification ; *Bass/microbiology ; *Sea Bream/microbiology ; Phylogeny ; *Fish Diseases/microbiology/diagnosis ; DNA, Bacterial/genetics/chemistry ; Sequence Analysis, DNA ; },
abstract = {Dysbiosis is associated with shifts in the diversity or relative abundance of beneficial versus harmful bacteria, leading to health issues in organisms. This study investigated gut bacterial dysbiosis associated with larval quality using 16S rRNA gene sequencing. The gut microbiome of gilthead sea bream and European sea bass, key commercial species and vertebrate models, was examined in high- and low-quality larvae batches from several European hatcheries. Larval quality, hatchery site and species influenced bacterial diversity in the gut. Individuals from larval batches that performed well had higher microbial diversity in the gut and individuals from batches that performed poorly had a gut microbiota dominated by pathogenic Vibrio (e.g., V. aestuarianus and V. cortegadensis). The bacterial dysbiosis index revealed a notable predominance of Fusobacteriota and Firmicutes phyla, Thermoanaerobacteria class and Lactobacillaceae, Moritellaceae, Clostridiaceae, Thiotrichaceae and Shewanellaceae families in good-quality larvae batches, and a prevalence of the Proteobacteria phylum, Gammaproteobacteria class, Sphingomonadaceae and Vibrionaceae families in the gut of individuals from poor-quality larvae batches. A positive dysbiosis index (cutoff > 0.4) was associated with a high risk of decreased larval performance and quality. Additionally, the abundance of Clostridium_sensu_stricto_15, Shewanellaceae_unclassified, Cetobacterium, Psychrilyobacter, Moritella and Latilactobacillus genera in the gut of good production batches, and the Vibrio genus in the gut of poor production batches, identified these genus as potential markers for diagnosing and mitigating bacterial dysbiosis in fish and potentially other vertebrates.},
}

Animals
*Dysbiosis/microbiology/diagnosis/veterinary
Larva/microbiology
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome
*Bacteria/genetics/classification/isolation & purification
*Bass/microbiology
*Sea Bream/microbiology
Phylogeny
*Fish Diseases/microbiology/diagnosis
DNA, Bacterial/genetics/chemistry
Sequence Analysis, DNA

@article {pmid41041899,
year = {2025},
author = {Ganamurali, N and Sabarathinam, S},
title = {β-Sitosterol targets the gut-brain-clock axis to ameliorate circadian disruption and metabolic dysfunction: A herb-pharmacomicrobiomic perspective.},
journal = {Chronobiology international},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/07420528.2025.2568586},
pmid = {41041899},
issn = {1525-6073},
abstract = {β-Sitosterol (BS) is a phytosterol that may contribute to circadian and metabolic regulation through multiple predicted mechanisms. Using network pharmacology, gene expression profiling, and microbiome analysis, this study suggests that BS could interact with nuclear receptors (PPARγ, PPARα, RORα, RORγ) and potentially influence CLOCK:BMAL1 transcriptional rhythms in peripheral tissues. BS was also predicted to be associated with PER2-related feedback and the synchronization of gluconeogenic and lipogenic pathways with the light-dark cycle. In addition, computational and preclinical evidence indicates that BS may influence the gut microbiome, supporting short-chain fatty acid-producing bacteria, intestinal barrier integrity, and inflammatory balance. Limited preclinical findings further suggest a potential role for BS in mitigating circadian misalignment and insulin resistance, with possible implications for lipid homeostasis. Future clinical studies are warranted to investigate BS supplementation across different chronotypes and dietary conditions in order to evaluate its chronotherapeutic potential. While the findings are promising, they remain preliminary, and human validation is essential to determine dosing strategies and therapeutic relevance. This study, therefore, highlights BS as a candidate compound with potential relevance to circadian disruptions and metabolic disorders, pending further experimental confirmation.},
}

@article {pmid41041846,
year = {2025},
author = {Zhao, Y and Yu, C and Zhang, J and Yao, Q and Zhu, X and Zhou, X},
title = {The gut‑skin axis: Emerging insights in understanding and treating skin diseases through gut microbiome modulation (Review).},
journal = {International journal of molecular medicine},
volume = {56},
number = {6},
pages = {},
doi = {10.3892/ijmm.2025.5651},
pmid = {41041846},
issn = {1791-244X},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Skin Diseases/therapy/microbiology ; *Skin/microbiology/pathology ; Probiotics/therapeutic use ; Animals ; Prebiotics ; },
abstract = {Emerging evidence indicates a significant association between the composition and functionality of the gut microbiome and various skin disorders, including psoriasis, atopic dermatitis, acne and several dermatological conditions. The gut‑skin axis theory describes a complex bidirectional communication network between the gut and the skin, providing mechanistic insights into the pathogenesis of certain cutaneous diseases. Specifically, the gut microbiome influences skin health through the regulation of systemic immunity, inflammatory responses and metabolic pathways. Advances in high‑throughput sequencing and bioinformatics technologies have substantially enhanced the understanding of the role of the gut microbiome in skin pathology. Clinical and preclinical studies have demonstrated that restoring gut microbial homeostasis via interventions such as faecal microbiota transplantation, probiotics and prebiotics can ameliorate symptoms of skin diseases. Furthermore, personalized microbiome‑based therapies, next‑generation probiotics and dietary modifications hold promise for refining gut‑skin interactions and advancing precision medicine in dermatology. Therapeutic strategies targeting the gut‑skin axis offer novel avenues for innovative dermatological treatments, with future breakthroughs potentially involving microbial community engineering, postbiotics and artificial intelligence in microbiome‑related diagnostics. This narrative review summarizes recent advances in gut‑skin axis research, explores its potential in the prevention and management of selected dermatoses and discusses future trends and scientific developments in the field.},
}

Humans
*Gastrointestinal Microbiome
*Skin Diseases/therapy/microbiology
*Skin/microbiology/pathology
Probiotics/therapeutic use
Animals
Prebiotics

@article {pmid41041828,
year = {2025},
author = {Wang, J and Jiang, Y and Kuzyakov, Y and Han, Z and Liu, S and Huang, Y and Smith, P and van Groenigen, KJ and Zou, J},
title = {Toward Climate-Smart Rice Systems: Moving Beyond Cultivar Improvement.},
journal = {Global change biology},
volume = {31},
number = {10},
pages = {e70545},
doi = {10.1111/gcb.70545},
pmid = {41041828},
issn = {1365-2486},
mesh = {*Oryza/genetics/growth & development/physiology ; *Climate Change ; *Agriculture/methods ; Methane/metabolism ; *Plant Breeding/methods ; Crops, Agricultural/growth & development ; },
abstract = {Rice is one of the world's most important staple crops and a major source of agricultural methane emissions. Breeding strategies such as photosynthate allocation modification and biomass enhancement show potential, but their effectiveness is highly context dependent, shaped by water regimes and soil organic carbon levels. Cultivars effective under continuous flooding may fail, or even increase emissions, under optimized water regimes. This perspective argues for integrated strategies that combine cultivar improvement with water and organic matter management, microbiome regulation, and climate-resilient breeding to build climate-smart rice systems that ensure both yield stability and methane mitigation.},
}

*Oryza/genetics/growth & development/physiology
*Climate Change
*Agriculture/methods
Methane/metabolism
*Plant Breeding/methods
Crops, Agricultural/growth & development

@article {pmid41041568,
year = {2025},
author = {Klatt, N and Swanson, E and Broedlow, C and Cherenack, E and Nogueira, N and Basting, C and Yue, P and Chakrawarti, A and Schroeder, T and Salazar, A and Acosta, L and Raccamarich, P and Gale, M and Fein, L and Alcaide, M},
title = {Host-microbe interactions characterized by gene expression of cervical adhesion molecules, cytokines, and growth factors define the recurrence of bacterial vaginosis.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7576831/v1},
pmid = {41041568},
issn = {2693-5015},
abstract = {Bacterial vaginosis (BV) is a common vaginal condition with a high recurrence rate after treatment. In this longitudinal multi-omics study, we integrated cervical microbial metatranscriptomics, host transcriptomics, cytokine profiles, and behavioral data to investigate factors driving BV recurrence in women from Miami-Dade county (N24). Recurrence at 6 months occurred in 46% of participants after metronidazole treatment. Recurrence was preceded by increased transcriptional activity of Gardnerella and Fannyhessea, enriched for glycogen and maltose metabolism and iron scavenging. Host transcriptomic analysis of cervical tissue revealed reduced CEACAM5-7 expression and increased IL6 and EREG, indicating impaired epithelial integrity and persistent inflammation. Cytokine-gene correlations and Bayesian mediation models identified CEACAM7 as a key mediator linking inflammation and microbial activity to recurrence. Intravaginal practices further amplified risk. These findings uncover for the first time dynamic host-microbiome disruptions that persist after treatment and reveals new targets for diagnostic and therapeutic strategies to reduce BV recurrence.},
}

@article {pmid41041532,
year = {2025},
author = {Niraula, S and Khan, I and Jung, J and Stirewalt, SL and Alagna, M and Du, J and Xiong, L and Elmasri, A and Wu, E and Seed, P and Green, SJ and Ho, KJ},
title = {Comparative study of sample storage conditions on gut dysbiosis in peripheral artery disease.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-7483387/v1},
pmid = {41041532},
issn = {2693-5015},
abstract = {BACKGROUND: Large-scale gut microbiome studies rely on fecal sample storage prior to batch sample preparation, sequencing, and analysis. Effects of storage methods have largely been studied using samples from healthy participants, where the microbial communities and the metabolic environment are in concordance. In diseased states, dysbiosis is more prone to environmental perturbation, which causes variable shifts in the communities. Cardiovascular diseases are associated with gut dysbiosis, but the effect of storage methods on the qualitative and quantitative aspects of dysbiosis is unknown. Thus, we examined the effects of 3 sample storage conditions on the fecal samples of patients with peripheral artery disease (PAD), a form of cardiovascular disease, and non-PAD controls.

METHODS AND RESULTS: This is a cross-sectional study of fecal samples collected from adults with PAD and non-PAD controls. All participants (12 non-PAD and 18 PAD) followed the home fecal sample collection protocol. Each sample was immediately frozen (IF), placed in modified Cary-Blair (CB), and stored in an OMNIgene•Gut vial. All samples were subjected to 16S rRNA gene amplicon sequencing of the hypervariable V4 region. A subset of glycerol stocks from IF and CB samples was thawed and cultured to compare revivification. We found significant differences in microbial composition and community structure between non-PAD and PAD groups based on storage conditions. Although we did not see the effect of an interaction term (disease group*storage condition) at the community level, we observed storage condition-specific differential abundance of genera in the PAD compared to the non-PAD group. The high number of differentially variable taxa in the PAD group samples further emphasize the need for standardizing storage conditions. The subset of samples stored in CB had less revivification potential than IF samples under both anaerobic and aerobic processing conditions.

CONCLUSIONS: Sample storage conditions and room temperature storage time differentially affect the microbial communities of fecal samples and revivification of glycerol stocks from non-PAD and PAD groups. The effects of storage conditions can bias microbiome-related disease biomarker discovery. Careful consideration should be given to sample storage conditions when analyzing fecal samples from diseased populations and when combining data from cohorts with samples stored in different conditions.},
}

@article {pmid41041324,
year = {2025},
author = {Alsayb, MA},
title = {Innovations in immunotherapy for autoimmune diseases: recent breakthroughs and future directions.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1647066},
pmid = {41041324},
issn = {1664-3224},
mesh = {Humans ; *Autoimmune Diseases/therapy/immunology ; *Immunotherapy/methods/trends ; Animals ; Antibodies, Bispecific/therapeutic use ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {Millions of people worldwide suffer from chronic and devastating autoimmune disorders, challenging contemporary medicine. These disorders develop when the immune system attacks its own tissues, causing inflammation and damage. Traditional treatments have focused on widespread immunosuppression, which can relieve symptoms but has serious adverse effects and does not address immunological dysregulation. This review discusses the current and future trends in immunotherapy for the management of autoimmune diseases, including advancements such as CAR T-cell therapy, bispecific antibodies, next-generation immune checkpoint modulators, targeted cytokine therapies, and microbiome-based interventions. The discussion is grounded in current scientific literature, focusing on mechanisms of action, recent breakthroughs, limitations, and potential future directions. Each of the related sections presents cutting-edge advancements, current challenges, and future opportunities for research and clinical translation.},
}

Humans
*Autoimmune Diseases/therapy/immunology
*Immunotherapy/methods/trends
Animals
Antibodies, Bispecific/therapeutic use
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid41041139,
year = {2025},
author = {Berlanga, M and Martín-García, A and Guerrero, R and Riu-Aumatell, M and López-Tamames, E},
title = {Changes in healthy Wistar rat gut microbiome by short-term dietary cava lees intervention.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1641612},
pmid = {41041139},
issn = {2296-861X},
abstract = {INTRODUCTION: The gut microbiome plays a crucial role in host health through complex host-microbe interactions. Beta-glucans, structural polysaccharides found in yeast cell walls, have emerged as promising modulators of immune function and microbial ecology. Cava lees, a by-product of sparkling wine production composed of Saccharomyces cerevisiae cell walls, represent a rich source of beta-glucans that could be upcycled for nutritional and therapeutic applications.

METHODS: Twenty-four Wistar rats (12 males, 12 females) were randomly divided into control and treatment groups. The treatment group received daily doses of 2,000 mg lees/kg body weight for 14 days. Shotgun metagenomic analysis was performed to assess microbial composition and functional changes.

RESULTS: A 14-day cava lees supplementation study revealed significant shifts in gut microbiota composition and function. Baseline microbiota was dominated by Bacillota (64-72%) and Bacteroidota (23-32%) with sex-specific differences at the family level. Post-supplementation analysis showed increased Shannon diversity across both sexes, with beneficial enrichment of Bifidobacteriaceae and Rikenellaceae families and reduction of Eubacteriaceae. While global metabolic profiles remained stable, targeted functional pathways were significantly changed, including butyrate production genes. Females exhibited particularly elevated secondary bile acid modification genes (Mann-Whitney-Wilcoxon test p = 0.032), and male oxidative stress response pathways (Mann-Whitney-Wilcoxon test p = 0.016) showing both a potentially sex-dependent responses to dietary intervention.

CONCLUSION: Working with healthy individuals provides a clear understanding of the normal, baseline microbiota composition and function before any intervention. These findings suggest a degree of plasticity of the gut microbiome and its responsiveness to dietary modifications. Beta-glucans from cava lees appear to create a favorable environment for beneficial bacteria, with sex-specific changes of certain bacterial families and functions. These findings provide a foundation for future translational research in humans. Nonetheless, to establish their true impact on human health, these observations in rodent models must be validated through appropriately designed human clinical studies.},
}

@article {pmid41041136,
year = {2025},
author = {Wang, W and Zhu, E and Yang, Y and Huang, Q and Xiao, X and Piao, S},
title = {An analysis of the intestinal microbiome combined with metabolomics to explore the mechanism of how Pangxiejiao tea improves metabolic disorders in HFFD-treated rats.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1653855},
pmid = {41041136},
issn = {2296-861X},
abstract = {INTRODUCTION: The high-fat and high-fructose diet (HFFD) can lead to various metabolic disorders. Pangxiejiao (PXJ), a natural plant widely used in folk practices, has been found to contain bioactive compounds that exhibit hypoglycemic effects in vitro. However, the potential of PXJ aqueous extract to ameliorate metabolic disorders in vivo and its underlying mechanisms remain unexplored. This study aims to investigate the effects of PXJ on metabolic disorders induced by HFFD in rats.

METHODS: An HFFD was employed to mimic unhealthy dietary habits, while PXJ was administered via oral gavage for 10 weeks. Perform biochemical assays, observe histopathological structures, and evaluate metabolic status in rats to investigate intrinsic alterations through detection of gut microbiota and plasma metabolites.

RESULTS: The results demonstrated that PXJ intervention reduced body weight, improved glucose and lipid metabolism, and decreased serum uric acid levels. PXJ alleviated oxidative stress and inflammation, as evidenced by reduced serum levels of IL-1β, IL-6, and TNF-α, along with ameliorated pathological inflammatory manifestations in metabolism-related organs, such as liver, pancreas, and colon. Furthermore, PXJ was found to decrease the Firmicutes/Bacteroidota ratio, modulated gut microbiota composition, and maintain microbial homeostasis. Nontargeted metabolomics analysis identified 39 upregulated metabolites, including hippuric acid, and 9 downregulated metabolites, such as LysoPG(18:2(9Z,12Z)/0:0). Correlation analysis further revealed that PXJ maintains metabolic homeostasis through complex network crosstalk. Specifically, four gut microbial taxa including Alloprevotella and six metabolites, including hippuric acid, demonstrated significant negative correlations with IL-6, TNF-α, and MDA. In contrast, Lachnospiraceae_NK4A136_group showed positive correlations with these metabolites and SOD.

DISCUSSION: In conclusion, early and sustained PXJ intervention alleviates HFFD-induced metabolic disorders, which is associated with restored gut microbiota balance, improved metabolism, and reduced inflammation and oxidative stress, demonstrating its potential as a novel functional tea for metabolic disorder prevention.},
}

@article {pmid41040929,
year = {2025},
author = {Cho, HY and Park, HJ and Choi, JS and Kim, SH and Ryu, MO and Seo, KW},
title = {Delineating the fecal microbiome of healthy domestic short-hair cats in South Korea.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1571107},
pmid = {41040929},
issn = {2297-1769},
abstract = {BACKGROUND: The gut microbiome is a vital component of an organism's health, influencing metabolism, immune function, and overall homeostasis. In this study, we aimed to characterize the gut microbiota of healthy domestic short-hair cats in South Korea and evaluate the effects of age, body condition score (BCS), sex, and diet on microbial composition.

METHODS: From August to December 2023, 40 healthy cats aged 1-14 years with a body condition score (BCS) of 5-9 were selected. Cats were excluded if they had taken probiotics or antibiotics, exhibited gastrointestinal symptoms within the last 6 months, or had blood work abnormalities. DNA quantification was performed, and libraries targeting the V3 and V4 regions were prepared according to the Illumina 16S metagenomic sequencing protocol with a read length of 2 × 300 bp. The relative abundance of bacteria at the phylum, genus, and species levels was assessed according to the age, sex, diet, and BCS of the cats, with major bacterial groups selected for chart analysis.

RESULTS: Examination of the fecal samples from 40 healthy cats (aged 0.5-14 years) using 16S rRNA gene sequencing revealed 2,721 bacterial amplicon sequence variants. The predominant phyla were Bacillota, Bacteroidota, and Actinomycetota. Although age did not significantly affect alpha diversity, a trend toward increased diversity was observed in cats aged 7-14 years. Phocaeicola was more abundant in older cats, suggesting a possible association with age-related conditions. Furthermore, Verrucomicrobiota was enriched in cats with a BCS of 8-9, and Ruminococcus torque was positively correlated with higher BCS. Sex-based differences indicated increased levels of Pseudomonadota, Finegoldia magna, and Sutterella massiliensis in neutered males, potentially linked to inflammatory pathways. Dietary analysis revealed an increased abundance of Blautia and Lachnoclostridium following a combination of dry and wet food.

CONCLUSION: Our findings provide critical insights into the core microbiota of domestic short-hair cats in South Korea, emphasizing the influence of geographic, physiological, and environmental factors on gut microbial diversity. The results offer a valuable foundation for advancing feline gut health research and enhancing health management strategies for felines, particularly in South Korea.},
}

@article {pmid41040880,
year = {2025},
author = {Wang, J and Gu, H and Gao, H and Zhang, T and Li, B and Zhang, M and Jiang, F and Song, P and Liang, C and Fan, Q and Xu, Y and Zhang, R},
title = {Developmental dynamics and functional adaptation of gut microbiota in Mongolian wild asses (Equus hemionus hemionus) across ontogenetic stages in arid desert ecosystems.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1659661},
pmid = {41040880},
issn = {1664-302X},
abstract = {Understanding the composition and function of gut microbiota is essential for elucidating how wild animals adapt to arid environments. The Mongolian wild ass (Equus hemionus hemionus), which inhabits harsh desert ecosystems, offers an ideal model for such investigations. This study employed metagenomic sequencing of fecal samples to characterize the composition and structure of the gut microbiota in adult, subadult, and juvenile Mongolian wild asses, with functional annotation based on the KEGG, CARD, and CAZy databases. Our study revealed that Bacillota and Bacteroidota were the dominant phyla, together accounting for over 85% of relative abundance, with their ratio (B/B value) showing clear age-dependent shifts. Juveniles were dominated by Bacillota (high B/B value), consistent with adaptation to a milk-based, protein- and lactose-rich diet, whereas adults shifted toward Bacteroidota dominance (low B/B value), with relative abundance increasing from 39.53% to 64.92%, reflecting enhanced polysaccharide and fiber degradation, thereby providing microecological support for adaptation to low-energy, high-fiber desert vegetation resources. Alongside this transition, α-diversity significantly increased with age, while β-diversity patterns shifted from dispersed to clustered, indicating a more complex, stable, and mature gut community. Over 58% of predicted genes were assigned to metabolic pathways, highlighting the essential contribution of gut microbes to herbivore digestion. Polysaccharide lyases, enriched in adults and subadults, were positively correlated with Bacteroidota abundance, highlighting their central role in fiber degradation and stable energy supply, thereby supporting adaptation to arid desert habitats. In contrast, juveniles were characterized by enrichment of the galactose metabolism pathway, high abundance of Pseudomonadota (LEfSe LDA > 4), and the largest number of antibiotic resistance genes (AROs), including 17 potential key AROs, reflecting greater microbial plasticity and higher environmental exposure risks during early development. This study provides the first systematic characterization of age-related gut microbiome dynamics and functional adaptations in the endangered Mongolian wild ass, offering novel insights into microbial contributions to host energy optimization and resilience in arid ecosystems, with implications for conservation strategies.},
}

@article {pmid41040874,
year = {2025},
author = {Zheng, M and Zhong, C and Pan, G and Xie, J and Zhang, S and Jin, J},
title = {Insights into microbiome-triterpenoid correlation in Poria cocos via comparative analysis of sclerotial and soil microenvironments.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1674216},
pmid = {41040874},
issn = {1664-302X},
abstract = {INTRODUCTION: Poria cocos (P. cocos) is a medicinal fungus renowned for its bioactive triterpenoids, particularly pachymic acid. However, the relationship between its specialized microbiota and the accumulation of this key metabolite remains poorly understood.

METHODS: This study systematically compared the microbial communities and pachymic acid distribution patterns between P. cocos and different soil microenvironments using integrated 16S rRNA/ITS1 sequencing and HPLC-QTOF-MS/MS analysis.

RESULTS: The results revealed significantly lower microbial diversity in P. cocos compared to the surrounding soil, with a dominance of Proteobacteria and Ascomycota, along with specific enrichments of Burkholderia-Caballeronia-Paraburkholderia and Scytalidium. Pachymic acid was found to accumulate predominantly within the sclerotia, with trace amounts detectable in adjacent soils. Significant positive correlations were identified between pachymic acid and these enriched microbial taxa.

DISCUSSION: These findings indicate that P. cocos forms a specialized microenvironment characterized by selective microbial enrichment associated with pachymic acid accumulation, offering valuable insights for optimizing cultivation strategies to improve its medicinal quality.},
}

@article {pmid41040873,
year = {2025},
author = {Sandoval, M and Shah, DD},
title = {Diversity and distribution of amino acid decarboxylase enzymes in the human gut bacteria-a bioinformatics investigation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1616635},
pmid = {41040873},
issn = {1664-302X},
abstract = {Biogenic amines play numerous biological functions that include neuromodulation, maintenance of the gut health and motility, gastric acid secretion, regulation of immune response, cell growth, and gene expression. Therefore, it is crucial to comprehend the potential modulation of these molecules by the human gut microbiota. A primary pathway for the generation of these molecules involves the decarboxylation of amino acids, a process facilitated by enzymes known as amino acid decarboxylases (AADCs). Here, we conducted a bioinformatic analysis to understand diversity and prevalence of AADCs from the most prevalent members of the human gut microbiome. This study aims to understand how human gut microbes generate metabolites that influence health and disease, through specific enzyme activities. Our results indicate that AADCs are most abundant in the prominent gut microbial genera, namely Bacteroides, Parabacteroides, Alistipes, and Enterococcus. Within these, Enterococcus faecalis harbors the most variety of amino acid decarboxylases, potentially playing an important role in driving decarboxylation chemistry in the human gut. Furthermore, among AADCs, arginine decarboxylases are the most common, present in approximately 60% of the frequently found members of the human gut microbiome, followed by aspartate 1-decarboxylases and glutamate decarboxylases. In addition, our sequence analyses of various AADCs demonstrated that a tetrad of amino acids in the PLP binding motif can provide functional identification for AADCs. We hypothesize that the diversity in AADCs and the microbes that harbor them has the potential to alter host metabolic outputs. This could provide a mechanism to use specific changes in microbial genera or species to understand possible metabolite modulations that might influence biological functions. Such studies could lay the groundwork for developing future disease markers or therapeutic interventions.},
}

@article {pmid41040871,
year = {2025},
author = {Zeng, L and Qian, Y and Cui, X and Zhao, J and Ning, Z and Cha, J and Wang, K and Ge, C and Jia, J and Dou, T and Chen, H and Liu, L and Bao, Z and Jian, Z},
title = {Immunomodulatory role of gut microbial metabolites: mechanistic insights and therapeutic frontiers.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675065},
pmid = {41040871},
issn = {1664-302X},
abstract = {The gut microbiota modulates host immunity through a wide array of metabolic products that function as signaling molecules, thereby linking microbial activity with both mucosal and systemic immune responses. Notably, short-chain fatty acids, secondary bile acids, tryptophan-derived indoles, polyamines, and lipid derivatives play pivotal roles in regulating innate and adaptive immune functions via G protein-coupled receptors, nuclear receptors, and epigenetic pathways. These metabolites modulate immune cell differentiation, epithelial barrier integrity, and the resolution of inflammation in a dose- and site-specific manner. Recent advancements in spatial metabolomics, synthetic biology, and nanomedicine have facilitated the spatiotemporal delivery of these immunomodulatory compounds, revealing novel therapeutic avenues for the treatment of inflammatory and autoimmune disorders. This review summarizes the biosynthesis and immunoregulatory functions of key microbial metabolites, highlights the compartmentalized and systemic mechanisms of action, and discusses emerging therapeutic approaches, including postbiotics, engineered probiotics, and receptor-targeting drugs. We also explore the challenges in achieving personalized microbiome-immune modulation and propose future directions integrating multiomics and AI-driven predictive modeling. Understanding the metabolite-immune axis paves the way for novel interventions targeting host-microbe symbiosis.},
}

@article {pmid41040819,
year = {2025},
author = {Han, X and Zhu, J and Zhao, W and Han, Y},
title = {Serum Metabolic and Gut Microbiome Differences in Age-Associated Fragile X Syndrome (FXS) Pediatric Patients May Benefit Clinical Therapy Development.},
journal = {International journal of general medicine},
volume = {18},
number = {},
pages = {5869-5882},
pmid = {41040819},
issn = {1178-7074},
abstract = {BACKGROUND: Fragile X syndrome (FXS) is a rare, genetically based neurodevelopmental disorder characterized by intellectual disability. While previous research has largely focused on its genetic mechanisms, the role of metabolism and the gut microbiome in FXS remains underexplored. This study aimed to investigate age-related metabolic differences in the gut flora and serum metabolites of children with FXS and their associations with clinical behavioral outcomes.

METHODS: A total of 32 children with FXS under 18 years were enrolled and divided into two age groups: younger (3-8 years) and older (8-18 years). Intestinal microbiota composition was analyzed using 16S rDNA gene sequencing, and serum metabolite profiles were assessed via ultra-performance liquid chromatography-mass spectrometry (UPLC-MS). Spearman correlation analysis was used to assess associations among gut flora, serum metabolites, and scores from the Social Responsiveness Scale (SRS) and Child Behavior Checklist (CBCL).

RESULTS: Significant differences in gut bacterial genera and 1,352 serum metabolites were observed between the age groups. The older group exhibited higher levels of phospholipids, steroids, and peptides, and enrichment in the steroid hormone biosynthesis pathway. Several metabolites were significantly correlated with SRS and CBCL scores, indicating potential links between metabolic changes and behavioral symptoms.

CONCLUSION: Age-associated metabolic and gut microbiota alterations in FXS may contribute to variations in clinical presentation. These findings suggest a metabolic basis for FXS and provide a foundation for future research into microbiome-targeted interventions in FXS management.},
}

@article {pmid41040777,
year = {2025},
author = {Multani, HK and Sraa, KK and Abbas, H and Gandhi, S and San Juan, LJ and Pan, EH and Riedel, F and Khan, S},
title = {Climate Change and Pediatric Skin Health: Emerging Threats, Innovations, and Equity Gaps.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e91397},
pmid = {41040777},
issn = {2168-8184},
abstract = {Climate change poses unique dermatologic risks to children due to immature skin barrier function, weakened immune systems, and dependence on caregivers. Under stable environmental conditions, pediatric skin maintains homeostasis through balanced barrier function, microbiome diversity, and immune regulation. The changing climate disrupts these protective mechanisms through rising temperatures, air pollution, ultraviolet (UV) radiation, and adverse weather conditions. Research demonstrates these environmental stressors exacerbate atopic dermatitis (AD), infectious dermatoses, and infestations, all while disproportionately affecting marginalized communities. Current clinical approaches often fail to address the climate-related dimensions of pediatric skin disease, relying on traditional therapies without environmental adaptation. Emerging solutions, such as climate-resilient skincare formulations, teledermatology, and community-based interventions, show promise for more effective management. This review examines the pathophysiological effects of climate change on pediatric skin, evaluates current and emerging care strategies, and identifies critical gaps in the literature. Challenges include limited pediatric-specific climate research, healthcare disparities in vulnerable populations, and inadequate integration of dermatologic concerns into climate policy. Despite these barriers, advances in preventive dermatology and community-based interventions offer opportunities to improve outcomes. Future progress will depend on interdisciplinary efforts to develop climate-adaptive skin care frameworks that protect children's health in a dynamic world.},
}

@article {pmid41040679,
year = {2025},
author = {DeVito, A and Kimm-Drapeau, AL and Higgins, WJ and Montecillo, M and Li, C and Bal, I and Dadhania, DM and Selbach, F and Lee, JR},
title = {Serial Blood Microbiome Profiles in Kidney Transplant Recipients: Evidence of Circulating Gut Bacteria.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.22.25330581},
pmid = {41040679},
abstract = {Innovation in sequencing techniques has enabled the identification of microbiome in low biomass sites. In this study, we sought to investigate the utility of 16S rRNA deep sequencing of whole blood in kidney transplant recipients and to assess a link between the gut microbiota and the blood microbiota. We recruited 63 kidney transplant recipients who provided 163 whole blood specimens over the first 140 days after transplantation. We profiled the blood microbiome using 16S rRNA gene sequencing of the V4-V5 hypervariable region and additionally evaluated the gut microbiota in a subset of kidney transplant recipients who had gut bacteria detected in the blood. We generated a median of 19,959 sequences per blood specimen and found that most whole blood microbiome profiles consisted of mitochondrial DNA. While we did not identify classically pathogenic bacteria in the blood such as Escherichia, Klebsiella , and Enterococcus , we identified 25 gut bacterial taxa at very low levels in the blood of 22 kidney transplant recipients. For 9 of these kidney transplant recipients the same bacterial taxa detected in the blood were also identified in the gut microbiota. Our study is one of the first to show the detection of gut bacterial DNA in the blood of kidney transplant patients.},
}

@article {pmid41040674,
year = {2025},
author = {Narváez Miranda, J and Sohn, MB and Velasquez-Portocarrero, D and Ejiofor, K and Gill, AL and Beblavy, R and Qiu, X and Laniewski, N and Brunner, J and Best, M and Leger, A and Macomber, A and Caddy, SL and Jiang, B and O'Connor, T and Gill, SR and Scheible, K},
title = {Early-life gut microbiome is associated with immune response to the oral rotavirus vaccine in healthy infants in the US.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.22.25336338},
pmid = {41040674},
abstract = {BACKGROUND: Rotavirus remains a leading cause of childhood mortality worldwide, despite the widespread introduction of oral rotavirus vaccines (ORVs). While emerging evidence supports a link between microbiome and vaccine response, findings have been inconsistent, especially across geographic and socioeconomic contexts, and none have been conducted in a US-based cohort. This study investigates the development of the infant gut microbiome and its association with immunogenicity following RotaTeq administration in U.S. infants.

METHODS: We conducted a longitudinal analysis of infants in Rochester, New York, using 16S rRNA sequencing data to assess microbiome composition. We used rotavirus-specific immunoglobulin A (Rotavirus-IgA) titers at the sixth-month study visit (M6) in plasma to determine the seroresponse to vaccination. Clinical metadata were used to evaluate the influence of different factors on microbial diversity over the first year of life and Rotavirus-IgA titers at the M6 visit. Microbiome data from the M1 visit and Rotavirus-IgA at the M6 visit were used to assess the relationship between the infant gut microbiome and ORV immune responses.

FINDINGS: The infant gut microbiome followed characteristic developmental patterns during the first year (N=264). At the M6 visit, 65 infants had a Rotavirus-IgA geometric mean titer of 455, 95% CI:[272-761]. In a sub-cohort that included the complete dataset of immunogenicity and microbiome (N=47), higher alpha diversity at the month 1 (M1) visit was significantly associated with higher Rotavirus-IgA titers at the M6 visit (ß= 2.151, 95% CI:[0.31-3.99], p=0.023). Specific taxa present at the M1 visit, including Collinsella (ß: 0.243, 95% CI:[0.076, 0.392], q= 0.037), Atopobium (ß: 0.262, 95% CI:[0.066, 0.458], q= 0.062), and Schaalia radingae (ß: 0.28, 95% CI:[0.116, 0.458], q=0.018), were positively associated with Rotavirus-IgA titers. In contrast, Bifidobacterium (ß: -0.204,95% CI:[-0.323, -0.085], q=0.012), Lactobacillus (ß: -0.17, 95% CI:[- 0.314, -0.035], q= 0.087), Klebsiella (ß: -0.195, 95% CI:[-0.331, -0.058], q= 0.042), Escherichia-Shigella (ß: - 0.128, 95% CI:[-0.245, -0.012], q= 0.162), Streptococcus salivarius (ß: -0.229, 95% CI:[-0.359, -0.098], q= 0.012), and Peptostreptococcus anaerobius (ß: -0.176, 95% CI:[-0.338, -0.014], q= 0.162) were negatively associated.

INTERPRETATION: In a healthy U.S.-infant cohort, we report a significant association between the early-life infant gut microbiome and RotaTeq-vaccinated infants' Rotavirus-IgA titers. This study contributes to a clearer understanding of microbiome-vaccine interactions, particularly in high-income settings where existing evidence has been limited.

FUNDING: Office of the Director of the National Institutes of Health, National Institute of Mental Health of the National Institutes of Health, and the National Center for Advancing Translational Sciences of the National Institutes of Health.},
}

@article {pmid41040575,
year = {2025},
author = {Liu, X and Zhang, Y and Liu, Q and Hou, C and Xu, L},
title = {A scientometric study on research trends and characteristics of halitosis.},
journal = {Journal of dental sciences},
volume = {20},
number = {4},
pages = {2467-2471},
pmid = {41040575},
issn = {2213-8862},
abstract = {BACKGROUND/PURPOSE: Halitosis is a condition characterized by unpleasant odors originating from the oral cavity. The purpose of this study was to analyze the scientometric characteristics and research trends of halitosis.

MATERIALS AND METHODS: All the papers on halitosis were comprehensively retrieved from the Scopus database. The years of publication were divided into before 2015 and after 2015 in the analysis of research trends.

RESULTS: There were 1252 papers on halitosis, with total citations of 26,932 and the h index of 76. Poor oral hygiene, periodontitis, periodontal disease, gingivitis, dental caries, xerostomia, periodontics, and smoking were halitosis-related conditions. The trend of clinical investigations has changed to prospective study, single blind procedure, tongue coating, complication, sensation, and quality of life after 2015. The trend of treatment, mainly drug therapy such as antiinfective agent, cetylpyridinium salt, chewing gum, zinc, and triclosan before 2015, has changed to photodynamic therapy, plant extract, and probiotic agent after 2015. Moreover, the trend of laboratory investigation has changed to biological marker, genetics, microbiome, and microflora after 2015. There have always been common keywords such as controlled study, mouth hygiene, sulfur compounds, hydrogen sulfide, microbiology, breath analysis, mouthwash, questionnaire, breath tests, and gas chromatography.

CONCLUSION: This scientometric study elucidated the current scenario and research trends of halitosis, and would help in improving in reciprocal collaboration and communication for investigations on this condition.},
}

@article {pmid41040559,
year = {2025},
author = {Chen, TP and Yu, HC and Lin, WY and Chang, YC},
title = {Bidirectional association between obesity and chronic periodontitis: Inflammatory pathways and clinical implications.},
journal = {Journal of dental sciences},
volume = {20},
number = {4},
pages = {2021-2025},
pmid = {41040559},
issn = {2213-8862},
abstract = {Obesity and chronic periodontitis are the prevalent chronic conditions significantly linked through shared common inflammatory and immune mechanisms. This review aimed to synthesize current knowledge on the association between obesity and chronic periodontitis, exploring biological mechanisms, epidemiological evidence, and clinical relevance. Obesity induces systemic low-grade inflammation marked by elevated pro-inflammatory cytokines, altered immune responses, and disrupted adipokine profiles that may influence periodontal inflammation. Conversely, chronic periodontitis, characterized by oral microbial dysbiosis and local inflammation, contributes to systemic inflammatory burden and potentially exacerbates obesity-related complications. Obesity-associated dietary habits further promote pathogenic oral microbiome shifts as well as aggravate periodontal inflammation. Clinically, obese patients frequently exhibit more severe chronic periodontitis and diminished responsiveness to conventional periodontal therapies, highlighting the need for tailored clinical interventions and integrated healthcare approaches. Public health efforts should make dental care easier to access, support teamwork between health professionals, and offer clear education to help manage both obesity and chronic periodontitis. Although researches have advanced significantly, the exact causal mechanisms still remain unclear. Further studies are needed to improve prevention as well as treatment strategies, ultimately reducing the global burden of obesity and chronic periodontitis.},
}

@article {pmid41040284,
year = {2025},
author = {Lefebvre, R and Rousseaux, T and Bendridi, N and Chanon, S and Arquier, D and Humbert, A and Bertocchini, N and Pillot, B and Meugnier, E and Vieille-Marchiset, A and Nawrot, M and Pinteur, C and Ayciriex, S and Loomba, R and Rieusset, J and Caussy, C},
title = {N-acetyl-phenylalanine induces hepatic steatosis in MASLD by disrupting ER-mitochondria calcium coupling and mitochondrial lipid oxidation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.24.678188},
pmid = {41040284},
issn = {2692-8205},
abstract = {BACKGROUND & AIMS: The gut-liver axis and hepatic ER-mitochondria miscommunication (at contact sites called MAMs) are involved in the development of metabolic dysfunction-associated steatotic liver disease (MASLD). We investigated the role of circulating aromatic amino acids (AAA) derived from phenylalanine and tyrosine in MASLD potentially through MAM alterations.

METHODS: We analyzed AAA metabolomic profiles in individuals with and without MASLD and validated findings in a biopsy-proven cohort. The pro-steatogenic effect of MASLD-associated AAAs was validated in vitro using lipid labeling, MAM structural/functional assays, and palmitate-induced respiration. In vivo effects were tested in mice fed with candidate AAAs, and MAM involvement was confirmed by expressing a specific organelle linker in vitro and in vivo .

RESULTS: N-acetyl-phenylalanine (NAPA) was strongly associated with hepatic steatosis and correlated with specific gut microbes. In vitro , NAPA promoted lipid accumulation by impairing ER-mitochondria calcium exchange via a LAT1-dependent electrogenic mechanism, reducing mitochondrial lipid oxidation. Chronic NAPA administration in mice induced steatosis and MAM disruption. Notably, enhancing ER-mitochondria contacts with an organelle linker prevented NAPA-induced steatosis in vitro and in vivo . Additionally, other phenylalanine- and tyrosine-derived AAAs reproduced NAPA's effects, suggesting a class-dependent mechanism.

CONCLUSION: NAPA emerges as a MASLD-promoting metabolite, contributing to hepatic steatosis by disrupting ER-mitochondria calcium coupling and mitochondrial lipid oxidation.

LAY SUMMARY: The gut-liver axis is a key component of the development of MASLD, and circulating gut-derived metabolites, notably AAAs derived from phenylalanine and tyrosine metabolism, have been associated with MASLD. However, the specific causal mechanisms of these AAA metabolites in MASLD development remain unexplored. Here, we identified NAPA, a gut microbiome linked metabolite elevated in MASLD patients, as a causal driver of hepatic steatosis both in vitro and in vivo. Mechanistically, NAPA alters ER-mitochondria calcium coupling leading to reduced mitochondrial lipid oxidation, highlighting a new mechanism with potential therapeutic implications.

HIGHLIGHTS: - Circulating NAPA levels are increased in MASLD patients and correlate with hepatic steatosis.- NAPA levels result from a complex host-microbiota interplay- NAPA induces lipid accumulation by dampening ER-mitochondria calcium coupling and mitochondrial lipid oxidation.- NAPA disrupts MAMs by a LAT1-mediated electrogenic mechanism.- Other Phe- and Tyr-mediated metabolites have the same pro-steatogenic effect than NAPA pointing to a class-dependent effect.},
}

@article {pmid41040224,
year = {2025},
author = {Ekalle, G and York, S and Gerard, M and Kerr, J},
title = {Association Between Vaginal Community States and Preeclampsia Status in Pregnant Individuals.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.18.677097},
pmid = {41040224},
issn = {2692-8205},
abstract = {Preeclampsia (PE) is a severe pregnancy complication affecting 3-8% of pregnancies. Recent evidence suggests the vaginal microbiome may influence PE risk. To investigate this, we reanalyzed publicly available 16S rRNA sequencing data (PRJNA798597) from vaginal samples of pregnant women with (n=10) and without PE (n=10) and assigned vaginal community state types which were previously uncharacterized. Overall microbial diversity did not differ significantly between groups; however, subtype differences in Lactobacillus spp. were observed. D-lactic acid-producing vaginal community state types were less common in PE, suggesting potential value for microbiome-based risk assessment.},
}

@article {pmid41040189,
year = {2025},
author = {Hansen, SC and Hamm, CW and Weaver, CT and Gray, MJ},
title = {Probiotic biogeography and sepsis prevention in the neonatal intestine.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.09.26.678848},
pmid = {41040189},
issn = {2692-8205},
abstract = {UNLABELLED: Neonatal infection is one of the leading causes of neonatal morbidity and mortality worldwide, particularly in those born prematurely or with low birth weight. Probiotic bacteria have been demonstrated to protect against the development of neonatal intestinal dysbiosis and are widely used in peri- and post-natal clinical settings. However, formulations and efficacy are highly variable, highlighting a critical gap in the current understanding of the mechanistic underpinnings of successful probiotic interventions in this population. Furthermore, current studies on probiotic efficacy largely rely on indirect or relative readouts of intestinal bacterial burden. Herein, we directly mapped the biogeography of intestinal colonization and quantify the probiotic effects of Escherichia coli Nissle 1917 (EcN) and Ligilactobacillus murinus strain V10 against Klebsiella pneumoniae dysbiosis across the span of the neonatal murine intestine. Despite substantial differences in biogeography within the intestine, both EcN and L. murinus V10 significantly reduced K. pneumoniae colonization and mortality from K. pneumoniae sepsis, with EcN doing so much more robustly. EcN's probiotic effect was partially dependent on its ability to respire oxygen. Contrary to the dominant paradigm and practice in the probiotic field, combining multiple probiotic strains did not necessarily increase efficacy. Simultaneous treatment with EcN and L. murinus V10 was less effective than EcN treatment alone at preventing death from sepsis. These results highlight important variables which must be taken into account in the design of effective future probiotic intervention strategies.

IMPORTANCE: In this work we use a mouse model of late-onset neonatal sepsis (LOS) to rigorously test fundamental assumptions that underlie the current paradigm for understanding the impact of probiotics on intestinal disease. We demonstrate that two distantly related probiotic bacteria (Escherichia coli Nissle 1917 and Ligilactobacillus murinus V10) can each effectively reduce both intestinal colonization and death caused by the LOS pathobiont Klebsiella pneumoniae , acting by distinct ecological and molecular mechanisms. Our results provide new evidence that will be critical for designing and implementing safe and effective probiotic treatment regimens for LOS, a devastating and difficult to treat disease. More broadly, our results show that ecological principles are key to understanding how interventions that modulate the gut microbiome work, and that some of the assumptions underlying current interventions need to be reevaluated, especially when it comes to combining multiple probiotic strains and species.},
}

@article {pmid41039986,
year = {2025},
author = {Crevecoeur, S and Phillips, L and Zastepa, A and Comte, J and Diep, N and Dove, A and Edge, T and Frenken, T and McKay, RM and Waston, SB},
title = {Spatio-Temporal Resolution of Microbial Functions and Taxa Associated With Cyanobacterial Harmful Algae Blooms Along a 500-Km Aquatic Continuum in the Lake Erie Watershed.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70183},
doi = {10.1111/1462-2920.70183},
pmid = {41039986},
issn = {1462-2920},
support = {//Canada's Genomics Research and Development Initiative/ ; //Canada's Great Lake Protection Initiative (GLPI)/ ; RGPIN-2019-03943//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 1P01ES02328939-01//Great Lakes Center for Fresh Waters and Human Health supported by the National Institute of Environmental Health Sciences (NIEHS)/ ; OCE-1840715//National Science Foundation/ ; },
mesh = {*Lakes/microbiology ; *Cyanobacteria/genetics/classification/growth & development/isolation & purification ; *Harmful Algal Bloom ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rivers/microbiology ; Microcystins ; Seasons ; Bacteria/classification/genetics/isolation & purification ; Spatio-Temporal Analysis ; },
abstract = {Biogeochemical processes rendered by the aquatic microbiome could influence the development of cyanobacterial harmful algal blooms (cHABs), but those biotic factors are poorly understood and rarely considered. We focused on the link between microbial functions, community composition and environmental gradients along the Thames River-Lake St. Clair-Detroit River-Lake Erie corridor across different seasons. We measured the abundance and expression (transcripts) of genes involved in nutrient cycling and microcystin toxin production with qPCR and determined microbial community composition with high-throughput sequencing of the 16S rRNA gene. Throughout the year, genes and transcripts involved in P acquisition, denitrification and N fixation were in higher abundance upstream in the Thames River and Lake St. Clair. Gene abundance, rather than expression, correlated with environmental variables, but functional changes were linked to changes in the aquatic microbiome and did not respond directly to larger environmental gradients. Network analysis revealed tighter connections between gene expression and biotic variables than gene presence, with ubiquitous and streamlined-genomes microbes associated with the dominant bloom-causing cyanobacteria, highlighting the cooperative dynamic of these associations. Overall, the results highlight the link between the changing microbiome, microbial processes and the watershed influence in the presence of cHABs.},
}

*Lakes/microbiology
*Cyanobacteria/genetics/classification/growth & development/isolation & purification
*Harmful Algal Bloom
*Microbiota
RNA, Ribosomal, 16S/genetics
Rivers/microbiology
Microcystins
Seasons
Bacteria/classification/genetics/isolation & purification
Spatio-Temporal Analysis

@article {pmid41039843,
year = {2025},
author = {Hui-Beckman, JW and Goleva, E and Leung, DYM},
title = {Predictive biomarkers for atopic dermatitis.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {36},
number = {10},
pages = {e70215},
doi = {10.1111/pai.70215},
pmid = {41039843},
issn = {1399-3038},
mesh = {Humans ; *Dermatitis, Atopic/diagnosis/metabolism/immunology ; *Biomarkers/metabolism ; *Skin/immunology/metabolism ; Cytokines/metabolism ; Child ; Microbiota ; },
abstract = {The discovery of early-life preclinical biomarkers for atopic dermatitis (AD) is an important area of research to prevent AD development and introduce treatment measures early to reduce AD severity. Birth cohort studies performed worldwide have given insights into skin barrier components, such as lipids and proteins, cytokine immunologic markers, and microbiome alterations that are present prior to the clinical diagnosis of AD. This article reviews the structure of the skin barrier and the early-life biomarkers that are present in children at risk for AD.},
}

Humans
*Dermatitis, Atopic/diagnosis/metabolism/immunology
*Biomarkers/metabolism
*Skin/immunology/metabolism
Cytokines/metabolism
Child
Microbiota

@article {pmid41039628,
year = {2025},
author = {Schols, R and Hammoud, C and Bisschop, K and Vanoverberghe, I and Huyse, T and Decaestecker, E},
title = {Schistosome species, parasite development, and co-infection combinations determine microbiome dynamics in the snail Biomphalaria glabrata.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {101},
pmid = {41039628},
issn = {2524-4671},
support = {B2/191/P1/MicroResist//Belgische Federale Overheidsdiensten/ ; PDMT2/24/045//KU Leuven/ ; 12T5622N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: Schistosomiasis is a snail-borne disease affecting over 200 million people worldwide. Despite dedicated control efforts and effective diagnostic tools, schistosomiasis remains prevalent. Novel and sustainable control measures are urgently needed. Bacteria might offer such a solution as links between bacteria, disease resistance and transmission potential of intermediate hosts have been established in other systems. To better understand the tripartite interaction potentially driving snail-schistosome compatibility patterns, microbial communities must be investigated throughout and across various parasite exposure conditions. Therefore, we studied Biomphalaria glabrata snails exposed to a high- and low-shedder population of Schistosoma mansoni and Schistosoma rodhaini in single and co-exposure experiments. Snails were sacrificed at different time points post-exposure and their bacterial communities and trematode (co-)infection status were determined through metabarcoding tools.

RESULTS: Snails infected by low- and high-shedder S. mansoni populations were more likely to have bacterial community dysbiosis than those infected by S. rodhaini but this was also affected by miracidial load. Moreover, the single-infection hierarchical effect on the bacterial component of the microbiome is not maintained under co-infection with S. rodhaini, which appears to stabilize the snail's bacterial profile even after being outcompeted by high-shedder S. mansoni. Finally, alpha diversity differed significantly between infected and uninfected snails around the onset period of shedding at 30 days post-miracidial exposure.

CONCLUSION: The timing of this bacterial shift suggests an intricate parasite-snail interaction around key parasite development moments. Future studies investigating the tripartite interaction are advised to consider the effect of outcompeted or prepatent infections on the snail's microbiome.},
}

@article {pmid41039566,
year = {2025},
author = {Wei, XY and Feng, HJ and Zhu, YY and Guo, SJ and Wang, H and Li, M and Mei, Q},
title = {The immune microenvironment of pathogen-associated cancers and current clinical therapeutics.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {232},
pmid = {41039566},
issn = {1476-4598},
support = {202303021221191//Shanxi Provincial Basic Research Program/ ; },
mesh = {Humans ; *Tumor Microenvironment/immunology/drug effects ; *Neoplasms/etiology/therapy/immunology/pathology ; Animals ; Immunotherapy/methods ; *Host-Pathogen Interactions/immunology ; },
abstract = {Pathogen-associated cancers account roughly 15-20% of all malignancies worldwide and arise from chronic infections by oncogenic viruses, bacteria and parasites. Pathogens can alter the tumor microenvironment (TME) into an immune-suppressive niche using multiple mechanisms, including immune checkpoint manipulation, chronic inflammation, metabolic reprogramming, and direct epigenetic modifications. Immune dysfunctions related to infections linked to cancers can include M2-polarized macrophages, expansion of MDSCs, exhausted T/NK cells, and tolerogenic dendritic cells, all progressing immune evasion and resistance to cancer therapy. Advances in therapeutics exist in prophylactic vaccines, immune checkpoint inhibitors, and next-generation methods such as the engineered Salmonella to deliver to hypoxic tumors and the targeting the microbiome. The advancement of pathogen-, cancer-, and patient-specific therapeutics is not without its challenges, including heterogeneity of the pathogens, absence of clinically useful biomarkers, concerns about the safety of the restoring anti-pathogen immunity and challenges of scale for manifold interventions. This review will provide a synthesis of the mechanistic aspects of pathogen-mediated TME remodeling, contemporary clinical therapeutics, and ongoing investigations into using pathogen/host dynamics to enhance measurable precision immunotherapy strategies.},
}

Humans
*Tumor Microenvironment/immunology/drug effects
*Neoplasms/etiology/therapy/immunology/pathology
Animals
Immunotherapy/methods
*Host-Pathogen Interactions/immunology

@article {pmid41039548,
year = {2025},
author = {Luo, D and Chen, Q and Li, Y and Yang, J and Tao, Y and Ji, L and Gong, X},
title = {Microbiome-metabolome interplay in pancreatic cancer progression: insights from multi-omics analysis.},
journal = {Molecular cancer},
volume = {24},
number = {1},
pages = {240},
pmid = {41039548},
issn = {1476-4598},
support = {2024JK2111//Key Research and Development Program of Hunan Province of China/ ; },
mesh = {Humans ; *Pancreatic Neoplasms/metabolism/pathology/microbiology/etiology ; *Metabolome ; *Metabolomics/methods ; Disease Progression ; *Microbiota ; Male ; Female ; Metabolic Networks and Pathways ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Aged ; Multiomics ; },
abstract = {BACKGROUND: Recent studies suggest that intratumoral microbiome and altered metabolic networks play crucial roles in pancreatic cancer (PC) progression. However, the precise interplay between microbial communities and tumor metabolism in PC remains poorly understood. This study aims to investigate the impact of the intratumoral microbiome, the metabolic landscape, and their interactions on PC development.

METHODS: 16S rDNA sequencing and Untargeted metabolomic profiling were performed on 47 paired pancreatic cancer and adjacent normal tissues to analyze their intratumoral microbiome and metabolic landscapes. Bioinformatics tools were used to conduct differential microbiome abundance analysis and pathway enrichment. A correlation analysis was performed to identify key microbiota-metabolite interactions.

RESULTS: 16S rDNA sequencing revealed significant differences in the abundance and diversity (α-diversity and β-diversity) of the intratumoral microbiome in PC. The predominant species in pancreatic cancer were Pseudomonas. Enrichment analysis showed that amino acid metabolic pathways, including Arginine and Proline Metabolism, Arginine Biosynthesis, were significantly enriched in PC. Untargeted metabolomics identified 298 metabolites that were significantly altered in PC (fold change > 1.5, P-value < 0.05). These included amino acid metabolites such as Lys-Leu, Pro-Leu, Arg-Leu, Lys-Val, His-Lys, and others. Functional enrichment analysis highlighted several metabolic pathways that play important roles in pancreatic cancer, including Glycine, Serine, and Threonine Metabolism, Amino Acid Biosynthesis, Metabolic Pathways and Cysteine and Methionine Metabolism. Correlation analysis between microbiome and metabolic data revealed significant associations between Pseudomonas and several metabolites, including Alpha-ketoisovaleric acid, 16-hydroxyhexadecanoic acid, Myristic acid, Nonanoic acid (the Spearman correlation coefficient r, 0.5 ≤|r|≤ 1 and P-value < 0.05).

CONCLUSION: This study suggests a relationship between the microbiome and metabolism in pancreatic cancer. We observed that Pseudomonas contributes to altered amino acid metabolism, but whether this interaction is causal and the mechanisms underlying it remain unclear. Further experimental validation is required before considering microbiome-targeted metabolic interventions as viable therapeutic strategies.},
}

Humans
*Pancreatic Neoplasms/metabolism/pathology/microbiology/etiology
*Metabolome
*Metabolomics/methods
Disease Progression
*Microbiota
Male
Female
Metabolic Networks and Pathways
Computational Biology/methods
RNA, Ribosomal, 16S/genetics
Middle Aged
Aged
Multiomics

@article {pmid41039515,
year = {2025},
author = {Kanika, NH and Ke, J and Mandal, RN and Guo, ZY and Cai, SL and Hou, X and Chen, XW and Wang, J and Wang, CH},
title = {Black-spot linked gut microbiota shifts in Oujiang color carp: insights from TYR knockout and metabolomic integration.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {102},
pmid = {41039515},
issn = {2524-4671},
support = {32172959//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Growing insights into gut microbiota reveal their surprising role in shaping external traits in fish, including the regulation of skin pigmentation. This study explores whether black-spot pigmentation influences the abundance of gut microbiota. We investigate how black-spot pigmentation in Oujiang color common carp shapes gut microbiome composition, gene expression, and metabolite, revealing a coordinated gut-skin color axis. To validate these findings, we used a TYR knockout group, which included both mutant black-spotted (TYR [+/-]) and non black-spotted (TYR [-/-]) fish, enabling functional comparison across pigmentation phenotypes.

RESULTS: We demonstrate that black-spotted (RB and WB) fish groups contained less total microbiome composition among them. We observed significant differences in microbiota composition, with genera such as Acinetobacter, Bacillus, and Staphylococcus being more less abundant in wild black-spotted (RB and WB) groups. Gene expression profiling revealed significant differential regulation, with 27 genes markedly upregulated in the black-spotted group. Interestingly, we identified RAB9B, JUN, EGR1, PURB, HS2ST1, and ARL8 as key genes functionally correlated with the gut microbiome and metabolite profiles. Notably, Xanthine metabolites were significantly upregulated in RB and WB groups, highlighting a strong connection to purine metabolism. These genes are primarily involved in tyrosine signaling transduction, the immune system, and metabolic pathways. In parallel, blood metabolomic analysis identified 3 significantly elevated metabolites associated with nucleotide, amino acid, and lipid metabolism. Furthermore, 9 lipid-derived nutrients from muscle tissue were significantly upregulated in the black-spotted group, underscoring a strong link between pigmentation phenotype and systemic metabolic alterations. To support this, knocking out TYR converted black-spotted fish to a white phenotype and showed total microbiome profiles, 5 selective bacterial taxa, and 4 consistently expressed genes that mirrored those of wild-type black-spotted fish. Moreover, human gut microbiome data showed Bacillus and Pseudomonas were less abundant in black skin populations, reflecting patterns seen in fish.

CONCLUSIONS: Our results draw a root map to uncover a potential gut-skin-color axis, where black-spot pigmentation not only marks external phenotypic variation but also aligns with distinct microbial signatures.},
}

@article {pmid41039491,
year = {2025},
author = {Song, J and Yang, X and Liu, X and Li, J},
title = {Gut bacteria: protective mediators, pathogenic contributors and novel therapeutic targets in Candida albicans infections.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {77},
pmid = {41039491},
issn = {1757-4749},
support = {24QNMP087//Health Commission of Sichuan Province Medical Science and Technology Program/ ; 24QNMP087//Health Commission of Sichuan Province Medical Science and Technology Program/ ; 24QNMP087//Health Commission of Sichuan Province Medical Science and Technology Program/ ; 24QNMP087//Health Commission of Sichuan Province Medical Science and Technology Program/ ; 2024ZYD0146//Central Government-Directed Project for Local Science and Technology Development/ ; 2024ZYD0146//Central Government-Directed Project for Local Science and Technology Development/ ; 2024ZYD0146//Central Government-Directed Project for Local Science and Technology Development/ ; 2024ZYD0146//Central Government-Directed Project for Local Science and Technology Development/ ; Q2024024//The Sichuan Medical Association Youth Innovation Project/ ; Q2024024//The Sichuan Medical Association Youth Innovation Project/ ; Q2024024//The Sichuan Medical Association Youth Innovation Project/ ; Q2024024//The Sichuan Medical Association Youth Innovation Project/ ; },
abstract = {Candida albicans is an opportunistic pathogen that resides in the human gut alongside a diverse array of microorganisms, including enteric bacteria, archaea, and viruses, which collectively form the gut microbiota. Recent studies have shown that the development of Candida albicans infections involves both weakened host immunity and enhanced invasiveness of Candida albicans, with intestinal microecology serving as a critical mediator of these processes. It has been demonstrated that disturbances in the gut microbiome can potentiate the invasive capacity of Candida albicans. Moreover, a compromised immune system, along with the use of antibiotics and immunosuppressive drugs, can lead to gut microbiome imbalances. Consequently, modulators of the intestinal microecology represent promising therapeutic interventions for managing Candida albicans infections. In this review, we examine the mechanisms underlying the increased invasiveness of Candida albicans following significant disruption of intestinal bacteria and highlighting the interplay among immune dysfunction, antibiotic use, and their effects on gut microbiome imbalance and Candida albicans infection. Additionally, we summarize the roles of microbiome-based therapies, such as probiotics, prebiotics, dietary interventions, and fecal microbiota transplantation (FMT), in addressing Candida albicans infections. This review provides a theoretical foundation and practical guidance for the development of more effective microecological therapeutic strategies in the future.},
}

@article {pmid41039273,
year = {2025},
author = {Phan, A and Thapa, K and Hashmi, MA and Mohapatra, A and Ho, G and Tholan, GN and Biswas, D},
title = {Prophylactic efficacy of probiotics and their metabolites against Staphylococcus epidermidis.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {621},
pmid = {41039273},
issn = {1471-2180},
support = {2018-5110628809//USDA-National Institute of Food and Agriculture/ ; 2018-5110628809//USDA-National Institute of Food and Agriculture/ ; 2018-5110628809//USDA-National Institute of Food and Agriculture/ ; },
abstract = {BACKGROUND: Staphylococcus epidermidis is a prevalent common microorganism found on the skin of most mammals, including humans. However, S. epidermidis is also known as an opportunistic pathogen that can cause diseases if the skin microbiome becomes skewed to favor its overgrowth. This situation can be worsened if the causative strains are antibiotic-resistant. To explore potential alternatives to replace conventional antibiotics, we aim to use probiotics, specifically Lacticaseibacillus rhamnosus and Lactiplantibacillus plantarum, in controlling the growth, colonization, and biofilm formation of a multidrug-resistant S. epidermidis.

RESULTS: Multidrug-resistant S. epidermidis was co-cultured with either L. rhamnosus or L. plantarum, and antimicrobial activity was assessed by counting S. epidermidis colonies at various timepoints. Under co-culture conditions, growth of S. epidermidis was decreased over time in the presence of either probiotic, specifically, a significant reduction was observed after 48 hours (p=0.0062). Additionally, S. epidermidis was treated with cell-free culture supernatant (CFCS) collected from probiotics to investigate the mechanism of inhibition. CFCS from 72-hour Lactobacilli cultures significantly inhibited S. epidermidis growth within 4 hours (p<0.05), and no S. epidermidis was detected after 72 hours (p=0.0003) when treated with 50% CFCS. Both CFCSs also reduced biofilm formation and bacterial counts after 24 hours, with complete inhibition by 48 h. Gene expression analysis revealed that exposure to CFCS led to downregulation of S. epidermidis genes associated with metabolism and cell division (arcC, gts, mutS, mur1, and ftsZ). Fluorescence microscopy indicated compromised cell wall integrity, evidenced by reduced HADA fluorescence and increased propidium iodide staining.

CONCLUSION: L. plantarum and L. rhamnosus possess strong antimicrobial activity against multidrug-resistantS. epidermidis, supporting their potential as alternative strategies to control S. epidermidis colonization.},
}

@article {pmid41039272,
year = {2025},
author = {Cao, Z and Wang, D and Cui, Y and Huang, F and Liu, Y and Dai, J and Wu, W and Dai, Z and Xie, J and Zhu, X and Hu, X and Xu, Y},
title = {Diet, nutrient characteristics and gut microbiome between summer and winter drive adaptive strategies of East China sika deer (Cervus nippon kopschi) in the Yangtze River basin.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {626},
pmid = {41039272},
issn = {1471-2180},
support = {32470552//National Natural Science Foundation of China/ ; 20242BAB25349//Natural Science Foundation of Jiangxi Province/ ; },
abstract = {BACKGROUND: Adaptation of species represents the outcome of interactions between organisms and their environment, as well as a product of natural selection and evolution.

METHOD: To elucidate how East China sika deer in TNNR respond to seasonal climatic selection pressures in the mid-lower Yangtze River basin, we investigated their seasonal adaptive strategies via analyses of dietary nutrition and the gut microbiome, using high-throughput sequencing of the trnL P6-loop of chloroplast and 16S rRNA.

RESULTS: In summer, sika deer consumed 174 plant species belonging to 183 genera and 107 families, exhibiting pronounced dietary generalization. Conversely, in winter, they fed on 130 species from 173 genera and 90 families, characterized by dietary specialization. The nutritional composition and availability of plants differed between the two seasons, driven by seasonal changes, which led to corresponding adjustments in foraging strategies. Notably, sika deer maintained a stable balance in nutrient intake across seasons. and industrialization of sika deer breeding in eastern China, whereas α-diversity was higher in winter. Microbiota in both seasons exhibited distinct correlations with consumed plant species and nutrients, but their microbial functions were predominantly enriched in metabolic processes. This pattern indicates that sika deer can flexibly reshape the structural and interaction networks of gut microbiota to enhance adaptive capacity to seasonal shifts. Overall, we demonstrated seasonal dynamics and provided new insights into understanding the diet diversity and nutrition components associated with gut microbiota in the adaptation of sika deer. These results will further facilitate genetic resource conservation, habitat improvement, food plant breeding, wild rescue, and industrialization of sika deer breeding in eastern China.},
}

@article {pmid41039266,
year = {2025},
author = {Tavanaeian, S and Feizabadi, MM and Falsafi, S and Aghdaei, HA and Houri, H},
title = {Oral and fecal microbiome alterations in pancreatic cancer: insights into potential diagnostic biomarkers.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {624},
pmid = {41039266},
issn = {1471-2180},
}

@article {pmid41039241,
year = {2025},
author = {Kang, C and Lee, J and Baek, MG and Kim, NE and Son, H and Yoo, S and Yi, H},
title = {Urinary microbiome in non-muscle invasive bladder cancer: impact of sample types and sex differences.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {623},
pmid = {41039241},
issn = {1471-2180},
support = {2022R1A2C1007966//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Previous research on urinary microbiomes in bladder cancer patients has yielded inconsistent results, highlighting the need for further investigation. This study aims to analyze microbiome dysbiosis in bladder cancer patients by comparing multiple sample types, incorporating negative controls, and assessing sex-based variations. Fifty patients who required transurethral resection of bladder tumor for treatment were selected. Three types of specimens were collected from each patient: midstream urine, catheterized urine, and normal bladder mucosal tissue. Microbiome was analyzed via 16 S rRNA gene amplificon sequencing.

RESULTS: Beta diversity analysis revealed significant differences in microbiome composition between mucosal tissue and urine samples, while no significant variation was observed between midstream and catheterized urine samples. Due to the low biomass of mucosal tissue-characterized by dominance of a few taxa and high variability across extraction kit lots-its susceptibility to contamination compromised reproducibility, leading to a focus on urine samples for further analysis. Midstream urine samples showed significant sex-related microbiome differences, whereas catheterized urine exhibited no such differences, suggesting midstream urine may not be ideal for bladder-specific microbiome studies. Catheterized urine analysis identified Curvibacter, particularly Curvibacter gracilis, as significantly more abundant in bladder cancer patients compared to controls, while overall microbiome composition remained unchanged between the groups. Curvibacter prevalence was not directly correlated with any single clinical marker but increased with bladder cancer severity when patients were classified into high-risk and low-risk groups based on biopsy and clinical criteria.

CONCLUSIONS: This study highlights the importance of selecting appropriate sample types for bladder microbiome analysis, with catheterized urine emerging as the most reliable option. The findings suggest that Curvibacter may be associated with bladder cancer severity, warranting further investigation into its potential role as a biomarker. Future research should focus on validating these findings in larger cohorts and exploring the mechanistic link between microbiome alterations and bladder cancer progression.},
}

@article {pmid41039239,
year = {2025},
author = {Li, C and Ji, Y and Li, X and Cai, J and Ye, J and Wu, Y and Liao, Q and Wang, Z and Sanganyado, E and Li, P and Sun, Y and Liang, B and Liu, W},
title = {Vibrio spp.: a potential critical pathogen for mammals with implications beyond marine aquaculture.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {598},
pmid = {41039239},
issn = {1471-2180},
support = {4200615//STU Scientists of China/ ; 4200615//National Science Foundation for Young Scientists of China/ ; GDNRC[2022]48//Key Program of Marine Economy Development (Six Marine Industries) Special Foundation of the Department of Natural Resources of Guangdong Province/ ; },
abstract = {BACKGROUND: Species-specific or health status specific microbiome composition of cetaceans is still poorly classified due to the limited samples. Despite a partial identification of the gut microbiota of melon-headed whales (Peponocephala electra), comparative analyses across anatomical systems are lacking. This study provides the first comprehensive analysis of the microbial communities habiting nine body sites - oral cavity, esophagus, foregut, midgut, hindgut, blowhole, and skin wounds (left anterior, dorsal fin, tail) - in a stranded melon-headed whale.

RESULTS: By 16 S rRNA gene sequencing, a decrease in microbial richness was observed from the oral cavity to the hindgut, accompanied by compositional shifts from Fusobacterium-dominated oral/esophageal niches to Vibrio-enriched gastrointestinal regions (21.81% Vibrio, 21.19% Fusobacterium, 12.50% Actinobacillus). The respiratory tract microbiota underwent a significant shift and was dominated by Ostreibacterium (57.5%), Helcococcus (6.59%), and Tenacibaculum (4.12%). Skin wounds showed environmental similarities, with Vibrio (47.84%), Pseudoalteromonas (17.84%), and Psychrobacter (12.36%). Pan-microbiome screening identified seven Vibrio species (V. alginolyticus, V. cidicii, V. cyclitrophicus, V. navarrensis, V. parahaemolyticus, V. salilacus, and V. splendidus) across all niches, along with V. cholerae in non-respiratory samples. Notably, V. profundi was exclusively localized to anterior and dorsal fin wounds. Functional profiling revealed enrichment of Vibrio-linked pathogenesis pathways (infection, pathogenic cycle) and metabolic modules that were correlated with immunocompromised states.

CONCLUSIONS: This study revealed significant bidirectional environment-host microbiome exchange dynamics across cetacean mucosal surfaces. Notably, Vibrio spp. emerged as the dominant genus in both gastrointestinal and cutaneous wound microbiomes, highlighting: (1) potential zoonotic transmission risks from pathogenic Vibrio strains, and (2) the critical need for habitat-specific microbial surveillance to inform marine mammal conservation strategies.},
}

@article {pmid41039235,
year = {2025},
author = {Ahmad, S and Wang, M and Zhang, H and Deng, Y and Liang, Q and He, B and Wen, R},
title = {Synergistic application of biochar and lime modulates rhizosphere microbiome, suppresses pathogens, and enhances disease resistance in sugarcane.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {622},
pmid = {41039235},
issn = {1471-2180},
support = {GuiKeNongAB24153009//Guangxi Key R&D Plan/ ; 2025GXNSFAA069449//Guangxi natural science foundation/ ; },
abstract = {Soil acidification disrupts microbial communities and exacerbates plant disease susceptibility in agriculture. This study demonstrates that combined application of biochar (15 t ha[-1]) and lime (1.5 t ha[-1]) in acidic sugarcane fields significantly elevates soil pH (up to 46.7%) and organic carbon (SOC), driving profound restructuring of the rhizosphere microbiome. High-throughput sequencing revealed suppression of potentially pathogenic bacteria (Solirubrobacteraceae, Acidothermus, Gaiella) and fungi (Curvularia, Scytalidium, Myrothecium), alongside qPCR-confirmed reduction in Fusarium abundance. Concurrently, we observed significant enrichment of beneficial taxa including plant-growth-promoting bacteria (Sinomonas, Bacillus, Brevibacillus, Micromonospora, Filomicrobium, OLB13, Arenimonas) and fungi (Trichoderma, Aspergillus, Talaromyces, Penicillium, Taifanglania, Redeckera). FUNGuild analysis confirmed decreased relative abundance of fungal plant pathogen guilds, particularly under the combined treatment. Redundancy analysis identified pH, SOC, and acid phosphatase as key environmental drivers of microbial assembly. These microbiome shifts correlated with enhanced plant defense responses: increased phenylalanine ammonia-lyase and superoxide dismutase activities, reduced malondialdehyde content, and significantly suppressed pokkah boeng disease incidence (82.57% reduction) and severity. Our findings establish that biochar-lime synergy ameliorates soil constraints, functionally modulates the rhizosphere microbiome to suppress pathogens, and systemically enhances plant immunity, providing a sustainable strategy for managing soil-borne diseases in acidified agroecosystems.},
}

@article {pmid41039214,
year = {2025},
author = {Cortez-Martínez, M and Medrano-Lozano, J and Blanco-Peña, K and Quesada-Alvarado, F and Solano-Campos, F},
title = {Seasonal and spatial dynamics of the intestinal microbiome in tropical freshwater fish: insights from Astyanax aeneus and Brycon costaricensis in the Peñas Blancas river basin, Costa Rica.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {595},
pmid = {41039214},
issn = {1471-2180},
abstract = {BACKGROUND: The intestinal microbiome plays a crucial role in fish development and health, facilitating essential functions such as nutrient uptake, immune system response, and disease resistance. However, the microbial communities of Neotropical freshwater fish, such as Astyanax aeneus and Brycon costaricensis, remain largely unexplored. Understanding how microbiomes vary in relation to environmental gradients is key to identifying potential sentinel species for ecosystem monitoring. To understand the dynamics of bacterial diversity and community structure, we collected intestinal content samples from 165 individuals of both species from six points along the Peñas Blancas river basin, Costa Rica, during the dry and rainy seasons and during an intermediate period.

RESULTS: Metabarcoding analysis of the 16 S rRNA gene revealed that the intestinal microbial communities of both species were dominated primarily by the genera Cetobacterium, Clostridium, Romboutsia and Plesiomonas. No significant differences were detected in the relative abundance of taxa, metabolic pathways or community structure between the two species and only at the Dam site, a significant increase in the Shannon index was detected in B. costaricensis. Conversely, distinct differences in microbial network properties were found, with A. aeneus showing a lower clustering coefficient and modularity, a shorter average path length and a greater number of hubs. Site and season influenced the microbial community structure of A. aeneus but not the relative abundance of taxa. Similarly, differentially abundant metabolic pathways, including xenobiotic degradation, were enriched in A. aeneus.

CONCLUSIONS: The similarities in microbiome diversity and structure in both species could arise from parallels in taxonomy, habitat and diet. However, temporal and spatial shifts in the A. aeneus microbial community structure may be associated with sensitivity to changes in environmental stressors such as precipitation, temperature, and runoff. Microbial network analysis revealed that taxa in A. aeneus are more tightly interconnected and form fewer distinct clusters, making it a promising bioindicator for monitoring water quality and anthropogenic impacts.},
}

@article {pmid41039213,
year = {2025},
author = {IJdema, F and Arias-Giraldo, LM and Vervoort, E and Struyf, T and Van den Ende, W and Raaijmakers, JM and Lievens, B and De Smet, J},
title = {Metagenome-based identification of functional traits of the black soldier fly gut microbiome associated with larval performance.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {612},
pmid = {41039213},
issn = {1471-2180},
support = {S008519N//ENTOBIOTA/ ; IMP20028//KU Leuven Impuls grant/ ; C3/22/041//KU Leuven CHITINERY grant/ ; G0C4622N//Fonds Wetenschappelijk Onderzoek/ ; },
abstract = {BACKGROUND: The relationship between microbiomes and their hosts has been the subject of intensive study in recent years. For black soldier fly larvae (BSFL) (Hermetia illucens L., Diptera: Stratiomyidae), correlations between shifts in its microbial gut community composition and its health and performance suggest that the BSFL gut microbiome encodes important functions that complement the insect's own immune system and metabolism. To date, most BSFL microbiome studies have been based on 16S rRNA sequencing data. Because this approach derives a lot of information from very short sequencing reads, it was hypothesized that more insight into bacterial functionality could be generated using more extensive sequencing technologies. Here, whole genome shotgun (WGS) metagenomic sequencing was employed to investigate which microbiome-associated taxa and functions were associated with increased performance of larvae reared on a chicken feed (CF) or artificial supermarket food waste (SFW) based diet.

RESULTS: Taxonomic and functional profiling of the BSFL gut microbiome revealed a significant shift in response to diet, where bacterial genes encoding specific metabolic functions, such as the metabolism of sorbitol, were significantly enriched in the microbiome of larvae reared on SFW-diet. This indicates that the nutritional composition of the substrate alters the gut bacterial composition by providing competitive benefits or new niches for specific bacteria that can utilise these compounds. Moreover, specific microbial functions, such as cobalamin synthesis, appear to be correlated with larval performance. Aside from metabolic functions, biosynthetic gene cluster analysis revealed potential antimicrobial competition and protective functions among bacterial species. Improved taxonomic resolution provided by WGS led to the identification of several metagenome assembled genomes (MAGs), including a potentially novel BSFL-associated Scrofimicrobium species. Furthermore, there were differences in larval performance between rearing diets, and larval growth was correlated with high abundance of several MAGs.

CONCLUSIONS: Variation in the nutritional and bacterial load of a diet can result in functional shifts in the gut microbiome of the larvae. Analysis of the BSFL metagenome identified several bacteria that are positively correlated with larval performance, which could potentially provide beneficial metabolic functions for the host that should be further explored.},
}

@article {pmid41039203,
year = {2025},
author = {Shang, L and Li, F and Wang, Z and Hu, Z and Zou, H and Lu, J and Tang, YZ and Deng, Y},
title = {Cobalt exposure induces the specific associated-bacterial microbiome potentially contributing to cobalt stress alleviation of the host dinoflagellate Scrippsiella acuminata.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {617},
pmid = {41039203},
issn = {1471-2180},
support = {42206215//the National Science Foundation of China/ ; 42406214//the National Science Foundation of China/ ; 42376138//the National Science Foundation of China/ ; },
abstract = {Dinoflagellates grow in tight association with the bacterial community, which exert impacts on the physiology and ecology of both partners. However, the changes of associated-bacterial microbiome with the physiologies of the host dinoflagellate under specific heavy metals (HMs) stress remain largely unknown. In this study, we characterized the bacterial microbiome associated with the laboratory-cultured dinoflagellate Scrippsiella acuminata, a cosmopolitan bloom-forming species, under different cobalt concentrations, via high-throughput sequencing of 16 S rRNA gene amplicons. The sequencing of a total of 72 Libraries generated 6,047,695 reads which were classified into 31 phyla, 97 classes, 215 orders, 367 families, and 782 genera. We found that cobalt stress could greatly affect the growth of S. acuminata as well as the ASV diversity and community composition of the associated bacterial community. Significant dose-dependent changes in the bacterial community were detected, which were found to be closely correlated with some specific bacterial genera. Excessive cobalt exerted significantly inhibitory effects on microalgae growth-promoting bacteria (Marinobacter, Roseobacter, Mameliella, Leifsonia, Roseovarius, and Stappia). A notable increase in the relative abundance of HM-resistant bacteria with siderophore-producing capacity (Alteromonas, Arthrobacter, Pseudoalteromonas, Brevundimonas, Staphylococcus, Microbacterium, and Bacillus) and/or HM bio-removal potential (Corynebacterium, Pseudomonas, Burkholderia, Rhodococcus, and Gemella) was detected upon elevated cobalt concentrations, which potentially contributed to the cobalt stress alleviation of the dinoflagellate host. Our work provided deeper insights into the relationship between the associated-bacterial assemblage and dinoflagellate, and also broadened the current knowledge pertaining to the potential contributions of bacterial microbiome to the HM tolerance of host alga.},
}

@article {pmid41039039,
year = {2025},
author = {da Silva, DMG and Costa, R and Keller-Costa, T},
title = {A genomic view of the bacterial family Endozoicomonadaceae in marine symbioses.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1418},
pmid = {41039039},
issn = {2399-3642},
support = {CEECIND/00788/2017//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020//Ministry of Education and Science | Fundação para a Ciência e a Tecnologia (Portuguese Science and Technology Foundation)/ ; },
mesh = {*Symbiosis ; *Genome, Bacterial ; *Aquatic Organisms/microbiology/physiology ; Genomics ; Phylogeny ; Microbiota ; },
abstract = {Endozoicomonadaceae bacteria are found in association with marine organisms across ocean ecosystems. Interactions may range from mutualistic to parasitic depending on host species and ecological context. Their genomic repertoire suggests metabolic versatility and capacity for rapid adaptation and transitioning between free-living and host-associated lifestyles. Some lineages, however, undergo genome reduction, are host-specific, and lack cultivability. Here we present an advanced genomic perspective and updated view on the functional diversity of Endozoicomonadaceae along the mutualism-parasitism continuum. We discuss their roles in marine symbioses, potential for microbiome engineering, and highlight knowledge gaps of their ecology to be addressed in future research.},
}

*Symbiosis
*Genome, Bacterial
*Aquatic Organisms/microbiology/physiology
Genomics
Phylogeny
Microbiota

@article {pmid41039005,
year = {2025},
author = {Abi Assaf, J and de Coriolis, JC and Godden, AM and Redhead, E and Bartram, J and Cohen-Krais, J and Silova, K and Crighton, Z and Le Gall, G and Sami, S and Khalid, SA and Immler, S},
title = {Gum Arabic modulates the microbiota-gut-brain axis and affects general fitness in zebrafish.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34465},
pmid = {41039005},
issn = {2045-2322},
support = {218467/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; SELECTHAPLOID-101001341/ERC_/European Research Council/International ; NE/S011188/1//Natural Environment Research Council/ ; },
mesh = {Animals ; *Zebrafish/microbiology/physiology ; *Gastrointestinal Microbiome/drug effects ; *Brain/metabolism/drug effects ; Male ; Female ; *Gum Arabic/pharmacology ; Dietary Supplements ; Reproduction/drug effects ; },
abstract = {Gum Arabic (GA) (Acacia senegal var. senegal) is an edible tree exudate and dietary fibre shown to improve health in humans and animals. We tested the ramifications of GAon organismal health across the microbiota-gut-brain axis by supplementing female and male zebrafish (Danio rerio) with two concentrations(6% or 60%) of GA (Acacia senegal var. senegal) for two weeks. We assessed the effects on the gut microbiome composition, intestinal and brain metabolic profiles, reproductive fitness, locomotion, and brain gene expression. GA supplementation induced a relative decrease in Proteobacteria and a relative increase in Fusobacteria, with a rise in the beneficial genus Cetobacterium. In the GA-supplemented fish, we detected increased intestinal glucose metabolism, evidenced by reduced glucose retention levels. Additionally, high levels of acetate were detected in the brain. Interestingly, the gene cart1, involved in appetite and hunger control, was significantly downregulated in female brains only. Consistently, we detected increased locomotion in GA-supplemented fish compared to Control fish. Interestingly, GA supplementation had a negative effect on female reproductive fitness and a positive effect on male reproductive fitness. .Our results emphasise the significance of evaluating the impact of dietary fibre at a systemic level to develop relevant nutritional guidelines that consider the different nutritional requirements of each sex.},
}

Animals
*Zebrafish/microbiology/physiology
*Gastrointestinal Microbiome/drug effects
*Brain/metabolism/drug effects
Male
Female
*Gum Arabic/pharmacology
Dietary Supplements
Reproduction/drug effects

@article {pmid41038976,
year = {2025},
author = {Majood, M and Rao, R},
title = {Human milk: insights on cell composition, organoids and emerging applications.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41038976},
issn = {1530-0447},
abstract = {Human milk is far more than a source of infant nutrition. It is a dynamic, living fluid packed with cells, bioactive molecules, and a complex microbiome that shapes neonatal development and lifelong health. Recent advances have illuminated the remarkable cellular diversity of human milk, including epithelial, immune, microbial and stem cells, each contributing essential biological functions. Milk contains distinct membrane-bound structures in the form of milk fat globules and extracellular vesicles that package a diverse cargo of lipids, proteins and nucleic acids for neonate nutrition, development and immune regulation. This review explores the composition of human milk, highlighting its nutrient and bioactive components and discussing growing concerns of xenobiotic and viral burden. We describe how milk-derived cells offer non-invasive windows into lactation biology and how emerging 3D mammary organoid models, particularly those generated from human milk cells, provide unprecedented tools to study breast development, lactation disorders, and regenerative therapies. We outline the potential of milk cells and extracellular vesicles in neonatal care, personalized medicine, and biobanking, while addressing current technical challenges and future research opportunities. By harnessing the unique properties of human milk, we stand at the threshold of transformative insights into maternal-infant health and novel biomedical applications. IMPACT: Up to date summary of bioactives, living cells and membrane bound compartments found in human milk. Primer on human mammary organoid technology, including advantages, recent advances and step by step methods. Highlights the unrealized potential of human milk in organoid technology, therapeutics, and regenerative medicine.},
}

@article {pmid41038964,
year = {2025},
author = {Liu, F and Zhang, Y and Zhang, L and Feng, W and Zhao, Y and Wei, J and Zhu, X and Zhao, S},
title = {Aqueous extract of Acer truncatum leaves retards Drosophila melanogaster senescence by regulating amino acid metabolism and gut microbiota.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34409},
pmid = {41038964},
issn = {2045-2322},
support = {2020QFY10-04//the Regional Innovation Capability Guiding Plan Project of Shaanxi Province/ ; 2020-120//the "Tianfu Scholar" Distinguished Expert Program of Sichuan Province/ ; },
mesh = {Animals ; *Drosophila melanogaster/drug effects/physiology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Plant Leaves/chemistry ; *Plant Extracts/pharmacology/chemistry ; *Acer/chemistry ; *Amino Acids/metabolism ; *Aging/drug effects ; Longevity/drug effects ; Tandem Mass Spectrometry ; Metabolomics ; },
abstract = {Acer truncatum is a unique tree species indigenous to northern China. The Chinese government approved the utilization of Acer truncatum leaves as a raw material for food. These leaves have been traditionally used in Inner Mongolia as a form of anti-aging medicine. However, the specific mechanism responsible for the anti-aging properties of Acer truncatum leaves remains unidentified. In this study, an aqueous extract of Acer truncatum leaves (AAL) was prepared and analyzed using UPLC-QTOF-MS/MS. the UPLC-MS/MS profile detected a total of 989 compounds in AAL, with 5 compounds of high concentration selected for quantitative analysis via UPLC-QTOF-MS/MS employing the internal standard method. Subsequently, Drosophila melanogaster served as a model organism to assess the impact of AAL on the lifespan and locomotor abilities. The results demonstrated a significant extension of the lifespan of D. melanogaster in response to AAL supplementation. Moreover, the addition of AAL to the medium enhanced the physical and anti-stress abilities of D. melanogaster, while preserving the integrity of their intestinal barrier. Gut microbiome analysis revealed that AAL administration positively influenced the structure and composition of gut microbes in aged D. melanogaster, notably reducing the prevalence of detrimental bacteria like Enterococcus and increasing beneficial bacteria such as Lactococcus. Metabolomic analysis annotated 30 potentially significant metabolites in AAL that contribute to delaying aging, predominantly associated with Phenylalanine metabolic pathways. Through a comprehensive multi-omics correlation analysis, a strong link was established between gut microbiota and metabolites following AAL treatment, highlighting how AAL prolongs the lifespan of D. melanogaster by modulating metabolic pathways via the gut microbiota. This study offers valuable insights into the anti-aging properties of AAL, emphasizing its ability to delay aging primarily through the regulation of metabolic pathways mediated by the gut microbiota and sets a foundation for the potential future application of AAL as a functional food.},
}

Animals
*Drosophila melanogaster/drug effects/physiology/metabolism
*Gastrointestinal Microbiome/drug effects
*Plant Leaves/chemistry
*Plant Extracts/pharmacology/chemistry
*Acer/chemistry
*Amino Acids/metabolism
*Aging/drug effects
Longevity/drug effects
Tandem Mass Spectrometry
Metabolomics

@article {pmid41038962,
year = {2025},
author = {Ali, S and Fuller, KD and Yurgel, SN and Forge, T and Lévesque, V and Mazzola, M},
title = {Exploring soil microbial and plant parasitic nematode communities involved in the apple replant disease complex in Nova Scotia.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34402},
pmid = {41038962},
issn = {2045-2322},
support = {J-002358//Agriculture and Agri-Food Canada/ ; J-002358//Agriculture and Agri-Food Canada/ ; J-002358//Agriculture and Agri-Food Canada/ ; J-002358//Agriculture and Agri-Food Canada/ ; },
mesh = {*Soil Microbiology ; Animals ; *Plant Diseases/parasitology/microbiology ; *Malus/parasitology/microbiology ; *Nematoda ; Fungi/genetics/isolation & purification/classification ; Nova Scotia ; *Microbiota ; Soil/parasitology ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Apple replant disease (ARD) is incited by a complex of causal agents including various fungi, oomycetes, and plant parasitic nematodes. These causal agents can differ significantly in abundance between orchard sites within a geographic region. Knowledge of the specific etiology of ARD is required in order to develop commercially viable soil management strategies to combat specific/individual components of the pathogen complex. In this study, we analyzed soil from six ARD affected orchard sites to assess the presence and composition of fungal, bacterial and oomycetes communities, as well as the prevalence of plant parasitic nematodes. Five fungal, and 17 bacterial classes were differentially represented in the soil microbiomes across the different locations. Mortierellomycetes was the most abundant fungal taxa represented followed by Sordariomycetes. Mortierella exigua, a fungal endophyte, was the most abundant fungal amplicon sequence variant (ASV) in the core microbiome. Among bacteria, Proteobacteria was the most prevalent phylum identified in these orchard soils. Several potential phytopathogenic fungi associated with ARD, as well as endophytes including Fusarium oxysporum, F. solani, Nectria ramulariae, Ilyonectria robusta and Nectriaceae, were identified in ARD soils. Among oomycetes, Pythium attrantheridium (Globisporangium attrantheridium), and P. irregulare (Globisporangium irregulare) were the most abundant taxa. Additionally, six different groups of plant-parasitic nematodes were found across the ARD orchard soils. Root-lesion nematodes, Pratylenchus spp., which are commonly associated with ARD, were identified in all orchard soils at population densities range from 12 to 33/100 cm[3] soil. This research enhances our understanding of the ARD pathogen complex and provide important insights for developing alternative disease management strategies in the apple industry.},
}

*Soil Microbiology
Animals
*Plant Diseases/parasitology/microbiology
*Malus/parasitology/microbiology
*Nematoda
Fungi/genetics/isolation & purification/classification
Nova Scotia
*Microbiota
Soil/parasitology
Bacteria/genetics/classification/isolation & purification

@article {pmid41038926,
year = {2025},
author = {Giner-Pérez, L and Jarquín-Díaz, VH and Leone, P and Giménez-Garzó, C and Mincheva, G and Mira, Á and Forslund-Startceva, SK and Rubio, T and Felipo, V and Pérez-Martínez, G and Llansola, M},
title = {Rifaximin-induced changes in the gut microbiome associated to improvement of neurotransmission alterations and learning in rats with chronic liver disease.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34382},
pmid = {41038926},
issn = {2045-2322},
support = {PID2020-113388RB-I00-AEI/10.13039/501100011033 and FPU2022/02975//Ministerio de Ciencia e Innovación/ ; PID2020-113388RB-I00-AEI/10.13039/501100011033 and FPU2022/02975//Ministerio de Ciencia e Innovación/ ; PID2020-113388RB-I00-AEI/10.13039/501100011033 and FPU2022/02975//Ministerio de Ciencia e Innovación/ ; CIPROM 2021/082 and CIBEFP/2022/58//Conselleria de Educación de la Generalitat Valenciana/ ; CIPROM 2021/082 and CIBEFP/2022/58//Conselleria de Educación de la Generalitat Valenciana/ ; CIPROM 2021/082 and CIBEFP/2022/58//Conselleria de Educación de la Generalitat Valenciana/ ; OP ERDF of Comunitat Valenciana 2014-2020//Generalitat Valenciana co-funded with European Regional Development Funds (ERDF)./ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Rifaximin/pharmacology ; Rats ; Male ; *Synaptic Transmission/drug effects ; Carbon Tetrachloride/toxicity ; Hepatic Encephalopathy ; *Learning/drug effects ; Feces/microbiology ; *Liver Diseases/microbiology/drug therapy ; Disease Models, Animal ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Rifaximin, a gut-targeted antibiotic, improves cognitive function and reduces the risk of hepatic encephalopathy (HE), yet its effects on the gut-brain axis remain unknown. This study explores how rifaximin influences gut microbiota functions and its association with cognitive function and molecular alterations in rats with liver injury. Liver injury was induced by chronic administration of carbon tetrachloride (CCl4), and rifaximin was administered daily. Fecal samples were collected after eight weeks of CCl4 administration, and taxonomic and functional changes in the gut microbiome were analyzed. Rifaximin altered microbiota diversity and composition, increasing α diversity in liver-injured rats but reducing diversity in healthy rats. It influenced microbiota interactions with neurotransmission alterations, where Dorea, Lachnospiraceae A2, and possibly Erysipelotricaceae might be important contributors. Functionally, butyric acid levels negatively correlated with gene orthologues associated with GABA, tryptophan, and glutamate degradation pathways. In healthy rats, fecal short-chain fatty acid (SCFA) levels were positively correlated with each other, a pattern absent in other groups. Rifaximin significantly influenced gut microbiota and promoted bacterial groups linked to improved cognition and neurotransmission in liver disease. Our findings underscored the direct relationship between a healthy microbiome and the maintenance of balanced SCFA concentrations.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Rifaximin/pharmacology
Rats
Male
*Synaptic Transmission/drug effects
Carbon Tetrachloride/toxicity
Hepatic Encephalopathy
*Learning/drug effects
Feces/microbiology
*Liver Diseases/microbiology/drug therapy
Disease Models, Animal
Anti-Bacterial Agents/pharmacology

@article {pmid41038906,
year = {2025},
author = {Yang, I and He, X and Jeon, J and Claussen, H and Arthur, R and Cushenan, P and Weaver, SR and Luo, R and Black, M and Shannahan, J and Wright, C},
title = {The impact of vaping behavior on functional changes within the subgingival microbiome.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {34374},
pmid = {41038906},
issn = {2045-2322},
support = {1R56DE031814-01/DE/NIDCR NIH HHS/United States ; 1R56DE031814-01/DE/NIDCR NIH HHS/United States ; 1R56DE031814-01/DE/NIDCR NIH HHS/United States ; 1R56DE031814-01/DE/NIDCR NIH HHS/United States ; 1R56DE031814-01/DE/NIDCR NIH HHS/United States ; },
mesh = {Humans ; *Vaping/adverse effects ; *Microbiota/drug effects ; Female ; Male ; Adult ; Electronic Nicotine Delivery Systems ; Volatile Organic Compounds/analysis ; Young Adult ; Adolescent ; Saliva/microbiology ; *Gingiva/microbiology ; Periodontal Diseases/microbiology/etiology ; },
abstract = {The use of Electronic Nicotine Delivery Systems (ENDS), or vaping devices, has raised concerns about their potential impact on oral health, particularly periodontal disease. While traditional smoking is a well-established risk factor for periodontal disease, the biological and microbial effects of ENDS use are less well understood. Our study examined how vaping and vaping behaviors influence the subgingival plaque microbiome and the associated metabolic pathways that may contribute to oral disease. We enrolled 70 healthy adults aged 18-35, including 48 regular ENDS users and 22 non-vaping controls. ENDS users were categorized by puffing behavior into low, medium, and high flow groups using a validated topography device. All participants underwent periodontal screening and provided saliva and subgingival plaque samples. To evaluate exposure profiles, ENDS users also submitted their personal devices for emissions testing, and volatile organic compounds (VOCs) were collected and analyzed using gas chromatography-mass spectrometry and high-performance liquid chromatography. Compared to non-vapers, ENDS users demonstrated distinct shifts in their oral microbiome, with reductions in beneficial taxa and increased bacteria associated with inflammation and periodontal disease. These changes were more pronounced in high-puff volume users, who also exhibited lower microbial diversity. Functional profiling revealed vaping-associated enrichment of pathways related to lipid metabolism, inflammation, and xenobiotic degradation. Untargeted salivary metabolomics identified metabolic disruptions consistent with these functional shifts. Integrative network analyses incorporating VOC measurements demonstrated correlations between microbial composition, puff volume, and metabolic disruptions, particularly in lipid-regulated and inflammatory pathways. To our knowledge, this is one of the first studies to integrate vaping behavior, oral microbiome profiling, salivary metabolomics, and VOC emissions analysis in a human cohort. These findings suggest ENDS use, especially at higher intensities, may disrupt oral microbial and metabolic homeostasis through both biological and chemical pathways potentially enhancing periodontal disease risk. These patterns point to potential biological and chemical pathways of concern, warranting further investigation and informing public health priorities.},
}

Humans
*Vaping/adverse effects
*Microbiota/drug effects
Female
Male
Adult
Electronic Nicotine Delivery Systems
Volatile Organic Compounds/analysis
Young Adult
Adolescent
Saliva/microbiology
*Gingiva/microbiology
Periodontal Diseases/microbiology/etiology

@article {pmid41038688,
year = {2025},
author = {Paz, HES and Stolf, CS and Bao, K and Monteiro, MF and Carvalho, LM and Silbereisen, A and Belibasakis, GN and Casarin, RCV and Bostanci, N},
title = {The Subgingival Host-Microbial Landscape in Mothers With Periodontitis and Their At-Risk Offspring.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70045},
pmid = {41038688},
issn = {1600-051X},
support = {2019/09740-3//São Paulo Research Foundation (FAPESP)/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES)/ ; 88887.717561/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior-Brasil (CAPES)/ ; FoUI-966140//Steering Group KI/Region Stockholm for Dental Research (SOF)/ ; FoUI-978687//Steering Group KI/Region Stockholm for Dental Research (SOF)/ ; },
abstract = {AIM: To evaluate the subgingival proteome and microbiome of mothers with periodontitis and their offspring, thereby assessing signatures of periodontal diseases.

METHODS: Forty participants in four groups were included: mothers with periodontitis and their offspring, as well as periodontally healthy mothers and their offspring. Periodontal clinical parameters were assessed. Gingival crevicular fluid (GCF) and subgingival biofilm were collected from the same sites. Proteome from GCF was investigated by liquid chromatography-tandem mass spectrometry with data-independent acquisition (DIA-PASEF). Bacterial DNA from subgingival biofilms was sequenced using the 16S rRNA gene for taxonomy assignment.

RESULTS: Overall, 6147 bacterial and human proteins (≥ 2 peptides) were quantified. Despite the absence of attachment loss, the offspring of mothers with periodontitis presented with similar proteotypes as their mothers, characterised by up-regulation of inflammatory response cascades and down-regulation of epithelial barrier proteins. They also displayed higher colonisation patterns by periodontopathogens while presenting with increased expression of bacterial virulence proteins compared with controls.

CONCLUSION: The study showed that the maternal periodontal microbiome and proteome associate with those of the offspring and relate to maternal periodontal status. These early ecological events may potentially promote offspring's susceptibility to dysbiosis and may predispose them to periodontitis.},
}

@article {pmid41038565,
year = {2025},
author = {Habiba, U and Noor, M and Kayani, MUR and Huang, L},
title = {Horizontal gene transfers differentially shape the functional potential of the infant gut metagenome.},
journal = {Life sciences},
volume = {},
number = {},
pages = {124006},
doi = {10.1016/j.lfs.2025.124006},
pmid = {41038565},
issn = {1879-0631},
abstract = {Horizontal gene transfer (HGT) is a major driver of microbial evolution, influencing the metabolic potential of microbial communities. Despite its significance, the consequences of HGT in shaping the microbial metabolic potential remain poorly understood, particularly in complex environments such as the human gut. This study aimed to assess the impact of HGT in infant gut microbiome from Caesarean section (CSD) and vaginal delivery (VD) groups during the first year of life. At Month 0, CSD infants exhibited a higher number of HGT events than VD infants. However, the numbers converged around Month 2 and remained comparable until Month 9, with no significant differences between groups (p > 0.05). HGT in VD was primarily driven by Coprococcus catus and Ruminococcus sp_5_1_39BFAA, while in CSD, Salmonella enterica and Klebsiella pneumoniae were dominant donors and acceptors. Functional analysis revealed that HGT in VD enriched genes related to carbohydrate metabolism and immune responses, whereas CSD was enriched for metabolic processes and biofilm formation. Additionally, HGT events were associated with Neonatal Intensive Care Unit Admission and diet transitions. These results suggest that HGT events in the VD and CSD groups differently shape the functional potential of the infant gut microbiome, with possible health implications that require further investigation. However, experimental validation is needed to establish a causal link.},
}

@article {pmid41038555,
year = {2025},
author = {Guo, C and Zhang, S and Zhang, H and Chen, L and Gao, S and Xu, M and Shi, H and Zhu, J},
title = {Per- and Polyfluoroalkyl Substances (PFAS) Disrupt Gut Microbiome Composition and Metabolism in Metabolic Syndrome: Evidence from a Host-Free In Vitro Colonic Model.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127189},
doi = {10.1016/j.envpol.2025.127189},
pmid = {41038555},
issn = {1873-6424},
abstract = {Metabolic syndrome (MetS) is a global health concern linked to metabolic abnormalities and increased risk of type 2 diabetes and cardiovascular disease. Recent studies suggest that exposure to per- and polyfluoroalkyl substances (PFAS) may contribute to MetS through alterations in gut microbiota and metabolism, but the underlying mechanisms remain unclear. This study aimed to investigate the effects of PFAS exposure on gut microbiota composition and metabolism in MetS using a three-stage, automated, computer-controlled in vitro Human Colonic Model (HCM) system. We introduced PFAS exposure to the gut microbiome in vitro at two concentrations (100 ng/mL and 1000 ng/mL) and analyzed microbial community structure using microbiome analysis, while changes in gut microbial metabolism were assessed through targeted and untargeted metabolomics. Our results showed that PFAS exposure significantly altered gut microbiota composition, with notable changes in key genera such as Morganella and Bilophila. Metabolomics analysis revealed an increase in short-chain fatty acid (SCFA) production at 1000 ng/mL of PFAS exposure, as well as significant alterations in other metabolites, including decreased acetophenone and taurocholic acid in both concentrations. These findings suggest that PFAS exposure may disrupt gut microbiota homeostasis and contribute to metabolic disturbances associated with MetS. This study highlights the need for further investigation into the mechanisms underlying PFAS-induced alterations in gut microbiota and their potential impact on human health.},
}

@article {pmid41038411,
year = {2025},
author = {Taoum, C and Devaux, A and Rouanet, P and Colombo, PE and Boucher, D and Bonnet, M},
title = {Gut microbiota and chemoradiotherapy response in rectal cancer: biomarker opportunities.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {104974},
doi = {10.1016/j.critrevonc.2025.104974},
pmid = {41038411},
issn = {1879-0461},
abstract = {The gut microbiota is increasingly recognized as a key factor in rectal carcinogenesis. This review synthesizes current clinical and preclinical evidence linking specific microbial signatures, such as Fusobacterium nucleatum, Duodenibacillus massiliensis and colibactin-producing Escherichia coli (CoPEC) to chemoradiotherapy (CRT) treatment efficacy and resistance. Microbiota-driven mechanisms include immune modulation, inflammation, and drug metabolism. We highlight emerging microbial biomarkers and therapeutic strategies such as antibiotics, probiotics, and fecal microbiota transplantation. Integrating microbiome profiling into clinical workflows could refine patient stratification and enhance CRT efficacy in rectal cancer. Ongoing clinical trials aim to validate these associations and establish robust microbial biomarkers for CRT response prediction in rectal cancer.},
}

@article {pmid41038408,
year = {2025},
author = {Meng, L and Xie, H and Duan, X and Liang, X and Tang, X and Luo, H and Xiao, X and Li, Z},
title = {Temporal shifts and cross-site relationships of oral, gut, and vaginal microbiota during the third trimester of pregnancy.},
journal = {Genomics},
volume = {},
number = {},
pages = {111123},
doi = {10.1016/j.ygeno.2025.111123},
pmid = {41038408},
issn = {1089-8646},
abstract = {BACKGROUND: The maternal microbiome during pregnancy influences maternal and neonatal health, yet its dynamics and cross-site relationships in the third trimester remain unclear.

METHODS: Oral, fecal, and vaginal samples were collected from 22 healthy pregnant women and analyzed using 16S rRNA gene sequencing.

RESULTS: As pregnancy progressed, gut microbial richness significantly increased, while vaginal richness significantly declined. Source tracking showed that the majority of microbes originated from their respective niches, although low-level cross-site contributions were also observed. Correlation-based network analysis revealed complex associations among microbial communities across sites. The oral microbiome exhibited distinct relative contributions and network relationships to the gut and vaginal microbiomes. Moreover, some low-abundance genera (relative abundance <1 %) played a critical role in maintaining ecological balance compared to high-abundance genera.

CONCLUSIONS: This study demonstrates dynamic, site-specific microbial changes and highlights potential microbial connections across body sites during late pregnancy, offering new ecological insights relevant to maternal-fetal health.},
}

@article {pmid41038354,
year = {2025},
author = {Qing, Z and Haibei, H and Hanxue, Y and Juan, S},
title = {Mitigation of tetracycline resistance genes in silage through targeted lactic acid bacteria inoculation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133416},
doi = {10.1016/j.biortech.2025.133416},
pmid = {41038354},
issn = {1873-2976},
abstract = {The dissemination of antibiotic resistance genes (ARGs) in silage ecosystems poses a critical challenge to ecological stability and public health security. This investigation focuses on tetracycline resistance genes (TRGs), the most prevalent subtype of ARGs in silage, employing a targeted selection strategy for lactic acid bacteria (LAB) inoculants. From 226 isolated LAB strains, four candidates (LP1-3: Lactiplantibacillus plantarum; LC1: Lacticaseibacillus paracasei) demonstrating superior growth kinetics (OD600 > 1.6 within 24 h) and rapid acidification capacity (pH < 3.9 within 24 h) were selected. Strains LP3 and LC1 exhibited minimal intrinsic TRGs content. These four strains reduced (p < 0.001) pH, ammonia-N concentration, and coliform bacterial counts of stylo silage. Metagenomic analysis revealed that strains LP1-3 promoted Lactiplantibacillus dominance (0.709-0.975 vs. 0.379-0.509 in the control), while LC1 enhanced Lacticaseibacillus abundance (0.449-0.612 vs. 0.002-0.013 in the control). Ensiling process downregulated 367 and upregulated 227 ARGs. Inoculation with the four LAB strains further enhanced the suppression of ARGs. Among the top 30 TRGs, 22 were reduced by strains LP1-3 and 20 by LC1. Quantitative PCR results showed that strains LP1-3 decreased (p < 0.05) the contents of tetA and tetG during 30 days fermentation. Among the TRGs increased, tetA(60), tetB(58), tet(T) were positively correlated with Lactiplantibacillus spp., tetA(58), tetB(60), tetA(46), tetB(46), tet(43) were significantly correlated with Lacticaseibacillus spp. (R > 0.4, p < 0.001). In conclusion, the fermentation process induced substantial ARGs profile modifications, LAB-mediated microbiome engineering enables TRGs suppression, providing a scientific foundation for precision silage management strategies targeting antimicrobial resistance mitigation.},
}

@article {pmid41038332,
year = {2025},
author = {Zhang, Y and Liu, Y and Wei, Y and Ren, Z and Jin, YH and Li, G},
title = {The role of rare ginsenosides in the prevention and treatment of liver diseases.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120666},
doi = {10.1016/j.jep.2025.120666},
pmid = {41038332},
issn = {1872-7573},
abstract = {Ginseng (Panax ginseng C. A. Mey.) is a traditional herb that occupies a very important position in traditional Chinese medicine (TCM). Many references have recorded the traditional application methods of ginseng and improve the effects of liver-blood insufficiency and chronic liver injury. Modern studies have found that rare ginsenosides are the key to their role and have therapeutic effects on a variety of liver diseases, further verifying their traditional applications.

AIM OF THIS REVIEW: This article reviews recent research advances on the structure, origin and pharmacological effects of rare ginsenosides to evaluate the preventive and therapeutic effects of rare ginsenosides on different types of liver diseases.

MATERIALS AND METHODS: This article utilized keywords like "Rare ginsenosides", "Source", "Drug-induced liver injury", "Metabolic dysfunction-associated fatty liver disease", "Liver fibrosis", "Hepatocellular carcinoma", and "Therapeutic interventions" to gather research on rare ginsenosides related to liver diseases from databases such as PubMed, Web of Science, and CNKI, up to February 2025. The collected information was then summarized and analyzed.

RESULTS: The structural characterization and preparation process of rare ginsenosides were clarified. In terms of pharmacological activities, rare ginsenosides possess a variety of activities, including anti-inflammatory, antioxidant, anti-tumor and immunomodulatory. In addition, rare ginsenosides showed protective effects against liver diseases through various mechanisms. However, their clinical application remains limited due to low content, poor water solubility, low oral bioavailability, and unclear mechanisms. Future efforts will accelerate translation through fermentation optimization, nanocarriers, structural modification, and microbiome research.

CONCLUSION: The multiple pharmacological activities of rare ginsenosides make them candidates for the treatment of various liver diseases and provide a broader direction for exploring the Chinese medicine treatment of liver diseases.},
}

@article {pmid41037885,
year = {2025},
author = {Goo, D and Lee, DJ and Kim, Y and Kim, WK},
title = {The effects of dietary levels of corn distillers dried grains with solubles and supplementation of valine and isoleucine on growth performance, intestinal health, and cecal microbiome in Ross 708.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105910},
doi = {10.1016/j.psj.2025.105910},
pmid = {41037885},
issn = {1525-3171},
abstract = {The current study was conducted to investigate the effects of additional valine and isoleucine in a high corn distillers dried grains with solubles (DDGS) diet on growth performance, intestinal health, and cecal microbiome in broilers. A total of 800 0-d-old male Ross 708 were allocated into 5 dietary treatments with 8 replicates. The five diet groups were as follows: 1) corn-soybean meal (SBM)-based control (CON) group; 2) 15 % DDGS (15D) group (replacing corn and SBM with 15 % DDGS); 3) 15D + additional valine and isoleucine to have the same leucine:valine and leucine:isoleucine ratios as the CON group (15DB); 4) 30 % DDGS (30D) group; and 5) 30D + additional valine and isoleucine to have the same leucine:valine and leucine:isoleucine ratios as the CON group (30DB). The reduction in growth performance, carcass weight, breast muscle, and lean weight was intensified with increasing dietary DDGS levels. The 15DB group showed similar body weight gain (BWG) and carcass weight compared to the CON group. The 30DB group showed significant differences in phylum- and family-level cecal bacterial diversities compared to the 30D group but did not create significant growth improvement. No significant differences were observed in growth performance, carcass weight, body composition, intestinal morphology, jejunal gene expression levels, and alpha and beta diversity of cecal microbiota between the 15D and 15DB, and 30D and 30DB groups. Additional valine and isoleucine did not show consistent improvements in intestinal health and growth performance in DDGS-supplemented diets. The effect of additional valine and isoleucine varied depending on how much corn and SBM was replaced with DDGS in the diet, which may have been affected by additional factors other than intestinal health. In conclusion, additional valine and isoleucine may play a role in growth and muscle deposition but not have significant impact on the intestinal health in broiler diets that replaced corn and SBM with high levels of DDGS.},
}

@article {pmid41037883,
year = {2025},
author = {Park, JW and Kim, H and Choi, SA and Lee, HK and Shin, DH},
title = {Effects of patulin on quail muscle cells and the potential for microbiome-mediated recovery.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {105872},
doi = {10.1016/j.psj.2025.105872},
pmid = {41037883},
issn = {1525-3171},
abstract = {Mycotoxins pose a significant threat to livestock health and productivity by compromising immunity and inducing various toxicities. This study investigated the potential of specific Bacillus strains to mitigate mycotoxin-induced muscle damage in poultry cells. We treated quail muscle clone 7 (QM7) muscle cells with patulin, a common mycotoxin, to induce cellular injury. Subsequently, the damaged QM7 cells were treated with the candidate microbial strains, B. subtilis and B. velezensis. Our findings revealed that patulin treatment elevated stress-inducible gene expression and apoptosis markers, concurrently disrupting normal myoblast differentiation, as evidenced by altered expression patterns of Paired Box 7 (PAX7) and Myogenic Differentiation 1 (MyoD) and impaired myotube formation. Notably, treatment with the Bacillus strains significantly reduced these negative effects, reducing stress and apoptosis indicators while promoting a different pattern of myotube development. Although the exact mechanism of muscle recovery warrants further functional assessment, our results highlight the potential of B. subtilis and B. velezensis as agents for mitigating mycotoxin-induced damage in poultry, and offer novel strategies for enhancing animal health and agricultural sustainability.},
}

@article {pmid41037658,
year = {2025},
author = {Sun, W and Ma, L and Feng, X and Fan, Y and Cai, Y and Li, X},
title = {Efficacy of gut microbiota-based therapy for autism Spectrum Disorder and attention Deficit Hyperactivity Disorder: a systematic review and meta-analysis.},
journal = {Psychology, health & medicine},
volume = {},
number = {},
pages = {1-25},
doi = {10.1080/13548506.2025.2565181},
pmid = {41037658},
issn = {1465-3966},
abstract = {The gut-brain axis is an emerging therapeutic target for neurodevelopmental conditions such as Autism Spectrum Disorder (ASD) and Attention Deficit Hyperactivity Disorder (ADHD). However, the overall efficacy of gut microbiome-based interventions remains unclear. This systematic review and meta-analysis, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines, aimed to synthesize the evidence on these interventions. Fifteen randomized controlled trials (RCTs) were identified from 1,080 records across PubMed, Embase, Web of Science, Cochrane, PsycInfo, MEDLINE, and ClinicalTrials.gov through August 2024. Interventions included probiotics, prebiotics, dietary changes, and fecal transplants. Using random-effects models, pooled analysis showed a small but significant overall benefit of gut microbiota-based interventions (Standardized Mean Difference, SMD = -0.12; 95% Confidence Interval, CI: -0.19 to -0.04), with low heterogeneity (I[2] = 5.9%). Effects differed by disorder: ADHD demonstrated greater improvement (SMD = -0.24; 95% CI: -0.42 to -0.06; I[2] = 50.4%) compared to ASD (SMD = -0.05; 95% CI: -0.15 to 0.04; I[2] = 0%). Duration-specific effects emerged: 8-week interventions showed significant outcomes (SMD = -0.32; 95% CI: -0.58 to -0.06), while shorter or longer durations lacked significance. Acceptability analysis from eight studies revealed comparable dropout rates between intervention and control groups (ASD: Risk Ratio, RR = 1.002; ADHD: RR = 0.943), with no serious adverse events reported. Subgroup analyses identified participant age, diagnosis type, and geographic location as heterogeneity sources. Despite methodological limitations and small sample sizes, findings suggest gut microbiome modulation may offer a safe adjunctive therapy, particularly for ADHD, with optimal effects emerging at 8 weeks. The gut-brain axis appears promising for neurodevelopmental disorders, but current evidence remains preliminary. Future research should prioritize large-scale RCTs with standardized protocols, mechanistic investigations, and long-term follow-up to establish clinical guidelines and clarify biological pathways. Findings underscore the need to tailor interventions to specific disorders and optimize treatment duration.},
}

@article {pmid41037624,
year = {2025},
author = {Tsai, HH and Tang, Y and Jiang, L and Xu, X and Dénervaud Tendon, V and Pang, J and Jia, Y and Wippel, K and Vacheron, J and Keel, C and Andersen, TG and Geldner, N and Zhou, F},
title = {Localized glutamine leakage drives the spatial structure of root microbial colonization.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6768},
pages = {eadu4235},
doi = {10.1126/science.adu4235},
pmid = {41037624},
issn = {1095-9203},
mesh = {*Plant Roots/microbiology/metabolism ; *Glutamine/metabolism ; Rhizosphere ; *Arabidopsis/microbiology/metabolism ; *Microbiota ; *Plant Exudates/metabolism ; Chemotaxis ; },
abstract = {Plant roots release exudates to encourage microbiome assembly, which influences the function and stress resilience of plants. How specific exudates drive spatial colonization patterns remains largely unknown. In this study, we demonstrate that endodermal Casparian strips-forming the root's extracellular diffusion barrier-restrict nutrient leakage into the rhizosphere, coinciding with and controlling spatial colonization patterns of rhizobacteria. We find that vasculature-derived glutamine leakage is a major bacterial chemoattractant and enhancer of proliferation, defining a previously unknown pathway for root exudate formation. Bacteria defective in amino acid chemoperception display reduced attraction toward leakage sites, and roots with Casparian strip defects display bacterial overproliferation, dependent on bacterial capacity for amino acid metabolization. Associated chronic immune stimulation suggests that endodermal nutrient restriction is crucial for regulating microbial colonization and assembly, limiting excessive proliferation that could compromise plant health.},
}

*Plant Roots/microbiology/metabolism
*Glutamine/metabolism
Rhizosphere
*Arabidopsis/microbiology/metabolism
*Microbiota
*Plant Exudates/metabolism
Chemotaxis

@article {pmid41037233,
year = {2025},
author = {Yamada, M and Kubo, M and Kaneshiro, K and Kai, M and Morisaki, T and Hayashi, S and Ochiai, Y and Sato, Y and Mizoguchi, K and Takao, Y and Arimura, A and Nakamura, M},
title = {Characterization of gut microbiota dysbiosis in breast cancer patients.},
journal = {Breast cancer (Tokyo, Japan)},
volume = {},
number = {},
pages = {},
pmid = {41037233},
issn = {1880-4233},
support = {JP21K19532//Japan Society for the Promotion of Science/ ; },
abstract = {BACKGROUND: While lifestyle factors are known to be associated with breast cancer development, the potential role of the gut microbiome, which is influenced by lifestyle, as a risk factor is not well understood. We conducted a comparative analysis of the intestinal microbiota between healthy individuals and breast cancer patients to investigate the potential impact of gut microbiome composition on breast cancer development. This study aimed to explore the role of intestinal microbial communities in breast cancer pathogenesis.

METHODS: We conducted a comparative analysis of fecal 16S rRNA amplicon sequencing data from 100 individuals in the general population and 79 breast cancer patients. We investigated the differences between the two groups in terms of relative abundance, absolute quantity, diversity, and functionality of the gut microbiota.

RESULTS: Breast cancer groups showed higher levels of Firmicutes and lower levels of Bacteroidota at the phylum level, and an increase in Fusobacteriota was found in the human epidermal growth factor receptor 2 (HER2)-negative breast cancer group. Additionally, certain genera were more or less common in breast cancer groups at the genus level. The study also indicated lower gut microbiota diversity and loss of heterogeneity in breast cancer groups and reduced functional genes and pathways.

CONCLUSION: Compared to the general population, breast cancer patients exhibited a distinct dysbiosis in their gut microbiota. Further investigation is warranted to determine if this dysbiotic state, linked to a predicted downregulation of functional pathways critical for homeostasis, plays a role in breast cancer development.},
}

@article {pmid41037094,
year = {2025},
author = {Wadop, YN and Bernal, R and Njamnshi, WY and Satizabal, CL and Beiser, A and Ruiz, A and Njamnshi, AK and Vasan, RS and Seshadri, S and Himali, JJ and Fongang, B},
title = {Altered gut microbiota mediates the association between APOE genotype and amyloid-β accumulation in middle-aged adults.},
journal = {Journal of neurology},
volume = {272},
number = {10},
pages = {670},
pmid = {41037094},
issn = {1432-1459},
support = {AG059421/AG/NIA NIH HHS/United States ; AG054076/AG/NIA NIH HHS/United States ; AG049607/AG/NIA NIH HHS/United States ; AG033090/AG/NIA NIH HHS/United States ; AG066524/AG/NIA NIH HHS/United States ; P30 AG066546/AG/NIA NIH HHS/United States ; 5P30AG059305-03/AG/NIA NIH HHS/United States ; RF1 AG061729A1/AG/NIA NIH HHS/United States ; 5U01AG052409-04/AG/NIA NIH HHS/United States ; UG3AG090675)/AG/NIA NIH HHS/United States ; NINDS (NS017950/AG/NIA NIH HHS/United States ; UF1NS125513/AG/NIA NIH HHS/United States ; K01NS126489/AG/NIA NIH HHS/United States ; P30AG066546//South Texas Alzheimer's Disease Research Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Middle Aged ; *Amyloid beta-Peptides/metabolism ; *Apolipoprotein E4/genetics ; *Apolipoproteins E/genetics ; *Dysbiosis/metabolism/microbiology/genetics ; *Alzheimer Disease/genetics/metabolism/microbiology ; Aged ; Genotype ; *Brain/metabolism ; },
abstract = {BACKGROUND: The apolipoprotein E (APOE) ε4 allele is the strongest genetic risk factor for Alzheimer's disease, yet the mechanisms linking APOE to amyloid-β (Aβ) pathology remain incompletely understood. Emerging evidence suggests that the gut microbiome may modulate neurodegeneration; however, its role as a mediator in the APOE-Aβ relationship remains unclear.

OBJECTIVE: Evaluate whether specific microbial taxa mediate APOE-related effects on brain Aβ burden in a population-based study.

METHODS: This study involved 227 participants from the Framingham Heart Study with stool 16S rRNA sequencing and carbon-11 Pittsburgh Compound-B imaging for Aβ collected at the third examination (2016-2019). Associations between gut microbiota and global/regional Aβ deposition were assessed using multivariable models. We stratified participants by APOE ε4 status and conducted mediation analysis to evaluate whether specific taxa mediated APOE-related effects on Aβ. Microbial functional potential was inferred to examine enrichment of metabolic pathways.

RESULTS: Higher Aβ burden was significantly associated with the depletion of protective genera (e.g., Faecalibacterium, Ruminococcus, Butyricicoccus) and the enrichment of pro-inflammatory taxa (e.g., Alistipes, Bacteroides) and Barnesiella. These associations were more pronounced in APOE ε4 carriers, who exhibited a broader spectrum of microbial dysbiosis. Mediation analysis showed that Ruminococcus, Butyricicoccus, Clostridium, and Christensenellaceae collectively mediated ~ 0.3-0.4% of the effect of APOE ε4 on global Aβ burden. Functional profiling revealed a reduced abundance of microbial genes involved in key metabolic pathways among individuals with higher Aβ levels.

CONCLUSION: Gut microbiome composition mediates the deleterious effect of APOE ε4 on cerebral amyloid deposition, suggesting that microbiome-targeted interventions may mitigate APOE-related risk.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Middle Aged
*Amyloid beta-Peptides/metabolism
*Apolipoprotein E4/genetics
*Apolipoproteins E/genetics
*Dysbiosis/metabolism/microbiology/genetics
*Alzheimer Disease/genetics/metabolism/microbiology
Aged
Genotype
*Brain/metabolism

@article {pmid41037066,
year = {2025},
author = {Scott, CM and Holman, DB and Gzyl, KE and Ibe, A and Taheri, AE},
title = {Production Systems and Age Influence Fecal Mycobiota Diversity and Composition in Swine.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {104},
pmid = {41037066},
issn = {1432-184X},
mesh = {Animals ; *Feces/microbiology ; Swine/microbiology ; *Fungi/classification/genetics/isolation & purification ; *Animal Husbandry/methods ; *Gastrointestinal Microbiome ; *Mycobiome ; Biodiversity ; DNA, Fungal/genetics ; Age Factors ; Female ; },
abstract = {The gut microbiome is an important factor in animal health and can be influenced by factors such as age, diet, stress, environmental conditions, and farming practices. Bacterial communities of the gut microbiome in many species have been extensively studied, but research on the fungal microbiota remains limited and underrepresented in the literature. The objective of this study was to characterize the fecal mycobiota of swine raised under two different production systems: outdoor pasture-based or conventional indoor systems. Fecal samples from nursery, growing-finishing, and sow pigs from both farming systems were collected, and the mycobiota was profiled using PCR amplification and sequencing of the universal fungal internal transcribed spacer 1 (ITS1) region. A significant difference in fungal community structure was observed between the conventionally raised and pasture-raised pigs, as well as among all three production phases. Four species, Arthrographis kalrae, Enterocarpus grenotii, Pseudallescheria angusta, and Sagenomella oligospora, were differentially abundant between the two farms, all of which had higher relative abundance in the pasture-raised pigs. Additionally, pasture-raised pigs hosted a more diverse fungal community with higher species richness in their gastrointestinal tract. In summary, farming practices and pig age influenced the pig fecal mycobiota.},
}

Animals
*Feces/microbiology
Swine/microbiology
*Fungi/classification/genetics/isolation & purification
*Animal Husbandry/methods
*Gastrointestinal Microbiome
*Mycobiome
Biodiversity
DNA, Fungal/genetics
Age Factors
Female

@article {pmid41036865,
year = {2025},
author = {Smith, S and Ciesielski, M and Clerkin, T and Ben-Horin, T and Noble, RT},
title = {Farmed oyster mortality follows consistent Vibrio community reorganization.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0107825},
doi = {10.1128/msystems.01078-25},
pmid = {41036865},
issn = {2379-5077},
abstract = {Mortality events in marine bivalves cause substantial economic losses in aquaculture, yet the microbial dynamics underlying these events remain poorly characterized. Here, we investigated succession patterns in oyster-associated Vibrio communities during mortality events by sampling eastern oysters (Crassostrea virginica) at a North Carolina commercial farm that has experienced repeated, unexplained mortality events. Through whole-genome sequencing of 110 Vibrio isolates from 26 oysters sampled across mortality events in two consecutive years, we identified six conserved phylogenetic clades with distinct temporal associations. Vibrio mediterranei and a clade of resident vibrios consistently dominated the initial cultured community at the onset of mortality. However, V. mediterranei was absent as mortality progressed, coinciding with increased abundance of V. harveyi, V. alginolyticus, V. diabolicus, and V. agarivorans. Comparative genomic analysis revealed that initial isolates were enriched in pathways associated with host colonization and complex carbon metabolism, while isolates from elevated mortality showed enrichment in virulence mechanisms and adaptation to degraded host tissues. Temporal separation between genetically distinct clades suggests microbial competition shapes community assembly during mortality events that ultimately reached >85% mortality in both years. This predictable succession from commensal to potentially pathogenic Vibrio species provides genome-level insight into microbial community dynamics during oyster mortality. The consistent loss of V. mediterranei prior to severe mortality suggests this species could serve as a bioindicator for early warning systems to mitigate economic losses in shellfish aquaculture.IMPORTANCEMortality events in aquaculture systems represent complex host-microbe-environment interactions that challenge our ability to predict and prevent disease. By characterizing succession patterns in oyster-associated Vibrio communities at whole-genome resolution, we reveal a consistent transition from metabolically versatile species associated with healthy oysters to functionally distinct Vibrio taxa enriched in virulence factors and tissue degradation pathways as mortality progresses. This genome-level evidence for predictable community reorganization suggests that monitoring commensal Vibrio populations, particularly the presence or absence of Vibrio mediterranei, could provide earlier warning of impending disease compared to tracking only known pathogens. This shift in monitoring approach could advance aquaculture disease management while expanding our fundamental understanding of how microbial community transitions contribute to host health and disease progression.},
}

@article {pmid41036846,
year = {2025},
author = {Schlievert, PM and Brennan, PE and Klem, RE and Reardan, DT},
title = {Antifungal, antibacterial, and anti-inflammatory activity of glycerol dithionomonolaurate, an analog of glycerol monolaurate.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0031825},
doi = {10.1128/msphere.00318-25},
pmid = {41036846},
issn = {2379-5042},
abstract = {UNLABELLED: Glycerol dithionomonolaurate (NB2) is an analog of the natural antimicrobial compound glycerol monolaurate (GML) with enhanced antimicrobial activity. The advantage of NB2 over GML is the presence of a dithionate to greatly reduce microbial cleavage through glycerol ester hydrolases, such as Staphylococcus aureus lipase. NB2 exhibited antimicrobial activity against Candida fungal species, including Candida auris, with comparable minimum bactericidal concentration (MBC) and minimum inhibitory concentration (MIC) of 50-100 µg/mL compared to 250-500 µg/mL for GML. NB2 exhibited a broad range of antibacterial activity including both gram-positive and gram-negative organisms, while sparing normal microbiome lactobacilli. When 10[8] C. auris and 10[9] S. aureus were incubated on Todd Hewitt agar plates in the presence of two times the MBC for NB2, no resistant colonies grew, likely the result of the large number of antimicrobial targets inhibited. Like GML, NB2 inhibited exotoxin production at non-antibacterial concentrations. NB2 exhibited anti-staphylococcal activity when tested topically on a dermatitis skin model on rabbits. NB2 inhibited the production of chemokines (interleukin-8 and macrophage inflammatory protein-3α) by human vaginal epithelial cells, suggesting anti-inflammatory activity. Unlike clear GML solutions, NB2 was pale yellow. The absorption spectrum of NB2 was not sufficient to raise Food and Drug Administration concerns over phototoxicity. Collectively, the data suggest that NB2 could become a useful topical agent for the prevention of both fungal and bacterial infections as a dual-active anti-infective, killing microbes and reducing harmful inflammation, such as seen in atopic dermatitis.

IMPORTANCE: Fungi and many bacteria commonly develop resistance to antimicrobial agents or have inherent resistance. Many microbes initiate infections through the skin and mucous membranes, in part by producing toxins and causing harmful inflammation. We describe a novel topical antimicrobial agent, glycerol dithionomonolaurate (NB2), effective against Candida and a wide range of gram-positive and gram-negative bacteria; the compound did not kill normal microbiome lactobacilli. NB2 is likely to have many microbial targets for killing, suggesting resistance to the molecule may not develop. At sub-antibacterial concentrations, glycerol dithionomonolaurate inhibited exotoxin production by Staphylococcus aureus. The molecule was not inactivated by staphylococcal lipase. Glycerol dithionomonolaurate effectively treated S. aureus dermatitis in a rabbit skin model and reduced chemokine production by human epithelial cells. Glycerol dithionomonolaurate may prove useful to treat many types of skin and mucous membrane infections by both antimicrobial and anti-inflammatory activities, such as in atopic dermatitis.},
}

@article {pmid41036840,
year = {2025},
author = {Diaz, B and Krishna, R and Schoeniger, JS and Mageeney, CM},
title = {Exploring phage-host interactions in Burkholderia cepacia complex bacterium to reveal host factors and phage resistance genes using CRISPRi functional genomics and transcriptomics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0193625},
doi = {10.1128/spectrum.01936-25},
pmid = {41036840},
issn = {2165-0497},
abstract = {Complex interactions of bacteriophages with their bacterial hosts determine phage host range and infectivity. While phage defense systems and host factors have been identified in model bacteria, they remain challenging to predict in non-model bacteria. In this paper, we integrate functional genomics and transcriptomics to investigate phage-host interactions, revealing active phage resistance and host factor genes in Burkholderia cenocepacia K56-2. Burkholderia cepacia complex species are commonly found in soil and are opportunistic pathogens in immunocompromised patients. We studied infection of B. cenocepacia K56-2 with Bcep176, a temperate phage isolated from Burkholderia multivorans. A genome-wide dCas9 knockdown library targeting B. cenocepacia K56-2 was constructed, and a pooled infection experiment identified 63 novel genes or operons coding for candidate host factors or phage resistance genes. The activities of a subset of candidate host factor and resistance genes were validated via single-gene knockdowns. Transcriptomics of B. cenocepacia K56-2 during Bcep176 infection revealed that expression of genes coding for host factor and resistance candidates identified in this screen was significantly altered during infection by 4 h post-infection. Identifying which bacterial genes are involved in phage infection is important to understand the ecological niches of B. cenocepacia and its phages, and for designing phage therapies.IMPORTANCEBurkholderia cepacia complex bacteria are opportunistic pathogens inherently resistant to antibiotics, and phage therapy is a promising alternative treatment for chronically infected patients. Burkholderia bacteria are also ubiquitous in soil microbiomes. To develop improved phage therapies for pathogenic Burkholderia bacteria, or engineer phages for applications, such as microbiome editing, it's essential to know the bacterial host factors required by the phage to kill bacteria, as well as how the bacteria prevent phage infection. This work identified 65 genes involved in phage-host interactions in Burkholderia cenocepacia K56-2 and tracked their expression during infection. These findings establish a knowledge base to select and engineer phages infecting or transducing Burkholderia bacteria.},
}