@article {pmid40624665,
year = {2025},
author = {Lin, F and Ma, L and Sheng, Z},
title = {Health disorders in menopausal women: microbiome alterations, associated problems, and possible treatments.},
journal = {Biomedical engineering online},
volume = {24},
number = {1},
pages = {84},
pmid = {40624665},
issn = {1475-925X},
support = {2022KY275//Zhejiang Provincial Medical and Health Science and Technology Project: "Research on the Impact of Hormone Therapy for Menopause on the Vaginal Microbiota of Perimenopausal Women Based on 16S rRNA High-throughput Gene Sequencing Technology/ ; 2022KY275//Zhejiang Provincial Medical and Health Science and Technology Project: "Research on the Impact of Hormone Therapy for Menopause on the Vaginal Microbiota of Perimenopausal Women Based on 16S rRNA High-throughput Gene Sequencing Technology/ ; 2022KY275//Zhejiang Provincial Medical and Health Science and Technology Project: "Research on the Impact of Hormone Therapy for Menopause on the Vaginal Microbiota of Perimenopausal Women Based on 16S rRNA High-throughput Gene Sequencing Technology/ ; },
abstract = {Perimenopause marks a critical transition in women's lives, characterized by declining estrogen levels that trigger profound physiological and psychological changes, impacting quality of life and increasing susceptibility to age-related degenerative diseases. This review systematically examines the intricate relationships among menopause, disease associations, microbiome alterations, and intervention strategies. Estrogen fluctuations disrupt the microbial balance in the vagina, intestine, urethra, and oral cavity, contributing to microecological imbalance and heightened disease risk. Menopause is closely linked to a spectrum of health issues, including reproductive system disorders (e.g., uterine fibroids, ovarian cancer microbiota changes), metabolic syndromes (obesity, type 2 diabetes), cardiovascular diseases (influenced by gut microbiota and dietary patterns), osteoporosis, and mental health disturbances. Current interventions-ranging from dietary modifications (cocoa polyphenols, dietary fiber, soy isoflavones) and menopausal hormone therapy (MHT) to probiotic supplementation, plant extracts (soybean, black cohosh, red clover), and traditional therapies-exhibit distinct advantages and limitations. Technological advancements in microbiome analysis, tissue processing, and cell isolation have revolutionized diagnostic and therapeutic approaches, while immune function, socioeconomic factors, and lifestyle choices significantly modulate health outcomes. Future research should prioritize exploring synergistic intervention strategies, developing personalized health management programs, and unraveling the mechanistic links between the microbiome and menopause-related diseases. This comprehensive synthesis aims to advance evidence-based strategies for improving the health and quality of life of menopausal women.},
}

@article {pmid40624638,
year = {2025},
author = {Yan, X and Lin, X and Wu, J and Zheng, L and Liu, Y and Wu, F and Lin, Y and Lu, Y and Huang, C and Shen, B and Liu, H and Huang, R and Hou, F and Zhou, Q and Song, M and Liu, K and Zhu, F and Li, S and Lin, Y and Wang, W and Li, P and Liao, W and Zhi, F},
title = {Mitigation of chemotherapy-induced gut dysbiosis and diarrhea by supplementation with heat-killed Bacteroides fragilis.},
journal = {BMC medicine},
volume = {23},
number = {1},
pages = {408},
pmid = {40624638},
issn = {1741-7015},
support = {Y20190159//Study on the Mechanism of FUT7 regulating CD15s+eTreg cells in the Pathogenesis of Ulcerative Colitis/ ; NO.2024B03J1282//Key Technology Project in Guangzhou/ ; NO. 201809010014//Innovation Leading Team Project in Guangzhou/ ; },
abstract = {BACKGROUND: The role of gut microbial dysbiosis in chemotherapy-induced diarrhea (CID) pathogenesis remains unclear in humans. This study investigates gut microbiota alterations in CID patients and evaluates the therapeutic potential of probiotic supplementation.

METHODS: To establish a paired cohort for longitudinal comparison and minimize confounding factors in assessing CID-related microbiota changes, strict inclusion/exclusion criteria were applied to gastrointestinal cancer patients. Fecal samples from eligible participants underwent shotgun metagenomic sequencing to comprehensively profile the gut microbiome composition and function. To evaluate probiotic efficacy and mechanisms, we utilized 6-8-week-old male BALB/c and C57BL/6 mice in established 5-FU- or CPT-11-induced CID models. Probiotic efficacy was assessed using primary (diarrhea severity) and secondary endpoints (body weight change, intestinal permeability). Mechanistic studies were conducted in murine models, complemented by IEC-6 cells and intestinal organoid experiments to elucidate microbiota-host interactions.

RESULTS: Analysis of paired fecal samples (pre- and post-chemotherapy) from 30 gastrointestinal cancer patients (n = 60) revealed chemotherapy-induced reduction of Bacteroides fragilis (B. f) via metagenomics sequencing, with baseline B. f relative abundance negatively correlating with CID severity (r =  - 0.93, p = 3.1e - 12). Building on these clinical observations, in 5-FU/CPT-11-induced CID murine models, oral gavage of heat-killed B. f (hk-B. f) outperformed live bacteria in diarrhea alleviation. Mechanistically, B. f-derived succinate exacerbated diarrhea, while its capsular polysaccharide (PSA) ameliorated mice diarrhea. This discovery explains the discrepant therapeutic effect between hk-B. f and live B. f. Fluorescence tracing confirmed hk-B. f transiently localized to the upper gastrointestinal tract without extraintestinal colonization. hk-B. f preserved epithelial integrity, mitochondrial function, and intestinal organoid development (higher budding count and larger organoid surface area). Moreover, hk-B. f upregulated the expression of BCL2 and downregulated the expression of BAX. Shifting the balance between BCL2 and BAX alleviates intestinal epithelial apoptosis. Caspase-3 inhibition or BCL2 silencing abrogated hk-B. f's anti-apoptotic effects in IEC-6 cells.

CONCLUSIONS: Pathological process of CID can be partially explained by compositional alterations in the gut microbiota. Supplementation with hk-B. f reduces 5-FU-stimulated epithelial injury through mitochondrial apoptotic pathway in CID murine models. These preclinical findings suggest hk-B. f merits further investigation as a potential strategy for improving CID, pending clinical validation.},
}

@article {pmid40624612,
year = {2025},
author = {De, T and Ma, T and Wang, W and An, X and Liu, D and Yin, H and Wang, Q and Zhao, T and Wang, H},
title = {Intestinal microbiota in adults with cholangiocarcinoma identifies the dysregulated Blautia species and bile acid metabolic pathways.},
journal = {BMC gastroenterology},
volume = {25},
number = {1},
pages = {506},
pmid = {40624612},
issn = {1471-230X},
support = {XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; XZ2024033//Ningxia Medical University Institutional Scientific Research Fund/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2022BSB03112//the Ningxia Gut Homeostasis and Chronic Disease Prevention and Treatment Scientific and Technological Innovation Team, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; 2023GKLRLX17//Program of Ningxia Science and Technology Leading Talent, China/ ; },
abstract = {BACKGROUND: Cholangiocarcinoma (CCA) represents a significant global health concern. The gut and bile microbiota, which can influence the gut-liver axis and disease progression, have not been thoroughly characterized in CCA patients.

METHODS: We selected two clinical centers at our hospital and collected stool samples from CCA patients and healthy controls (HC). These samples underwent whole-genome metagenomic shotgun sequencing, followed by analysis using both marker gene-based and assembly-based methods. Additionally, KEGG pathway enrichment was performed using the cholangiocarcinoma (CHOL) RNA-seq samples.

RESULTS: Our results revealed distinct dysbiosis of the gut microbiota in our regional CCA patients. The results revealed greater heterogeneity in the gut microbiome of CCA patients compared to HC samples. We found Blautia species to be significantly less abundant in CCA samples, and can distinguish CCA patients from HC. Blautia can also play a role in influencing the modification of secondary bile acids. Additionally, down-regulation of arachidonic acid and linoleic acid metabolism was observed in the tumor tissues of CHOL patients. In summary, the results revealed significant heterogeneity difference in the gut microbiome of CCA patients compared to HC samples, and detected the specifically decreased Blautia species in CCA patients, suggesting that Blautia may influence bile acid metabolic pathways. Further investigation is warranted to explore Blautia as a potential biomarker for CCA.},
}

@article {pmid40624576,
year = {2025},
author = {Liu, H and Su, Y and Ye, C and Zuo, D and Wang, L and Mei, X and Deng, W and Liu, Y and Huang, H and Hao, J and Zhao, J and Wang, D and Zhang, X and Zhu, Y and Liu, J and Yang, M and Zhu, S},
title = {Nucleotides enriched under heat stress recruit beneficial rhizomicrobes to protect plants from heat and root-rot stresses.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {160},
pmid = {40624576},
issn = {2049-2618},
support = {6254033//Beijing Municipal Natural Science Foundation/ ; U23A20202//Natural Science Foundation of China/ ; 2021YFD1601003//National Key Research and Development Program of China/ ; 2021JH002//Major Science and Technology Project of Kunming/ ; 202102AE090042//Major Science and Technology Projects in Yunnan Province/ ; },
abstract = {BACKGROUND: Plants thrive under biotic and abiotic stresses with the help of rhizomicrobiota. Root exudates play a pivotal role in recruiting beneficial microbes that assist plants in surviving environmental challenges, but the mechanisms of plant-microbiome interactions to resist multiple stresses remain elusive. We investigated how heat stress alters the rhizomicrobiomes of Panax notoginseng and how these heat stress-regulated microbes confer enhanced heat tolerance and disease resistance.

RESULTS: We revealed that heat stress at 36 °C caused thermal damage to plants while enhancing heat tolerance and disease resistance for the survival of subsequent plants. Specifically, the beneficial microbes Burkholderia sp. and Saitozyma podzolica were recruited by the heat-stressed P. notoginseng and were confirmed to be responsible for resisting multiple stresses. Heat stress-induced plant roots secrete nucleotides such as purines and pyrimidines to promote the proliferation of these two beneficial microbes rather than root-rot pathogens. The exogenous application of these nucleotides to natural soil also resulted in the enrichment of the same beneficial microbes. Cross-species validation experiments in Capsicum annuum (pepper) and Solanum lycopersicum (tomato) further demonstrated that co-application of nucleotides with beneficial microbes synergistically enhanced heat tolerance.

CONCLUSIONS: Our findings highlight a plant strategy for thriving under multiple adversities and propose a potential pathway by leveraging nucleotide-mediated recruitment of beneficial microbes for enhancing plant resilience against multiple stresses. Video Abstract.},
}

@article {pmid40624564,
year = {2025},
author = {Zhu, J and Jiang, MZ and Chen, X and Li, M and Wang, YL and Liu, C and Liu, SJ and Chen, WH},
title = {Systematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {161},
pmid = {40624564},
issn = {2049-2618},
support = {2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; 2022YFA1304100//Ministry of Science and Technology of the People's Republic of China/ ; },
abstract = {BACKGROUND: Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

METHODS: We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the "PairInteraX" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

RESULTS: Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

CONCLUSIONS: This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.},
}

@article {pmid40624562,
year = {2025},
author = {Ferreira, IM and Mantovani, HC and Viquez-Umana, F and Granja-Salcedo, YT and E Silva, LFC and Koontz, A and Holder, V and Pettigrew, JE and Rodrigues, AA and Rodrigues, AN and de Abreu, MJI and de Almeida, STR and Vidigal, PMP and Siqueira, GR and de Resende, FD},
title = {Feeding amylolytic and fibrolytic exogenous enzymes in feedlot diets: effects on ruminal parameters, nitrogen balance and microbial diversity of Nellore cattle.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {96},
pmid = {40624562},
issn = {1674-9782},
support = {2022/00989-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2023/10911-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2017/50339-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {BACKGROUND: The environmental impact of feedlot operations is a growing concern, as cattle excrete a significant portion of feed nutrients as waste. Exogenous feed enzymes (EFE) have gained interest for their potential to enhance feed efficiency in ruminants by improving nutrient digestion. However, EFE effects on ruminal parameters have shown inconsistencies, with limited research on nitrogen metabolism and rumen microbiome impacts. Moreover, the synergistic effects of combining different EFEs remain unclear. This study aimed to evaluate the effects of individual and combined EFE products in feedlot diets on ruminal fermentation parameters, nitrogen metabolism, and ruminal microbial communities. Ten rumen-cannulated Nellore steers [543 ± 28.6 kg of body weight (BW)] were distributed in a replicated Latin-square design (5 × 5) in individual pens. Treatments included: control (CON, no EFE supplementation), amylase [AML, 0.5 g/kg of diet dry matter (DM)], xylanase (FBL, 0.9 g/kg DM), half dose combination (HD, 0.25 g of AML + 0.45 g of FBL/kg of DM), and full dose combination (FD, 0.5 g of AML + 0.90 g of FBL/kg of DM). The experimental period lasted 19 d and included total urine and feces collection (d 15 to 18) and rumen fluid sampling (d 19) at 0, 4, 8, 12, and 16 h post-feeding for ammonia, volatile fatty acids (VFA), pH and microbiome analysis.

RESULTS: EFE supplemented animals exhibited lower ruminal ammonia concentrations (P = 0.040), and higher acetate proportions (P < 0.001) compared to the control group. EFE supplementation resulted in reduced nitrogen (N) excretion in feces (P = 0.049) and urine (P = 0.036), contributing to improved N retention and efficiency (P = 0.045). Additionally, EFE products induced shifts in various microbial taxa at family and genera levels (P ≤ 0.10), which may be associated with the changes observed in ruminal fermentation.

CONCLUSIONS: Our findings demonstrate that EFE supplementation enhances nitrogen retention, reduces ruminal ammonia, and alters ruminal fermentation profiles and microbial populations in feedlot cattle. While the expected synergism between amylase and xylanase did not significantly impact rumen fermentation parameters, it did induce shifts in the rumen microbiome. These results suggest that EFE supplementation may be a promising strategy for improving nutrient utilization and potentially reducing the environmental impact of feedlot operations.},
}

@article {pmid40624448,
year = {2025},
author = {Mitropoulou, G and Karapantzou, I and Prapa, I and Papanikolaou, D and Charovas, V and Kourkoutas, Y},
title = {Physicochemical, microbial, and microbiome dynamics in winery waste composting.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {40624448},
issn = {1614-7499},
support = {ΑΜΘΡ7-0074893//The European Union and National Resources under the Operational Programme "Eastern Macedonia and Thrace" 2014-2020/ ; MIS number: 5076618//The European Union and National Resources under the Operational Programme "Eastern Macedonia and Thrace" 2014-2020/ ; },
abstract = {Compared to more extensively studied composting substrates like food waste or animal manure, winery waste presents unique challenges and opportunities. Its high content of lignin, cellulose, and polyphenolic compounds demands specific microbial consortia for efficient degradation and can potentially inhibit microbial activity if not properly balanced. In the present study, analysis of winery waste composting that combines traditional microbial enumeration with high-resolution microbiome profiling, an approach rarely applied to this type of agro-industrial residue, was implemented. Moreover, a practical proof-of-concept study, for using the composted product as a partial substrate replacement in grapevine cultivation, closing the loop in vineyard waste management, was conducted. Key parameters, such as moisture content, pH, temperature, conductivity, and C/N ratio were monitored, over a 60-day period, along with changes in enzymatic activity and shifts in microbial populations, indicating dynamic microbial activity. At the end of the process, a reduction in the carbon-to-nitrogen (C/N) ratio was observed, pH was stabilized to neutral values, and dehydrogenases activity was notably decreased. Microbiome analysis revealed eight bacterial and six fungal phyla. Acidobacteria, Armatimonadetes, Bacteroidetes, Candidatus Saccharibacteria, Chloroflexi, Cyanobacteria, Planctomycetes were identified. The Ascomycota, Basidiomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, and Mucoromycota fungal phyla were also detected. The compost exhibited no phytotoxicity and supported grapevine growth comparable to commercial substrates. Winery waste microbial composting led to stable biofertilizer production, evidenced by physicochemical stability, lack of phytotoxicity, and effectiveness in promoting grapevine growth suggesting the potential of composting as a sustainable waste management solution in the winemaking industry.},
}

@article {pmid40624404,
year = {2025},
author = {Gao, T and Yun, J and Zheng, Y and Mu, C and Zhao, B},
title = {Time-dependent microbiome dynamics in orthodontic thermoplastic materials: comparing PETG and TPU.},
journal = {Clinical oral investigations},
volume = {29},
number = {8},
pages = {374},
pmid = {40624404},
issn = {1436-3771},
support = {202240182//Shanghai Municipal Health Commission/ ; SHH-2022-YJ-A01//Shanghai Stomatological Hospital/ ; },
abstract = {OBJECTIVES: This study compares the effects of thermoplastic polyurethane (TPU) and polyethylene terephthalate glycol (PETG) aligners on the oral microbiome and salivary pH during orthodontic treatment.

MATERIALS AND METHODS: Ten participants wore TPU and PETG aligners for 24 h. At five time points (1 min, 4, 8, 12, and 24 h), saliva was collected for pH analysis, and microbial samples were taken from both aligner and supragingival plaque surfaces for 16S rRNA sequencing. Statistical analyses included repeated Measures ANOVA for pH, Kruskal-Wallis test for alpha diversity, PERMANOVA for beta diversity, and two-way ANOVA for microbial composition.

RESULTS: In Group PETG, salivary pH significantly decreased from T0 to T4 (p < 0.05). No significant changes in alpha or beta microbiota diversity were observed in either group. Microbial shifts in supragingival plaque microbiomes were detected at T8 in Group PETG, while in Group TPU, these changes became evident between T12 and T24. In aligner microbiomes, Group TPU showed significant reductions in Veillonella, Actinomyces, and Fusobacterium at T24 (p < 0.05). In contrast, Group PETG exhibited significant increases in Streptococcus from T4 to T24 (p < 0.05) and Fusobacterium from T0 to T4 (p < 0.05), followed by a decline from T4 to T24 (p < 0.01).

CONCLUSIONS: PETG aligners caused significant reductions in salivary pH at T4 and triggered pronounced fluctuations at T8 in supragingival plaque microbiomes. TPU aligners caused a delayed decline in salivary pH between T8 and T12 and drove distinct structural shifts during prolonged wear from T12 to T24.

CLINICAL RELEVANCE: Material choice based on microbial impact highlights the need for personalized aligner materials and cleaning cycles.},
}

@article {pmid40624250,
year = {2025},
author = {Fukuda, T and Takagaki, M and Kaimori, J and Motooka, D and Nakamura, S and Kawabata, S and Nakamura, H and Ozaki, T and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Isaka, Y and Kishima, H},
title = {Differences in gut microbiome between autosomal dominant polycystic kidney disease with and without intracranial aneurysms.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24204},
pmid = {40624250},
issn = {2045-2322},
support = {22K09282//Japan Society for the Promotion of Science/ ; 21K09072//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Polycystic Kidney, Autosomal Dominant/microbiology/complications ; *Gastrointestinal Microbiome ; *Intracranial Aneurysm/microbiology/complications ; Female ; Male ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Adult ; Feces/microbiology ; Aged ; Bacteria/genetics/classification/isolation & purification ; },
abstract = {Autosomal dominant polycystic kidney disease (ADPKD) is a genetic disorder characterized by cyst formation in the kidneys, and is associated with an elevated risk of intracranial aneurysms (IAs). Although a family history is a recognized risk factor for IAs in patients with ADPKD, emerging research suggests that gut microbiome composition may influence IA development. We investigated the relationship between the gut microbiome and the development of IA in patients with ADPKD. We recruited patients with ADPKD with (IA group) and without (non-IA group) IA from Osaka University between October 2021 and December 2023. Fecal samples were analyzed using 16S rRNA sequencing. Data were processed using the QIIME 2 pipeline to determine microbial diversity and composition. We included 60 patients: 26 in the IA and 34 in the non-IA groups. There were significant differences in microbial beta diversity between the groups. The IA group had higher abundances of Eubacterium siraeum group, Oscillibacter, Fournierella, Negativibacillus, Colidextribacter, and Adlercreutzia. The non-IA group had higher abundances of Bifidobacterium, Megamonas, Acidaminococcus, Megasphaera, and Merdibacter. There was a significant association between the gut microbiome composition and the presence of IAs in patients with ADPKD. Specific bacterial taxa were differentially abundant between patients with ADPKD with and without IAs, suggesting a potential role of the gut microbiome in the pathogenesis of IAs in this genetically predisposed population.},
}

Humans
*Polycystic Kidney, Autosomal Dominant/microbiology/complications
*Gastrointestinal Microbiome
*Intracranial Aneurysm/microbiology/complications
Female
Male
Middle Aged
RNA, Ribosomal, 16S/genetics
Adult
Feces/microbiology
Aged
Bacteria/genetics/classification/isolation & purification

@article {pmid40624247,
year = {2025},
author = {Lin, YT and Sayols-Baixeras, S and Baldanzi, G and Dekkers, KF and Hammar, U and Nguyen, D and Nielsen, N and Eklund, AC and Varotsis, G and Holm, JB and Nielsen, HB and Lind, L and Bergström, G and Smith, JG and Engström, G and Ärnlöv, J and Sundström, J and Orho-Melander, M and Fall, T},
title = {The association between the gut microbiome and 24-h blood pressure measurements in the SCAPIS study.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {276},
pmid = {40624247},
issn = {2730-664X},
support = {ERC-STG-2018-801965, ERC-CoG-2014-649021, ERC-STG-2015-679242//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 2019-01471; 2018-02784; 2018-02837; 2021-03291//Vetenskapsrådet (Swedish Research Council)/ ; 2023-0687; 20200711 (M.O-M.); 20180343, 20210357; 20200173; 20190526//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; NNF20OC0063886//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; LUDC-IRC 15-0067//Stiftelsen för Strategisk Forskning (Swedish Foundation for Strategic Research)/ ; },
abstract = {BACKGROUND: There is mounting evidence supporting the role of the microbiota in hypertension from experimental studies and population-based studies. We aimed to investigate the relationship between specific characteristics of the gut microbiome and 24-h ambulatory blood pressure measurements.

METHODS: The association of gut microbial species and microbial functions, determined by shotgun metagenomic sequencing of fecal samples, with 24-h ambulatory blood pressure measurements in 3695 participants and office blood pressure was assessed in multivariable-adjusted models in 2770 participants without antihypertensive medication from the Swedish CArdioPulmonary bioImage Study.

RESULTS: Gut microbiome alpha diversity was negatively associated with diastolic blood pressure variability. Additionally, four microbial species were associated with at least one of the 24-h blood pressure traits. Streptococcus sp001556435 was associated with higher systolic blood pressure, Intestinimonas massiliensis and Dysosmobacter sp001916835 with lower systolic blood pressure, Dysosmobacter sp001916835 with lower diastolic blood pressure, and ER4 sp900317525 with lower systolic blood pressure variability. Moreover, office blood pressure data from a subsample without ambulatory blood pressure measurements replicated the association of Intestinimonas massiliensis with systolic blood pressure and Dysosmobacter sp001916835 with diastolic blood pressure. Species associated with 24-h blood pressure were linked to a similar pattern of metabolites.

CONCLUSIONS: In this large cross-sectional analysis, gut microbiome alpha diversity negatively associates with diastolic blood pressure variability, and four gut microbial species associate with 24-h blood pressure traits.},
}

@article {pmid40624229,
year = {2025},
author = {Lau, HC and Zhang, X and Yu, J},
title = {Gut microbiome in metabolic dysfunction-associated steatotic liver disease and associated hepatocellular carcinoma.},
journal = {Nature reviews. Gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
pmid = {40624229},
issn = {1759-5053},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease worldwide, affecting billions of the global population. It can gradually progress to more severe diseases, including steatohepatitis, cirrhosis and hepatocellular carcinoma. Studies have highlighted the importance of the gut microbiome in the pathogenesis and progression of MASLD. On the other hand, increasing evidence has revealed the clinical potential of targeting the gut microbiome to treat MASLD. In this Review, we summarize gut microbial alterations in MASLD, metabolic dysfunction-associated steatohepatitis and hepatocellular carcinoma. The mechanisms by which a dysregulated gut-liver axis contributes to disease progression are also described, including intestinal barrier dysfunction, chronic inflammation, and altered metabolic pathways (for example, bile acids) and microbial-derived metabolites (for example, short-chain fatty acids, tryptophan derivatives and endogenous ethanol). In addition, we discuss the clinical implications of utilizing the gut microbiome as a diagnostic biomarker and the therapeutic approaches to treat MASLD and related diseases such as faecal microbiota transplantation, probiotics and engineered bacteria, prebiotics and postbiotics, microbial-derived metabolites, antimicrobials and bacteriophages. Finally, we discuss current challenges in basic and translational research on the microbiome in MASLD and propose future directions to drive progress in this field.},
}

@article {pmid40624207,
year = {2025},
author = {Liu, J and Ye, Z and Zhang, Y and You, S and Sun, S and Lu, L and Su, W and Liu, J and Pu, J and Pan, H and Zhu, H and Deng, K and Yao, Y and Hu, X and Zhang, S},
title = {Multi-omics study reveals gut microbiota dysbiosis and tryptophan metabolism alterations in GH-PitNET progression.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24261},
pmid = {40624207},
issn = {2045-2322},
support = {pumch201911867//Youth Science Foundation of Peking Union Medical College Hospital/ ; 2022-PUMCH-B-114 and 2022-PUMCH-A-026//National High Level Hospital Clinical Research Funding/ ; 2022-PUMCH-B-114 and 2022-PUMCH-A-026//National High Level Hospital Clinical Research Funding/ ; 82270405//Chinese Natural Science Foundation/ ; 20220484031//Beijing Nova Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/metabolism ; *Tryptophan/metabolism ; Male ; Female ; Adult ; Metabolomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Disease Progression ; Feces/microbiology ; *Neuroendocrine Tumors/metabolism/microbiology/pathology ; *Growth Hormone-Secreting Pituitary Adenoma/metabolism/microbiology/pathology ; Case-Control Studies ; Multiomics ; Indoleacetic Acids ; },
abstract = {Growth hormone-secreting pituitary neuroendocrine tumors (GH-PitNETs) arise from the anterior pituitary gland and constitute 20-30% of all PitNETs, representing a significant subset of functional pituitary tumors. Despite their prevalence, the precise mechanisms underlying the development of these tumors remain elusive due to the complex pathophysiology of pituitary neoplasia. To investigate the potential role of the gut microbiome in GH-PitNETs, we conducted a comprehensive study involving 16S rRNA gene sequencing and metabolomics analysis of fecal and serum samples from 20 GH-PitNET patients and 30 healthy controls at Peking Union Medical College Hospital. Our findings revealed a distinct gut microbiota profile in GH-PitNET patients compared to healthy individuals, characterized by dysbiosis with increased abundance of Bacteroides and decreased abundance of Blautia and Bifidobacterium. Notably, alterations in specific bacterial taxa, including Intestinibacter bartlettii, Fusicatenibacter faecihominis, and Massilioclostridium, were observed in GH-PitNET patients. Concomitantly, serum metabolomics analysis identified 154 differentially abundant metabolites in GH-PitNET patients, with significant enrichment in pathways related to tryptophan metabolism. Among these metabolites, 3-indoleacetic acid (IAA) exhibited a obvious change, suggesting its potential research value for disease processing of GH-PitNETs. To further elucidate the mechanistic link between the gut microbiome and GH-PitNETs, we conducted in vitro and in vivo experiments, our results demonstrated that IAA could promote the proliferation of GH3 cells and significantly enhance growth hormone secretion by activating the cAMP pathway. These findings collectively suggest that gut microbiota dysbiosis may contribute to in the development and progression of GH-PitNETs by contributing to metabolic disturbances.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/metabolism
*Tryptophan/metabolism
Male
Female
Adult
Metabolomics/methods
Middle Aged
RNA, Ribosomal, 16S/genetics
Disease Progression
Feces/microbiology
*Neuroendocrine Tumors/metabolism/microbiology/pathology
*Growth Hormone-Secreting Pituitary Adenoma/metabolism/microbiology/pathology
Case-Control Studies
Multiomics
Indoleacetic Acids

@article {pmid40624115,
year = {2025},
author = {Liu, L and Wei, L and Mou, FX and Zhang, W and Wang, RF and Wang, Q and Wang, F},
title = {Oral microbiome dysbiosis in women with a history of pregnancy loss: a metagenomic cross-sectional study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24242},
pmid = {40624115},
issn = {2045-2322},
support = {Grant No. YJS-BD-19//the Special Fund for Doctoral Student Training of The Second Hospital of Lanzhou University in 2019/ ; Grant No. 071100107//The Science Foundation of Lanzhou University/ ; },
mesh = {Humans ; Female ; *Dysbiosis/microbiology ; Pregnancy ; Adult ; Cross-Sectional Studies ; Metagenomics/methods ; *Microbiota/genetics ; *Abortion, Spontaneous/microbiology ; Mouth Mucosa/microbiology ; Metagenome ; *Mouth/microbiology ; Young Adult ; },
abstract = {Pregnancy loss is a prevalent condition among women of reproductive age, significantly affecting fertility and psychological well-being. Despite advances in understanding the etiology of pregnancy loss, the role of the oral microbiome-its composition and metabolic activity-in influencing pregnancy outcomes remains underexplored. Previous studies have suggested that imbalances in the microbiota may contribute to adverse health outcomes, but few have investigated its association with pregnancy loss specifically. A total of 182 women of childbearing age were recruited for this study and divided into two groups: those with a history of pregnancy loss (n = 70) and a control group with no history of adverse pregnancy outcomes (n = 112). Clinical data and buccal mucosa samples were collected for metagenomic analysis. The inclusion of participants was based on their reproductive history, with particular attention to selecting women with at least one confirmed pregnancy loss and those with at least one successful live birth to serve as controls. The oral microbiota of women in the pregnancy loss group exhibited significantly lower richness and diversity compared to the control group (p < 0.05). Notably, specific genera such as Faecalibacterium, Roseburia, and Bacteroides were positively correlated with pregnancy loss, whereas Pseudomonas and Leptotrichia were correlated with it. These findings suggest a potential microbial dysbiosis associated with pregnancy loss. Our study identifies significant oral microbiota dysbiosis in women with pregnancy loss, characterized by reduced diversity and altered metabolic pathways. These findings underscore the potential role of oral microbial imbalance in adverse pregnancy outcomes. While our cross-sectional design and sample heterogeneity limit causal inference, they highlight the need for longitudinal cohorts and mechanistic studies. Future research integrating multi-niche microbiome profiling (e.g., gut and vaginal microbiota) is essential to unravel systemic interactions and advance targeted interventions for reproductive health.},
}

Humans
Female
*Dysbiosis/microbiology
Pregnancy
Adult
Cross-Sectional Studies
Metagenomics/methods
*Microbiota/genetics
*Abortion, Spontaneous/microbiology
Mouth Mucosa/microbiology
Metagenome
*Mouth/microbiology
Young Adult

@article {pmid40624095,
year = {2025},
author = {Pellowe, SD and Zhang, A and Bignell, DRD and Peña-Castillo, L and Walsh, CJ},
title = {Gut microbiota composition is related to anxiety and aggression scores in companion dogs.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24336},
pmid = {40624095},
issn = {2045-2322},
support = {20220468//MITACS eAccelerate Program/ ; 20201328//Seed, Bridge & Multidisciplinary Fund, Memorial University of Newfoundland, Canada/ ; },
mesh = {Animals ; Dogs ; *Gastrointestinal Microbiome ; *Aggression ; *Anxiety/microbiology ; *Pets/microbiology ; Behavior, Animal ; Male ; Feces/microbiology ; Female ; },
abstract = {There is mounting evidence for a link between behaviour and the gut microbiome in animal and human health. However, the role of the gut microbiome in the development and severity of behavioural issues in companion dogs is not yet fully understood. Here, we investigated the relationship between gut microbiota composition and aggression or anxiety in pet dogs. Dogs were assigned to higher or lower anxiety and aggression groups based on their owner's responses to the Canine Behavioral Assessment & Research Questionnaire (C-BARQ). Then, the gut microbiota composition of each animal, sequenced from microbial DNA extracted from fecal samples, was assessed for association with the dog's assigned behavioural group using multiple approaches. While minimal differences in relative abundance were seen between behavioural groups, machine-learning and compositional balance models could predict behavioural group based on gut microbiota composition. The genus Blautia was identified consistently across analyses, suggesting a link between this genus and anxiety in pet dogs. This study provides insight into specific bacteria that are linked to increased anxiety and aggression in pet dogs. Further research is required to identify bacteria to the species level, and to better understand the specific role of Blautia in the canine gut-brain axis.},
}

Animals
Dogs
*Gastrointestinal Microbiome
*Aggression
*Anxiety/microbiology
*Pets/microbiology
Behavior, Animal
Male
Feces/microbiology
Female

@article {pmid40624071,
year = {2025},
author = {Lee, YQ and Choi, YM and Park, SY and Kim, SK and Lee, M and Kim, D and Koduru, L and Lakshmanan, M and Jung, S and Kim, MJ and Choe, YH and Lee, DY},
title = {Genome-scale metabolic model-guided systematic framework for designing customized live biotherapeutic products.},
journal = {NPJ systems biology and applications},
volume = {11},
number = {1},
pages = {73},
pmid = {40624071},
issn = {2056-7189},
support = {32136-05-1-HD050//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; 32136-05-1-HD050//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry and Fisheries/ ; 2021-DD-UP-0369//Ministry of Science and ICT, South Korea/ ; RS-2024-00351458//Ministry of Science and ICT, South Korea/ ; 2021-DD-UP-0369//Ministry of Science and ICT, South Korea/ ; },
mesh = {Humans ; *Biological Products ; Models, Biological ; Microbiota/genetics ; Precision Medicine/methods ; },
abstract = {For the successful development of live biotherapeutic products (LBPs), which are promising microbiome-based therapeutics, it is required to rigorously evaluate their quality, safety, and efficacy. To this end, we present a model-guided framework where genome-scale metabolic models (GEMs) can be exploited for characterizing LBP candidate strains and their metabolic interactions with adjacent microbiome and host cells at a systems level. In this perspective, we outline a GEM-based strategy for screening, assessment, and design of personalized multi-strain LBPs.},
}

Humans
*Biological Products
Models, Biological
Microbiota/genetics
Precision Medicine/methods

@article {pmid40624015,
year = {2025},
author = {Wang, C and Zhang, L and Kan, C and He, J and Liang, W and Xia, R and Zhu, L and Yang, J and Jiang, X and Ma, W and Liang, Z and Xiao, Z and Zhang, J and Zhong, J and Sun, X and Chang, D and Wang, Z and Zhang, G and Li, M},
title = {Benefits and challenges of host depletion methods in profiling the upper and lower respiratory microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {130},
pmid = {40624015},
issn = {2055-5008},
support = {Z211100002121135//Beijing Nova Program/ ; 32100098//National Natural Science Foundation of China/ ; 2021097//Youth Innovation Promotion Association of the Chinese Academy of Sciences/ ; KCXFZ20211020163545004//Shenzhen Scientific and Technological Foundation/ ; SZZYSM202311009//Sanming Project of Medicine in Shenzen Municipality/ ; 2022YFA1304300//National Key Research and Development Program of China/ ; },
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; *Respiratory Tract Infections/microbiology/diagnosis ; Oropharynx/microbiology ; *Respiratory System/microbiology ; },
abstract = {Metagenomic sequencing for respiratory pathogen detection faces two challenges: efficient host DNA depletion and the representativeness of upper respiratory samples for lower tract infections. In this study, we benchmarked seven host depletion methods, including a new method (F_ase), using bronchoalveolar lavage fluid (BALF), oropharyngeal swab (OP), and mock samples. All methods significantly increased microbial reads, species richness, genes richness, and genome coverage while reduced bacterial biomass, introduced contamination, and altered microbial abundance. Some commensals and pathogens, including Prevotella spp. and Mycoplasma pneumoniae, were significantly diminished. F_ase demonstrated the most balanced performance. High-resolution microbiomes profiling revealed distinct microbial niche preferences and microbiome disparities between the upper and lower respiratory tract. In pneumonia patients, 16.7% of high-abundance species (>1%) in BALF were underrepresented (<0.1%) in OP, highlighting OP's limitations as lower respiratory proxies. This study underscores both the potential and challenges of metagenomic sequencing in advancing microbial ecology and clinical research.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
*Respiratory Tract Infections/microbiology/diagnosis
Oropharynx/microbiology
*Respiratory System/microbiology

@article {pmid40623969,
year = {2025},
author = {Kobel, CM and Leu, A and Vera-Ponce de León, A and Øyås, O and Lai, W and Altshuler, I and Hagen, LH and Wollenberg, RD and Søndergaard, MT and Bakshani, CR and Willats, WGT and Nicoll, L and McIlroy, SJ and Hvidsten, TR and Schmidt, O and Greening, C and Tyson, GW and Roehe, R and Aho, VTE and Pope, PB},
title = {Protozoal populations drive system-wide variation in the rumen microbiome.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {6238},
pmid = {40623969},
issn = {2041-1723},
support = {0054575-SuPAcow//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; No.101000213//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; FT230100560//Department of Education and Training | Australian Research Council (ARC)/ ; },
mesh = {Animals ; *Rumen/microbiology/parasitology ; *Gastrointestinal Microbiome ; Bacteria/classification/genetics/metabolism/isolation & purification ; Cattle ; *Microbiota ; },
abstract = {While rapid progress has been made to characterize the bacterial and archaeal populations of the rumen microbiome, insight into how they interact with keystone protozoal species remains elusive. Here, we reveal two distinct system-wide rumen community types (RCT-A and RCT-B) that are not strongly associated with host phenotype nor genotype but instead linked to protozoal community patterns. We leveraged a series of multi-omic datasets to show that the dominant Epidinium spp. in animals with RCT-B employ a plethora of fiber-degrading enzymes that present enriched Prevotella spp. a favorable carbon landscape to forage upon. Conversely, animals with RCT-A, dominated by genera Isotricha and Entodinium, harbor a more even distribution of fiber, protein, and amino acid metabolizers, reflected by higher detection of metabolites from both protozoal and bacterial activity. Our results indicate that microbiome variation across key protozoal and bacterial populations is interlinked, which should act as an important consideration for future development of microbiome-based technologies.},
}

Animals
*Rumen/microbiology/parasitology
*Gastrointestinal Microbiome
Bacteria/classification/genetics/metabolism/isolation & purification
Cattle
*Microbiota

@article {pmid40623769,
year = {2025},
author = {Basoya, R and Singh, B and Basi, A and Aggarwal, S},
title = {Role of microbiome in cancer progression.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {79-106},
doi = {10.1016/bs.ircmb.2024.12.013},
pmid = {40623769},
issn = {1937-6448},
mesh = {Humans ; *Neoplasms/microbiology/pathology/therapy ; *Disease Progression ; *Microbiota ; Animals ; },
abstract = {The human microbiome plays a crucial role in maintaining health and preventing disease. Dysbiosis, or imbalance, in the microbiome, has been linked to various diseases, including cancer. This chapter explores the influence of microbiomes on different organs, immune system modulation, and cancer development. Specific microorganisms, such as Helicobacter pylori, Escherichia coli, and human papillomavirus (HPV), contribute to gastric, colorectal, and cervical cancer through mechanisms like immunomodulation and proliferative signaling pathways. Dysbiosis-induced cancer progression involves NF-κB, Wnt/β-catenin, and JAK/STAT signaling. Recent studies highlight the microbiome's potential in cancer diagnosis and immunotherapy. Fecal Microbiota Transplantation (FMT) and predictive biomarkers, such as Porphyromonas gingivalis and Escherichia-Shigella, show promise in treating colorectal cancer. The microbiome influences tumor biology and immune response, affecting immunotherapeutic efficacy. Understanding microbiome-cancer interactions offers new opportunities for improved diagnosis and personalized therapy. This chapter provides comprehensive insights into the role of microbiome in cancer progression, emphasizing the importance of microbiome research in developing effective cancer treatments.},
}

Humans
*Neoplasms/microbiology/pathology/therapy
*Disease Progression
*Microbiota
Animals

@article {pmid40623767,
year = {2025},
author = {Abdel-Wahab, R and Kerr, TD and McGrail, DJ and Diab, A and Bentebibel, SE},
title = {The role of microbiome in CAR-T cell therapy.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {197-212},
doi = {10.1016/bs.ircmb.2024.12.015},
pmid = {40623767},
issn = {1937-6448},
mesh = {Humans ; *Immunotherapy, Adoptive/methods ; Animals ; *Receptors, Chimeric Antigen/metabolism/immunology ; *Microbiota/immunology ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; },
abstract = {Chimeric Antigen Receptor (CAR) T-cell therapy represents a significant advancement in treating hematologic malignancies. However, its therapeutic efficacy against solid tumors remains hindered by several challenges, including suboptimal antitumor activity, high toxicity, and the emergence of resistance mechanisms. In recent years, the microbiome has emerged as a critical modulator of cancer immunotherapy outcomes. Yet, the precise molecular and cellular pathways through which the microbiome influences CAR-T cell efficacy remain largely unexplored. This chapter provides a comprehensive review of current knowledge regarding the interactions between CAR-T cell therapy and the microbiome, with particular emphasis on gut microbial dynamics. Additionally, it underscores the existing gaps in our understanding of these interactions and highlights key preclinical and clinical findings. We also discuss innovative strategies aimed at manipulating the microbiome to enhance CAR-T cell function, thereby presenting potential avenues for optimizing therapeutic outcomes.},
}

Humans
*Immunotherapy, Adoptive/methods
Animals
*Receptors, Chimeric Antigen/metabolism/immunology
*Microbiota/immunology
*Gastrointestinal Microbiome/immunology
*Neoplasms/therapy/immunology/microbiology

@article {pmid40623766,
year = {2025},
author = {Karimi, N and De Anda, AB and Yang, R and Aksan, E and Grimaldo, MT and Moghaddam, SJ},
title = {The multipotential effect of microbiome in lung cancer development and progression.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {171-196},
doi = {10.1016/bs.ircmb.2024.12.011},
pmid = {40623766},
issn = {1937-6448},
mesh = {Humans ; *Lung Neoplasms/microbiology/pathology/therapy ; *Disease Progression ; Animals ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {Lung cancer is the leading cause of cancer-related deaths worldwide. Despite the introduction of numerous drugs to cure this deadly disease, treatment outcomes differ significantly among patients. This differential response has drawn attention to individual patient characteristics, particularly the microbiome. In recent years, the microbiome has garnered significant interest from scientists in various fields including autoimmune, inflammatory, and cancer research. These studies have primarily focused on the composition and diversity of the gut microbiome, pointing out its fundamental effect on the development and progression of diseases such as asthma, chronic obstructive pulmonary disease (COPD), cystic fibrosis, and lung cancer. Recent findings have also highlighted the impact of the gut microbiome on the efficacy of immunotherapy in lung cancer patients. In this chapter, we will delve into the multifaceted role of microbiome in lung cancer prevention, progression, and treatment outcome.},
}

Humans
*Lung Neoplasms/microbiology/pathology/therapy
*Disease Progression
Animals
*Microbiota
*Gastrointestinal Microbiome

@article {pmid40623765,
year = {2025},
author = {Vig, M and Dubey, S},
title = {Gut microbiome and tumor immunotherapy.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {147-170},
doi = {10.1016/bs.ircmb.2024.12.014},
pmid = {40623765},
issn = {1937-6448},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy/methods ; Animals ; },
abstract = {Multiple innovative molecular techniques have established compelling connections between the gut microbiome and cancers. Studies have also revealed that the microbiome and microbiome-specific metabolites can significantly influence cancer treatments like chemotherapy, radiotherapy, and immunotherapy. Advancements in cancer immunotherapy driven by a targeted immune system approach have considerably improved the treatment landscape in cancer. However, the full potential of tumor immunotherapy remains to be explored, and many challenges need to be addressed. This review provides a summary of the current evidence regarding the presence of microbiota and how it can impact the response to Food and Drug Administration (FDA) approved cancer immunotherapies, such as immune checkpoint inhibitors (ICIs) or chimeric antigen receptor T (CAR-T) cell therapy. Additionally, it addresses the challenges and limitations of gut microbiome and cancer immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Neoplasms/therapy/immunology/microbiology
*Immunotherapy/methods
Animals

@article {pmid40623764,
year = {2025},
author = {Richards, J and Davis, EL and Shakila, L and Narayanan, J and Aggarwal, S and Mishra, A and Venkata, KKM and Walther, BK and Dominic, A},
title = {Microbiome-mediated immune modulation in tumor microenvironment.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {107-145},
doi = {10.1016/bs.ircmb.2024.12.012},
pmid = {40623764},
issn = {1937-6448},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Neoplasms/immunology/microbiology/pathology ; *Microbiota/immunology ; Animals ; },
abstract = {This chapter explores the complex interplay between the tumor microenvironment (TME), the microbiome, and the immune system. It focuses on how microbes and their metabolites influence tumor development, progression, and the subsequent immune responses. The TME is a highly complex environment made up of cancer cells, immune cells, and the extracellular matrix, where immune cells can either inhibit or promote tumor growth depending on the context. The chapter highlights several key mechanisms of interaction, including microbial metabolites, the presentation of microbial antigens by tumor or immune cells, and the role of immune checkpoints, such as PD-L1, in modulating immune responses. Certain bacteria, viruses, and fungi can trigger immune responses that lead to the destruction of cancer cells, often through processes such as immunogenic cell death (ICD). Conversely, dysbiosis, or an imbalance in microbial communities, can create a pro-tumorigenic environment, aiding in tumor progression through chronic inflammation, immune suppression, and metabolic alterations. The chapter categorizes microbial interactions with cancer into three areas: microbes directly causing cancer (e.g., Epstein-Barr virus and HPV), cancers that induce infections (e.g., obstructing the respiratory or digestive systems), and tumors located in organs with natural microbiomes, such as the gastrointestinal tract. In addition to these mechanisms, the chapter also illuminates how microbial antigens can serve as potential identifiers and tools for cancer diagnosis and treatment, offering new avenues for personalized medicine. The insights gained from this exploration are important for advancing microbial-based therapies and improving the effectiveness of immunotherapies in cancer treatment.},
}

Humans
*Tumor Microenvironment/immunology
*Neoplasms/immunology/microbiology/pathology
*Microbiota/immunology
Animals

@article {pmid40623763,
year = {2025},
author = {Agrawal, P and Mendhey, P and Kumar, R and Patel, S and Kaushik, PK and Dadsena, A and Kumar, S},
title = {Introduction to microbiomes in health and diseases.},
journal = {International review of cell and molecular biology},
volume = {394},
number = {},
pages = {1-42},
doi = {10.1016/bs.ircmb.2024.12.010},
pmid = {40623763},
issn = {1937-6448},
mesh = {Humans ; *Microbiota ; *Health ; *Disease ; Animals ; },
abstract = {The human microbiome is a complex ecological system of commensal, symbiotic, and pathogenic microorganisms that plays a crucial role in human health and disease. The microbiome includes both the living microorganisms also called microbiota and their synthesized metabolites and structural components. It is distributed to the gastrointestinal tract, skin, respiratory system, and oral cavity, each with a distinct microbial composition. Dysbiosis, or imbalance in the microbiome is linked to numerous diseases such as eczema, gastric ulcers, cardiovascular diseases, and cancer. The axes of microbial activity and their connections to disease, including the gut-skin, gut-lung, gut-brain, and gut-kidney play a crucial role in health and disease conditions. Also, the role of the microbiome in cancer development and response to therapy is examined. This book chapter underscores the importance of maintaining a balanced microbiome for overall health and the potential for microbiome-based interventions in disease prevention and treatment.},
}

Humans
*Microbiota
*Health
*Disease
Animals

@article {pmid40623407,
year = {2025},
author = {Leti, M and Garidou, L and Cuisiat, SV and Stennevin, A and Doat, G and Mias, C},
title = {Plant Extracts in Acne Management: a narrative review.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-51},
doi = {10.1159/000547149},
pmid = {40623407},
issn = {1421-9832},
abstract = {BACKGROUND: Acne is a chronic inflammatory skin disease associated with impaired pilosebaceous unit function leading to the development of noninflammatory and inflammatory lesions and, in some cases, persistent post-inflammatory erythema, hyperpigmentation and scarring. Acne pathophysiology is complex, involving altered sebum production and composition, abnormal keratinization, microbiome dysbiosis, and skin inflammation. Conventional therapies, such as topical retinoids, antibiotics and benzoyl peroxide, are the first-line treatments for mild-to-moderate acne, but antibiotic resistance and local adverse effects can have a negative impact on therapeutic outcomes, leading to a growing interest in alternative strategies for disease management. The use of dermocosmetics is increasingly being recognized as a useful strategy to improve treatment outcomes and patient adherence. In particular, there has been a recent increase in research aiming to identify natural plant-based ingredients with properties that target the multiple pathogenic mechanisms involved in acne, but which have less impact on skin barrier function.

SUMMARY: This review provides a summary of the anti-acne properties of the most well-characterized plant extracts and phytocompounds used in dermocosmetic anti-acne products, based on insights gained from in vitro, ex vivo and in vivo studies. Evidence gained from clinical trials evaluating the effectiveness and safety of topical formulations containing these herbal ingredients is also presented. Finally, several less well-characterized herbal extracts and phytocompounds with promising anti-acne properties are described.

KEY MESSAGES: Although research is ongoing for many of the anti-acne herbal ingredients identified so far, this review highlights the effectiveness of topical plant-based formulations for reducing lesion counts and disease severity in acne patients, as well as the rebalancing effects of herbal ingredients on sebum composition, microbial diversity, and pilosebaceous unit cell differentiation. Taken together with the antibiofilm, anti-inflammatory, antioxidant, and skin barrier repair properties demonstrated for many of these extracts, current evidence suggests that dermocosmetics with plant-based ingredients show great promise for acne management, either as monotherapies, maintenance treatments, or in combination with conventional drugs.},
}

@article {pmid40622960,
year = {2025},
author = {Farda, B and Pellegrini, M and Coppari, L and Cacchio, P and Lunghi, E},
title = {Isolation and Identification of Bacterial Strains from Skin of Terrestrial Amphibians.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {220},
pages = {},
doi = {10.3791/67862},
pmid = {40622960},
issn = {1940-087X},
mesh = {Animals ; *Skin/microbiology ; *Bacteria/isolation & purification/classification ; *Amphibians/microbiology ; *Bacteriological Techniques/methods ; Microbiota ; },
abstract = {The microbiota is a vital element of higher organisms, with the cutaneous microbiota significantly contributing to the organism's defense against external agents. There is no standard method to sample Speleomantes (Amphibia: Plethodontidae) skin microbial communities for the microbial culturing approach. To address this, we have developed a practical protocol for isolating bacteria from the skin of individuals and a best practice for handling and storing samples. The steps are straightforward: swabs are stored in a physiological saline solution supplemented with glycerol upon sampling. Once transferred in the laboratory, swabs can be stored at +4 °C for a maximum of 10 days to ensure the integrity of the microbial community. This study offers interesting insights into the cutaneous microbiota investigation of terrestrial amphibian species, such as those belonging to the genus Speleomantes. This approach contributes to implementing, monitoring and conserving measures for endangered species and might improve the knowledge of microbiota's function in the health and ecology of amphibians. This protocol may also have broader significance for microbiome research in many wildlife conservation scenarios.},
}

Animals
*Skin/microbiology
*Bacteria/isolation & purification/classification
*Amphibians/microbiology
*Bacteriological Techniques/methods
Microbiota

@article {pmid40622660,
year = {2025},
author = {Kong, L and Zhu, B and Zhuang, Y and Lai, J and Hu, S},
title = {Viewing Psychiatric Disorders Through Viruses: Simple Architecture, Burgeoning Implications.},
journal = {Neuroscience bulletin},
volume = {},
number = {},
pages = {},
pmid = {40622660},
issn = {1995-8218},
abstract = {A growing interest in the comprehensive pathogenic mechanisms of psychiatric disorders from the perspective of the microbiome has been witnessed in recent decades; the intrinsic link between microbiota and brain function through the microbiota-gut-brain axis or other pathways has gradually been realized. However, little research has focused on viruses-entities characterized by smaller dimensions, simpler structures, greater diversity, and more intricate interactions with their surrounding milieu compared to bacteria. To date, alterations in several populations of bacteriophages and viruses have been documented in both mouse models and patients with psychiatric disorders, including schizophrenia, major depressive disorder, autism spectrum disorder, and Alzheimer's disease, accompanied by metabolic disruptions that may directly or indirectly impact brain function. In addition, eukaryotic virus infection-mediated brain dysfunction provides insights into the psychiatric pathology involving viruses. Efforts towards virus-based diagnostic and therapeutic approaches have primarily been documented. However, limitations due to the lack of large-scale cohort studies, reliability, clinical applicability, and the unclear role of viruses in microbiota interactions pose a challenge for future studies. Nevertheless, it is conceivable that investigations into viruses herald a new era in the field of precise psychiatry.},
}

@article {pmid40622649,
year = {2025},
author = {G R, SK and V, M},
title = {Scaling Up Postbiotics Production: A Prospective Review of Processes and Health Benefits.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40622649},
issn = {1867-1314},
abstract = {Postbiotics are bioactive compounds produced by probiotic bacteria that have taken the spotlight for their significant health benefits. These postbiotics include digestive enzymes, short-chain fatty acids, cell wall components, bacteriocins, exopolysaccharides, and vitamins. Among many health benefits, postbiotics possess immunomodulatory effect; cholesterol regulation; antimicrobial, antioxidant, and anti-inflammatory properties; enhanced gut health; and reduced risk of cardiovascular diseases, although the mechanism of action of these health benefits is yet to be fully understood. Forecast indicates a rising industrial demand for postbiotic production. This review summarizes the tools and techniques employed in optimizing postbiotic production that aid in overcoming those challenges that currently interrupt industrial scale-up. Plackett-Burman design, response surface methodology (RSM), Taguchi method, and central composite design (CCD) are significant tools for optimizing postbiotic production conditions. Molecular techniques including genetic engineering, synthetic biology tools such as CRISPR-Cas9, and metabolic engineering are potential techniques to enhance postbiotic production. Despite these advancements, challenges remain in industrial scale-up (stability, quality, yield, and consistency). Understanding the correlation between high cell density and postbiotic yield is crucial for industrial scale-up and optimized production. However, further in-depth research is in demand for industrial production of postbiotics. This review would benefit researchers exploring the mechanism of action and industrial production of postbiotics.},
}

@article {pmid40622577,
year = {2025},
author = {Holle, J and Behrens, F and Koppe, L},
title = {Pediatric and adult point of view on the gut-kidney axis in CKD.},
journal = {Pediatric nephrology (Berlin, Germany)},
volume = {},
number = {},
pages = {},
pmid = {40622577},
issn = {1432-198X},
abstract = {Chronic non-communicable diseases pose a significant global health challenge, with the human gut microbiota emerging as a key player in several (patho) physiological functions, including immunity, metabolic homeostasis, and inflammation. While dysbiosis, or imbalance in taxonomy and function of gut microbiota, has been implicated in chronic kidney disease (CKD), whether it is a cause or consequence of the disease remains controversial. Understanding the gut microbiota's role in CKD pathogenesis is essential for developing novel therapeutic interventions. CKD in children presents unique opportunities for studying disease-specific mechanisms due to the absence of comorbidities typically seen in adults, such as diabetes, obesity, and hypertension, although few studies exist. On the other hand, unlike the relatively stable gut microbiota of healthy adults, the infant's microbiome undergoes significant development and maturation during the early years of life. Integrating knowledge from both pediatric and adult populations may provide a comprehensive understanding of gut microbiota dysbiosis in CKD. This review aims to provide an overview of the gut microbiota's development in healthy individuals and CKD patients and discusses how these findings can inform personalized treatment approaches to CKD.},
}

@article {pmid40622440,
year = {2025},
author = {Woltsche, J and Pacher-Deutsch, C and Fürst, S and Gulden, L and Schwarzl, J and Feldbacher, N and Nepel, M and Celcer, L and Hasl, N and Rieper, V and Stadlbauer, V and Horvath, A},
title = {Microbial Dysbiosis in the Urinary Microbiome of Patients with Cirrhosis.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000003634},
pmid = {40622440},
issn = {1572-0241},
abstract = {INTRODUCTION: Cirrhosis is associated with microbiome alterations beyond the gut, including skin, saliva, and serum. This study investigated the urinary microbiome (UMB) in patients with cirrhosis, who have an increased risk of urinary tract infections (UTIs).

METHODS: Midstream urine from 137 patients was analysed via 16S rRNA sequencing; 68 patients with cirrhosis and 32 non-cirrhotic controls met inclusion criteria.

RESULTS: Patients with cirrhosis showed significantly reduced alpha-diversity. The UMB of controls was enriched in Streptococcus species.

DISCUSSION: Reduced microbial diversity and lower Streptococcus abundance in patients with cirrhosis might help to explain their heightened susceptibility to UTIs.},
}

@article {pmid40622379,
year = {2025},
author = {Mars Brisbin, M and Acord, M and Davitt, R and Bent, S and Van Mooy, BAS and Flaum, E and Norlin, A and Turner, J and Krinos, A and Alexander, H and Saito, M},
title = {Exploring the Phaeosphere: Characterizing the microbiomes of Phaeocystis antarctica colonies from the coastal Southern Ocean and laboratory culture.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70051},
pmid = {40622379},
issn = {1529-8817},
support = {874439//Simons Foundation/ ; OPP-2224611//National Science Foundation/ ; },
abstract = {Interactions between phytoplankton and bacteria play critical roles in shaping marine ecosystems. However, the intricate relationships within these communities-particularly in rapidly changing polar environments-remain poorly understood. We use targeted methods to directly characterize the microbiomes of individual colonies of Phaeocystis antarctica, a keystone phytoplankton species in the Southern Ocean, and showed that colony microbiomes were consistent across individual colonies collected 108 nautical miles apart. These results suggest that hosting specific colony microbiomes is a shared trait across colony-forming Phaeocystis species, with different species hosting colony microbiomes suited to their respective environments. The bacterial orders Alteromonadales, Oceanospirillales, and Sphingomonadales dominated the microbiomes of all field-collected P. antarctica colonies. The relative abundances of bacterial taxa comprising the majority of field-collected colony microbiomes-for example, Paraglaciecola sp. (Alteromonadales) and Nitrincolaceae (Oceanospirillales)-correlated with Phaeocystis abundance in surface waters, highlighting their potential roles in bloom dynamics and carbon cycling. After a year of laboratory culture, we observed a reduction in colony microbiome diversity, and Caulobacterales, Cellvibrionales, and Rhodobacterales dominated the cultured colony microbiomes. Notably, abundant genera in field-collected colony microbiomes that were lost in culture were psychrophiles. The shift in microbiome structure emphasizes the importance of field-based studies to capture the complexity of microbial interactions, especially for species from polar environments that are difficult to replicate in laboratory conditions. This research provides valuable insights into the ecological significance of prokaryotic interactions with a key phytoplankton species and underscores the necessity of considering these dynamics in the context of climate-driven shifts in marine ecosystems.},
}

@article {pmid40622159,
year = {2025},
author = {Hernandez, JB and Hayer, SS and Alvarez, S and Fischer, A and Hassenstab, HR and Cooper, K and Alsafwani, ZW and Benson, AK and Suhr Van Haute, MJ and Izard, J and Song, H-S and Clayton, JB},
title = {Microbiome and metabolome association network analysis identifies Clostridium_sensu_stricto_1 as a stronger keystone genus candidate than Bifidobacterium in the gut of common marmosets.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0021425},
doi = {10.1128/msystems.00214-25},
pmid = {40622159},
issn = {2379-5077},
abstract = {The common marmoset (Callithrix jacchus), a nonhuman primate species, is a model organism of great interest due to its translational value in a variety of research settings, including the field of microbiomics. While the composition of the marmoset's gut microbiome has been somewhat described in captivity, little is known about how gut microbiota interact with each other over time and how they relate to metabolite production. To help answer this, we characterized interactions in the gut microbiome of the common marmoset by calculating the Spearman correlation coefficient between 16S rDNA-derived relative genera abundance data and targeted metabolomics data collected longitudinally from 10 captive marmosets. Association network graphs were used to visualize significant correlations and identify genera and metabolites that have high degree centrality, marking them as more influential within the microbiome. The genus Clostridium_sensu_stricto_1 engaged in the most metabolomic associations, indicating that it potentially plays a gatekeeping role over metabolites involved in microbial growth and signaling. Its associations with downregulated taurine and bile acids further suggest Clostridium_sensu_stricto_1 modifies bile acids to exert its influence. Flavonifractor and several Bacteroidales members had the most bacterial associations and were negatively associated with Bifidobacterium, indicating a potential competitive relationship. To further characterize microbiome interactions, we performed hierarchical clustering on significant within-dataset associations and developed a new "Keystone Candidate Score" metric that identified Clostridium_sensu_stricto_1 and Alloprevotella as the most influential bacteria (so-called candidate keystone genera) in the marmoset gut microbiome.IMPORTANCEPrevious studies have identified significant individuality within the gut microbiome of common marmosets. The reasons for this inter-subject variability and how it relates to health in captivity are poorly understood, owing to a lack of knowledge regarding dynamic interactions between specific microbiota. To that end, this study characterized significant temporal associations between the gut microbiome and metabolome of healthy captive marmosets. Our findings suggest that certain microbial taxa exert a stronger influence within the gut than others. Specifically, Bifidobacterium was the most abundant genus and primary driving force behind subject-specific microbiome differences, while Clostridium_sensu_stricto_1 and bacteria from the order Bacteroidales were the main sources, respectively, for significant bacteria-metabolite and bacteria-bacteria associations. Together, this suggests that Bifidobacterium may compete with the other taxa for resources and a metabolic niche in the marmoset microbiome.},
}

@article {pmid40621937,
year = {2025},
author = {Choi, A and Pia, L and Kaspar, JR},
title = {Seven genome sequences of Rothia spp. isolated from human saliva.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0046525},
doi = {10.1128/mra.00465-25},
pmid = {40621937},
issn = {2576-098X},
abstract = {Rothia are understudied commensal bacteria within the human oral cavity and respiratory tract and can cause opportunistic infections. We report the complete genome sequences of seven Rothia spp. strains isolated from pooled human saliva, including four strains of Rothia mucilaginosa (59.5% GC) and three strains of Rothia dentocariosa (53.8% GC).},
}

@article {pmid40621936,
year = {2025},
author = {Kolar, O and Appleberry, H and Wolfe, AJ and Kula, A and Putonti, C},
title = {Complete genome sequence of vaginal swab isolate Enterococcus faecalis UMB6935B, including two complete plasmids.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0036825},
doi = {10.1128/mra.00368-25},
pmid = {40621936},
issn = {2576-098X},
abstract = {Enterococcus faecalis has been identified as a member of the vaginal community of healthy females, in addition to its association with vaginitis and urinary tract infections. Here we present the hybrid assembly of an E. faecalis strain, UMB6935B, isolated from a vaginal swab from a female with overactive bladder symptoms.},
}

@article {pmid40621926,
year = {2025},
author = {Samson, R and Kumar, S and Dastager, S and Khairnar, K and Dharne, M},
title = {Deciphering the comprehensive microbiome of glacier-fed Ganges and functional aspects: implications for one health.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0172024},
doi = {10.1128/spectrum.01720-24},
pmid = {40621926},
issn = {2165-0497},
abstract = {Glacier-fed rivers are significant ecological components of the river catchments, yet their microbial diversity and the associated antimicrobial potential remain underexplored. The Ganges is a glacier-fed river of immense cultural, religious, and ecological significance that supports over 400 million people downstream, providing essential water for agriculture, industry, and daily use. Despite its importance, the microbial community composition and antimicrobial potential, across its relatively pristine origin, remain largely underexplored. One possible explanation for this could be the lower microbial load in the upstream glacier-fed region, which likely results in a reduced DNA yield, insufficient for whole-metagenome sequencing, in contrast to the more biologically diverse and nutrient-rich lower reaches. In this study, we developed an efficient DNA extraction and amplification method using low-input DNA to sequence the microbiome from sediments of the glacier-fed Ganges River in pre-monsoon and post-monsoon over 2 years. Taxonomic and functional diversity of bacterial and viral (phage) communities were analyzed, together with the seasonal variations in their composition. Significant differences in microbial communities were observed in response to seasonal shifts (P < 0.05). During the dry season, Proteobacteria and Actinobacteria were predominant, while Bacteroidetes and Firmicutes were abundant post-monsoon (P < 0.05). The microbiome harbors potential for the biosynthesis of streptomycin, phenylpropanoid, penicillin, and cephalosporins. Bacteriophages from Podoviridae, Myoviridae, and Siphoviridae showed lytic potential against putrefying and pathogenic bacteria. This first comprehensive study on the glacier-fed Ganges River highlights significant seasonal shifts in microbial diversity. The initial insights into the functional profile of the bacterial and phage diversity offer opportunities to explore various natural compounds and enzymes to tackle antimicrobial resistance under the one-health canopy.IMPORTANCEThis study addresses a knowledge gap by exploring the microbial diversity and antimicrobial potential of the glacier-fed Ganges River across different seasons. The findings reveal various taxa with biosynthetic capabilities for antimicrobial compounds. Additionally, the presence of bacteriophages with lytic potential opens up opportunities for their exploration and application spanning various domains of one health. These findings lay a foundational basis for understanding the unique properties of this riverine ecosystem and offer valuable insights into environmental conservation and the potential to tackle antimicrobial resistance.},
}

@article {pmid40621718,
year = {2025},
author = {Rai, SK and Hu, Y and Ding, M and Hu, FB and Wang, M and Chavarro, JE and McCormick, N and Choi, HK and Sun, Q},
title = {Long-term lignan intake, whole grain foods, and the risk of gout: results from two prospective cohort studies.},
journal = {Arthritis care & research},
volume = {},
number = {},
pages = {},
doi = {10.1002/acr.25596},
pmid = {40621718},
issn = {2151-4658},
abstract = {OBJECTIVE: Multiple plant-based dietary patterns are inversely associated with gout, although the individual constituents driving this association remain unclear. Dietary lignans, a major group of phytoestrogens abundant in plant foods, are metabolized by the gut microflora and may modulate gout risk. We examined the associations between dietary lignan intake, certain whole grain foods rich in lignans, and incident gout.

METHODS: We analyzed data from 122,680 individuals in the Health Professionals Follow-up Study and Nurses' Health Study. We administered a food frequency questionnaire every 2-4 years. We used Cox models to evaluate associations between dietary lignans, whole grain foods, and confirmed gout.

RESULTS: Higher intakes of matairesinol (hazard ratio [HR] and 95% confidence interval [CI] comparing extreme quintiles: 0.78 [0.69, 0.90]; P trend=0.002) and secoisolariciresinol (0.78 [0.68, 0.89]; P trend=0.002) were both associated with lower gout risk, while pinoresinol and lariciresinol were not associated with gout. We found inverse associations of whole grain cold breakfast cereals (HR for those consuming ≥1 serving/day 0.62 [0.53, 0.73]), cooked oatmeal/oat bran (HR for those consuming ≥2 servings/week 0.78 [0.70, 0.86]), and bran added to food (HR for those consuming ≥2 servings/week 0.84 [0.74, 0.95]), but not dark breads or other cooked breakfast cereals, with gout.

CONCLUSION: Higher intakes of matairesinol and secoisolariciresinol, as well as whole grain cold breakfast cereals, oatmeal, and added bran, were each significantly associated with lower gout risk. These findings support adherence to healthful plant-based diets for gout and suggest a potential role of the gut microbiome in gout pathogenesis.},
}

@article {pmid40621717,
year = {2025},
author = {Liu, S and Li, Y and Shi, Y and Rao, Z and Zhang, Y and Zhang, Y and Wang, T and Kong, H and Zhu, S and Zhu, DM and Yu, Y and Zhu, J},
title = {Multi-omics analyses of the gut microbiome, fecal metabolome, and multimodal brain MRI reveal the role of Alistipes and its related metabolites in major depressive disorder.},
journal = {Psychological medicine},
volume = {55},
number = {},
pages = {e190},
doi = {10.1017/S003329172510072X},
pmid = {40621717},
issn = {1469-8978},
support = {82471952//National Natural Science Foundation of China/ ; 82371928//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Depressive Disorder, Major/microbiology/metabolism/diagnostic imaging/physiopathology ; *Gastrointestinal Microbiome/physiology ; Male ; Magnetic Resonance Imaging ; Adult ; *Feces/microbiology/chemistry ; Female ; *Metabolome ; Middle Aged ; *Brain/diagnostic imaging ; Metabolomics ; Case-Control Studies ; *Dysbiosis/microbiology ; Multiomics ; },
abstract = {BACKGROUND: Compelling evidence claims that gut microbial dysbiosis may be causally associated with major depressive disorder (MDD), with a particular focus on Alistipes. However, little is known about the potential microbiota-gut-brain axis mechanisms by which Alistipes exerts its pathogenic effects in MDD.

METHODS: We collected data from 16S rDNA amplicon sequencing, untargeted metabolomics, and multimodal brain magnetic resonance imaging from 111 MDD patients and 102 healthy controls. We used multistage linked analyses, including group comparisons, correlation analyses, and mediation analyses, to explore the relationships between the gut microbiome (Alistipes), fecal metabolome, brain imaging, and behaviors in MDD.

RESULTS: Gut microbiome analysis demonstrated that MDD patients had a higher abundance of Alistipes relative to controls. Partial least squares regression revealed that the increased Alistipes was significantly associated with fecal metabolome in MDD, involving a range of metabolites mainly enriched for amino acid, vitamin B, and bile acid metabolism pathways. Correlation analyses showed that the Alistipes-related metabolites were associated with a wide array of brain imaging measures involving gray matter morphology, spontaneous brain function, and white matter integrity, among which the brain functional measures were, in turn, associated with affective symptoms (anxiety and anhedonia) and cognition (sustained attention) in MDD. Of more importance, further mediation analyses identified multiple significant mediation pathways where the brain functional measures in the visual cortex mediated the associations of metabolites with behavioral deficits.

CONCLUSION: Our findings provide a proof of concept that Alistipes and its related metabolites play a critical role in the pathophysiology of MDD through the microbiota-gut-brain axis.},
}

Humans
*Depressive Disorder, Major/microbiology/metabolism/diagnostic imaging/physiopathology
*Gastrointestinal Microbiome/physiology
Male
Magnetic Resonance Imaging
Adult
*Feces/microbiology/chemistry
Female
*Metabolome
Middle Aged
*Brain/diagnostic imaging
Metabolomics
Case-Control Studies
*Dysbiosis/microbiology
Multiomics

@article {pmid40621291,
year = {2025},
author = {Mima, Y and Yamamoto, M and Iozumi, K},
title = {Tacrolimus Ophthalmic Suspension Can Be an Effective Treatment Option for Biologic-Induced Refractory Conjunctivitis.},
journal = {Cureus},
volume = {17},
number = {6},
pages = {e85373},
pmid = {40621291},
issn = {2168-8184},
abstract = {Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disease characterized by intense pruritus. It is a multifactorial condition involving complex interactions among skin barrier dysfunction, immune dysregulation, genetic predisposition, and alterations in the skin microbiome. The disease is primarily driven by Th2-associated cytokines such as interleukin (IL)-4, IL-13, and IL-31, which contribute to inflammation and exacerbate pruritus, perpetuating the "itch-scratch cycle." Recently, biologics targeting Th2 cytokines - such as dupilumab, lebrikizumab, and tralokinumab - have emerged as effective treatment options for moderate-to-severe AD. Conjunctivitis is a common adverse effect associated with biologic therapies. In severe cases of conjunctivitis, continuation of biologic therapy may be difficult, highlighting the importance of appropriate ophthalmologic management. Herein, we report a case of AD successfully controlled with lebrikizumab, in which the patient developed conjunctivitis refractory to artificial tears and fluorometholone eye drops. Switching to tacrolimus ophthalmic suspension resulted in marked improvement. While tacrolimus eye drops are not approved for conjunctivitis, they are indicated for vernal keratoconjunctivitis and may be considered in severe cases of AD-related conjunctivitis in consultation with ophthalmologists.},
}

@article {pmid40620903,
year = {2025},
author = {Gao, C and Huang, Q and Yang, X and Cui, X and Wen, K and Liu, Y and Wang, C and Dai, Q and Xie, J and Zhu, L},
title = {Diet and environment drive the convergence of gut microbiome in wild-released giant pandas and forest musk deer.},
journal = {iScience},
volume = {28},
number = {7},
pages = {112837},
pmid = {40620903},
issn = {2589-0042},
abstract = {Reintroduction is important for recovering endangered species, and gut microbiome is crucial for successful wildlife reintroduction. This study utilized 16S rRNA high-throughput sequencing of 791 fecal samples to examine the gut microbial changes in giant pandas (Ailuropoda melanoleuca) and forest musk deer (Moschus berezovskii) across captivity, semi-release, and release stages. Our results revealed a similar transitional pattern in the gut microbiome of both species, with semi-release stage displaying an intermediate state between captive and wild microbiome. We also observed that both species are enriched in Pseudomonas and functional pathways related to amino acid metabolism, ATP-binding cassette transporters, and acetyl-CoA/propionyl-CoA carboxylase. Furthermore, the SourceTracker analysis indicated putative contributions of plant and soil microbiome to the gut microbiome of forest musk deer. These findings suggest that similar herbivorous diets and same environment may contribute to the convergence of gut microbiome. In conclusion, our study provides valuable insights for reintroducing endangered wildlife.},
}

@article {pmid40620665,
year = {2025},
author = {Jinyu, K and Jian, W and Yiwen, L and Ruonan, L and Shegan, G},
title = {Role of Oral and Esophageal Microbiota in Esophageal Squamous Cell Carcinoma.},
journal = {Clinical Medicine Insights. Oncology},
volume = {19},
number = {},
pages = {11795549251350185},
pmid = {40620665},
issn = {1179-5549},
abstract = {In China, esophageal cancer (EC) is one of the most prevalent malignant tumors of the digestive system. EC has a high incidence and mortality rate, of which esophageal squamous cell carcinoma (ESCC) accounts for more than 90%. Due to a lack of effective prevention and treatment methods, the 5 year survival rate is less than 30%. In recent years, microecology has become a hot spot in cancer research, and dysbiosis may play an important role in the etiology of EC. Presently, research on the relationship between the microbiome and ESCC remains in its early stages. This narrative review examines the relationship between the oral and esophageal microbiota and ESCC. A better understanding of this relationship may facilitate early detection and the optimization of treatment strategies.},
}

@article {pmid40620607,
year = {2025},
author = {Liu, J and Chen, Y and Wan, Q},
title = {Immune Cell Characteristics in a Gut-Kidney Axis-Induced Mouse Model of IgA Nephropathy: The Upregulated Dendritic Cells and Neutrophils.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {8579-8592},
pmid = {40620607},
issn = {1178-7031},
abstract = {BACKGROUND: IgA nephropathy (IgAN) is the leading type of primary glomerulonephritis, significantly contributing to chronic kidney disease (CKD) and renal failure. The pathogenesis of IgAN is the multi-hit hypothesis regarding overproduction and accumulation of galactose-deficient (Gd-IgA1). Recent findings have revealed gut microbiota dysbiosis and immune responses are essential in the development of IgAN, attracting increasing attention. This study aimed to map mucosal immune cells in IgAN influenced by gut microbiota, investigating the role of innate immune cells in kidney damage.

METHODS: Fecal samples were acquired from both patients and controls for subsequent animal experiments. Mice received a broad-spectrum antibiotic cocktail to eliminate their intestinal microflora, followed by a gavage with fecal microbiota from clinical individuals. Murine intestinal and kidney tissues were collected for flow cytometry. Intestine and kidney histopathology, immunofluorescence, and inflammatory cytokine expression were assessed in the murine models. The mucosal epithelium's structure and function, along with the innate immune cell response, were analyzed.

RESULTS: Mice exhibited the IgAN phenotype following colonization with gut microbiota from IgAN patients. These mice (IgAN-FMT mice) showed renal dysfunction and increased pathology of tissue injury in both intestine and kidneys. IgAN-FMT mice showed heightened pro-inflammatory cytokine (IL-6 and TNF-α) activity, greater antibody (IgA and complement C3) deposition and decreased expression of mucosal barrier protein (ZO-1, Occludin) compared to the control group. Furthermore, CD11c[+]dendritic cells were more abundant in the murine intestine and kidneys compared to the control group.

CONCLUSION: The gut-kidney axis, including microbiota homeostasis and innate immune cell response, contributes to the pathogenesis of IgAN. Gut dysbiosis and hyperactivated immune cells like CD11c[+]dendritic cells can affect the mucosal barrier and exacerbate the renal damage, being novel insights into immunotherapeutic strategies for IgAN.},
}

@article {pmid40620487,
year = {2025},
author = {Luo, W and Zhang, S and Sun, J and Xu, J and Huang, W and Hao, R and Ou, Z and Wen, Z and Wang, D and Xiao, G and Dong, H},
title = {Microbial and clinical disparities in pneumonia: insights from metagenomic next-generation sequencing in patients with community-acquired and severe pneumonia.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1538109},
pmid = {40620487},
issn = {1664-302X},
abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is a major global cause of death, with its varying symptoms and severity complicating diagnosis and treatment. Severe pneumonia (SP), a more critical form of CAP, has higher mortality and often requires intensive care. The identification of clinical markers to differentiate CAP from SP has the potential to improve treatment protocols and patient outcomes. Concurrently, metagenomic next-generation sequencing (mNGS) demonstrates significant promise in pathogen detection and in elucidating microbiome disparities between CAP and SP.

METHODS: This retrospective study analyzed clinical and pathogen data from 204 patients diagnosed with CAP and 25 patients diagnosed with SP in the Department of Respiratory and Critical Care Medicine at the Zengcheng Branch of Nanfang Hospital, Southern Medical University, spanning the period from September 2022 to June 2023. Clinical characteristics were compared, and bronchoalveolar lavage fluid (BALF) samples underwent mNGS for microbial detection and characterization. Statistical analyses, encompassing Chi-square, Fisher's exact test, Student's t-test, and LEfSe analysis, were employed to compare clinical and microbiological data between the CAP and SP cohorts.

RESULTS: Patients with SP were significantly older and exhibited higher incidences of sepsis, hypotension, tachycardia, multilobar infiltrates, and consciousness disorders compared to those with CAP. Elevated levels of C-reactive protein (CRP) and procalcitonin (PCT) were more frequently observed in SP patients. mNGS analysis identified diagnostic microbiology profiles between groups. Diverse microbiological profiles (> 5 species) were more common in SP patients (> 30% detection rate). Beta diversity analysis demonstrated significant differences in microbial community composition between CAP and SP groups (p = 0.001), though alpha diversity metrics showed no significant differences. Both LEfSe and ANCOM-BC2 analyses consistently identified Pseudomonas as a potential biomarker for SP and Streptococcus for CAP.

CONCLUSION: The substantial differences observed in clinical characteristics, pathogen profiles, and microbiomes between patients with CAP and those with SP highlight the imperative need for comprehensive diagnostic methodologies in the management of pneumonia. mNGS has demonstrated substantial utility in informing personalized treatment strategies, with the potential to enhance clinical outcomes. Future research should prioritize elucidating the dynamics of microbial communities and their impact on pneumonia severity, with the objective of refining and optimizing therapeutic strategies.},
}

@article {pmid40620214,
year = {2025},
author = {Lee, SM and Eom, KH and Jung, J and Kang, JC and Ryu, JS and Ahn, YM and Park, JY},
title = {Stress exacerbates DNCB-induced atopic dermatitis in BALB/c mice: association with modulation of the gut microbiome.},
journal = {Stress (Amsterdam, Netherlands)},
volume = {28},
number = {1},
pages = {2525801},
doi = {10.1080/10253890.2025.2525801},
pmid = {40620214},
issn = {1607-8888},
mesh = {Animals ; *Dermatitis, Atopic/microbiology/chemically induced ; *Gastrointestinal Microbiome/physiology ; Mice ; Dinitrochlorobenzene ; Mice, Inbred BALB C ; *Stress, Psychological/complications/microbiology ; Immunoglobulin E/blood ; Disease Models, Animal ; Corticosterone/blood ; Restraint, Physical ; Male ; Pruritus/microbiology ; },
abstract = {Atopic dermatitis (AD) is a widely recognized chronic inflammatory skin disease influenced by dietary habits, stress, genetic factors, and environmental factors. This study aimed to explore the impact of stress on AD exacerbation, as well as the associated changes in the gut microbiota. We utilized a 2,4-dinitrochlorobenzene (DNCB)-induced AD mouse model subjected to chronic restraint stress (CRS). The animals were divided into four groups: normal, sham control (sham), AD, and AD+CRS. Scratching behavior was significantly increased in the AD+CRS group compared to the AD group on day 28, indicating that stress exacerbates pruritus in AD. Relative abundance analysis of the gut microbiota at the phylum level revealed an increased relative abundance of Bacteroidota in both the AD and AD+CRS groups. Principal coordinate analysis revealed distinct patterns between the AD and AD+CRS groups. The relative abundance of Heminiphilus was negatively correlated with immunoglobulin E (IgE) levels, while the relative abundance of Ruminococcus exhibited significant and negative correlations with both corticosterone and IgE levels. Alistipes, which is known to aggravate AD, was notably elevated in the AD+CRS group. These findings confirm that stress-related changes in the gut microbiota composition may contribute to the exacerbation of AD, highlighting the connection among stress, immune response, and microbiome dynamics in AD progression.},
}

Animals
*Dermatitis, Atopic/microbiology/chemically induced
*Gastrointestinal Microbiome/physiology
Mice
Dinitrochlorobenzene
Mice, Inbred BALB C
*Stress, Psychological/complications/microbiology
Immunoglobulin E/blood
Disease Models, Animal
Corticosterone/blood
Restraint, Physical
Male
Pruritus/microbiology

@article {pmid40620081,
year = {2025},
author = {Fraser, L and Bedendo, A and O'Neill, M and Taylor, J and Hackett, J and Horridge, K and Cade, J and Richardson, G and Phung, TH and Beresford, B and McCarter, A and Hewitt, C},
title = {The risks, benefits, and resource implications of different diets in gastrostomy-fed children: The YourTube mixed method study.},
journal = {Health technology assessment (Winchester, England)},
volume = {29},
number = {25},
pages = {1-21},
doi = {10.3310/RRREF7741},
pmid = {40620081},
issn = {2046-4924},
mesh = {Humans ; *Gastrostomy ; Female ; Male ; Infant ; Child, Preschool ; *Enteral Nutrition/methods/adverse effects ; Quality of Life ; Child ; *Diet ; Parents/psychology ; Food, Formulated ; Focus Groups ; Qualitative Research ; Cohort Studies ; },
abstract = {BACKGROUND: Many children receive some or all their nutritional intake via a gastrostomy. More parents are using home-blended meals to feed their children, reporting beneficial effects, such as improved gastro-oesophageal reflux and less distress.

AIM: To compare safety, outcomes and resource use of those on home-blended diets compared to formula diets.

METHODS: A mixed-methods study of gastrostomy-fed children.

WORKSTREAM 1: Qualitative study involving semistructured interviews with parents (n ≈ 20) and young people (n ≈ 2) and focus groups with health professionals (n ≈ 41).

WORKSTREAM 2: Cohort study; data were collected on 180 children at months 0, 12 and 18 from parents and clinicians using standardised measures. Data included gastrointestinal symptoms, quality of life, sleep (child and parent), dietary intake, anthropometry, healthcare usage, safety outcomes and resource use. Outcomes were compared using propensity scored weighted multiple regression analyses.

RESULTS: WORKSTREAM 1: Participants believed the type of diet would most likely affect gastrointestinal symptoms, time spent on feeding, sleep and physical health.

WORKSTREAM 2: Baseline: Children receiving a home-blended diet and those receiving a formula diet were similar in terms of diagnoses and age, but those receiving a home-blended diet were more likely to live in areas of lower deprivation and their parents had higher levels of education. They also had a higher dietary fibre intake and demonstrated significantly better gastrointestinal symptom scores compared to those receiving a formula diet (beta 13.8, p < 0.001). The number of gut infections and tube blockages were similar between the two groups, but stoma site infections were lower in those receiving a home-blended diet. Follow-up: There were 134 (74%) and 105 (58%) children who provided follow-up data at 12 and 18 months. Gastrointestinal symptoms were lower at all time points in the home-blended diet group, but there was no difference in change over time within or between the groups. The nutritional intake of those on a home-blended diet had higher calories/kg and fibre, and both home-blended and formula-fed children have values above the Dietary Reference Values for most micronutrients. Safety outcomes were similar between groups and over time. Total costs to the statutory sector were higher among children who were formula fed, but costs of purchasing special equipment for home-blended food and the total time spent on child care were higher for families with home-blended diet.

CONCLUSION: Findings show that home-blended diets for children who are gastrostomy fed should be seen as a safe alternative to formula feeding for children unless there is a clinical contraindication.

LIMITATIONS: The target sample for children in workstream 1 was not achieved. The observational study design means unmeasured confounding may still be an issue. Children in this cohort had been on their home-blended diets for different periods of time. A lack of good reference data for nutritional and anthropometric data for disabled children does hinder further interpretation of nutritional adequacy.

FUTURE WORK: Future research on: impact of a home-blended diet on the gut microbiome in children who are gastrostomy fed and equality of access. Children's experiences of living with a gastrostomy, nutritional requirements and quality of life should also be prioritised.

FUNDING: This synopsis presents independent research funded by the National Institute for Health and Care Research (NIHR) Health Technology Assessment programme as award number 17/76/06.},
}

Humans
*Gastrostomy
Female
Male
Infant
Child, Preschool
*Enteral Nutrition/methods/adverse effects
Quality of Life
Child
*Diet
Parents/psychology
Food, Formulated
Focus Groups
Qualitative Research
Cohort Studies

@article {pmid40619937,
year = {2025},
author = {Deshmukh-Reeves, E and Shaw, M and Bilsby, C and Gourlay, CW},
title = {Biofilm Formation on Endotracheal and Tracheostomy Tubing: A Systematic Review and Meta-Analysis of Culture Data and Sampling Method.},
journal = {MicrobiologyOpen},
volume = {14},
number = {4},
pages = {e70032},
doi = {10.1002/mbo3.70032},
pmid = {40619937},
issn = {2045-8827},
support = {//This study was supported by an industrial CASE studentship between University of Kent and ICU Medical Inc./ ; },
mesh = {*Biofilms/growth & development ; Humans ; *Tracheostomy/instrumentation/adverse effects ; *Intubation, Intratracheal/instrumentation/adverse effects ; *Bacteria/classification/isolation & purification/genetics ; Trachea/microbiology ; Pneumonia, Ventilator-Associated/microbiology ; Equipment Contamination ; Microbiota ; },
abstract = {Biofilm formation on tracheal tubing is a key risk factor for ventilator-associated pneumonia. Endotracheal tube microbiology has been systematically reviewed, but tracheostomy tube profiles have not. Analysis of the tube-associated microbiome is not standardised, and sampling methods are varied. We compared the reported microbiomes of endotracheal and tracheostomy tubes and examined the impact of sampling by tracheal aspiration or direct culture. We searched PubMed, SCOPUS, and Web of Knowledge for clinical microbiology studies from 2000-2024, extracting tubing type, sampling method, and the most prevalent genera identified. Genera were compared by Spearman's rank correlation and pairwise analyses by Šidák's test. Extraction from 49 studies identified 30 genera. Pseudomonas was the most prevalent in all conditions followed by Klebsiella, Staphylococcus, and Acinetobacter. 25 studies performed tracheal aspiration, and 22, direct culture. Two studies used both methods. Correlation was observed between endotracheal and tracheostomy tubes, and aspirates and direct cultures (Spearman's rho = 0.69; 0.59). Pseudomonas were more prevalent in tracheostomy tubes (p < 0.0001). Coagulase-positive Staphylococci were more common in tracheal aspirates, and coagulase-negative Staphylococci in direct culture. The microbial profiles of endotracheal and tracheostomy tubes are comparable, with Pseudomonas being the most common coloniser. Our analyses suggest that tracheal aspiration can effectively identify the constituents of biofilms without requiring tube removal, making it a valuable tool for clinical researchers to analyse or monitor biofilms before extubation or device failure using existing microbiology procedures.},
}

*Biofilms/growth & development
Humans
*Tracheostomy/instrumentation/adverse effects
*Intubation, Intratracheal/instrumentation/adverse effects
*Bacteria/classification/isolation & purification/genetics
Trachea/microbiology
Pneumonia, Ventilator-Associated/microbiology
Equipment Contamination
Microbiota

@article {pmid40619849,
year = {2025},
author = {Yu, W and Liu, N and Gui, P and Huang, X and Feng, X and Liu, L and Yang, D and Guo, G and Xiong, C},
title = {Research trends and hotspots of nanomaterials in inflammatory bowel disease: a bibliometric analysis.},
journal = {Nanomedicine (London, England)},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/17435889.2025.2527594},
pmid = {40619849},
issn = {1748-6963},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a chronic and nonspecific gastrointestinal disorder, imposing significant physical, emotional, and economic burdens on patients. In recent years, nanomaterials have shown great potential in the management of IBD. This study employs bibliometric analysis to map global research trends and intellectual landscapes in nanomaterials application for IBD.

METHOD: A comprehensive search was conducted on the Web of Science Core Collection database for studies pertaining to nanomaterials and IBD. Bibliometric and visual analysis of the included publications were facilitated by the utilization of Bibliometrix R, VOSviewer and CiteSpace software.

RESULT: A total of 879 studies were included. China, the United States, and Germany are the leading countries in this field. Georgia State University emerged as the most productive institution, while Didier Merlin and Zhang Mingzhen were identified as influential core authors. International Journal of Pharmaceutics was the most productive journal, and Journal of Controlled Release was the most cited journal. Keyword analysis highlighted "drug delivery," "gut microbiota," "reactive oxygen species" and "anti-inflammation" as dominant research frontiers, with burst keywords such as "polymeric nanoparticles" and "gut microbiotasignaling emerging trends.

CONCLUSION: These findings underscore nanomaterials' transformative potential in IBD management, particularly in targeted therapies and microbiome modulation, while emphasizing the need for interdisciplinary collaboration to address clinical translation challenges.},
}

@article {pmid40619813,
year = {2025},
author = {Sabih Ur Rehman, S and Nasar, MI and Mesquita, CS and Al Khodor, S and Notebaart, RA and Ott, S and Mundra, S and Arasardanam, RP and Muhammad, K and Alam, MT},
title = {Integrative systems biology approaches for analyzing microbiome dysbiosis and species interactions.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf323},
pmid = {40619813},
issn = {1477-4054},
support = {G00005310//UAEU-ZU/ ; G00004960//UPAR/ ; G00004540//UPAR/ ; G00004152//UPAR/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; *Systems Biology/methods ; *Microbiota ; Metagenomics ; Metabolomics ; Proteomics ; },
abstract = {Microbiomes are crucial for human health and well-being, with microbial dysbiosis being linked to various complex diseases. Therefore, understanding the structural and functional changes in the microbiome, along with the underlying mechanisms in disease conditions, is essential. In this review, we outline the structure and function of different human microbiomes and examine how changes in their composition may contribute to diseases. We highlight critical information associated with microbial dysbiosis and explore various therapeutic strategies for restoring a healthy microbiome, including microbiota transplantation, phage therapy, probiotics, prebiotics, dietary interventions, and drug-based approaches. Further, to better understand microbiome dysbiosis, we discuss multi-omics approaches including metagenomics, metatranscriptomics, metaproteomics, and meta-metabolomics, alongside computational modeling approaches such as ecological and metabolic network analysis. We outline key challenges associated with multi-omics techniques and emphasize the importance of integrative systems biology approaches that combine multi-omics data with computational modeling. These approaches are crucial for effectively analyzing microbiome data, providing deeper insights into species interactions and microbiome dynamics. Finally, we offer insights into future research directions in the field of microbiome research. This review makes a unique contribution to microbiome research by presenting a holistic framework that integrates multi-omics data with multi-scale modeling to elucidate microbial interactions, microbiome dysbiosis, and their modulation in disease-associated contexts.},
}

Humans
*Dysbiosis/microbiology
*Systems Biology/methods
*Microbiota
Metagenomics
Metabolomics
Proteomics

@article {pmid40619698,
year = {2025},
author = {Demirli Atıcı, S},
title = {Microbiome, mechanics, and morphology: Rethinking the etiopathogenesis of pilonidal sinus disease.},
journal = {Turkish journal of surgery},
volume = {},
number = {},
pages = {},
doi = {10.47717/turkjsurg.2025.2025-5-2},
pmid = {40619698},
issn = {2564-6850},
}

@article {pmid40619655,
year = {2025},
author = {Jia, D and He, Y and Chen, Q and Zhang, Y},
title = {Gut Microbiota-Induced Long Non-Coding RNA Snhg9 Regulates the Development of Human Malignant Tumors.},
journal = {Current molecular medicine},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115665240366916250629064055},
pmid = {40619655},
issn = {1875-5666},
abstract = {Gut microbes influence the progression of human malignancies through their recognition by the immune system and their effects on numerous metabolic pathways. Long non-coding RNA is a key target of intestinal microbiota involved in the progression of human malignant tumors. Current research shows that there is a close cross-talk between long non-coding RNA Snhg9 and intestinal microorganisms, and it is widely involved in the progression of human malignant tumors. An in-depth study of the interaction between long non-coding RNA and intestinal flora and the intrinsic regulatory mechanism of snhg9 will provide new and powerful therapeutic targets for future research on human malignant tumors.},
}

@article {pmid40619214,
year = {2025},
author = {Bai, X and Ihara, E and Tanaka, Y and Minoda, Y and Wada, M and Hata, Y and Esaki, M and Ogino, H and Chinen, T and Ogawa, Y},
title = {The interplay of gut microbiota and intestinal motility in gastrointestinal function.},
journal = {Journal of smooth muscle research = Nihon Heikatsukin Gakkai kikanshi},
volume = {61},
number = {},
pages = {51-58},
doi = {10.1540/jsmr.61.51},
pmid = {40619214},
issn = {1884-8796},
mesh = {Humans ; *Gastrointestinal Motility/physiology ; *Gastrointestinal Microbiome/physiology ; Bile Acids and Salts/metabolism ; Animals ; Irritable Bowel Syndrome/microbiology/physiopathology/therapy ; Probiotics/therapeutic use ; *Gastrointestinal Tract/microbiology/physiology ; Interstitial Cells of Cajal/physiology ; Fecal Microbiota Transplantation ; Prebiotics ; Constipation/microbiology ; Gastrointestinal Diseases/microbiology/therapy ; Fatty Acids, Volatile/metabolism ; },
abstract = {The relationship between gut microbiota and intestinal motility is crucial for maintaining gastrointestinal health. Intestinal motility refers to the coordinated movements of the digestive tract, essential for effective digestion, nutrient absorption, and timely waste elimination. Recent studies have demonstrated that microbiota play a crucial role not only in the maturation of intestinal motility but also in the ongoing maintenance of established motility patterns. Disruptions in motility can lead to various disorders, such as chronic constipation, irritable bowel syndrome, and chronic idiopathic pseudo-obstruction. Gut microbiota significantly influence intestinal motility through mechanisms like bile acid metabolism and the production of short-chain fatty acids. In patients with diarrhea-predominant irritable bowel syndrome, elevated primary-to-secondary bile acid ratios suggest a complex interaction between gut bacteria and bile acids that can enhance motility via receptors like TGR5. Additionally, the role of interstitial cells of Cajal in facilitating non-neuronal contractions has revolutionized our understanding of motility regulation, highlighting both neural and non-neural factors. Various therapeutic approaches, including prebiotics, probiotics, and fecal microbiota transplantation, have been explored to improve intestinal motility, although their effectiveness has been limited. Advancements in gene-related research and innovative diagnostic methods are vital for a deeper understanding of how the gut microbiome regulates motility. This review synthesizes current knowledge on the interplay between gut microbiota and intestinal motility, emphasizing the need for interdisciplinary research to develop effective treatments targeting gut microbiota for gastrointestinal disorders. By unraveling these complex interactions, we can pave the way for novel therapeutic strategies that enhance intestinal health and improve the quality of life for those affected by motility-related disorders.},
}

Humans
*Gastrointestinal Motility/physiology
*Gastrointestinal Microbiome/physiology
Bile Acids and Salts/metabolism
Animals
Irritable Bowel Syndrome/microbiology/physiopathology/therapy
Probiotics/therapeutic use
*Gastrointestinal Tract/microbiology/physiology
Interstitial Cells of Cajal/physiology
Fecal Microbiota Transplantation
Prebiotics
Constipation/microbiology
Gastrointestinal Diseases/microbiology/therapy
Fatty Acids, Volatile/metabolism

@article {pmid40619188,
year = {2025},
author = {Hackman, NM and Hoyt-Austin, AE and Fernández, CR and Kair, LR},
title = {Recent Advancements and Best Practices in Supporting Newborn Feeding: A Narrative Review.},
journal = {Pediatric clinics of North America},
volume = {72},
number = {4},
pages = {581-595},
doi = {10.1016/j.pcl.2025.04.001},
pmid = {40619188},
issn = {1557-8240},
mesh = {Humans ; Infant, Newborn ; *Breast Feeding/methods ; *Infant Nutritional Physiological Phenomena ; *Infant Care/methods ; Practice Guidelines as Topic ; },
abstract = {Care of the newborn can be complex and very rewarding. The pediatric clinician will face the important challenge of balancing and supporting a family's feeding plan with the health care needs of the newborn and lactating parent. This narrative review focuses on several important topics and provides valuable resources and guidance in the complex care of newborn feeding. The health benefits of breastfeeding, benefits of skin to skin, guidance on unique or complex newborn feeding situations, response to newborn weight loss, vitamin supplementation, as well as consideration of the social determinants of health in the context of infant feeding are reviewed.},
}

Humans
Infant, Newborn
*Breast Feeding/methods
*Infant Nutritional Physiological Phenomena
*Infant Care/methods
Practice Guidelines as Topic

@article {pmid40619159,
year = {2025},
author = {Hou, J and Weng, A and Yang, Z and Huang, X and Chen, W and Wang, X},
title = {Unveiling the Link Between Oral Microbiome Diversity and Biological Ageing: A Cross-Sectional Study.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.14172},
pmid = {40619159},
issn = {1600-051X},
abstract = {AIM: To investigate the relationship between oral microbiome diversity and biological ageing acceleration in a nationally representative U.S.

METHODS: Data from 7716 participants in NHANES (2009-2012) were analysed. Oral microbiome diversity was assessed, and biological ageing acceleration was calculated using a validated algorithm. Generalised linear models, restricted cubic splines and smooth curve fitting were applied to evaluate associations.

RESULTS: Higher α-diversity of the oral microbiome was significantly negatively correlated with biological ageing acceleration. Stratified analyses revealed that this protective effect was particularly pronounced in men and individuals with hypertension and diabetes. β-Diversity analysis showed significant differences in the association between microbial community composition and biological ageing acceleration, with immune functions potentially modulating these effects. Furthermore, key intervals of α-diversity were identified, which may serve as potential targets for future research on delaying ageing.

CONCLUSIONS: In the general U.S. population, greater oral microbiome diversity was associated with lower biological ageing acceleration, especially among men and those with hypertension and diabetes. This association was also observed in Mexican and Hispanic populations.},
}

@article {pmid40619037,
year = {2025},
author = {Karine da Rosa Dias, K and Tochetto, C and Muterle Varela, AP and Loiko, MR and Caroline Dos Santos, A and Frazzon, J and Roehe, PM and Mayer, FQ},
title = {Impact of weaning on piglet microbiota: differences in bacterial taxa and metabolic pathways associated with diarrhea.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107878},
doi = {10.1016/j.micpath.2025.107878},
pmid = {40619037},
issn = {1096-1208},
abstract = {In modern pig farming, early weaning increases pigs' vulnerability to intestinal diseases due to the immaturity of their digestive and immune systems. Post-weaning diarrhea is a common issue in Brazil, leading to weight loss and slow growth, which significantly impacts the swine industry's performance. The intestinal microbiota plays a crucial role during this phase, as it is determinant for the animals' health and productivity. This study aimed to compare the microbiota of post-weaning piglets with and without diarrhea, identifying differences in the bacterial composition and microbial metabolic pathways. The most frequent phyla in both groups were Bacillota followed by Bacteriodota and Pseudomonadota, which together accounted for nearly 90% of microbiota. However, one phylum and eight bacterial families were enriched in the control group (minimum fold change of 4.6), whereas only the Fusobacteriaceae family was enriched in diarrhea group (fold change of 6.5). Moreover, 16 genera were enriched in the control group, while 12 were enriched in the diarrhea group. These findings indicate distinct microbiota compositions between the groups, suggesting an association with dysbiosis. Variations in metabolic pathways were also observed. In the diarrhea group, six pathways were enriched (fold changes of 8.12 to 263.23), most of which were associated with pathogenic and inflammatory processes. In addition, an increase in pathways linked to bacterial metabolism suggested heightened microbial activity, potentially exacerbating diarrhea. In contrast, seven metabolic pathways were enriched in the control group, many of which are essential for immune system development and strengthening, supporting healthy growth. These results highlight key differences in the microbiota and metabolic activity of piglets with and without diarrhea, providing insights that may aid in developing strategies to promote intestinal health and improve post-weaning performance.},
}

@article {pmid40619005,
year = {2025},
author = {Hullar, MAJ and Kahsai, O and Curtis, KR and Navarro, SL and Zhang, Y and Randolph, TW and Levy, L and Shojaie, A and Kratz, M and Neuhouser, ML and Lampe, PD and Raftery, D and Lampe, JW},
title = {Metabolic plasticity of the gut microbiome in response to diets differing in glycemic load in a randomized, crossover, controlled feeding study.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.06.026},
pmid = {40619005},
issn = {1938-3207},
abstract = {BACKGROUND: Dietary patterns characterized by low-glycemic, minimally processed plant foods are associated with lower risk of several chronic diseases.

OBJECTIVE: Evaluate the effects of a low glycemic load (LGL) versus a high glycemic load (HGL) dietary pattern on stool bacterial community structure and metabolism.

METHODS: Participants in this crossover-controlled feeding study were healthy men and women (n=69). We identified genera, species, and genes and transcripts of metabolic pathways and bacterial enzymes using 16S rRNA gene, metagenomic and metatranscriptomic sequencing, and bioinformatic analysis.

RESULTS: Overall community structure measured by alpha and beta diversity were not significantly different across the diets although diet did significantly increase the abundance of 13 out of 161 genera (padj<0.05) and 5 species in the LGL and 7 species in the HGL diet. Gene expression in the hexitol fermentation pathway (β=-1.15, SE=0.24 with 95% CI (-1.63, -0.67); padj=0.002) was significantly higher in the HGL diet, whereas expression in the L-lysine biosynthesis pathway (β =0.20, SE=0.05 with 95% CI (0.09, 0.30); padj=0.03); was enriched in the LGL diet. The beta diversity of expressed carbohydrate-active enzymes (CAZymes) was significantly different between the diets (MiRKAT, p<0.001). CAZymes enriched in the HGL diet reflected dietary additives while CAZymes enriched in the LGL diet reflected diverse phytochemical intake. There was a significant interaction between HOMA IR and the Coenzyme A biosynthesis I pathway involved in bacterial fatty acid biosynthesis (padj=0.035) that was positive in the HGL diet (β=0.20, SE=0.09 with 95% CI (0.02, 0.39)) and negative in the LGL diet (β =-0.23, SE=0.09 with 95% CI (-0.40, -0.06)).

CONCLUSION: In healthy humans, diet impacts microbial metabolism and enzymatic activity but not the overall diversity of the gut microbiome. This emphasizes the relevance of dietary components in activating expression of specific bacterial genes and their impact on host metabolism. This trial was registered at clinicaltrials.gov as NCT00622661.},
}

@article {pmid40618920,
year = {2025},
author = {Kongsintaweesuk, S and Tunbenjasiri, K and Pongking, T and Roytrakul, S and Charoenlappanit, S and Anutrakulchai, S and Pairojkul, C and Intuyod, K and Tanasuka, P and Blair, D and Pinlaor, S and Pinlaor, P},
title = {Microcystin-LR exacerbates chronic kidney disease in rats: Insights into gut microbiome and host proteome dysregulation.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123840},
doi = {10.1016/j.lfs.2025.123840},
pmid = {40618920},
issn = {1879-0631},
abstract = {AIMS: This study aimed to investigate the effects of microcystin-leucine arginine (MC-LR), an environmental nephrotoxin, on the gut-kidney axis in chronic kidney disease (CKD), focusing on interactions between the gut microbiome and host proteome.

MATERIALS AND METHODS: Male Sprague-Dawley rats were administered adenine (200 mg/kg/day) for 10 days to induce kidney injury, followed by MC-LR (10 μg/mL/kg, i.p., every other day for 4 weeks). Renal function (Blood urea nitrogen (BUN), Serum creatinine (SCr), and urine albumin to creatinine ratio (uACR)) and kidney pathology (EGTI histology scores and picrosirius-red staining) were assessed. Expression of kidney injury (KIM-1), fibrosis (CTGF), inflammation (HMGB1 and CD3), oxidative stress (H2AX) markers were evaluated by immunohistochemical staining. Gut microbiota was analyzed by 16S rRNA sequencing, and fecal proteomics by LC-MS/MS.

KEY FINDINGS: MC-LR markedly exacerbated adenine-induced kidney injury, leading to impair kidney function (elevated BUN, Cr, and uACR levels) and worsen kidney histopathology (higher EGTI histology scores and prominent fibrosis). Elevated expression levels of KIM1, HMBG1, CTGF, H2AX and CD3 were observed following MC-LR exposure. Notably, pro-inflammatory bacterial families (Enterococcaceae, Enterobacteriaceae) were elevated, while beneficial taxa (Bifidobacteriaceae, Muribaculaceae) decreased in the combination group. Proteomic analysis revealed upregulation of inflammatory markers (TXNIP, Itgb3bp), which correlated with Enterococcaceae abundance. Bifidobacteriaceae negatively correlated with kidney injury markers.

SIGNIFICANCE: Our study reveals that MC-LR exacerbates chronic kidney disease progression by disrupting the gut-kidney axis. We highlight gut barrier integrity and inflammation as crucial therapeutic targets, offering novel insights and intervention strategies for CKD management, particularly in beyond early stages.},
}

@article {pmid40618877,
year = {2025},
author = {Luo, Y and Tan, C and Yang, J and Zhang, G and Wu, J},
title = {Maternal exposure to tris (2-chloroethyl) phosphate during pregnancy and suckling period alters gut microbiota and SCFAs metabolism in offspring of rats.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126777},
doi = {10.1016/j.envpol.2025.126777},
pmid = {40618877},
issn = {1873-6424},
abstract = {Tris(2-chloroethyl) phosphate (TCEP), one of the most widely used organophosphate flame retardants, is frequently detected in environmental and biological samples. However, its toxic effects on the offspring remain unknown. To explore the health risks posed by TCEP in susceptible populations, we investigated the intergenerational transmission of TCEP, gut microbiome, and disruptive effects of intestinal metabolites in the offspring. Different doses of TCEP were administered orally to female Sprague-Dawley (SD) rats throughout pregnancy or during both pregnancy and lactation periods. Concentrations of TCEP and its metabolite, BCEP, composition of the gut microbiota, and fecal concentrations of short-chain fatty acids were measured. The concentration of TCEP in the placenta of rats in the high-dose group was significantly higher than that in the control group, and BCEP was also present. Serum and fecal samples from immature offspring contained TCEP; however, no BCEP was detected in serum. Exposure to TCEP altered the intestinal microbiota of both the maternal rats and their offspring. The relative abundance of Coelenterata was significantly increased in the immature offspring. Exposure to TCEP altered the concentration of SCFAs in the feces of the rats and their offspring. Lower concentrations of acetic, propionic, and butyric acids were observed in the feces of immature offspring. Holdemanella had a significant mediating effect between TCEP exposure and intestinal concentrations of acetic and propionic acids. Maternal exposure to TCEP affects the gut microbiota balance and metabolism of offspring, suggesting the presence of a long-term risk associated with metabolic disease.},
}

@article {pmid40618613,
year = {2025},
author = {Nie, S and Shen, C and Qu, S and Chen, B and Liu, S and Ge, Y},
title = {Predicting the impact of climate warming on soil quality using bacteria and machine learning.},
journal = {Journal of environmental management},
volume = {391},
number = {},
pages = {126473},
doi = {10.1016/j.jenvman.2025.126473},
pmid = {40618613},
issn = {1095-8630},
abstract = {In the context of global warming, a substantial portion of global soil is in a state of degradation, which poses a significant threat to biodiversity and food production worldwide. Moreover, monitoring soil quality typically requires measuring numerous physical, chemical, and biological indicators, resulting in high costs. In this study, 286 soil samples were obtained from the climate-sensitive Tibetan Plateau and subjected to 16S rRNA amplicon sequencing to reveal the relationships between soil quality, soil bacteria, and climate warming. The results indicated that climate-sensitive bacteria could effectively predict soil quality indices through machine learning (R[2] > 0.76). This suggests that 16S rRNA sequencing can replace numerous soil indicators, providing comprehensive information on soil quality and reducing the costs associated with soil quality monitoring. Additionally, model predictions demonstrated a slight increase in soil quality when only the average annual temperature increased by 1.5 °C. However, when other climatic factors (precipitation and temperature during specific periods) also changed (future climate scenarios for 2021-2040 and 2080-2100), which is more realistic than only increasing the average annual temperature, soil quality declined and the greater the increase in temperature, the more severe the decline in soil quality. These findings provide valuable insights for soil management in the face of increasingly severe climate warming conditions. In summary, our research offers new perspectives for soil quality monitoring from a microbiome standpoint and indicates that future climate warming could pose a threat to soil quality.},
}

@article {pmid40618567,
year = {2025},
author = {Schäfer, L and Grundmann, SM and Hepp, V and Herrero-Encinas, J and Rühl, M and Most, E and Ringseis, R and Eder, K},
title = {Influence of Pleurotus sapidus fruiting bodies on the performance, cecal microbiome, and gene expression in the liver and breast muscle of broilers.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105517},
doi = {10.1016/j.psj.2025.105517},
pmid = {40618567},
issn = {1525-3171},
abstract = {Mushrooms, the fruiting bodies of edible fungi, are widely used as food for humans. However, their potential, as well as that of fungal mycelia, as feed components for poultry is less acknowledged. Recent studies have shown that feeding the vegetative mycelium of Pleurotus sapidus does not affect growth performance or nutrient digestibility and causes only minimal changes in the cecal microbiota structure, liver transcriptome, and plasma metabolome of broilers. The present study aimed to comprehensively investigate the effects of feeding the fruiting bodies of P. sapidus on performance metrics, ileal nutrient digestibility, cecal microbiota composition, cecal integrity, liver transcriptome, and the expression of genes involved in protein turnover in breast muscle of broilers. A total of 72 male, 1-day-old Cobb 500 broilers were randomly assigned to three groups and fed three distinct diets containing either 0 g (PSA-F0), 25 g (PSA-F25), or 50 g (PSA-F50) of freeze-dried P. sapidus fruiting bodies per kg diet in a 35-day, three-phase feeding regimen. Final body weights and weight gain during the finisher and the whole period were significantly lower in groups PSA-F50 and PSA-F25 compared to group PSA-F0 (P < 0.05). Feed intake during the finisher and the whole period tended to be lower in groups PSA-F50 and PSA-F25 compared to group PSA-F0 (P < 0.1). Average daily apparently digested amounts of most indispensable amino acids were lower in group PSA-F50 than in group PSA-F0 (P < 0.05). Cecal microbial α-diversity indicators (Chao1 and Richness) were significantly higher in the PSA-F50 group compared to the PSA-F0 group (P < 0.05), whereas β-diversity indicators were similar between groups. Taxonomic analysis showed a higher abundance of the class Bacilli and the species unknown_Erysipelatoclostridium and a lower abundance of the class Clostridia in the PSA-F50 group compared to the PSA-F0 group (P < 0.05). Concentrations of total and individual short-chain fatty acids, including acetic acid and propionic acid, in the cecal digesta were lower in the PSA-F50 group compared to the PSA-F0 group (P < 0.05). A total of 66 differentially expressed transcripts were identified in the liver between PSA-F50 and PSA-F0 groups based on filter criteria (FC > 1.3 or FC < -1.3, P < 0.05). The mRNA levels of genes involved in critical pathways such as protein synthesis and degradation-including the mammalian target of rapamycin pathway, myogenesis, the ubiquitin-proteasome system, autophagy-lysosomal pathway, and GCN2/eIF2α pathway-did not vary across the groups. Plasma lipopolysaccharide concentration was similar across all groups. The mRNA levels of CLDN3, MUC2, and MUC5AC were elevated in the PSA-F50 group compared to the PSA-F0 group (P < 0.05), while mRNA levels of CLDN5, OCLN, MUC13, and several pro-inflammatory genes in cecal mucosa remained unchanged across groups. The observed impairment in growth performance suggests that P. sapidus fruiting bodies cannot be recommended as dietary components for broilers at the tested doses. Considering the higher β-glucan content of fruiting bodies compared to vegetative mycelia, the negative effects observed on broiler performance may be associated with their β-glucan content.},
}

@article {pmid40618523,
year = {2025},
author = {Yin, YL and Xu, YX and Wang, MT and Yang, DZ and Wang, XY and Zhou, XK and Huang, MM and Yang, S and Fei, H},
title = {Integrative analysis of microbiome and metabolome reveals the effect of deoxynivalenol on growth performance, liver and intestinal health of largemouth bass (Micropterus salmoides).},
journal = {Journal of hazardous materials},
volume = {495},
number = {},
pages = {139148},
doi = {10.1016/j.jhazmat.2025.139148},
pmid = {40618523},
issn = {1873-3336},
abstract = {This study explored the toxic effects of deoxynivalenol (DON) intake at low (100 µg·Kg[-1], LD group) and high doses (300 µg·Kg[-1], HD group) on largemouth bass (Micropterus salmoides). After a 56-day feeding trial, the HD group exhibited significantly reduced growth performance and weakened antioxidant capacity, along with elevated activities of enzymes related to metabolic dysregulation. Histopathological analysis showed an increase in hepatic cell vacuoles, as well as a shortened intestinal villi in both LD and HD groups. Notably, high-dose DON intake markedly down-regulated the expression of intestinal epithelial tight junction-related genes and proteins. Microbiome analysis indicated a significant increase in the Delftia and Acinetobacteria relative abundance, accompanied by diminished in Mycoplasma abundance in the HD group. Metabolomic profiling demonstrated that the dysregulated metabolites were mainly associated with the lysine biosynthesis pathway. Integrative multi-omics analysis revealed that pyridoxamine and diferuloylputrescine served as key biomarkers associated with Acinetobacteria. Collectively, we confirmed that high-dose DON intake induces hepatointestinal damage, thereby impairing the growth performance of largemouth bass. Our findings also further highlighted the link between DON-induced gut microbiota alterations and metabolic disorders, offering new intervention targets for alleviating DON toxicity.},
}

@article {pmid40618487,
year = {2025},
author = {Schober, JM and Wilson, N and Seyoum, MM and Lyte, JM and Bergman, MM and Oluwagbenga, EM and Fraley, GS},
title = {Effects of semi-open water and non-water enrichment on welfare, production, behavior, and microbial exposure of grow-out Pekin ducks.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105477},
doi = {10.1016/j.psj.2025.105477},
pmid = {40618487},
issn = {1525-3171},
abstract = {Environmental enrichment plays an important role in the welfare, behavior, and health of commercially raised Pekin ducks. We assessed the effects of three enrichment treatments and a control: Nipple line (CON), whiffle ball (EED), preening cup (PC), and Pekino (PEK) on duck welfare, behavior and bacterial exposure. 525 grow-out Pekin ducks were housed in 4 pens/4 rooms with one of the four enrichment types (N = 4 pens/treatment). Body weights and body condition scores of 10 ducks/pen and FCR, ammonia level, and litter moisture % were recorded weekly. On 16 and 44 days of age, 3 ducks/pen were euthanized and their organs were weighed and whole brains collected. Behavior data were collected using scan sampling with video being recorded for 72 continuous hours for 3 weeks after enrichment placement. Weekly samples were also collected for viable bacterial counts, and 16S rRNA gene sequencing at baseline and 6 h after baseliner. Body morphometrics, FCR, ammonia levels, litter moisture % and viable bacteria were analyzed by 2-way ANOVA with repeated measures. Body condition scores were analyzed with PROC LOGISTIC (SAS 9.4). GLIMMIX procedure (SAS 9.4) was used to analyze behavior. Bacterial communities were characterized using 16S rRNA gene sequencing, and functional potential was predicted using PICRUSt2. PEK and PC ducks were largest in weight (p < 0.0001) and better nostril scores (p = 0.0005) but had dirtier feathers (p < 0.0001), worse litter conditions (p < 0.0001) and more viable bacteria in their water sources (p < 0.0001), while the PC and EED ducks had worse feather quality (p = 0.0021). Alpha and beta diversity metrics revealed that microbiota composition was significantly (p < 0.05) dependent on environmental enrichment type. Likewise, functional pathway analyses revealed distinct (p < 0.05) metabolic capacities, including aerobic respiration and amino acid biosynthesis, between microbiotas of each respective environmental enrichment niche. Our study suggests that semi-open water sources and EEDs may lead to an increase in feather pecking and a decrease in feather quality with a low number of ducks per enrichment as well as an increase in bacteria load and litter moisture.},
}

@article {pmid40618377,
year = {2025},
author = {Le, TT and Hoang, TN and Do, DH and Nguyen, XH and Huynh, C and Viet, HD and Dat, VQ and Zengler, K and Gilbert, JA and Avedissian, SN and Tran, TM and Le, J},
title = {Current state of microbiota clinical applications in neonatal and pediatric bacterial infections.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2529400},
doi = {10.1080/19490976.2025.2529400},
pmid = {40618377},
issn = {1949-0984},
mesh = {Humans ; Infant, Newborn ; Child ; *Bacterial Infections/microbiology/therapy ; Dysbiosis/microbiology/therapy ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/therapeutic use ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; Infant ; Bacteria/classification/isolation & purification/genetics ; Child, Preschool ; },
abstract = {The microbiota plays a crucial role in pediatric health by shaping immune development and influencing infection susceptibility. In infants and children, an immature microbiota may compromise immune defense, increasing the risk of bacterial infections. This review evaluates clinical trials on the microbiota's role in neonatal and pediatric bacterial infections, including sepsis, infections in pediatric cancer patients, and Clostridioides difficile-associated dysbiosis. We summarized original research articles published from 2000 to May 2024 on the microbiota and bacterial infections in neonates and children. A balanced microbiota is essential for infection prevention, particularly in premature infants and immunocompromised children. Studies of microbiome signatures in the gut, oral cavity, and nasopharynx have highlighted how microbiota composition influences infection risk, treatment response, and adverse effects from antibiotics and chemotherapy. Disruptions from antibiotic exposure, chemotherapy, and hematopoietic stem cell transplantation frequently lead to dysbiosis, characterized by depletion of commensal bacteria and overgrowth of pathobionts, including antibiotic-resistant strains such as C. difficile. Conversely, microbiota-restorative interventions, such as probiotics and fecal microbiota transplantation, show promise in reducing bacterial infections by enhancing microbial resilience. The microbiota plays a critical role in predicting and potentially treating bacterial infections in children. While antibiotics remain essential, their widespread use has significant consequences for microbiota health. Striking a balance between effective infection control and microbiota preservation is crucial, particularly in vulnerable pediatric populations. Implementing judicious antibiotic use and exploring microbiota-based therapies may mitigate long-term microbiota disruptions, ultimately improving infection outcomes and overall pediatric health.},
}

Humans
Infant, Newborn
Child
*Bacterial Infections/microbiology/therapy
Dysbiosis/microbiology/therapy
*Gastrointestinal Microbiome
Anti-Bacterial Agents/therapeutic use
Fecal Microbiota Transplantation
Probiotics/therapeutic use
Infant
Bacteria/classification/isolation & purification/genetics
Child, Preschool

@article {pmid40618373,
year = {2025},
author = {Li, L and Yang, Z and Yi, Y and Song, Y and Zhang, W},
title = {Gut microbiota and radiation-induced injury: mechanistic insights and microbial therapies.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2528429},
doi = {10.1080/19490976.2025.2528429},
pmid = {40618373},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/radiation effects ; *Radiation Injuries/therapy/microbiology ; Animals ; Fecal Microbiota Transplantation ; Probiotics ; Signal Transduction ; Oxidative Stress ; Neoplasms/radiotherapy ; Radiotherapy/adverse effects ; Prebiotics ; },
abstract = {Radiotherapy represents a crucial therapeutic modality in cancer treatment, yet its efficacy is frequently limited by radiation-induced toxicity. Growing evidence indicates that gut microbiota and their metabolites serve as key regulators of both radioprotective and radiosensitizing effects. This review systematically examines three fundamental regulatory mechanisms through which gut microbiota and its metabolites mitigate radiation-induced injury: (1) modulation of intestinal epithelial cell regeneration and tumor cell apoptosis via Wnt/β-catenin and PI3K/AKT/mTOR pathways; (2) immunomodulation via Toll-like receptor activation and NF-κB signaling; (3) oxidative stress management via Nrf2 signaling. We also evaluate various microbiota-targeted interventions, ranging from probiotics and prebiotics to fecal microbiota transplantation and emerging engineered microbial therapies, highlighting their potential in clinical radiotherapy. Finally, we emphasize current limitations and future research directions, underscoring the need to overcome existing challenges in microbiome analysis and therapeutic durability to fully realize the potential of precision radio-microbiome medicine, which may provide valuable references for developing personalized radiotherapy strategies based on gut microbiota and their metabolites.},
}

Humans
*Gastrointestinal Microbiome/physiology/radiation effects
*Radiation Injuries/therapy/microbiology
Animals
Fecal Microbiota Transplantation
Probiotics
Signal Transduction
Oxidative Stress
Neoplasms/radiotherapy
Radiotherapy/adverse effects
Prebiotics

@article {pmid40618372,
year = {2025},
author = {Healy, DB and Wang, S and Patangia, D and Grimaud, G and Ross, RP and Stanton, C and Dempsey, EM},
title = {Late-onset sepsis treatment in very preterm infants alters longitudinal microbiome trajectory with lower abundance of Bifidobacterium despite probiotic supplementation.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2523808},
doi = {10.1080/19490976.2025.2523808},
pmid = {40618372},
issn = {1949-0984},
mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Longitudinal Studies ; Infant, Newborn ; Male ; *Sepsis/microbiology/drug therapy/therapy ; Female ; *Bifidobacterium/isolation & purification/genetics/growth & development ; Feces/microbiology ; Anti-Bacterial Agents/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Infant, Premature ; Bacteria/classification/genetics/isolation & purification ; Dietary Supplements ; Infant ; },
abstract = {INTRODUCTION: Taxonomic instability within the dynamic gut microbiome of very preterm infants can be associated with various adverse outcomes. This longitudinal study was designed to follow the trajectory of microbiome composition and abundance in a cohort of probiotic supplemented very preterm infants with and without sepsis.

METHODS: Stool samples (n = 180) from probiotic-supplemented participants with culture-positive sepsis (n = 8) and matched healthy controls (n = 10) were analyzed using 16S rRNA sequencing. Calculation of total copy number per gram (TCN/g) by DNA spiking provided estimates of total microbial load.

RESULTS: TCN/g was significantly different between infants with and without sepsis, the latter having more rapid increase and overall higher TCN/g. In adjusted analysis, sepsis was associated with a significant abundance of Escherichia-Shigella (p = 0.02) and Veillonella (p = 0.01). Microbial load and composition appeared to fluctuate following antibiotic administration. Analysis of pre-sepsis samples showed a non-significant trend toward lower Bifidobacterium abundance and higher Escherichia-Shigella abundance in infants with subsequent sepsis. Antibiotic administration was independently associated with significantly lower (on average 250-fold lower) Bifidobacterium (p = 0.005) abundance, which remained significant after adjustment for confounders.

CONCLUSIONS: Estimation of absolute abundance reveals fluctuations and blooms in key genera within the gut microbiome of very preterm infants that may not be recognized using relative abundance alone. Very preterm neonates with sepsis have a significantly different longitudinal trajectory of microbiome development, which may, in part, extend to lower Bifidobacterium and higher Escherichia-Shigella abundance prior to the onset of sepsis. Bifidobacterium abundance appears to be particularly affected by antibiotic administration compared to other genera.},
}

Humans
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/drug effects
Longitudinal Studies
Infant, Newborn
Male
*Sepsis/microbiology/drug therapy/therapy
Female
*Bifidobacterium/isolation & purification/genetics/growth & development
Feces/microbiology
Anti-Bacterial Agents/therapeutic use
RNA, Ribosomal, 16S/genetics
Infant, Premature
Bacteria/classification/genetics/isolation & purification
Dietary Supplements
Infant

@article {pmid40618170,
year = {2025},
author = {Shin, C and Ruhno, KE and Shin, JH and Hwang, S and Go, JR and Kang, M and Kim, HJ and Moon, JH and Kim, HJ},
title = {Spatial transcriptome analysis of myenteric plexus and intestinal epithelium of colon in patients with Parkinson's disease.},
journal = {Acta neuropathologica communications},
volume = {13},
number = {1},
pages = {146},
pmid = {40618170},
issn = {2051-5960},
support = {2022R1A2C2091254//National Research Foundation of Korea/ ; 11-2022-5010//Seoul National University Hospital/ ; },
mesh = {Humans ; *Myenteric Plexus/metabolism/pathology ; Male ; Female ; *Parkinson Disease/metabolism/genetics/pathology ; *Colon/metabolism/pathology ; Aged ; *Intestinal Mucosa/metabolism/pathology ; Middle Aged ; Gene Expression Profiling ; *Transcriptome ; alpha-Synuclein/metabolism ; },
abstract = {Alpha-synuclein (AS) accumulation is found in the nerve plexuses of the gastrointestinal tract in patients with Parknison's disease (PD). Moreover, alterations in microbiome composition and its metabolites were confirmed in the colon of patients with PD. However, there has been no study that evaluates transcriptomic alterations of the nerve plexus and intestinal epithelium simultaneously using in vivo tissue of patients with PD. Therefore, we aimed to investigate the gene expression profiles of the myenteric plexus and intestinal epithelium of the colon of patients with PD. Ten full-depth slides of paraffin-embedded surgical specimens of the colon or rectum from five patients with PD and five controls were included. AS accumulation was found in the myenteric plexus in all patients with PD. We performed spatial-specific transcriptomic profiling of the myenteric plexus and epithelium using the GeoMX Digital Spatial Profiler. Forty-one differentially expressed genes (DEGs) (36 up-regulated and 5 down-regulated) were identified in the myenteric plexus of patients with PD compared to controls. In the intestinal epithelium, 240 DEGs (81 up-regulated and 159 down-regulated) were identified. Pathway analysis showed upregulated response to type II interferon and lymphocyte activation, while downregulated cellular response to zinc and copper ions in the intestinal epithelium of patients with PD. In the myenteric plexus, neuroepithelial cell differentiation and axon development were upregulated. Network analysis showed the following key genes: and HLA-DRA, SERPINA1, and metallothioneins in the intestinal epithelium, and LAMP1, TUBB2A, and S100B in the myenteric plexus. This study suggests that inflammatory processes may occur in the intestinal epithelium, while neuronal regeneration mechanisms may be active in the myenteric plexus in patients with overtly developed PD. A spatial transcriptomic analysis of the brain and the gastrointestinal tract will enable a better understanding of the gut-brain axis in PD.},
}

Humans
*Myenteric Plexus/metabolism/pathology
Male
Female
*Parkinson Disease/metabolism/genetics/pathology
*Colon/metabolism/pathology
Aged
*Intestinal Mucosa/metabolism/pathology
Middle Aged
Gene Expression Profiling
*Transcriptome
alpha-Synuclein/metabolism

@article {pmid40618036,
year = {2025},
author = {Sato, K and Nakashima, A and Fukuda, S and Inoue, J and Kim, YG},
title = {Fasting builds a favorable environment for effective gut microbiota modulation by microbiota-accessible carbohydrates.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {414},
pmid = {40618036},
issn = {1471-2180},
support = {JPMJSP2123//JST SPRING/ ; 2346//Sylff Research Grant/ ; JP23H02718//Japan Society for the Promotion of Science/ ; JP 23K18223//Japan Society for the Promotion of Science,Japan/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Fasting ; Feces/microbiology/chemistry ; Animals ; *Bacteria/classification/genetics/isolation & purification ; Male ; Mice ; Immunoglobulin A/analysis ; Humans ; },
abstract = {Dietary nutrients are an important determinant of gut microbial composition (Asnicar et al, Nat Med 27:321-332, 2021; Arifuzzaman. et al, Nature 611:578-584, 2022; Bolte. et al, Gut 70:1287-1298, 2021). Commensal bacteria compete and cross-feed on host-derived nutrients to maintain stable gut microbial communities (Kolodziejczyk. et al, Nat Rev Microbiol. 17:742-753, 2019; Ma. et al, Gut Microbes 12:1785252, 2020). However, the changes to the gut bacteria induced by fasting are not well-defined. Here, we propose a powerful method to selectively and effectively increase specific gut bacteria by combining fasting and administration of microbiota-accessible carbohydrates (MACs). Fasting alters the gut microbial community structure, and the fasting + MAC intervention has profound effects on the gut microbiome with increased specific bacteria and fecal IgA levels than MAC administration alone. The changes in gut microbiota composition are specific to the type of MAC administered. We identified the most effective protocol to combine with fasting + MAC to increase the levels of specific bacteria such as Bifidobacterium. Overall, the integrating fasting with MACs effectively alters the gut microbiome, suggesting that fasting can prepare the environment for gut microbial modulation by MACs.},
}

*Gastrointestinal Microbiome/physiology
*Fasting
Feces/microbiology/chemistry
Animals
*Bacteria/classification/genetics/isolation & purification
Male
Mice
Immunoglobulin A/analysis
Humans

@article {pmid40617918,
year = {2025},
author = {Jamaluddin, NF and Brovkina, O and Nor Rashid, N and Al-Maleki, AR and Lim, YA and Tan, MP and Lee, SC and Duvallet, C and Corzett, CH and Alm, E and Groussin, M and Poyet, M and Ibrahim, F},
title = {Gut microbiota profiles of peninsular Malaysian populations are associated with urbanization and lifestyle.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {24066},
pmid = {40617918},
issn = {2045-2322},
support = {RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; RK019-2018//Universiti Malaya Partnership Grant/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Project-ID 261376515 - SFB 1182//German Science Foundation and Collaborative Research Center (CRC)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; Flex Fund grant, DFG project no. 28/1 AOBJ: 700895 Bio4ALL, NFDI4Microbiota//German National Research Data Infrastructure (NFDI)/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; IF030-2018//Center for Microbiome Informatics and Therapeutics, MIT/ ; },
mesh = {Humans ; Malaysia ; *Gastrointestinal Microbiome ; *Life Style ; Male ; Female ; *Urbanization ; Adult ; Middle Aged ; Rural Population ; Urban Population ; Bacteria/classification/genetics ; Young Adult ; Diet ; RNA, Ribosomal, 16S/genetics ; },
abstract = {There is increasing evidence of distinct gut microbiome compositions between populations living industrialized and non-industrialized lifestyles worldwide. However, whether populations of Malaysia exhibit variations in their microbiome, and to what extent host lifestyle correlates with these variations, remains unclear. Malaysia's extensive geographical and sociocultural diversity provides a unique opportunity to explore how lifestyle and environmental exposures are associated with the human gut microbiome. Here, we characterized the gut microbiome of three populations in peninsular Malaysia, each representing different lifestyle contexts, and identified host factors associated with microbiome variation. Our findings suggest that lifestyle-related factors are strongly associated with differences in microbial community composition across populations. In particular, urban and rural individuals harbor gut microbiota with distinct community structures. We further identified specific taxa as potential microbial signatures of host lifestyle, with the genera Prevotella and Cryptobacteroides enriched in rural populations, while Phocaeicola, Vescimonas, and Megasphaera were more prevalent among urban individuals. In addition to lifestyle, demographic factors such as age, sex, and BMI were also associated with variation in the gut microbiome. This study highlights the influence of urbanization, lifestyle, and diet on the gut microbiome landscape of Malaysian populations and underscores the importance of considering sociocultural context in future microbiome research.},
}

Humans
Malaysia
*Gastrointestinal Microbiome
*Life Style
Male
Female
*Urbanization
Adult
Middle Aged
Rural Population
Urban Population
Bacteria/classification/genetics
Young Adult
Diet
RNA, Ribosomal, 16S/genetics

@article {pmid40617850,
year = {2025},
author = {Liu, Q and Fang, W and Zheng, P and Xie, S and Jiang, X and Luo, W and Han, L and Zhao, L and Lu, L and Zhai, L and Yu, DJ and Yang, W and Lin, C and Fang, X and Bian, Z},
title = {Multi-kingdom microbiota analysis reveals bacteria-viral interplay in IBS with depression and anxiety.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {129},
pmid = {40617850},
issn = {2055-5008},
support = {ITC RC/IHK/4/7//Health@InnoHK Initiative Fund of the Hong Kong Special Administrative Region Government/ ; S/N Ref: 2023-0045//Jockey Club Traditional Chinese Medicine-driven Mental Wellness Project/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/psychology/virology/complications ; *Gastrointestinal Microbiome ; *Depression/microbiology/virology ; Female ; Male ; *Bacteria/classification/virology/genetics/isolation & purification ; Prospective Studies ; *Anxiety/microbiology/virology ; Adult ; *Bacteriophages/genetics/classification/isolation & purification ; Hong Kong ; Middle Aged ; Virome ; Feces/microbiology/virology ; },
abstract = {Irritable Bowel Syndrome (IBS) is a common gastrointestinal disorder frequently accompanied by psychological symptoms. Bacterial microbiota plays a critical role in mediating local and systemic immunity, and alterations in these microbial communities have been linked to IBS. Emerging data indicate that other intestinal organisms, including bacteriophages, are closely interlinked with the bacterial microbiota and their host, yet their collective role remains to be elucidated. Here, we analyze the gut multi-kingdom microbiota of 360 IBS patients from a prospective cohort study in Hong Kong, with participants phenotyped through psychological assessment. Our findings reveal significantly lower intra-community correlations in IBS patients compared to healthy controls and highlight unique taxa patterns associated with IBS and mental disorders. Utilizing multi-omic data alongside machine learning techniques, we successfully predicted psychiatric comorbidities in IBS, achieving an average AUC of 0.78. Notably, gut viruses emerged as significant contributors to our predictive model, indicating a vital role for bacteriophages in the gut microbiome of IBS patients. We found that lysogenic phages in IBS displayed a broader host range, with Bilophia containing the most abundant prophages. Our analysis further indicates that IBS patients with depression exhibited a higher prevalence of viral-encoded auxiliary metabolic genes, specifically those involved in the sulfur metabolic pathway related to ubiquinone biosynthesis. The gut virome is increasingly reported to play an important role in the pathogenesis of many diseases. The study provides a systematic characterization of the drivers of the gut viral community and further expands our knowledge of the distinct interaction of gut viruses with their prokaryotic hosts, which is critical for understanding the viral-bacterial environment in IBS.},
}

Humans
*Irritable Bowel Syndrome/microbiology/psychology/virology/complications
*Gastrointestinal Microbiome
*Depression/microbiology/virology
Female
Male
*Bacteria/classification/virology/genetics/isolation & purification
Prospective Studies
*Anxiety/microbiology/virology
Adult
*Bacteriophages/genetics/classification/isolation & purification
Hong Kong
Middle Aged
Virome
Feces/microbiology/virology

@article {pmid40617811,
year = {2025},
author = {Zhu, B and Liang, L and Chen, S and Li, H and Huang, Y and Wang, W and Zhang, H and Zhou, J and Xiong, D and Li, X and Li, J and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Multi-kingdom microbial changes and their associations with the clinical characteristics in schizophrenia patients.},
journal = {Translational psychiatry},
volume = {15},
number = {1},
pages = {228},
pmid = {40617811},
issn = {2158-3188},
mesh = {Humans ; *Schizophrenia/microbiology/metabolism/physiopathology ; Male ; Female ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Feces/microbiology ; Case-Control Studies ; Metabolic Networks and Pathways ; Fungi ; },
abstract = {Accumulating evidence has highlighted alterations in the gut microbiome in schizophrenia (SZ); however, the role of multi-kingdom microbiota in SZ remains inadequately understood. In this study, we performed metagenomic sequencing of fecal samples from 36 SZ patients and 55 healthy controls (HC) to profile bacterial, fungal, archaeal, and viral communities, along with functional pathways. We also conducted co-occurrence network analysis to explore the relationships among differential microbial species and metabolic pathways separately. Additionally, we assessed the associations of these differential species and functional pathways with clinical characteristics. Our findings revealed significant differences in species between SZ patients and HC, identifying not only 17 bacterial species, but also 8 fungal, 26 archaeal, and 19 viral species. Functional pathway analysis revealed 21 metabolic pathways significantly altered in SZ patients, including an increase in tryptophan metabolism, while biosynthesis of amino acids was decreased. Network analysis further uncovered more complex inter-kingdom interactions in SZ patients, with specific fungal species appearing exclusively in the SZ network. Importantly, significant associations were observed between microbial species and functional pathways with clinical characteristics, including symptom severity, cognitive function, and clinical biochemical marker. For instance, the abundance of Streptococcus vestibularis was positively correlated with homocysteine levels; the ubiquinone and other terpenoid-quinone biosynthesis was positively correlated with both symptom severity and C-reactive protein. Our findings reveal the intricate microbial dysbiosis present in SZ patients, suggesting multi-kingdom microbial interactions play a crucial role in SZ patients, highlighting promising avenues for potential diagnostic and therapeutic applications.},
}

Humans
*Schizophrenia/microbiology/metabolism/physiopathology
Male
Female
*Gastrointestinal Microbiome
Adult
Middle Aged
Feces/microbiology
Case-Control Studies
Metabolic Networks and Pathways
Fungi

@article {pmid40617665,
year = {2025},
author = {Koutoukoglou, P and Mountzios, G},
title = {Beyond Programmed Death-Ligand 1: Gut Microbiome Composition as a Biomarker For First-Line Chemoimmunotherapy in Advanced NSCLC.},
journal = {Journal of thoracic oncology : official publication of the International Association for the Study of Lung Cancer},
volume = {20},
number = {7},
pages = {831-833},
doi = {10.1016/j.jtho.2025.04.011},
pmid = {40617665},
issn = {1556-1380},
}

@article {pmid40617511,
year = {2025},
author = {Arikawa, AY and Waterman, A and Mishra, SP and Labyak, C and Williams, C and Chaudhari, DS and Shukla, R and Kumar, V and Masternak, M and Holland, P and Golden, A and Dangiolo, M and Kociolek, J and Fraser, A and Agronin, M and Aymat, M and Yadav, H and Jain, S},
title = {Cognitive impairment is associated with alterations in diet quality and inflammatory biomarkers in older adults: a cross-sectional analysis of data collected from the Microbiome in Aging Gut and Brain (MiaGB) consortium cohort.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.026},
pmid = {40617511},
issn = {1541-6100},
abstract = {BACKGROUND: Research suggests that gut inflammation and alterations in intestinal barrier function may be important mechanisms linking diet, systemic inflammation, and cognitive outcomes.

OBJECTIVE: The objective of this study was to explore the relationship between diet, cognitive health, and inflammatory markers in older adults. It was hypothesized that cognitive impairment would be associated with lower diet quality and higher levels of inflammatory markers.

METHODS: A cross-sectional analysis was conducted using data from the Microbiome in Aging Gut and Brain (MiaGB) consortium cohort. Participants aged 60 years and older were assessed for cognitive status using the Montreal Cognitive Assessment (MoCA), diet quality using the Healthy Eating Index-2020 (HEI-2020), and dietary inflammatory potential using the Dietary Inflammatory Index (DII). Inflammatory biomarkers were measured in plasma and stool samples, including interleukin (IL)-6, IL-1β, lipopolysaccharide binding protein (LBP), Toll-like receptor 4 (TLR4), and zonula occludens-1 (ZO-1).

RESULTS: Among 217 participants, 33.6% presented with cognitive impairment based on MoCA scores. There were no differences in DII and HEI-2020 scores between participants with and without cognitive impairment. The only significant finding related to the components of the HEI was a higher adequacy of dairy intake in those without cognitive impairment (54.8%) compared with those with cognitive impairment (44.4%, p=0.035). Key inflammatory markers, including IL-6, IL-1β, LBP, and TLR4, were elevated in those with cognitive impairment, while plasma ZO-1 levels were reduced. Stool calprotectin levels were notably higher in those with cognitive impairment, suggesting increased intestinal inflammation. There was a weak but significant correlation between stool calprotectin and DII score (rs=0.283, p=0.046).

CONCLUSION: The findings suggest that elevated inflammatory markers and disrupted intestinal barrier integrity may contribute to cognitive decline. These results highlight the need to develop dietary interventions to mitigate cognitive impairment through modulation of inflammation.},
}

@article {pmid40617320,
year = {2025},
author = {Lu, Y and Yi, F and Chen, W and Tan, X and Li, K and Yang, C and Lin, Y},
title = {Involvement of oxidative stress, lipid dysmetabolism and gut microbiol dysbiosis in oxaliplatin-induced fatty liver disease: evidence from a tree shrew model.},
journal = {Clinics and research in hepatology and gastroenterology},
volume = {},
number = {},
pages = {102645},
doi = {10.1016/j.clinre.2025.102645},
pmid = {40617320},
issn = {2210-741X},
abstract = {BACKGROUND: Oxaliplatin is cornerstone treatment for colorectal cancer, yet a significant proportion of patients develop drug-induced fatty liver disease (DILI). How it induces such liver injury is poorly understood and whether the gut microbiome is involved remains unknown.

METHODS: A male tree shrew model of oxaliplatin-induced DILI was established by six intraperitoneal injections (7 mg/kg every two weeks). During the early and late phases of liver injury, liver tissue was analyzed in terms of histopathology, oxidative stress and transcriptional profiling, while feces were subjected to microbial profiling based on 16S rRNA sequencing.

RESULTS: The model recapitulated key features of DILI, including severe hepatocyte steatosis and ballooning in the early phase after the final treatment, mild hepatic steatosis with sinusoidal dilatation in the late phase, and persistent hepatic oxidative stress during both phases. Transcriptional analysis of liver tissue identified 1503 differentially expressed genes (DEGs) between oxaliplatin-treated and control animals, of which 601 DEGs differed between treated animals in the early or late phases after the final treatment of DILI. Pathway enrichment revealed significant dysregulation in oxidative stress (e.g. NDUFA12, OSR1, MPO) and lipid metabolism (e.g., LDAH, ACACB, CH25H, LIPE) genes. Gut microbiota profiling showed an increase in the relative abundance of potentially harmful bacteria (e.g., Parabacteroides, Rikenella, Alistipes and Faecalitalea) and a concurrent decrease in the abundance of anti-oxidative bacteria (e.g., Lactococcus and Flavobacterium). Notably, abundance of several microbial genera in the gut correlated with liver expression of genes involved in oxidative stress and lipid metabolism as well as with levels of oxidative stress markers, and/or fat deposition in the liver.

CONCLUSION: Our results suggest that our tree shrew model can faithfully replicate key characteristics of oxaliplatin-induced fatty liver disease, and that such disease involves oxidative stress and lipid dysmetabolism in the liver as well as dysbiosis of microbiota in the gut.},
}

@article {pmid40617300,
year = {2025},
author = {Martin, EM and Xue, J and Smith, CJ},
title = {Effects of environmental toxicant exposures on oxytocin and vasopressin systems in the developing brain: Factors imparting risk and resilience.},
journal = {Behavioural brain research},
volume = {},
number = {},
pages = {115723},
doi = {10.1016/j.bbr.2025.115723},
pmid = {40617300},
issn = {1872-7549},
abstract = {Environmental toxicants are increasingly prevalent worldwide and associated with numerous neurodevelopmental and psychiatric health outcomes. Exposure to these toxicants, particularly during gestation and the early postnatal period, alters maternal and offspring stress responses, inflammation, and behavioral outcomes. Oxytocin (OT) and arginine vasopressin (AVP) are highly conserved neuropeptides with myriad roles in the regulation of social behavior, stress responses, and more. While developmental stress is well known to impact OT and AVP systems, a growing body of literature suggests that early-life exposure to toxicants also impacts OT and AVP system development. Here we review the evidence demonstrating that perinatal exposures to environmental toxicants program developmental trajectories of the OT and AVP systems. Perinatal exposure to flame retardants, pesticides, plastics, and air pollution induces a variety of changes to OT and AVP systems in the brain, affecting the neuropeptides themselves as well as their primary central receptors, the oxytocin receptor (OTR) and the vasopressin receptor 1a (V1aR), respectively. Next, we discuss two biological mechanisms of action that may underlie the effects of toxicant exposure on OT and AVP: endocrine disruption and maternal immune activation. Finally, we explore key factors that promote either risk or resilience to toxicant exposures, including psychosocial experience, sex, the gut microbiome, and dosage/timing of exposure. Cumulatively, the literature reviewed suggests that preventing psychosocial stress to mothers during the perinatal period while promoting positive psychosocial experiences may lessen the impact of toxicants on offspring outcomes. Furthermore, the gut microbiome may be an important intermediary, and therefore target for intervention, between toxicant exposures and OT and AVP systems in the brain.},
}

@article {pmid40617206,
year = {2025},
author = {Mu, Y and Liu, L and He, J and Zhang, H and Yu, S and Zhu, Z and Huang, Y and Mou, M and Zhang, C},
title = {Investigating the variations in microbiome and volatilome characteristics of sauce-flavor Muqu across different grades and production rounds.},
journal = {Food chemistry},
volume = {492},
number = {Pt 1},
pages = {145394},
doi = {10.1016/j.foodchem.2025.145394},
pmid = {40617206},
issn = {1873-7072},
abstract = {Muqu is the starter of high-temperature Daqu; however, the mechanisms underlying its quality formation remain unclear. Therefore, the effects of grade and round on Muqu quality were investigated. Biochemical activities were closely associated with grade, while moisture and fat content were linked to round. The volatilome was also significantly influenced by grade, with levels of differential compounds such as trimethylpyrazine, 2,3-butanediol, and methyl hexanoate showing a positive correlation with grade. In contrast, bacterial and fungal diversities were regulated by grade and round, respectively, resulting in distinct interaction patterns within the co-occurrence network. Acidity and amino acid nitrogen levels were key factors driving community assembly, and Virgibacillus, Kroppenstedtia, Thermoactinomyces, Aspergillus, and Byssochlamys were identified as the primary flavor producers. Functional predictions indicated the pivotal role of bacterial communities in flavor synthesis and fungal communities in carbohydrate metabolism. These findings provide new insights into improving Daqu quality via the Muqu grading strategy.},
}

@article {pmid40617156,
year = {2025},
author = {Sola-Leyva, A and Pérez-Prieto, I and Di Nisio, V and Panagiotis-Deligiannis, S and Blanco-Rodríguez, L and Acharya, G and Saare, M and Papaikonomou, K and Damdimopoulou, P and Salumets, A and Altmäe, S},
title = {Assessing the ovarian microbiome: lack of a distinguishable microbial signature beyond contamination.},
journal = {Reproductive biomedicine online},
volume = {51},
number = {3},
pages = {104988},
doi = {10.1016/j.rbmo.2025.104988},
pmid = {40617156},
issn = {1472-6491},
abstract = {RESEARCH QUESTION: Do the ovaries harbour commensal microbes?

DESIGN: Twenty-two ovarian tissue samples (cortex and medulla), six follicular fluid samples from gender-reassignment patients (GRP, n = 11) and five ovarian cortex tissue samples from Caesarean sections (n = 5), together with positive and negative controls, were analysed by bacterial 16S rRNA gene sequencing. Negative controls were obtained from saline storage buffer, air contaminants from the laboratory and operating room, and samples from clinicians and researchers handling the samples.

RESULTS: Of the 33 ovarian tissue and follicular fluid samples analysed, 63.6% did not result in any bacterial DNA amplification on PCR. As a result, only 1 out of 6 follicular fluid samples from GRP resulted in DNA amplification, while two ovarian cortex and four medulla samples from GRP, together with five ovarian samples from women undergoing Caesarean section, presented detectable bacterial DNA. Following sequencing, quality filtering and decontamination, negligible microbial reads were detected in these 12 samples. Despite strict protocols to avoid contamination during sample collection and processing, a high proportion of contaminant reads (30.3-100%, median 62.1%) were found in all the samples.

CONCLUSIONS: These findings do not support the existence of a specific ovarian microbiome in the ovaries of healthy participants. It can be concluded that the incidental detection of low-biomass bacterial genera is probably attributable to contamination.},
}

@article {pmid40617143,
year = {2025},
author = {Corrivetti, G and Monaco, F and Vignapiano, A and Marenna, A and Panarello, E and Di Gruttola, B and Landi, S and Malvone, R and Vecchi, C and Leo, S and Carmellini, P and Steardo, L and Solmi, M and Panella, R and Fasano, A},
title = {Precision medicine for depression: Improving treatment response and remission.},
journal = {Asian journal of psychiatry},
volume = {110},
number = {},
pages = {104585},
doi = {10.1016/j.ajp.2025.104585},
pmid = {40617143},
issn = {1876-2026},
abstract = {This review synthesises current knowledge to improve understanding of the pathophysiology of major depressive disorder (MDD) and optimise diagnostic, therapeutic and prognostic approaches. It examines the interplay between genetic, epigenetic, inflammatory, neurotransmitter and gut microbiome factors, together with environmental stressors and different clinical symptom presentations, in shaping MDD presentation and treatment response. Studies have revealed potential biomarkers predictive of treatment response, allowing differentiation of MDD subtypes and facilitating remission monitoring. While studies have identified potential biomarkers predictive of treatment response and enabling MDD subtype differentiation, significant challenges remain in achieving fully optimized therapeutic efficacy and widespread remission. A holistic, data-driven approach is key to addressing the complex aetiology of MDD, ultimately improving outcomes for patients and reducing the substantial burden of this prevalent disorder.},
}

@article {pmid40616950,
year = {2025},
author = {Jain, CK and Maurya, S and Singh, A},
title = {Bioinformatics-driven salivary microbial and functional profiling for identifying biomarkers in oral cancer and tobacco abusers in the Indian population.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106346},
doi = {10.1016/j.archoralbio.2025.106346},
pmid = {40616950},
issn = {1879-1506},
abstract = {OBJECTIVE: To investigate alterations in the salivary microbiome and its functional potential in Oral Squamous Cell Carcinoma (OSCC) patients, tobacco abusers, and healthy individuals in order to identify microbial biomarkers and gain insight into OSCC pathogenesis.

DESIGN: Saliva-derived 16S rRNA gene sequences from OSCC patients, tobacco users, and healthy controls were obtained from the Indian Biological Data Centre (IBDC). Taxonomic classification was performed using QIIME2, and functional prediction was conducted with MicFunPred. Alpha and beta diversity, differential abundance, and pathway enrichment analyses were used to compare microbial communities and functions among the groups.

RESULTS: OSCC samples showed significantly reduced alpha diversity and distinct microbial community profiles relative to healthy controls. Genera including Porphyromonas, Streptococcus, Rothia, and Parvimonas were enriched in OSCC and are associated with inflammation and carcinogenesis. Tobacco users exhibited increased microbial richness, with dominance of Prevotella, Veillonella, and Peptostreptococcus, indicative of adaptation to chemical exposure. Functional predictions in OSCC samples indicated enrichment in pathways related to bacterial chemotaxis, lipopolysaccharide biosynthesis, glycolysis, and DNA repair. Tobacco-associated microbiota showed elevated oxidative stress response and detoxification pathways.

CONCLUSIONS: Microbial dysbiosis and functional alterations in the oral microbiome are strongly associated with OSCC and tobacco use. The identification of disease-specific microbial signatures and pathways highlights the potential of the oral microbiome as a non-invasive biomarker and therapeutic target for precision medicine in OSCC, particularly in the Indian population.},
}

@article {pmid40616901,
year = {2025},
author = {Flygel, TT and Bargheet, A and Abotsi, RE and Claassen-Weitz, S and Simms, V and Hjerde, E and Mwaikono, KS and Mchugh, G and Hameiri-Bowen, D and Pettersen, VK and Ferrand, RA and Nicol, M and Cavanagh, JP and Flaegstad, T and Sovershaeva, E},
title = {Effect of long-term azithromycin treatment on gut microbial diversity in children and adolescents with HIV-associated chronic lung disease.},
journal = {EBioMedicine},
volume = {118},
number = {},
pages = {105832},
doi = {10.1016/j.ebiom.2025.105832},
pmid = {40616901},
issn = {2352-3964},
abstract = {BACKGROUND: HIV-associated chronic lung disease (HCLD) is common in children and adolescents growing up with HIV. The use of azithromycin (AZM) reduces the rate of acute respiratory exacerbations in this population, however, impact of this treatment on the gut microbiota and associations with blood-derived inflammatory markers have not been studied.

METHODS: Children and adolescents with HCLD in Harare, Zimbabwe and Blantyre, Malawi were recruited in a double-blind, placebo-controlled trial of once-weekly AZM or placebo for 48 weeks (BREATHE trial, NCT02426112). Rectal swabs were collected at inclusion (N = 346), 48 weeks (treatment end, N = 313), and 72 weeks (six months after treatment cessation, N = 244). The bacterial composition of fecal swabs was determined using 16S rRNA gene sequencing. Plasma biomarkers at inclusion and 48 weeks were measured using Luminex multiplex bead assay.

FINDINGS: At 48 weeks, bacterial α-diversity was significantly lower in the AZM group, with 27 bacterial genera showing differential abundance between the study groups. The placebo group exhibited higher interconnectivity between bacterial genera at 48 weeks compared to the AZM group. Correlations between the top seven differentially abundant genera and biomarkers observed at inclusion were no longer significant at 48 weeks in both groups. Depletion of Campylobacter persisted for six months after cessation of AZM treatment.

INTERPRETATION: Long-term AZM treatment in HCLD patients affects their gut bacterial composition at least 6 months after its cessation. The consequences of reduced bacterial diversity, such as altered interaction with the immune system and risk of resistance, need further investigation to understand how to optimise gut health during long-term antibiotic treatments.

FUNDING: The study was funded by the Norwegian Research Council and Helse Nord (HNF 1387-17).},
}

@article {pmid40616741,
year = {2025},
author = {Renton, N and Pillinger, MH and Toprover, M},
title = {Gout, Hyperuricemia, and the Intestinal Microbiome.},
journal = {Inflammation},
volume = {},
number = {},
pages = {},
pmid = {40616741},
issn = {1573-2576},
abstract = {Gout is a disease of hyperuricemia (HU) leading to monosodium urate crystal deposition in the joint, resulting in inflammation and joint damage. Recently, efforts have been made to characterize the intestinal microbiome of patients who suffer from HU and gout, and pre-clinical studies have evaluated the utility of prebiotics and probiotics in alleviating gout. Herein we review recent notable studies addressing these topics. In brief, the "gouty" microbiome is characterized by reduced diversity, an elevated Bacteroides: Firmicutes ratio, and reduced presence of Akkermansia and Bifidobacterium. In anserine models, supplementation with Lactobacillus probiotic strains appears to reduce serum urate (SU) and HU-induced inflammation. Murine models suggest that the chicory-derived prebiotic inulin may reduce SU, and oral supplementation with the anti-inflammatory short-chain fatty acid butyrate may lower SU by enhancing urate excretion and alleviate HU-induced tissue inflammation. Many of these studies are limited by modest numbers of participants and/or incompletely documented experimental controls, and, in the case of animal models, questionable reproducibility in humans. Many studies have been geographically limited. There remains a need for more information regarding the features of the "gouty" microbiome in wider populations, as well as for additional well-controlled probiotic and prebiotic studies in more physiologically relevant animal models prior to clinical trials.},
}

@article {pmid40616291,
year = {2025},
author = {Facchin, S and Bonazzi, E and Tomasulo, A and Bertin, L and Lorenzon, G and Maniero, D and Zingone, F and Cardin, R and Barberio, B and Ghisa, M and Savarino, EV},
title = {Could modulation of the esophageal microbiome be the answer for eosinophilic esophagitis treatment?.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2025.2530606},
pmid = {40616291},
issn = {1747-4132},
abstract = {INTRODUCTION: The oral and esophageal microbiota are gaining recognition for their significance in managing Eosinophilic Esophagitis (EoE). They serve as diagnostic biomarkers and therapeutic targets.

AREAS COVERED: The primary goal of EoE treatment is to alleviate symptoms such as dysphagia, heartburn, nausea, and chest pain. These symptoms are often associated with dysfunction of the esophageal barrier, closely linked to the esophageal microbiota. The composition of the esophageal microbiota can be affected by pharmacological treatments, particularly proton pump inhibitors, corticosteroids, and dietary interventions suggested for EoE management. As a result, the intestinal microbiota may also be influenced by these pharmacological approaches. Emerging research points to the potential of probiotic treatments as a complementary option to pharmacological therapy in the management of EoE. Publications linking "EoE" to "microbiome-microbiota" from 2013 to 2025 have been considered.

EXPERT OPINION: Further investigation into probiotics could expand the range of therapeutic options available alongside conventional treatments, potentially improving EoE remission rates, enhancing patient compliance, and reducing treatment-related side effects.},
}

@article {pmid40615889,
year = {2025},
author = {Park, K and Kim, Y and Kim, D and Oh, SM and Koo, TJ and Yoo, SM and Yoon, SH},
title = {Regulation of the tagatose catabolic gene cluster and development of a tagatose-inducible expression system in the probiotic Escherichia coli Nissle 1917.},
journal = {Microbial cell factories},
volume = {24},
number = {1},
pages = {158},
pmid = {40615889},
issn = {1475-2859},
support = {NRF-2022R1A2C2004292//National Research Foundation of Korea/ ; RS-2024-00401518//National Research Foundation of Korea/ ; },
mesh = {*Escherichia coli/genetics/metabolism ; *Probiotics/metabolism ; *Hexoses/metabolism ; *Gene Expression Regulation, Bacterial ; *Multigene Family ; Escherichia coli Proteins/genetics/metabolism ; Humans ; },
abstract = {BACKGROUND: The probiotic Escherichia coli Nissle 1917 (EcN) is a promising microbial chassis for therapeutic and industrial applications. However, its broad utility is limited by a lack of reliable inducible gene expression systems that precisely control gene expression.

RESULTS: We developed a tagatose-inducible expression system in EcN using D-tagatose, a naturally occurring sugar with established safety in humans, as a metabolizable inducer. Through differential RNA sequencing and sequence analysis, we identified the key regulatory elements governing D-tagatose catabolism in EcN and demonstrated that the DeoR family regulator (TagR) functions as a tagatose-responsive repressor. The developed system exhibited a strong dose-dependent response to D-tagatose, ensuring uniform and tunable gene activation across cell populations. Additionally, a catabolite repression-enabled auto-induction strategy facilitated robust biomass accumulation, followed by targeted protein production. This expression system was successfully applied to overexpress recombinant proteins under both aerobic and anaerobic conditions.

CONCLUSIONS: D-Tagatose is a naturally occurring low-calorie sugar that can serve as an inducer in vivo, including within the human gut microbiome. Thus, the tagatose-inducible expression system provides EcN with an additional tunable option for gene regulation, which may be valuable in applications such as synthetic biology and metabolic engineering.},
}

*Escherichia coli/genetics/metabolism
*Probiotics/metabolism
*Hexoses/metabolism
*Gene Expression Regulation, Bacterial
*Multigene Family
Escherichia coli Proteins/genetics/metabolism
Humans

@article {pmid40615864,
year = {2025},
author = {Kim, H and Chae, Y and Cho, JH and Song, M and Kwak, J and Doo, H and Choi, Y and Kang, J and Yang, H and Lee, S and Keum, GB and Wattanaphansak, S and Kim, S and Kim, HB},
title = {Understanding the diversity and roles of the canine gut microbiome.},
journal = {Journal of animal science and biotechnology},
volume = {16},
number = {1},
pages = {95},
pmid = {40615864},
issn = {1674-9782},
support = {RS-2023-00230754//Rural Development Administration/ ; },
abstract = {The canine gut microbiome plays a vital role in overall health and well-being by regulating various physiological functions, including digestion, immune responses, energy metabolism, and even behavior and temperament. As such, a comprehensive understanding of the diversity and functional roles of the canine gut microbiome is crucial for maintaining optimal health and well-being. In healthy dogs, the gut microbiome typically consists of a diverse array of bacterial phyla, including Firmicutes, Bacteroidetes, Actinobacteria, Fusobacteria, and Proteobacteria. These microbial communities form a complex ecosystem that interacts with the host to support canine health and homeostasis. A well-balanced microbiome, known as eubiosis, represents an optimized microbial composition that enhances host health and metabolic functions. Eubiosis is shaped by interactions between host physiology and environmental factors. However, dysbiosis, a disruption of eubiosis, can contribute to various health issues, such as weight fluctuations, metabolic disorders, and behavioral changes. Maintaining eubiosis in the canine gut microbiome requires customized management strategies that consider both physiological traits and environmental influences. In this review, we explored the structure and function of the canine gut microbiome, with particular emphasis on its role in health and the key factors that influence and support its maintenance.},
}

@article {pmid40615853,
year = {2025},
author = {Li, S and Xu, Z and Diao, H and Zhou, A and Tu, D and Wang, S and Feng, Y and Feng, X and Lai, Y and Yang, S and Tang, B},
title = {Gut microbiome alterations and hepatic encephalopathy post-TIPS in liver cirrhosis patients.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {745},
pmid = {40615853},
issn = {1479-5876},
abstract = {BACKGROUND: The transjugular intrahepatic portosystemic shunt (TIPS), a crucial tool for treating complications related to portal hypertension in patients with liver cirrhosis, is often associated with an increased risk of postoperative complications such as hepatic encephalopathy. Accurate preoperative prediction of the risk of developing hepatic encephalopathy is critical for optimizing the rational clinical application of TIPS.

METHODS: In this study, stool samples from 67 patients were collected preoperatively and 1 month postoperatively and metagenomic sequencing was performed to assess the composition of the gut microbiota. The differential abundances of species and MetaCyc pathways were analyzed using microbiome multivariate associations with linear models. Correlations between variables, including species abundance, the MetaCyc pathway, and clinical characteristics, were assessed using the Pearson correlation test. Prognostic models were developed from metagenomic sequencing cohorts to predict hepatic encephalopathy (HE) and elevated blood ammonia levels.

RESULTS: We demonstrated that the abundance of Phocaeicola vulgatus increased after TIPS, and the urea cycle decreased. A positive correlation was observed between P.vulgatus and elevated blood ammonia levels (P < 0.05). Patients exhibiting increased blood ammonia after TIPS showed significant enrichment of P.vulgatus (LDA > 2.5), accompanied by a reduction in the urea cycle (P < 0.05) and associated enzymes (P < 0.05). Similar microbiota alterations were identified in patients who experienced postoperative hepatic encephalopathy. Furthermore, a comprehensive genetic profile of P.vulgatus was developed, highlighting its ability to increase amino acid metabolism. Many models have shown that the use of gut microbiota characteristics has greater predictive performance.

CONCLUSION: Multiple machine learning models revealed that P.vulgatus may serve as a significant predictive microbe for hepatic encephalopathy after TIPS, which may be closely related to its ability to metabolize ammonia. These findings establish a microbiome-based framework for postoperative complication risk stratification and personalized preoperative interventions and offer unexplored targets for future research.},
}

@article {pmid40615821,
year = {2025},
author = {Upadhyay, P and Kumar, S and Tyagi, A and Tyagi, AR and Barbhuyan, T and Gupta, S},
title = {Gut Microbiome rewiring via fecal transplants: Uncovering therapeutic avenues in Alzheimer's disease models.},
journal = {BMC neuroscience},
volume = {26},
number = {1},
pages = {39},
pmid = {40615821},
issn = {1471-2202},
support = {File no.R.12014/20/2018//Department of Health Research, India/ ; DBT Core grant//National Institute of Immunology New Delhi India/ ; },
abstract = {BACKGROUND: Emerging evidence implicates the gut microbiome in Alzheimer's disease (AD) pathogenesis, yet the underlying mechanisms remain elusive. This study elucidates the bidirectional relationship between gut microbiota and AD using fecal microbiota transplantation (FMT) in a mouse model.

RESULT: Through meticulous experimentation, we conducted reciprocal FMT between AD (5xFAD) and healthy (C57BL/6) mice to unravel the impact of gut microbiome alterations on cognitive function and neuroinflammation. FMT from 5xFAD to C57BL/6 mice induced profound memory impairment and cognitive deficits, accompanied by elevated inflammatory cytokine levels, oxidative stress markers, and systemic inflammation, as evidenced by increased plasma cytokines. Conversely, transplanting healthy microbiota into 5xFAD mice yielded remarkable behavioral improvements, including enhanced spatial memory performance in the Morris water maze, directly correlating with cognitive recovery. Our findings underscore the pivotal role of the gut microbiome in AD pathogenesis and offer a promising therapeutic avenue.

CONCLUSION: Targeted modulation of the gut microbiome through strategies like FMT may offer potential benefits in Alzheimer's disease by influencing neuroinflammation, oxidative stress, and cognitive function. This comprehensive study provides novel insights into the gut-brain axis dynamics and paves the way for innovative microbiome-based interventions in AD management.},
}

@article {pmid40615170,
year = {2025},
author = {Chowdhury, R and Maddheshiya, A and Taneja, S and Bhandari, N and Majumder, PP and Strand, TA and Pandey, RM and Kurpad, AV and Mukherjee, S},
title = {Impact of an Integrated Intervention Package During Preconception, Pregnancy, and Early Childhood on the Gut Microbiome at Six Months of Age: Findings from the Women and Infants Integrated Growth Study (WINGS) Randomized Controlled Trial.},
journal = {The Journal of nutrition},
volume = {155},
number = {7},
pages = {2355-2366},
doi = {10.1016/j.tjnut.2025.04.016},
pmid = {40615170},
issn = {1541-6100},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; Infant ; Adult ; Young Adult ; Adolescent ; Male ; Feces/microbiology ; *Preconception Care ; },
abstract = {BACKGROUND: The infant gut microbiome is essential for healthy growth and development. However, limited research has explored how interventions targeting maternal and infant health, nutrition, and psychosocial conditions during preconception, pregnancy, and early childhood impact microbiome development. To address this research gap and better understand the potential impact of such interventions, this study was designed to evaluate their effects on the infant gut microbiome.

OBJECTIVE: The aim was to evaluate the effects of an integrated intervention package on infant gut microbiome at 6 mo of age compared with routine care.

METHODS: The study was embedded in a randomized factorial trial involving women aged 18-30 y. Participants were randomly assigned to receive either a preconception intervention package or routine care until pregnancy. Pregnant women were then randomly assigned to receive a pregnancy and early childhood intervention package or routine care. The intervention included health care for growth-related conditions, nutrition, water, sanitation, and hygiene (WASH), and psychosocial care. Stool samples from 392 infants (185 from the preconception, pregnancy, and early childhood intervention group and 207 from the routine care group) were collected at 6 mo, followed by microbiome DNA isolation and high-throughput sequencing of the V3-V4 region of 16S rRNA gene. Generalized linear models were used to estimate the mean relative abundance of core gut microbiome phyla, genera, and species between the intervention and routine care groups.

RESULTS: Infants in the group who received preconception, pregnancy, and early childhood intervention had a significantly lower mean relative abundance of Klebsiella genus under the Pseudomonadota phylum (45% lower; 95% confidence interval [CI]: 18, 63) and Klebsiella pneumoniae species (38% lower; 95% CI: 8, 59) compared with routine care group. In contrast, the relative abundance of Megasphaera (72% higher; 95% CI: 7, 175), Prevotella (72% higher; 95% CI: 3, 187), and Bifidobacterium breve (34% higher; 95% CI: 2, 79) was significantly higher in the group received preconception, pregnancy and early childhood intervention compared with routine care.

CONCLUSIONS: The findings indicate that improving maternal and infant health, nutrition, and psychosocial conditions enhances the relative abundance of beneficial gut bacteria at 6 mo of age, supporting healthy growth and development. This trial was registered at Clinical Trials Registry-India as CTRI/2020/10/028770; https://ctri.nic.in/Clinicaltrials/advsearch2.php.},
}

Humans
Female
*Gastrointestinal Microbiome
Pregnancy
Infant
Adult
Young Adult
Adolescent
Male
Feces/microbiology
*Preconception Care

@article {pmid40615087,
year = {2025},
author = {Wang, H and Liang, Y and Boor, PJ and Khanipov, K and Zhang, Y and Yu, X and Ambati, CSR and Putluri, N and Khan, MF},
title = {Protective role of dietary short chain fatty acid propionate against autoimmune responses and pathology of systemic lupus erythematosus in MRL-lpr mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.06.031},
pmid = {40615087},
issn = {1541-6100},
abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a chronic autoimmune disease (AD) that affects multiple organs, including skin and kidney. The etiology of SLE remains unclear but involves hormonal, environmental and genetic factors. Environmental factors, such as diet and microbiota-derived metabolites, among which short chain fatty acids (SCFAs) are major players, can influence AD pathogenesis.

OBJECTIVE: This study investigates the involvement of SCFAs in the pathogenesis of SLE and further investigated the effect of propionate (PA) supplementation on SLE disease outcome in MRL-lpr mice.

METHODS: Cecal SCFAs from mouse models with varying degrees of SLE disease activities (C57BL/6, MRL+/+ and MRL-lpr) were determined by LC-MS analysis. Five-week-old MRL-lpr mice were supplemented with PA (200 mM, via drinking water) for 6 weeks, and assessed autoimmunity and disease markers.

RESULTS: LC-MS analysis of cecal SCFAs showed a significant decrease of PA in MRL-lpr mice (p < 0.001). PA treatment ameliorated the autoimmune response, evident from reduced serum autoantibodies (p < 0.05 for both ANA and anti-dsDNA) and a significant alleviation of glomerulonephritis (p < 0.05). Furthermore, it restored the imbalances in gut microbiome composition and SCFAs, especially propionate (p < 0.01). Additionally, PA treatment resulted in decreased splenic activated CD4 T cells (p < 0.05) and alterations in renal inflammatory signaling pathways.

CONCLUSIONS: Our findings support the beneficial effects of propionate in alleviating SLE, and therapeutic potential of propionate or propionate-producing bacteria for SLE.},
}

@article {pmid40615083,
year = {2025},
author = {Duan, Y and Li, Y and Xu, C and Wang, W and Wang, X and Zheng, W and Hsing, JC and Wu, J and Myers, A and Hsing, AW and He, W and Zhu, S},
title = {Fried food consumption-related gut microbiota is associated with obesity, fat distribution and cardiometabolic diseases: results from two large longitudinal cohorts with sibling comparison analyses.},
journal = {The American journal of clinical nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajcnut.2025.06.025},
pmid = {40615083},
issn = {1938-3207},
abstract = {BACKGROUND: In prospective cohort studies, the relationship between fried food consumption, gut microbiota, obesity, and cardiometabolic diseases remains unknown.

OBJECTIVE: We aimed to explore associations of fried food consumption with gut microbiota and associations of fried food consumption-related microbiota with obesity and related disorders.

METHODS: We analyzed 6,637 individuals from the WELL-China cohort (baseline 2016-2019) and 3,466 from the Lanxi cohort (baseline 2017-2019), with follow-up until June 24, 2024. Face-to-face interviews provided data on fried food consumption and other covariates. Analysis of 16S rRNA data from fecal samples collected at baseline identified microbial genera. Body composition was evaluated using dual-energy X-ray absorptiometry (DXA). The Microbiome Multivariable Associations with Linear Models (MaAsLin) helped identify genera associated with frequency of fried food consumption in the cross-sectional analysis. Cox regression models examined the relationship of fried food consumption-related microbiota with cardiometabolic diseases during follow-up. Sibling comparison analyses were used to control for unmeasured familial confounders using the between-within (BW) model.

RESULTS: Twenty-five microbial genera were significantly associated with fried food consumption frequency. Using these genera, we constructed a fried food consumption-related microbiota index. Meta-analysis of both cohorts found a positive relationship of this index with overall adiposity measures (BMI) (β coefficient, 0.26; 95% confidence interval (CI), 0.19-0.32) and central fat distribution parameters (including android-gynoid fat ratio (β, 1.48; 95% CI, 1.14-1.82)). Longitudinal analyses indicated that a higher fried food consumption-related microbiota index was linked to a higher risk of developing cardiometabolic diseases, with adjusted hazard ratios (95% CI) of 1.16 (1.07-1.27) for diabetes and 1.16 (1.06-1.26) for major adverse cardiovascular events. Sibling comparison analyses yielded similar results.

CONCLUSIONS: Fried food consumption-related microbiome is associated with a higher risk of obesity, central fat distribution, and cardiometabolic diseases, emphasizing the importance of dietary choices in the management and prevention of chronic diseases.},
}

@article {pmid40615058,
year = {2025},
author = {Vanhatalo, A and L'Heureux, JE and Black, MI and Blackwell, JR and Aizawa, K and Thompson, C and Williams, DW and van der Giezen, M and Winyard, PG and Jones, AM},
title = {Ageing modifies the oral microbiome, nitric oxide bioavailability and vascular responses to dietary nitrate supplementation.},
journal = {Free radical biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.freeradbiomed.2025.07.002},
pmid = {40615058},
issn = {1873-4596},
abstract = {This study evaluated whether changes in the oral microbiome in response to dietary nitrate and antiseptic mouthwash treatments were related to changes in nitric oxide bioavailability and vascular function. Thirty-nine young (18-30 years) and thirty-six older (67-79 years) males and females completed a placebo-controlled, double-blind cross-over intervention including three 2-week conditions separated by 2-week washouts: placebo beetroot juice (PL), nitrate-rich beetroot juice (BR) and antiseptic mouthwash (MW). The oral microbiomes of young and older adults responded differently to BR (post BR non-metric multidimensional scaling P=0.01), while the oral microbiomes of both age groups were unaffected by PL and MW interventions. Older people, who had elevated baseline mean arterial pressure (MAP; 95±9 mmHg) compared to young adults (87±7 mmHg, P<0.001), showed decreased brachial MAP (-4±4 mmHg, P=0.003) after BR while this effect was absent in the young. Flow mediated dilatation (FMD) variables were not affected by the interventions in older adults, while in the young there was a difference in changes (from pre to post) in ΔFMD% between the MW and BR conditions (P=0.04). Decreased blood pressure in older adults correlated with increased plasma nitrite concentration (change in central MAP vs. [NO2[-]] r=-0.41, P=0.02), which in turn correlated with decreases within the co-occurring module of bacteria dominated by the genus Prevotella (P. intermedia r=-0.72, P=0.001; P. dentalis r=-0.88, P<0.0001; Crassaminicella sp. SY095 r=-0.81, P<0.0001). Greater blood pressure benefits from supplemental dietary nitrate in older compared to younger people are mediated primarily by the suppression of potentially harmful oral bacteria, that have been associated with ammonia production.},
}

@article {pmid40614920,
year = {2025},
author = {Yadav, S and Raj, RG},
title = {Parkinson's disease and the gut microbiota connection: unveiling dysbiosis and exploring therapeutic horizons.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.07.003},
pmid = {40614920},
issn = {1873-7544},
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder marked by dopaminergic neuronal loss, α-synuclein aggregation, and sustained neuroinflammation. Emerging evidence supports the gut-brain-microbiota axis as a pivotal player in the disease's pathogenesis. Dysbiosis, disruptions in the gut microbial composition, has been consistently observed in individuals with PD, with notable reductions in beneficial, short-chain fatty acid-producing bacteria and elevations in pro-inflammatory microbial species. These alterations contribute to increased intestinal permeability, systemic inflammation, and heightened neuroinflammatory responses that may drive α-synuclein misfolding and dopaminergic degeneration. In addition, microbial metabolites, including lipopolysaccharides and amyloid proteins such as curli, may promote neurodegeneration via immune and molecular mimicry pathways. Recent advances highlight the bidirectional influence of the microbiota-gut-brain axis on PD symptoms, ranging from motor deficits to non-motor features like constipation, depression, and cognitive decline. Several microbiota-modulating interventions, including probiotics, prebiotics, dietary strategies, antibiotics, and fecal microbiota transplantation, have demonstrated neuroprotective potential in both preclinical and clinical contexts. However, inter-individual variability, methodological heterogeneity, and the absence of longitudinal, multi-omics-integrated studies limit current understanding. The gut microbiome also holds promise as a non-invasive biomarker for early PD detection and prognosis, though standardization remains a challenge. Future research must clarify causal mechanisms, optimize therapeutic delivery, and integrate genetic, metabolic, and environmental data to advance precision medicine approaches. This review consolidates current knowledge on gut microbiota's role in PD pathophysiology and therapeutic innovation, providing a roadmap for future research directions.},
}

@article {pmid40614884,
year = {2025},
author = {Dong, TS and Jann, K and Wang, DJ and Church, A},
title = {Understanding Whole Person Systems in Brain-Gut-Microbiome Research Through Ultra-High-field MRI Imaging.},
journal = {NeuroImage},
volume = {},
number = {},
pages = {121360},
doi = {10.1016/j.neuroimage.2025.121360},
pmid = {40614884},
issn = {1095-9572},
abstract = {The brain-gut-microbiome (BGM) axis regulates interoception, metabolism, and immunity, with dysfunction linked to IBS, obesity, and mood disorders. Ultra-high-field (UHF) MRI advances neural imaging, enhancing resolution of vagal and spinal circuits mediating gut-brain communication. UHF enables real-time tracking of interventions like vagus nerve stimulation and probiotics, linking microbiome shifts to neural adaptations. Despite challenges like signal distortions, innovations in coil design are improving imaging fidelity. Integrating neuroimaging with multi-omic profiling fosters a systems-level approach, advancing personalized therapies for BGM disorders. This commentary underscores UHF MRI's transformative potential in bridging neuroscience, microbiome science, and clinical applications.},
}

@article {pmid40614851,
year = {2025},
author = {Yang, X and Huang, X and Zheng, B and Gao, F and He, L and Xu, Q},
title = {Natural-Setting Evidence of Stochastic-to-Deterministic Gut Microbiome Assembly and Metabolic Shifts in Regenerating Tropical Sea Cucumber Stichopus monotuberculatus.},
journal = {Environmental research},
volume = {},
number = {},
pages = {122260},
doi = {10.1016/j.envres.2025.122260},
pmid = {40614851},
issn = {1096-0953},
abstract = {Holothurians exhibit a distinctive ability to eviscerate and regenerate internal organs, making them an ideal model for investigating host-microbe interactions. This study examined the dynamics of the gut microbiome and the associated metabolome during intestinal regeneration in the tropical sea cucumber Stichopus monotuberculatus under natural conditions. Through a combination of 16S rDNA sequencing and GC-MS-based metabolomics, we determined stage-specific shifts in gut microbial communities and metabolite profiles. Early regeneration was characterized by a stochastic influx of environmental microbes, low microbial network connectivity, and high metabolite-microbe correlation complexity, which suggested that the host relied on metabolic signals to coordinate the initial colonization of a diverse microbial community sourced from environment. As regeneration advanced, the microbial network grew increasingly cohesive, environmental contribution diminished, and metabolite-microbe correlation decreased. The reestablished gut microbiome exhibited no significant structural differences compared to pre-evisceration communities. This process reflected a transition from stochastic recruitment to host-filtered deterministic assembly, ultimately restoring a stable microbiome. Core microbial taxa such as Roseburia, Faecalibacterium, and Ruegeria were associated with pathways related to nutrient provisioning, energy production, and immune regulation, suggesting their potential contributions to intestinal recovery. Metabolomic analysis revealed significant alterations in amino acid, lipid, and carbohydrate metabolism, highlighting the functional integration between the gut bacteria and regenerated host tissue. Our findings provide novel insight into the interactions among host, microbe, and environment during gut microbiome assembly, as well as highlight the balance between stochastic and deterministic factors in the formation of marine holobiont communities.},
}

@article {pmid40614836,
year = {2025},
author = {Yu, J and Zhu, H and Yu, X and Liu, Y and Zhang, J and Jiang, L and Zhang, X},
title = {Calcitriol/Vitamin D Receptor Ameliorates Fructose-Induced Enteritis-Hepatitis Axis Dysregulation in Mice.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110017},
doi = {10.1016/j.jnutbio.2025.110017},
pmid = {40614836},
issn = {1873-4847},
abstract = {Emerging evidence associates excessive fructose consumption with intestinal inflammation and metabolic dysfunction-associated steatotic liver disease (MASLD), though the underlying mechanisms remain elusive. This preclinical study systematically investigated the therapeutic potential of calcitriol/vitamin D receptor (VDR) signaling in counteracting fructose-induced gut-liver axis dysregulation using female C57BL/6J mice. Experimental groups included: (1) Control (C), (2) Fructose (F; 20% w/v fructose water for 8 weeks), (3) Fructose+Calcitriol (F+V; 300 ng/kg calcitriol gavage during weeks 4-8), and (4) Calcitriol alone (V). Key findings revealed that chronic fructose exposure induced gut microbiota dysbiosis (characterized by decreased Firmicutes/Bacteroidetes ratio), compromised intestinal barrier integrity through downregulation of tight junction proteins, depleted secretory cells (Goblet/Paneth cells), and triggered apoptosis with concomitant elevation of pro-inflammatory cytokines (TNF-α, IL-6). These intestinal alterations culminated in endotoxemia-mediated hepatic inflammation and fibrogenesis, accompanied by persistent NF-κB pathway activation. Notably, calcitriol intervention significantly restored VDR expression, enhanced autophagic flux, stimulated mucin/antimicrobial peptide production, and suppressed NF-κB-mediated inflammatory responses. In vitro validation using Caco2 and RAW264.7 cells demonstrated that VDR activation effectively reversed fructose-impaired autophagy and NF-κB hyperactivation. Microbiome analysis further indicated calcitriol's partial normalization of fructose-induced microbial shifts, suggesting microbiota-mediated mechanisms. Collectively, these findings establish that calcitriol/VDR signaling mitigates fructose-driven gut-liver axis dysfunction through coordinated regulation of autophagy, mucosal defense systems, and inflammatory pathways. This mechanistic framework positions the VDR pathway as a promising therapeutic target for enteritis-hepatitis axis disorders, warranting further clinical investigation.},
}

@article {pmid40614808,
year = {2025},
author = {He, S and Chen, C and Cao, L and Nauta, A and Liu, X and Chen, H and Spoelstra, J and Yang, B},
title = {Metabolic diversity and competitive interactions of infant-derived bifidobacteria in human milk oligosaccharides and galacto-oligosaccharides utilization.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26559},
pmid = {40614808},
issn = {1525-3198},
abstract = {Human milk oligosaccharides (HMO) play a pivotal role in shaping the infant gut microbiome and immune system, primarily by selectively promoting Bifidobacterium species. Although the metabolic pathways of individual bifidobacterial strains for HMO are well-characterized, competitive interactions among multiple strains under single-HMO conditions remain poorly understood. Here, we evaluated metabolic capabilities of 15 infant-derived Bifidobacterium strains on 3 substrates: 2'-fucosyllactose (2'-FL), lacto-N-tetraose (LNT), and high-purity galacto-oligosaccharides (GOS-HP). Monoculture and mixed-culture analyses were conducted using growth kinetics, substrate consumption assays, and genomic profiling. Monoculture results demonstrated most strains exhibited robust growth on LNT and GOS-HP, whereas 2'-FL utilization varied. Genomic analysis indicated efficient HMO metabolism correlated with glycosyl hydrolase gene diversity and copy numbers. In mixed cultures, B. dentium initially dominated through monosaccharide consumption but was subsequently outcompeted by B. longum ssp. infantis and B. breve, highlighting oligosaccharide-driven competition. The LNT mixed culture resulted in a bifidobacterial community composition resembling that of breastfed infants. These findings guide oligosaccharide selection for infant formula design to better emulate human milk's microbiome-modulating benefits.},
}

@article {pmid40614713,
year = {2025},
author = {Cowan, CM and Pietras, EM},
title = {From symbiote to bad neighbor: The intestinal microbiome as a driver of CHIP.},
journal = {Cell stem cell},
volume = {32},
number = {7},
pages = {1036-1037},
doi = {10.1016/j.stem.2025.06.003},
pmid = {40614713},
issn = {1875-9777},
mesh = {*Gastrointestinal Microbiome ; Humans ; Animals ; *Hematopoietic Stem Cells/metabolism ; *Clonal Hematopoiesis ; Mice ; },
abstract = {Hematopoietic stem cells (HSCs) with mutations that can cause clonal hematopoiesis of indeterminate potential (CHIP) accumulate during aging. Agarwal et al.[1] demonstrate in Nature that intestinal barrier permeability increases with age and enables the microbial metabolite ADP-heptose to reach the bone marrow, thus driving the expansion of DNMT3A-mutant HSCs.},
}

*Gastrointestinal Microbiome
Humans
Animals
*Hematopoietic Stem Cells/metabolism
*Clonal Hematopoiesis
Mice

@article {pmid40614655,
year = {2025},
author = {Ghosh, R and Sui, P and Fritze, D and Fernandez, S and Torres, A and Woodworth, J and Cigarroa, FG and Halff, GA and Kumar, AP},
title = {Characterization of metabolomic associated with pancreatic cancer patients with overweight and obesity.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {240-251},
doi = {10.1016/j.clnu.2025.06.015},
pmid = {40614655},
issn = {1532-1983},
abstract = {BACKGROUND AND AIMS: The near equal incidence and mortality rates of pancreatic cancer, combined with projections that by 2050 pancreatic cancer will be the second-most fatal cancer, underscore the need to identify patients with early disease and thus interrupt this trajectory. Obesity, weight gain and waistline have been implicated in increasing the risk of pancreatic cancer. Factors such as inflammation, insulin resistance, and changes in intestinal microbiome have been suggested to be involved in obesity. Although metabolomic analyses of pancreatic cancer patients have established correlations between phospholipids, lysophospholipids with treatment outcomes, the association between metabolites, obesity, and pancreatic cancer remains largely understudied. We hypothesized that global metabolomic profile of obese and overweight pancreatic cancer patients will be different compared with healthy weight subjects with no cancer.

METHODS: Global metabolic profiles were determined in obese and overweight pancreatic cancer patients compared with healthy weight subjects using ultrahigh performance liquid chromatography-tandem mass spectroscopy.

RESULTS: Analysis of the data using the Benjamini & Hochberg method to control the false discovery rate revealed statistically significant changes in branched chain amino acids, lipid metabolites including monoacyl glycerol, and fructose in overweight/obese pancreatic cancer patients relative to healthy weight.

CONCLUSION: Our findings suggest that metabolomic pathways as potential targets for high-risk pancreatic cancer patients.},
}

@article {pmid40614652,
year = {2025},
author = {Korotetskiy, I and Kuznetsova, T and Shilov, S and Zubenko, N and Ivanova, L and Korotetskaya, N and Izmailov, T},
title = {Metagenomic data insights into chicken microbiome diversity across various regions of Kazakhstan.},
journal = {Poultry science},
volume = {104},
number = {9},
pages = {105488},
doi = {10.1016/j.psj.2025.105488},
pmid = {40614652},
issn = {1525-3171},
abstract = {Understanding the gut microbiome of poultry is essential for ensuring the health, productivity, and safety of poultry products. This study aimed to assess the regional diversity and composition of chicken microbiota in Kazakhstan using high-throughput metagenomic sequencing. Tracheal and cloacal swabs were collected from chickens on private farms in five geographic locations. Pooled DNA and RNA samples were sequenced using the Ion Torrent PGM platform, and taxonomic classification was performed using Kaiju, with subsequent alpha and beta diversity analyses in R. The results revealed considerable differences in the microbial profiles between regions. Notably, Chlamydia was abundant in the Shymkent samples (>48 %) but was nearly absent elsewhere. In contrast, Pseudomonas was disproportionately dominant in Almaty (32.7 %), suggesting possible dysbiosis. This study provides the first metagenomic characterization of poultry microbiota in Kazakhstan. This highlights region-specific microbial risks and underscores the importance of spatial microbiome monitoring in poultry health management. These findings provide a basis for future strategies aimed at preventing disease outbreaks and controlling zoonotic pathogens in poultry.},
}

@article {pmid40614627,
year = {2025},
author = {Pecyna, P and Bykowska-Derda, A and Gabryel, M and Mankowska-Wierzbicka, D and Nowak-Malczewska, DM and Jaskiewicz-Rajewicz, K and Jaworska, MM and Grzymislawski, M and Dobrowolska, A and Czlapka-Matyasik, M and Gajecka, M},
title = {Blautia spp. in the gut microbiome: Its relation to dietary choices and to the nutritional status of patients with irritable bowel syndrome.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {138},
number = {},
pages = {112836},
doi = {10.1016/j.nut.2025.112836},
pmid = {40614627},
issn = {1873-1244},
abstract = {OBJECTIVES: Uncontrolled growth of certain Blautia spp. species could be associated with symptoms identified in patients with irritable bowel syndrome (IBS). As no studies have thus far focused on the relationship between nutrition habits, body composition, and the abundance of Blautia spp. in patients with IBS, this study aimed to determine the above-mentioned aspects.

METHODS: The gut microbiota of patients with IBS (n = 73) and a control group (n = 54) were subjected to 16S ribosomal RNA sequencing. Food frequency intake, physical activity, and socioeconomic status were measured by the Dietary Habits and Nutrition Beliefs Questionnaire KomPAN. Body composition was assessed by the air plethysmography method (BodPod, Life Measurement Inc., Concord, CA, USA).

RESULTS: Blautia spp. was more abundant in the gut microbiota of patients with IBS than in control participants. In patients with IBS, a relation was observed between the frequency of fruit intake and Blautia spp. abundance (odds ratio [OR] = 0.35; 95% confidence interval [95% CI]: 0.12-1.01; P = 0.04). When comparing all study participants, individuals with a high relative Blautia spp. abundance consumed white bread more frequently than the remaining participants (OR = 2.26; 95% CI: 1.03-4.96; P = 0.04). In turn, the high-frequency intake of wholegrain bread and legumes was related to decreased Blautia spp. abundance OR = 0.29; 95% CI: 0.10-0.94; P = 0.03 and OR = 0.38; 95% CI: 0.17-0.83; P = 0.01, respectively). A body fat percentage over 40% was related to high Blautia spp. abundance (OR = 2.85; 95% CI: 0.99-8.16; P = 0.04).

CONCLUSIONS: A diet high in wholegrain bread, legumes, and vegetables may influence Blautia spp. abundance in the gut microbiota. High levels of Blautia spp. in the gut are also related to body composition.},
}

@article {pmid40614495,
year = {2025},
author = {Su, X and Liu, M and Chen, Y and Feng, D and Xu, J and He, Y},
title = {Microplastics aging potentially enlarge the ecological risk to wetland sediments as revealed by their interactive effects on γ-HCH dissipation and methane production.},
journal = {Water research},
volume = {285},
number = {},
pages = {124137},
doi = {10.1016/j.watres.2025.124137},
pmid = {40614495},
issn = {1879-2448},
abstract = {Microplastics (MPs) have garnered global concern, yet the environmental implications of their aging remain poorly understood. Especially, their interactions with co-occurring pollutants and impacts on biogeochemical processes in wetland sediments require further investigation. Through microcosm experiments, this study systematically elucidated the differential effects of pristine vs. aged MPs on γ-hexachlorocyclohexane (γ-HCH) behavior and methanogenesis. Aged MPs exhibited enhanced γ-HCH adsorption (666.7 vs. 500.0 mg kg[-1] for pristine MPs), yet paradoxically inhibited γ-HCH dissipation in wetland sediments. This demonstrates that previous studies might oversimplify the interaction between MPs and pollutants. Concurrently, Dhc functional gene abundance on aged MP-surface biofilms declined sharply from 3015.4 to 811.4 copies g[-1] dw over 60 days, suggesting impaired functional microorganisms. Notably, aged MPs amplified CH4 production (1.64 ± 0.10 vs. 1.25 ± 0.15 mg kg[-1] day[-1] pristine MPs) and H2O2 generation (2.62 ± 0.12 vs. 2.06 ± 0.05 mmol L[-1] pristine MPs), with reduced microbial complexity and stability. Mechanistically, aging altered MP surface properties, selectively enriching mcrA functional genes and methanogenic archaea (Methanomassiliicoccus and Methanosarcina). These findings show aged MPs in suppressing pollutant dissipation (γ-HCH) while accelerating elemental cycling (CH4), driven by reactive oxygen species and microbiome shifts. Given the widespread occurrence of aged MPs in wetlands, this study underscores their underappreciated yet critical influence on wetland sediment biogeochemistry, urging prioritized research to mitigate their cascading potential risks.},
}

@article {pmid40613995,
year = {2025},
author = {Ghamari, M and Sabzi, S and Rajabi, E and Khodadadi, G and Navidifar, T and Sadeghi, Z and Bostanghadiri, N},
title = {Probiotics, Prebiotics, Synbiotics, Postbiotics, and Bioactive Agents in Modulating Harmful Oral Biofilms.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40613995},
issn = {1867-1314},
abstract = {Oral biofilms are intricate microbial communities that can enhance oral health, yet their equilibrium is susceptible to disruption, leading to oral infectious diseases. The most prevalent of these are dental caries, periodontitis, and peri-implant infections. The formation of pathogenic biofilms is the primary cause of these diseases, and their resistance to antimicrobial agents and immune responses poses significant treatment challenges. Researchers have recently implemented microbiome-based strategies, including probiotics, prebiotics, synbiotics, and postbiotics, to modulate biofilm composition and restore microbial equilibrium. Probiotics exert their health effects by competitively inhibiting pathogenic bacteria, producing antimicrobial compounds, and interacting with the immune system. Moreover, prebiotics can selectively stimulate beneficial bacteria, while synbiotics and postbiotics increase these effects using synergistic mechanisms. Recent studies suggest that integrating these strategies into oral healthcare can offer effective, non-invasive approaches to manage biofilm-related oral infections. Notwithstanding the challenges, issues pertaining to strain-specific efficacy, probiotic viability, and long-term colonization remain to be addressed. This review has collated recent research in this area and highlights promising therapeutic directions for improving oral health outcomes.},
}

@article {pmid40613917,
year = {2025},
author = {Zakerska-Banaszak, O and Ladziak, K and Kruszka, D and Maciejewski, K and Wolko, L and Krela-Kazmierczak, I and Zawada, A and Vibeke Vestergaard, M and Dobrowolska, A and Skrzypczak-Zielinska, M},
title = {New potential biomarkers of ulcerative colitis and disease course - integrated metagenomic and metabolomic analysis among Polish patients.},
journal = {Journal of gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {40613917},
issn = {1435-5922},
support = {2020/04/X/NZ2/02172//Narodowe Centrum Nauki/ ; 2021/02//Institute of Human Genetics, Polish Academy of Sciences, in Poznan, Poland/ ; },
abstract = {BACKGROUND & AIM: The course of ulcerative colitis (UC) involves successive periods of remission and exacerbation but is difficult to predict. Gut dysbiosis in UC has already been intensively investigated. However, are periods of exacerbation and remission associated with specific disturbances in the composition of the intestinal microbiota and its metabolome? Our goal was to answer this question and to identify bacteria and metabolites necessary to maintain the remission.

METHODS: We enrolled 65 individuals, including 20 UC patients in remission, 15 in exacerbation, and 30 healthy controls. Metagenomic profiling of the gut microbial composition was performed based on 16S rRNA V1-V9 sequencing. Stool and serum metabolic profiles were studied by chromatography combined with mass spectrometry.

RESULTS: We revealed significant differences in the gut bacterial and metabolic composition between patients in active UC and those in remission, as well as in healthy controls. As associated with UC remission we have identified following bacteria: Akkermansia, Agathobacter, Anaerostipes, Enterorhabdus, Coprostanoligenes, Colinsella, Ruminococcus, Subdoligranulum, Lachnoclostridium, Coriobacteriales, Erysipelotrichaceae, and Family XII, and compounds - 1-hexadecanol, phytanic acid, squalene, adipic acid, cis-gondoic acid, nicotinic acid, tocopherol gamma, ergosterol and lithocholic acid. Whereas, in the serum lithocholic acid, indole and xanthine were found as potential candidates for biomarkers of UC remission.

CONCLUSION: We have demonstrated that specific bacteria, metabolites, and their correlations could be crucial in the remission of UC among Polish patients. Our results provide valuable insights and a significant source for developing new hypotheses on host-microbiome interactions in diagnosis and course of UC.},
}

@article {pmid40613843,
year = {2025},
author = {Huang, R and Jin, X and Liu, Q and Bai, X and Wu, Y and Wang, Y and He, X and Jiang, Z and Wang, L and Zhu, W},
title = {Genetic evidence for causal links between diet, gut microbiota, and hepatobiliary cancer: a Mendelian randomization study.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {100},
pmid = {40613843},
issn = {2191-0855},
support = {81874182//National Natural Science Foundation of China/ ; 81874056//National Natural Science Foundation of China/ ; 201940043//the Public Health Bureau Foundation of Shanghai/ ; 202240240//the Public Health Bureau Foundation of Shanghai/ ; 2022YFE0125300//National Key Research and Development Plan of the Ministry of Science and Technology/ ; 22ZR1413300//Shanghai Natural Science Foundation Project/ ; },
abstract = {Emerging evidence suggests a complex interplay among dietary habits, gut microbiota, and hepatobiliary cancers, yet the causal relationships remain unclear. Here, we conducted a comprehensive two-sample Mendelian randomization (MR) analysis using genetic instruments from large European cohorts to assess causality among 88 dietary components, 1080 microbiota traits, liver cancer (500 cases, 314,193 controls), and biliary tract cancer (1207 cases, 314,193 controls). We identified significant causal associations of 17 dietary and 101 microbial traits with hepatobiliary cancer risk, while 11 dietary and 70 microbiota traits showed evidence of reverse causality, indicating potential disease-driven alterations. Importantly, a two-step MR mediation analysis revealed that 43 microbial taxa and 6 metabolic pathways significantly mediated dietary influences on hepatobiliary cancer risk; notably, Mollicutes RF9 mediated 31% of the protective effect exerted by zinc on biliary tract cancer. These findings provide genetic evidence delineating gut microbiota as key intermediaries connecting dietary intake to hepatobiliary cancers, highlighting microbiome-targeted dietary strategies as potential preventive interventions. Further research is required to confirm these causal mechanisms and facilitate the development of targeted prevention and therapeutic approaches.},
}

@article {pmid40613581,
year = {2025},
author = {Dang, T and Lysenko, A and Boroevich, KA and Tsunoda, T},
title = {VBayesMM: variational Bayesian neural network to prioritize important relationships of high-dimensional microbiome multiomics data.},
journal = {Briefings in bioinformatics},
volume = {26},
number = {4},
pages = {},
doi = {10.1093/bib/bbaf300},
pmid = {40613581},
issn = {1477-4054},
support = {JP20H03240//JSPS KAKENHI/ ; JP24K15175//JSPS KAKENHI/ ; JPMJCR2231//JST CREST/ ; },
mesh = {Bayes Theorem ; *Microbiota ; *Neural Networks, Computer ; *Metagenomics/methods ; Humans ; *Computational Biology/methods ; Algorithms ; Multiomics ; },
abstract = {The analysis of high-dimensional microbiome multiomics datasets is crucial for understanding the complex interactions between microbial communities and host physiological states across health and disease conditions. Despite their importance, current methods, such as the microbe-metabolite vectors approach, often face challenges in predicting metabolite abundances from microbial data and identifying keystone species. This arises from the vast dimensionality of metagenomics data, which complicates the inference of significant relationships, particularly the estimation of co-occurrence probabilities between microbes and metabolites. Here we propose the variational Bayesian microbiome multiomics (VBayesMM) approach, which aims to improve the prediction of metabolite abundances from microbial metagenomics data by incorporating a spike-and-slab prior within a Bayesian neural network. This allows VBayesMM to rapidly and precisely identify crucial microbial species, leading to more accurate estimations of co-occurrence probabilities between microbes and metabolites, while also robustly managing the uncertainty inherent in high-dimensional data. Moreover, we have implemented variational inference to address computational bottlenecks, enabling scalable analysis across extensive multiomics datasets. Our large-scale comparative evaluations demonstrate that VBayesMM not only outperforms existing methods in predicting metabolite abundances but also provides a scalable solution for analyzing massive datasets. VBayesMM enhances the interpretability of the Bayesian neural network by identifying a core set of influential microbial species, thus facilitating a deeper understanding of their probabilistic relationships with the host.},
}

Bayes Theorem
*Microbiota
*Neural Networks, Computer
*Metagenomics/methods
Humans
*Computational Biology/methods
Algorithms
Multiomics