@article {pmid40653355,
year = {2025},
author = {Murakonda, SP and Balusu, S and Chava, H and Murakonda, AB and Polneedi, R and Bodduluri, S and Gupta, SC and Challagundla, KB},
title = {Influence of gut microbiota on systemic immune responses and cancer immunotherapy.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {23-66},
doi = {10.1016/bs.ircmb.2024.12.005},
pmid = {40653355},
issn = {1937-6448},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immunotherapy/methods ; *Neoplasms/therapy/immunology/microbiology ; Animals ; *Immunity ; },
abstract = {The gut microbiota is increasingly being recognized as a key player in the onset and progression of several human diseases, including malignancies. Recent research has shed light on the complex relationships between the gut microbiome and the effectiveness of cancer immunotherapy. Gaining a thorough understanding of how the gut microbiota influences immune responses during cancer treatments is critical for medical advancements. This review aims to delve into the intricate interactions between gut microbiota, the systemic immune system, and cancer immunotherapy. Additionally, as the gut microbiota can contribute to immune-related adverse effects, we explored possible interventions to alleviate these side effects and reviewed microbiota-targeted strategies that could enhance the success of cancer immunotherapies.},
}

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

@article {pmid40653354,
year = {2025},
author = {Gupta, R and Gaur, S},
title = {Effect of diet and lifestyle on microbiome composition.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {157-174},
doi = {10.1016/bs.ircmb.2024.12.008},
pmid = {40653354},
issn = {1937-6448},
mesh = {Humans ; *Life Style ; *Diet ; *Microbiota ; Animals ; },
abstract = {Microbes are major drivers of many important physiological pathways in the human body. A well-adapted and established microbial community at key body sites performs a wide range of functions, including digestive and immunological roles. However, the structure of these microbial communities depends on numerous factors, both genetic and external. Diet and lifestyle are the most common external factors influencing microbiome composition. A healthy diet and lifestyle promote the growth of beneficial microbes, while disturbances in these factors can alter the entire microbial dynamics, potentially leading to pathogenesis. These perturbations can occur at any stage of life, from birth to old age, and may result in serious clinical conditions such as obesity, diabetes, cancers, metabolic syndromes, and many others. Therefore, it is essential to identify the dietary and lifestyle factors that support a healthy microbiome and prevent dysbiosis. This chapter aims to discuss the role of various component of diet and life style that can ultimately shape the human microbiome.},
}

Humans
*Life Style
*Diet
*Microbiota
Animals

@article {pmid40653353,
year = {2025},
author = {Jain, P and Joshi, N and Sahu, V and Dominic, A and Aggarwal, S},
title = {Autoimmune diseases and microbiome targeted therapies.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {133-156},
doi = {10.1016/bs.ircmb.2024.12.007},
pmid = {40653353},
issn = {1937-6448},
mesh = {Humans ; *Autoimmune Diseases/microbiology/therapy/immunology ; *Gastrointestinal Microbiome/drug effects ; Animals ; },
abstract = {Previously regarded solely as a digestive entity, the human gut has been revealed to harbor a rich diversity of microbial flora, pivotal in maintaining overall health and organ functionality. Contrary to conventional wisdom, certain microbes confer notable benefits rather than posing threats. The gut microbiota, consisting of Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, plays a crucial role in health maintenance, and dysbiosis can precipitate disease onset. Autoimmune disorders stem from immune system dysregulation, resulting in self-cell attacks. Recent microbiome research underscores a correlation between altered gut microbiota and autoimmune diseases. This chapter delves into the impact of the gut microbiome in autoimmune diseases and presents gut microbiome targeting therapy as a possible treatment alternative.},
}

Humans
*Autoimmune Diseases/microbiology/therapy/immunology
*Gastrointestinal Microbiome/drug effects
Animals

@article {pmid40653352,
year = {2025},
author = {Singh, K and Bhadauriya, AS},
title = {Effect of microbial dysbiosis on autoimmune associated inflammation.},
journal = {International review of cell and molecular biology},
volume = {395},
number = {},
pages = {1-22},
doi = {10.1016/bs.ircmb.2024.12.016},
pmid = {40653352},
issn = {1937-6448},
mesh = {Humans ; *Dysbiosis/complications/microbiology/immunology ; *Autoimmune Diseases/microbiology/immunology ; *Inflammation/microbiology/immunology/complications ; Animals ; *Gastrointestinal Microbiome/immunology ; },
abstract = {Trillions of microorganisms inhabit the human body, playing crucial roles in the development of the immune system, maintaining balance within the gut's immune system, and overall well-being. When these microbial communities experience imbalance, known as dysbiosis, it can lead to localized inflammatory conditions such as colitis and inflammatory bowel diseases, as well as systemic autoimmune disorders like type 1 diabetes, rheumatoid arthritis, and multiple sclerosis. Gut microbes engage with the immune system through various means, including influencing host microRNAs to regulate gene expression and generating metabolites that interact with cellular receptors such as TLRs and GPCRs. These interactions impact critical immune processes like the differentiation of lymphocytes, the production of interleukins, and the maintenance of gut barrier function. Looking into, how gut microbes contribute to or defend against systemic autoimmune diseases is crucial for developing strategies to manage or prevent these conditions. These approaches may include dietary or lifestyle modifications, microbiome-targeted therapies such as prebiotics or probiotics, the identification of diagnostic biomarkers for predicting disease risk, and monitoring and intervening in shifts in microbial populations during autoimmune flare-ups. Recognizing the microbiome's significance in systemic autoimmune diseases offers promise for transforming these presently challenging-to-treat conditions into more controllable or preventable ones.},
}

Humans
*Dysbiosis/complications/microbiology/immunology
*Autoimmune Diseases/microbiology/immunology
*Inflammation/microbiology/immunology/complications
Animals
*Gastrointestinal Microbiome/immunology

@article {pmid40653335,
year = {2025},
author = {Kramer, A and Dahl, MB and Bengtsson, MM and Boyce, JM and Heckmann, M and Meister, M and Papke, R and Pittet, D and Reinhard, A and Slevogt, H and Wang, H and Zwicker, P and Urich, T and Seifert, U},
title = {Response to the comment on the article "No detrimental effect on the hand microbiome of health care staff by frequent alcohol-based antisepsis".},
journal = {American journal of infection control},
volume = {53},
number = {8},
pages = {916-917},
doi = {10.1016/j.ajic.2025.04.013},
pmid = {40653335},
issn = {1527-3296},
}

@article {pmid40653334,
year = {2025},
author = {Huda, NU and Javed, R and Ibrahim, H},
title = {Letter to editor: No detrimental effect on the hand microbiome of health care staff by frequent alcohol-based antisepsis.},
journal = {American journal of infection control},
volume = {53},
number = {8},
pages = {915},
doi = {10.1016/j.ajic.2025.04.007},
pmid = {40653334},
issn = {1527-3296},
}

@article {pmid40653216,
year = {2025},
author = {Ren, F and Wu, F and Jie, Y and Wu, X and Gao, L},
title = {Carbon-nitrogen metabolic coupling for optimized protein production of corn stover polysaccharides: From molecular mechanisms to buffalo rumen microbiome.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {145901},
doi = {10.1016/j.ijbiomac.2025.145901},
pmid = {40653216},
issn = {1879-0003},
abstract = {The efficient bioconversion of polysaccharide-rich lignocellulosic agricultural residues into high-value products remains a significant challenge in sustainable agriculture. We investigated the molecular mechanisms of carbon‑nitrogen metabolic coupling during corn stover bioconversion through solid-state fermentation with Trichoderma longibrachiatum. Statistical optimization of fermentation conditions enhanced substrate nutritional value, achieving 17.57 % true protein content (53.45 % increase) and substantial lignocellulose degradation (cellulose 24.89 %, hemicellulose 23.54 %, lignin 22.28 %). Transcriptomic analysis revealed key metabolic coupling mechanisms, with cysteine supplementation significantly enhancing cellulolytic enzyme activities and protein accumulation. The optimized fermented corn stover increased dry matter intake and nutrient digestibility in buffalo feeding trials, while rumen microbiome analysis demonstrated shifts towards beneficial taxa and metabolic pathways. This study reveals the molecular interplay between polysaccharide metabolism and protein synthesis, providing a comprehensive strategy with dual benefits: environmental sustainability through efficient agricultural waste valorization and enhanced animal production through improved feed digestibility and nutrient utilization. This approach simultaneously addresses global food security concerns and environmental challenges associated with agricultural waste management.},
}

@article {pmid40653001,
year = {2025},
author = {Pudipeddi, A and Bijle, MN and Yiu, C},
title = {Effect of arginine-based synbiotics on multispecies biofilm.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {105974},
doi = {10.1016/j.jdent.2025.105974},
pmid = {40653001},
issn = {1879-176X},
abstract = {OBJECTIVE: To examine the effect of arginine (Arg)-based synbiotics on multispecies biofilm.

METHODS: In vitro biofilms (Streptococcus mutans UA159, S. gordonii DL1, S. sanguinis DSS-10) were grown on HA discs under anaerobic conditions (37°C, 5% CO₂, 24 h) and treated with: (1) Arg (0.25%, 0.5% w/v.), (2) Lacticaseibacillus rhamnosus GG (LRG) at 10⁷ CFU/mL, or (3) their combinations, 2× daily for 3 days. At 96 h, biofilm matrix components (exoproteins, eDNA, and carbohydrates) and microbial viability (confocal microscopy and PMA-qPCR) were quantified. Relative gene expression analysis was also conducted with species-specific genes (gtfB, sagP, arcA, argG, argH).

RESULTS: For carbohydrates, no significant difference was identified among treatment groups (p>0.05). Protein content for 0.5% Arg+LRG was significantly lower than LRG (p<0.05). The lowest eDNA content was observed in LRG (p<0.05); while eDNA content of 0.5% Arg+LRG, was similar to 0.5% Arg and control (p>0.05). Using confocal imaging, the highest proportion of live cell was found in 0.5% Arg+LRG (p<0.05), followed by 0.25% Arg+LRG, 3-D biofilm imaging demonstrated increased biomass with smoother architecture in biofilms treated with 0.5% Arg+LRG (p<0.05). 0.5% Arg+LRG significantly enhanced growth of commensal streptococci (S. gordonii, S. sanguinis) compared to monotherapies and control, while also reducing viability of S. mutans compared to control (p<0.05). Gene expression analysis revealed downregulation of S. mutans virulence (gtfB) and upregulation of commensal metabolism (sagP, arcA) for 0.5% Arg+LRG (p<0.05).

CONCLUSION: The 0.5% Arg+LRG synbiotics uniquely integrates ecological modulation by regulating biochemical matrix components, promoting commensal enrichment and suppressing cariogenic pathogens.

CLINICAL SIGNIFICANCE: A deliverable Arg-LRG synbiotics for caries prevention addresses a global public health priority. This strategy aligns with microbial homeostasis principles, presenting a novel paradigm for caries prevention. The Arg-LRG synbiotics can counter the limitations of fluorides to establish a diverse oral microbiome, imparting an ecologically driven approach to caries prevention.},
}

@article {pmid40652984,
year = {2025},
author = {Wu, S and Huang, M},
title = {Letter to the editor: "Association between oral microbiome and depression: A population-based study".},
journal = {Journal of affective disorders},
volume = {},
number = {},
pages = {119897},
doi = {10.1016/j.jad.2025.119897},
pmid = {40652984},
issn = {1573-2517},
}

@article {pmid40652765,
year = {2025},
author = {Chen, C and Qin, J and Li, G and Gu, Y and Gao, C and Meng, X and Yang, L},
title = {Effects of plant essential oils on intestinal microflora and growth performance of Lingshan native hens.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105539},
doi = {10.1016/j.psj.2025.105539},
pmid = {40652765},
issn = {1525-3171},
abstract = {This study examined the effects of dietary supplementation with citronella oil and cinnamon oil on the abundance and diversity of the intestinal microbiome in Lingshan native hens and explored how these changes may enhance chicken quality by influencing metabolic pathways. After three months of supplementation, the relative abundance of Firmicutes decreased, whereas Bacteroidota and Proteobacteria increased significantly in the experimental group. Correspondingly, the fatty acid content decreased, whereas the levels of free amino acids and inosine monophosphate (IMP) increased. Correlation analysis revealed a significant positive correlation between IMP content and Proteobacteria, whereas the abundances of Erysipelatoclostridium, Barnesiella, and Faecalitalea were significantly negatively correlated with IMP variation. The abundance of Rikenellaceae_RC9_intestine_group differed across all experimental groups and was strongly correlated with IMP content, suggesting that it is a key microbial factor influencing community composition and chicken traits.},
}

@article {pmid40652649,
year = {2025},
author = {Kong, T and Sun, X and Gao, P and Huang, W and Guan, X and Xu, Z and Li, B and Sun, W},
title = {Investigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.},
journal = {Water research},
volume = {286},
number = {},
pages = {124170},
doi = {10.1016/j.watres.2025.124170},
pmid = {40652649},
issn = {1879-2448},
abstract = {Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.},
}

@article {pmid40652256,
year = {2025},
author = {Tang, Y and Zhan, P and Wu, Y and Zhang, T and Yin, D and Gao, Y and Yu, Y and Qiu, S and Zhao, J and Zhang, X and Ma, Z and Chen, Y and Zhao, L and Mao, S and Huang, J and Chen, WH and Liu, J},
title = {Landscape of mobile genetic elements and their functional cargo across the gastrointestinal tract microbiomes in ruminants.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {162},
pmid = {40652256},
issn = {2049-2618},
mesh = {Animals ; *Ruminants/microbiology ; *Gastrointestinal Microbiome/genetics ; *Interspersed Repetitive Sequences ; Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Plasmids/genetics ; Gene Transfer, Horizontal ; *Gastrointestinal Tract/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Mobile genetic elements (MGEs) drive horizontal gene transfer and microbial evolution, spreading adaptive genes across microbial communities. While extensively studied in other ecosystems, the role of MGEs in shaping ruminant gastrointestinal microbiomes-especially their impact on diversity, adaptation, and dietary responsiveness-remains largely unexplored. This study systematically profiles MGE distribution and functionality across gastrointestinal regions in multiple ruminant species to advance our understanding of microbial adaptation.

RESULTS: Across 2458 metagenomic samples from eight ruminant species, we identified 4,764,110 MGEs-a ~ 216-fold increase over existing MGE databases. These elements included integrative and conjugative elements, integrons, insertion sequences, phages, and plasmids, with mobilization patterns largely confined to closely related microbial lineages. The distribution of MGEs varied by GIT regions, often reflecting nutritional gradients. In a validation cohort, GH1-carrying plasmids enriched in carbohydrate-active enzymes were found to predominate in the stomach, showing notable responsiveness to forage-based diets. All annotated MGEs have been compiled into a publicly accessible database, rumMGE (https://rummge.liulab-njau.com), to support further research.

CONCLUSIONS: This study substantially expands the catalog of known MGEs in ruminants, revealing their diverse roles in microbial evolution and functional adaptation to dietary changes. The findings provide a valuable resource for advancing research on microbial functionality and offer insights with potential applications for enhancing ruminant health and productivity, through strategies aimed at modulating the microbiome in agricultural contexts. Video Abstract.},
}

Animals
*Ruminants/microbiology
*Gastrointestinal Microbiome/genetics
*Interspersed Repetitive Sequences
Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Plasmids/genetics
Gene Transfer, Horizontal
*Gastrointestinal Tract/microbiology
Metagenome

@article {pmid40652165,
year = {2025},
author = {Guzmán-Guzmán, P and Etesami, H and Santoyo, G},
title = {Trichoderma: a multifunctional agent in plant health and microbiome interactions.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {434},
pmid = {40652165},
issn = {1471-2180},
mesh = {*Trichoderma/physiology ; *Microbiota ; Soil Microbiology ; *Plants/microbiology ; Rhizosphere ; Plant Diseases/microbiology ; Microbial Interactions ; Plant Development ; Crops, Agricultural/microbiology ; },
abstract = {The beneficial fungus Trichoderma is a key component of agricultural soils, contributing to sustainable crop production through multiple mechanisms. Among its major roles are the suppression of plant pathogens, promotion of plant growth, and activation of plant immune responses. This study reviews recent advances in understanding the modes of action of Trichoderma spp. related to pathogen control and plant growth promotion, using comparative analysis of its interactions across different plant-associated habitats. In recent years, considerable progress has been made in elucidating how Trichoderma interacts with plants in the rhizosphere, endosphere, and phyllosphere, where it exhibits distinct colonization patterns and functional traits. Additionally, this review explores emerging but less-studied topics, such as the involvement of Trichoderma in the pathobiome concept. Finally, we discuss the synergistic interactions between Trichoderma and other plant-associated microorganisms, highlighting their importance in shaping complex microbial networks within agroecosystems.},
}

*Trichoderma/physiology
*Microbiota
Soil Microbiology
*Plants/microbiology
Rhizosphere
Plant Diseases/microbiology
Microbial Interactions
Plant Development
Crops, Agricultural/microbiology

@article {pmid40652088,
year = {2025},
author = {Venkatraman, A and Jacobs, K and Binns, J and An, R and Rey, F and Thibeault, SL},
title = {Effects of psychosocial stress on laryngeal microbiology and epithelial barrier integrity.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25278},
pmid = {40652088},
issn = {2045-2322},
support = {F32DC021367/NH/NIH HHS/United States ; R01DC004336/NH/NIH HHS/United States ; 2023//AshFoundation New Investigator Grant/ ; 2023//American Bronchoesphagological Association Young Investigator Award/ ; },
mesh = {*Stress, Psychological/microbiology ; Female ; Male ; Animals ; *Microbiota ; Mice ; RNA, Ribosomal, 16S/genetics ; *Larynx/microbiology ; Vocal Cords/microbiology ; },
abstract = {Psychosocial stress and laryngeal physiology are linked. However, the biological mechanisms of psychosocial stress on voice have not been studied. This study delineated the effects of psychosocial stress on laryngeal microbiota composition and vocal fold epithelial integrity. We hypothesized that stress would result in reduced microbial diversity and abundance in laryngeal microbiota, and reduced vocal fold epithelial barrier integrity, with more pronounced differences in females and with increased duration of stress. One hundred and eight, conventionally-raised, C56BL/7 mice (8-10 weeks of age, 54 males, 54 females) were allocated to short stress, prolonged stress or control groups. Psychosocial stress involved restraint stress for 7 days (short stress) and 14 days (prolonged stress). Laryngeal microbiota profiles were compared across stress groups using 16S rRNA sequencing (N = 66). Outcome measures of alpha and beta diversity, differentially abundant taxa were obtained. Independently, stress-altered epithelial targets were delineated using RT-qPCR (N = 24) and immunofluorescence (N = 18).We found that prolonged stress, but not short stress, altered measures of alpha, beta diversity, indicating distinct laryngeal microbiota composition compared to control samples. Prolonged stress samples were dominated by Firmicutes phyla, whereas, short stress and control groups by Actinobacteria, and Proteobacteria phyla. Within genera, prolonged psychosocial stress decreased relative abundance of Corynebacterium and increased Streptococcus. Laryngeal microbial differences were more pronounced in females following psychosocial stress, as hypothesized. In addition, short and prolonged psychosocial stress downregulated gene and/or protein expression of inflammatory cytokines, sensory receptors, adherens and tight junction (E cadherin, Zo-1), TLRs and mucins (MUC2) within the larynx, with more severe effects in the prolonged stress group. Short and prolonged psychosocial stress alters laryngeal microbiota composition and vocal fold epithelial barrier integrity. Future studies should delineate causal host epithelial-microbiome interactions in the larynx in response to stress.},
}

*Stress, Psychological/microbiology
Female
Male
Animals
*Microbiota
Mice
RNA, Ribosomal, 16S/genetics
*Larynx/microbiology
Vocal Cords/microbiology

@article {pmid40652009,
year = {2025},
author = {Wang, J and Cong, Y and Tang, B and Liu, J and Pu, K},
title = {Integrative analysis of multi-omics data and gut microbiota composition reveals prognostic subtypes and predicts immunotherapy response in colorectal cancer using machine learning.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {25268},
pmid = {40652009},
issn = {2045-2322},
support = {CBY21-QD31//The Intramural Fund of North Sichuan Medical College/ ; CBY23-NCR06//Nanchong City Talent Development Fund/ ; 23JCYJPT0056//Fund of Bureau of Science&Technology Nanchong City/ ; },
mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/genetics/mortality/immunology ; *Gastrointestinal Microbiome ; *Machine Learning ; Prognosis ; *Immunotherapy/methods ; Female ; Male ; Tumor Microenvironment ; Middle Aged ; Aged ; Multiomics ; },
abstract = {Colorectal cancer (CRC) exhibits substantial heterogeneity in molecular subtypes and clinical outcomes. We performed an integrative analysis of multi-omics data from 274 CRC patients to investigate the impact of gut microbiota composition on prognosis, identify novel subtypes, and develop a machine learning-based prognostic model. Our microbiome analysis revealed significant differences between CRC and normal tissues. Multi-omics clustering identified two major CRC subtypes, CS1 and CS2, with distinct molecular characteristics and survival outcomes. We developed the Multi-Omics Integrative Clustering and Machine Learning Score (MCMLS) model, which demonstrated strong prognostic value in predicting patient survival and outperformed existing models. The MCMLS low-score group exhibited higher immune cell infiltration, increased metabolic pathway activity, and potentially better immunotherapy response. In contrast, the MCMLS high-score group showed higher mutation burden, fibroblast infiltration, and enrichment of cell adhesion and migration pathways. Bacterial analysis revealed differentially abundant bacteria associated with prognosis. Importantly, MCMLS consistently predicted immunotherapy response across six independent datasets. Our findings highlight the complex interplay between the gut microbiome, tumor microenvironment, and immune landscape in CRC, providing valuable insights for improving patient stratification and personalized treatment strategies.},
}

Humans
*Colorectal Neoplasms/therapy/microbiology/genetics/mortality/immunology
*Gastrointestinal Microbiome
*Machine Learning
Prognosis
*Immunotherapy/methods
Female
Male
Tumor Microenvironment
Middle Aged
Aged
Multiomics

@article {pmid40651630,
year = {2025},
author = {Wu, Q and Gao, G and Kwok, LY and Lv, H and Sun, Z},
title = {Insomnia: the gut microbiome connection, prospects for probiotic and postbiotic therapies, and future directions.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2025.07.005},
pmid = {40651630},
issn = {2090-1224},
abstract = {BACKGROUND: The gut microbiota is influenced by a complex interplay of factors including the host's genetics, diet, and lifestyle. It plays a crucial role in regulating metabolic processes and is linked to various diseases. Growing evidence suggests that the gut-brain axis, which involves bidirectional communication between the gut microbiota and the brain, plays a crucial role in regulating sleep patterns and has significant implications in the development of sleep disorders.

AIM OF REVIEW: This comprehensive review aims to summarize the current knowledge on the mechanisms underlying insomnia and its association with the gut microbiota and metabolome. Probiotics and postbiotics are beneficial microorganisms and their components and metabolites, which offer potential in modulating the gut microbiota of the host and alleviating insomnia. We present an overview of recent progress in probiotic and postbiotic intervention trials for managing insomnia, highlighting both the potential benefits and limitations of existing research in this domain. Additionally, we offer suggestions for future directions in this field. Probiotics can regulate sleep-wake behavior by modulating gut microbiota and its metabolites, influencing endocrine, neuronal, and immune responses. In addition, to understand the role of probiotics in improving insomnia, a standardized sleep behavior index and sleep monitoring method are needed.},
}

@article {pmid40651395,
year = {2025},
author = {Gustafsson, F and Hansen, AE and Fuursted, K and Andersen, N and Riley, CH and Lebech, AM and Ørbæk, M},
title = {Borrelia afzelii-associated seronegative Lyme neuroborreliosis in an immunocompromised patient.},
journal = {Diagnostic microbiology and infectious disease},
volume = {113},
number = {3},
pages = {116999},
doi = {10.1016/j.diagmicrobio.2025.116999},
pmid = {40651395},
issn = {1879-0070},
abstract = {This case highlights the diagnostic complexity of Lyme neuroborreliosis (LNB) in immunosuppressed patients. A 62-year-old man with a history of follicular lymphoma, previously treated with R-Bendamustine and currently rituximab, presented with generalized symptoms and systemic inflammation. Lymphoma relapse was excluded and diagnostic evaluations for infectious, metabolic, and autoimmune etiologies yielded unremarkable results. Several antibiotic treatments were without effect. An amplicon-based microbiome blood analysis using next-generation sequencing identified Borrelia afzelii, confirmed by specific PCR. Cerebrospinal fluid analysis revealed pleocytosis and elevated CXCL13. Blood serology and intrathecal Borrelia burgdorferi antibodies were negative. Treatment with doxycycline led to clinical and laboratory improvement corroborating LNB diagnosis. The case underscores that B-cell-depleting therapy can impair antibody responses, resulting in false-negative serology and LNB may present atypically. In cases like this advanced diagnostics like PCR and CXCL13 measurement can be valuable tools. Clinicians must consider the impact of immunosuppression on both disease presentation and diagnostic reliability.},
}

@article {pmid40651297,
year = {2025},
author = {Chen, LJ and Liu, Y and Liu, JL and Chen, ZJ and Zhao, W and Li, JH and Hsu, C and Chen, L and Zeng, JH and Li, XW and Yang, JZ and Li, JH and Xie, XL and Tao, SH and Wang, Q},
title = {Lycopene ameliorates Di-(2-ethylhexyl) phthalate-induced neurotoxicity in mice via the gut-brain axis.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {157057},
doi = {10.1016/j.phymed.2025.157057},
pmid = {40651297},
issn = {1618-095X},
abstract = {BACKGROUND: Di(2-ethylhexyl) phthalate (DEHP), a ubiquitous plasticizer present in numerous consumer products, poses a substantial neurotoxic risk through environmental and dietary exposure. Growing evidence highlights a critical association between DEHP-induced neurotoxicity and gut microbiota dysbiosis. Renowned for its potent antioxidant and anti-inflammatory capabilities, the natural carotenoid lycopene (Lyc) demonstrates therapeutic promise in treating various neurological disorders.

PURPOSE: The potential neuroprotective mechanisms of Lyc against DEHP-induced neurotoxicity in mice were investigated in this study, with a specific focus on its interaction with the gut-brain axis.

METHODS: For 35 consecutive days, mice received daily intragastric administrations of DEHP or Lyc. A comprehensive approach involving integrated transcriptome, microbiome, and molecular biology analyses, in conjunction with bacteriotherapy, was utilized to thoroughly investigate the underlying mechanisms.

RESULTS: Our findings demonstrated that Lyc administration or fecal microbiota transplantation (FMT) from Lyc-treated mice effectively ameliorated DEHP-induced anxiety- and depression-like behaviors. At the molecular level, Lyc mitigated neuroinflammation in the hippocampus, potentially through modulation of the NOD-like receptor signaling pathway. Furthermore, Lyc treatment improved gut microbiota composition by promoting the growth of beneficial bacteria, such as Akkermansiaceae, and enhanced intestinal barrier integrity via increased expression of tight junction proteins. Lyc also regulated the LPS-TLR4/MyD88 signaling pathway in the colon, thereby reducing local inflammation.

CONCLUSION: These results provide compelling evidence that Lyc confers protection against DEHP-induced neurotoxicity through a multifaceted strategy involving modulation of gut-brain axis, suppression of neuroinflammation, and restoration of gut homeostasis. We propose a novel therapeutic strategy to alleviate the risks posed by DEHP to both neurological and intestinal health. This approach involves either supplementation with Lyc or the application of bacteriotherapy.},
}

@article {pmid40651180,
year = {2025},
author = {Gorczyca, A and Przemieniecki, SW and Bednarz, S and Niemiec, M and Szerement, J and Kula-Maximenko, M and Guzik, M},
title = {Closing the loop: Agricultural applications of hydrolyzed polyhydroxyalkanoates production waste.},
journal = {Waste management (New York, N.Y.)},
volume = {205},
number = {},
pages = {115006},
doi = {10.1016/j.wasman.2025.115006},
pmid = {40651180},
issn = {1879-2456},
abstract = {The increasing global demand for sustainable materials and circular economy solutions has driven research into innovative applications of polyhydroxyalkanoates (PHA) and their by-products. While PHAs are well-recognized biodegradable bioplastics, the potential reuse of waste streams generated during their production remains largely unexplored. This study investigates the feasibility of utilizing hydrolysates derived from PHA post-fermentation biomass as biostimulants for rapeseed (Brassica napus L.) growth. Waste biomass from two bacterial fermentation processes - Zobellella denitrificans and Pseudomonas putida CA-3 - was subjected to acid hydrolysis to generate liquid formulations suitable for soil application. Their effects on plant growth, photosynthetic efficiency, phytohormone profiles, soil chemical composition, and microbiome dynamics were evaluated through microbiotests and pot experiments. Results indicated that hydrolysate application enhanced biomass accumulation and improved soil nutrient content, while also modulating key physiological responses, including chlorophyll fluorescence dynamics and hormone levels, suggesting a role in stress resilience. Additionally, hydrolysates induced a shift in the rhizosphere microbiome, decreasing bacterial dominance while enhancing diversity, particularly through the promotion of plant growth-associated microbial taxa. These findings support the integration of PHA production residues into agriculture, aligning with circular bioeconomy principles by converting industrial by-products into value-added biostimulants. Future research should focus on optimizing hydrolysate formulations, assessing their long-term agronomic impact, and evaluating their commercial feasibility for sustainable crop production.},
}

@article {pmid40651111,
year = {2025},
author = {Špulák, M and Nelic, D and Randáková, A and Konečná, K and Janďourek, O and Smutná, L and Kubíček, V and Gathergood, N and Pourová, J and Pávek, P and Pour, M and Svoboda, D and Ďurinová, A and Jakubík, J and Trejtnar, F},
title = {Evaluation of pharmacokinetics, pharmacodynamics, and toxicity of potential quinazoline bronchodilators derived from vasicinone.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {392},
number = {8},
pages = {103636},
doi = {10.1016/j.jpet.2025.103636},
pmid = {40651111},
issn = {1521-0103},
abstract = {Various synthetic modifications of the alkaloid (-)-vasicinone are known to exhibit a remarkable bronchodilatory effect. This study aimed to examine selected pharmacological and toxicological properties of 2 quinazolines derived from vasicinone with previously proven bronchodilatory action to consider their potential applicability for further preclinical development. Both compounds were found to have relatively low in vitro toxicity in a standard hepatic cell model. Pharmacokinetic studies in rats using oral and intravenous administration showed significant differences in oral availability (0.66 ± 0.11% vs 0.36 ± 0.18%), distribution volume, and elimination parameters of the 2 tested agents (for all parameters, P < .05). The different pharmacokinetic properties offer the possibility to select more convenient compounds for inhalation or systemic administration in further stages of development. The performed pharmacodynamic studies using an in vitro model showed that the tested quinazolines bind to the allosteric site on muscarinic acetylcholine receptors with micromolar affinity (pKB higher than pKI for M1 and M3 receptors, P < .05) and exert functional antagonism of carbachol-induced response. The main effect is not accompanied by a concomitant antibiotic effect. The proven inhibition of muscarinic receptors including the M3 subtype is analogous to the effects of clinically used anticholinergic bronchodilators. Therefore, the findings suggest that the bronchodilating effect of the tested compounds is likely mediated by a similar mechanism. The muscarinic receptor blocking effect based on allosteric binding to the receptors may potentially allow the development of a new group of highly selective M3 antagonists. SIGNIFICANCE STATEMENT: Two tested synthetic quinazoline derivatives with proven bronchodilator action exhibit allosteric binding to muscarinic receptors. Since the extracellular domain at which allosteric modulators commonly bind varies among subtypes of muscarinic receptors, this characteristic may allow further development of highly selective M3 antagonists. The examined compounds exhibit low toxicity as well as no concomitant antimicrobial effect that would potentially affect the bronchial microbiome.},
}

@article {pmid40651052,
year = {2025},
author = {Arutselvan, R and Kumar, S and Akash, AU and Greeshma, K and Sinha, SS and Khan, AS and Pati, K and Chauhan, VBS and Gowda, KH and Pradhan, S and Jeeva, ML and Veena, SS and Makeshkumar, T and Meena, M and Sangeetha, BG and Laxminarayana, K and Nedunchezhiyan, M},
title = {Deciphering the complex signaling networks in phytophthora infected plants: Insights into microbiome interactions and plant defense mechanisms.},
journal = {Plant physiology and biochemistry : PPB},
volume = {228},
number = {},
pages = {110222},
doi = {10.1016/j.plaphy.2025.110222},
pmid = {40651052},
issn = {1873-2690},
abstract = {Phytophthora species are destructive plant pathogens that cause severe economic losses in agriculture and natural ecosystems, known for their rapid spread through soil and water and resistance to conventional control methods. Understanding the complex signaling networks activated in plants during Phytophthora infection is crucial for developing effective management strategies. This review summarizes research findings on Phytophthora-plant interactions, with special emphasis on Phytophthora-plant microbiome interactions. Initially, molecular mechanisms involved in the plant response to Phytophthora infection are discussed, further emphasizing key signaling pathways activated by Phytophthora in host plants. The role of phytohormones in imparting resistance to Phytophthora infections is explored in depth. Additionally, the interaction and effects of Phytophthora and the plant immune system with the plant microbiome are examined, highlighting how these interactions facilitate disease and/or aid in plant defense. Various biotechnological approaches for enhancing plant resistance to Phytophthora, including recent technologies like CRISPR-Cas systems, are also reviewed. The conclusion addresses the need for further research into signaling networks within Phytophthora-plant-microbiome interactions and their future implications for crop protection.},
}

@article {pmid40650586,
year = {2025},
author = {Xu, S and Wang, C and Zhou, Q and Wang, Y and Yan, H and Tang, J and Zhang, R and Li, H and Zhao, X and Jiang, X and Liu, G and Luo, H and Wu, D and Che, L},
title = {Effects of 25-hydroxycholecalciferol supplementation during gestation on sow performance, offspring development and intestinal microbiota in sows and piglets.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf228},
pmid = {40650586},
issn = {1525-3163},
abstract = {The 25-hydroxycholecalciferol (25OHD3) is a metabolite of vitamin D (VD) and status biomarker of VD in blood. We investigate the effect of dietary 25OHD3 supplementation on gestation sow litter performance, milk composition, nutrient metabolism, the growth performance of offspring, and intestinal microbiota. A total of 60 sows were randomly allocated to receive VD3 diet (CON, 50 µg·kg-1, n = 30) or 25OHD3 diet (50 µg·kg-1, n = 30). All sows had the same diet during lactation. No difference was observed in litter size at farrowing and piglet performance at weaning between treatments. Sows fed 25OHD3 diet had increased plasma concentrations of prolactin (P = 0.05) and tended to have increased estradiol concentrations (P = 0.09) at farrowing. Sows fed 25OHD3 diet tended to have higher dry matter and fat contents in milk on day 10 of lactation (P = 0.08), increased plasma calcium concentration in newborn piglets (P < 0.05), and proportions of tibia and femur to body weights (P < 0.05) in weaning piglets. Newborn piglets from sows fed 25OHD3 diet had increased crypt depth (P < 0.05), and decreased ratio of villus height to crypt depth (P < 0.05). Compared with the VD3 diet, sows fed the 25OHD3 diet tended to have more fecal Firmicutes (P = 0.09) and fewer Campylobacterota (P < 0.05) at farrowing, and had fewer Bacteroidota and Spirochaetota (P < 0.05) at the end of lactation. Moreover, the weaning piglets from sows fed 25OHD3 diet had a higher abundance of Pseudomonas (P < 0.05), and a lower abundance of Bacteroides, Megasphaera, CAG-873, and Olsenella (P < 0.05) in colonic chyme. We conclude that 25OHD3 supplementation in gestation sows improves milk composition, increases the blood calcium concentration of newborn piglets, the tibia and femur weight of weaned piglets, and alters the intestinal microbiota of both sows and piglets.},
}

@article {pmid40650585,
year = {2025},
author = {Shin, YH and Bang, S and Xavier, R and Clardy, J},
title = {Eggerthella lenta Produces a Cryptic Pro-inflammatory Lipid.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c08613},
pmid = {40650585},
issn = {1520-5126},
abstract = {Eggerthella lenta is both one of the most studied and least understood members of the human gut microbiome. Most of the interest in this Gram-positive anaerobe originates from multiple robust associations of its population with a variety of autoimmune diseases, perhaps most notably inflammatory bowel disease (IBD). The links between bacteria and inflammation are only partially known. Inflammation is driven by Th17 cells and their inflammatory cytokine IL-17, and the population of these cells is promoted by a transcription factor, RORγt. Bacterial metabolites appear to activate RORγt in a cell- and antigen-independent fashion, but the metabolites and their activating mechanism are unknown. This report describes an assay-driven search for pro-inflammatory metabolites from E. lenta that revealed a plasmalogen-triggered plasmalogen pair that forms a single molecule signal transduction device. Small electrophiles characteristic of inflammatory environments react with the plasmalogen's sensitive vinyl ether moiety to create a lipid signal, a lysoglycoglycerolipid that upregulates the inflammatory cytokines TNF-α and IL-6 through a TLR receptor. This provides a molecular mechanism that allows E. lenta to upregulate inflammatory responses in a cell- and antigen-independent fashion. This molecular mechanism is similar to an endogenous signaling system that upregulates RORγt through a triggered mammalian plasmalogen signal, 1-18:0-lysophosphatidylethanolamine.},
}

@article {pmid40650575,
year = {2025},
author = {Guigard, L and Nazaret, F and Almario, J and Bertolla, F and Boubakri, H and Cantarel, AAM and Cournoyer, B and Favre-Bonté, S and Florio, A and Galia, W and Hazard, C and Henry, G and Belaroussi, AH and Chong, SKTF and Lavire, C and Lobreau, C and Luis, P and Maréchal, M and Meyer, T and Pozzi, ACM and Minard, G and Nazaret, S and Nicol, GW and Prigent-Combaret, C and Richaume, A and Rodriguez, V and Sanchez-Cid, C and Moro, CV and Vial, L and Vigneron, A and Wisniewski-Dye, F and Shade, A},
title = {The connections of climate change with microbial ecology and their consequences for ecosystem, human, and plant health.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxaf168},
pmid = {40650575},
issn = {1365-2672},
abstract = {The climate crisis presents an urgent challenge for Earth's living creatures and the habitats in which they have been adapted to thrive. Climate-related stress presents risks to microorganisms, the stability of the functions they provide, and their maintenance of beneficial interactions with their hosts and ecosystems. Microbes move across the continuum of anthropogenic influence on Earth's ecosystems, from pristine to human-managed to fully urbanized environments. Because microbial feedback within and across this continuum exists at multiple, connected scales from molecules to ecosystem-level processes, predicting microbial responses to climate stress and their potentially wide-ranging consequences remains difficult. Here, we discuss the broad implications of microbial and microbiome responses to climate change as they interface with human, plant, and ecosystem health. For each section on human, plant and ecosystem health, we briefly discuss the state of knowledge for each and follow with proposed future research, including some directions that are promising but require more work to evaluate. We end by considering overarching microbial ecology research needs across these systems and microbial solutions under investigation as possible climate-resilient interventions to maintain human, plant, and ecosystem health. This work draws on diverse expertise to identify broad research directions across typically separated disciplines and builds a holistic framework for considering their interrelationships.},
}

@article {pmid40650475,
year = {2025},
author = {Zhai, T and Zou, X and Zhang, Z and Wang, Y and Shi, L and Ren, W and Huang, J},
title = {Circadian rhythms of gut microbiota and plaque vulnerability: mechanisms and chrono-microbiota modulation interventions.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2532703},
doi = {10.1080/19490976.2025.2532703},
pmid = {40650475},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; *Plaque, Atherosclerotic/microbiology/physiopathology ; Animals ; Probiotics/administration & dosage ; Circadian Clocks ; Chronotherapy ; },
abstract = {The stability of atherosclerotic plaques constitutes the fundamental pathological basis for acute cardiovascular events, and their circadian rhythm characteristics highlight the essential role of dynamic interactions between the host and microorganisms. This review systematically elucidates the multifaceted mechanisms by which disruptions in the circadian rhythm of the gut microbiota contribute to plaque destabilization. Specifically, the microbiota modulates endothelial function, immune homeostasis, and vascular inflammation via rhythmic variations in metabolites. Perturbations in this rhythm compromise the structural integrity of plaques through a synergistic "metabolic-immune-vascular" network. Furthermore, the review unveils the bidirectional regulation between the host's circadian clock and the microbiota's rhythm. Innovatively, we propose "Chronotherapy-based Microbiome Modulation (CMM)," a strategy that reestablishes synchrony between the host and microbiota rhythms through time-restricted feeding, time-specific probiotics, and drugs targeting the circadian clock, thereby, it is possible to improve plaque stability by regulating the host's gut microbiota. The clinical translation of these findings requires overcoming technical challenges, such as personalized time window prediction and microbiota ecological risk assessment, and integrating multi-omics dynamic monitoring with AI modeling and optimization strategies. This review presents a novel perspective on the regulation of plaque stability.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Circadian Rhythm/physiology
*Plaque, Atherosclerotic/microbiology/physiopathology
Animals
Probiotics/administration & dosage
Circadian Clocks
Chronotherapy

@article {pmid40650267,
year = {2025},
author = {Borowik, A and Wyszkowska, J and Zaborowska, M and Kucharski, J},
title = {Regulation of the Microbiome in Soil Contaminated with Diesel Oil and Gasoline.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136491},
pmid = {40650267},
issn = {1422-0067},
support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; Regional Initiative of Excellence Program//Minister of Education and Science in the range of the program entitled Funded by the Minister of Science/ ; },
mesh = {*Soil Microbiology ; *Gasoline/analysis ; *Microbiota/drug effects ; *Soil Pollutants ; Fungi/drug effects/genetics/classification ; Bacteria/genetics/classification/drug effects ; Biodegradation, Environmental ; Zea mays/growth & development ; Soil/chemistry ; },
abstract = {Petroleum-derived contaminants pose a significant threat to the soil microbiome. Therefore, it is essential to explore materials and techniques that can restore homeostasis in disturbed environments. The aim of the study was to assess the response of the soil microbiome to contamination with diesel oil (DO) and gasoline (G) and to determine the capacity of sorbents, vermiculite (V), dolomite (D), perlite (P) and agrobasalt (A), to enhance the activity of microorganisms under Zea mays cultivation conditions in pot experiments. The restoration and activity of the soil microbiome were evaluated based on the abundance and diversity of bacteria and fungi, using both classical microbiological methods and Next Generation Sequencing (NGS). Bioinformatic tools were employed to calculate the physicochemical properties of proteins. DO increased the abundance of cultured microorganisms, whereas G significantly reduced it. Both DO and G increased the number of ASVs of Proteobacteria and decreased the relative abundance of Gemmatimonadetes, Chloroflexi, Acidobacteria, Verrucomicrobia, Planctomycetes, and fungal OTUs. These contaminants stimulated the growth of bacteria from the genera Rhodanobacter, Sphingomonas, Burkholderia, Sphingobium, and Mycobacterium, as well as fungi belonging to the Penicillium genus. Conversely, they had a negative effect on Kaistobacter, Rhodoplanes, and Ralstonia, as well as the fungi Chaetomium, Pseudaleuria, and Mortierella. DO caused greater changes in microbial alpha diversity than G. The stability of microbial proteins was higher at 17 °C than at -1 °C. The most stable proteins were found in bacteria and fungi identified within the core soil microbiome. These organisms exhibited greater diversity and more compact RNA secondary structures. The application of sorbents to contaminated soil altered the composition of bacterial and fungal communities. All sorbents enhanced the growth of organotrophic bacteria (Org) and fungi (Fun) in DO-contaminated soils, and actinobacteria (Act) and fungi in G-contaminated soils. V and A had the most beneficial effects on cultured microorganisms. In DO-contaminated soils, all sorbents inhibited the growth of Rhodanobacter, Parvibaculum, Sphingomonas, and Burkholderia, while stimulating Salinibacterium and Penicillium. In G-contaminated but otherwise unamended soils, all sorbents negatively affected the growth of Burkholderia, Sphingomonas, Kaistobacter, Rhodoplanes, Pseudonocardia, and Ralstonia and increased the abundance of Gymnostellatospora. The results of this study provide a valuable foundation for developing effective strategies to remediate soils contaminated with petroleum-derived compounds.},
}

*Soil Microbiology
*Gasoline/analysis
*Microbiota/drug effects
*Soil Pollutants
Fungi/drug effects/genetics/classification
Bacteria/genetics/classification/drug effects
Biodegradation, Environmental
Zea mays/growth & development
Soil/chemistry

@article {pmid40650181,
year = {2025},
author = {Udawatte, NS and Liu, C and Staples, R and Han, P and Kumar, PS and Arumugam, TV and Ivanovski, S and Seneviratne, CJ},
title = {Short-Term Probiotic Colonization Alters Molecular Dynamics of 3D Oral Biofilms.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136403},
pmid = {40650181},
issn = {1422-0067},
support = {HREC No. 2023000467//Australian Dental Association/ ; },
mesh = {*Biofilms/growth & development/drug effects ; *Probiotics/pharmacology/administration & dosage ; Humans ; RNA, Ribosomal, 16S/genetics ; *Streptococcus salivarius/physiology/growth & development/genetics ; Microbiota ; Saliva/microbiology ; Bifidobacterium/genetics ; Mouth Mucosa/microbiology ; Pilot Projects ; *Mouth/microbiology ; In Situ Hybridization, Fluorescence ; },
abstract = {Three-dimensional (3D) scaffold systems have proven instrumental in advancing our understanding of polymicrobial biofilm dynamics and probiotic interactions within the oral environment. Among oral probiotics, Streptococcus salivarius K12 (Ssk12) has shown considerable promise in modulating microbial homeostasis; however, its long-term therapeutic benefits are contingent upon successful and sustained colonization of the oral mucosa. Despite its clinical relevance, the molecular mechanisms underlying the adhesion, persistence, and integration of Ssk12 into the native oral microbiome/biofilm remain inadequately characterized. In this pilot study, we explored the temporal colonization dynamics of Ssk12 and its impact on the structure and functional profiles of salivary-derived biofilms cultivated on melt-electrowritten poly(ε-caprolactone) (MEW-mPCL) scaffolds, which emulate the native oral niche. Colonization was monitored via fluorescence in situ hybridization (smFISH), confocal microscopy, and RT-qPCR, while shifts in community composition and function were assessed using 16S rRNA sequencing and meta-transcriptomics. A single administration of Ssk12 exhibited transient colonization lasting up to 7 days, with detectable presence diminishing by day 10. This was accompanied by short-term increases in Lactobacillus and Bifidobacterium populations. Functional analyses revealed increased transcriptional signatures linked to oxidative stress resistance and metabolic adaptation. These findings suggest that even short-term probiotic colonization induces significant functional changes, underscoring the need for strategies to enhance probiotic persistence.},
}

*Biofilms/growth & development/drug effects
*Probiotics/pharmacology/administration & dosage
Humans
RNA, Ribosomal, 16S/genetics
*Streptococcus salivarius/physiology/growth & development/genetics
Microbiota
Saliva/microbiology
Bifidobacterium/genetics
Mouth Mucosa/microbiology
Pilot Projects
*Mouth/microbiology
In Situ Hybridization, Fluorescence

@article {pmid40650144,
year = {2025},
author = {Gáspár, Z and Lakatos, B},
title = {Mapping the Gut Microbiota Composition in the Context of Raltegravir, Dolutegravir, and Bictegravir-A Scoping Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136366},
pmid = {40650144},
issn = {1422-0067},
mesh = {*Gastrointestinal Microbiome/drug effects ; Pyridones/pharmacology ; Humans ; *Heterocyclic Compounds, 3-Ring/pharmacology/therapeutic use ; Piperazines/pharmacology ; Oxazines/pharmacology ; *Raltegravir Potassium/pharmacology/therapeutic use ; *HIV Integrase Inhibitors/pharmacology/therapeutic use ; *HIV Infections/drug therapy/microbiology ; Amides ; *Heterocyclic Compounds, 4 or More Rings/pharmacology/therapeutic use ; },
abstract = {(1) Background: Second-generation integrase strand transfer inhibitors (INSTIs) are now the preferred first-line therapies for human immunodeficiency virus (HIV). However, concerns regarding their side effects, such as weight gain and metabolic disturbances, have emerged. This scoping review aims to assess the effects of INSTIs on the gut microbiota, with a focus on differences between agents and their clinical implications. (2) Methods: A scoping review was conducted using PubMed, Web of Science, and Embase, with reports collected following PRISMA for Scoping Reviews (PRISMA-ScR). (3) Results: The majority of available evidence focused on dolutegravir, which demonstrated beneficial effects on microbiota diversity and composition. However, factors such as younger age, lower CD4+ counts, and extreme BMI were associated with proinflammatory changes. Limited data on bictegravir also suggested favorable alterations in the gut microbiota. Raltegravir, a first-generation INSTI, was associated with improvements in alpha diversity and microbial composition, although these changes were not consistently beneficial. Moreover, associated changes in inflammatory and microbial translocation markers suggested unfavorable alterations. (4) Conclusions: Based on the evidence mapped, second-generation INSTIs may generally induce favorable changes in the gut microbiota. However, further research is needed to explore the clinical implications of these microbiota alterations, particularly in specific patient groups.},
}

*Gastrointestinal Microbiome/drug effects
Pyridones/pharmacology
Humans
*Heterocyclic Compounds, 3-Ring/pharmacology/therapeutic use
Piperazines/pharmacology
Oxazines/pharmacology
*Raltegravir Potassium/pharmacology/therapeutic use
*HIV Integrase Inhibitors/pharmacology/therapeutic use
*HIV Infections/drug therapy/microbiology
Amides
*Heterocyclic Compounds, 4 or More Rings/pharmacology/therapeutic use

@article {pmid40650070,
year = {2025},
author = {Bai, Y and Li, Z and Chen, Z and Luo, L and Wang, J and Yao, S and Yun, K and Gao, C and Guo, X},
title = {Integrated Metabolomic and Gut Microbiome Profiles Reveal Postmortem Biomarkers of Fatal Anaphylaxis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136292},
pmid = {40650070},
issn = {1422-0067},
support = {82271925//National Natural Science Foundation of China/ ; 81971790//National Natural Science Foundation of China/ ; 2024KY364//the Postgraduate Education Innovation Project of Shanxi/ ; },
mesh = {*Anaphylaxis/metabolism/microbiology/diagnosis/blood/mortality ; *Biomarkers/blood/metabolism ; Animals ; *Gastrointestinal Microbiome ; Rats ; *Metabolomics/methods ; Male ; RNA, Ribosomal, 16S/genetics ; Rats, Sprague-Dawley ; Humans ; Immunoglobulin E/blood ; *Metabolome ; Disease Models, Animal ; Myocardial Infarction/diagnosis/metabolism ; Tryptophan/blood ; Feces/microbiology ; },
abstract = {The incidence of fatal anaphylaxis is increasing, but there is still no recognized "golden standard" for forensic diagnosis. Due to its non-specific symptoms, especially cardiovascular symptoms without cutaneous changes, it can easily be misdiagnosed as acute myocardial infarction. Here, we established rat models (n = 12) of fatal anaphylaxis (FA), acute myocardial infarction (AMI), and coronary atherosclerosis with anaphylaxis (CAA). The untargeted metabolomics of plasma and 16S rRNA sequencing of fecal matter was performed, and a random forest was used to identify potential biomarkers. Three metabolites (tryptophan, trans-3-indole acrylic acid, and imidazole acetic acid) and three microbial genera (g_Prevotellaceae_Ga6A1_group, g_UCG_008, and g_Eubacterium_hallii_group) were identified as potential biomarkers for distinguishing anaphylaxis and non-anaphylaxis. The classification model of plasma metabolites showed a much better discriminatory performance than that of microbial genus, serum IgE, and tryptase. The performance of the microbial genera was superior to the serum IgE but inferior to the serum tryptase. Forensic samples of fatal anaphylaxis and non-anaphylaxis deaths (n = 12) were collected for untargeted metabolomics detection. The results showed that among the three identified metabolic biomarkers, tryptophan has better stability in cadaveric blood samples. Its diagnostic performance (AUC = 87.1528) was superior to serum IgE and tryptase, making it more suitable as a postmortem biomarker of fatal anaphylaxis.},
}

*Anaphylaxis/metabolism/microbiology/diagnosis/blood/mortality
*Biomarkers/blood/metabolism
Animals
*Gastrointestinal Microbiome
Rats
*Metabolomics/methods
Male
RNA, Ribosomal, 16S/genetics
Rats, Sprague-Dawley
Humans
Immunoglobulin E/blood
*Metabolome
Disease Models, Animal
Myocardial Infarction/diagnosis/metabolism
Tryptophan/blood
Feces/microbiology

@article {pmid40650060,
year = {2025},
author = {Baek, KR and Singh, S and Hwang, HS and Seo, SO},
title = {Using Gut Microbiota Modulation as a Precision Strategy Against Obesity.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136282},
pmid = {40650060},
issn = {1422-0067},
support = {Research Program//SeoulTech (Seoul National University of Science and Technology)./ ; },
mesh = {*Obesity/microbiology/therapy/metabolism/prevention & control ; *Gastrointestinal Microbiome/physiology ; Humans ; Probiotics/therapeutic use ; Animals ; Prebiotics/administration & dosage ; Energy Metabolism ; },
abstract = {Obesity is a complex metabolic disorder with high global prevalence. Recent studies have highlighted the crucial role of gut microbiota in obesity's onset and progression. This review explores the relationship between gut microbiota composition and obesity, emphasizing how changes in microbial communities can influence host metabolism, energy balance, and fat storage. By reviewing current evidence regarding the interactions between specific microbial taxa; their metabolic byproducts, such as short-chain fatty acids; and host signaling pathways, we aim to clarify the mechanisms through which the gut microbiome contributes to obesity. Furthermore, we discuss the potential of microbiota engineering through precision strategies such as the use of probiotics, prebiotics, and genetically engineered microbial strains. Collectively, this review highlights the targeted modulation of the gut microbiome as a promising and innovative approach to the prevention and treatment of obesity.},
}

*Obesity/microbiology/therapy/metabolism/prevention & control
*Gastrointestinal Microbiome/physiology
Humans
Probiotics/therapeutic use
Animals
Prebiotics/administration & dosage
Energy Metabolism

@article {pmid40650015,
year = {2025},
author = {Yang, L and Cui, R and Li, Z and Xue, M and Chan, S and Xue, P and Yang, X and Zhang, L and Lv, F and Fang, M},
title = {Gut Microbiota-Bile Acid Crosstalk Contributes to Meat Quality and Carcass Traits of Tan and Dorper Sheep.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136224},
pmid = {40650015},
issn = {1422-0067},
support = {U21A20246//the National Natural Science Foundation of China/ ; 2021YFD1200900//the National Key Research and Development Program-Key Projects/ ; },
mesh = {Animals ; *Bile Acids and Salts/metabolism ; *Gastrointestinal Microbiome/physiology ; Sheep/metabolism ; *Meat/analysis ; Transcriptome ; Colon/metabolism ; },
abstract = {Tan sheep outperform Dorper sheep in meat-quality traits, including muscle fiber characteristics and fatty acid composition, while Dorper sheep excel in carcass weight. However, the molecular mechanisms underlying these breed-specific traits, especially gut microbiota-bile acid (BA) interactions, remain poorly understood. As host-microbiota co-metabolites, BAs are converted by colonic microbiota via bile salt hydrolase (BSH) and dehydroxylases into secondary BAs, which activate BA receptors to regulate host lipid and glucose metabolism. This study analyzed colonic BA profiles in 8-month-old Tan and Dorper sheep, integrating microbiome and longissimus dorsi muscle transcriptome data to investigate the gut-muscle axis in meat-quality and carcass trait regulation. Results showed that Tan sheep had 1.6-fold higher secondary BA deoxycholic acid (DHCA) levels than Dorper sheep (p < 0.05), whereas Dorper sheep accumulated conjugated primary BAs glycocholic acid (GCA) and tauro-α-muricholic acid (p < 0.05). Tan sheep exhibited downregulated hepatic BA synthesis genes, including cholesterol 7α-hydroxylase (CYP7A1) and 27-hydroxylase (CYP27A1), alongside upregulated transport genes such as bile salt export pump (BSEP), sodium taurocholate cotransporting polypeptide (NTCP), and ATP-binding cassette subfamily B member 4 (ABCB4), with elevated gut BSH activity (p < 0.05). DHCA was strongly correlated with g_Ruminococcaceae_UCG-014, ENSOARG00000001393, and ENSOARG00000016726, muscle fiber density, diameter, and linoleic acid (C18:2n6t) (|r| > 0.5, p < 0.05). In contrast, GCA was significantly associated with g_Lachnoclostridium_10, g_Rikenellaceae_RC9_gut_group, ENSOARG0000001232, carcass weight, and net meat weight (|r| > 0.5, p < 0.05). In conclusion, breed-specific colonic BA profiles were shaped by host-microbiota interactions, with DHCA potentially promoting meat quality in Tan sheep via regulation of muscle fiber development and fatty acid deposition, and GCA influencing carcass traits in Dorper sheep. This study provides novel insights into the gut microbiota-bile acid axis in modulating ruminant phenotypic traits.},
}

Animals
*Bile Acids and Salts/metabolism
*Gastrointestinal Microbiome/physiology
Sheep/metabolism
*Meat/analysis
Transcriptome
Colon/metabolism

@article {pmid40649958,
year = {2025},
author = {Roznovan, CN and Măruțescu, LG and Gradisteanu Pircalabioru, G},
title = {Immuno-Oncology at the Crossroads: Confronting Challenges in the Quest for Effective Cancer Therapies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136177},
pmid = {40649958},
issn = {1422-0067},
mesh = {Humans ; *Neoplasms/therapy/immunology ; Tumor Microenvironment/immunology ; *Immunotherapy/methods ; Precision Medicine ; Cancer Vaccines/therapeutic use/immunology ; Animals ; Immune Checkpoint Inhibitors/therapeutic use ; *Medical Oncology/methods ; },
abstract = {Immuno-oncology has rapidly evolved into a cornerstone of modern cancer therapy, offering promising avenues for durable responses and personalized treatment strategies. This narrative review provides a thorough overview of the mechanisms underlying tumor-immune system interactions and the therapeutic innovations emerging from this knowledge. Central to this discussion is the tumor microenvironment (TME), a complex ecosystem of immune and stromal cells that supports tumor growth and shapes therapeutic outcomes. Key cellular and molecular factors within the TME are examined, along with diverse immune escape strategies. We further analyze the landscape of immunotherapeutic approaches, including immune checkpoint inhibitors, cancer vaccines, adoptive cell therapies such as CAR-T cells, and cytokine-based interventions. This review also addresses the increasing importance of predictive biomarkers in immuno-oncology, particularly in patient stratification, monitoring resistance, and managing immunotherapy-related toxicity. Finally, we explore the emerging role of the microbiome as a modulator of immunotherapy efficacy, shedding light on host-microbe-immune interactions that may influence clinical outcomes. By integrating current biological insights with therapeutic innovation, this review outlines the challenges and opportunities ahead in immuno-oncology and emphasizes the need for translational research and cross-disciplinary collaboration to optimize cancer immunotherapy in the era of precision medicine.},
}

Humans
*Neoplasms/therapy/immunology
Tumor Microenvironment/immunology
*Immunotherapy/methods
Precision Medicine
Cancer Vaccines/therapeutic use/immunology
Animals
Immune Checkpoint Inhibitors/therapeutic use
*Medical Oncology/methods

@article {pmid40649947,
year = {2025},
author = {Pinheiro, I and Bolca, S and Van den Bossche, L and Vanhove, W and Van Ryckeghem, S and Gottardi, D and Laukens, D and Possemiers, S},
title = {MH002, a Novel Butyrate-Producing Consortium of Six Commensal Bacterial Strains Has Immune-Modulatory and Mucosal-Healing Properties.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136167},
pmid = {40649947},
issn = {1422-0067},
mesh = {Animals ; Humans ; *Butyrates/metabolism ; *Gastrointestinal Microbiome ; Mice ; Caco-2 Cells ; *Inflammatory Bowel Diseases/microbiology/immunology/therapy ; Rats ; *Intestinal Mucosa/microbiology/immunology/metabolism ; Male ; Colitis/chemically induced/microbiology ; Leukocytes, Mononuclear/metabolism ; Mice, Inbred C57BL ; *Bacteria/metabolism ; Wound Healing ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic relapsing inflammatory condition of the gastrointestinal tract. It is generally accepted that IBD is characterized by an inappropriate immune response to the intestinal microbiome in genetically susceptible individuals. Despite the available treatment options ranging from salicylates and corticosteroids, to immunosuppressants and biologics, there is still a high unmet medical need for patients who respond poorly to drugs or are not able to tolerate them. Microbiome-based therapeutics offer a valid treatment strategy for IBD with enhanced safety. A butyrate-producing consortium of six commensal strains (MH002) was evaluated in a series of in vitro, ex vivo, and in vivo experiments mimicking multiple IBD-related dysfunctions, namely disrupted intestinal permeability and immune activation. MH002 rapidly produced high levels of butyrate in fed-batch cultures, and significantly increased butyrate levels within one day after administration to IBD-derived gut microbial communities in vitro. Both in Caco-2/peripheral blood mononuclear cells (PBMCs) co-cultures, and IBD patients-derived organoids and colonic explants, MH002 reduced inflammation and restored epithelial barrier integrity. In addition, MH002 promoted wound repair in vitro. Finally, MH002 protected mice and rats from chemically induced colitis. Altogether, results showed that MH002 presents a novel therapeutic avenue for the treatment of IBD.},
}

Animals
Humans
*Butyrates/metabolism
*Gastrointestinal Microbiome
Mice
Caco-2 Cells
*Inflammatory Bowel Diseases/microbiology/immunology/therapy
Rats
*Intestinal Mucosa/microbiology/immunology/metabolism
Male
Colitis/chemically induced/microbiology
Leukocytes, Mononuclear/metabolism
Mice, Inbred C57BL
*Bacteria/metabolism
Wound Healing

@article {pmid40649930,
year = {2025},
author = {Lin, SH and Lin, RJ and Chu, CL and Chen, YL and Fu, SC},
title = {Associations Between Gut Microbiota Composition and Impulse Control Disorders in Parkinson's Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136146},
pmid = {40649930},
issn = {1422-0067},
support = {MOST 111-2628-M-A49-004-MY3//National Science and Technology Council/ ; NSTC 113-2314-B-259 -001 -MY3//National Science and Technology Council/ ; },
mesh = {*Parkinson Disease/microbiology/complications ; Humans ; *Gastrointestinal Microbiome/genetics ; Male ; RNA, Ribosomal, 16S/genetics ; Female ; Middle Aged ; *Disruptive, Impulse Control, and Conduct Disorders/microbiology/etiology ; Aged ; Bacteria/genetics/classification ; },
abstract = {Impulse control disorders (ICDs) are a debilitating non-motor symptom of Parkinson's disease (PD), often associated with dopaminergic therapy. However, their occurrence in some patients but not others suggests additional biological mechanisms, including the gut microbiome. In this study, we analyzed 191 PD patients (14 with ICDs, 177 without) using 16S rRNA gene sequencing to explore the association between gut microbiota and ICDs. No significant differences were observed in alpha or beta diversity between groups, but several bacterial taxa showed differential abundances. Notably, Methanobrevibacter and Intestinimonas butyriciproducens were enriched in ICD patients. Functional pathway analysis revealed differences in metabolic pathways, including enrichment of xenobiotic degradation and nicotinate metabolism in the ICD group. These findings suggest that specific gut microbial taxa and their associated metabolic functions may contribute to ICDs in PD, highlighting a potential non-dopaminergic mechanism and opening new avenues for microbiome-targeted intervention.},
}

*Parkinson Disease/microbiology/complications
Humans
*Gastrointestinal Microbiome/genetics
Male
RNA, Ribosomal, 16S/genetics
Female
Middle Aged
*Disruptive, Impulse Control, and Conduct Disorders/microbiology/etiology
Aged
Bacteria/genetics/classification

@article {pmid40649842,
year = {2025},
author = {Muttiah, B and Wahid, W and Sukri, A and Hanafiah, A},
title = {Towards Effective Helicobacter pylori Eradication: Emerging Therapies in the Wake of Antibiotic Resistance.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26136064},
pmid = {40649842},
issn = {1422-0067},
support = {DIP-2024-005//National University of Malaysia/ ; },
mesh = {Humans ; *Helicobacter pylori/drug effects ; *Helicobacter Infections/drug therapy/microbiology ; *Anti-Bacterial Agents/therapeutic use/pharmacology ; *Drug Resistance, Bacterial/drug effects ; Probiotics/therapeutic use ; Antimicrobial Peptides/therapeutic use/pharmacology ; Animals ; },
abstract = {Helicobacter pylori (H. pylori) infection is a leading cause of gastritis, peptic ulcers, and gastric cancer, affecting more than half of the global population. Its persistence in the acidic gastric environment and its ability to evade host immunity present major treatment challenges. Although antibiotics remain the standard therapy, rising antimicrobial resistance has reduced treatment efficacy, prompting the search for alternative and adjunct approaches. Emerging therapies include probiotics, antimicrobial peptides (AMPs), and plant-derived compounds, which target H. pylori through membrane disruption, immunomodulation, or direct antimicrobial activity. Novel drug delivery systems and microbiota-sparing interventions are also being investigated. Additionally, vaccine development offers a promising strategy for long-term protection, though challenges related to antigenic variability and host-specific responses remain. Despite these advances, treatment variability and the limited clinical validation of alternatives hinder progress. A multifaceted approach integrating microbiome research, host-pathogen interactions, and new therapeutic agents is essential for future success.},
}

Humans
*Helicobacter pylori/drug effects
*Helicobacter Infections/drug therapy/microbiology
*Anti-Bacterial Agents/therapeutic use/pharmacology
*Drug Resistance, Bacterial/drug effects
Probiotics/therapeutic use
Antimicrobial Peptides/therapeutic use/pharmacology
Animals

@article {pmid40649705,
year = {2025},
author = {Borbélyová, V and Szabó, J and Sušienková, P and Potvin, J and Belvončíková, P and Groß, T and Jančovičová, A and Bačová, Z and Rašková, B and Szadvári, I and Antal, M and Pirník, Z and Karhánek, M and Šoltys, K and Gardlík, R and Celec, P and Ostatníková, D and Tomova, A},
title = {The Effect of Parental Faecal Microbiome Transplantation from Children with Autism Spectrum Disorder on Behavior and Gastrointestinal Manifestations in the Male Offspring of Shank3 Mice.},
journal = {International journal of molecular sciences},
volume = {26},
number = {13},
pages = {},
doi = {10.3390/ijms26135927},
pmid = {40649705},
issn = {1422-0067},
support = {APVV-20-0114//Slovak Research and Development Agency/ ; VEGA 1/0062/21//Ministry of Education, Science, Research, and Sport of the Slovak Republic/ ; },
mesh = {Animals ; *Autism Spectrum Disorder/therapy/microbiology/genetics ; *Fecal Microbiota Transplantation ; Mice ; Male ; Female ; *Nerve Tissue Proteins/genetics/metabolism ; Humans ; Behavior, Animal ; Pregnancy ; Gastrointestinal Microbiome ; Mice, Knockout ; Disease Models, Animal ; Child ; Prenatal Exposure Delayed Effects ; Microfilament Proteins ; },
abstract = {The increasing incidence of autism spectrum disorder (ASD) increases the urgency of establishing the mechanism of its development for effective prevention and treatment. ASD's etiology includes genetic predisposition and environmental triggers, both of which can play a role in the changed microbiota. Recent research has proved the impact of maternal microbiota on the neurodevelopment of the child. To investigate the co-play of genetic and microbiota factors in ASD development, we performed fecal microbiota transplantation (FMT) from children with ASD to female Shank3b[+/-] mice and studied the autism-like symptoms in the male Shank3b[-/-] and wild-type (WT) offspring. WT animals with prenatal exposure to ASD microbiota had delayed neurodevelopment and impaired food intake behavior, but also elevated plasma leptin concentration and body weight. Shank3b[-/-] mice after FMT ASD exhibited impaired learning and exacerbated anxiety-like behavior in adulthood. Interestingly, FMT ASD improved learning in adolescent Shank3b[-/-] mice. Prenatal exposure to ASD microbiota decreased the activity of hypocretin neurons of the lateral hypothalamic area in both genotypes. The combination of genetic predisposition and FMT ASD led to an increased colon permeability, evaluated by zonula occludens (ZO1, ZO3) and claudin factors. These results suggest the effect of parental FMT exposure on shaping offspring behavior in Shank3b[-/-] mice and the potential of microbiota in the modulation of ASD.},
}

Animals
*Autism Spectrum Disorder/therapy/microbiology/genetics
*Fecal Microbiota Transplantation
Mice
Male
Female
*Nerve Tissue Proteins/genetics/metabolism
Humans
Behavior, Animal
Pregnancy
Gastrointestinal Microbiome
Mice, Knockout
Disease Models, Animal
Child
Prenatal Exposure Delayed Effects
Microfilament Proteins

@article {pmid40649157,
year = {2025},
author = {Cannizzaro, R and Maiero, S and Pelizzo, P and Gulotta, M and Facchin, S and Tessarolo, G and Zucchetto, A and Matrone, F and Realdon, S and Bortolus, R},
title = {Microencapsulated Sodium Butyrate in the Prevention of Acute Radiotherapy Proctitis: Single-Center Prospective Study.},
journal = {Journal of clinical medicine},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/jcm14134783},
pmid = {40649157},
issn = {2077-0383},
abstract = {Background/Objectives: Prostate cancer is the most frequent cancer in men, for which Radiotherapy (RT) is used as a radical or post-surgical treatment. Actinic proctitis is one of the most disabling side effects of RT. Intestinal microbiome studies have highlighted the importance of short-chain fatty acids, in particular butyric acid, for their beneficial effects over intestinal epithelial cells. The aim of this prospective study is to evaluate if treatment with micro-encapsulated sodium butyrate (MESB) can reduce the incidence of actinic proctitis during RT in prostate cancer patients. Methods: In total, 122 consecutive patients with prostate cancer treated in Radiotherapy Unit, Centro di Riferimento Oncologico, IRCCS Aviano, were enrolled. Patients received MESB (3 tablets/day) from one week before until four weeks after RT. They completed a diary, tracking daily bowel movements, rectal bleeding, abdominal pain, and perceived health status before, at the end, and one month after RT. Results: Although an improvement in symptoms was observed, when comparing interpatient data before RT vs. one month after the end of RT, statistically significant differences emerged only regarding abdominal pain (94.2% vs. 81.6% vs. 81.6%) (McNemar's test p < 0.002). Conclusions: MESB appears effective in reducing radiation-induced bowel toxicity during RT, minimizing stool changes, incontinence, and abdominal pain. Although patients' health perception declined at RT completion, it improved after one month, suggesting MESB may support clinical recovery post-treatment.},
}

@article {pmid40649085,
year = {2025},
author = {Adames, SM and Naz, S and Dai, J and Wang, Y and Shirwaikar Thomas, A},
title = {The Impact of Fecal Diversion on Immune Checkpoint Inhibitor Adverse Gastrointestinal Toxicities.},
journal = {Journal of clinical medicine},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/jcm14134711},
pmid = {40649085},
issn = {2077-0383},
abstract = {Background/Objective: Immune checkpoint inhibitors (ICIs) are highly effective cancer therapies used across a broad spectrum of malignancies. They function by disrupting immune inhibitory pathways, resulting in an amplified immune response against tumors. However, this heightened immune activity can predispose patients to immune-mediated colitis (IMC), which is graded using the Common Terminology Criteria for Adverse Events (CTCAE) and can range from mild diarrhea to severe colitis. Prior studies have shown that fecal stream diversion can modify the gut microbiome and influence the severity of intestinal inflammation. This study investigates the impact of fecal stream diversion on IMC outcomes in cancer patients receiving ICIs. Methods: We conducted a retrospective cohort study of patients treated with ICIs from 2016 to 2023 who had a history of fecal stream diversion. Demographic, oncologic, and toxicity-related data were collected. Patients with active gastrointestinal infections, autoimmune GI diseases, or graft-versus-host disease were excluded. Descriptive statistics and univariate and multivariate logistic regression analyses were performed using SAS version 9.4. Results: A total of 44 patients were included and categorized into two groups based on the timing of bowel stoma creation relative to the IMC event. CTCAE grade for diarrhea was used to assess GI toxicity. While overall CTCAE grade distribution for diarrhea did not differ significantly between groups (p = 0.22), Hispanic ethnicity was significantly associated with a lower CTCAE grade compared to non-Hispanic or Latino individuals (OR [95% CI] = 0.12 [0.02, 0.62], p = 0.011). In contrast, higher CTCAE grades were significantly associated with ileostomy versus colostomy (OR [95% CI] = 3.21 [1.01, 10.18], p = 0.048) and in patients without an ostomy at the time of diarrhea onset compared to those with an ostomy (OR [95% CI] = 8.87 [2.51, 31.31], p = 0.0007). Conclusions: Our findings suggest that the CTCAE diarrhea grade is significantly associated with ethnicity, type of stoma, and presence of ostomy at the time of diarrhea. Limitations include the retrospective study design and small sample size. These results contribute to understanding potential strategies for mitigating the serious gastrointestinal toxicities of ICIs.},
}

@article {pmid40648949,
year = {2025},
author = {Shiina, N and Shimpo, Y and Kikuchi, K and Sekiya, T and Tomonari, H},
title = {Effects of 0.05% Cetylpyridinium Chloride Mouthwash on Halitosis and Tongue Microbiota in Patients Undergoing Orthodontic Treatment: A Double-Blind Randomized Clinical Trial.},
journal = {Journal of clinical medicine},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/jcm14134576},
pmid = {40648949},
issn = {2077-0383},
abstract = {Background: Halitosis is frequently observed in patients undergoing orthodontic treatment with multibracket appliances, primarily due to volatile sulfur compounds (VSCs) produced by oral anaerobic bacteria. Cetylpyridinium chloride (CPC) is a widely used antimicrobial agent in oral care products and may help alleviate halitosis.This study aimed to evaluate the effects of 0.05% CPC mouthwash on halitosis, oral hygiene indices, and the tongue microbiota in orthodontic patients with elevated VSC levels. Methods: In this randomized, double-blind, placebo-controlled clinical trial, 30 orthodontic patients with elevated VSCs (≥150 ppb) were assigned to a CPC mouthwash group or a placebo group. Participants used the assigned mouthwash three times daily for 1 month. Halitosis was quantitatively assessed by gas chromatography (Oral Chroma™), and oral hygiene parameters including Plaque Index (PI), Gingival Index (GI), Tongue Coating Index (TCI), and unstimulated salivary flow rate were evaluated at baseline and after the intervention. The tongue microbiota was analyzed by 16S rRNA sequencing. Results: The CPC mouthwash group showed significant reductions in total VSCs, hydrogen sulfide, methyl mercaptan, PI, GI, and TCI (p < 0.05), while salivary flow rate and dimethyl sulfide remained unchanged. Microbiome analysis revealed decreases in halitosis-associated genera (Actinomyces, Corynebacterium, Tannerella) and increases in beneficial species such as Streptococcus salivarius. Conclusions: CPC mouthwash (0.05%) effectively reduced halitosis and improved oral hygiene parameters in orthodontic patients, likely through modulation of the tongue microbiota. This mouthwash may serve as a safe and practical adjunct to conventional oral hygiene practices during orthodontic treatment.},
}

@article {pmid40648819,
year = {2025},
author = {Hoying, D and Sangwan, N and Chaaban, MR},
title = {Investigating the Role of the Sinus Microbiome and Cytokine Profile in the SNOT-22 Response After Functional Endoscopic Sinus Surgery in Chronic Rhinosinusitis Patients.},
journal = {Journal of clinical medicine},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/jcm14134446},
pmid = {40648819},
issn = {2077-0383},
abstract = {Background: Functional endoscopic sinus surgery (FESS) is the treatment of choice for medically refractory CRS. However, the success rate of FESS is dependent on both baseline medical and demographic characteristics. Consequently, we performed an analysis of systemic/nasal cytokines and the sinus microbiome to assess their impact on the SNOT-22 response after functional endoscopic sinus surgery (FESS). Methods: A prospective observational study was performed on 44 patients with chronic rhinosinusitis undergoing FESS between December 2021 and September 2022. Diseased sinus tissue from 25 patients was subjected to whole-exome sequencing (WES) for taxonomical profiling of the sinus bacterial composition. Additional data collection included demographics, comorbidities, baseline sinonasal outcome test scores, post-operative sinonasal outcome test scores (at 3-4 months), and nasal/systemic cytokines. Results: Our analysis demonstrated that CRSwNP patients in the surgical responder cohort had statistically significantly higher median [P25, P75] levels of intra-nasal IL-5, indicating type 2 sinonasal disease (63 pg/μL [28, 118] versus 17 pg/μL [16.6, 18], p = 0.04). At the genus level, the relative abundance of Staphylococcus was significantly higher in the surgical non-responder cohort compared to the responder group. An ROC curve was highly accurate at distinguishing responders versus non-responders to FESS based on a microbiota-based random forest model (AUC = 0.92). Conclusions: Intra-nasal IL-5 levels and the bacterial composition of the sinus microbiome may be important predictors of symptomatic response after sinus surgery.},
}

@article {pmid40647985,
year = {2025},
author = {Perelló, A and Romero-Munar, A and Martinez, SI and Busquets, A and Cañellas, M and Quetglas, BM and Bosch, R and Vadell, J and Cabot, C and Gomila, M},
title = {Xylem Sap Mycobiota in Grapevine Naturally Infected with Xylella fastidiosa: A Case Study: Interaction of Xylella fastidiosa with Sclerotinia sclerotiorum.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/plants14131976},
pmid = {40647985},
issn = {2223-7747},
abstract = {Grapevine (Vitis vinifera) is a key crop in Mediterranean agriculture, now increasingly threatened by Xylella fastidiosa subsp. Fastidiosa (Xff), the causal agent of Pierce's disease. This study investigated: (1) the diversity of culturable fungal endophytes in the xylem sap of naturally Xff-infected grapevines, and (2) the interaction between Xff and the pathogenic fungus Sclerotinia sclerotiorum identified in the sap. The xylem sap was collected from Cabernet Sauvignon vines in Mallorca, Spain, and fungal communities were characterized using culture-dependent methods. Both beneficial fungi (e.g., Aureobasidium pullulans, Rhodotorula mucilaginosa) and pathogenic species (e.g., S. sclerotiorum, Cladosporium sp., Alternaria alternata, and the Phoma complex) were isolated from both Xff-positive and Xff-negative plants, indicating similar community profiles. Although limited by small sample size, these findings offer preliminary evidence of complex ecological interactions between Xff and the xylem-associated mycobiota, with potential implications for grapevine health and disease development under varying environmental and management conditions. Further experiments under controlled conditions revealed that grapevines co-inoculated with Xff and S. sclerotiorum showed increased disease severity, suggesting a synergistic interaction. These preliminary results highlight the complex interplay between Xff and the fungal endophytic microbiome, which may modulate grapevine susceptibility depending on environmental and management conditions.},
}

@article {pmid40647668,
year = {2025},
author = {Chudzicka-Strugała, I and Gołębiewska, I and Brudecki, G and Elamin, W and Banaszewska, B and Chudzicka-Adamczak, M and Strugała, D and Zwoździak, B},
title = {Proinflammatory Cytokines in Women with PCOS in Atypical Pathogen Infections.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/diagnostics15131669},
pmid = {40647668},
issn = {2075-4418},
abstract = {Background/Objectives: Polycystic ovary syndrome (PCOS) is one of the most frequently diagnosed endocrine and metabolic disorders in women of reproductive age before menopause. It is associated with excess androgens and ovarian dysfunction, reduced fertility, the presence of obstetric disorders, but also metabolic disorders, and, among others, insulin resistance, obesity and type II diabetes. Its close relationship with changes in the diversity of the vaginal microbiome, vaginal inflammation and changes in the vaginal microenvironment, which can pave the way for pathogenic microorganisms, is emphasized. Methods: The research in the presented paper focuses on a group of women with PCOS (n = 490) of reproductive age (26-43 years), in whom the frequency of infections of the reproductive system caused by atypical pathogens, Chlamydia trachomatis, Mycoplasma hominis and Ureaplasma spp., were analyzed, and then the immune system response was assessed in terms of the level of serum proinflammatory cytokines, IL-1β, IL-6 and TNF-α. Results: Our results showed a 40% infection rate in the studied group of patients with PCOS, with C. trachomatis being the most common pathogen (17.7%), followed by Ureaplasma spp. (10%) and M. hominis (4.9%). In some cases, co-infections such as Mycoplasma and Ureaplasma were also observed in 3.1% or all three atypical bacteria, M. hominis, Ureaplasma spp. and C. trachomatis, in 4.3% of patients with PCOS. In our study, in women with PCOS and confirmed infection with any atypical pathogen (n = 196), we analyzed the levels of proinflammatory cytokines, IL-1 β a, IL-6 and TNF-α. The results were compared with a control group (control group A) consisting of patients with the same underlying disease, i.e., PCOS (n = 39), who did not experience infection with atypical pathogens or symptoms of gynecological infection. Additionally, a control group B (n = 28) consisting of healthy women (without PCOS and without infection) was introduced. The results regarding the levels of cytokines studied in this work (IL-1β, IL-6, TNF-α) may suggest that the presence of intracellular C. trachomatis in the infection will play a dominant role in the immune system response. In the infections with atypical pathogens analyzed in this study in patients with PCOS, no characteristic clinical features were observed, apart from indications in the form of an increase in the number of leukocytes in the assessment of the vaginal biocenosis, suggesting cervicitis and reported reproductive failure or lower abdominal pain. An additional problem is the inability to detect the presence of atypical pathogens in routine microbiological tests; therefore, confirmation of such etiology requires referral of the patient for targeted tests. Conclusions: Invasion of host cells by atypical pathogens such as C. trachomatis and infections with "genital mycoplasmas" can disrupt the function of these cells and lead to many complications, including infertility. The immune response with the production of proinflammatory cytokines such as TNF-α, IL-1β, and IL-6, observed in response to infection with C. trachomatis, M. hominis, and Ureaplasma spp., induces or amplifies inflammation by activating immune cells or controlling infection, but may lead to the facilitation of the survival of pathogenic microorganisms and irreversible damage to fallopian tube tissues. Especially in the case of the proinflammatory cytosine TNF-α, there seems to be a close correlation with infections with atypical pathogens and a marked immune response, as well as with increased IL-1β and IL-6 values compared with the absence of infection (both in the presence and absence of PCOS). The presented study may suggest the importance of extended diagnostics to include atypical pathogens in the case of PCOS and the importance of research in this area also from the point of view of the immune response.},
}

@article {pmid40647560,
year = {2025},
author = {Unrug-Bielawska, K and Sandowska-Markiewicz, Z and Piątkowska, M and Czarnowski, P and Goryca, K and Zeber-Lubecka, N and Dąbrowska, M and Kaniuga, E and Cybulska-Lubak, M and Bałabas, A and Statkiewicz, M and Rumieńczyk, I and Pyśniak, K and Mikula, M and Ostrowski, J},
title = {Comparative Analysis of Gut Microbiota Responses to New SN-38 Derivatives, Irinotecan, and FOLFOX in Mice Bearing Colorectal Cancer Patient-Derived Xenografts.},
journal = {Cancers},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/cancers17132263},
pmid = {40647560},
issn = {2072-6694},
support = {2018/31/B/NZ7/02675//National Science Center/ ; },
abstract = {BACKGROUND: Symbiotic gut microbiota can enhance cancer therapy efficacy, while treatment-induced dysbiosis may reduce effectiveness or increase toxicity. Our preclinical study compared the anticancer effects and impact on fecal microbiota and metabolites of two water-soluble SN-38 derivatives (BN-MePPR and BN-MOA), with those observed after treatment with Irinotecan, and the FOLFOX regimen in NOD scid gamma mice bearing patient-derived colon adenocarcinoma xenografts (CRC PDX).

METHODS: Five individual experiments with Irinotecan and its derivatives and eight individual experiments with FOLFOX were conducted using eight CRC PDX models. Chemotherapeutics were administered intraperitoneally 4-5 times at 5-day intervals. Fecal samples were collected before and after treatment. Microbiota composition was analyzed by 16S rRNA gene (V3-V4 regions) sequencing. Mass spectrometry was used to quantify short-chain fatty acids (SCFAs) and amino acids (AAs).

RESULTS: All treatments significantly inhibited tumor growth versus controls. However, no significant changes were observed in gut microbiota α- and β-diversity between treated and untreated groups. Tumor progression in controls was associated with increased abundance of Marvinbryantia, Lactobacillus, Ruminococcus, and [Eubacterium] nodatum group. FOLFOX-treated mice showed increased Marvinbryantia, Bacteroides, and Candidatus Arthromitus, and decreased Akkermansia. No distinct taxa changes were found in the Irinotecan or derivative groups. SCFA levels remained unchanged across groups, while BN-MePPR, BN-MOA, and Irinotecan all increased AA concentrations.

CONCLUSIONS: Contrary to earlier toxicological data, these findings indicate a relatively limited impact of the tested chemotherapeutics on the gut microbiome and metabolome, emphasizing the importance of research method selection in preclinical studies.},
}

@article {pmid40647535,
year = {2025},
author = {Palkovsky, M and Modrackova, N and Neuzil-Bunesova, V and Liberko, M and Hlodakova, A and Soumarova, R},
title = {Role of Human Microbiome in Development and Management of Head and Neck Squamous Cell Carcinoma.},
journal = {Cancers},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/cancers17132238},
pmid = {40647535},
issn = {2072-6694},
abstract = {Despite decades of research, cancer remains a major global health problem [...].},
}

@article {pmid40647494,
year = {2025},
author = {Fajkić, A and Lepara, O and Jahić, R and Hadžović-Džuvo, A and Belančić, A and Chupin, A and Pavković, D and Sher, EK},
title = {Ultra-Processed Diets and Endocrine Disruption, Explanation of Missing Link in Rising Cancer Incidence Among Young Adults.},
journal = {Cancers},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/cancers17132196},
pmid = {40647494},
issn = {2072-6694},
abstract = {The global increase in early-onset cancers among adolescents and young adults has happened at the same time as the rise in the consumption of ultra-processed foods (UPFs). Far beyond their poor nutritional quality, UPFs are increasingly seen as Trojan horses, complex biological agents that interfere with many functions of the human organism. In this review, we utilise the Trojan horse model to explain the quiet and building health risks from UPFs as foods that seem harmless, convenient, and affordable while secretly delivering endocrine-disrupting chemicals (EDCs), causing chronic low-grade inflammation, altering the microbiome, and producing epigenetic alterations. We bring together new proof showing that UPFs mess up hormonal signals, harm the body's ability to fight off harmful germs, lead to an imbalance of microbes, and cause detrimental changes linked to cancer. Important components, such as bisphenols and phthalates, can migrate from containers into food, while additional ingredients and effects from cooking disrupt the normal balance of cells. These exposures are especially harmful during vulnerable developmental periods and may lay the groundwork for disease many years later. The Trojan horse model illustrates the hidden nature of UPF-related damage, not through a sudden toxin but via chronic dysregulation of metabolic, hormonal, and genetic control. This model changes focus from usual diet worries to a bigger-picture view of UPFs as causes of life-disrupting damage. Ultimately, this review aims to identify gaps in current knowledge and epidemiological approaches and highlight the need for multi-omics, long-term studies and personalised nutrition plans to assess and reduce the cancer risk associated with UPFs. Recognising UPFs as a silent disruptor is crucial in shaping public health policies and cancer prevention programs targeting younger people.},
}

@article {pmid40647355,
year = {2025},
author = {Chu, J and No, CW and Joung, H and Kim, KH and Shin, CH and Lee, J and Ha, JH},
title = {Modulation of Gut Microbial Composition by Lactobacillus delbrueckii subsp. lactis CKDB001 Supplementation in a High-Fat-Diet-Induced Obese Mice.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132251},
pmid = {40647355},
issn = {2072-6643},
support = {RS-2023-00227274//National Research Foundation of Korea/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Male ; Mice, Inbred C57BL ; *Obesity/microbiology/etiology/therapy ; *Lactobacillus delbrueckii/physiology ; *Probiotics/administration & dosage/pharmacology ; Mice ; *Dietary Supplements ; Feces/microbiology ; Mice, Obese ; Disease Models, Animal ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background/Objectives:Lactobacillus delbrueckii subsp. lactis CKDB001 (LL) has demonstrated anti-inflammatory, antioxidant, and lipid-regulatory effects in vitro and in vivo, including attenuation of hepatic steatosis and modulation of lipid metabolism. Given the known interactions between host metabolism and gut microbiota, these findings suggest a potential role for LL in modulating microbial composition under conditions of diet-induced obesity. This study aimed to investigate the microbiome-related effects of LL using an established murine model. To evaluate the effect of LL supplementation on gut microbial composition and predict microbial metabolic functions in mice with high-fat diet-induced obesity. Methods: Male C57BL/6J mice were fed a high-fat diet and administered LL orally for 12 weeks. Fecal samples were collected and analyzed using 16S rRNA gene sequencing. Microbial taxonomic profiles were assessed using linear discriminant analysis effect size, and functional predictions were performed using PICRUSt2. Results: LL supplementation significantly altered the gut microbiota by increasing the relative abundance of Lactobacillus and other commensal taxa while reducing the prevalence of pro-inflammatory genera such as Alistipes and Bilophila. Functional prediction analysis revealed a downregulation of lipopolysaccharide and ADP-L-glycero-β-D-manno-heptose biosynthesis pathways. Microbial functions associated with carbohydrate metabolism and short-chain fatty acid production were enriched in the LL-treated group. Conclusions: LL modulated gut microbial composition and suppressed pro-inflammatory microbial pathways while enhancing beneficial metabolic functions in high-fat diet-fed mice. These findings support the potential of LL as a safe and effective microbiota-targeted probiotic for managing obesity-related metabolic disorders.},
}

Animals
*Gastrointestinal Microbiome
*Diet, High-Fat/adverse effects
Male
Mice, Inbred C57BL
*Obesity/microbiology/etiology/therapy
*Lactobacillus delbrueckii/physiology
*Probiotics/administration & dosage/pharmacology
Mice
*Dietary Supplements
Feces/microbiology
Mice, Obese
Disease Models, Animal
RNA, Ribosomal, 16S/genetics

@article {pmid40647335,
year = {2025},
author = {Chojnacki, M and Błońska, A and Kaczka, A and Chojnacki, J and Walecka-Kapica, E and Romanowska, N and Przybylowska-Sygut, K and Popławski, T},
title = {Assessment of the Gut Microbiome in Patients with Coexisting Irritable Bowel Syndrome and Chronic Fatigue Syndrome.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132232},
pmid = {40647335},
issn = {2072-6643},
support = {503/6-006-05//UMED/ ; UK/US/06/2022/01/00004//ALAB/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/complications/urine ; Female ; *Fatigue Syndrome, Chronic/microbiology/complications/urine ; *Gastrointestinal Microbiome/physiology ; Adult ; Middle Aged ; Tryptophan/metabolism ; Dysbiosis/microbiology ; },
abstract = {Background: The gut microbiome is a key modulator of the gut-brain axis and may contribute to the pathophysiology of both gastrointestinal and systemic disorders. This study aimed to evaluate gut microbiota composition and tryptophan/phenylalanine metabolism in women with unclassified irritable bowel syndrome (IBS-U), with or without coexisting chronic fatigue syndrome (CFS). Methods: Eighty women were enrolled and divided into two groups: IBS-U without CFS (Group I, n = 40) and IBS-U with coexisting CFS (Group II, n = 40). Microbial composition and diversity were assessed using the GA-map™ Dysbiosis Test, including the dysbiosis index (DI) and Shannon Diversity Index (SDI). Hydrogen and methane levels were measured in breath samples. Urinary concentrations of selected microbial and neuroactive metabolites-homovanillic acid (HVA), 5-hydroxyindoleacetic acid (5-HIAA), kynurenine (KYN), kynurenic acid (KYNA), xanthurenic acid (XA), quinolinic acid (QA), hydroxyphenylacetic acid (HPA), and 3-indoxyl sulfate (3-IS)-were quantified using LC-MS/MS. Fatigue severity was assessed using the Chalder Fatigue Questionnaire (CFQ-11) and the fatigue severity scale (FSS). Results: Compared to Group I, patients with IBS-CFS showed significantly greater microbial diversity, higher breath methane levels, and elevated urinary concentrations of QA, XA, 3-IS, and HVA, alongside lower concentrations of 5-HIAA and KYN. Fatigue severity was positively correlated with urinary XA and QA levels. Conclusions: Women with IBS and coexisting CFS exhibit distinct gut microbiota and tryptophan metabolite profiles compared to those without fatigue. The observed metabolite-symptom associations, particularly involving neuroactive kynurenine derivatives, warrant further investigation. These preliminary findings should be interpreted as hypothesis-generating and require validation through high-resolution microbiome analyses, functional pathway profiling, and longitudinal or interventional studies to clarify causality and clinical significance.},
}

Humans
*Irritable Bowel Syndrome/microbiology/complications/urine
Female
*Fatigue Syndrome, Chronic/microbiology/complications/urine
*Gastrointestinal Microbiome/physiology
Adult
Middle Aged
Tryptophan/metabolism
Dysbiosis/microbiology

@article {pmid40647334,
year = {2025},
author = {Szudzik, M and Zajdel, M and Samborowska, E and Perlejewski, K and Radkowski, M and Ufnal, M},
title = {High-Fat Diet with Normal Caloric Intake Elevates TMA and TMAO Production and Reduces Microbial Diversity in Rats.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132230},
pmid = {40647334},
issn = {2072-6643},
support = {2020/37/B/NZ5/00366//National Science Center/ ; },
mesh = {Animals ; *Methylamines/metabolism/urine ; *Gastrointestinal Microbiome ; *Diet, High-Fat/adverse effects ; Rats, Sprague-Dawley ; Male ; Rats ; *Energy Intake ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification ; },
abstract = {Background/Objectives: Trimethylamine (TMA), produced by gut microbiota, and its derivative trimethylamine N-oxide (TMAO) are both associated with cardiometabolic diseases. While the effects of high-fat diets (HFDs) and high-disaccharide diets (HDDs) on gut microbiota in the context of obesity have been well studied, their impact on TMA/TMAO production, particularly alongside physiological caloric intake, remains obscure. This study investigates how standard HFDs and HDDs alongside physiological caloric intake influence gut microbiota composition and TMA/TMAO production in rats. Methods: Sprague Dawley rats were fed one of three diets a standard diet, an HFD, or an HDD for 12 weeks, with chow availability adjusted by age to maintain physiological caloric intake. Gut bacterial diversity was analyzed using 16S rRNA gene sequencing, and metabolites were quantified via High-Performance Liquid Chromatography-Mass Spectrometry (HPLC-MS) in urine and plasma. Results: The HFD group had significantly higher urinary levels of TMA and TMAO compared to the control and HDD groups. Gut bacterial diversity in the HFD group was markedly reduced, displaying the lowest species richness and phylogenetic diversity among all the groups. Notably, Pasteurellaceae (within the order Pasteurellales) and S24-7 (within the order Bacteroidales) were positively correlated with TMAO levels. The demonstrated HDD group increased microbial diversity compared to both the control and HFD groups. Conclusions: A high-fat diet during controlled and physiological caloric intake increases TMA/TMAO production and reduces gut microbial diversity. This underscores the role of diet composition, beyond caloric excess, in shaping gut microbiota and the related cardiometabolic biomarkers.},
}

Animals
*Methylamines/metabolism/urine
*Gastrointestinal Microbiome
*Diet, High-Fat/adverse effects
Rats, Sprague-Dawley
Male
Rats
*Energy Intake
RNA, Ribosomal, 16S/genetics
Bacteria/classification

@article {pmid40647305,
year = {2025},
author = {Almatani, MF and Rompato, G and Stewart, EC and Hayden, M and Case, J and Rice, S and Hintze, KJ and Benninghoff, AD},
title = {Dynamic Microbiome Responses to Structurally Diverse Anthocyanin-Rich Foods in a Western Diet Context.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132201},
pmid = {40647305},
issn = {2072-6643},
support = {2021-67018-33938//United States Department of Agriculture/ ; UTA-01456//Utah Agricultural Experiment Station/ ; },
mesh = {Animals ; *Anthocyanins/pharmacology/chemistry/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Mice, Inbred C57BL ; *Fruit/chemistry ; *Diet, Western/adverse effects ; Male ; Mice ; Feces/microbiology ; Dietary Supplements ; RNA, Ribosomal, 16S/genetics ; Ribes/chemistry ; Vaccinium myrtillus/chemistry ; Polyphenols ; Rubus/chemistry ; },
abstract = {Background/Objectives: Anthocyanin (ACN)-rich foods are known to influence the gut microbiota composition, but the temporal dynamics and structural specificity of these effects remain poorly understood. This study investigated how distinct ACN-rich fruit supplements impact the gut microbiome over time in the context of a Western-style diet. We hypothesized that ACN-induced microbial shifts would occur rapidly, differ by ACN source, and require continued intake to persist. Methods: C57BL/6J mice were fed the total Western diet (TWD) supplemented with freeze-dried powders from bilberry (BB), tart cherry (TC), chokeberry (CB), elderberry (EB), black currant (BC), or black raspberry (BRB) for 0, 1, 3, or 7 days. Cocoa polyphenols (CPs) were included as a comparator with a distinct polyphenol profile. Fecal microbiota were collected at 0, 1, 3, and 7 days post exposure and analyzed by 16S rRNA sequencing. Results: ACN-rich supplements induced rapid microbial shifts detectable within one day of exposure. However, most changes reverted toward the baseline within days of supplement withdrawal, indicating limited persistence. Among the ACNs, BRB produced the most sustained microbiome alterations. Microbial responses varied by ACN source, suggesting that differences in glycoside and aglycone structures influence the community composition. Conclusions: ACN-rich foods can induce rapid but largely transient alterations in the gut microbiome, with variability linked to the polyphenol structure. These findings highlight the ecological sensitivity of the microbiome to specific dietary components and underscore the importance of sustained intake for maintaining microbial shifts.},
}

Animals
*Anthocyanins/pharmacology/chemistry/administration & dosage
*Gastrointestinal Microbiome/drug effects
Mice, Inbred C57BL
*Fruit/chemistry
*Diet, Western/adverse effects
Male
Mice
Feces/microbiology
Dietary Supplements
RNA, Ribosomal, 16S/genetics
Ribes/chemistry
Vaccinium myrtillus/chemistry
Polyphenols
Rubus/chemistry

@article {pmid40647290,
year = {2025},
author = {Zdybel, K and Śliwka, A and Polak-Berecka, M and Polak, P and Waśko, A},
title = {Postbiotics Formulation and Therapeutic Effect in Inflammation: A Systematic Review.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132187},
pmid = {40647290},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Inflammation/therapy ; *Anti-Inflammatory Agents ; Inflammatory Bowel Diseases ; },
abstract = {Background: Postbiotics are bioactive compounds derived from inactivated probiotic microorganisms that show potential for preventing and treating inflammatory diseases. This review aimed to evaluate the evidence on their therapeutic effects in inflammatory conditions. Methods: A search of PubMed, Scopus, and Web of Science databases from 2014 to 2024 identified 39 eligible studies. Article selection was conducted using the Rayyan platform, risk of bias was assessed with the Cochrane ROB 2 tool, and results were visualized with ROBVIS. Bibliometric networks were constructed using VOSviewer. Due to data heterogeneity, a meta-analysis was not performed; therefore, results were described and presented graphically. Results: The most commonly used microorganisms belonged to the Lactobacillaceae and Bifidobacteriaceae families, with heat inactivation as the predominant method. Postbiotics exert multifaceted anti-inflammatory effects by modulating cytokine expression, influencing immune cell signaling pathways, and strengthening epithelial barrier integrity. They regulate immune mechanisms such as the Th1/Th2 and Treg/Th17 balance, indicating their potential in treating inflammatory bowel diseases, autoimmune diseases, and metabolic syndrome. However, the heterogeneity of studies, their limitations, and risk of bias require cautious interpretation. Conclusions: Future research should focus on standardizing postbiotic preparations, conducting long-term clinical trials, and analyzing synergistic effects of different strains. Postbiotics offer a promising approach to managing inflammation, with potential applications in functional foods and nutraceuticals.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Inflammation/therapy
*Anti-Inflammatory Agents
Inflammatory Bowel Diseases

@article {pmid40647269,
year = {2025},
author = {Lamichhane, G and Godsey, TJ and Liu, J and Franks, R and Zhang, G and Emerson, SR and Kim, Y},
title = {Twelve-Week Curcumin Supplementation Improves Glucose Homeostasis and Gut Health in Prediabetic Older Adults: A Pilot, Double-Blind, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132164},
pmid = {40647269},
issn = {2072-6643},
support = {Barbara K. Pass//Oklahoma State University/ ; 1-503351//Ottogi Ham Taiho Foundation/ ; },
mesh = {Humans ; *Curcumin/administration & dosage/pharmacology ; Double-Blind Method ; *Prediabetic State/drug therapy/blood ; Aged ; Male ; Female ; Pilot Projects ; *Blood Glucose/drug effects/metabolism ; Glycated Hemoglobin/metabolism ; Gastrointestinal Microbiome/drug effects ; Middle Aged ; *Homeostasis/drug effects ; *Dietary Supplements ; Diabetes Mellitus, Type 2/prevention & control ; Insulin/blood ; Overweight ; Body Mass Index ; },
abstract = {Background: The prevalence of diabetes increases with age, and food bioactive compounds have shown potential in mitigating its development. This study aimed to evaluate the efficacy of curcumin in preventing type 2 diabetes mellitus (T2DM) in older adults with prediabetes. We hypothesized that curcumin, due to its insulin-sensitizing effects, would help maintain glucose homeostasis, metabolic health, and gut health. Methods: This randomized, double-blind, placebo-controlled trial included 28 older adults (aged 60 years or older) with prediabetes or overweight/obesity. Participants were randomly assigned to receive either curcumin (80 mg) or placebo capsules for 12 weeks. The primary outcome measures were glucose homeostasis markers, including hemoglobin A1c (HbA1c), blood glucose, and insulin levels. Secondary outcomes included body composition, body mass index (BMI), body weight, lipid profiles, and gut microbiome composition. Data normality was assessed using the Shapiro-Wilk test, and two-way repeated-measures ANOVA with multiple comparisons was used to find differences between groups and over time. Results: A total of 23 participants (age = 66.52 ± 5.76 years; 14 in the curcumin group and 9 in the placebo group) completed the 12-week intervention. HbA1c levels significantly decreased in the curcumin group, whereas levels remained stable in the placebo group. While the curcumin group observed an increase in AST levels, the ALT level was reduced in the placebo group. Both the curcumin and placebo groups showed a reduced ALT/AST ratio by the end of the intervention. Body mass index, lipid profiles, and body composition showed no significant changes over the study period. Gut microbiome analysis revealed no significant changes in alpha diversity or beta diversity of microbiome; however, there was marginal enrichment of beneficial bacteria such as Bacteroidota (phylum), Bacteroidaceae (family), Agathobacter, Bacteroides, and Roseburia (genera) in the curcumin-supplemented group over time. Conclusions: Curcumin supplementation improved or favorably maintained glucose homeostasis and showed modest improvements in beneficial gut microbiota in older adults with prediabetes, potentially reducing the risk of developing diabetes. Long-term studies with larger sample sizes are needed to confirm these findings and determine the clinical relevance of curcumin supplementation for prediabetes prevention.},
}

Humans
*Curcumin/administration & dosage/pharmacology
Double-Blind Method
*Prediabetic State/drug therapy/blood
Aged
Male
Female
Pilot Projects
*Blood Glucose/drug effects/metabolism
Glycated Hemoglobin/metabolism
Gastrointestinal Microbiome/drug effects
Middle Aged
*Homeostasis/drug effects
*Dietary Supplements
Diabetes Mellitus, Type 2/prevention & control
Insulin/blood
Overweight
Body Mass Index

@article {pmid40647261,
year = {2025},
author = {Ding, Q and Xue, D and Ren, Y and Xue, Y and Shi, J and Xu, Z and Geng, Y},
title = {Apple Cider Vinegar Powder Mitigates Liver Injury in High-Fat-Diet Mice via Gut Microbiota and Metabolome Remodeling.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132157},
pmid = {40647261},
issn = {2072-6643},
support = {32372302//National Natural Science Foundation of China/ ; 32101964//National Natural Science Foundation of China/ ; 31970746//National Natural Science Foundation of China/ ; 2024YFF0619500//National Key Research and Development Program of China/ ; 2023M731346//China Postdoctoral Science Foundation/ ; BK20241755//Natural Science Foundation of Jiangsu Province/ ; BJ2023046//Top Talent Support Program for young and middle-aged people of Wuxi Health Committee/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; Male ; Mice ; *Acetic Acid/pharmacology ; *Metabolome/drug effects ; Powders ; *Malus/chemistry ; Liver/drug effects/metabolism/pathology ; Dysbiosis ; },
abstract = {Background/Objectives: High-fat-diet (HFD) consumption drives chronic liver injury via gut dysbiosis and metabolic disturban. Apple cider vinegar, rich in polyphenols and organic acids, shows potential in metabolic regulation. This study aimed to investigate whether apple cider vinegar powder (ACVP) alleviates HFD-induced liver injury by modulating the gut-liver axis. Methods: For 12 weeks, C57BL/6 J mice received daily ACVP gavage while being fed a HFD. A series of biological assessments were conducted, including systemic metabolic evaluations (body weight, serum alanine aminotransferase (ALT)/aspartate aminotransferase (AST), and lipid/glucose levels), hepatic steatosis (hematoxylin and eosin (H&E) staining), intestinal microbiome characterization (16S rRNA gene genomic analysis), and comprehensive metabolite profiling of cecal contents (non-targeted metabolomics). Pearson correlation networks integrated multi-omics data. Results: ACVP attenuated HFD-induced weight gain by 26.3%, hepatomegaly and dyslipidemia, as well as reduced hepatic lipid vacuoles and serum ALT (48%)/AST (21.5%). ACVP restored gut microbiota diversity, enriching Muribaculaceae. Cecal metabolomics identified 38 HFD-perturbed metabolites reversed by ACVP, including indolelactate, hyocholate, and taurocholic acid. the Kyoto encyclopedia of genes and genomes (KEGG) analysis revealed ACVP-mediated recovery of linoleic acid metabolism. Correlation networks linked Akkermansia to anti-inflammatory metabolites (e.g., trans-ferulic), while Desulfobacterota correlated with pro-inflammatory oxylipins (e.g., 12,13-dihydroxy-9Z-octadecenoic acid (DHOME)). Conclusions: ACVP mitigates HFD-induced liver injury by remodeling gut microbiota, restoring microbial metabolites, and enhancing gut-liver crosstalk.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Diet, High-Fat/adverse effects
Mice, Inbred C57BL
Male
Mice
*Acetic Acid/pharmacology
*Metabolome/drug effects
Powders
*Malus/chemistry
Liver/drug effects/metabolism/pathology
Dysbiosis

@article {pmid40647258,
year = {2025},
author = {Fekete, M and Lehoczki, A and Kryczyk-Poprawa, A and Zábó, V and Varga, JT and Bálint, M and Fazekas-Pongor, V and Csípő, T and Rząsa-Duran, E and Varga, P},
title = {Functional Foods in Modern Nutrition Science: Mechanisms, Evidence, and Public Health Implications.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132153},
pmid = {40647258},
issn = {2072-6643},
support = {TKP2021-NKTA-47//Ministry of Innovation and Technology of Hungary/ ; RRF-2.3.1-21-2022-00003//National Cardiovascular Laboratory Program/ ; },
mesh = {Humans ; *Functional Food ; *Public Health ; *Nutritional Sciences ; Gastrointestinal Microbiome ; Nutrigenomics ; Nutritive Value ; Cardiovascular Diseases/prevention & control ; Prebiotics ; },
abstract = {In recent years, functional foods have garnered increasing scientific and public health interest due to their potential to confer physiological benefits beyond basic nutritional value. International bodies such as EFSA, FDA, and WHO define functional foods as those containing bioactive components that may contribute to the prevention and management of chronic non-communicable diseases, including cardiovascular disease, type 2 diabetes, and certain cancers. The evolving paradigm of "food as medicine" reflects a broader shift in nutritional science towards proactive, health-oriented dietary strategies. This article provides a comprehensive, interdisciplinary overview of functional foods by examining their biological mechanisms, clinical evidence, public health significance, regulatory frameworks, and future prospects-particularly in the context of advances in personalized nutrition and nutrigenomics. A thorough literature review was conducted, drawing from recent peer-reviewed studies and guidelines from key health authorities. The review highlights the roles of specific compounds such as probiotics and prebiotics in modulating the gut microbiome, flavonoids and polyphenols in anti-inflammatory processes, omega-3 fatty acids in cardiometabolic regulation, and vitamins and minerals in supporting immune function. While an expanding body of clinical trials and meta-analyses supports the health benefits of these compounds-including reductions in LDL cholesterol, improved insulin sensitivity, and mitigation of oxidative stress-the integration of functional foods into everyday diets remains challenging. Socioeconomic disparities and limited health literacy often impede their accessibility and widespread adoption in public health practice. Functional foods represent a promising component of prevention-focused modern healthcare. To maximize their impact, a coordinated, evidence-based approach is essential, involving collaboration among healthcare professionals, nutrition scientists, policymakers, and the food industry. Looking forward, innovations in artificial intelligence, microbiome research, and genomic technologies may unlock novel opportunities for the targeted and effective application of functional foods in population health.},
}

Humans
*Functional Food
*Public Health
*Nutritional Sciences
Gastrointestinal Microbiome
Nutrigenomics
Nutritive Value
Cardiovascular Diseases/prevention & control
Prebiotics

@article {pmid40647253,
year = {2025},
author = {Zhang, D and Leitman, M and Pawar, S and Shera, S and Hernandez, L and Jacobs, JP and Dong, TS},
title = {The Association Between Prevotella copri and Advanced Fibrosis in the Progression of Metabolic Dysfunction-Associated Steatotic Liver Disease.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132145},
pmid = {40647253},
issn = {2072-6643},
mesh = {Animals ; Gastrointestinal Microbiome ; Humans ; Disease Progression ; *Liver Cirrhosis/microbiology ; Mice ; *Prevotella/genetics ; Male ; *Fatty Liver/microbiology ; Diet, High-Fat/adverse effects ; Disease Models, Animal ; Mice, Inbred C57BL ; Lipid Metabolism/genetics ; RNA, Ribosomal, 16S/genetics ; Liver/pathology/metabolism ; Female ; Obesity/microbiology/complications ; Middle Aged ; *Non-alcoholic Fatty Liver Disease/microbiology ; Metabolic Syndrome/microbiology/complications ; },
abstract = {Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD), driven by obesity and metabolic syndrome, is increasingly prevalent and a significant contributor to liver fibrosis, cirrhosis, and liver-related mortality. Emerging research implicates the gut microbiome as a critical player in MASLD progression, yet specific microbial drivers remain poorly understood. Here, we explore the role of Prevotella copri (P. copri) in MASLD progression through both human patient cohorts and a mouse model of diet-induced obesity. Methods/Results: Using 16S rRNA sequencing, we identified elevated P. copri abundance in MASLD patients with advanced fibrosis, linked with significant shifts in microbial diversity and bacterial network connectivity. To investigate causality, experimental colonization of P. copri in mice on a high-fat diet worsened MASLD progression, with P. copri-colonized mice showing significant increases in hepatic steatosis, liver triglyceride accumulation, and body weight, independent of caloric intake. At the molecular level, P. copri colonization downregulated key lipid metabolism genes, such as carnitine palmitoyltransferase 1 and adipose triglyceride lipase, and impaired tight intestinal junction integrity through the downregulation of occludin. Collectively, our findings position P. copri as a possible driver of MASLD progression by promoting hepatic steatosis through lipid and triglyceride accumulation and fibrosis through decreased tight junction integrity. These insights suggest a promising therapeutic avenue to target specific microbial signatures like P. copri to curb MASLD progression and mitigate the associated risk of advanced fibrosis.},
}

Animals
Gastrointestinal Microbiome
Humans
Disease Progression
*Liver Cirrhosis/microbiology
Mice
*Prevotella/genetics
Male
*Fatty Liver/microbiology
Diet, High-Fat/adverse effects
Disease Models, Animal
Mice, Inbred C57BL
Lipid Metabolism/genetics
RNA, Ribosomal, 16S/genetics
Liver/pathology/metabolism
Female
Obesity/microbiology/complications
Middle Aged
*Non-alcoholic Fatty Liver Disease/microbiology
Metabolic Syndrome/microbiology/complications

@article {pmid40647243,
year = {2025},
author = {Lei, O and Yang, J and Kang, HH and Li, Z},
title = {Impact of a 12-Week Hypocaloric Weight Loss Diet with Mixed Tree Nuts vs. Pretzels on Trimethylamine-N-Oxide (TMAO) Levels in Overweight Adults.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132137},
pmid = {40647243},
issn = {2072-6643},
support = {NCT03159689//Center for Human Nutrition and the International Tree Nut Council Nutrition Research and Education Foundation/ ; },
mesh = {Humans ; Female ; Male ; *Methylamines/blood ; *Overweight/diet therapy/blood ; *Nuts ; Middle Aged ; Adult ; *Diet, Reducing/methods ; Weight Loss ; Choline/administration & dosage ; },
abstract = {UNLABELLED: Trimethylamine N-oxide (TMAO), a gut microbiome metabolite linked to cardiovascular health, can be influenced by dietary factors like choline intake and diet quality. This study compared the effects of mixed tree nuts (MTNs) and pretzels, as part of a 12-week hypocaloric weight loss diet, on TMAO levels and identified dietary predictors.

METHODS: Plasma samples from 95 overweight individuals consuming either 1.5 oz. of mixed tree nuts (MTNs, n = 56) or isocaloric pretzels (n = 39) daily for 12 weeks were analyzed. Nutritional data were collected at baseline and week 12 through dietary recall using the Automated Self-Administered 24 h Dietary Assessment Tool (ASA24), and the overall diet quality was assessed via the Healthy Eating Index (HEI) score. TMAO levels were determined and analyzed using linear mixed-effect models, adjusting for covariates. Wilcoxon signed-rank tests compared baseline and week 12 TMAO and weight. Multiple linear regression identified baseline predictors of TMAO.

RESULTS: Baseline demographics, anthropometric measures, HEI scores, and dietary choline intake were similar between the MTN and pretzel groups. A significant positive association was observed between baseline dietary choline and plasma TMAO levels (p = 0.012). The 12-week hypocaloric diet led to significant weight reduction in both groups (p < 0.01), but the magnitude of weight loss did not differ significantly between the MTN (-3.47 lbs) and pretzel (-4.25 lbs) groups (p = 0.18). Plasma TMAO levels decreased significantly in both groups (p < 0.01), but the between-group difference in reduction was not significant. (MTNs: -0.34 vs. pretzels: -0.37; p = 0.43). HEI scores and dietary choline intake remained unchanged, with no significant time-intervention interaction. Participants with low baseline HEI scores (≤53.72) had a more pronounced reduction in TMAO levels in the MTN group compared to the pretzel group (MTN: -0.54 vs. pretzel: -0.23; p = 0.045) over 12 weeks, despite similar weight loss. This difference was not observed in participants with higher HEI scores.

CONCLUSIONS: The 12-week hypocaloric diet reduced body weight and plasma TMAO levels similarly in both MTN and pretzel groups. Participants with lower dietary quality saw a greater reduction in TMAO levels in the MTN group, suggesting MTNs may better modulate TMAO levels, especially for those with poorer baseline diets.},
}

Humans
Female
Male
*Methylamines/blood
*Overweight/diet therapy/blood
*Nuts
Middle Aged
Adult
*Diet, Reducing/methods
Weight Loss
Choline/administration & dosage

@article {pmid40647237,
year = {2025},
author = {Kalman, D and Hewlings, S and Madelyn-Adjei, A and Ebersole, B},
title = {Dietary Heme Iron: A Review of Efficacy, Safety and Tolerability.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132132},
pmid = {40647237},
issn = {2072-6643},
mesh = {Humans ; *Heme/administration & dosage/adverse effects/pharmacokinetics ; *Iron, Dietary/adverse effects/administration & dosage/pharmacokinetics ; *Anemia, Iron-Deficiency/prevention & control ; Dietary Supplements ; Biological Availability ; Intestinal Absorption ; *Iron/adverse effects ; Animals ; },
abstract = {Iron is a fundamental micronutrient essential for oxygen transport, enzymatic activity, and metabolic homeostasis. Yet it remains the most deficient nutrient in the world, with more than 2 billion people estimated with iron deficiency anemia. In the diet, animal foods provide iron primarily as heme iron. Dietary heme iron is absorbed through the active transport pathways catalyzed by heme oxygenase in the intestinal enterocyte. This form of heme differs in its bioavailability, absorption mechanisms, and tolerability compared to non-heme forms of iron, including iron salts and chelates. Adding more heme iron to a diet, including through iron supplements, may help to reduce the prevalence of iron deficiency. Future research should focus on research of heme iron supplementation strategies to enhance absorption efficiency, gut microbiome health, and safety, ensuring optimal iron status across diverse populations.},
}

Humans
*Heme/administration & dosage/adverse effects/pharmacokinetics
*Iron, Dietary/adverse effects/administration & dosage/pharmacokinetics
*Anemia, Iron-Deficiency/prevention & control
Dietary Supplements
Biological Availability
Intestinal Absorption
*Iron/adverse effects
Animals

@article {pmid40647225,
year = {2025},
author = {Shakhman, S and Pfeffer-Gik, T and Elial-Fatal, S and Broitman, Y and Yanai, H and Gophna, U and Dotan, I and Godny, L},
title = {Industrial Bread Composition: Potential Implications for Patients with Inflammatory Bowel Disease.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132120},
pmid = {40647225},
issn = {2072-6643},
support = {G-2203-05892//Leona M. and Harry B. Helmsley Charitable Trust/ ; },
mesh = {*Bread/analysis ; Humans ; *Inflammatory Bowel Diseases/etiology/microbiology ; *Food Additives/analysis/adverse effects ; Food Handling ; Emulsifying Agents/analysis/adverse effects ; Gastrointestinal Microbiome ; Israel ; Food Preservatives/analysis/adverse effects ; },
abstract = {Background: Ultra-processed food (UPF) intake, particularly that of industrial breads rich in food additives (FAs) like emulsifiers, has been linked to higher risk of inflammatory bowel diseases (IBD). Here, we screened the ingredients and FAs used in the bread industry and reviewed their potential biological effects. Methods: We consecutively screened breads available at supermarket and health food store chains in Israel. Bread products were analyzed by dietitians and categorized into three categories based on their composition: low processed (traditional ingredients), medium processed (additives like malt and fibers), and highly processed (FAs like emulsifiers and preservatives). We conducted a literature review to explore the links between the identified FAs, microbial composition and intestinal inflammation. Results: Of the 233 breads screened, 195 (84%) were highly processed, 9 (4%) medium-processed and 29 (12%) low-processed. We identified 37 different FAs and ingredients used. Most breads contained preservatives-189 (81%), and emulsifiers-178 (76%). Calcium propionate (E-282) was the most prevalent preservative present in 112 (48%) breads, while sodium-stearoyl-2-lactylate (SSL-E-481) was the most prevalent emulsifier present in 86 (37%) breads. The literature review revealed that 19 (51%) FAs used in the bread industry were associated with the exacerbation of inflammation or gut microbiome dysbiosis by increasing cytokine production and adversely affecting microbial composition. Conclusions: Most of the available breads in Israel are highly processed, containing FAs that may mediate intestinal inflammation. Low-processed breads are available and may be more recommended to patients with IBD. Further understanding of the role of FAs in IBD etiology may guide dietary recommendations.},
}

*Bread/analysis
Humans
*Inflammatory Bowel Diseases/etiology/microbiology
*Food Additives/analysis/adverse effects
Food Handling
Emulsifying Agents/analysis/adverse effects
Gastrointestinal Microbiome
Israel
Food Preservatives/analysis/adverse effects

@article {pmid40647222,
year = {2025},
author = {Braszczyńska-Sochacka, J and Sochacki, J and Mik, M},
title = {The Gut's Secret Code: Bowel Microbiota as a Biomarker for Adaptation.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132117},
pmid = {40647222},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Short Bowel Syndrome/microbiology/physiopathology/therapy ; Biomarkers/metabolism ; *Adaptation, Physiological ; Dysbiosis ; *Intestinal Failure/microbiology/therapy/physiopathology ; Intestine, Small/microbiology/surgery ; Parenteral Nutrition ; },
abstract = {Background: Chronic intestinal failure (CIF), most commonly caused by short bowel syndrome (SBS), necessitates complex care. This review explores the gut microbiota's role in intestinal adaptation in SBS, examining its potential as both a biomarker and therapeutic target. SBS results from extensive small bowel resection, leading to malabsorption and dependence on parenteral nutrition (PN). Post-resection, the gut microbiota undergoes significant alterations. While the small bowel microbiome typically comprises Streptococcus, Veillonella, and others, SBS patients often exhibit increased Gram-negative Proteobacteria. Dysbiosis is linked to adverse outcomes like liver disease and impaired growth, but beneficial effects such as energy salvage also occur. Intestinal adaptation, a process of increasing absorptive surface area in the remaining bowel, involves acute, remodeling, and maintenance phases. Preservation of ileum and stimulation with the oral diet are crucial. Biomarkers are needed to predict success, with gut microbiota composition emerging as a promising non-invasive option. The precise mechanisms driving adaptation remain incompletely understood. Conclusions: GLP-1 and GLP-2 analogues show promise in enhancing adaptation and reducing PN dependence. Surgical rehabilitation aims to maximize intestinal absorptive capacity, while transplantation remains a last resort due to high complication risks. Further research is needed to fully elucidate the microbiota's role and harness its potential in managing SBS.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Short Bowel Syndrome/microbiology/physiopathology/therapy
Biomarkers/metabolism
*Adaptation, Physiological
Dysbiosis
*Intestinal Failure/microbiology/therapy/physiopathology
Intestine, Small/microbiology/surgery
Parenteral Nutrition

@article {pmid40647165,
year = {2025},
author = {Sultan, N and Tuck, CJ and Cheng, E and Kellow, NJ and Biesiekierski, JR},
title = {The Impact of Egg Consumption on Gastrointestinal Health: A Systematic Literature Review and Meta-Analysis.},
journal = {Nutrients},
volume = {17},
number = {13},
pages = {},
doi = {10.3390/nu17132059},
pmid = {40647165},
issn = {2072-6643},
support = {APP2025943//National Health and Medical Research Council/ ; GROW005//Australian Eggs/ ; },
mesh = {Humans ; *Eggs ; *Gastrointestinal Microbiome/physiology ; Methylamines/blood ; *Gastrointestinal Tract/microbiology/physiology ; Choline/blood ; C-Reactive Protein/metabolism ; Adult ; Female ; *Diet ; Biomarkers/blood ; Male ; },
abstract = {OBJECTIVE: Eggs are a valuable source of nutrients and bioactive compounds that may influence the gastrointestinal tract by modulating the microbiome, promoting the production of gastrointestinal-related metabolites, and mediating inflammation. Limited human studies have explored the effects of whole egg intake on indices of gastrointestinal health. This systematic literature review aimed to synthesise research investigating the impact of whole egg consumption on markers of gastrointestinal health.

METHODS: Five databases were searched from inception until July 2024. Studies were included if they examined the link between whole egg consumption and gastrointestinal markers, including symptoms, gut microbiome composition, inflammation, colonic fermentation, and egg-derived metabolites such as trimethylamine N-oxide (TMAO) in healthy adults. Two reviewers independently conducted title and abstract and full-text screening, with conflicts resolved by a third reviewer. Similarly, two authors conducted data extraction, which was verified by a third. A risk of bias assessment was conducted using validated tools. Random effects meta-analyses were performed to summarise the effect of egg consumption on TMAO, choline, and C-reactive protein (CRP).

RESULTS: Twenty-two studies were included in a narrative synthesis and ten in the meta-analyses. Nine were randomised controlled trials (RCTs), three were non-randomised intervention trials, eight were cross-sectional, and two were prospective cohort studies. Meta-analyses indicated that egg consumption did not impact plasma TMAO (n = 6, p = 0.22) or CRP (n = 3, p = 0.45) concentrations but did increase plasma choline (n = 5, p < 0.001) in the short term (≤4 weeks). Four studies found correlations between habitual egg consumption and specific gut bacteria, although results varied as egg consumption was both positively and negatively associated with butyrate-producing genera.

CONCLUSIONS: This review found conflicting results regarding egg consumption and most gastrointestinal outcomes, highlighting that future studies are needed to explore links between habitual egg intake and plasma TMAO, microbial diversity, and inflammation (PROSPERO registration: 408532).},
}

Humans
*Eggs
*Gastrointestinal Microbiome/physiology
Methylamines/blood
*Gastrointestinal Tract/microbiology/physiology
Choline/blood
C-Reactive Protein/metabolism
Adult
Female
*Diet
Biomarkers/blood
Male

@article {pmid40647144,
year = {2025},
author = {Sreenesh, B and Varghese, E and Kubatka, P and Samuel, SM and Büsselberg, D},
title = {Prebiotic Potential of Dietary Polyphenols in Colorectal Cancer Immunomodulation.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/foods14132392},
pmid = {40647144},
issn = {2304-8158},
support = {NPRP14S-0311-210033//Qatar National Research Fund/ ; },
abstract = {Molecular crosstalk between the gut microbiome and human diet represent a potential therapeutic avenue requiring further investigation as it can be applied to human health management and treatment. Colon cancer, the third leading cause of cancer mortality, is often linked to the gut microbiome. In vitro and in vivo studies and metagenomic research have revealed alterations in gut microbial flora among diseased individuals. The human diet is connected to these changes in microbial inhabitants related to the pathophysiology underlying colorectal cancer (CRC). Polyphenols are well-studied, naturally occurring plant secondary metabolites recognized for their anti-inflammatory and antioxidant properties. The anticancer activities of these compounds are increasingly reported, offering insights into the administration of these natural molecules for managing various types of cancer and developing novel medications from them. Recent investigations have highlighted the prebiotic-like effects of these compounds on gut microbial dysbiosis and their metabolism concerning colorectal cancer, influencing colon cancer by interfering with multiple signaling pathways. This review will focus on the existing literature regarding the prebiotic potential of dietary polyphenols, and further research in this area would be valuable, as the integration of artificial intelligence (AI) and machine learning (ML) can enable analysis of the connections between unique gut microbiome profiles and other dependent factors such as physiological and genetic variables, paving the way for personalized treatment strategies in gut microbiome-based health management and precision medicine.},
}

@article {pmid40647126,
year = {2025},
author = {Zhou, B and Xing, Z and Wang, Y and Guan, X and Wang, F and Yin, J and Li, Z and Zhao, Q and Hou, H and Sang, X},
title = {Apple Juice Fermented with Lactiplantibacillus plantarum Improves Its Flavor Profile and Probiotic Potential.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/foods14132373},
pmid = {40647126},
issn = {2304-8158},
support = {2024YFD2401904//National Key Research and Development Program Project of China/ ; 2024-MSLH-049//Liaoning Provincial Natural Science Foundation Program Project/ ; HDYJ202201//Dalian Ocean University Doctoral Initiation Project/ ; },
abstract = {Fermented apple juice (FAJ), a nutrient-dense beverage rich in vitamins, offers multiple health benefits, including improved digestion, enhanced fat metabolism, and sustained energy provision with reduced caloric intake. To advance the development of probiotic-enriched flavored and functional juices, this study establishes Lactiplantibacillus plantarum (L. plantarum) as a safe and effective starter culture for apple juice fermentation. The selected strain exhibited minimal biogenic amine synthesis, producing only 30.55 ± 1.2 mg/L of putrescine and 0.59 ± 0.55 mg/L of cadaverine, while histamine and tyramine were undetectable. Furthermore, the strain demonstrated no hemolytic activity and exhibited robust biofilm-forming capacity, reinforcing its suitability for fermentation applications. An electronic nose analysis revealed that L. plantarum significantly enriched the volatile compound profile of FAJ, leading to an improved flavor profile. The strain also displayed excellent growth adaptability in the apple juice matrix, further optimizing fermentation efficiency and sensory quality. Crucially, 16S rRNA sequencing demonstrated that FAJ specifically restructures the gut microbiota in obese individuals, significantly elevating the relative abundance of beneficial genera, including Enterococcus, Parabacteroides, and Bifidobacterium (p < 0.05). Concurrently, FAJ enhanced glycolytic activity, suggesting a potential role in metabolic regulation. Collectively, these findings confirm that L. plantarum-fermented FAJ combines favorable sensory properties and safety with promising anti-obesity effects mediated through gut microbiome modulation and metabolic pathway activation. This study provides a critical scientific foundation for designing next-generation functional fermented beverages with targeted health benefits.},
}

@article {pmid40647113,
year = {2025},
author = {Terpou, A and Dahiya, D and Nigam, PS},
title = {Evolving Dynamics of Fermented Food Microbiota and the Gut Microenvironment: Strategic Pathways to Enhance Human Health.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/foods14132361},
pmid = {40647113},
issn = {2304-8158},
abstract = {The growing interest in health-promoting diets has brought fermented foods into the spotlight due to their unique microbial compositions and bioactive metabolites. Fermented foods and their beneficial microbiota are expected to stimulate the overall industry's expansion over the next few years as their beneficial health effects become established. This narrative review explores the evolving dynamics of fermented food microbiota and their interactions with the gut microenvironment, emphasizing strategic pathways to enhance human health. Fermented foods, both industrially produced and traditionally prepared, serve as carriers of beneficial microorganisms such as lactic acid bacteria, yeasts, and certain fungi that transform food substrates into bioactive compounds including short-chain fatty acids (SCFAs), exopolysaccharides, and bioactive peptides. Simultaneously, their bioactive metabolites are the subject of passionate investigation by the scientific community, uncovering novel beneficial aspects that have not been elucidated until now. These metabolites contribute to improved gut barrier function, modulation of immune responses, and overall metabolic health. Notably, microbial fermentation can reshape the intrinsic properties of food, offering therapeutic potential beyond basic nutrition. The interactions between food-derived microbes and the host gut microbiota suggest a synergistic mechanism influencing gastrointestinal and systemic health outcomes. Nevertheless, there remains a significant gap in the comprehensive evaluation of the existing literature in this specific research area. Further research is needed to standardize fermented food formulations, validate the effects of individual microbial strains, and optimize their application in personalized nutrition and functional food development. Accordingly, this review highlights the association between the microbiota of fermented foods and their metabolites with the gut microenvironment, emphasizing their potential health-promoting properties.},
}

@article {pmid40647075,
year = {2025},
author = {Sun, C and Zhang, Z and Sun, Y and Sun, X and Jin, Y and Zhu, J and Yu, J and Wu, T},
title = {Enteric Delivery of Probiotics: Challenges, Techniques, and Activity Assays.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/foods14132318},
pmid = {40647075},
issn = {2304-8158},
support = {23ZYCGSN00970//Tianjin Science and Technology Plan Project/ ; },
abstract = {Probiotics, as live microbial agents, play a pivotal role in modulating host microbiota balance, enhancing immunity, and improving gastrointestinal health. However, their application is hindered by critical challenges, such as inactivation during processing, storage, and gastrointestinal delivery, as well as low colonization efficiency. This article comprehensively reviews recent advances in probiotic delivery systems, focusing on innovative technologies, including hydrogels, nanocoatings, emulsions, and core-shell microgels. It provides an in-depth analysis of natural polyphenol-based nanocoatings and metal-phenolic network (MPN) single-cell encapsulation strategies for enhancing bacterial survival rates while highlighting the unique potential of microalgae-based bio-carriers in targeted delivery. Research demonstrates that well-designed edible delivery systems can effectively preserve probiotic viability and enable controlled intestinal release, offering novel strategies to reshape a healthy gut microbiome. While these systems show promise in maintaining probiotic activity and gut colonization, challenges remain in safety, scalable production, and clinical translation. Overcoming these barriers is crucial to fully harnessing probiotics for human health.},
}

@article {pmid40647044,
year = {2025},
author = {Park, I and Mannaa, M},
title = {Fermented Foods as Functional Systems: Microbial Communities and Metabolites Influencing Gut Health and Systemic Outcomes.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/foods14132292},
pmid = {40647044},
issn = {2304-8158},
support = {2024//This work was supported by Youngsan University research fund of/ ; },
abstract = {Fermented foods represent an intricate ecosystem that delivers live microbes and numerous metabolites, influencing gut health. In this review, we explore how complex microbial communities and metabolites generated during food fermentation modulate the gut microbiome and affect human health. We discuss fermentation-induced biochemical transformations, including enhanced fiber fermentability; nutrient availability; and the synthesis of bioactive metabolites such as short-chain fatty acids, exopolysaccharides, bacteriocins, and modified polyphenols. We describe the dynamic microbial ecology of fermented foods, influenced by ingredient variations, highlighting its effect on health-related metabolic outcomes. Fermented products when consumed transiently introduce beneficial microbes and bioactive compounds into the gut, thereby boosting microbial diversity, resilience, and barrier function. We review clinical and preclinical studies to substantiate the roles of fermented foods in immune regulation, metabolic homeostasis, cognitive function, and inflammation mitigation. Individual variability in response to fermented foods has been emphasized, underscoring the potential for personalized nutrition strategies informed by advanced omics technologies. By integrating microbial ecology, metabolomics, and clinical evidence, this review positions fermented food intake as a strategic dietary intervention for microbiome modulation and health promotion.},
}

@article {pmid40646988,
year = {2025},
author = {Shi, L and Yang, L and You, J and Wu, W and Xiong, G and Wang, L and Yin, T},
title = {Integrated Microbiome and Metabolomics Insights into Meat Quality Changes in Rice-Field Eel Slices During Refrigeration Storage: Effects of ε-Polylysine, Vitamin C, Epigallocatechin Gallate, and Phloretin.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {13},
pages = {},
doi = {10.3390/foods14132236},
pmid = {40646988},
issn = {2304-8158},
support = {2024BBB079, 2024BBB078//Hubei Provincial Technology Innovation Program Project/ ; CARS-46//China Agriculture Research System/ ; },
abstract = {Rice-field eel (Monopterus albus) slices, an important aquatic product in Southeast Asia, are prone to spoilage and deterioration during cold chain storage. In this study, the effects of a composite preservative (ε-polylysine, Vitamin C (Vc), epigallocatechin gallate (EGCG), and phloretin) on the muscle quality (color, texture, water holding capacity (WHC)) of rice-field eel slices during refrigeration storage at 4 °C for up to 7 days was investigated, and the underlying mechanism was elucidated by the integrated microbiome and metabolomics, in addition to Elisa and Low-Field Nuclear Magnetic Resonance (LF-NMR). After 7 days of storage, the WHC, shear force, and a* decreased by 11.39%, 34.37%, and 49.20% in treated samples, and by 19.18%, 38.38%, and 54.87% in control samples, respectively. The addition of the composite preservative significantly increased Hexokinase, Pyruvate kinase, and Creatine kinase, while it decreased the total viable count (TVC), total volatile basic nitrogen (TVB-N), thiobarbituric acid reactive substance (TBARS), and Lactic acid. Preservative treatment maintained the moisture content of the eel slices during storage and prevented bright red oxymyoglobin from transforming into brown metmyoglobin. Microbiota composition (especially Pseudomonas) and metabolic pathways (including amino acid and its metabolites, nucleotide and its metabolite, and organic acid and its derivatives, etc.) were obviously altered by the preservative treatment. Pseudomonas, tryptophan-aspartic acid (Trp-Asp), D-Glucose 6-phosphate, Succinic Acid, Biliverdin 1, 5-Diaminopentane, and Tyramine, etc., are potential biomarkers for the quality changes of eel slices during refrigeration. These findings provide an in-depth understanding of the improvement of the eel slice quality during refrigeration storage by the composite preservative.},
}

@article {pmid40646874,
year = {2025},
author = {Longshaw, M and Quest, B and Miller, W and Oba, PM and Swanson, OR and Swanson, KS and Miller, K},
title = {The Safety of FeedKind Pet[®] (Methylococcus capsulatus, Bath) as a Cultured Protein Source in the Diet of Adult Dogs and Its Effect on Feed Digestibility, Fecal Microbiome, and Health Status.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131975},
pmid = {40646874},
issn = {2076-2615},
support = {N/A - internal funding//Calysta (Inc)/ ; N/A - internal funding//Calysta (Inc)/ ; },
abstract = {Thirty-two healthy adult dogs (16 males and 16 females) were fed control kibble diets for one month, followed by six months (Weeks 0 to 25) of diets containing either 0, 4, 6, or 8% cultured protein derived from Methylococcus capsulatus (FeedKind Pet[®], FK), then they were fed control diets (0% FK) for a further two months (Weeks 25 to 34). The diets were isonitrogenous, isolipidic, and isocaloric and stage- and age-specific. The dogs were assessed for overall health, weight gain, and body condition score (BCS). Blood samples were collected 1 week prior to randomization, during acclimation, then in Weeks 5, 13, 25, 30, 32, and 34 for hematology, coagulation, and clinical chemistry; urine was collected according to the same time schedule for urinalysis. Feces were assessed for parasite load and presence of occult blood during Weeks 5, 9, 13, 17, 21, and 25. Fecal samples were collected during acclimation and Weeks 25 and 34 for fecal microbiome analysis and in Week 25 for apparent total gastrointestinal tract digestibility (ATTD). All dogs maintained a healthy weight and BCS throughout the study. Hematology parameters were within normal limits at the end of each phase of the study. With the exception of a decrease in serum phosphorus level and in urine pH in all groups at the end of the study, urine and serum chemistry results were within normal limits at the end of each phase. ATTD values for organic matter, protein, and energy exceeded 80%, whilst digestibility values for copper were around 20%. The fecal microbiome was dominated by Firmicutes. Alpha diversity increased during the safety phase before returning to baseline levels during the washout phase. The dominant genera in all groups were Megamonas, Peptoclostridium, Turicibacter, Catenibacterium, Fusobacterium, Romboutsia, and Blautia. The study has shown that the inclusion of cultured protein at up to 8% of the total diet of adult dogs can provide sufficient nutrition and is safe with no long-term effects on a range of health parameters.},
}

@article {pmid40646872,
year = {2025},
author = {Yu, SS and Xiang, JW and Zhang, L and Guo, XH and Wang, Y and Ding, GH and Hu, HL},
title = {Integrated Microbiome-Metabolome Analysis Reveals Intestine-Liver Metabolic Associations in the Moustache Toad.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131973},
pmid = {40646872},
issn = {2076-2615},
support = {2024-HZ12//County-School Cooperation Project in Suichang County, China/ ; N/A//Ecological Discipline Construction Fund of Lishui University, China/ ; },
abstract = {The intestinal microbiota regulates host metabolic homeostasis through production of bioactive microbial metabolites. These microorganisms facilitate digestion, enhance immune function, maintain osmoregulation, and support physiological balance via these bioactive compounds, thereby enhancing environmental adaptation. Our study investigated intestinal microbiota-liver metabolic interactions in Leptobrachium liui using 16S rRNA gene sequencing and non-targeted liquid chromatography-tandem mass spectrometry metabolomics. Key findings include (1) comparable alpha diversity but distinct microbial community structures between the small intestine (SI) and large intestine (LI), with the SI dominated by Enterobacteriaceae (72.14%) and the LI by Chitinophagaceae (55.16%); (2) segment-specific microbe-metabolite correlations, with predominantly positive correlations in the SI and complex patterns in the LI involving fatty acids, amino acids, and energy metabolites; and (3) significant correlations between specific bacterial families (Aeromonadaceae, Enterobacteriaceae, Chitinophagaceae) and hepatic metabolites related to fatty acid metabolism, amino acid synthesis, and energy pathways, indicating potential gut-liver axis associations. These findings provide insights into amphibian intestinal microbiota-hepatic metabolite associations and may inform future studies of host-microbe interactions.},
}

@article {pmid40646853,
year = {2025},
author = {Liu, H and Xiao, L and Liu, Z and Deng, Y and Zhu, J and Yang, C and Liu, Q and Tian, D and Cui, X and Peng, J},
title = {Impacts of Captive Domestication and Geographical Divergence on the Gut Microbiome of Endangered Forest Musk Deer.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131954},
pmid = {40646853},
issn = {2076-2615},
support = {No. 31470570//The People's Republic of China Wildlife Protection Program of the Central Forestry Reform and Development Fund of the State Forestry Administration, and the National Natural Science Foundation of China/ ; },
abstract = {Forest musk deer (Moschus berezovskii Flerov), a critically endangered ruminant species, faces extinction risks, with captive populations further threatened by prevalent digestive and immune disorders. This study utilized comparative metagenomic sequencing to assess intestinal microbiota structure and functional profiles between wild populations in Chongqing and Hunan and captive individuals. Wild populations exhibited a Pseudomonadota-dominated gut microbiota (significantly more abundant than in captive counterparts), enriched with lignin-degrading genera Novosphingobium and Acinetobacter. In contrast, the captive group demonstrated increased abundances of Bacillota/Bacteroidota, alongside abnormal proliferation of Escherichia and Clostridium. Both alpha and beta diversity analyses confirmed significant compositional divergences among the three groups, with wild populations maintaining higher diversity than captive populations. Notably, while substantial disparities in microbial abundance existed between wild populations (attributed to habitat vegetation differences), core microbial diversity and carbohydrate metabolic functions exhibited convergence. Functional analyses marked divergences in metabolic pathways: Captive microbiota showed enrichment in translation and glycan metabolism pathways, whereas wild populations displayed pronounced enrichment in immune regulation and environmental sensing pathways. These findings establish a theoretical foundation for optimizing wild population conservation strategies and developing science-based captive management protocols.},
}

@article {pmid40646851,
year = {2025},
author = {Mrenoshki, S and Temerario, L and Mastrorocco, A and Visci, G and Notario, E and Marzano, M and Martino, NA and Mrenoshki, D and Lacalandra, GM and Pesole, G and Dell'Aquila, ME},
title = {Taxonomic Profile of Cultivable Microbiota from Adult Sheep Follicular Fluid and Its Effects on In Vitro Development of Prepubertal Lamb Oocytes.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131951},
pmid = {40646851},
issn = {2076-2615},
abstract = {The aims of the present study were to analyze the taxonomic profile and to evaluate the functional effects of sheep FF cultivable microbiota on prepubertal lamb oocytes PLOs developmental potential. Ovarian FFs were recovered from slaughtered adult sheep via the aspiration of developing follicles and used for microbiota propagation. Bacterial pellets underwent 16S rRNA gene sequencing and targeted culturomics, whereas cell-free supernatants were used as supplements for the in vitro maturation (IVM) of slaughtered PLOs. For the first time, bacteria presence in adult sheep FF was detected, with the first report of Streptococcus infantarius subsp. infantarius (as a species) and Burkholderia cepacia (as a genus and species) in either animal or human FF. The short- and long-term effects of bacterial metabolites on PLO maturation and embryonic development were demonstrated. As short-term effects, the addition of FF microbiota metabolites did not affect the oocyte nuclear maturation and mitochondria distribution pattern, except in one of the examined supernatants, which reduced all quantitative bioenergetic/oxidative parameters. As long-term effects, one of them reduced the total cleavage rate after in vitro embryo culture (IVC). In conclusion, microbiota/bacteria are present in adult sheep FF and may influence reproductive outcomes in vitro. Future studies may reveal the beneficial in vitro effects using the microbiome from preovulatory follicles.},
}

@article {pmid40646844,
year = {2025},
author = {Kerek, Á and Szabó, Á and Jerzsele, Á},
title = {Amoxicillin Resistance: An In Vivo Study on the Effects of an Approved Formulation on Antibiotic Resistance in Broiler Chickens.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131944},
pmid = {40646844},
issn = {2076-2615},
support = {RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; },
abstract = {Background: Antimicrobial resistance (AMR) is a growing global concern in poultry production, where antibiotic use can disrupt gut microbiota and enrich antimicrobial resistance genes (ARGs). Objectives: This study aimed to assess the in vivo effects of a veterinary-approved amoxicillin formulation on gut microbiome composition and ARG profiles in broiler chickens. Methods: A total of 120 Ross-308 broiler chickens were randomly allocated into 12 experimental groups (n = 10 per group), with three replicates per treatment. Birds received either full-dose (1×), a subtherapeutic quarter-dose (¼×) of amoxicillin, a placebo (starch), or no treatment. Cloacal swabs were collected on days 0, 14, and 28 for shotgun metagenomic sequencing. One-way ANOVA was used to evaluate treatment effects on body weight, with significant differences observed from day 14 onward (p < 0.0001). Results: The ¼× dose caused a more pronounced microbiome shift than the 1× dose, with a marked reduction in Pseudomonadota and increase in Bacillota and Bacteroidota. ARG abundance declined in the ¼× group (from 1386 to 1012). While TEM-type ESBL genes were ubiquitous, CTX-M-1 emerged only after ¼× treatment. Worryingly, 20 types of vancomycin resistance genes were detected across all samples. Plasmid-borne ARGs and mobile genetic elements decreased in the ¼× group. Conclusions: Even subtherapeutic antibiotic exposure significantly reshapes the gut microbiota composition and ARG landscape, highlighting the need for refined risk assessments and microbiome-conscious antimicrobial policies in poultry farming.},
}

@article {pmid40646835,
year = {2025},
author = {Kyrtsoudis, D and Alvanou, MV and Loukovitis, D and Gourdouvelis, D and Bampidis, VA and Chatziplis, D and Mitsopoulos, IK},
title = {Influence of Oregano Essential Oil on the Rumen Microbiome of Organically Reared Alpine Goats: Implications for Methanobacteria Abundance.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131937},
pmid = {40646835},
issn = {2076-2615},
support = {20957//Rural Development Project (RDP) 2014-2020, project code M16ΣΥΝ2-00144, Agricultural European Innovation Partnership (EIP AGRI)/ ; },
abstract = {The present study aimed to evaluate the effects of dietary supplementation with organic oregano (Origanum vulgare) essential oil (OEO) on the rumen microbial population, with a focus on methanogenic archaea, in lactating dairy goats. A total of nine age-matched goats (mean body weight 49 ± 1.8 kg) were assigned to three experimental groups (n = 3 per group) in a completely randomized design. All animals were fed a basal diet consisting of a corn-based concentrate and a forage mix composed of alfalfa hay, wheat straw and corn silage. Group 1 was the control group while Groups 2 and 3 received an OEO supplement at dosages of 1 mL/day and 2 mL/day per animal, respectively, incorporated into the concentrate feed. Rumen fluid samples were collected on days 15, 30 and 45 of the feeding trial and their microbial profile was assessed using NGS analysis. The results demonstrated a reduction in the relative abundance of methanobacteria in both OEO-supplemented groups compared to the control group. Statistical analysis revealed significant differences between feeding groups and days of sampling. These findings suggest that OEO has the potential to modulate the rumen microbiome by reducing methane-producing archaeal populations. In conclusion, dietary supplementation with OEO may serve as a natural strategy to mitigate enteric methane emissions in Alpine dairy goats.},
}

@article {pmid40646827,
year = {2025},
author = {Hu, X and Zhu, S and Chen, Y and Zhang, L and Tan, H and Wu, C and Zhang, X and Deng, X and Li, Y},
title = {Bioaccumulation, Ecotoxicity, and Microbial Responses in Hoplobatrachus rugulosus Tadpoles Following Co-Exposure to Imidacloprid and Microplastics.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131928},
pmid = {40646827},
issn = {2076-2615},
support = {221CXTD1015//Hainan Provincial Natural Science Foundation of China/ ; 42107501//National Natural Science Foundation of China/ ; 1630042025002//Central Public-interest Scientific Institution Basal Research Fund/ ; },
abstract = {Agricultural organic pollutants have been identified as a key factor contributing to amphibian population decline, particularly during early developmental stages when tadpoles are frequently exposed to neonicotinoids (NEOs) and microplastics (MPs). In this study, Hoplobatrachus rugulosus tadpoles were exposed to imidacloprid (IMI: 0.045, 0.45, and 4.5 mg L[-1]) and polyethylene-derived MPs (10 mg L[-1]) from agricultural mulch films, both individually and in combination. We systematically evaluated acute toxicity, bioaccumulation, developmental and oxidative stress responses, and changes in the skin and gut microbiota. The results showed that the 96 h median lethal concentration (LC50) of IMI was 44.8 mg L[-1] in the IMI-only group and was 40.5 mg L[-1] in the IMI + MPs group, indicating the negligible impact of MPs on acute toxicity. However, in the highest co-exposure group (IMI4.5 + MPs), tadpole body length and weight decreased by 14.7% and 22.6%, respectively, alongside marked changes in oxidative stress, whereby catalase (CAT) and superoxide dismutase (SOD) activities were suppressed, while malondialdehyde (MDA) levels increased by 35%, indicating elevated lipid peroxidation. Furthermore, the micronucleus frequency in erythrocytes was significantly elevated, suggesting genotoxic effects. Microbial community analysis revealed significant shifts in the relative abundance of gut and skin microbiota under IMI + MPs exposure, with a notable enrichment of Proteobacteria, Fusarium, Actinomycetota, and Bacteroidota, indicating the disruption of host-microbiome interactions. This study proposes a comprehensive multi-tiered assessment framework encompassing environmental exposure, bioaccumulation, toxicological endpoints, oxidative stress biomarkers, and microbiome shifts. Our findings provide new mechanistic insights and quantitative evidence on the compound threats posed by IMI and MPs to amphibians in aquatic environments.},
}

@article {pmid40646826,
year = {2025},
author = {Rey, AI and Higueras, C and Olmeda, P and Sainz, A and Gálvez, BG and Larrosa, M},
title = {Markers of Gut Health in Small Animals: Focus on Fatty Acids and Amino Acids as Indicators of Intestinal Functionality and Microbiome Activity.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131927},
pmid = {40646826},
issn = {2076-2615},
abstract = {Chronic inflammatory enteropathies (CIEs) in companion animals represent a group of idiopathic, immune-mediated gastrointestinal disorders in which the intestinal epithelium can be altered, affecting intestinal functionality, nutrient absorption, and microbiota composition. This review presents an overview of markers that could be used for the assessment of intestinal health, focusing extensively on functional biomarkers, with particular attention to fatty acids (including short-chain fatty acids, SCFAs) and amino acids. Studies have consistently shown reduced concentrations of SCFAs in companion animals with CIEs compared to healthy groups. These alterations occur with varying intensity depending on the type of enteropathy. Alterations in saturated, monounsaturated, and long-chain polyunsaturated fatty acids have also been reported in blood and feces, particularly in omega-3 and omega-6 derivatives, as well as in the elongase and desaturase indices responsible for endogenous synthesis. In addition, amino acids serve as precursors to key metabolites involved in mucosal immunity, oxidative stress regulation, and microbial homeostasis. In CIEs, alterations in systemic and fecal amino acid profiles have been observed, reflecting both host metabolic adaptation and microbial dysbiosis. Integrating fatty acid and amino acid profiles can help distinguish different types of enteropathies, providing additional discriminatory power for determining response to dietary treatment. Future research should aim to elucidate the causal relationships between metabolic alterations and disease pathogenesis, which could lead to novel dietary interventions targeting metabolic interactions between the microbiota and the host.},
}

@article {pmid40646806,
year = {2025},
author = {Irving, J and Pineau, V and Shultz, S and Ter Woort, F and Julien, F and Lambey, S and van Erck-Westergren, E},
title = {Impact of Low-Starch Dietary Modifications on Faecal Microbiota Composition and Gastric Disease Scores in Performance Horses.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131908},
pmid = {40646806},
issn = {2076-2615},
support = {2625299/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NA//Lambey SAS/ ; },
abstract = {Equine gastric disease (EGD) is a common condition in performance horses (Equus caballus), potentially compromising behaviour, performance, and welfare. EGD is often attributed to high-starch, high-sugar feeds and limited forage. Evidence for diet-induced changes on digestive microbiota is lacking. Nine elite showjumping horses were housed at the same performance yard with standardised diet and management throughout the study. Horses were transitioned from a high-sugar and -starch (31%) feed to a low-starch and -sugar (16.5%) concentrate feed. Gastroscopies, blood, and faecal samples were taken pre- and 12 weeks post-diet change. Squamous and glandular ulceration was blindly graded a posteriori using 0-4 scores and faecal microbiota profiled using 16S rRNA gene amplicon sequencing. Total (t(1,8) = -6.17, p < 0.001; Pre: 4 [0-5], Post: 1 [0-2]), squamous (t(1,8) = -5.32, p < 0.001; Pre: 1 [0-3], Post: 0 [0-1]), and glandular (t(1,8) = -2.53, p = 0.04; Pre: 2.5 [0-4], Post: 0 [0-2]) disease improved following the introduction of a low-starch diet. Diet change did not impact microbiota communities (PERMANOVA: F(1,16) = 1.37, p = 0.15, r[2] = 0.08), but Firmicute to Bacteroidota (F/B) ratio reduced (t(1,8) = -3.13, p = 0.01; Pre: 2.07 ± 0.21 vs. Post: 1.29 ± 0.14). Lower F/B ratios were associated with reduced total EGD scores (ChiSq(1,17) = 3.83, p = 0.05). Low-starch diets did not influence faecal microbiota diversity but aided gastric disease healing and reduced F/B ratios in elite showjumpers during a competition season without medication.},
}

@article {pmid40646733,
year = {2025},
author = {Pettett, L and Ebrahimie, E and Chinkangsadarn, T and Mohammadi Dehcheshmeh, M and Trott, DJ and Bird, PS},
title = {The Oral Microbiome in Queensland Free-Ranging Koalas (Phascolarctos cinereus) and Its Association with Age and Periodontal Disease.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131834},
pmid = {40646733},
issn = {2076-2615},
abstract = {This study was developed to profile the oral microbiome of free-ranging Queensland koalas and its association with age, gingivitis and periodontitis. Using next-generation sequencing of 16S rRNA genes, the microbiota of oral plaque samples from eight koalas across different age groups (joey, juvenile, adult and old) were compared. The findings revealed significant shifts in microbiota composition with age and disease presence. At the phylum level, Proteobacteria were the most dominant phylum, especially in younger koalas. Proteobacteria abundance decreased with age, while Bacteroidetes, Fusobacteria and Actinobacteria increased. At the genus level, Acinetobacter declined with age. Fusobacterium and Porphyromonas became more prominent genera in older koalas and those with periodontal disease. The beneficial genus Lactobacillus was detected only in the joey, suggesting a potential loss of protective microbes with age. Alpha diversity analysis showed high variability within individuals based on age. Alpha diversity was remarkably lower in younger koalas and increased with periodontal disease. Beta diversity suggested distinct microbiota composition differences between younger (joey and juvenile) and older (adult and old) koalas, although statistical significance was limited by sample size. This is the first detailed characterization of the oral microbiome in Queensland's free-ranging koalas and highlights its association with age and oral health status. Findings may contribute to better understanding of oral disease progression in koalas and support conservation and health management efforts.},
}

@article {pmid40646729,
year = {2025},
author = {Lawless, C and Kovacs, K and Mohammadi Dehcheshmeh, M and Ebrahimie, E and Messele, YE and Snowball, M and Trott, DJ and McLelland, DJ},
title = {Higher Dietary Fibre Increases the Faecal Microbiome Diversity of Golden Lion Tamarins (Leontopithecus rosalia).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/ani15131831},
pmid = {40646729},
issn = {2076-2615},
support = {Donation//This research was in part funded by a generous donation to The University of Adelaide by As-sociate Professor Phil Bird./ ; },
abstract = {Gut microbiota influences host energetics, metabolic rate, and overall health. Optimising the diet, such as by increasing dietary fibre, is a key strategy for promoting a healthy microbiome and improving host energy balance. In this study, we compared the faecal microbiome of five zoo-housed golden lion tamarins (Leontopithecus rosalia) before and after a dietary fibre increase using 16S rRNA gene sequencing. Prevotella, the most abundant genus, declined significantly (FDR-corrected p < 0.05) following the introduction of a higher-fibre diet. The dietary change also significantly altered the overall gut microbial composition, including the emergence of Eisenbergiella (FDR-adjusted p < 0.05), a butyrate-producing genus whose relative abundance increased from 0% to 0.005% (FDR-adjusted p < 0.05). Given the role of Eisenbergiella in butyrate synthesis, this shift may enhance host energy metabolism and microbial interactions. Additionally, both alpha and beta diversity increased significantly (p < 0.05) after the dietary fibre intervention. A significant reduction in Desulfobacterota (FDR-adjusted p < 0.05) following dietary fibre enrichment was observed, suggesting a shift away from microbial groups that may be associated with pathogenicity or pro-inflammatory effects. Collectively, these changes represent a positive shift in the microbiome, supporting improved host energetics and metabolic health.},
}

@article {pmid40646691,
year = {2025},
author = {Zhou, D and Wu, C and Li, C and Li, M and Li, Z and Li, J and Zhang, Y and Zhao, H and Wang, Y and Liang, L and Xu, L and Li, Y and Zhong, LL and Feng, S and Tian, GB},
title = {SLAMF7 regulates goblet cell mucus production and negatively impacts gut homeostasis and commensalism.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2527857},
doi = {10.1080/19490976.2025.2527857},
pmid = {40646691},
issn = {1949-0984},
mesh = {Animals ; Homeostasis ; *Goblet Cells/metabolism ; *Gastrointestinal Microbiome ; Mice ; Intestinal Mucosa/microbiology/metabolism ; Macrophages/metabolism/immunology ; *Signaling Lymphocytic Activation Molecule Family/genetics/metabolism ; Mice, Inbred C57BL ; *Mucus/metabolism ; Symbiosis ; Mice, Knockout ; Inflammatory Bowel Diseases/microbiology ; Male ; Akkermansia ; },
abstract = {Crosstalk between the intestinal mucosal barrier and the gut microbiota contributes to maintaining intestinal homeostasis. Accumulating evidence suggests that diverse mechanisms are involved in maintaining intestinal homeostasis. Any disturbance in these pathways can compromise gut homeostasis and trigger chronic inflammatory diseases such as inflammatory bowel disease (IBD). However, how host factors regulate the intestinal mucosal barrier and change the gut microbiome has not been well defined. Here, we discovered that disruption of SLAMF7 protects against intestinal inflammation. SLAMF7 deficiency significantly altered the intestinal microbiota composition, specifically the expansion of the mucus-specific bacterium Akkermansia muciniphila. Moreover, SLAMF7 deficiency resulted in goblet cell generation by increasing the number of M2-like C1q+ macrophages, which may contribute to a thicker mucosal barrier. Mechanistically, SLAMF7 deficiency increased goblet cell generation through C1q+ M2-like macrophage polarization, which partly led to a thicker mucosal barrier. Depletion of SLAMF7 in intestinal macrophages upregulated C1q via activation of the STAT6-MafB pathway. The upregulation of C1q in macrophages resulted in a bias toward the M2 phenotype in response to damage-associated molecular patterns (DAMPs) stimulation. Accordingly, SLAMF7 activation induced a shift in macrophage polarization and reduced mucus secretion, which partially aggravated intestinal inflammation. Conversely, SLAMF7 knockdown mitigated DSS-induced intestinal inflammation to some extent. This work reveals the previously unrecognized functions of SLAMF7 in regulating intestinal inflammation and tissue homeostasis.},
}

Animals
Homeostasis
*Goblet Cells/metabolism
*Gastrointestinal Microbiome
Mice
Intestinal Mucosa/microbiology/metabolism
Macrophages/metabolism/immunology
*Signaling Lymphocytic Activation Molecule Family/genetics/metabolism
Mice, Inbred C57BL
*Mucus/metabolism
Symbiosis
Mice, Knockout
Inflammatory Bowel Diseases/microbiology
Male
Akkermansia

@article {pmid40646653,
year = {2025},
author = {Wu, W and Cheng, J and Hou, Z and Yan, Q and Wang, X and He, J and Zhu, Y and Li, J},
title = {Association between the dietary index for gut microbiota and all-cause/cardiovascular mortality in patients with metabolic dysfunction-associated steatotic liver disease.},
journal = {Diabetology & metabolic syndrome},
volume = {17},
number = {1},
pages = {263},
pmid = {40646653},
issn = {1758-5996},
support = {82270915//the National Natural Science Foundation of China/ ; 202304051001021//Special Fund for Science and Technology Innovation Teams of Shanxi Province/ ; 2022//Shanxi Funding for High Level Overseas Returns/ ; 202103021224425//Basic Research Program of Shanxi/ ; BYJL010//Shanxi Province Higher Education "Billion Project" Science and Technology Guidance Project/ ; },
abstract = {BACKGROUND: Nutrient interactions with the gut microbiome modulate the development of metabolic dysfunction-associated steatotic liver disease (MASLD) and cardiovascular disease. The dietary index for gut microbiota (DI-GM) is an innovative and comprehensive diet index to assess quality for health of gut microbiota.

METHOD: This is a cohort study from the interview date to the date of death or the end of follow-up (December 31, 2019). Involving 13,390 participants in National Health and Nutrition Examination Survey (NHANES), including 3538 with MASLD and 9852 without MASLD. DI-GM was calculated using 14 foods and nutrients with clear positive or negative impacts on gut microbiota, and MASLD was assessed based on liver steatosis and cardiometabolic risk factors, with all-cause and cardiovascular mortality determined through probabilistic matching and death certificate review. Restricted Cubic Spline (RCS) analysis and Cox regression were palyed for the DI-GM-mortality correlation. Subgroup analyses to identify the interactive factors that influence their relationship in MASLD. Six sensitivity analyses reinforced findings.

RESULTS: MASLD participants exhibited lower DI-GM levels, which were statistically associated with higher mortality. Each DI-GM unit increase in MASLD was associated with a 13% lower all-cause mortality (HR = 0.87, 95% CI 0.78-0.98) and a 19.5% lower cardiovascular mortality (HR = 0.805, 95% CI 0.690-0.938). In advanced fibrosis MASLD, this increase was linked to a 20% lower cardiovascular mortality risk (HR = 0.800, 95% CI 0.691-0.927). Age and prediabetes significantly modified DI-GM's effect on mortality risk.

CONCLUSIONS: The study revealed a significant inverse correlation between the DI-GM and all-cause/cardiovascular mortality in patients with MASLD, which provide dietary suggestions and guidance for MASLD patients in preventing early mortality. However, limitations such as the cross-sectional design, potential residual confounding, and population-specific generalizability should be considered when interpreting these findings.},
}

@article {pmid40646642,
year = {2025},
author = {Peng, Q and Sun, S and Ma, J and Chen, S and Gao, L and Du, X and Liu, X and Zhu, F and Peng, W and Liu, Y and Su, P and Cernava, T and Zhang, D},
title = {The effect of developmental stages on microbiome assembly in the phyllosphere and rhizosphere of rice grown in urban area soil.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {86},
pmid = {40646642},
issn = {2524-6372},
support = {32302316//Natural Science Foundation of China/ ; 32302316//Natural Science Foundation of China/ ; 32302316//Natural Science Foundation of China/ ; 2023YFD1400200//National Key R&D Program of China/ ; },
abstract = {BACKGROUND: The plant microbiome can support plant health and fitness in the face of biotic and abiotic stress. Research has mostly focused on plant growth in natural and agricultural soils. However, as urban areas continue to expand and soils change in the Anthropocene, microbiome assembly during development of plants grown in urban area soil remains largely elusive. Here, we examined the effect of developmental stages on the phyllosphere and rhizosphere microbiomes of rice grown in soil from an urban area during the vegetative growth stages.

RESULTS: We found that the microbial alpha and beta diversity, networks, and functions of the phyllosphere and rhizosphere microbiomes significantly differed among rice seedling, tillering, and elongation stages. Notably, we observed that bacteria assigned to potential animal parasites or symbionts not only exhibited significantly higher relative abundances in the phyllosphere compared to the rhizosphere but are also influenced by the developmental stages. Plants grown in the urban area soil had a higher relative abundance of Bacteroidales and enriched bacteria assigned to potential animal parasites or symbionts in the phyllosphere in contrast to plants grown in field. Some of these bacteria were shown to significantly influence the assembly of the phyllosphere microbiome and to prevalently engage in negative interactions with other microbes.

CONCLUSION: Our study provides new insights into developmental stage-resolved microbiome assembly of plants grown in urban areas. The insights could help in the development of strategies for promoting 'One Health' by highlighting the role of plants as alternative host for bacterial groups that are prevalently associated with animals.},
}

@article {pmid40646631,
year = {2025},
author = {Wang, N and Ping, L and Mei, X and Zhang, Y and Zhang, Y and Yang, X and Guo, Y and Gao, Y and Xu, Y and Shen, Q and Yang, T and Wei, Z},
title = {Succinic acid reduces tomato bacterial wilt disease by recruiting Sphingomonas sp.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {85},
pmid = {40646631},
issn = {2524-6372},
support = {2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; 2022YFD1500202//the National Key Research and Development Program of China/ ; GuiKe AA24010003//Guangxi Science and Technology Program/ ; },
abstract = {BACKGROUND: Root exudates are key mediators in maintaining plant health by mediating interactions with the rhizosphere microbiome. Plants release specific exudates to defend against pathogens, either directly by inhibiting pathogen growth or indirectly through alterations in the microbial community. However, the mechanisms by which root exudates influence the rhizosphere microbiome to enhance plant resistance remain poorly understood. In this study, we evaluated the effects of 23 root exudates on the growth of the pathogen Ralstonia solanacearum and tomato bacterial wilt.

RESULTS: Seventeen of the exudates reduced the disease index, with most having neutral or even promotive effects on R. solanacearum growth. Notably, succinic acid (SA) completely suppressed bacterial wilt without directly affecting the pathogen or tomato plants in the absence of the rhizosphere microbiome. We further explored the impact of SA on the rhizosphere bacterial community in both tomato rhizosphere and bulk soil. Only the bacterial community in the rhizosphere responded significantly to SA addition, with indicator species and network analyses identifying Sphingomonas sp. WX113 as the key taxa associated with this response. A subsequent greenhouse experiment showed that co-applying Sphingomonas sp. WX113 with SA achieved 100% biocontrol efficiency, outperforming either treatment alone. In vitro assays further demonstrated that SA enhanced the antagonistic activity of Sphingomonas sp. WX113 against R. solanacearum.

CONCLUSIONS: Our findings emphasize the host-mediated role of root exudates, such as succinic acid, in selectively promoting beneficial Sphingomonas sp., thereby enhancing plant resistance to bacterial wilt. These results offer new perspectives on the combination of beneficial microbes and their matching compounds for soil-borne diseases management.},
}

@article {pmid40646629,
year = {2025},
author = {Koutromanos, I and Legaki, E and Dovrolis, N and Vassilopoulos, E and Stem, A and Vasiliou, V and Tzavellas, E and Gazouli, M},
title = {Integrating gut microbiome and neuroplasticity genomics in alcohol use disorder therapy.},
journal = {Human genomics},
volume = {19},
number = {1},
pages = {78},
pmid = {40646629},
issn = {1479-7364},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Alcoholism/genetics/therapy/microbiology ; *Neuronal Plasticity/genetics ; Male ; Female ; Adult ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; *Genomics/methods ; Prospective Studies ; Dysbiosis/genetics/microbiology ; },
abstract = {BACKGROUND: Alcohol Use Disorder (AUD) is a chronic neuropsychiatric condition with substantial public health impact. The interplay between gut microbiota and neuroplasticity-related genes presents a novel approach to understand AUD pathophysiology and treatment response. While microbial dysbiosis has been implicated in AUD, its correlation with gene expression changes in neuroplasticity pathways remains unexplored. This study investigates microbiome composition, microbial metabolic pathways, and their correlation with neuroplasticity-related genes in AUD patients undergoing treatment.

METHODS: We conducted a prospective observational study integrating gut microbiome 16S rRNA sequencing and host neuroplasticity-related gene expression profiling in AUD patients undergoing treatment which combines psychotherapeutic intervention along with oral diazepam administration followed by Pythagorean Self Awareness Intervention. Patients were classified as responders or non-responders, and microbial composition, functional pathways, and host-microbiota interactions were analyzed using multi-omic correlation frameworks.

RESULTS: Responders exhibited a microbiome enriched in short-chain fatty acid (SCFA)-producing bacteria (e.g., Lachnospiraceae), linked to gut barrier integrity and neurotransmitter synthesis. In contrast, non-responders demonstrated enrichment of inflammation-associated taxa (Succinivibrionaceae) and oxidative stress-related metabolic pathways. Correlation analysis revealed microbiome-mediated modulation of neuroplasticity-related genes measured from peripheral blood, including BDNF, GRIA1, CAMK2G, and EGR family genes, suggesting a gut-brain-genomic axis in AUD treatment response.

CONCLUSIONS: This study highlights the role of gut microbiota as a modulator of neuroplasticity-related gene expression in AUD patients. Integrating microbiome and host genomic signatures could improve biomarker-based prediction of treatment response and inform precision medicine approaches for AUD. Future studies should expand these findings by incorporating multi-omic approaches, including epigenomics and exposomics, to refine microbiome-targeted interventions for addiction therapy.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Alcoholism/genetics/therapy/microbiology
*Neuronal Plasticity/genetics
Male
Female
Adult
Middle Aged
RNA, Ribosomal, 16S/genetics
*Genomics/methods
Prospective Studies
Dysbiosis/genetics/microbiology

@article {pmid40646012,
year = {2025},
author = {Soler, Z and Serrano-Gómez, G and Pons-Tarín, M and Vega-Abellaneda, S and Xie, Z and Manjón, I and Cognard, C and Varela, E and Yañez, F and Noguera-Segura, A and Roca-Bosch, M and Manichanh, C},
title = {A contributory citizen science project reveals the impact of dietary keys to microbiome health in Spain.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {131},
pmid = {40646012},
issn = {2055-5008},
support = {FI21/00262//Instituto de Salud Carlos III/ ; FI21/00262//Instituto de Salud Carlos III/ ; SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; 72190278//Agencia Nacional de Investigación y Desarrollo/ ; PI20/00130//Instituto de Salud Carlos III (ISCIII), Spain/ ; },
mesh = {Humans ; Spain/epidemiology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome ; *Diet ; Middle Aged ; *Inflammatory Bowel Diseases/microbiology ; Dysbiosis/microbiology ; Young Adult ; Vegetables ; Fruit ; Aged ; *Bacteria/classification/genetics/isolation & purification ; Adolescent ; Feces/microbiology ; },
abstract = {Low consumption of whole grains, fruits, and vegetables has been identified as dietary risks for non-communicable diseases such as inflammatory bowel diseases (IBDs). We explore how individual and lifestyle factors influence these risks by shaping gut microbiome composition. 1001 healthy participants from all Spanish regions provided personal and dietary data at baseline, six, and twelve months, yielding 2475 responses. Gut microbiome data were analyzed for 500 healthy participants and 321 IBD patients. Our findings reveal that adherence to national dietary guidelines-characterized by diets rich in nuts, seeds, fruits, and vegetables-was associated with greater microbial diversity and reduced IBD-related dysbiosis. Finally, we observed variations in dietary patterns and microbiome diversity and composition across age groups, genders, regions, seasons, and transit time. This study is among the first to uncover dietary intake associated with IBD-related dysbiosis and to propose an interactive website for participants (https://manichanh.vhir.org/POP/en).},
}

Humans
Spain/epidemiology
Male
Female
Adult
*Gastrointestinal Microbiome
*Diet
Middle Aged
*Inflammatory Bowel Diseases/microbiology
Dysbiosis/microbiology
Young Adult
Vegetables
Fruit
Aged
*Bacteria/classification/genetics/isolation & purification
Adolescent
Feces/microbiology

@article {pmid40645765,
year = {2025},
author = {Fusco, W and Adolph, T and Cammarota, G and Gasbarrini, A and Ianiro, G and Tilg, H},
title = {Gut microbiota and atherosclerosis.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-335610},
pmid = {40645765},
issn = {1468-3288},
abstract = {Atherosclerosis reflects a chronic inflammatory process of arteries. The origin of chronic vascular inflammation has been associated over a long time primarily with lipid disorders, but evidence from the past years has suggested that lipid-independent pathways are also involved. Recent research has demonstrated that the gastrointestinal microbiota has an impact on the development of atherosclerosis. Many clinical studies have revealed that there exist altered gut microbiota and increased intestinal abundance of bacteria from the oral cavity in atherosclerosis-related disorders such as cardiovascular disease or stroke, while several studies have demonstrated insights into underlying mechanisms. Various microbial-derived metabolites, such as the pathogen-associated molecular pattern endotoxin, trimethylamine N-oxide or imidazole propionate, contribute to atherosclerosis, while other bacterial metabolites, such as some tryptophan derivatives, might be protective. Furthermore, gut microbiota and lipid pathways are highly interactive, and the gut microbiota affects lipid absorption and storage, and the gut microbiota also contributes to vascular ageing. Interference with the gut microbiota by prebiotics, probiotics and antibiotics has demonstrated beneficial effects on atherosclerosis mainly in preclinical models. Overall, the gut microbiota has appeared as an important rheostat for vascular inflammation in atherosclerosis, which is controlled by host-microbe interactions that may be therapeutically exploited in the future.},
}

@article {pmid40645672,
year = {2025},
author = {Li, H and Leaman, AA and Zheng, Q},
title = {The cancer microbiome.},
journal = {Advances in clinical chemistry},
volume = {127},
number = {},
pages = {1-61},
doi = {10.1016/bs.acc.2025.04.001},
pmid = {40645672},
issn = {2162-9471},
mesh = {Humans ; *Neoplasms/microbiology ; *Microbiota ; Tumor Microenvironment ; Animals ; },
abstract = {The cancer microbiome is an emerging concept that is referred to as the microorganism communities associated with cancer. There has been controversy in terms of the bona fide functions of the microbiome in carcinogenesis and cancer development, since the microorganisms were first observed within tumor tissues. Recently, there has been growing evidence showing that the microbiome indeed plays a role in cancer initiation, development, diagnosis, and treatment through diverse mechanisms and interactions between host cells and microbes. Rather than contaminants or artifacts, the cancer microbiome has been proven to be alive in the tumor microenvironment and possess significantly differential physiological and morphological properties compared to the corresponding environmental microorganisms. However, due to the low abundance of microbes within cancer tissues (especially the intratumoral microbiota) and lack of efficient analytical tools (e.g., sensitive antibodies, sensors, and probes), there are still a number of challenges and question marks in this fast-growing field. In this chapter, we made a systematic summary of the cancer microbiome, specifically focusing on its discovery and the recent research advances with respect to the studies on its functions and corresponding technology development.},
}

Humans
*Neoplasms/microbiology
*Microbiota
Tumor Microenvironment
Animals

@article {pmid40645376,
year = {2025},
author = {Zemko, P and Canevelli, M and Pavanello, S and Cesari, M and Bonsembiante, F and Campisi, M and Cannella, L and Buscarnera, S and Zotti, A and Banzato, T},
title = {Markers of biological age in dogs.},
journal = {Ageing research reviews},
volume = {111},
number = {},
pages = {102814},
doi = {10.1016/j.arr.2025.102814},
pmid = {40645376},
issn = {1872-9649},
abstract = {As human life expectancy continues to rise, ageing and age-related diseases have become critical societal challenges, driving extensive research across genetics, molecular biology, biochemistry, and behavioral sciences. In this context, domestic dogs (Canis lupus familiaris) offer a unique model for ageing research due to their shared environmental exposures with humans, diverse genetic profiles, and relatively short lifespans. This review aims to identify potential biomarkers of ageing in dogs, facilitating a deeper understanding of age-related mechanisms and supporting the evaluation of interventions designed to promote healthy ageing. We present a research of peer-reviewed literature on age-related variations of various parameters across multiple biological systems, including epigenetic, telomere, immune, metabolic, and cognitive markers in dogs. Our findings highlight several robust biomarkers, such as DNA methylation-based epigenetic clocks, telomere attrition, CD4+/CD8+ T-cell ratio, hematological markers (e.g., globulin levels), and cognitive function scores. These biomarkers demonstrate strong parallels with human ageing processes, particularly concerning genomic and epigenetic alterations. However, challenges remain, including breed-specific variability, body size differences, and inconsistent evidence regarding inflammageing markers, such as pro-inflammatory cytokines. Despite these limitations, indicators of chronic inflammation (e.g., anemia of chronic disease and elevated globulins) are evident in older dogs. Future research directions include the standardization of biomarker protocols for dogs, the development of longitudinal studies to track dynamic age-related changes, and further exploration of emerging biomarkers, such as those related to microbiome composition and oxidative stress.},
}

@article {pmid40645338,
year = {2025},
author = {Gudi, CR and Wannemuehler, MJ and Mansell, TJ},
title = {Gut-brain-immune interactions: exploring probiotics as a drug delivery platform for neurological disease.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115650},
doi = {10.1016/j.addr.2025.115650},
pmid = {40645338},
issn = {1872-8294},
abstract = {The gut-brain-immune (GBI) axis, connecting gut microbes, neural tissue, and the cells of the immune system, plays a critical role in human health, particularly in relation to neurological diseases. Research in this field over the last few decades shows that disruptions in the microbiome have been linked to chronic inflammation, which may contribute to neurological conditions, including Parkinson's disease, Alzheimer's disease, and other mental health disorders. As we gain a greater understanding of the links between these systems, novel therapeutic strategies are being explored to treat disease by modulation of the GBI axis. One of the most promising approaches is the use of live biotherapeutics, such as engineered probiotics, as next-generation drug delivery systems. These live microorganisms can be designed to deliver specific therapeutic compounds to the gut and brain in order to modulate immune responses and reduce inflammation at the source. Probiotics and live biotherapeutics can offer a targeted approach to treating neurological diseases by influencing both the microbiome and immune system. In this review, we outline the research and mechanisms that have been implicated in GBI interactions and highlight the potential of these innovative therapies in treating neurological disorders, emphasizing their role in improving precision medicine through targeted, microbiome-based interventions.},
}

@article {pmid40645337,
year = {2025},
author = {du Toit-Thompson, T and Leck, L and Gillson, J and Pavlakis, N and Gill, AJ and Samra, JS and Mittal, A and Sahni, S},
title = {Overcoming therapy resistance in pancreatic cancer: challenges and emerging strategies.},
journal = {Advanced drug delivery reviews},
volume = {},
number = {},
pages = {115647},
doi = {10.1016/j.addr.2025.115647},
pmid = {40645337},
issn = {1872-8294},
abstract = {Pancreatic cancer (PC) is one of the deadliest types of cancer, with a 5-year survival rate of ∼12.5 %. It is expected to become the second leading cause of cancer-related deaths by 2030. Despite recent advances in treatment options by advent of various targeted and immunotherapies, their benefits have not been actualized for PC patients and chemotherapy remains the mainstay systemic therapeutic option for these patients. However, the majority of PC tumours have a highly chemo-resistant phenotype, leading to therapeutic failure. This review provides a comprehensive overview of the established mechanisms related to chemoresistance in PC and provides insight into emerging theories, including the potential role of the microbiome in modulating therapeutic responsiveness. It further discusses potential opportunities to explore to overcome this critical clinical problem.},
}

@article {pmid40645301,
year = {2025},
author = {Melamed, E and Rungratanawanich, W and Liangpunsakul, S and Maki, KA and McCullough, RL and Llorente, C},
title = {Alcohol, Aging, and the Gut Microbiome: Intersections of Immunity, Barrier Dysfunction, and Disease.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2025.07.001},
pmid = {40645301},
issn = {1873-6823},
abstract = {Alcohol consumption exerts complex, dose- and context-dependent effects on human health, particularly by influencing the gut microbiome, intestinal barrier integrity, immune regulation, and aging processes. Genetic variation and advancing age are two major, and often interacting, factors that modify the risk of alcohol-related diseases. Among genetic factors, the prevalent aldehyde dehydrogenase 2 polymorphism (ALDH2*2) compromises acetaldehyde clearance, driving toxic metabolite accumulation, oxidative stress, and increased intestinal permeability that disrupts gut microbial communities, even at low levels of alcohol consumption. Heavy and chronic alcohol use further disrupts gut microbial communities, erodes mucosal integrity, and drives systemic inflammation, contributing to alcohol-associated liver disease (ALD), neuroinflammation, and multi-organ injury. Aging independently worsens these effects by promoting chronic low-grade inflammation and impaired immune responses, heightening susceptibility to alcohol-induced pathology. In specific contexts, such as certain autoimmune diseases, low to moderate alcohol intake may exert immunomodulatory effects and influence the gut microbiome, potentially contributing to reduced inflammation and alterations in microbial composition. This review synthesizes current mechanistic insights into how alcohol, host genetics, the gut microbiome, immune regulatory pathways, and aging intersect to influence disease risk. As global populations age and the burden of alcohol-related health issues rises, there is an urgent need for integrated, systems-level approaches. Future research should prioritize precision-based, gut-targeted strategies aimed at restoring microbial balance, maintaining intestinal barrier integrity, and mitigating alcohol-related harm across the lifespan.},
}

@article {pmid40645237,
year = {2025},
author = {Hofford, RS and Sens, JP and Shipman, AL and Kimble, VM and Coric, C and Meckel, KR and Kiraly, DD},
title = {Brief exposure to oral antibiotics has age-dependent effects on morphine reward and gene expression in the medial prefrontal cortex of adolescent and adult mice.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.07.005},
pmid = {40645237},
issn = {1090-2139},
abstract = {Adolescence is a critical period for the initiation of problematic drug use, which significantly increases the risk of developing substance use disorders later in life. This heightened vulnerability is partly attributed to the immaturity of the prefrontal cortex, a brain region both essential for decision-making and implicated in drug reward. During adolescence, peripheral systems, such as the gut microbiome, also undergo substantial changes. Emerging evidence suggests that disruptions to the gut microbiome can influence gene expression and drug reward behaviors in rodent models. In this study, we investigated the effects of oral antibiotics on morphine reward and prefrontal cortical gene expression in adolescent and adult mice. Using oral antibiotics to transiently disrupt the microbiome, we found that short-term antibiotic exposure reduced morphine place preference specifically in adolescent mice. In a separate cohort, we observed that antibiotic treatment altered the transcriptomic response to morphine in the medial prefrontal cortex across all age groups. Notably, the transcriptomic changes induced by antibiotics and morphine were age-specific, with distinct gene expression patterns observed in adolescents compared to adults. These findings establish a foundation for future research into the role of the gut microbiome in opioid reward and highlight potential gene pathways underlying age-dependent differences in opioid sensitivity.},
}

@article {pmid40645132,
year = {2025},
author = {Mckirdy, S and Koutsos, A and Nichols, B and Anderson, M and Dhami, S and Chowdhury, CR and Mascellani Bergo, A and Havlik, J and Gerasimidis, K},
title = {Micronutrient supplementation influences the composition and diet-originating function of the gut microbiome in healthy adults.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {51},
number = {},
pages = {293-303},
doi = {10.1016/j.clnu.2025.06.020},
pmid = {40645132},
issn = {1532-1983},
abstract = {BACKGROUND & AIMS: Studies in-vitro and in animals propose that vitamins and minerals can alter the human gut microbiome. Human trials replicating these findings are scarce or used micronutrient supplementation in supraphysiological doses. We explored the effect of multivitamin/multimineral (MVMM) supplementation on the gut microbiome, and how participant's background diet can modify this effect.

METHODS: In a randomised, controlled, cross-over study, 28 healthy adults (68 % female, mean [SD], 33 [13] years]) received either a MVMM supplement containing dosages close to the UK dietary recommendations for 23 micronutrients (intervention period) or no supplement (control period), for 10-days, separated by a 15-day washout period. Participants' diet was recorded and replicated between the two periods. Faecal microbiota composition was profiled using 16S rRNA sequencing, metabolome with [1]H NMR, short chain fatty acids (SCFAs) with gas chromatography, and sulphide concentration with colorimetry. Associations between background diet and microbiome responses during MVMM supplementation were explored using machine learning.

RESULTS: Following MVMM supplementation, the absolute abundance of Lachnoclostridium and UCG_005 taxa were lower, while the concentrations of total SCFAs, specifically propionate and butyrate, and total sulphide were higher than the control period. Compared to baseline, MVMM supplementation decreased the absolute abundance of Desulfobacterota, Actinobacteriota, Bifidobacteriaceae, Erysipelatoclostridiaceae and Veillonellaceae, and increased the concentration of propionate. Background dietary intakes of saturated fat and total carbohydrates related with the MVMM-induced effect of decreasing Desulfobacterota. Likewise, the intakes of vitamins B2, B12, and E, along with iron, related with the effect of MVMM on decreasing Erysipelatoclostridiaceae. No changes were observed within the control period.

CONCLUSION: In healthy adults, short-term MVMM supplementation influences the gut microbiota composition and diet-originating microbial metabolites and potentially host health.

REGISTRATION: This trial was registered at clinicaltrials.gov as NCT05371704.},
}

@article {pmid40645053,
year = {2025},
author = {Zhao, M and Xiong, S and Du, T and Xu, X and Li, H and Zhang, L and Xu, Y and Wei, T and Xiong, T and Xie, M},
title = {Elucidating microbial succession dynamics and flavor metabolite formation in korean style spicy cabbage fermentation: Integration of flavoromics, amplicon sequencing, and metagenomics.},
journal = {Food chemistry},
volume = {492},
number = {Pt 2},
pages = {145464},
doi = {10.1016/j.foodchem.2025.145464},
pmid = {40645053},
issn = {1873-7072},
abstract = {Korean style spicy cabbage (KSC) is a prominent fermented vegetable consumed globally. Nevertheless, microbial succession dynamics, interactions, and flavor-core microbiome correlations lack comprehensive understanding. Metabolomics revealed eight taste-active compounds and sixteen aroma-active compounds as key flavor determinants throughout fermentation. Amplicon sequencing elucidated dynamic shifts in bacterial and fungal community structures during KSC fermentation, with subsequent analyses identifying free sugars as the primary drivers of microbial succession. Spearman correlation analysis further identified Psychrobacter, Latilactobacillus, Weissella, Pseudomonas, Rothia, Candida, Vishniacozyma, Kazachstania, and Cutaneotrichosporon as core microbes driving the formation of characteristic flavor metabolites in KSC. Through metagenomic analysis, we reconstructed the metabolic network underlying the formation of characteristic flavor compounds. Our study elucidates microbial diversity dynamics and flavor metabolite formation during KSC fermentation, offering actionable insights for identifying critical fermentation phases and optimizing inoculated starter culture.},
}

@article {pmid40645046,
year = {2025},
author = {Liu, Z and Forde, CG and Stieger, M and Rubert, J},
title = {Chewing behavior and bolus particle size of rice influence carbohydrate digestion and gut microbiome metabolism in vitro.},
journal = {Food chemistry},
volume = {492},
number = {Pt 2},
pages = {145404},
doi = {10.1016/j.foodchem.2025.145404},
pmid = {40645046},
issn = {1873-7072},
abstract = {The size of ingested bolus particles and their surface area affect how accessible the substrates are to digestive enzymes and the gut microbiota. This study aimed to investigate the impact of oral breakdown of rice on the human gut microbiota in vitro. Three rice varieties with different fiber contents were chewed in vivo, then subjected to in vitro digestion and fecal batch cultures. Increasing the number of chews per bite from 5 to 40 led to higher structural breakdown and more extensive early starch hydrolysis, resulting in up to 14 % increase in the degree of starch hydrolysis during in vitro digestion, and 26-47 % smaller rice bolus particles after in vitro digestion. Higher bile salt hydrolase activity and total short-chain fatty acid levels (5-13 %) were found in less chewed rice. Untargeted lipidomics highlighted that the number of chews influenced numerous metabolites beyond SCFA.},
}

@article {pmid40645018,
year = {2025},
author = {Huang, A and Lin, B and Hu, T and Lan, J},
title = {Unraveling functional dyspepsia: Pathophysiological mechanisms, microbiota interactions, and emerging therapeutic strategies.},
journal = {Pathology, research and practice},
volume = {272},
number = {},
pages = {156118},
doi = {10.1016/j.prp.2025.156118},
pmid = {40645018},
issn = {1618-0631},
abstract = {This comprehensive review elucidates the latest advancements in understanding functional dyspepsia (FD). The article delves into the pathophysiological mechanisms of FD, including gastrointestinal motility disorders, visceral hypersensitivity, impaired gastric accommodation, compromised intestinal barrier function, and microbiota dysbiosis. It particularly emphasizes the crucial role of gut microbiota in FD pathogenesis, providing a detailed analysis of how microbiome-host interactions influence intestinal barrier function, immune regulation, and the brain-gut axis. The review also synthesizes current treatment strategies for FD, encompassing dietary modifications, pharmacological interventions, behavioral therapies, and Traditional Chinese Medicine approaches. This review uniquely integrates microbiome-barrier-immune-brain-gut axis interactions and combines Western-TCM therapeutic paradigms, providing a comprehensive framework for personalized FD management.},
}

@article {pmid40644733,
year = {2025},
author = {Zhou, Y and Wen, C and Zhang, Q and Gu, Z and Lian, L and Xue, K and Xu, T and Lin, Z and Wang, W and Zhu, H},
title = {Characteristics of oral microbiomics with soldiers in the army before and after high-intensity physical training.},
journal = {Archives of oral biology},
volume = {178},
number = {},
pages = {106347},
doi = {10.1016/j.archoralbio.2025.106347},
pmid = {40644733},
issn = {1879-1506},
abstract = {OBJECTIVES: This paper aims to investigate the changes in soldiers' oral microbiome and metabolic levels after a month of high-intensity training.

DESIGN: We collected saliva samples from 10 soldiers with good oral health and hygiene habits before and after training. Subsequently, DNA extraction, metagenomic sequencing, and phylogenetic analysis of the oral microbiome were conducted.

RESULTS: 7733 bacterial species from 113 known bacterial phyla and 2017 genera detected in 20 samples. The diversity and richness of saliva microorganisms before and after training were similar (p > 0.05), while beta diversity analysis showed structural differences in microbiota at the phylum and genus levels (p < 0.05). The relative abundance of 27 genera such as Proteobacteria, Neisseria, Morococcus cerebrosus and Eikenella in soldiers' saliva significantly increased after high-intensity training (p < 0.05). Conversely, the relative abundance of 20 genera such as Bacteroidota, Veillonella, Parvimonas micra, Prevotella oris, Peptostreptococcus, and Treponema decreased (p < 0.05). At the metabolic level, training resulted in a relative increase (p < 0.05) in various pathways, including amino acid metabolism, sulfur metabolism, glutathione metabolism, and Tyrosine metabolism. By comparison, after training, carbohydrate metabolism, glycan biosynthesis, metabolism, the HIF-1 signaling pathway, and necroptosis revealed a relative decrease (p < 0.05).

CONCLUSIONS: This paper reveals the changes in the saliva microbiome of soldiers after one month of high-intensity training, in which the relative abundance of biomarkers of periodontal disease, caries, and other oral diseases represented by peptostreptococcus, prevotella oris, treponema, etc., are significantly reduced, suggesting that long-term high-intensity training may have a positive effect on oral health.},
}

@article {pmid40644647,
year = {2025},
author = {Barragan-Carrillo, R and Zengin, ZB and Pal, SK},
title = {Microbiome Modulation for the Treatment of Solid Neoplasms.},
journal = {Journal of clinical oncology : official journal of the American Society of Clinical Oncology},
volume = {},
number = {},
pages = {JCO2500374},
doi = {10.1200/JCO-25-00374},
pmid = {40644647},
issn = {1527-7755},
abstract = {The interplay between the human gut microbiome and the immune system has sparked growing interest in microbiome modulation as a therapeutic strategy in oncology. Preclinical studies have identified specific bacterial species linked to improved responses to immune checkpoint inhibitors (ICIs), leading to clinical investigations in melanoma, renal cell carcinoma (RCC), and non-small cell lung cancer (NSCLC). The stool bacterial abundance of Ruminococcaceae, Akkermansia, and Bifidobacterium correlates with favorable clinical outcomes, whereas the disruption of the gut microbiome through antibiotics before or during ICI initiation is associated with higher rates of primary resistance and shorter survival. Biomarkers such as TOPOSCORE have been developed to better predict ICI benefits and estimate dysbiosis and treatment responses. Several microbiome-modulating strategies have shown potential in patients receiving treatment with ICIs-for instance, high dietary fiber intake may be linked to improved outcomes. As a separate strategy, certain probiotics appear to enhance clinical activity in early trials when incorporated into ICI-based regimens. Finally, fecal microbiota transplantation has shown safety and efficacy in ICI-refractory melanoma and yielded encouraging results in treatment-naïve patients with melanoma, NSCLC, and RCC. Although several compelling signals have been observed to date with microbiome manipulation, the field is lacking large, definitive randomized trials-these are indeed a prerequisite for any of the highlighted strategies to become a standard of care.},
}

@article {pmid40644597,
year = {2025},
author = {Hamza, YP and Kacem, MABH and Al Molawi, NH and Yassine, HM and AlKhatib, HAM and Benslimane, F and Al-Remaihi, HIKB and Awni El Kahlout, R and Ahmed El Kahlout, BI and Al Khalili, H and Al Khalili, MA and Doiphode, SH and Elmagboul, EBI and Akhter, J and Al Kuwari, EAE and Coyle, PV},
title = {Patients in hospital with confirmed bacterial airway infection are significantly more likely to have a respiratory virus co-infection.},
journal = {Journal of medical microbiology},
volume = {74},
number = {7},
pages = {},
doi = {10.1099/jmm.0.001996},
pmid = {40644597},
issn = {1473-5644},
mesh = {Humans ; *Coinfection/microbiology/virology/epidemiology ; Male ; *Respiratory Tract Infections/microbiology/virology ; Female ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Aged ; Bacteria/genetics/isolation & purification/classification ; *Virus Diseases/virology/microbiology/epidemiology/complications ; Adult ; Bronchoalveolar Lavage Fluid/microbiology/virology ; *Bacterial Infections/microbiology ; Real-Time Polymerase Chain Reaction ; Aged, 80 and over ; },
abstract = {Introduction. Respiratory viruses are seen as cofactors in bacterial airway infection, often leading to bacterial pneumonia. This study addressed their role in hospitalized patients with bacterial infection confirmed by culture, 16S real-time PCR (16S RT-PCR) and 16S rRNA sequencing (16S Sequencing). The potential for using 16S RT-PCR and 16S Sequencing as diagnostic tools was also addressed.Gap Statement. The significance of virus infections on the lung microbiome and on bacterial superinfection in hospitalized patients needs additional evidence from real-world studies.Aim. The primary objective was to assess the impact of respiratory viruses on bacterial airway infection, with the secondary objective to see if 16S Sequencing had potential as a faster diagnostic tool that could augment culture.Methodology. A total of 83 lower airway samples - 36 bronchoalveolar lavage fluids, 39 bronchial washes, 5 sputa and 3 endotracheal aspirates - were tested for respiratory virus and bacterial co-infection. Bacteria were tested by (a) culture, (b) 16S RT-PCR and (c) 16S Sequencing. The performance of culture-independent assays against culture was assessed, and the impact of confirmed viral infections on the airway bacterial load was determined.Results. Virus infections reflected those co-circulating in the community and were significantly associated with culture and 16S Sequencing-confirmed bacterial infections [1-tailed mid P exact test (χ[2]: P=0.04; P=0.05)]. There was substantive agreement of culture and 16S RT-PCR and 16S Sequencing: kappa score: 0.66 (CI: 0.50-0.82); diagnostic accuracy 83.13% (73.32-90.46%). Virus infections were highly associated with increased bacterial load by 16S RT-PCR [2-tailed χ[2] (χ[2]: 2.4 P=0.003)]. Altered microbial diversity by 16S Sequencing was seen for samples stratified by culture but not by virus detection.Conclusion. Acute respiratory viral infections were significantly associated with bacterial airway infections confirmed by culture and 16S Sequencing. Airway dysbiosis was seen with bacterial-confirmed but not viral-confirmed infections, even though the latter were highly associated with increased bacterial loads using 16S RT-PCR. This suggests that virus infections induce changes in lung bacteria missed by culture and sequencing. The study supported a potential role for 16S Sequencing and 16S RT-PCR alongside culture.},
}

Humans
*Coinfection/microbiology/virology/epidemiology
Male
*Respiratory Tract Infections/microbiology/virology
Female
Middle Aged
RNA, Ribosomal, 16S/genetics
Aged
Bacteria/genetics/isolation & purification/classification
*Virus Diseases/virology/microbiology/epidemiology/complications
Adult
Bronchoalveolar Lavage Fluid/microbiology/virology
*Bacterial Infections/microbiology
Real-Time Polymerase Chain Reaction
Aged, 80 and over

@article {pmid40644523,
year = {2025},
author = {Li, T and Felton, J and Lewis, J and Cheng, Q and Meredith, R and Lu, HT and Benken, A and Dutta, PP and Liao, J and Zhao, XD and Matvekas, A and Baker, J and Hasler, WL and Babiskin, A and Walenga, R and Fang, LL and Lionberger, R and Pai, MP and Sun, D and Gianchandani, YB},
title = {An ingestible device for automated sampling and location tracing in gastrointestinal tract.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327667},
doi = {10.1371/journal.pone.0327667},
pmid = {40644523},
issn = {1932-6203},
mesh = {Animals ; *Gastrointestinal Tract/metabolism ; Dogs ; },
abstract = {Fluids sampled from the gastrointestinal (GI) tract are of interest for evaluating the bioequivalence of oral medications, and more generally for evaluating GI-related diseases, and for profiling the individual gut microbiome. Existing options for capturing multiple fluid samples from specific locations in the GI tract are limited and invasive, particularly for the small intestine. Here, we report the development of an ingestible capsule for the collection of multiple fluid samples along the GI tract; we additionally report the use of data from sensors within the capsule to determine the sampling regions. The capsule has an ingestible size of Φ14 × 42 mm3. Within this volume, it includes three separate cartridges that capture and retain samples within capillaries; a stepper motor for positioning the sampling cartridges at a sampling port; a 3-axis accelerometer that enables a new method of correlating sample location; a microcontroller with wireless communication and sensor data storage capabilities; and batteries to power the device. We describe in vitro characterization and in vivo tests performed with canine models that have successfully verified the capabilities of the capsule. Fluid samples from the stomach, small intestine, and colon regions of the GI tract are identified by inertial measurements taken within the capsule, and correlated to measurements of the concentration of mesalamine (a drug used for testing) and the bile salt profile in each region, respectively.},
}

Animals
*Gastrointestinal Tract/metabolism
Dogs

@article {pmid40643767,
year = {2025},
author = {Ghasemipoor, M and Yaghoubi-Avini, M and Azimirad, M and Nabavi-Rad, A and Looha, MA and Doulberis, M and Schulz, C and Yadegar, A},
title = {Gastric microbiome-derived Lacticaseibacillus casei strain RIGLD MG-1 relieves Helicobacter pylori-induced inflammation in gastric epithelial cells in vitro.},
journal = {Molecular biology reports},
volume = {52},
number = {1},
pages = {702},
pmid = {40643767},
issn = {1573-4978},
support = {RIGLD 1281//Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran/ ; },
mesh = {Humans ; *Helicobacter pylori/pathogenicity/drug effects ; *Probiotics/pharmacology ; *Helicobacter Infections/microbiology/therapy ; Epithelial Cells/microbiology/metabolism ; *Lacticaseibacillus casei/physiology/isolation & purification/metabolism ; Inflammation/microbiology ; *Gastrointestinal Microbiome ; Gastric Mucosa/microbiology/metabolism ; Male ; Female ; Cell Line ; Adult ; Middle Aged ; },
abstract = {BACKGROUND: The burden of Helicobacter pylori infection is exacerbated by rising antibiotic resistance. Probiotics, especially Lactobacillus species, have shown potential as adjunctive therapies for H. pylori infection. This study aimed to isolate a Lactobacillus strain from the gastric microbiome of healthy individuals and assess its probiotic properties against H. pylori.

METHODS AND RESULTS: Gastric biopsies were obtained from a cohort of 10 subjects, and used for bacterial isolation. The Lactobacillus strain was identified to species level using PCR and sequencing, followed by safety assessments. MTT assay was employed to measure AGS cell viability after exposure to various concentrations of H. pylori, as well as live and pasteurized Lactobacillus. Anti-inflammatory properties of the probiotic strain were assessed in AGS cells using RT-qPCR and ELISA. Additionally, the strain's potential to inhibit H. pylori adhesion and invasion was examined. Probiotic Lacticaseibacillus casei strain RIGLD MG-1 was isolated and characterized as non-pathogenic and found to be tolerant to acidic and bile-rich environments, and susceptible to several antibiotics. Live and pasteurized L. casei downregulated the expression of NF-κB, IL-8, TNF-α, and β-catenin, meanwhile upregulated the expression of IL-10 in H. pylori-treated cells. They also alleviated H. pylori-induced proinflammatory response by lowering IL-8 and TNF-α, and boosting IL-10 production. Additionally, both probiotic forms inhibited H. pylori adhesion and invasion in AGS cells.

CONCLUSION: Our results show that L. casei strain RIGLD MG-1 is safe and demonstrates significant immunomodulatory and anti-adhesion effects, making it a potential probiotic for use as adjunctive therapy to mitigate H. pylori-induced inflammation.},
}

Humans
*Helicobacter pylori/pathogenicity/drug effects
*Probiotics/pharmacology
*Helicobacter Infections/microbiology/therapy
Epithelial Cells/microbiology/metabolism
*Lacticaseibacillus casei/physiology/isolation & purification/metabolism
Inflammation/microbiology
*Gastrointestinal Microbiome
Gastric Mucosa/microbiology/metabolism
Male
Female
Cell Line
Adult
Middle Aged

@article {pmid40643580,
year = {2025},
author = {Alcala-Gonzalez, LG and Hinchcliff, M and McMahan, ZH},
title = {Gastrointestinal manifestations of systemic sclerosis: current approaches and emerging therapies.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
pmid = {40643580},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: This review highlights recent advances in the understanding and management of gastrointestinal manifestations in systemic sclerosis (SSc). It is intended for clinicians and researchers aiming to improve diagnostic accuracy and therapeutic strategies in managing SSc-related gastrointestinal disease.

RECENT FINDINGS: Gastrointestinal involvement in SSc is highly variable in terms of clinical presentation, symptom severity, progression, timing of onset, and response to treatment. Emerging research highlights early immune-mediated damage to neural and muscular gastrointestinal tissues, microbiome alterations, and vascular dysfunction - particularly in patients with late-onset gastrointestinal disease - as key factors guiding the development of personalized, precision-based approaches for well defined patient subgroups. Recent studies underscore the value of early, objective assessment of gastrointestinal motility using tools like whole-gut transit scintigraphy and abdominal vascular ultrasound. New treatment strategies are also being explored for severe manifestations, including investigating mechanisms behind acid-suppressive therapy-resistant gastroesophageal reflux disease and implementing adjunctive therapies for gastrointestinal dysmotility.

SUMMARY: Gastrointestinal involvement in SSc poses a complex clinical challenge, particularly in patients with severe dysmotility and symptoms refractory to standard management strategies. This review offers timely, evidence-based insights to support clinicians in delivering more personalized and effective patient care and highlights critical gaps to address in future research.},
}

@article {pmid40643564,
year = {2025},
author = {Popowitch, EB and Boiditswe, SC and Patel, MZ and Aquino, JN and Hurst, JH and Steenhoff, AP and Cunningham, AL and Yoon, JW and Seed, PC and Kelly, MS},
title = {Corynebacterium rhinophilum sp. nov. isolated from the human upper respiratory tract.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {75},
number = {7},
pages = {},
doi = {10.1099/ijsem.0.006835},
pmid = {40643564},
issn = {1466-5034},
mesh = {*Corynebacterium/classification/isolation & purification/genetics ; *Phylogeny ; Humans ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/analysis ; Base Composition ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Genome, Bacterial ; Nucleic Acid Hybridization ; United States ; Whole Genome Sequencing ; *Respiratory System/microbiology ; },
abstract = {Twelve strains of a novel Corynebacterium species were cultured from human respiratory samples collected in the USA and Botswana. Five strains underwent detailed phenotypic and chemotaxonomic characterization, while all 12 strains were included in phylogenomic analyses. Optimal growth was observed on brain heart infusion solid medium and in liquid media, including brain heart infusion and tryptic soy broth when supplemented with Tween 80, a source of the fatty acid oleic acid. Cells were Gram-positive, non-spore-forming, non-motile bacilli that exhibited catalase activity but lacked oxidase activity. Major fatty acids were 18 : 1 ω9c (oleic acid) and 16 : 0 (palmitic acid). Analysis of 16S ribosomal RNA gene sequences identified these strains as belonging to the genus Corynebacterium (family Corynebacteriaceae), with the closest relatives being Corynebacterium accolens and Corynebacterium macginleyi. Whole-genome sequencing revealed that the genomes are 2.47-2.62 Mbp in size and have a G+C content of 58.7-59.0 mol%. Average nucleotide identity and in silico DNA-DNA hybridization values for comparisons of these genomes to those of closely related phylogenetic neighbours were 93.19-93.62% and 19.9-36.3%, respectively. These results indicate that these strains represent a novel species of Corynebacterium, for which we propose the name Corynebacterium rhinophilum sp. nov., with the type strain MSK072[T] (=DSM 118652[T]=JCM 37534[T]).},
}

*Corynebacterium/classification/isolation & purification/genetics
*Phylogeny
Humans
RNA, Ribosomal, 16S/genetics
Fatty Acids/analysis
Base Composition
DNA, Bacterial/genetics
Bacterial Typing Techniques
Sequence Analysis, DNA
Genome, Bacterial
Nucleic Acid Hybridization
United States
Whole Genome Sequencing
*Respiratory System/microbiology