@article {pmid41308014,
year = {2025},
author = {Barat, B and Ghosh, K and Kulkarni, B and Banerjee, P and Ghosh, K},
title = {Enteric microbiome and obesity: a multidimensional narrative review.},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001562},
pmid = {41308014},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Obesity/microbiology ; Probiotics ; Animals ; },
abstract = {Obesity (henceforth called the pathologic condition) is a global epidemic affecting nearly 20% of adults worldwide and transcends genetic, ethnic and civilizational barriers in this era of globalization. Various ways of stemming the progress of the disease have been considered. One significant finding in this condition is an altered enteric microbiome. This review elucidates multiple mechanisms by which an altered enteric microbiome may contribute to the pathologic condition. Key roles include the microbiome's ability to process dietary roughage into absorbable nutrients, modulate intestinal physiology, enhance nutrient absorption and influence the endocrine function of adipose tissue and the liver to regulate appetite and hunger. The gut microbiome also interacts with the entero-insular axis, optimizing food utilization, and communicates with the central nervous system to alter appetite, satiety and food-seeking behaviour. Additional mechanisms include immunomodulation, chronic inflammation, epigenetic regulation and the production of vitamins and antioxidants. Promising therapeutic avenues, including engineering beneficial gut bacteria, developing targeted probiotic formulations and designing specialized food programmes can help combat this pathologic condition and potentially provide effective, non-invasive strategies to address this widespread condition.},
}

Humans
*Gastrointestinal Microbiome
*Obesity/microbiology
Probiotics
Animals

@article {pmid41307551,
year = {2025},
author = {Tamura, T and Ohsugi, Y and Katagiri, S and Kusano, A and Handa, T and Lin, P and Liu, A and Toyoshima, K and Takagi, S and Shiwaku, H and Sugihara, G and Takahashi, H},
title = {Oral Microbiota Associated With Cognitive Impairment in Schizophrenia: Composition and PICRUSt2-Predicted Functional Pathways.},
journal = {Schizophrenia bulletin},
volume = {},
number = {},
pages = {},
doi = {10.1093/schbul/sbaf212},
pmid = {41307551},
issn = {1745-1701},
support = {24K18736//KAKENHI JP/ ; 24K12944//KAKENHI JP/ ; 24K02619//KAKENHI JP/ ; //Ministry of Education, Culture, Sports, Science and Technology of Japan/ ; //Enomoto Mental Health Association/ ; },
abstract = {BACKGROUND AND HYPOTHESIS: Cognitive impairment is a core disabling feature of schizophrenia (SZ). Changes in gut microbiota have been linked to cognitive dysfunction in SZ; however, changes in the oral microbiota in relation to immune dysregulation have only been recently reported, and their relevance to cognition remains unclear. The objective of this study was to explore the relationship between oral microbiota alterations and cognitive impairment in patients with SZ and to evaluate potential mediating mechanisms, including neuroinflammation and microbial functions.

STUDY DESIGN: In this cross-sectional study, we recruited 68 patients with SZ and 32 healthy controls (HC). Cognitive function was assessed using the Wechsler Adult Intelligence Scale-Fourth Edition. Oral microbiota composition was characterized by 16S rRNA gene sequencing, and microbial functions were predicted using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) based on the 16S profiles. Neuroinflammation was assessed using peripheral kynurenine (KYN) pathway activity as a proxy.

STUDY RESULTS: The patients with SZ exhibited significantly lower oral microbiota alpha diversity (driven by reduced evenness) and showed greater cognitive impairment and differences in the KYN pathway markers (neuroinflammation proxies) compared to HC. They also showed shifts in specific bacterial genera and the PICRUSt2-predicted functional pathways. Importantly, the oral microbiota alterations were significantly associated with cognitive impairment. Exploratory mediation analysis suggested that several pathways, including glycan biosynthesis and metabolism, may play a role in this association. In contrast, KYN pathway markers showed no significant association.

CONCLUSIONS: Our findings show an association between the oral microbiota alpha diversity and cognitive impairment in SZ, with the PICRUSt2-predicted functional pathways potentially implicated.},
}

@article {pmid41307322,
year = {2025},
author = {Baima, G and Dabdoub, S and Thumbigere-Math, V and Ribaldone, DG and Caviglia, GP and Tenori, L and Fantato, L and Vignoli, A and Romandini, M and Ferrocino, I and Aimetti, M},
title = {Multi-Omics Signatures of Periodontitis and Periodontal Therapy on the Oral and Gut Microbiome.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70055},
pmid = {41307322},
issn = {1600-0765},
support = {CUP B83C22004800006//Next Generation EU/ ; DM 1557 11.10.2022//Next Generation EU/ ; Prot. P2022YEX5R//Next Generation EU Program and the Italian Ministry of University and Research/ ; },
abstract = {AIM: To characterize the impact of periodontitis and of Steps I-II of periodontal therapy on microbiome composition, function, and metabolic output across the oral and gut environments.

METHODS: A multi-omics analysis was performed on saliva and stool samples collected from 50 systemically healthy individuals with and without Stage III-IV periodontitis. For participants with periodontitis, samples were analyzed both at baseline and 3 months after Steps I-II of periodontal therapy. High-throughput whole metagenome sequencing was used to profile microbial taxa and functional genes, NMR-based metabolomics profiled host-microbial metabolites. Single-omic differential abundance analysis between healthy samples and periodontitis samples was performed with MaAsLin2, while analysis between pre- and post-treatment was conducted with timeOmics. Variable selection and subsequent supervised multivariate analysis to determine group-separating markers utilized multi-level sparse Partial Least Squares Discriminant Analysis (sPLS-DA) through mixOmics. KEGG pathway enrichment was analyzed using clusterProfiler, whereas multi-omic data integration was performed with multi-block Partial Least Squares regression analysis.

RESULTS: Periodontitis was associated with significant compositional and functional changes in both saliva and stool, with increased abundance of pathobionts and loss of health-associated taxa in both niches. A subset of species was shared across oral and gut habitats, with detectable differences across clinical groups. As functional potential, periodontitis enriched microbial pro-inflammatory pathways (lipopolysaccharide biosynthesis, bacterial motility) and depleted beneficial short-chain fatty acid (SCFA)- and vitamin-producing functions. Metabolomic profiles revealed reduced SCFAs and amino acids in periodontitis, with elevated pro-inflammatory metabolites (succinate, trimethylamine) in both saliva and stool. Following therapy, microbial communities and their metabolic output partially reverted toward health-associated profiles, particularly in saliva. Stool samples showed subtler but consistent shifts, including a decrease in some typically oral species and decreased succinate and methylamine and restoration of amino acid and SCFA-related metabolites.

CONCLUSIONS: Periodontitis is associated with coordinated microbial and metabolic signatures across the oral and gut environments. Non-surgical periodontal therapy promotes partial ecological restoration in both niches, supporting the view of oral health as a modifiable target for influencing systemic microbial homeostasis.

TRIAL REGISTRATION: ClinicalTrials.gov identification number: NCT04826926.},
}

@article {pmid41307148,
year = {2025},
author = {Mclaughlin, MS and Yurgel, SN and Abbasi, PA and Ali, S},
title = {Changes in Environmental Conditions Differentially Affect the Bacterial Microbiome Communities in Different Apple Fruit Tissues.},
journal = {Environmental microbiology reports},
volume = {17},
number = {6},
pages = {e70225},
doi = {10.1111/1758-2229.70225},
pmid = {41307148},
issn = {1758-2229},
support = {J-003004//Agriculture and Agri-Food Canada/ ; J-002516//Agriculture and Agri-Food Canada/ ; J-002861//Agriculture and Agri-Food Canada/ ; //Nova Scotia Fruit Gorwer Association/ ; 2090-21600-040-00D//USDA/ ; },
mesh = {*Malus/microbiology ; *Microbiota ; *Fruit/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Seasons ; RNA, Ribosomal, 16S/genetics ; },
abstract = {The maintenance and manipulation of the beneficial plant microbiome is a new frontier in ecofriendly disease management, particularly during post-harvest storage. However, the fruit microbiome is highly variable and can be influenced by both biotic and abiotic factors. A comprehensive understanding of how these factors influence microbial communities is necessary in order to unlock the microbiome for sustainable disease management. In this study, we demonstrate the impacts of the growing season and management strategy on the composition and structure of the bacterial microbiome of 'Honeycrisp' apples at harvest from seven different orchards in the Atlantic Maritime Ecozone, over the course of two growing seasons. We show that the bacterial communities associated with core and peel tissues respond differently to changes in external environmental conditions, underscoring the need to include multiple tissue types in future fruit microbiome research. Finally, we characterize the microbial cooperation networks of apple core and peel tissues and identify key microbial taxa influencing these networks.},
}

*Malus/microbiology
*Microbiota
*Fruit/microbiology
*Bacteria/classification/genetics/isolation & purification
Seasons
RNA, Ribosomal, 16S/genetics

@article {pmid41307098,
year = {2025},
author = {Pangga, GM and Bamford, S and Richmond, A and Corcionivoschi, N and Ijaz, UZ and Gundogdu, O},
title = {The Transgenerational Link: Breeder Gut Microbiota and Broiler Progeny Development.},
journal = {MicrobiologyOpen},
volume = {14},
number = {6},
pages = {e70174},
doi = {10.1002/mbo3.70174},
pmid = {41307098},
issn = {2045-8827},
support = {//This work was supported by the Biotechnology and Biological Sciences Research Council (grant number BB/T008709/1)./ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Chickens/microbiology/growth & development ; Female ; Reproduction ; },
abstract = {The gut microbiome of breeder hens plays a pivotal role in reproductive efficiency, egg quality, and progeny development. Its composition is shaped by host factors such as age and genetics, as well as environmental influences, including diet and management practices. Importantly, the breeder gut microbiome is not only dynamic but also responsive to targeted interventions that can enhance intestinal health, metabolic function, and laying performance. Vertical transmission of maternal microbes through the cloaca and egg components provides offspring with a foundational microbial community, with the yolk sac serving as a critical reservoir for early colonisers that influence gut maturation, immunity, and growth. Emerging evidence further demonstrates that maternal nutritional strategies can programme the gut microbiota of progeny and intestinal development, highlighting the breeder microbiome as both a determinant and mediator of transgenerational performance. These insights underscore the potential of microbiome-focused approaches to improve reproductive success and sustainability in poultry production.},
}

Animals
*Gastrointestinal Microbiome
*Chickens/microbiology/growth & development
Female
Reproduction

@article {pmid41306971,
year = {2025},
author = {Han, T and Zhang, Y and Zheng, G and Guo, Y},
title = {From pathogenic mechanisms to therapeutic perspectives: a review of gut microbiota and intestinal mucosal immunity in inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1704651},
pmid = {41306971},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Immunity, Mucosal ; *Intestinal Mucosa/immunology/microbiology ; *Inflammatory Bowel Diseases/therapy/immunology/microbiology/etiology ; Animals ; Dysbiosis/immunology ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; },
abstract = {Inflammatory bowel diseases (IBDs), which comprises Crohn's disease (CD) and ulcerative colitis (UC), is a multifactorial disorder with an as-yet undetermined etiology, with its global incidence rising rapidly, particularly in developing and Western countries. Although the exact etiology remains unclear, recent research implicates genetic predisposition, environmental factors, gut microbiota, and immune responses in the pathogenesis of IBD. Notably, dysbiosis of the gut microbiota-characterized by a reduction in the abundance and diversity of specific bacterial genera-has been suggested as a potential trigger for the onset of IBD, accompanying with dysregulated intestinal mucosal immunity involving in immune cells and nonimmune cells. Understanding and restoring the imbalanced gut microbiota, as well as identifying key bacterial species involved in IBD, are critical for elucidating disease mechanisms and developing therapeutic strategies. In this review, we explore the role of gut microbiota and intestinal mucosal immunity in the pathogenesis of IBD and offers insights into microbiota-centered therapeutic interventions, including probiotics, fecal microbiota transplantation, and microbial metabolites, that aim to modulate the gut microbiota for the treatment of IBD.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Immunity, Mucosal
*Intestinal Mucosa/immunology/microbiology
*Inflammatory Bowel Diseases/therapy/immunology/microbiology/etiology
Animals
Dysbiosis/immunology
Fecal Microbiota Transplantation
Probiotics/therapeutic use

@article {pmid41306925,
year = {2025},
author = {Corr, S and Lowe, C and Vos, M},
title = {Reciprocal transplantation experiments reveal local adaptation of seaweed-associated bacteria.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf205},
pmid = {41306925},
issn = {2730-6151},
abstract = {Seaweed microbiomes are diverse and frequently species-specific. By actively attracting and repelling settling bacteria through exuded metabolites, seaweeds are thought to exert a strong selective pressure on their microbiomes. However, to what degree seaweed-associated bacteria are adapted to their host has received little attention. Here, we retrieve cultivable seaweed bacterial communities from Palmaria palmata (Dulse) and Fucus serratus (Serrated Wrack) and use reciprocal transplant experiments to test whether bacterial isolates have the greatest fitness on their host seaweed species. We used agar derived from host seaweed extracts for bacterial isolation, which was found to be superior to a generic marine agar formulation based on both 16S rRNA gene amplicon alpha- and beta-diversity comparisons to uncultured samples. We then demonstrate that bacterial isolates from both seaweed species exhibit higher fitness in media derived from their native host compared to a non-native host. Although epibacterial fitness varied between hosts, bacterial isolates on average outperformed non-native counterparts in their native environment. By integrating amplicon sequencing with laboratory experiments, we demonstrate that bacteria are locally adapted to their seaweed host species. These findings contribute to the growing body of research exploring the evolutionary and ecological drivers that shape bacterial communities, with implications for ecosystem management, disease control, and microbial biotechnology.},
}

@article {pmid41306772,
year = {2025},
author = {Wu, J and Wu, L and Liu, R and Xuan, L and Qian, J and Fang, C and Wang, H and Guo, J and Du, L and Miao, Y and Liu, B and Liu, Y and Tang, G},
title = {Fabrication of Single-Bacterium Microgel with Gas-Shearing Strategy for Precision Probiotic Delivery in IBD Therapy.},
journal = {Research (Washington, D.C.)},
volume = {8},
number = {},
pages = {0955},
pmid = {41306772},
issn = {2639-5274},
abstract = {The human gut microbiome is essential for maintaining health, as it substantially impacts immune regulation and overall balance within the body. Accordingly, disruptions in this microbial community are associated with various diseases. Probiotics offer a promising solution, but their effectiveness is often hampered by challenges related to gastrointestinal delivery. To overcome the issue of probiotic survival in the gastrointestinal system, researchers have explored various encapsulation techniques. However, traditional coarse encapsulation techniques lack precision and effective targeting, limiting the delivery of viable organisms to the colon. Current methods face challenges such as inadequate particle size control, leakage, and poor survival in complex gastrointestinal environments. This research introduces a novel approach for encapsulating individual bacteria to create single-bacterium microgels, utilizing gas-shearing technology to enhance the survival and targeting capabilities of probiotics. This approach also demonstrates the capability to coat multiple microbial species, including bacteria and fungi, while ensuring good biocompatibility and mechanical support. Focusing on Escherichia coli Nissle 1917, we demonstrate that this method significantly improves therapeutic efficacy in treating inflammatory bowel disease compared to unencapsulated strains. Our results suggest that gas-shearing encapsulation represents a promising strategy for the fabrication of single-bacterium microgels, facilitating the development of effective probiotic therapies with potential applications in both biomedical and nutraceutical fields.},
}

@article {pmid41306540,
year = {2025},
author = {Cordi, CV and Hurley, JM},
title = {The Link Between Circadian Disruption and Alzheimer's Disease and Related Dementias: Insights from Peripheral Inflammation.},
journal = {Current opinion in physiology},
volume = {46},
number = {},
pages = {},
pmid = {41306540},
issn = {2468-8673},
abstract = {Circadian rhythms are essential for maintaining physiological homeostasis, influencing biological processes from the sleep-wake cycle to metabolism and immune responses. Disruption of these rhythms is increasingly linked to the pathogenesis of Alzheimer's Disease and Related Dementias (ADRDs), conditions characterized by cognitive decline and neuropsychiatric symptoms through various pathways including increases in inflammation. While many studies link the effects of circadian disruption on neuroinflammation to ADRDs, this review explores the potential link between the circadian disruption of peripheral inflammation and ADRDs. We discuss the evidence of how circadian misalignment can exacerbate neuroinflammation through the activation of the peripheral immune system. We further examine the role of peripheral factors such as insulin dysregulation, melatonin levels, and gut microbiome imbalances in amplifying these peripheral inflammatory responses. These data underscore the significance of circadian regulation in maintaining immune homeostasis, highlighting potential therapeutic avenues for mitigating ADRDs through the restoration of circadian integrity.},
}

@article {pmid41306408,
year = {2025},
author = {Vijendra, A and Kunkle, C and Jordan, J and Erickson, A and Osei-Karikari, K and Ratley, G and Myles, IA},
title = {Molecular connections between inflammation and social determinants of health.},
journal = {Frontiers in epidemiology},
volume = {5},
number = {},
pages = {1683955},
pmid = {41306408},
issn = {2674-1199},
abstract = {Chronic inflammatory diseases such as autoimmune disorders, cancer, cardiovascular diseases and neurodegenerative disorders are a significant cause of morbidity and mortality in the industrialized world. Socioeconomically disadvantaged communities bear a disproportionately high burden of these inflammatory diseases. This review synthesizes evidence linking various domains of the Social Determinants of Health (SDoH)-economic stability, education access and quality, healthcare access and quality, neighborhood and built environment, and social and community context-to inflammatory pathways and mechanisms. Across domains, biological mechanisms such as cytokine dysregulation, toll-like receptor (TLR) activation, hypothalamic-pituitary-adrenal (HPA) axis alterations and gut microbiome disruption act together to sustain proinflammatory states that drive adverse health outcomes in marginalized communities. Although causality is obscured by interrelated determinants, identifying inflammation as a shared pathway between various determinants highlights the need for structural interventions to reduce chronic disease burden.},
}

@article {pmid41306340,
year = {2025},
author = {Kim, H and Kim, HL and Boo, M and Choi, H and Han, J and Nam, S and Kang, SJ and Kim, JK and Han, Y and Jung, JH and Kim, W and Kim, KI and Um, JY and Park, J and Otterbein, LE and Kim, HI and Ko, SG},
title = {Herbal Combination of Angelica gigas, Zingiber officinale, and Aconitum carmichaeli Alleviates High Fat Diet-Induced Non-Alcoholic Fatty Liver Disease in Mice Through NRF2-Mediated Regulation of Adipogenesis and Non-Shivering Thermogenesis.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71199},
pmid = {41306340},
issn = {2048-7177},
abstract = {Obesity is a complex metabolic disorder characterized by excessive fat accumulation and is closely associated with non-alcoholic fatty liver disease (NAFLD), a condition that increases the risk of metabolic complications such as insulin resistance, type 2 diabetes, and cardiovascular diseases. JI017 is a recently optimized multi-herbal formula composed of Angelica gigas, Zingiber officinale , and processed Aconitum carmichaeli. Clinical records of these three herbs indicate their potentially synergistic anti-obesity effects. This study was conducted to verify the effects of JI017 in an animal model of obesity-associated NAFLD. The effect of JI017 on glucose metabolism, white adipose tissue (WAT) adipogenesis, brown adipose tissue (BAT) thermogenesis, liver oxidative stress, and gut microbiota composition was assessed. The results showed that JI017 improved glucose sensitivity, reduced WAT mass by suppressing PPARγ and C/EBPα expression, and increased BAT thermogenesis through upregulation of UCP1 and PGC-1α. Additionally, JI017 reduced liver oxidative stress by increasing HO-1 and NRF2 expression and modulated the gut microbiota by restoring the Firmicutes/Bacteroidetes ratio. These findings on the multi-targeted effects of JI017 suggest its potential as a promising therapeutic approach for metabolic diseases including NAFLD.},
}

@article {pmid41306277,
year = {2025},
author = {Peng, Y and Ma, L and Zhou, H and Li, J and Wang, J},
title = {1DCNN-BiLSTM-transformer hypertension risk prediction model based on APW.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1714654},
pmid = {41306277},
issn = {1664-302X},
abstract = {INTRODUCTION: Hypertension has a multifactorial etiology. Recent studies have revealed a link between hypertension and gut microbiota dysbiosis. Pulse wave analysis holds significant clinical value for hypertension risk assessment. While research on deep learning models utilizing photoplethysmography (PPG) for hypertension classification has advanced, limitations persist. PPG offers limited richness and accuracy for characterizing blood pressure-related pathological information. In contrast, Arterial Pressure Waveform (APW) provides richer pathological information and exhibit stronger correlations with clinically interpretable features. However, deep learning research using APW for hypertension classification remains limited, as existing studies focus primarily on local feature extraction and neglect global temporal dynamics.

METHODS: To address these challenges, we propose a novel 1D-CNN-BiLSTM-Transformer architecture for hypertension risk assessment based on APW, where the 1D-CNN module extracts waveform morphology features from signals within individual pressure segments, the BiLSTM module models long-range temporal dependencies from signals within each segment, and the Transformer module explicitly captures nonlinear interaction from signals across different pressure segments through multi-head self-attention mechanisms.

RESULTS: We use the multi-channel APW database from the Population Health Data Archive (PHDA), containing hypertensive and non-hypertensive cases with APW signals acquired from six traditional Chinese medicine points (left-cun, left-guan, left-chi, right-cun, right-guan, and right-chi) to evaluate the model's performance. The model outperforms the current state-of-the-art methods in accuracy, precision, recall, and F1 score across all six points.

CONCLUSION: The proposed model enhances classification performance. The physiologically driven interpretable analysis demonstrates that APW can reflect pathophysiological features associated with gut microbiota dysbiosis. The model-driven interpretable analysis offers a decision-making basis for clinical diagnosis.},
}

@article {pmid41306171,
year = {2025},
author = {Ng, MK and Jacofsky, DJ and Barsoum, WK and Mont, MA},
title = {Human Health Applications of Calcium Montmorillonite Clay: A Systems-Based Review.},
journal = {Cureus},
volume = {17},
number = {10},
pages = {e95449},
pmid = {41306171},
issn = {2168-8184},
abstract = {Calcium montmorillonite (CMM) clay is a naturally occurring mineral with a longstanding history in medical applications, now receiving increased scientific attention for its broad therapeutic potential. Known for its ability to bind a range of harmful substances, including bacterial toxins, heavy metals, mycotoxins, and inflammatory mediators, it exerts its effects without systemic absorption, acting locally within the gastrointestinal tract or at the skin surface. This narrative review synthesizes current clinical and preclinical evidence on the human health applications of calcium montmorillonite, with focused sections on the gastrointestinal/metabolic, dermatologic, immune, and musculoskeletal systems. The gastrointestinal section covers its documented role in treating pediatric diarrhea, radiation enteritis, and dietary toxin exposure. In dermatology, the clay has been incorporated into topical preparations for acne, rashes, and wound care, supported by both laboratory data and real-world use. Hepatic and metabolic studies suggest that it may reduce liver fat accumulation, improve glucose metabolism, and modulate the gut microbiome, particularly in models of non-alcoholic fatty liver disease and obesity. Additional sections explore its potential relevance in renal toxin clearance, immune regulation, mucosal healing, and surgical recovery. Across these systems, calcium montmorillonite has demonstrated a strong safety profile, with minimal nutrient interaction and no evidence of systemic toxicity when properly sourced and used in appropriate contexts. With growing access to carefully studied, pharmaceutical-grade formulations, CMM may offer safe and consistent benefits across clinical and preventive care settings.},
}

@article {pmid41305918,
year = {2025},
author = {Shao-Yu, Y and Niu, D and Chen, J and Li, WY and Wang, X and Meng, QW and Song, WJ and Yang, YG and Wang, H and Li, RR and Li, BY and Zhang, LG and Hu, CJ and Xu, LF and Wang, HH and Zhang, L and Liang, CZ and Du, HX},
title = {Antibiotic cocktail-induced changes in gut microbiota drive alteration of bile acid metabolism to restrain Th17 differentiation through the FXR-NLRP3 axis.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2582944},
doi = {10.1080/19490976.2025.2582944},
pmid = {41305918},
issn = {1949-0984},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Th17 Cells/drug effects/immunology/cytology ; Male ; *Bile Acids and Salts/metabolism ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; Mice ; *NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics ; Humans ; *Receptors, Cytoplasmic and Nuclear/metabolism/genetics ; Mice, Inbred C57BL ; Cell Differentiation/drug effects ; Fecal Microbiota Transplantation ; *Prostatitis/immunology/microbiology/drug therapy ; Disease Models, Animal ; Interleukin-17 ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Antibiotics influence both gut microbial composition and immune regulation, but the detailed mechanisms are still undefined. Shifts in the microbiome caused by antibiotic exposure can modulate immune activity through various pathways. Therefore, we aimed to explore how antibiotics affect immune-inflammation by regulating Th17 cells through the gut microbiota of mice with experimental autoimmune prostatitis (EAP). Antibiotic-driven shifts in gut microbial communities and metabolite profiling in EAP mice were performed by integrating 16S rRNA sequencing with mass spectrometry-driven metabolomic analysis. Antibiotic cocktail (ABX) therapy mitigated EAP, modified the gut microbiome composition, and influenced bile acid metabolism. Fecal microbiota transplantation (FMT) using microbiota from ABX-treated feces into EAP mice effectively altered gut microbiome composition and alleviated disease symptoms, indicating that microbiome intervention reduces autoimmune inflammation and decreases deoxycholic acid (DCA) in mice. Subsequent experiments demonstrated that DCA suppresses farnesol X receptor (FXR) expression which can inhibit the NLRP3‒ IL17A axis, thus promoting Th17 cell development and exacerbating inflammatory cell infiltration of the prostate. Our initial clinical examination of patients with prostatitis and antibiotic treatment indicated that bile acid metabolism and Th17 cell development are affected by antibiotic therapy. This work revealed that antibiotic-induced gut microbiota dysbiosis decreases the bile acid metabolite DCA, further restraining Th17 cell differentiation via the FXR‒NLRP3 axis to alleviate autoimmune prostatitis. Our results reveal new perspectives regarding the interconnected dynamics of antibiotics, gut microbiota, bile acid metabolism, and immune regulation, with potential relevance for therapies targeting immune-mediated diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Th17 Cells/drug effects/immunology/cytology
Male
*Bile Acids and Salts/metabolism
*Anti-Bacterial Agents/pharmacology/administration & dosage
Mice
*NLR Family, Pyrin Domain-Containing 3 Protein/metabolism/genetics
Humans
*Receptors, Cytoplasmic and Nuclear/metabolism/genetics
Mice, Inbred C57BL
Cell Differentiation/drug effects
Fecal Microbiota Transplantation
*Prostatitis/immunology/microbiology/drug therapy
Disease Models, Animal
Interleukin-17
RNA, Ribosomal, 16S/genetics

@article {pmid41305672,
year = {2025},
author = {Arishi, RA and Cheema, AS and McEachran, JL and Gridneva, Z and Furst, A and Roman, A and Bode, L and Lai, CT and Payne, MS and Geddes, DT and Stinson, LF},
title = {Development of the Breastfed Infant Oral Microbiome Is Associated with Concentrations and Intakes of Human Milk Oligosaccharides.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223622},
pmid = {41305672},
issn = {2072-6643},
mesh = {Humans ; *Milk, Human/chemistry ; *Oligosaccharides/administration & dosage/analysis ; Infant ; *Breast Feeding ; Female ; *Microbiota ; *Mouth/microbiology ; Male ; RNA, Ribosomal, 16S/genetics ; Adult ; },
abstract = {Background/Objectives: Human milk oligosaccharides (HMOs) are bioactive carbohydrates abundant in human milk that shape the infant gut microbiome, yet their influence on the oral microbiome remains poorly understood. This study investigated associations between HMO concentrations and infant HMO intakes and the composition of the oral microbiome in predominantly (n = 2) and exclusively (n = 54) breastfed infants. Methods: We profiled infant oral samples collected at 2 months of age using full-length 16S rRNA gene sequencing, alongside paired milk HMO analyses from 56 mother-infant dyads from the Western Australian BLOSOM cohort. Daily HMO intakes were calculated using 24 h milk intake data. Results: Concentrations of human milk 3FL and LNFPIII were negatively associated with infant oral Shannon diversity (p = 0.027) and richness (p = 0.037), respectively. LNFPII concentration and daily intake were linked to increased abundance of Neisseria subflava (both p = 0.025), while daily intakes of DFLNT and DFLNH were positively associated with Streptococcus parasanguinis (p = 0.028 and p = 0.040). Notably, the associations observed for daily HMO intakes were modest in effect size. Conclusions: These findings demonstrate a statistically significant but biologically limited effect of HMOs on the development of the infant oral microbiome. By clarifying how specific components of human milk shape early microbial development, this work provides mechanistic insights relevant to nutritional and supportive interventions that promote breastfeeding success.},
}

Humans
*Milk, Human/chemistry
*Oligosaccharides/administration & dosage/analysis
Infant
*Breast Feeding
Female
*Microbiota
*Mouth/microbiology
Male
RNA, Ribosomal, 16S/genetics
Adult

@article {pmid41305652,
year = {2025},
author = {Dargenio, VN and Sgarro, N and Grasta, G and Begucci, M and Castellaneta, SP and Dargenio, C and Paulucci, L and Francavilla, R and Cristofori, F},
title = {Hidden Hunger in Pediatric Obesity: Redefining Malnutrition Through Macronutrient Quality and Micronutrient Deficiency.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223601},
pmid = {41305652},
issn = {2072-6643},
mesh = {Humans ; *Micronutrients/deficiency ; Child ; *Pediatric Obesity/complications/physiopathology ; Gastrointestinal Microbiome ; *Nutrients/deficiency ; *Malnutrition/etiology ; *Hunger ; Inflammation ; Diet ; Biomarkers ; },
abstract = {Background: Pediatric obesity exemplifies the paradox of energy excess coexisting with nutritional inadequacy. Despite high caloric intake, children with obesity often display deficiencies in essential macro- and micronutrients that impair growth, metabolic regulation, and long-term health. This review critically examines the mechanisms underlying malnutrition in pediatric obesity, emphasizing the interplay between dietary quality, inflammation, microbiota alterations, and biomarker profiles, and identifies research gaps limiting precision nutrition approaches. Methods: A comprehensive narrative review of studies addressing macro- and micronutrient intake, metabolic and inflammatory biomarkers, and gut microbiota-host interactions in pediatric obesity was conducted. Evidence from both clinical and experimental models was integrated to evaluate mechanistic pathways, diagnostic criteria, and preventive strategies. Results: Obesity-related malnutrition arises from poor dietary quality, systemic inflammation, and microbiota dysbiosis, leading to impaired nutrient utilization and metabolic dysfunction. Deficiencies in vitamin D, calcium, iron, magnesium, and B vitamins are common and often coexist with macronutrient imbalances. Diets rich in saturated fats and refined carbohydrates exacerbate inflammation and metabolic risk, whereas plant-based proteins, unsaturated fats, and fiber support metabolic resilience. Precision nutrition and biomarker-guided monitoring show promise but require validation in pediatric cohorts. Evidence on microbiota modulation and nutrient-gene interactions remains inconsistent, reflecting methodological heterogeneity. Conclusions: Malnutrition in pediatric obesity should be recognized as a distinct clinical phenotype characterized by qualitative nutrient deficiency within a state of energy surplus. Addressing this paradox demands harmonized diagnostic criteria, longitudinal biomarker surveillance, and individualized dietary strategies informed by genetics and microbiome profiling. Multilevel interventions, linking clinical practice, policy, and food system reform, are essential to prevent lifelong metabolic complications and promote healthy growth trajectories.},
}

Humans
*Micronutrients/deficiency
Child
*Pediatric Obesity/complications/physiopathology
Gastrointestinal Microbiome
*Nutrients/deficiency
*Malnutrition/etiology
*Hunger
Inflammation
Diet
Biomarkers

@article {pmid41305634,
year = {2025},
author = {Blady, K and Pomianowski, B and Strugała, M and Smółka, L and Kursa, K and Stanek, A},
title = {Vitamin D in Atopic Dermatitis: Role in Disease and Skin Microbiome.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223584},
pmid = {41305634},
issn = {2072-6643},
mesh = {Humans ; *Vitamin D/metabolism/pharmacology ; *Dermatitis, Atopic/microbiology/immunology/drug therapy ; *Skin/microbiology/immunology/drug effects ; *Microbiota/drug effects ; Animals ; Skin Microbiome ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disorder associated with immune dysregulation, skin barrier dysfunction, and microbial dysbiosis characterized by Staphylococcus aureus overcolonization and reduced bacterial diversity. Beyond its classical role in calcium homeostasis, Vitamin D (VD) influences skin immunity and microbial composition. This review summarizes current knowledge on VD metabolism, its immunological pathways in AD, and its interactions with the skin microbiome. Recent evidence positions the skin as an active immunological organ rather than a passive barrier. Commensal bacteria such as Staphylococcus epidermidis not only inhibit pathogens by producing bacteriocins and modulins but also generate ceramides and short-chain fatty acids (SCFAs) that stabilize the lipid barrier. Moreover, dermal fibroblasts and preadipocytes produce antimicrobial peptides, while resident γδ T cells release growth factors like fibroblast growth factor 7 (FGF7), linking host defense with tissue regeneration. VD modulates AD by suppressing T helper 2 cells/T helper 17 cell responses, enhancing regulatory T cell development, inducing antimicrobial peptides, and strengthening skin and gut barrier integrity. Its interaction with the microbiome and pathways such as SCFA and aryl hydrocarbon receptor (AhR) signaling supports its potential as an adjunctive therapy in AD management. Evidence from mechanistic studies and animal models suggests that VD supplementation may modulate inflammation and microbial diversity. Clinical implications, therapeutic perspectives, and future research directions highlight the potential of VD as a therapeutic adjunct in AD management.},
}

Humans
*Vitamin D/metabolism/pharmacology
*Dermatitis, Atopic/microbiology/immunology/drug therapy
*Skin/microbiology/immunology/drug effects
*Microbiota/drug effects
Animals
Skin Microbiome

@article {pmid41305619,
year = {2025},
author = {Tanjung, C and Shibata, R and Fikri, B and Prawitasari, T and Zainuddin, AA and Juliaty, A and Yullyana, DS and Sundjaya, T and Kuswanto, H and Clarensia, J and Shimojo, N and Koletzko, B and Ohno, H and Massi, N},
title = {Longitudinal Microbiome and Metabolome Shifts After Successful Intervention in Impending Stunting in Indonesian Infants.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223570},
pmid = {41305619},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Infant ; Indonesia ; *Growth Disorders/microbiology/prevention & control ; *Metabolome ; Male ; Female ; Feces/microbiology ; Dietary Supplements ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Bacteria/classification ; },
abstract = {Background/Objectives: Stunting and weight faltering (WF) remain pressing public health challenges in low- and middle-income countries, with long-term consequences for child growth, development, and survival. While the role of gut health in early growth is increasingly recognized, evidence on how the gut microbiome and metabolome respond to nutritional interventions in WF infants is scarce. This study explored gut microbiome and metabolome changes in Indonesian infants aged 6-12 months who overcame WF following a one-month intervention. Methods: Infants were assigned to either a Nutritional Advice (NA) group or a Nutritional Advice plus Oral Nutritional Supplements (NAONS) group. Stool samples were collected before and after the intervention for microbiome (16S rRNA sequencing) and metabolome (LC-MS) analysis. Results: Significant shifts in gut microbial composition (beta diversity) and species richness (Chao1 index) were observed in both groups, suggesting enhanced microbial diversity and gut resilience. Within-group analysis revealed increases in beneficial genera such as Faecalibacterium and Peptostreptococcus, and a reduction in pro-inflammatory Fusobacterium in the NA group. The NAONS group showed a notable decrease in Proteus, a potentially pathogenic genus. Between-group comparisons indicated higher abundances of Lactococcus and Leuconostoc in the NAONS group, likely reflecting the influence of milk protein-rich supplements on microbial colonization, favoring lactic acid bacteria over SCFA-producing taxa, leading to better gut health. Metabolome analysis revealed significant changes in the NA group, increases in metabolites like Threonine, Tryptophan, and Xylose pointed to improved energy metabolism and gut health, while a decrease in Oxalic Acid suggested better metabolic efficiency. In contrast, the NAONS group, while benefiting from rapid weight gain, displayed a distinct metabolic profile influenced by high milk protein intake. No significant correlations were found between microbiome and metabolome changes, highlighting the complexity of gut-host interactions, suggesting that the interventions led to independent shifts in the aforementioned profiles. Conclusions: Overall, the findings suggest that nutritional interventions may enhance gut health and support recovery from weight faltering, providing insights into strategies that may contribute to restoring healthy growth trajectories and preventing stunting by modulating gut health.},
}

Humans
*Gastrointestinal Microbiome/physiology
Infant
Indonesia
*Growth Disorders/microbiology/prevention & control
*Metabolome
Male
Female
Feces/microbiology
Dietary Supplements
Longitudinal Studies
RNA, Ribosomal, 16S/genetics
Bacteria/classification

@article {pmid41305616,
year = {2025},
author = {Dale, HF and Kolby, M and Valeur, J},
title = {Ultra-Processed Food Consumption and Irritable Bowel Syndrome: Current Evidence and Clinical Implications.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223567},
pmid = {41305616},
issn = {2072-6643},
mesh = {Humans ; *Irritable Bowel Syndrome/etiology/epidemiology ; Gastrointestinal Microbiome ; *Fast Foods/adverse effects ; *Diet/adverse effects ; *Food Handling ; Food, Processed ; },
abstract = {Irritable bowel syndrome (IBS) is a prevalent disorder of gut-brain interaction (DGBI) with an adverse impact on quality of life. The global consumption of ultra-processed foods (UPF) is rapidly increasing, and UPF intake has recently been linked to a wide range of metabolic and chronic diseases. The potential role of UPF consumption in the onset and symptom generation of IBS is emerging but remains unclear. This narrative review synthesizes epidemiological evidence on the association between UPF consumption and IBS, integrates mechanistic insights from experimental and clinical studies and suggests clinical implications based on the current state of knowledge. Observational studies suggest that higher UPF intake may be associated with increased risk of IBS, although the evidence base is limited and subject to methodological challenges. Mechanistic studies indicate that additives including emulsifiers and non-nutritive sweeteners can alter pathways relevant to IBS symptom generation, such as gut microbiota composition, impair intestinal barrier function and trigger low-grade inflammation. Current evidence supports a possible link between UPF consumption and IBS. Increasing overall dietary quality and reducing UPF intake are promising complementary strategies to established dietary interventions. Future intervention trials may provide insights into relevant biological mechanisms, particularly if such changes co-occur with symptom improvement.},
}

Humans
*Irritable Bowel Syndrome/etiology/epidemiology
Gastrointestinal Microbiome
*Fast Foods/adverse effects
*Diet/adverse effects
*Food Handling
Food, Processed

@article {pmid41305603,
year = {2025},
author = {He, Y and Peng, K and Tan, J and Hao, Y and Zhang, S and Gao, C and Li, L},
title = {Short-Chain Fatty Acids and Colorectal Cancer: A Systematic Review and Integrative Bayesian Meta-Analysis of Microbiome-Metabolome Interactions and Intervention Efficacy.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223552},
pmid = {41305603},
issn = {2072-6643},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/metabolism/ethnology/prevention & control ; *Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/physiology ; Bayes Theorem ; *Metabolome ; Female ; Adenoma/microbiology ; },
abstract = {Objective: Existing studies on short-chain fatty acids (SCFAs) and colorectal cancer (CRC) yield contradictory conclusions and are limited to single ethnic groups or sample types. This study aimed to (1) quantify associations between total SCFAs/subtypes (acetate, propionate, butyrate) and CRC/advanced colorectal adenoma (A-CRA) risks; (2) identify modifiers (ethnicity, sample type, intervention); and (3) clarify SCFA-gut microbiota interaction mechanisms via integrative Bayesian meta-analysis and multi-ancestry data integration. Methods: We systematically searched PubMed, Embase, Cochrane Library, and Web of Science (inception to September 2025) using keywords: "Short-chain fatty acids", "SCFAs", "Colorectal cancer", "CRC", "Gut microbiota", "Dietary fiber", and "High-amylose maize starch butyrate". Eligible studies included 14 peer-reviewed original studies (7 observational, cohort/case-control/cross-sectional; 7 RCTs) covering Europeans, Asians, and African Americans. Inclusion criteria: Quantitative SCFA data (total/≥3 subtypes), clear ethnic grouping, reported CRC/A-CRA risks or intervention outcomes. Exclusion criteria: Reviews, animal/in vitro studies, incomplete data, low-quality studies (Newcastle-Ottawa Scale [NOS] <6 for observational; high Cochrane risk for RCTs), or limited populations (single gender/rare genetics). A Bayesian hierarchical random-effects model quantified effect sizes (Odds Ratio [OR]/Mean Difference [MD], 95% credible intervals [CrI]), with heterogeneity analyzed via multi-ancestry stratification, intervention efficacy, and microbiota interaction analyses (Preferred Reporting Items for Systematic Reviews and Meta-Analyses [PRISMA] 2020; International Prospective Register of Systematic Reviews [PROSPERO]: CRD420251157250). Results: Total SCFAs were negatively associated with CRC (OR = 0.78, 95% CrI: 0.65-0.92) and A-CRA (OR = 0.72, 95% CrI: 0.59-0.87), with butyrate showing the strongest protective effect (CRC: OR = 0.63, 95% CrI: 0.51-0.77). Ethnic heterogeneity was significant: Europeans had the strongest protection (OR = 0.71), Asians had weaker protection (OR = 0.86), and African Americans had the lowest fecal SCFA levels and the highest CRC risk. Fecal SCFAs showed a stronger CRC association than serum/plasma SCFAs (OR = 0.73 vs. 0.85). High-Amylose Maize Starch Butyrate (HAMSB) outperformed traditional fiber in increasing fecal butyrate (MD = 4.2 mmol/L vs. 2.8 mmol/L), and high butyrate-producing bacteria (Clostridium, Roseburia) enhanced SCFA protection (OR = 0.52 in high-abundance groups). Conclusions: SCFAs (especially butyrate) protect against CRC and precancerous lesions, with effects modulated by ethnicity, sample type, and gut microbiota. High-Amylose Maize Starch Butyrate is a priority intervention for high-risk populations (e.g., familial adenomatous polyposis, FAP), and differentiated strategies are needed: 25-30 g/d dietary fiber for Europeans, 20-25 g/d for Asians, and probiotics (Clostridium) for African Americans. Future Perspectives: Expand data on underrepresented groups (African Americans, Latinos), unify SCFA detection methods, and conduct long-term RCTs to validate intervention efficacy and "genetics-microbiota-metabolism" crosstalk-critical for CRC precision prevention.},
}

Humans
*Colorectal Neoplasms/microbiology/metabolism/ethnology/prevention & control
*Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome/physiology
Bayes Theorem
*Metabolome
Female
Adenoma/microbiology

@article {pmid41305578,
year = {2025},
author = {Rehner, J and Gund, M and Becker, SL and Hannig, M and Rupf, S and Schattenberg, JM and Keller, A and The Imagine Consortium, and Molano, LG and Keller, V},
title = {Joint Bacterial Traces in the Gut and Oral Cavity of Obesity Patients Provide Evidence for Saliva as a Rich Microbial Biomarker Source.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223527},
pmid = {41305578},
issn = {2072-6643},
support = {469073465//DFG/ ; },
mesh = {Humans ; *Saliva/microbiology ; *Obesity/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Mouth/microbiology ; Male ; Female ; Biomarkers/analysis ; Middle Aged ; Adult ; Dental Plaque/microbiology ; *Bacteria/isolation & purification/classification/genetics ; Metagenome ; },
abstract = {Background: The human microbiome holds promise for identifying biomarkers and therapeutic targets. In obesity, interactions between oral and gut communities are increasingly implicated and end in organ injury. Methods: From the IMAGINE study, we analyzed 418 shotgun metagenomes from three specimen types (dental plaque (n = 143; 65 non-obese, 78 obese), saliva (n = 166; 75 non-obese, 91 obese), and stool (n = 109; 57 non-obese, 52 obese)) to compare site-specific microbial shifts between obese (BMI > 30 kg/m[2]) and non-obese individuals. Differential abundance was assessed with ANCOM-BC; effect sizes were summarized as Cohen's d. Results: Across all samples, we detected 240 bacterial species in plaque, 229 in saliva, and 231 in stool, with 46 species present across all three sites. Absolute effect sizes were significantly larger in plaque (mean |d| = 0.26) and saliva (0.25) than in stool (0.21; p = 9 × 10[-3]). Several taxa showed an opposite directionality between oral and gut sites, including Streptococcus salivarius and Bifidobacterium longum, indicating site-specific associations. Notably, Actinomyces sp. and Streptococcus sp. exhibited promising effect sizes as diagnostic markers. Conclusions: The oral and gut microbiomes capture complementary obesity-related signals, with stronger shifts observed in oral sites. We suggest that integrating oral and gut profiling could enhance diagnostic and therapeutic strategies in obesity.},
}

Humans
*Saliva/microbiology
*Obesity/microbiology
*Gastrointestinal Microbiome
Feces/microbiology
*Mouth/microbiology
Male
Female
Biomarkers/analysis
Middle Aged
Adult
Dental Plaque/microbiology
*Bacteria/isolation & purification/classification/genetics
Metagenome

@article {pmid41305571,
year = {2025},
author = {Verstegen, REM and Zuurveld, M and Thijssen, S and de Bruijn, MJW and van Ark, I and Diks, MAP and Garssen, J and Folkerts, G and Kostadinova, AI and Hendriks, RW and Willemsen, LEM},
title = {A Specific Ratio of Dietary Short-Chain and Long-Chain Fructo-Oligosaccharides Shifts the Immune Response Away from Type 2 in a Murine Model for House Dust Mite-Induced Asthma.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223520},
pmid = {41305571},
issn = {2072-6643},
support = {10.1.19.001//Health Holland/ ; 10.1.19.001//Lung Foundation Netherlands/ ; },
mesh = {Animals ; *Asthma/immunology/microbiology ; *Oligosaccharides/administration & dosage/pharmacology ; *Pyroglyphidae/immunology ; Mice, Inbred BALB C ; Disease Models, Animal ; Gastrointestinal Microbiome/drug effects ; Mice ; Fatty Acids, Volatile ; Female ; Dietary Supplements ; Lung/immunology ; Feces/microbiology ; Bronchoalveolar Lavage Fluid ; Dietary Fiber/administration & dosage ; Th2 Cells/immunology ; },
abstract = {Background/Objectives: The gut microbiome has an important role in immune regulation, and dietary interventions that support a balanced microbiota may help to prevent the development of allergic asthma. Dietary fibers can beneficially affect the intestinal microbiome, but due to the diversity of fiber types, the effects differ. In this study, we investigate the preventive effects of two mixes of short-chain and long-chain (1:1 and 9:1 ratio) fructo-oligosaccharides (FOS) in a mouse model of house dust mite (HDM)-induced allergic asthma. Methods: BALB/c mice received FOS-supplemented (1% w/w) diets before and during intranasal exposures to HDM. Endpoint airway hyperreactivity measurements were performed, followed by the collection of bronchoalveolar lavage fluid (BALF), lung, serum and cecum content. Fecal microbiome composition was determined by DNA sequencing and short-chain fatty acid (SCFA) levels were determined in the cecum, serum and lung. Results: Fecal microbiome analyses revealed an increased abundance of Prevotellaceae after FOS1:1 supplementation in HDM-allergic mice. Additionally, FOS1:1 protected against an HDM-induced increase in basal airway resistance. Both FOS1:1 and FOS9:1 restored the systemic acetate levels in HDM-allergic mice. The two FOS supplementations did not affect HDM-induced inflammatory cell influx in the BALF. However, FOS1:1 increased the frequency of Th1-cells and prevented an HDM-induced increase in the Th2/Th1 balance. Upon ex vivo restimulation with HDM, lung cell suspensions of FOS1:1-fed mice produced less type 2-related cytokines compared to control-supplemented mice, and FOS9:1 followed a similar pattern. Conclusions: Specific short-chain and long-chain FOS ratios differentially affect the microbiome and immune system in a mouse model with HDM-induced allergic airway inflammation. Dietary supplementation with FOS1:1 shifts the immune response away from type 2, suggesting that dietary fibers like FOS1:1 may contribute as a part of a broader strategy to modulate HDM-induced allergic asthma.},
}

Animals
*Asthma/immunology/microbiology
*Oligosaccharides/administration & dosage/pharmacology
*Pyroglyphidae/immunology
Mice, Inbred BALB C
Disease Models, Animal
Gastrointestinal Microbiome/drug effects
Mice
Fatty Acids, Volatile
Female
Dietary Supplements
Lung/immunology
Feces/microbiology
Bronchoalveolar Lavage Fluid
Dietary Fiber/administration & dosage
Th2 Cells/immunology

@article {pmid41305568,
year = {2025},
author = {Liu, C and Zhao, Y and Li, J and Gao, S and Cao, J and Jing, N and Han, X and He, H and Liang, W and Wang, N},
title = {Limosilactobacillus fermentum IOB802 Protects Against Blue Light-Induced Retinopathy via Gut Microbiota Modulation.},
journal = {Nutrients},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/nu17223517},
pmid = {41305568},
issn = {2072-6643},
support = {No. 202228040//Jinan Innovation Team Project/ ; No.24ZYCGSY00390//Tianjin Science and Technology Achievement Transfer and Transformation Project/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Limosilactobacillus fermentum ; *Light/adverse effects ; *Retinal Diseases/prevention & control/etiology/microbiology ; Humans ; *Probiotics/pharmacology ; Cell Line ; Male ; Mice, Inbred C57BL ; Retina/radiation effects ; Lactobacillus plantarum ; Cytokines/metabolism ; Antioxidants/metabolism ; Disease Models, Animal ; Blue Light ; },
abstract = {BACKGROUND: Blue light-induced retinal photodamage represents a growing public health concern globally. Lactic acid bacteria and their bioactive metabolites represent a promising therapeutic strategy for mitigating such damage.

METHODS: This study evaluated the protective efficacy of Limosilactobacillus fermentum IOB802 and Lactobacillus plantarum subsp. plantarum IOB602 against blue light-induced retinal injury using both in vitro and in vivo models.

RESULTS: In ARPE-19 cells exposed to blue light, treatment with postbiotics from IOB802 and IOB602 significantly restored cell viability (p < 0.05), enhanced antioxidant enzyme activities (GSH-Px, SOD, and CAT, p < 0.05), and reduced inflammatory cytokine levels (IL-6, IL-1β, TNF-α, and VEGF, p < 0.05). Subsequent validation in a murine blue light-induced retinal damage model demonstrated that IOB802 notably preserved retinal architecture, upregulated antioxidant defenses, and promoted the expression of tight junction proteins. Mechanistically, IOB802 suppressed inflammation by inhibiting the phosphorylation of the IκBα/NF-κB pathway. Through 16S rDNA sequencing and short-chain fatty acid (SCFA) profiling, IOB802 was further shown to restore gut microbial diversity, increase beneficial bacteria, including Lachnospiraceae, Rikenellaceae, and Bacteroidaceae (p < 0.05), and elevate concentrations of key SCFAs (butyrate, acetate, and propionate; p < 0.05), underscoring the role of the gut-retina axis in mediating retinal protection.

CONCLUSIONS: In summary, IOB802 and its postbiotics alleviate blue light-induced retinopathy through antioxidative, anti-inflammatory, and microbiota-modulating mechanisms, offering novel insights into microbiome-based interventions for retinal diseases.},
}

Animals
*Gastrointestinal Microbiome/drug effects
Mice
*Limosilactobacillus fermentum
*Light/adverse effects
*Retinal Diseases/prevention & control/etiology/microbiology
Humans
*Probiotics/pharmacology
Cell Line
Male
Mice, Inbred C57BL
Retina/radiation effects
Lactobacillus plantarum
Cytokines/metabolism
Antioxidants/metabolism
Disease Models, Animal
Blue Light

@article {pmid41305378,
year = {2025},
author = {Lee, SJ and Seong, J and Lee, JA and Lee, Y and Kim, JH and Ahn, JY and Ku, NS and Choi, JY and Yeom, JS and Jeong, SJ},
title = {Respiratory Microbiome of Carbapenem-Resistant Acinetobacter baumannii Ventilator-Associated Pneumonia: A Pilot Study from the Republic of Korea.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111141},
pmid = {41305378},
issn = {2076-0817},
mesh = {Humans ; *Pneumonia, Ventilator-Associated/microbiology/mortality ; *Acinetobacter baumannii/drug effects/genetics/isolation & purification ; Male ; *Carbapenems/pharmacology ; Female ; Republic of Korea ; Pilot Projects ; Middle Aged ; Aged ; *Microbiota ; *Acinetobacter Infections/microbiology/mortality ; RNA, Ribosomal, 16S/genetics ; Anti-Bacterial Agents/pharmacology ; Intensive Care Units ; Prognosis ; },
abstract = {Ventilator-associated pneumonia (VAP) is one of the most common hospital-acquired infections. Several studies have explored the potential role of the lung microbiome as a biomarker for identifying and predicting the prognosis of VAP. However, research on the respiratory microbiome in individuals with VAP caused by carbapenem-resistant Acinetobacter baumannii (CRAB) remains limited. Therefore, we aimed to analyze the respiratory microbiome of patients with CRAB VAP. Respiratory specimens were collected from patients who developed CRAB VAP. Microbiome diversity and composition were analyzed using 16S rRNA gene pyrosequencing. Patients were categorized into two groups based on mortality outcomes: intensive care unit (ICU) mortality or 28-day mortality after ICU discharge. Twenty patients with CRAB VAP were enrolled, including nine in the mortality group. No significant differences were observed in α-diversity indices between the study groups. However, multivariable Firth's logistic regression revealed a significant association between a relative abundance of the Enterococcus genus ≥ 1% and mortality outcomes (odds ratio: 0.06; 95% confidence interval: 0.00-0.771; p = 0.029). This study characterized the respiratory microbiome of patients with CRAB VAP and highlighted the potential role of microbiome analysis in predicting disease prognosis. Further studies with larger sample sizes are warranted to validate these findings.},
}

Humans
*Pneumonia, Ventilator-Associated/microbiology/mortality
*Acinetobacter baumannii/drug effects/genetics/isolation & purification
Male
*Carbapenems/pharmacology
Female
Republic of Korea
Pilot Projects
Middle Aged
Aged
*Microbiota
*Acinetobacter Infections/microbiology/mortality
RNA, Ribosomal, 16S/genetics
Anti-Bacterial Agents/pharmacology
Intensive Care Units
Prognosis

@article {pmid41305374,
year = {2025},
author = {Zhou, J and Fu, Z and Gao, Y and An, C and Zhang, Z and Zhong, X and Tian, L and Yang, X and Zhang, J and Zhang, Q and Wang, D and Li, N},
title = {Gut Microbiotas, Plasma Metabolites, and Autism Spectrum Disorder: A Bidirectional Mendelian Randomization Analysis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111137},
pmid = {41305374},
issn = {2076-0817},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Autism Spectrum Disorder/microbiology/genetics/blood ; Mendelian Randomization Analysis ; Genome-Wide Association Study ; Linkage Disequilibrium ; Metabolome ; Male ; Female ; },
abstract = {Background: Previous studies have indicated that the gut microbiome and plasma metabolites play key roles in autism spectrum disorder (ASD), but their causal relationships remain unclear. Linkage disequilibrium score regression (LDSC) and Mendelian randomization (MR) are powerful tools for assessing genetic causality. This study uses LDSC and MR to investigate the genetic links between the gut microbiome and ASD and explore the mediating role of plasma metabolites. Methods: To explore the genetic relationships between the gut microbiome, plasma metabolites, and ASD, we obtained summary statistics from large-scale genome-wide association studies (GWAS). Gut microbiome data came from a MiBioGen consortium meta-analysis (N = 18,340), ASD data from the Danish Psychiatric Central Research Register (DPCRR) (N = 18,382), and plasma metabolite data from the Canadian Longitudinal Study of Aging (CLSA) (N = 8299). We applied LDSC and bidirectional MR to analyze the genetic associations between the gut microbiome and ASD and plasma metabolites and ASD. Mediation MR was used to assess the mediating role of plasma metabolites in the gut microbiome-ASD relationship. Results: LDSC analysis revealed significant genetic correlations between the gut microbiota Lachnospiraceae NK4A136 group and Sellimonas with ASD. Moreover, bidirectional MR demonstrated causal effects of five gut microbial genera on ASD risk, as indicated by inverse variance weighted (IVW) methods. Similarly, we identified 49 plasma metabolites that exhibited genetic correlations with ASD, and 58 metabolites had causal effects on ASD in MR analysis. Mediation analysis revealed that specific bacteria, Ruminiclostridium5, reduce the occurrence of ASD through metabolites Delta-CEHC and Docosadioate (C22-DC). Furthermore, Ruminococcaceae UCG005 and Sutterella modulate ASD by inhibiting Serotonin and N-acetyl-L-glutamine, respectively. Conclusions: This study provides evidence of a causal relationship between the gut microbiome and ASD, with plasma metabolites acting as a potential mediator. Our findings offer new insights into the causal mechanisms linking the gut microbiome and ASD and provide a theoretical foundation for microbiome-based therapeutic strategies.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Autism Spectrum Disorder/microbiology/genetics/blood
Mendelian Randomization Analysis
Genome-Wide Association Study
Linkage Disequilibrium
Metabolome
Male
Female

@article {pmid41305349,
year = {2025},
author = {Ruden, DM},
title = {The Human Archaeome: Commensals, Opportunists, or Emerging Pathogens?.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/pathogens14111111},
pmid = {41305349},
issn = {2076-0817},
support = {5P42ES030991-07/NH/NIH HHS/United States ; 5P30ES036084-06/NH/NIH HHS/United States ; },
mesh = {Humans ; *Archaea/physiology/pathogenicity/classification ; *Microbiota ; *Symbiosis ; },
abstract = {Archaea, one of the three domains of life, are increasingly recognized as consistent, though often underappreciated, members of the human microbiome, yet their roles in health and disease remain poorly understood. Unlike bacteria, no archaeal species have been conclusively identified as primary mammalian pathogens, but their widespread presence across diverse body sites suggests potential indirect contributions to host physiology and pathology. Current evidence is synthesized on archaeal diversity and habitat specificity across multiple human-associated sites, encompassing the gastrointestinal, aerodigestive, and urogenital tracts as well as the skin. Methanogens dominate the lower gastrointestinal tract (LGT), where they influence fermentation dynamics and methane production, while members of the class Nitrososphaeria are prevalent on the skin and upper aerodigestive tract (UAT), reflecting ecological specialization. Variability in archaeal composition across niches highlights possible links to disease processes: methanogens have been associated with irritable bowel syndrome (IBS), inflammatory bowel disease (IBD), obesity, and colorectal cancer (CRC); Methanobrevibacter oralis is enriched in periodontal disease; and archaea have been detected in the lungs of cystic fibrosis patients. Although archaea lack canonical bacterial virulence factors, they may contribute indirectly through metabolic cross-feeding, immune modulation, synergy in polymicrobial infections, and alteration of host-microbiome network dynamics. This review explores the emerging concept of the human "archaeome", evaluates current evidence for archaeal involvement in disease, and highlights emerging technologies, such as bacteria-MERFISH and multi-omics profiling, that enable translational applications including microbiome diagnostics, therapeutic targeting, and microbiome engineering.},
}

Humans
*Archaea/physiology/pathogenicity/classification
*Microbiota
*Symbiosis

@article {pmid41304681,
year = {2025},
author = {Zhou, X and Zhu, X and Fan, X and Huang, X and Ma, H and Cheema, HN and Zhang, K and Zheng, S},
title = {Exogenous Plant Growth-Promoting Rhizobacteria Enhance the Promoting Effect of Polyaspartic Acid on Potato Growth by Improving Rhizosphere Nutrient Availability and Reshaping Microbial Community.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223530},
pmid = {41304681},
issn = {2223-7747},
support = {2021YFYZ0005 and 2021YFYZ0019//the Sichuan Provincial Science and Technology Program Breeding Research Project/ ; sccxtd-2025-09//the National Modern Agricultural Industry Technology System Sichuan Tuber Crops Innovation Team Project/ ; SNSBJKJJHXM2024001//the Innovation and Application of Key Technologies for Green and Sustainable Yield Increase in New Potato Varieties/ ; 2522229017//the Key Technologies for Enhancing Potato Yield in Red Revolutionary Base Areas Training Program/ ; },
abstract = {Polyaspartic acid (PASP), a biodegradable and eco-friendly fertilizer synergist that shows potential to enhance nutrient use efficiency in agricultural systems, has its integrative role with rhizosphere microorganisms remain insufficiently explored. This study integrated outdoor pot experiments, soil biochemical analysis, and microbiome sequencing to investigate the effects of co-application of PASP and the plant growth-promoting rhizobacterium (PGPR) Enterobacter asburiae S13 on potato growth, with four treatments set up including blank control (CK), sole application of PASP (S0P1), sole inoculation of PGPR (S1P0), and co-application of PASP and PGPR (S1P1), and 25 pots per treatment as replicates. The results showed that, compared with the S0P1 treatment, the S1P1 treatment significantly increased plant height (9.59%), stem diameter (28.39%), root length (38.61%), as well as root and shoot biomass (21.26% and 25.17%, respectively) (ANOVA, Duncan's test, p < 0.05). It also enhanced ammonium nitrogen (40.00%), nitrate nitrogen (57.70%), available potassium (47.56%), and urease activity in the rhizosphere soil (ANOVA, Duncan's test, p < 0.05). 16S rRNA sequencing revealed that the S1P1 treatment enriched beneficial taxa such as Paucibacter and Massilia, while suppressing competitive genera such as Duganella and Pedobacter. Redundancy analysis (RDA) indicated that available potassium and ammonium nitrogen were the key factors shaping the microbial community structure. In conclusion, combining PASP with PGPR synergistically improves soil nutrient availability and reshapes the rhizosphere microbiome, resulting in enhanced potato growth, thus demonstrating its potential as a dual-function biostimulant for eco-efficient and sustainable potato production systems.},
}

@article {pmid41304632,
year = {2025},
author = {Wang, B and Meng, F and Cheng, T and Niu, J and Rao, D and Han, Z and Zhang, W and Zhang, Z},
title = {Comprehensive Responses of Physiology and Rhizosphere Microbiome to Saline-Alkaline Stress in Soybean Seedlings with Different Tolerances.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223480},
pmid = {41304632},
issn = {2223-7747},
support = {2023YFD2300100//National Key Research and Development Program of China/ ; CARS-04-PS15//China Agriculture Research System/ ; JLARS-2025030101//Jilin Agriculture Research System/ ; },
abstract = {Soil salinization severely threatens global crop production. Understanding the relationship between crop saline-alkaline tolerance physiology and the rhizosphere microbiome, and leveraging beneficial microorganisms to enhance crop stress resistance, holds importance for sustainable agricultural development. This study investigated the physiological and rhizosphere microbial responses of two soybean cultivars with different saline-alkaline tolerance to stress. Under saline-alkaline conditions, the tolerant cultivar exhibited superior physiological performance, including higher chlorophyll content, photosynthetic efficiency, and elevated activities of antioxidant enzymes (SOD, POD, and CAT), alongside reduced oxidative damage (MDA) and greater biomass accumulation. Combined metagenomic and physiological analyses revealed significant correlations of Bradyrhizobium and Solirubrobacter with key physiological indicators, including dry weight, PIABS, φpo, and MDA. The tolerant cultivar selectively enriched distinct marker microbes, such as Bradyrhizobium sp. and Bradyrhizobium liaoningense, in its rhizosphere. We conclude that the tolerant cultivar exhibits strong intrinsic physiological resistance. This resistance is further enhanced by a beneficially assembled rhizosphere microbiome, while the host plant's physiology remains the dominant factor.},
}

@article {pmid41304557,
year = {2025},
author = {Huang, S and Li, H and Wei, J and Zhou, H and Tang, Y and Gui, Y and Zhu, K},
title = {Drought-Driven Rhizosphere Microbiome and Metabolome Remodeling in Wild vs. Cultivated Saccharum arundinaceum.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/plants14223407},
pmid = {41304557},
issn = {2223-7747},
support = {2023GXNSFBA026223, 2023GXNSFBA026194//Natural Science Foundation of Guangxi/ ; GuikeAA24206005-4, GuikeAA24206006, GuikeAA23073001-1-22//Science and Technology Major Key Project of Guangxi Province/ ; 32160486, 32201766//National Natural Science Foundation of China/ ; CARS-17//China Agriculture Research System/ ; },
abstract = {Sugarcane is highly sensitive to the variations in soil moisture content capacity, and upregulated water stress efficiency restricts its development and crop output. Rhizospheric microbes and metabolites play key roles to mitigate the adverse effects of abiotic stresses, i.e., drought stress. The drought-tolerant wild sugarcane relative, Saccharum arundinaceum Retz., remains poorly characterized with respect to its rhizosphere microbial community dynamics under water limitation. To address this, we analyzed drought-associated shifts in the rhizosphere microbiome and metabolome by comparing native plants from a long-term arid habitat in Guangxi, China, with plants from an irrigated cultivation environment. We analyzed the effects of agronomic traits, soil properties, enzyme activities, and 16S rRNA sequencing and untargeted metabolomics to characterize microbial communities and metabolites, with correlation analyses. Results demonstrated that wild plants possessed thicker stems, higher proline levels, and increased antioxidant enzyme activity. Their rhizospheres were enriched with Actinobacteria, Proteobacteria, and Chloroflexi, which exhibited upregulated urease and acid phosphatase activities. Metabolites linked to phosphotransferase systems and sugar metabolisms were also more abundant. Positive correlations between these microbes, metabolites, and drought traits reveal site-specific microbial-metabolic modules that confer drought resilience, providing valuable insights for sugarcane breeding programs.},
}

@article {pmid41304481,
year = {2025},
author = {Zhou, R and Zhu, M and Chen, M},
title = {Gut Microbiota Dysbiosis and Toxic Metabolite Pathways Linked to Childhood Obesity in Eastern China.},
journal = {Toxics},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/toxics13110929},
pmid = {41304481},
issn = {2305-6304},
support = {82273668//National Natural Science Foundation of China/ ; 82574133//National Natural Science Foundation of China/ ; 25KJA330002//Key Natural Science Foundation of the Jiangsu Higher Education Institutions of China/ ; NA//Excellent Young Backbone Teachers of "Qinglan Project" of Colleges and Universities in Jiangsu Province/ ; NA//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; },
abstract = {Childhood obesity is a newly emerging public health and an emerging concern in environmental health in rapidly urbanized areas of China. This preliminary study investigated the gut microbiome composition and toxic metabolite pathways of school-aged children in Nanjing. Using 16S rRNA sequencing and PICRUSt2-based functional predictions, we observed significant microbial structural changes between the normal weight group and the overweight/obese group, although α diversity was similar. Overweight and obese children exhibited a markedly higher Firmicutes/Bacteroidetes ratio as well as an enrichment of genera such as Subdoligranulum, Ruminococcus, and Lachnospira, indicating increased energy harvesting and inflammation. Functionally, the downregulation of tryptophan metabolism in obese children suggests a reduction in anti-inflammatory indole and an increase in the production of pro-inflammatory kynurenine. In contrast, the upregulation of thiamine metabolism may be linked to enhanced carbohydrate utilization and lipid biosynthetic activity. Our toxicology network analysis and molecular docking experiments suggest that AhR and thiamine-related metabolic enzymes are targets of tryptophan and thiamine metabolism, respectively, and that PPARG is also a potential molecular target mediating thiamine metabolism in childhood obesity. These findings highlight the environment-microbiome-host axis as a potential pathway for metabolic toxicity in childhood obesity. Further studies are needed to validate these toxicological mechanisms and identify microbial biomarkers for early intervention.},
}

@article {pmid41304326,
year = {2025},
author = {Liu, Y and He, P and Liu, D and Song, Y and Jia, C and Wang, D and Jin, Q and Song, G and Wei, Q},
title = {Analysis of Gut Microbial Communities and Functions in Passer ammodendri Under Two Extreme Environments.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112642},
pmid = {41304326},
issn = {2076-2607},
support = {2021YFC2302002, 2022YFC2602200, 2022YFC2602301//the National Key Research and Development Project/ ; },
abstract = {The gut microbiome regulates multiple physiological processes of the host and plays a significant role in the adaptation of wild animal hosts to extreme environments. The saxaul sparrow (Passer ammodendri) is a typical bird species found in the northwest of China, characterized by its strong adaptability to extreme environments. Studying it can help reveal the microbial adaptation mechanisms of the host to extreme environments. Therefore, we conducted a comparative analysis of the intestinal microbial community characteristics and functions of the saxaul sparrow in high-altitude (Pamir Plateau) and desert (Tazhong Town) habitats in Xinjiang. The results of full-length 16S rRNA sequencing and species annotation indicated that the bacterial species composition (relative abundance > 0.1%) of the intestinal microbiota community of the saxaul sparrow was Candidatus Arthromitus sp. SFB rat Yit, Escherichia coli, Enterococcus faecium, Enterococcus faecalis, and Klebsiella pneumoniae, in sequence. In addition, Lysinibacillus sphaericus is a unique strain specific to the Tazhong group, while Stenotrophomonas maltophilia has a much higher abundance in the Tazhong group than in the Pamir Plateau group. It is worth noting that both groups of samples contain potential opportunistic pathogenic bacteria, such as Escherichia coli and Klebsiella pneumoniae. The Shannon index of the Pamir Plateau group was lower than that of the Tazhong Town group (p = 0.0026), indicating that the intestinal microbial diversity of the Pamir Plateau group was lower than that of the Tazhong Town group. However, there was no significant difference in the ACE index between the two groups and it was not statistically significant (p > 0.05). The Beta diversity analysis revealed that the distance between the two groups of samples was considerable (p = 0.001), indicating a significant separation. The functional annotation results indicated that the Pamir Plateau group exhibited enhanced capabilities in carbohydrate metabolism, energy metabolism, and DNA damage repair, while the Tazhong Town group demonstrated enhanced lipid metabolism and detoxification abilities. These findings will help reveal the possible impact of the living environment on the composition and function of the intestinal microbiota of the saxaul sparrow, fill the gap in comparative studies of the intestinal microbiota characteristics of the saxaul sparrow in two extreme environments, and provide new theoretical support for subsequent related research.},
}

@article {pmid41304325,
year = {2025},
author = {Garzon, A and Portillo-Gonzalez, R and Habing, G and Weimer, BC and Schlesener, C and Silva-Del-Rio, N and Karle, BM and Miramontes, C and Pereira, RV},
title = {Co-Occurrence Patterns of Bacterial Communities and Resistance Genes: A Comprehensive Multi-Pen Fecal Microbiome and Resistome Study in Dairy Farms.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112641},
pmid = {41304325},
issn = {2076-2607},
support = {2018-68003-27466//USDA National Institute of Food and Agriculture/ ; },
abstract = {Antimicrobial resistance (AMR) poses a critical public health threat, with rising multidrug resistance cases compromising treatment effectiveness. Knowledge about the resistome in dairy production systems remains limited, particularly regarding lactating cows. This study investigated the microbiome and resistome across the hospital, fresh, and mid-lactation pens on 18 conventional dairy farms in California and Ohio using shotgun metagenomic sequencing of pooled fecal samples. Pooled fecal pat samples were collected as part of a larger field study using a quasi-experimental design that assigned farms to the training intervention group (six per state) or the control group (three per state). For the training intervention group, farm worker(s), identified as having the task of diagnosing and treating adult cows on the farm, participated in a training program on antimicrobial stewardship practices. Pooled fecal samples (n = 7) were collected at enrollment and 3 months after the intervention was completed on each participating farm (n = 18). A total of 10,221 bacterial species and 345 AMR genes conferring resistance to 22 antimicrobial classes were identified. The hospital pen exhibited a higher AMR gene diversity compared to fresh and mid-lactation pens (p < 0.05). Several AMR genes showed bimodal distribution, suggesting complex transmission mechanisms. Network analysis revealed distinct gene correlation profiles across pens, with the hospital pen showing fewer gene interactions. Our findings suggest that farm-level antimicrobial drug use may not be the sole or primary driver of resistome composition in pooled fecal samples from dairy cattle, highlighting the need to investigate other factors influencing AMR dynamics in livestock systems.},
}

@article {pmid41304317,
year = {2025},
author = {Zhang, Y and Feng, D and Huo, J and Xu, J and Wang, Y and Liu, Q and Bai, W and Liu, Q and Zhang, Y},
title = {Cultivar-Dependent Differences in Agronomic Characteristics, Nutritional Value, Fermentation Quality, and Bacteriome Profile of Whole-Plant Sorghum Silage.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112634},
pmid = {41304317},
issn = {2076-2607},
support = {CARS-06-14.5-A30//the National Millet Sorghum Industrial Technology System/ ; 32202703//the national natural science foundation of China/ ; },
abstract = {Forage scarcity in semi-arid regions necessitates the identification of optimal sorghum cultivars for high-quality silage production. This study systematically evaluated varietal differences in agronomic characteristics, nutritive value, fermentation quality, and bacterial community structure of whole-plant sorghum silage. A completely randomized design was implemented with four sorghum cultivars representative of semi-arid northwestern China: Liaotian1 (LT1), Jinnuo3 (JN3), Jinza2001 (JZ2001), and Jinza1531 (JZ1531). Five quadrats per cultivar in experimental fields were randomly designated as biological replicates for silage production. The plants were harvested at the dough stage, chopped, and ensiled in laboratory-scale silos (n = 20, 4 cultivars × 5 replicates) for 120 days. Analyses included agronomic measurements, chemical composition, fermentation parameters, microbial plate enumeration, and bacterial community profiling via 16S rRNA gene amplicon sequencing of the V3-V4 hypervariable region. The results showed that cultivar significantly influenced (p < 0.01) all agronomic traits and most nutritional parameters. The forage-type cultivar LT1 showed the highest biomass yield but the lowest nutritional quality, with higher neutral detergent fiber (47.77% vs. 29.21-32.35%; p < 0.05) and lower starch (10.94% vs. 18.10-24.30%; p < 0.05) contents as well as higher dry matter losses (1.39% vs. 0.91-1.23%; p < 0.05) than grain-type cultivars. In contrast, the grain-type cultivar JN3 exhibited balanced yield-quality traits with the highest (p < 0.05) starch (24.30%) and crude protein (7.50%) contents. Most fermentation parameters differed significantly (p < 0.01) among cultivars, with JN3 showing elevated ammonia-nitrogen (0.24 g/kg) but within acceptable ranges. Microbial diversity analysis revealed cultivar-driven differences in bacterial communities, with JN3 enriched in Leuconostoc and early-colonizing taxa (p < 0.05 and LDA Score > 4). It is concluded that the grain-type cultivar JN3 is the most suitable cultivar for whole-plant sorghum silage production in water-limited regions due to its optimal yield-quality balance. The findings underscore the importance of integrated cultivar evaluation and suggest the potential of targeted microbial inoculants for enhancing silage quality.},
}

@article {pmid41304316,
year = {2025},
author = {Hu, P and Carr, AN and Parlov, M and Swift, D and Tiesman, JP and Ramji, N and Schoch, JJ and Teufel, AG},
title = {Metagenomics Investigation on Baby Diaper Area Microbiome and Its Association with Skin pH and Dermatitis in the Diapered Area.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112632},
pmid = {41304316},
issn = {2076-2607},
abstract = {Dermatitis in the diapered area (DDA) is the most common skin condition in infants and can cause significant pain and discomfort, leading to disturbed sleep, changes in temperament, and heightened concern and anxiety for caregivers. This study investigates the relationship between skin pH, microbiome composition, and DDA severity in 158 infants from China, the US, and Germany, focusing on the buttocks, perianal, and thigh regions. Significant variations in DNA biomass and microbiota profiles were noted. Escherichia coli and Veillonella atypica were linked to higher rash scores and elevated skin pH, while Bifidobacterium longum showed a negative correlation with buttocks pH and rash severity but not with perianal rash. Correlation patterns emerged for other species, like Enterococcus faecalis, between perianal and buttocks rashes. Functional analysis identified key categories, including lipid and fatty acid metabolism, cofactor, amino acid, and carbohydrate metabolism, homeostasis and osmolarity stress, and microbial virulence and oxidative stress response, which are vital for skin health, DDA, and pH regulation in infants. These findings underscore the importance of maintaining a mildly acidic skin pH and minimizing fecal and urine residues for optimal infant skin health, suggesting that microbiota significantly influence DDA development, and provide insights for future preventive strategies and therapeutic interventions.},
}

@article {pmid41304309,
year = {2025},
author = {Paoli, JE and Thongthum, T and Bassett, M and Beardsley, J and Tagliamonte, MS and Cash, MN and Spertus Newman, J and Smith, LM and Anderson, BD and Salemi, M and Subramaniam, K and von Fricken, ME and Braun de Torrez, E and Mathis, V and Mavian, CN},
title = {Virome and Microbiome of Florida Bats Illuminate Viral Co-Infections, Dietary Viral Signals, and Gut Microbiome Shifts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112625},
pmid = {41304309},
issn = {2076-2607},
support = {Department of Pathology EPIG RAS 2021-2022//University of Florida/ ; Florida Informatics Institute SEED 2022-2023//University of Florida/ ; Biodiversity Institute SEED 2022-2023//University of Florida/ ; },
abstract = {Florida's bat virome remains poorly characterized despite the state's high bat species diversity and conservation importance. We characterized viral metagenomes from rectal tissues, anal swabs, and feces of Myotis austroriparius and Tadarida brasiliensis sampled across north Florida. We recovered a near-complete Hubei virga-like virus 2 (HVLV2) genome from T. brasiliensis feces, a finding consistent with an arthropod-derived dietary signal rather than active bat infection. An Alphacoronavirus (AlphaCoV) was detected in two M. austroriparius specimens, including one with a putative co-infection involving an Astrovirus (AstV), the first detection of AstV in Florida bats to date. Parallel profiling of the M. austroriparius gut microbiome highlighted compositional differences in the co-infected individual relative to AlphaCoV-only and virus-negative bats, suggestive of potential associations between viral detection and gut microbial shifts. Our study expands the known viral diversity in Florida bat populations, and demonstrates how metagenomics can simultaneously illuminate host diet, viral exposure, and gut microbial ecology. This approach provides a scalable framework for monitoring how diet, microbiome composition, and environmental pressures shape the bat virome, and inform conservation and zoonotic risk assessments.},
}

@article {pmid41304301,
year = {2025},
author = {Martinez, A and St-Pierre, B},
title = {Metagenomic Identification and Characterization of Novel Vitamin B12 Synthesizers from the Rumen of Beef Cattle Fed High-Lipid Inclusion Diets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112617},
pmid = {41304301},
issn = {2076-2607},
support = {SD00H866-26//South Dakota State University Agricultural Experiment Station Hatch funds (USDA National In-stitute of Food and Agriculture)/ ; },
abstract = {Beef production in intensive systems requires optimal nutrition to maximize growth and profitability. While triglycerides contain twice the energy per unit weight compared to polysaccharides, they are not nearly as commonly used as a supplemental source of energy compared to starch, largely in part due to their negative effects on rumen physiology when their inclusion levels are too high. To gain further insights into the response of rumen microbial communities to elevated dietary lipid levels, we took advantage of rumen samples collected as part of a previously published study that tested high inclusion (4% and 8%) of tallow or linseed oil in beef cattle as part of a 5 × 5 Latin square design, with corn used as a base dietary ingredient. Using a 16S rRNA gene-based profiling approach, two uncharacterized candidate rumen bacterial Operational Taxonomic Units (OTUs), referred to as Bt-995 and Bt-1367, were found to be in higher abundance in rumen samples collected from steers when they were fed diets with higher inclusion of linseed oil. Using a metagenomics approach to assemble contigs corresponding to genomic regions of these OTUs, various predicted metabolic functions were found to be shared. Consistent with the dietary treatments of the original animal study, functions associated with starch utilization and triglyceride metabolism were identified. Unexpectedly, however, contig sets from both OTUs also encoded genes predicted to be involved in vitamin B12 biosynthesis, as well as ethanolamine utilization, a function that is dependent on vitamin B12 as a co-factor. Together, these results indicate that vitamin B12-related functions may provide an advantage to rumen bacteria under conditions of high dietary triglyceride inclusion.},
}

@article {pmid41304278,
year = {2025},
author = {Qiao, T and Zhu, Z},
title = {Multi-Kingdom Gut Microbiome Interaction Characteristics Predict Immune Checkpoint Inhibitor Efficacy Across Pan-Cancer Cohorts.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112595},
pmid = {41304278},
issn = {2076-2607},
support = {2025A04J5264//Guangzhou Basic and Applied Basic Research Project/ ; 2023A1515010744//Guangdong Basic and Applied Basic Research Foundation/ ; },
abstract = {An increasing number of studies have confirmed that the gut microbiota, especially bacteria, is closely related to the efficacy of immune checkpoint inhibitor (ICI) therapy. However, the effectiveness of multi-kingdom microbiota and their interactions in predicting the therapeutic effect of ICI therapy remains uncertain. We integrated extensive gut metagenomic databases, including 1712 samples of 10 cohorts from 7 countries worldwide, to conduct rigorous differential analysis and co-occurrence network analysis targeting multi-kingdom microbiota (bacteria, fungi, archaea, and virus). We ultimately identified two subtypes (C1 and C2) by employing a weighted similarity network fusion (WSNF) method. Subtype C2 exhibited higher microbial diversity, better treatment response, and improved prognosis compared to subtype C1. Notably, subtype C2 was associated with higher abundance of beneficial genera such as Bacteroides and Kluyveromyces, while subtype C1 contained potentially detrimental taxa like Malassezia. A multi-kingdom model incorporating 32 genera demonstrated superior predictive accuracy for ICI therapy efficacy compared to single-kingdom models. Co-occurrence network analysis revealed a more robust and interconnected microbiome in subtype C2, suggesting a stable gut environment correlates with effective ICI therapy efficacy. This study highlights the potential of a multi-kingdom signature in predicting the efficacy of ICI therapy, offering a novel perspective for personalized therapy in oncology.},
}

@article {pmid41304268,
year = {2025},
author = {Bednarska, NG and Reitlo, LS and Beisvag, V and Stensvold, D and Haberg, AK},
title = {Microbial Signatures Mapping of High and Normal Blood Glucose Participants in the Generation 100 Study.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112582},
pmid = {41304268},
issn = {2076-2607},
abstract = {Intestinal dysbiosis has been linked to metabolic disorders, including insulin resistance and type 2 diabetes mellitus (T2DM). T2DM typically follows a prediabetic stage, during which insulin resistance develops. During the early stages of T2DM, its development can be corrected, thus potentially preventing or delaying the onset of the disease. This secondary, exploratory, cross-sectional comparison study aimed to contrast the gut microbiome of individuals with elevated fasting blood glucose to that of individuals with glucose levels within the normal range. This study involved 65 older adults (ages 76-83 years) enrolled from the randomized controlled trial entitled the "Generation 100 Study", all of whom consented to provide their gut microbiome samples. We employed a high-throughput sequencing of the bacterial 16S rRNA gene to obtain metagenomic microbial profiles for all participants. These profiles were then correlated with clinical measures. Overall, microbial alpha diversity was significantly reduced in the high glucose group. We have also observed distinct patterns of microbial beta diversity between high and normal glucose groups. At the phylum level, we found that Synergistes, Elusimicobia, Euryarchaeota, Verrucomicrobia, and Proteobacteria were all significantly decreased in participants with high blood glucose. Additionally, P. copri (ASV 909561) was significantly elevated (10-fold increase) in the high glucose groups, suggesting that it may serve as an early T2DM marker. In contrast to prior reports on the Fusobacterium genus, we found that it was significantly increased in the normal glucose group, with a significant 151-fold increase compared to the high glucose group. Directly linking gut microbiota profiles with clinical indicators such as fasting blood glucose and T2DM diagnosis allows the identification of specific microbial features associated with glucose dysregulation, providing preliminary population-level evidence to guide future translational research. Our results indicate significant changes in the microbiome that may provide valuable insights for early intervention in pre-diabetic states.},
}

@article {pmid41304266,
year = {2025},
author = {Santoyo, G},
title = {Advances in the Plant Microbiome: Rhizosphere, Endosphere, and Phyllosphere.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112581},
pmid = {41304266},
issn = {2076-2607},
abstract = {The continuous growth of the global human population demands sustainable production systems that move away from synthetic fertilizers, pesticides, and other agrochemicals, which pose serious toxicological, environmental, and public health risks [...].},
}

@article {pmid41304258,
year = {2025},
author = {Viana, J and Ferro, T and Pitschieller, R and Machado, V and Su, N and Mendes, JJ and Botelho, J},
title = {Neutrophils at the Crossroads of Oral Microbiome Dysbiosis and Periodontal Disease.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112573},
pmid = {41304258},
issn = {2076-2607},
support = {10.54499/UIDB/04585/2020//FCT/ ; },
abstract = {Neutrophils are the most abundant circulating leukocytes and essential components of innate immunity. Through mechanisms such as phagocytosis, reactive oxygen species (ROS) production, degranulation, and neutrophil extracellular trap (NET) formation, they play a crucial role in host defense. However, dysregulated neutrophil responses are linked to chronic inflammatory conditions, including periodontitis. This review summarizes current evidence on neutrophil biology in periodontal health and disease, focusing on functional mechanisms, recruitment pathways, the influence of dysbiosis, and their potential as biomarkers and therapeutic targets. Neutrophils display a dual role in periodontal tissues: while protecting against microbial invasion, their excessive or impaired activity contributes to tissue destruction. Altered chemotaxis, defective phagocytosis, and uncontrolled NET release perpetuate inflammation and alveolar bone loss. Neutrophil-derived enzymes, including myeloperoxidase, elastase, and matrix metalloproteinases, emerge as promising biomarkers for early diagnosis. In parallel, therapeutic strategies targeting oxidative stress, NET regulation, or neutrophil hyperactivity are being explored to preserve periodontal tissues. Neutrophils are central players in periodontal pathophysiology. Understanding their regulation and interaction with the oral microbiome may enable the development of novel diagnostic and therapeutic approaches, ultimately improving periodontal disease management.},
}

@article {pmid41304256,
year = {2025},
author = {Mateescu, DM and Ilie, AC and Cotet, I and Guse, C and Muresan, CO and Pah, AM and Badalica-Petrescu, M and Iurciuc, S and Craciun, ML and Avram, A and Margan, MM and Enache, A},
title = {Gut Microbiome Dysbiosis in COVID-19: A Systematic Review and Meta-Analysis of Diversity Indices, Taxa Alterations, and Mortality Risk.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112570},
pmid = {41304256},
issn = {2076-2607},
support = {"Victor Babes" University of Medicine and Pharmacy Timisoara//"Victor Babes" University of Medicine and Pharmacy Timisoara/ ; },
abstract = {COVID-19 is associated with gut microbiome alterations that may influence disease outcomes through immune and inflammatory pathways. This systematic review and meta-analysis evaluated global evidence on gut dysbiosis in COVID-19. We searched PubMed/MEDLINE, Embase, Web of Science, Scopus, and Cochrane Library up to 5 October 2025 (PROSPERO CRD420251160970). Alpha-diversity indices and microbial taxa log-fold changes (logFC) were analyzed using random-effects models. The pooled standardized mean difference (SMD) for the Shannon index was -0.69 (95% CI -0.84 to -0.54; I[2] = 42%), confirming reduced microbial diversity. Faecalibacterium prausnitzii showed a significant pooled depletion (logFC = -1.24; 95% CI -1.68 to -0.80; k = 10; I[2] = 74%), while Enterococcus spp. was increased (logFC = 1.45; 95% CI 1.12-1.78). Egger's test did not suggest publication bias (p = 0.32). Gut dysbiosis was consistently associated with reduced microbial diversity and enrichment of pathogenic taxa, correlating with increased disease severity and mortality (HR = 1.67). These findings highlight the potential of microbiome profiling as a prognostic tool in COVID-19, although clinical translation requires further validation.},
}

@article {pmid41304252,
year = {2025},
author = {Ramírez-López, M and Bautista-Cruz, A and Toledo-López, A and Aquino-Bolaños, T},
title = {Rhizospheric and Endophytic Plant Growth-Promoting Bacteria Associated with Coffea arabica L. and Coffea canephora Pierre ex Froehner: A Review of Their Agronomic Potential.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112567},
pmid = {41304252},
issn = {2076-2607},
support = {SIP-20240857and SIP-20252379//Instituto Politécnico Nacional/ ; },
abstract = {Plant growth-promoting bacteria (PGPB) associated with Coffea arabica L. and Coffea canephora Pierre ex Froehner offer a viable strategy to reduce synthetic inputs and enhance resilience in coffee agroecosystems. This review synthesizes evidence from the past decade on rhizosphere-associated and endophytic taxa, their plant growth-promotion and biocontrol mechanisms and the resulting agronomic outcomes. A compartment-specific core microbiome is reported, in the rhizosphere of both hosts, in which Bacillus and Pseudomonas consistently dominate. Within endophytic communities, Bacillus predominates across tissues (roots, leaves and seeds), whereas accompanying genera are host- and tissue-specific. In C. arabica, endophytes frequently include Pseudomonas in roots and leaves. In C. canephora, root endophytes recurrently include Burkholderia, Kitasatospora and Rahnella, while seed endophytes are enriched for Curtobacterium. Functionally, coffee-associated PGPB solubilize phosphate; fix atmospheric nitrogen via biological nitrogen fixation; produce auxins; synthesize siderophores; and express 1-aminocyclopropane-1-carboxylate deaminase. Indirect benefits include the production of antifungal and nematicidal metabolites, secretion of hydrolytic enzymes and elicitation of induced systemic resistance. Under greenhouse conditions, inoculation with PGPB commonly improves germination, shoot and root biomass, nutrient uptake and tolerance to drought or nutrient limitation. Notable biocontrol activity against fungal phytopathogens and plant-parasitic nematodes has also been documented. Key priorities for translation to practice should include (i) multi-site, multi-season field trials to quantify performance, persistence and economic returns; (ii) strain-resolved omics to link taxa to functions expressed within the plant host; (iii) improved bioformulations compatible with farm management and (iv) rationally designed consortia aligned with production goals and biosafety frameworks.},
}

@article {pmid41304248,
year = {2025},
author = {Chen, F and He, X and Liu, Q and Gao, F and Zeng, C and Li, D},
title = {Bio-Organic Fertilizer Modulates the Rhizosphere Microbiome to Enhance Sugarcane Growth and Suppress Smut Disease.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112563},
pmid = {41304248},
issn = {2076-2607},
support = {2023YFD1902802//National Key Research and Development Program of China/ ; },
abstract = {Sugarcane smut, caused by the fungal pathogen Sporisorium scitamineum, leads to significant economic losses in the global sugarcane industry. Bio-organic fertilizers (BF) offer a promising and sustainable strategy to mitigate smut incidence and enhance sugarcane growth. While the application of BF is known to modulate root exudates and rhizosphere microbial community structure, thereby promoting disease resistance, the precise mechanisms underpinning BF-mediated suppression of sugarcane smut remain largely unclear. This study investigated the microbiological mechanisms of smut suppression using a pot experiment, comparing a novel BF treatment (composted substrate enriched with Bacillus subtilis, Bacillus altitudinis, Bacillus cereus, Trichoderma harzianum, and Trichoderma longibrachiatum, biochar, and calcium carbonate) with a control receiving only conventional organic fertilizer. BF application significantly increased plant height (by 95.2%), dry weight (137.5%), fresh weight (253.3%), and sugar content (43.1%) relative to the control. Furthermore, the BF treatment enhanced catalase activity by 167.8% and peroxidase activity by 102.3% in sugarcane leaves, while the control effectiveness against the incidence of smut disease reached 88.0%. Analysis of the rhizosphere microbiome revealed that BF application significantly altered microbial alpha- and beta-diversity. Specifically, the BF treatment notably enriched beneficial genera such as Pseudomonas and Meyerozyma. Beta-diversity analysis revealed distinct microbial community structures in BF-treated rhizosphere soil compared to the control. Correlation and random forest analyses identified Pseudomonas and Meyerozyma as key taxa that were positively associated with sugarcane growth parameters and negatively correlated with smut incidence. These findings elucidate the dual role of this novel BF in enhancing sugarcane growth and suppressing smut incidence through the strategic reshaping of the rhizosphere microbiome.},
}

@article {pmid41304231,
year = {2025},
author = {Fadiji, AE and Adeniji, A and Lanrewaju, AA and Adedayo, AA and Chukwuneme, CF and Nwachukwu, BC and Aderibigbe, J and Omomowo, IO},
title = {Key Challenges in Plant Microbiome Research in the Next Decade.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112546},
pmid = {41304231},
issn = {2076-2607},
abstract = {The plant microbiome is pivotal to sustainable agriculture and global food security, yet some challenges hinder fully harnessing it for field-scale impact. These challenges span measurement and integration, ecological predictability and translation across environments and seasons. Key obstacles include technical challenges, notably overcoming the limits of current sequencing for low-abundance taxa and whole-community coverage, integrating multi-omics data to uncover functional traits, addressing spatiotemporal variability in microbial dynamics, deciphering the interplay between plant genotypes and microbial communities, and enforcing standardized controls, metadata, depth targets and reproducible workflows. The rise of synthetic biology, omics tools, and artificial intelligence offers promising avenues for engineering plant-microbe interactions, yet their adoption requires regulatory, ethical, and scalability issues alongside clear economic viability for end-users and explicit accounting for evolutionary dynamics, including microbial adaptation and horizontal gene transfer to ensure durability. Furthermore, there is a need to translate research findings into field-ready applications that are validated across various soils, genotypes, and climates, while ensuring that advances benefit diverse regions through global, interdisciplinary collaboration, fair access, and benefit-sharing. Therefore, this review synthesizes current barriers and promising experimental and computational strategies to advance plant microbiome research. Consequently, a roadmap for fostering resilient, climate-smart, and resource-efficient agricultural systems focused on benchmarked, field-validated workflows is proposed.},
}

@article {pmid41304229,
year = {2025},
author = {Watanabe, K and Yanagi, U},
title = {Comparison of QIIME1 and QIIME2 for Analyzing Fungal Samples from Various Built Environments.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112545},
pmid = {41304229},
issn = {2076-2607},
support = {21ek0410055//Japan Agency for Medical Research and Development/ ; 22ek0410097//Japan Agency for Medical Research and Development/ ; 21LA1005//Ministry of Health Labour and Welfare/ ; 21LA1501//Ministry of Health Labour and Welfare/ ; },
abstract = {This study evaluates the differences between bioinformatics pipelines by analyzing samples collected from various built environments. Previous comparative studies of microbial community analysis pipelines have largely focused on bacterial communities, mock communities, or soil fungi, often with small sample sizes, and have not specifically targeted built environments. Our results highlight key differences between OTU (QIIME1) and ASV (QIIME2) analyses. OTU analysis clusters OTUs at 97% similarity and tends to show higher diversity values in diversity analyses. Regarding abundantly detected fungi, OTU analysis identified more genera than ASV analysis. However, the OTU method has a high rate of false positives and false negatives, indicating low error-removal capability and suggesting that many fungal genera may have been detected. Therefore, a combined approach using OTU analysis combined with ASV analysis allows for both the comprehensive detection of dominant taxa and the inclusion of rare species. Overall, our findings emphasize that the choice of pipeline significantly influences the composition of the observed fungal community in built environments. Careful consideration of both OTU and ASV strategies can enhance the reliability and completeness of fungal metabarcoding studies, particularly when studying complex indoor microbial communities.},
}

@article {pmid41304219,
year = {2025},
author = {Cui, J and Tang, L and Li, Z and Wang, S and Zhou, J and Yan, H and Wang, X},
title = {Active Factors in the Adult Pig Colon: Microbial Transplantation Versus Supplementation with Metabolites in Weaned Piglets.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112533},
pmid = {41304219},
issn = {2076-2607},
support = {No. 2022YFD1300402//the Key Program of the National Natural Science Foundation of China/ ; No. 32202715//National Natural Science Foundation of China/ ; No. 23DAA00403//the National Natural Science Foundation of China/ ; No. 2023B10564001//the Double first-class discipline promotion project under grant/ ; },
abstract = {The adult pig intestinal microbiota boosts piglet intestinal and microbiome development, thereby improving growth. However, the functional bacteria, metabolites, and their region-specific intestinal roles remain to be characterized. Administration of adult colon microbiota (CM; devoid of metabolites) to piglets promoted intestinal development post-weaning, as indicated by increased intestinal mucosal weight, villus-to-crypt ratio of the ileum (p < 0.05), and stimulated mucin secretion (p < 0.05). This effect was potentially mediated by modulating beneficial microbiota, including ASV50_Prevotella 7, ASV52_Prevotella 1, and ASV81_Coprococcus 1. Adult colon-derived microbiota was found to preferentially colonize the piglet colon, supported by significantly higher bacterial loads in colonic contents. Piglets receiving adult colon supernatant (CS; without bacterial cells) showed improved feed efficiency (FE; p < 0.05), with numerically higher body weight (BW) and average daily gain (ADG) compared to the control (CON) group. Additionally, CS transplantation (CST) promoted intestinal development, potentially by modulating abundances of beneficial bacteria species, including ASV95_Turicibacter, and ASV109_Ruminococcaceae, which correlated with increased production of antioxidant and anti-inflammatory chemicals, including protocatechuic acid (PCA, p < 0.01). Adult colon-derived microbiota and metabolites enhanced intestinal development in piglets. CS supplementation improved growth and immunity, mitigating post-weaning stress potentially through enriching growth-linked bacteria (e.g., Turicibacter and Ruminococcaceae) and metabolites production (e.g., prephenate and PCA). These findings highlight these functional microbiota and metabolites as promising direct-fed microbial or metabolite additives for piglet growth and intestinal health post-weaning.},
}

@article {pmid41304215,
year = {2025},
author = {Arruda, ISA and Cavalcante, CDS and Rubens, RS and Castro, LNPF and Nóbrega, YKM and Dalmolin, TV},
title = {Changes in the Gut Microbiota of Patients After SARS-CoV-2 Infection: What Do We Know?.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112529},
pmid = {41304215},
issn = {2076-2607},
support = {DPI/BCE nº 01/2025//University of Brasilia/ ; FAPDF nº 09/2023//Fundação de Apoio à Pesquisa do Distrito Federal/ ; },
abstract = {COVID-19 can cause long-term symptoms, such as a post-infection syndrome, known as Long-COVID. Among the symptoms present during this period, the most reported are gastrointestinal symptoms. This study discusses the effects of changes in the gut microbiota of post-COVID-19 patients. SARS-CoV-2 infection is associated with significant alterations in gut microbial composition, disturbing its homeostasis and promoting a reduction in the abundance of beneficial symbiotic bacteria and an increase in the abundance of opportunistic pathogens. Furthermore, the composition of the gut microbiota may play a role in the prognosis of patients with post-COVID-19 infection. The microbiota of the intestinal tract and the respiratory tract influence each other; therefore, the gut-lung axis has attracted increasing interest in understanding COVID-19. Moreover, the brain-gut axis has been studied, since there have been reports of anxiety and depression along with post-COVID-19 gastrointestinal symptoms. Treatments options for intestinal dysbiosis in Long-COVID patients include probiotics, prebiotics, and fecal microbiota transplantation. These treatments may serve as an approach to improve gastrointestinal symptoms during Long-COVID, increasing microbiome diversity, strengthening the integrity of intestinal barrier functions, and consequently influencing the treatment of COVID-19.},
}

@article {pmid41304207,
year = {2025},
author = {Uhegwu, CC and Anumudu, CK},
title = {Probiotic Potential of Traditional and Emerging Microbial Strains in Functional Foods: From Characterization to Applications and Health Benefits.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112521},
pmid = {41304207},
issn = {2076-2607},
abstract = {Global consumer demand for probiotic-enriched functional foods has increased as consumers become increasingly aware of the connection between what they eat and its role in their long-term health. Compared with conventional foods that primarily deliver fundamental nutrients, functional foods include biologically active compounds capable of influencing physiological processes. While traditionally used probiotic strains like Lactobacillus and Bifidobacterium are still at the center of this trend, there is growing interest in the exploration of emerging and novel microbial candidates that harbor new functional properties. This review addresses the characterization, modes of action, technological limitations, regulatory guidelines, and prospective health benefits of new probiotic strains in functional foods. The review further highlights the need for precise strain selection, novel encapsulation technologies for viability, and strict safety assessments in accordance with EFSA's QPS (Qualified Presumption of Safety) and the United States FDA GRAS (Generally Recognized As Safe) specifications. Current research focuses on the classical benefits of probiotics, including gut microbiota modulation, immunomodulation, antimicrobial activity, lowering of cholesterol, and mental health. However, long-term clinical validation, strain specificity, personalized application, and effective communication to consumers are some areas where gaps remain. Addressing these challenges through the incorporation of omics technologies, synthetic biology, and more detailed microbiome-host interaction studies will be the key to unlocking the full potential of next-generation probiotics and sustaining consumer trust in this emerging market.},
}

@article {pmid41304202,
year = {2025},
author = {Feng, JJ and Maddirala, NR and Saint Fleur, A and Zhou, F and Yu, D and Wei, F and Zhang, Y},
title = {Gut Microbiome and Immune System Crosstalk in Chronic Inflammatory Diseases: A Narrative Review of Mechanisms and Therapeutic Opportunities.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112516},
pmid = {41304202},
issn = {2076-2607},
abstract = {The gut microbiota, a complex community of trillions of microorganisms residing in the gastrointestinal tract, plays a vital role in maintaining host health and regulating a wide range of physiological functions. Advances in molecular biology have greatly expanded our understanding of the dynamic interactions between the gut microbiome and the immune system. Disruption of this microbial community, known as dysbiosis, can compromise epithelial barrier integrity, trigger aberrant immune activation, and lead to the production of proinflammatory metabolites. These changes are increasingly recognized as contributing factors in the pathogenesis of chronic inflammatory diseases. Emerging research highlights the gut microbiota as a key modulator of immune homeostasis, influencing both local and systemic inflammatory processes during the initiation and progression of these diseases. Understanding the mechanisms underlying gut microbiota-immune interactions will offer new avenues for therapeutic interventions. This review focuses on six representative chronic inflammatory diseases, including rheumatoid arthritis, inflammatory bowel disease, psoriasis, systemic lupus erythematosus, asthma, and vasculitis, all of which are characterized by dysregulated immune responses and persistent inflammation. Our goal is to synthesize the recent research on the role of gut microbiome in the pathogenesis of the diseases listed above and provide insights into the development of microbiota-based therapies, particularly fecal microbiota transplant, dietary modifications, prebiotic and probiotic interventions, for their treatment.},
}

@article {pmid41304199,
year = {2025},
author = {Zhang, J and Jiang, F and Li, X and Song, P and Zhang, T},
title = {Metagenome-Based Functional Differentiation of Gut Microbiota and Ecological Adaptation Among Geographically Distinct Populations of Przewalski's Gazelle (Procapra przewalskii).},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112513},
pmid = {41304199},
issn = {2076-2607},
support = {QHEG-2024-04//the 2023 award fund of Qinghai Provincial Key Laboratory of Animal Ecological Genomics/ ; 2024-ZZ-14//Independent Project of State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Univer-sity/ ; 2024T170992//the China Postdoctoral Science Foundation/ ; },
abstract = {Przewalski's gazelle (Procapra przewalskii) is an endangered ungulate endemic to the Qinghai-Tibet Plateau, with a small population size and exposure to multiple ecological pressures. Its gut microbiota may play a crucial role in host environmental adaptation. To investigate the functional divergence of gut microbial communities, we performed high-throughput metagenomic sequencing on 105 wild fecal samples collected from 10 geographic regions around Qinghai Lake. The results revealed significant regional differentiation in key functional modules related to metabolism, antibiotic resistance mechanisms, and virulence-associated pathways. All populations showed enrichment in core metabolic pathways such as carbohydrate and amino acid metabolism, with carbohydrate-active enzymes dominated by glycoside hydrolases (GHs) and glycosyltransferases (GTs), exhibiting overall functional conservation. Although populations shared many antibiotic- and virulence-related reference genetic markers, the marker composition associated with distinct resistance mechanisms and pathogenic processes exhibited clear population-specific patterns, suggesting differential microbial responses to local environmental pressures. Correlation network analysis further identified core taxa (e.g., Arthrobacter and Oscillospiraceae/Bacteroidales lineages) as key genera linking community structure with core metabolic, resistance-related, and virulence-associated marker functions. Overall, the gut microbiota of Przewalski's gazelle exhibits a complex spatially structured functional differentiation, reflecting host-microbiome co-adaptation under region-specific ecological pressures. These findings provide critical methodological and theoretical support for microecological health assessment and regionally informed conservation management of this endangered species.},
}

@article {pmid41304185,
year = {2025},
author = {Shijimaya, T and Tahara, T and Shimogama, T and Yamazaki, J and Kobayashi, S and Nakamura, N and Takahashi, Y and Honzawa, Y and Tomiyama, T and Naganuma, M},
title = {The Gastric Microbiome Communities and Endoscopic Mucosal Morphologies Associated with Premalignant Conditions.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112499},
pmid = {41304185},
issn = {2076-2607},
support = {22K08089.//JSPS KAKENHI Grant-in-Aid for Scientists (C)/ ; },
abstract = {The risk of Helicobacter pylori (H. pylori)-related gastric tumorigenesis is closely associated with the degree of chronic gastritis, although other gastric mucosa microbes may be relevant in this process. The morphological identification of the gastric mucosa associated with the cancer-promoting microbiome may have important implications for gastric cancer prevention. This study characterized gastric mucosa microbiome communities in relation to their mucosal morphologies. A total of 94 biopsies from non-neoplastic gastric bodies underwent 16S rRNA sequencing. Microbiome structures were characterized in relation to their mucosal morphologies, which were obtained using narrow-band imaging with magnifying endoscopy. H. pylori infection- and inflammatory mucosa-associated gastric mucosal morphologies exhibited decreased bacterial alpha diversity measures and an increase in the abundance of the Helicobacter genus, while the mucosal morphology associated with severely atrophic mucosa exhibited increased bacterial alpha diversity measures and a decrease in the abundance of the Helicobacter genus. This type of mucosal morphology was also associated with increased levels of well-known gastric cancer-related bacteria, e.g., Streptococcus. The microbial dysbiosis associated with gastric mucosa morphology also correlated well with the occurrence of gastric cancer and the DNA methylation status. Our results suggest that gastric microbiome communities correlate well with their premalignant condition-associated mucosal morphologies.},
}

@article {pmid41304176,
year = {2025},
author = {Lee, KC and Lee, H and Kim, OS and Sul, WJ and Lee, H and Kim, HJ},
title = {Case Study on Shifts in Human Skin Microbiome During Antarctica Expeditions.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112491},
pmid = {41304176},
issn = {2076-2607},
support = {Excellent Student Scholarship in 2023//Chung-Ang University/ ; 2024ER211600//Korea National Institute of Health/ ; 2023-NI-019-02//National Institute of Health/ ; },
abstract = {The human skin microbiome plays a crucial role in maintaining skin health by acting as a barrier against pathogens and modulating immune regulation. This case study investigates the skin microbiome of two healthy Korean male individuals in their 20s during Antarctic expeditions, focusing on microbial changes, reversion to pre-expedition states, and the influence of environmental and lifestyle factors. Notable microbial alterations were observed, including increases in Pseudomonadota and decreases in Actinomycetota, indicating pronounced microbial shifts in response to harsh environmental factors such as low temperature and humidity. Post-expedition revealed incomplete recovery to pre-expedition states, with Host A showing a higher resilience index, suggesting faster microbial recovery. Correlation analyses revealed associations between microbial changes and environmental factors (e.g., temperature, humidity, atmospheric pressure) as well as lifestyle factors (e.g., sunblock usage, outdoor activities), highlighting complex interactions between host behaviors and microbiome dynamics. Despite the study's limited sample size, these findings offer insights into the adaptability and resilience of the skin microbiome under extreme environments, with potential implications for health management and skincare strategies during isolated and prolonged expeditions.},
}

@article {pmid41304167,
year = {2025},
author = {Vitezić, BM and Franović, B and Renko, I and Kuiš, D and Begić, G and Blašković, M and Gabrić, D and Nikolić, M and Vranić, TŠ and Veljanovska, D and Cvijanović Peloza, O},
title = {Microbiome Profiling of Biofilms Formed on d-PTFE Membranes Used in Guided Bone Regeneration.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112478},
pmid = {41304167},
issn = {2076-2607},
support = {2170-137-08-24-19//UNIRI-biomed/ ; IP-2020-02-7875//the Croatian Science Foundation/ ; },
abstract = {In guided bone regeneration (GBR) procedures, d-PTFE membranes are often used as a barrier to promote alveolar ridge regeneration. The aim of this randomized clinical trial was to examine the microbial diversity and structure of biofilms on two types of d-PTFE membranes, Permamem[®] and Cytoplast™, over four-week oral cavity exposure periods. Bacterial biofilm analysis was performed using 16S rRNA next-generation sequencing (NGS) on 36 samples (20 Permamem[®] and 16 Cytoplast™). The results showed significant differences in the microbial profiles: Cytoplast™ membranes showed reduced microbial diversity and an enhanced proportion of pathobionts like Selenomonas, Segatella, Fusobacterium and Parvimonas, which are associated with periodontal and peri-implant diseases and alveolar bone loss. Permamem[®] membranes promoted colonization by bacteria associated with healthy oral conditions, such as the genera Streptococcus, Kingella and Corynebacterium. Overall, our results showed that Cytoplast™ membranes generate a specific type of biofilm, leading to reduction in health-related bacterial species and facilitating growth conditions for dysbiosis shift. Further research and patient follow-ups are essential to thoroughly evaluate the clinical implications of different d-PTFE membranes used in guided bone regeneration.},
}

@article {pmid41304151,
year = {2025},
author = {Reveles, KR and Meehan, J and Tillotson, G},
title = {Fecal Microbiota Transplantation in Animals: Therapeutics, Conservation, and Farming.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112465},
pmid = {41304151},
issn = {2076-2607},
abstract = {Fecal microbiota transplantation (FMT) is increasingly used in both human and veterinary settings to restore gut microbiota and promote health. Advances in sequencing technologies and microbiome analysis have expanded our understanding of microbial communities and enabled broader FMT applications. As insights grow into what constitutes a healthy microbiome, interest in using FMT across a range of animal contexts has also increased. This narrative review highlights recent progress in the use of FMT to improve the welfare of farm animals, manage infectious and chronic conditions in companion animals, and support the health of wildlife in conservation and reintroduction programs. Representative examples from each domain are discussed.},
}

@article {pmid41304147,
year = {2025},
author = {Lee, JY and Shin, H and Yu, J and Kong, HG},
title = {Changes in the Structure of Strawberry Leaf Surface Bacterial and Fungal Communities by Plant Biostimulants.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112461},
pmid = {41304147},
issn = {2076-2607},
support = {2024-DD-RD-0122-01-201//This research was supported by the Innopolis Korea Innovation Foundation's support program (Project Name: Technology Transfer Steps Towards the Commercialization of Research Re-sults[B24006], Project Number: 2024-DD-RD-0122-01-201), Republic of Korea./ ; },
abstract = {The application of plant biostimulants to enhance fruit quality is increasing, yet their impact on the phyllosphere microbiome remains understudied. This study investigated the effects of a sugar-based biostimulant on the bacterial and fungal communities on strawberry leaf surfaces using Illumina MiSeq sequencing. The sweetener treatment significantly decreased bacterial alpha diversity (Shannon and Simpson indices). Compositional analysis revealed a lower relative abundance of the phylum Pseudomonadota, whereas the fungal phylum Ascomycota increased and Basidiomycota decreased. At the family level, Sphingobacteriaceae, Bacillaceae, and Micrococcaceae were significantly enriched in the treated group. Furthermore, we isolated bacterial strains, including Sphingomonas zeae St1 and Frigoribacterium faeni TSAY2, which increased in abundance post-treatment and demonstrated enhanced growth using the sweetener as a sole nutrient source. These findings suggest that sugar-based biostimulants directly reshape the composition and functional potential of the phyllosphere microbiome, which may, in turn, influence nutrient uptake, plant growth, and immunity.},
}

@article {pmid41304144,
year = {2025},
author = {Schnabl, JT and Sandini, S and Stärkel, P and Hartmann, P},
title = {Serum Levels of Candida albicans 65-kDa Mannoprotein (CaMp65p) Correlate with Liver Disease in Patients with Alcohol Use Disorder.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112458},
pmid = {41304144},
issn = {2076-2607},
support = {1K12HD105271-05/NH/NIH HHS/United States ; 1KL2TR001444-01/NH/NIH HHS/United States ; 1P30DK120515-01/NH/NIH HHS/United States ; PNC22-159963//American Association for the Study of Liver Diseases Foundation/ ; T.0217.18//Fondation nationale de recherche scientifique (FNRS)/ ; T.0195.22//Fondation nationale de recherche scientifique/ ; J.0195.24//Fondation nationale de recherche scientifique/ ; },
abstract = {Alcohol-associated liver disease is a global health burden with high morbidity and mortality, and the fungal microbiome is important for its progression. In particular, Candida albicans and C. albicans-reactive T helper 17 (Th17) cells contribute to alcohol-associated liver disease. Specific C. albicans antigens that activate Th17 cells during this disease are unknown. The C. albicans 65 kDa mannoprotein (CaMp65p) is one of the most abundant and immunodominant proteins of C. albicans, and is capable of eliciting robust T cell and interleukin (IL)-17A responses. The aim of this study was to measure levels of CaMp65p in serum of patients with alcohol use disorder and liver disease. Serum CaMp65p levels were measured in the serum of 60 patients with alcohol use disorder using an indirect competitive Enzyme-Linked Immunoabsorbent Assay (ELISA). Serum CaMp65p levels were correlated with liver disease severity. Serum CaMp65p levels positively correlated with several clinical and biochemical markers of liver injury and disease within the patient group with alcohol use disorder, including serum aspartate aminotransferase (AST; R = 0.33, p = 0.0092), alanine aminotransferase (ALT; R = 0.27, p = 0.037), gamma-glutamyl transferase (GGT; R = 0.35, p = 0.0055) and alkaline phosphatase (R = 0.36, p = 0.0052), and with the circulating M65 fragment of cytokeratin 18 (CK18-M65; R = 0.51, p = 0.0012), a marker of hepatocyte death. In addition, patients with alcohol use disorder in the upper quartile had significantly higher liver stiffness (p = 0.0022). Serum CaMp65p was significantly higher in patients with fibrosis stage F2-F4 as compared with patients with no or minimal fibrosis F0-F1 (p = 0.0082). The area under the curve (AUC) for detecting F2-F4 fibrosis was 0.70. Elevated serum CaMp65p levels are associated not only with more severe hepatic injury, but also with liver fibrosis in patients with alcohol use disorder. Therefore, CaMp65p may serve as a non-invasive biomarker for fibrosis assessment in patients with alcohol use disorder.},
}

@article {pmid41304138,
year = {2025},
author = {Callac, N and Giraud, C and Perez, V and Ansquer, D and Lam, JS and Boulo, V and Pham, D and Wabete, N},
title = {Potential Bacterial Biomarkers Associated with Penaeus stylirostris Shrimp Larvae to Infer Holobiont Health and Dysbiosis Across Larvae Stages.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112452},
pmid = {41304138},
issn = {2076-2607},
abstract = {Microbiota play a pivotal role in holobionts, influencing nutrient intake, growth, and overall health. In this context, microbial dysbiosis of Penaeus stylirostris larvae seem to be associated with huge larval mortalities in hatcheries in New Caledonia. To understand larval dysbiosis establishment, our purpose was to identify bacterial biomarkers, as bioindicators, related to a given larval stage and health condition. To this end, larvae were sampled daily to access their active microbiota through sequencing of the V4 region of the 16S rRNA molecule, while their stage and their health were also observed. We identified three biomarkers strongly related to healthy zoea, and some may act as probiotics or play key roles in larval ontogeny and nutrition. We also found six biomarkers linked to unhealthy zoea and eight related to healthy mysis. Biomarkers were mostly related to diseased shrimps (Lewinella) or healthy shrimps (Cognitishimia, Thalassolituus) or were known to prey on cells (P30B-42), suggesting that the larvae might be battling against detrimental conditions. No biomarker related to unhealthy mysis was identified. Finally, our data showed that bacterial bioindicators could be used as an effective biosurveillance proxy in hatcheries, to monitor larval development, and as an early warning tool to predict rearing outcomes.},
}

@article {pmid41304128,
year = {2025},
author = {Zmysłowska-Polakowska, E and Płoszaj, T and Skoczylas, S and Grzybowska-Adamowicz, J and Palatyńska-Ulatowska, A and Łukomska-Szymańska, M and Zmysłowska, A},
title = {Evaluation of the Oral Microbiome in Patients with Alström and Bardet-Biedl Syndromes and Their Heterozygous Family Members.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112442},
pmid = {41304128},
issn = {2076-2607},
abstract = {Alström (ALMS) and Bardet-Biedl syndromes (BBS) are rare ciliopathies characterized by obesity and hyperglycemia that lead to type 2 diabetes, but also other disorders, including neurodegeneration. However, isolated clinical manifestations can be observed in carriers of heterozygous mutations in the ALMS1 and BBS genes. Recently, the influence of oral bacteria on the presence of obesity, type 2 diabetes, and neurodegenerative processes has been widely discussed. The purpose of the research project was to analyze the profile of the microbiome in the oral cavity by sequencing the 16S rRNA gene in ALMS/BBS patients and carriers of causative variants in these genes. Oral mucosal swabs were taken from 8 ALMS/BBS patients, 24 family members, 20 obese patients, and 29 healthy individuals. Streptococcus (30.7%), Haemophilus (18.9%), and Prevotella (11%) were the most common bacteria in the study group. Comparison between groups showed a higher abundance of Prevotella, Enterococcus, Eikenella, Capnocytophaga, Parvimonas, Selenomonas, and Corynobacterium, and a lower abundance of Lactobacillus in the study group compared to other groups. The specific profile of the oral microbiome found in patients with variants in the ALMS1 and BBS genes may enable the identification of the modulatory role of the oral microbiome in these disorders and point to new directions for additional therapy for these patients and heterozygous family members in the future.},
}

@article {pmid41304108,
year = {2025},
author = {Liu, B and Yang, C and Wan, X and Chen, S and Tao, Y and Li, Q and Zhao, H and Wang, X},
title = {Microbial Community Restructuring and Functional Response in Giant Duckweed (Spirodela polyrhiza) Fronds Driven by Cadmium Stress.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112423},
pmid = {41304108},
issn = {2076-2607},
support = {2024NSFSC1202//the Natural Science Foundation of Sichuan Province/ ; 2025ZNSFSC0254//the Natural Science Foundation of Sichuan Province/ ; GR-2023-E-03//the Key Laboratory of Dry-hot Valley Characteristic Bio-Resources Development at University of Sichuan Province/ ; grant no. Z3785//the start-up funds provided by Chengdu University/ ; },
abstract = {As a typical heavy metal pollutant, cadmium (Cd) poses significant threats to ecosystems and human health. Giant duckweed (Spirodela polyrhiza), a small aquatic plant characterized by rapid growth and efficient heavy metal accumulation, holds great promise for phytoremediation. However, the mechanisms by which S. polyrhiza enriches Cd-particularly the contributions of its surface-associated microbiota-remain poorly understood. In this study, S. polyrhiza fronds were exposed to 0, 1, and 10 μM Cd, and we observed a concentration-dependent increase in the abundance of epiphytic microorganisms on the frond surfaces. High-throughput 16S rRNA gene sequencing revealed that Cd stress significantly altered the diversity of the frond-epiphytic bacterial community. Notably, the relative abundances of the genera Herbaspirillum, Enterobacter, and Pantoea increased significantly with rising Cd concentrations. Functional prediction using PICRUSt2 indicated enrichment under Cd stress of specific traits-such as the nitrate/nitrite transporter NarK, signal transduction mechanisms, and ion channel proteins-suggesting these taxa may actively participate in Cd uptake and tolerance. Together, our results reveal a synergistic S. polyrhiza-microbiome response to Cd and identify taxa/functions as targets and biomarkers for microbe-augmented remediation.},
}

@article {pmid41304102,
year = {2025},
author = {Liscano, Y and Muñoz Morales, D and Suarez Daza, F and Vidal Cañas, S and Martinez Guevara, D and Artunduaga Cañas, E},
title = {Microbial Interventions for Inflammatory Skin Diseases: A Systematic Review and Meta-Analysis of Atopic Dermatitis and Psoriasis.},
journal = {Microorganisms},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/microorganisms13112416},
pmid = {41304102},
issn = {2076-2607},
support = {under call No. DGI-01-2025.//Universidad Santiago de Cali/ ; },
abstract = {Inflammatory dermatological diseases represent a significant global health burden, with emerging evidence suggesting that modulation of the gut-skin axis microbial interventions may offer therapeutic benefits. However, current evidence is fragmented, with considerable heterogeneity limiting definitive conclusions. A systematic review and a meta-analysis were conducted following PRISMA guidelines, registered in PROSPERO (CRD42024629809). Seven databases were searched for randomized controlled trials evaluating probiotics, synbiotics, or postbiotics in inflammatory skin conditions. Primary outcomes included disease severity scores (SCORAD for atopic dermatitis, PASI for psoriasis). Statistical analysis employed random-effect models with standardized mean differences (SMDs) and Hedges' g as effect size measures, using R software. Heterogeneity among studies was assessed using Q statistics and the I[2] index. Results: In total, 19 studies encompassing 1104 participants met the inclusion criteria. For atopic dermatitis, a meta-analysis of 12 studies (n = 817) demonstrated significant clinical improvement with microbial interventions versus placebo (SMD = -0.72; 95% CI: -1.26 to -0.17; p = 0.015), though substantial heterogeneity in the treatment effects was observed across studies (I[2] = 85.1%). The psoriasis results were more variable, with five studies (n = 287) showing non-significant pooled effects (SMD = -0.63; 95% CI: -1.74 to 0.48; p = 0.192). Multi-strain formulations and synbiotic combinations appeared to show greater efficacy compared to single-strain preparations. Safety profiles remained consistently favorable across all interventions. Microbial interventions represent a promising adjunctive therapeutic approach for inflammatory dermatological diseases, particularly atopic dermatitis, acting via gut-skin axis mechanisms. The substantial heterogeneity between the included studies emphasizes the need for standardized protocols and personalized medicine approaches integrating microbiome profiling to optimize clinical outcomes.},
}

@article {pmid41303688,
year = {2025},
author = {Sciandrone, B and Squarzanti, DF and Malfa, P and Regonesi, ME},
title = {Probiotic Modulation in Aging: Strain-Specific Geroprotective Effects in Caenorhabditis elegans.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262211205},
pmid = {41303688},
issn = {1422-0067},
support = {no number//private funding from SynBalance srl, 21040 Origgio, VA, Italy./ ; },
mesh = {Animals ; *Caenorhabditis elegans/physiology/drug effects ; *Probiotics/pharmacology ; *Aging/drug effects ; Longevity/drug effects ; Oxidative Stress/drug effects ; Reactive Oxygen Species/metabolism ; Caenorhabditis elegans Proteins/metabolism/genetics ; Bifidobacterium ; Locomotion/drug effects ; Lipofuscin/metabolism ; },
abstract = {Elderly individuals are more vulnerable to disease due to their increased frailty. Emerging evidence highlights the potential of probiotics as geroprotective agents by maintaining gut health and modulating key physiological processes involved in aging, such as inflammation, cognitive functions, and metabolism. Here, we investigated the geroprotective potential of four probiotic strains (Lacticaseibacillus paracasei LPC1114, Limosilactobacillus reuteri PBS072, Bifidobacterium breve BB077, and Bifidobacterium animalis subsp. lactis BL050) using Caenorhabditis elegans as an aging model. Mid-life healthspan parameters were assessed, including lifespan, motility, ROS levels, lipofuscin accumulation, and cognitive capabilities. The probiotics exhibited strain-specific effects. L. reuteri PBS072 and B. lactis BL050 significantly increased locomotion by 20% and decreased ROS levels by 70% and 30% respectively, suggesting enhanced oxidative stress response and neuromuscular maintenance. B. breve BB077, L. paracasei LPC1114, and L. reuteri PBS072 enhanced associative learning performance, whereas B. lactis BL050 improved chemotactic response. Notably, only L. paracasei LPC1114 and L. reuteri PBS072 extended the maximum lifespan by 4 and 5 days, respectively, an effect mediated by the longevity-related genes skn1, sir2.1, and daf16. Our findings highlight the multifaceted, strain-specific geroprotective properties of probiotics and support their potential as microbiome-based interventions to promote healthy aging.},
}

Animals
*Caenorhabditis elegans/physiology/drug effects
*Probiotics/pharmacology
*Aging/drug effects
Longevity/drug effects
Oxidative Stress/drug effects
Reactive Oxygen Species/metabolism
Caenorhabditis elegans Proteins/metabolism/genetics
Bifidobacterium
Locomotion/drug effects
Lipofuscin/metabolism

@article {pmid41303678,
year = {2025},
author = {Santos, KO and Sassaki, LY and Brusco De Freitas, M and Baima, JP and Faria, MH and Bizotto, AL and Benício, JP and Magalhães, AC},
title = {Salivary Biomarkers in Crohn's Disease and Ulcerative Colitis: A Scoping Review and Evidence Map.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262211195},
pmid = {41303678},
issn = {1422-0067},
support = {03/2025//Karina Oliveira Santos has received a schorlaship from Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - Brasil (CAPES)/ ; },
mesh = {Humans ; *Biomarkers/metabolism/analysis ; *Colitis, Ulcerative/metabolism/diagnosis/microbiology ; *Saliva/metabolism/chemistry ; *Crohn Disease/metabolism/diagnosis/microbiology ; Cytokines/metabolism ; MicroRNAs/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Salivary biomarkers have been explored as potential non-invasive tools for the diagnosis and monitoring of inflammatory bowel diseases (IBD), including Crohn's Disease (CD) and Ulcerative Colitis (UC). This study presents a scoping review and evidence mapping on the use of saliva as a matrix in which biomarkers can be identified for these conditions. A systematic search of multiple databases and studies was conducted until 28 January 2025, resulting in the selection of 12 relevant articles. The quantified evidence synthesis identified eight molecular and microbial categories. Of these, four classes, including cytokines, microRNAs, calprotectin, and the microbiome, have demonstrated the most consistent potential. Alterations in these biomarkers, such as an increase in the Prevotella genus within the microbiome, and elevated PSMA7 levels, may reflect disruptions in intestinal barrier integrity and immune response. However, factors such as oral health status, hygiene habits, and medication must be carefully considered. Therefore, further clinical research is essential to validate specific biomarkers.},
}

Humans
*Biomarkers/metabolism/analysis
*Colitis, Ulcerative/metabolism/diagnosis/microbiology
*Saliva/metabolism/chemistry
*Crohn Disease/metabolism/diagnosis/microbiology
Cytokines/metabolism
MicroRNAs/metabolism
Gastrointestinal Microbiome

@article {pmid41303565,
year = {2025},
author = {Ivanova, EA and Ryabova, EV and Komissarov, AE and Slepneva, EE and Stulov, AA and Bulat, SA and Sarantseva, SV},
title = {Swiss Cheese Gene Is Important for Intestinal Barrier, Microbiome, and Lipid Metabolism Regulation in Drosophila Gut.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262211085},
pmid = {41303565},
issn = {1422-0067},
support = {24-74-00165//Russian Science Foundation/ ; },
mesh = {Animals ; *Lipid Metabolism/genetics ; *Drosophila melanogaster/genetics/metabolism/microbiology ; *Drosophila Proteins/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Humans ; *Intestinal Mucosa/metabolism ; *Lysophospholipase/genetics/metabolism ; Enterocytes/metabolism ; Intestines/microbiology ; Acyltransferases ; Phospholipases ; },
abstract = {Mutations in the human patatin-like lysophospholipase domain containing the 6 gene PNPLA6 encode an evolutionarily conserved (lyso)phospholipase, leading to the development of a complex hereditary spastic paraplegia 39 (SPG 39) and a number of rare severe syndromes in humans. Diseases disrupt the functioning of the nervous and reproductive systems and the gastrointestinal tract. The study aims to investigate the role of the Drosophila melanogaster swiss cheese gene, an ortholog of the human PNPLA6 gene, in gut function. We showed that the swiss cheese gene knockout leads to changes in the morphology of the midgut, disruption of the septate junction structure and the intestinal barrier permeability, and a decrease in the lipid droplet number in enterocytes. As a result of such disturbances, intestinal stem cells (ISCs) proliferation is activated, and the gut microbiome is altered. Ectopic expression of human PNPLA6 leads to the recovery of the intestinal barrier in the fly gut. The example of Drosophila demonstrates the important role of evolutionarily conserved (lyso)phospholipase in intestinal homeostasis.},
}

Animals
*Lipid Metabolism/genetics
*Drosophila melanogaster/genetics/metabolism/microbiology
*Drosophila Proteins/genetics/metabolism
*Gastrointestinal Microbiome/genetics
Humans
*Intestinal Mucosa/metabolism
*Lysophospholipase/genetics/metabolism
Enterocytes/metabolism
Intestines/microbiology
Acyltransferases
Phospholipases

@article {pmid41303442,
year = {2025},
author = {Aliuș, C and Breazu, A and Pantu, C and Toader, C and Șerban, M and Covache-Busuioc, RA and Munteanu, O and Dumitru, AV},
title = {The Endocannabinoid-Microbiota-Neuroimmune Super-System: A Unifying Feedback Architecture for Systems Resilience, Collapse Trajectories, and Precision Feedback Medicine.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262210959},
pmid = {41303442},
issn = {1422-0067},
mesh = {*Endocannabinoids/metabolism ; Humans ; Animals ; *Microbiota ; Feedback, Physiological ; *Precision Medicine/methods ; *Neuroimmunomodulation ; },
abstract = {Modern biomedicine frequently contextualizes disease around isolated molecular or organ-specific mechanisms, but numerous chronic diseases, including Alzheimer's disease, multiple sclerosis, depression, diabetes, and sepsis, share common trajectories of systemic destabilization. An increasing body of evidence indicates that health is not a property of single organs but the emergent property of interdependent feedback networks linking the microbiome, endocannabinoidome, neuroimmune system, and metabolic regulators. We propose the Endocannabinoid-Microbiota-Neuroimmune Super-System (EMN-S) as an evolutionarily conserved conceptual model that describes how these fields of influence reciprocally interact through feedback control. The microbial communities constituting the EMN-S encode environmental and dietary inputs, endocannabinoid signaling serves as an integrative regulator that synchronizes neural and immune activity, and neuroimmune circuits effectuate adaptive behaviors that alter microbiotal and lipid ecosystems. This review formalizes the EMN-S, contending that it is a unitary and cohesive model of physiological resilience, as well as offering a framework for precision feedback therapeutics. We describe how three mechanisms-encoder drift, integrator detuning, and executor overutilization-convert stabilizing negative feedback into runaway feedback cascades that underlie chronic, recurrent, and multisystemic disease. We then specify the EMN-S signature-integrated microbiome, lipidomic, and immune readouts-as an early indicator of resilience collapse and prospective preclinical state. Finally, we recapitulate the potential of AI-driven digital twins to illuminate feedback collapse, predict tipping points, and direct closed-loop intervention and treatments to restore dynamic equilibrium. By anchoring complexity in concrete and measurable feedback principles, the EMN-S shifts focus to investigate pathophysiology as opposed to reductionist lesion models of systemic derangements and embraces a systemic, empirically testable theory of stability.},
}

*Endocannabinoids/metabolism
Humans
Animals
*Microbiota
Feedback, Physiological
*Precision Medicine/methods
*Neuroimmunomodulation

@article {pmid41303363,
year = {2025},
author = {Pacyga, K and Tabiś, A and Pacyga, P},
title = {Medicinal Plants for a Healthy Gut Microbiome: Scientific Insights into Modern Herbal Applications.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262210875},
pmid = {41303363},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Plants, Medicinal/chemistry ; Anti-Inflammatory Agents/pharmacology ; Phytochemicals/pharmacology/chemistry ; Prebiotics ; *Plant Extracts/pharmacology/chemistry ; Antioxidants/pharmacology ; Animals ; Dysbiosis ; },
abstract = {The human gut microbiome is a complex ecosystem of microorganisms fundamental to human health, influencing metabolism, immunity, and neurological function. Dysbiosis, or an imbalance in this microbial community, is increasingly linked to a range of chronic diseases, from inflammatory bowel disease to metabolic syndrome. This article explores the therapeutic potential of several common botanicals in modulating the gut microbiota and promoting intestinal health. We delve into the phytochemical composition and pharmacological properties of nine medicinal plants: globe artichoke, aloe vera, German chamomile, pot marigold, Ceylon cinnamon, dandelion, fennel, garlic, ginger, and green tea. We focus on their anti-inflammatory, antioxidant, antimicrobial, and prebiotic effects. The article also discusses the scientific evidence supporting their use, acknowledges the limitations of current research, and highlights considerations for safe and effective application. We conclude by summarising the significant role of these herbal remedies in modern complementary medicine and proposing future research directions to further elucidate their mechanisms of action and optimise their use for gut health.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Plants, Medicinal/chemistry
Anti-Inflammatory Agents/pharmacology
Phytochemicals/pharmacology/chemistry
Prebiotics
*Plant Extracts/pharmacology/chemistry
Antioxidants/pharmacology
Animals
Dysbiosis

@article {pmid41303351,
year = {2025},
author = {Tarbeeva, S and Kliuchnikova, A and Kozlova, A and Sarygina, E and Ilgisonis, E and Ponomarenko, E},
title = {Unraveling Obesity: A Five-Year Integrative Review of Transcriptomic Data.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262210864},
pmid = {41303351},
issn = {1422-0067},
support = {24-14-00006//Russian Science Foundation/ ; },
mesh = {Humans ; *Obesity/genetics/metabolism ; *Transcriptome ; Epigenesis, Genetic ; Biomarkers/metabolism ; Insulin Resistance/genetics ; Lipid Metabolism ; Gene Expression Profiling ; Energy Metabolism ; RNA, Long Noncoding/genetics ; Animals ; },
abstract = {Omics approaches have advanced insight into molecular mechanisms of human obesity. We reviewed transcriptomic studies published between January 2020 and June 2025 that used human tissues or human cell lines and applied high-throughput RNA methods. Across these works three convergent themes emerged: (1) immune-inflammatory activation-particularly interferon-stimulated and innate immune signatures-linked to insulin resistance and visceral adiposity; (2) dysregulation of lipid and energy-metabolism pathways, including reduced lipolysis and β-oxidation in adipose tissue and liver; and (3) epigenetic and post-transcriptional regulation mediated by DNA methylation, histone modification, long noncoding RNAs, microRNAs and circular RNAs. Multi-omics integration (transcriptome with proteome, metabolome and microbiome) improved mechanistic interpretation and biomarker discovery but was limited by cohort heterogeneity and technical variation. We conclude that standardized, integrative multi-omics analyses in well-characterized, longitudinal human cohorts are required to translate molecular signatures into robust biomarkers and personalized therapeutic strategies for obesity.},
}

Humans
*Obesity/genetics/metabolism
*Transcriptome
Epigenesis, Genetic
Biomarkers/metabolism
Insulin Resistance/genetics
Lipid Metabolism
Gene Expression Profiling
Energy Metabolism
RNA, Long Noncoding/genetics
Animals

@article {pmid41303325,
year = {2025},
author = {Diaconescu, IB and Dumitru, AV and Tataru, CP and Toader, C and Șerban, M and Covache-Busuioc, RA and Eva, L},
title = {From Electron Imbalance to Network Collapse: Decoding the Redox Code of Ischemic Stroke for Biomarker-Guided Precision Neuroprotection.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262210835},
pmid = {41303325},
issn = {1422-0067},
mesh = {Humans ; Oxidation-Reduction ; Animals ; *Ischemic Stroke/metabolism/pathology ; Biomarkers/metabolism ; Oxidative Stress ; *Neuroprotection ; Mitochondria/metabolism ; },
abstract = {Ischemic stroke remains one of the most catastrophic diseases in neurology, in which, due to a disturbance in the cerebral blood flow, the brain is acutely deprived of its oxygen and glucose oligomer, which in turn rapidly leads to energetic collapse and progressive cellular death. There is now increasing evidence that this type of stroke is not simply a type of 'oxidative stress' but rather a programmable loss-of-redox homeostasis, within which electron flow and the balance of oxidants/reductants are cumulatively displaced at the level of the single molecule and at the level of the cellular area. The advances being made in cryo-electron microscopy, lipidomics, and spatial omics are coupled with the introduction of a redox code produced by the interaction of the couples NADH/NAD[+], NADPH/NADP[+], GSH/GSSG, BH4/BH2, and NO/SNO, which determine the end results of the fates of the neurons, glia, endothelium, and pericytes. Within the mitochondria, pathophysiological events, including reverse electron transport, succinate overflow, and permeability transition, are found to be the first events after reperfusion, while signals intercommunicating via ER-mitochondria contact, peroxisomes, and nanotunnels control injury propagation. At the level of the tissue, events such as the constriction of the pericytes, the degradation of the glycocalyx, and the formation of neutrophil extracellular traps underlie microvascular failure (at least), despite the effective recanalization of the vessels. Systemic influences such as microbiome products, oxidized lipids, and free mitochondrial DNA in cells determine the redox imbalance, but this generally occurs outside the brain. We aim to synthesize how the progressive stages of ischemic injury evolve from the cessation of flow to the collapse of the cell structure. Within seconds of injury, there is reverse electron transport (RET) through mitochondrial complex I, with bursts of superoxide (O2•[-]) and hydrogen peroxide (H2O2) being produced, which depletes the stores of superoxide dismutase, catalase, and glutathione peroxidase. Accumulated succinate and iron-induced lipid peroxidation trigger ferroptosis, while xanthine oxidase and NOX2/NOX4, as well as uncoupled eNOS/nNOS, lead to oxidative and nitrosative stress. These cascades compromise the function of neuronal mitochondria, the glial antioxidant capacity, and endothelial-pericyte integrity, leading to the degradation of the glycocalyx with microvascular constriction. Stroke, therefore, represents a continuum of redox disequilibrium, a coordinated biochemical failure linking the mitochondrial metabolism with membrane integrity and vascular homeostasis.},
}

Humans
Oxidation-Reduction
Animals
*Ischemic Stroke/metabolism/pathology
Biomarkers/metabolism
Oxidative Stress
*Neuroprotection
Mitochondria/metabolism

@article {pmid41303313,
year = {2025},
author = {Biesbrock, AR and Xie, S and Hu, P and Tansky, CS and Wei, X and Ye, H and Circello, B and Zini, A and Tobias, G and Tamura, M and Parlov, M},
title = {Identification of Bacterial Networks and Relationship to Host Responses in Early Periodontitis Population over 24 Months.},
journal = {International journal of molecular sciences},
volume = {26},
number = {22},
pages = {},
doi = {10.3390/ijms262210823},
pmid = {41303313},
issn = {1422-0067},
support = {n/a//Procter & Gamble (United States)/ ; },
mesh = {Humans ; *Periodontitis/microbiology/therapy/metabolism ; Male ; Female ; Adult ; Middle Aged ; Cytokines/metabolism ; *Bacteria/genetics/isolation & purification ; *Microbiota ; Oral Hygiene/methods ; Dental Plaque/microbiology ; Interleukin-1beta/metabolism ; Biomarkers ; Gingiva/microbiology ; Toll-Like Receptors/metabolism ; },
abstract = {This research examined the effects of daily application of an oral hygiene regimen on the subgingival microbiome over 24 months. Generally healthy adults (107 enrolled, 87 completed) with early periodontitis used a home-care regimen (stannous fluoride paste, cetylpyridinium chloride rinse, power toothbrush, and floss) or usual care (control). Subgingival plaque samples were analyzed enzymatically for bacterial toxins. TLR ligands were measured using TLR-SEAP and TLR-ATP assays. Proinflammatory cytokines and metalloproteinases were quantified via immunoassays. Subgingival DNA was sequenced using a shotgun approach to assess microbial diversity. Increasing levels of bacteria, toxins, TLR activation, inflammatory cytokines, and MMPs were observed for periodontitis versus gingivitis and gingivitis versus healthy sites. The regimen significantly reduced levels of the critical proinflammatory cytokine IL-1β, as well as MMP-1 and MMP-9, at 24 months. By month 6, TLR ligands within subgingival plaques decreased. The abundance of pathogenic bacteria correlated with levels of virulence factors, proinflammatory cytokines, MMPs, and severity of clinical measures. Two distinct constellations of pathogenic bacteria were identified. Gingival sites were categorized into responders and non-responders per clinical symptoms and biomarkers. The regimen yielded more responder sites (70%) versus the control (47%), p = 0.0002914. The regimen reduced pathogenic bacteria, IL-1β, MMP1, and MMP-9, paralleling clinical reductions in periodontal disease.},
}

Humans
*Periodontitis/microbiology/therapy/metabolism
Male
Female
Adult
Middle Aged
Cytokines/metabolism
*Bacteria/genetics/isolation & purification
*Microbiota
Oral Hygiene/methods
Dental Plaque/microbiology
Interleukin-1beta/metabolism
Biomarkers
Gingiva/microbiology
Toll-Like Receptors/metabolism

@article {pmid41303157,
year = {2025},
author = {Almuhanna, Y},
title = {Microbial Biofilms as Barriers to Chronic Wound Healing: Diagnostic Challenges and Therapeutic Advances.},
journal = {Journal of clinical medicine},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/jcm14228121},
pmid = {41303157},
issn = {2077-0383},
abstract = {Wound healing is a complex and multistage process that incorporates precise cellular and molecular coordination. The presence of biofilms in chronic wounds adversely affects the wound healing process, as it prolongs the closure of the wound, thus sustaining chronic inflammation. Current data suggest that biofilms are present in almost all chronic wounds, which leads to significant challenges in diagnosis and treatment. Traditional detection methods, such as cultures and light microscopy, often fail to detect biofilms; however, sophisticated molecular and imaging techniques are constrained by their expense and accessibility. Chronic wound management, therefore, has progressed from conventional antimicrobial application to integrated methodologies that incorporate biofilm debridement, antibiofilm dressing, negative pressure wound therapy, and innovative enzyme or nanoparticle interventions. This review highlights the clinical significance of biofilm presence as a barrier in chronic wound healing, assesses diagnostic and therapeutic innovations, and stresses the urgent need to improve patient outcomes.},
}

@article {pmid41303068,
year = {2025},
author = {Voroneanu, L and Covic, A and Iliescu, S and Baluta, CV and Agavriloaei, BD and Stefan, AE and Amărandi, RM and Văcărean-Trandafir, IC and Ivanov, IC and Covic, A},
title = {Distinct Gut Microbiome Signatures in Hemodialysis and Kidney Transplant Populations.},
journal = {Journal of clinical medicine},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/jcm14228032},
pmid = {41303068},
issn = {2077-0383},
support = {10841/20.05.2022.//University of Medicine and Pharmacy "Grigore. T. Popa" Iasi, project number 10841/20.05.2022./ ; },
abstract = {Background: Gut microbiota plays a critical role in host metabolism, immunity, and intestinal barrier integrity. Both chronic kidney disease (CKD) and kidney transplantation (KTR) are associated with gut dysbiosis, driven by uremic toxins, comorbidities, and immunosuppressive therapy. However, direct comparisons between hemodialysis (HD), KTR, and healthy controls (HC), while accounting for dietary factors, remain limited. Methods: We conducted a cross-sectional study including 48 HD patients, 75 KTR patients, and 13 HC. Stool patient samples were analyzed using 16S rRNA amplicon sequencing targeting the V4-V4 region to assess microbial composition and diversity. Data on clinical status, laboratory parameters, and dietary intake were collected and integrated with microbiome profiling. Results: Firmicutes and Bacteroidota dominated all groups, with Akkermansia enriched in HD and SCFA-producing genera (Faecalibacterium, Roseburia) more abundant in KTR. LEfSe and sPLS-DA analyses identified Akkermansia and Clostridia-related taxa as discriminants of HD, while Acidaminococcus and Megasphaera characterized KTR. HD patients exhibited higher alpha diversity (Faith's PD and Chao1) than KTR (p < 0.05). Dietary intake differed across groups, but explained only a small proportion of microbial variance. Conclusions: Both HD and KTR patients display persistent gut dysbiosis with distinct microbial signatures. While transplantation partially restores SCFA producers, immunosuppression and diet shape new ecological shifts. These findings underscore the potential of microbiota as a biomarker and therapeutic target in renal replacement therapies.},
}

@article {pmid41303019,
year = {2025},
author = {Caballero-Mateos, AM and Brunet-Mas, E and Gros, B},
title = {Systemic Consequences of Inflammatory Bowel Disease Beyond Immune-Mediated Manifestations.},
journal = {Journal of clinical medicine},
volume = {14},
number = {22},
pages = {},
doi = {10.3390/jcm14227984},
pmid = {41303019},
issn = {2077-0383},
abstract = {Inflammatory bowel disease (IBD) management traditionally focuses on intestinal inflammation, yet extraintestinal manifestations can substantially impair patient quality of life. In this perspective, we emphasize the broad systemic impact of IBD-from highly prevalent conditions such as anemia, metabolic dysfunction-associated steatotic liver disease, or fatigue to rare but severe complications like interstitial lung disease and drug-induced glomerulonephritis. We review underlying mechanisms linking gut inflammation to distant organs, including immune dysregulation, microbial translocation, and metabolic derangements. Advances in diagnostics-such as biomarker panels, high-resolution imaging, and genomic/microbiome profiling-enable early detection and risk stratification. Emerging therapies, including targeted biologics (anti-TNF, anti-integrin, anti-IL-23), JAK and S1P modulators, precision nutrition, and microbiome modulation, offer new opportunities to address systemic inflammation. A multidisciplinary framework integrating gastroenterology with hepatology, hematology, neurology, nephrology, endocrinology, dermatology, pulmonology, and cardiology is essential to recognize hidden complications, facilitate timely intervention, and deliver personalized, comprehensive care for IBD.},
}

@article {pmid41302890,
year = {2025},
author = {Arpellino, A and Elsayed, AMA and Gonella, E and Alma, A},
title = {Effects of Host Plant on the Bacterial Community of the Leafhopper Scaphoideus titanus.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111144},
pmid = {41302890},
issn = {2075-4450},
support = {Next-GenerationEU (PIANO NAZIONALE DI RIPRESA E RESILIENZA (PNRR) - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4 - D.D. 1032 17/06/2022, CN00000022, Agritech national Research Center//European Union/ ; },
abstract = {The Nearctic leafhopper Scaphoideus titanus is the primary vector of Flavescence Dorée, a severe grapevine disease in Europe. This insect can complete its life cycle on both cultivated Vitis vinifera and American Vitis species, including rootstock-derived plants that have gone wild. While the movement of S. titanus between wild and cultivated vines is well documented, its biological implications remain unclear, particularly regarding the role of the insect-associated microbiome. In this study, we investigated how rearing S. titanus nymphs on different host plants, including American Vitis and several V. vinifera cultivars, affects its bacterial community. 16S rRNA metabarcoding revealed that the bacterial microbiome was dominated by two obligate symbionts, namely 'Candidatus Karelsulcia' and 'Candidatus Cardinium', with moderate but significant differences in microbial diversity among host plants and developmental stages. When these dominant symbionts were excluded, variability in the remaining bacterial community increased, indicating a modulation of minor taxa according to the plant offered. These findings suggest that host plant species influence the microbiome structure, potentially affecting the insect performance and the microbial exchange between wild and cultivated vines in the field, contributing to disease dynamics.},
}

@article {pmid41302881,
year = {2025},
author = {Huang, Z and Zhang, L and Tian, Y and Gao, J and Liu, F and Li, Y},
title = {Composition of the Gut Microbiome and Its Response to Rice Stripe Virus Infection in Laodelphax striatellus (Hemiptera: Delphacidae).},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111135},
pmid = {41302881},
issn = {2075-4450},
support = {32572831//the National Natural Science Foundation of China/ ; },
abstract = {The small brown planthopper (SBPH), Laodelphax striatellus, transmits rice stripe virus (RSV), a devastating pathogen that causes significant yield losses in rice. The components of the gut microbiota in SBPH and the effects of RSV infection on gut microorganisms are unclear. In this study, high-throughput sequencing of 16S rRNA was utilized to evaluate the composition of gut microorganisms in SBPH. The gut microbiota of SBPH was primarily composed of Proteobacteria, Firmicutes and Bacteroidetes at ratios of 94.79%, 3.04% and 1.39%, respectively; furthermore, the composition of bacteria in the gut microbiota was relatively conserved with differences at the genus level. To elucidate the response of the SBPH gut microbiota to RSV infection, we compared its composition and abundance in viruliferous and naïve SBPH. Interestingly, RSV infection was associated with increased diversity in the SBPH gut microbiota. Comparative analysis demonstrated that RSV infection elevated the relative abundance of Proteobacteria while reducing that of Firmicutes. Population counts demonstrated that RSV infection reduced the gut loads of Stenotrophomonas, Brevundimonas, and Brevibacillus, whereas the gut load of Staphylococcus was significantly increased. Further functional predictive assays revealed that RSV infection enhanced the functions of the SBPH gut microbiota in terms of metabolism, cellular processes, genetic and environmental information processing, and organismal systems. Our results indicate that RSV reshapes the composition, abundance, and functions of the SBPH gut microbiota, offering insights into virus-host-microbiome interactions.},
}

@article {pmid41302874,
year = {2025},
author = {Berlanga, M and Miñana-Galbis, D and Guerrero, R},
title = {Disentangling Gut Bacterial Community Patterns in Cryptocercus punctulatus and Comparing Their Metagenomes with Other Xylophagous Dyctioptera Insects.},
journal = {Insects},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/insects16111128},
pmid = {41302874},
issn = {2075-4450},
support = {project PID2021-123735OB-C22.//MCIN/ ; },
abstract = {Gut microbiota enable wood-feeding insects to digest recalcitrant diets. Two DNA-based analyses were performed. Amplicon sequencing of gut microbiota samples from Cryptocercus punctulatus showed inter-individual heterogeneity with visually distinct ordination patterns; however, no statistically significant differences were detected. Shotgun metagenomics was used to compare the taxonomic and functional profiles of C. punctulatus gut microbiota with those of other xylophagous Dictyoptera. Despite taxonomic differences, C. punctulatus microbiota revealed functional convergence with termites (Mastotermes darwiniensis and Nasutitermes sp.). Carbohydrate metabolism was performed by different bacterial phyla across all insects. All insect species possessed metabolic potential for cellulose, hemicellulose, pectin, and starch digestion, but lignin degradation capabilities were not detected. Termites showed higher abundance of chitin and xylan degradation pathways and nitrogen fixation genes, though nitrogen fixation was also present in Cryptocercus cockroaches. Genes for oxidative stress tolerance were present across all species but were most abundant in cockroaches, particularly, Cryptocercus. All insects harbored antibiotic resistance genes, with highest levels found in cockroaches. These findings indicate that metabolic requirements for wood digestion shape gut microbial community assembly across xylophagous insects, with distinct microbial taxa contributing to cellulose and hemicellulose breakdown. Moreover, the widespread presence of antibiotic resistance genes raises concerns about the potential transmission of antibiotic resistance within insect-associated microbiomes.},
}

@article {pmid41302671,
year = {2025},
author = {Chattopadhyay, S and Malayil, L and Sapkota, AR},
title = {Viable, Multi-Drug-Resistant Bacteria Recovered from E-Liquids Used with Commercial Electronic Cigarettes.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {11},
pages = {},
doi = {10.3390/ijerph22111725},
pmid = {41302671},
issn = {1660-4601},
mesh = {*Electronic Nicotine Delivery Systems ; *Drug Resistance, Multiple, Bacterial ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/isolation & purification ; Nicotine/pharmacology ; Microbial Sensitivity Tests ; Flavoring Agents/pharmacology ; },
abstract = {The use of electronic cigarettes has increased in the U.S. with menthol and mint flavors showing notably higher sales. While research on the bacterial microbiome of traditional tobacco products is growing, particularly regarding menthol and nicotine effects, data regarding potential microbial contaminants within electronic liquids (e-liquids) remain limited. Additionally, the potential antibacterial properties of e-liquids remain sparse. To address these gaps, we evaluated the prevalence of viable bacteria in e-liquids; characterized their antimicrobial susceptibility patterns; and tested the antibacterial activity of the e-liquids. Two e-liquid flavors (menthol and non-menthol) across three different nicotine concentrations (0, 6 and 12 mg/mL) were tested using culture-based methods and Sanger sequencing. Antimicrobial susceptibility testing and e-liquid antibacterial activity assays were performed using the Kirby Bauer disc diffusion method. The majority of the isolates (63.15%) were identified as Pseudomonas aeruginosa and Bacillus spp. (B. pumilus, B. megaterium and B. cereus). Notably, P. aeruginosa and P. fluorescens isolates exhibited multidrug resistance against penicillin, tetracyclines, and phenicols. The e-liquids also demonstrated antimicrobial activity, inhibiting the growth of B. cereus, P. aeruginosa, and Staphylococcus aureus, with greater inhibition of P. aeruginosa growth at higher (12 mg/mL) compared to lower (0 mg/mL) nicotine concentrations across the menthol-flavored samples. These findings offer preliminary evidence of viable, multidrug-resistant bacteria and antibacterial properties in e-liquids, underscoring potential public health concerns regarding user exposure risks and microbial interactions, and emphasizing the need for continued surveillance of microbial safety in electronic cigarette products.},
}

*Electronic Nicotine Delivery Systems
*Drug Resistance, Multiple, Bacterial
*Anti-Bacterial Agents/pharmacology
*Bacteria/drug effects/isolation & purification
Nicotine/pharmacology
Microbial Sensitivity Tests
Flavoring Agents/pharmacology

@article {pmid41302420,
year = {2025},
author = {Wojciechowska, K and Dos Santos Szewczyk, K},
title = {The Skin Microbiome and Bioactive Compounds: Mechanisms of Modulation, Dysbiosis, and Dermatological Implications.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {22},
pages = {},
doi = {10.3390/molecules30224363},
pmid = {41302420},
issn = {1420-3049},
mesh = {Humans ; *Skin/microbiology/drug effects ; *Dysbiosis/microbiology ; *Microbiota/drug effects ; Animals ; Prebiotics ; Probiotics/therapeutic use ; Skin Microbiome ; },
abstract = {Maintaining the balance between the host and commensal microorganisms is essential for skin health. The disruption of this equilibrium (dysbiosis) can contribute to inflammatory and infectious diseases and accelerate skin aging. Dysbiosis also accompanies skin cancers and may influence their progression. Causes of dysbiosis include exogenous factors such as cosmetics, UV radiation, pollution, and diet, as well as endogenous factors like stress, hormonal imbalances, and aging. Standard antibacterial treatments often eliminate beneficial microbes and may exacerbate conditions. Consequently, there is growing interest in alternative strategies-notably natural plant- and animal-derived products-that can modulate the skin microbiome more selectively and gently. This review presents current knowledge on skin microbiome physiology and dysbiosis and discusses natural compounds and microbiome-based therapies (probiotics, prebiotics, postbiotics) that modulate the skin microbiota. Unlike prior reviews, we provide a comparative perspective on emerging compound classes (e.g., peptides, lipids) and integrate the skin-gut axis concept into the framework, highlighting mechanistic insights at molecular and clinical levels. Our synthesis emphasizes distinct modes of action and evidence levels-from in vitro mechanisms to clinical outcomes-and offers guidance for formulation of microbiome-compatible products.},
}

Humans
*Skin/microbiology/drug effects
*Dysbiosis/microbiology
*Microbiota/drug effects
Animals
Prebiotics
Probiotics/therapeutic use
Skin Microbiome

@article {pmid41302239,
year = {2025},
author = {Dubois, N and Vincent, C and Giroux, I},
title = {Efficacy of Gut Microbiome-Targeted Interventions on Mental Health Symptoms in Women Across Key Hormonal Life Stages: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {22},
pages = {},
doi = {10.3390/healthcare13222851},
pmid = {41302239},
issn = {2227-9032},
abstract = {Background: Women are disproportionately affected by depression and generalized anxiety disorder compared to men throughout their lives. Hormonal changes during the menstrual cycle, pregnancy, postpartum, and menopause are often associated with mood disturbances. Evidence suggests that modulating the gut microbiome through gut-targeted interventions may offer a novel therapeutic approach for various mental health conditions. Objective: This systematic review and meta-analysis aimed to synthesize evidence from randomized controlled trials (RCTs) on the efficacy of gut microbiome-targeted interventions in improving mental health symptoms in women during key hormonal transitions. Methods: A systematic search was conducted from inception to August 2025 across Embase, MEDLINE (PubMed), Web of Science, PsycINFO, CINAHL, Scopus, FSTA, CENTRAL, the WHO International Clinical Trials Registry Platform, and ClinicalTrials.gov. Two reviewers independently screened, extracted data, and assessed study quality. Methodological quality was evaluated using Cochrane's risk-of-bias tool (RoB 2.0). Statistical analyses were performed with Comprehensive Meta-Analysis software (version 4). Results: Eleven RCTs were included, of which eight were used in the meta-analyses. Gut microbiome-targeted interventions significantly reduced depressive symptoms (Standardized Mean Difference (SMD) = -0.848; 95% Confidence Interval (CI): -1.470 to -0.226; p = 0.008) and anxiety symptoms (SMD = -0.997; 95% CI: -1.684 to -0.311; p = 0.004) versus controls. Heterogeneity was high (depression: Cochran's Q = 87.1, I[2] = 92%, τ[2] = 0.729; anxiety: Q = 35.3, I[2] = 89%, τ[2] = 0.535), but sensitivity analyses confirmed robustness. Meta-regressions indicated that treatment duration was not a significant moderator (depression: p = 0.12; anxiety: p = 0.28). Conclusions: Gut-targeted interventions significantly reduced symptoms of both depression and anxiety, highlighting their potential as complementary therapeutic strategies for managing mood disorders in women across hormonal life stages. However, high heterogeneity limits the ability to determine optimal standardized clinical recommendations, highlighting the need for further research to guide clinical applications and inform individualized approaches to treatment.},
}

@article {pmid41302187,
year = {2025},
author = {Marginean, IC and Cazacu, SM and Popescu, M and Iacob, GA and Sandulescu, LD and Iordache, S and Marginean, CM and Vere, CC},
title = {The Vicious Circle of Metabolic Dysfunction-Associated Steatotic Liver Disease When Micronutrient Deficiency Drives Microbial Imbalance and Liver Injury.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/life15111764},
pmid = {41302187},
issn = {2075-1729},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is an escalating global health burden and a leading cause of chronic liver disease. Without intervention, MASLD can progress to steatohepatitis, fibrosis, cirrhosis, and hepatocellular carcinoma. Although lifestyle modification is the cornerstone of management, specific dietary patterns are a primary driver of its development. The progression of MASLD is closely linked to micronutrient status, as these nutrients are critical for key biological functions such as antioxidant defense and immune regulation. Micronutrient deficiencies-particularly in essential vitamins and minerals-have been widely studied as independent contributors to MASLD pathogenesis. Similarly, the role of the gut microbiota in disease development has gained attention. However, the interplay between micronutrient deficiencies and gut dysbiosis is often underestimated. Emerging evidence suggests that micronutrient depletion not only directly exacerbates MASLD but also alters gut microbial composition, perpetuating a cycle of metabolic and hepatic dysfunction. This review aims to highlight the bidirectional relationship between micronutrient deficiency and gut microbiome imbalance in MASLD. It explores how dysbiosis impairs the bioavailability of micronutrients, thereby reinforcing a vicious cycle of disease progression. Therefore, effective MASLD management should address both nutritional deficiencies and microbial imbalances. Interventions such as prebiotic and probiotic supplementation may help restore microbial equilibrium and improve micronutrient absorption. Looking forward, personalized therapeutic strategies that combine targeted microbiota modulation with micronutrient repletion may offer promising approaches to curb the rising global burden of MASLD.},
}

@article {pmid41302083,
year = {2025},
author = {Farzand, A and Rohin, MAK and Awan, SJ and Ahmad, AMR and Akram, H and Saleem, T and Imran, MM},
title = {Nutrigenomics of Obesity: Integrating Genomics, Epigenetics, and Diet-Microbiome Interactions for Precision Nutrition.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/life15111658},
pmid = {41302083},
issn = {2075-1729},
abstract = {Obesity is a highly complex, multifactorial disease influenced by dynamic interactions among genetic, epigenetic, environmental, and behavioral determinants that explicitly position genetics as the core. While advances in multi-omic integration have revolutionized our understanding of adiposity pathways, translation into personalized clinical nutrition remains a critical challenge. This review systematically consolidates emerging insights into the molecular and nutrigenomic architecture of obesity by integrating data from large-scale GWAS, functional epigenomics, nutrigenetic interactions, and microbiome-mediated metabolic programming. The primary aim is to systematically organize and synthesize recent genetic and genomic findings in obesity, while also highlighting how these discoveries can be contextualized within precision nutrition frameworks. A comprehensive literature search was conducted across PubMed, Scopus, and Web of Science up to July 2024 using MeSH terms, nutrigenomic-specific queries, and multi-omics filters. Eligible studies were classified into five domains: monogenic obesity, polygenic GWAS findings, epigenomic regulation, nutrigenomic signatures, and gut microbiome contributions. Over 127 candidate genes and 253 QTLs have been implicated in obesity susceptibility. Monogenic variants (e.g., LEP, LEPR, MC4R, POMC, PCSK1) explain rare, early-onset phenotypes, while FTO (polygenic) and MC4R (monogenic mutations as well as common polygenic variants) represent major loci across populations. Epigenetic mechanisms, dietary composition, physical activity, and microbial diversity significantly recalibrate obesity trajectories. Integration of genomics, functional epigenomics, precision nutrigenomics, and microbiome science presents transformative opportunities for personalized obesity interventions. However, translation into evidence-based clinical nutrition remains limited, emphasizing the need for functional validation, cross-ancestry mapping, and AI-driven precision frameworks. Specifically, this review systematically identifies and integrates evidence from genomics, epigenomics, nutrigenomics, and microbiome studies published between 2000 and 2024, applying structured inclusion/exclusion criteria and narrative synthesis to highlight translational pathways for precision nutrition.},
}

@article {pmid41302050,
year = {2025},
author = {François, AC and Taminiau, B and Renaud, B and Gonza-Quito, IE and Massey, C and Hyde, C and Piercy, RJ and Douny, C and Scippo, ML and Daube, G and Gustin, P and Delcenserie, V and Votion, DM},
title = {In Vitro Investigation of Equine Gut Microbiota Alterations During Hypoglycin A Exposure.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/ani15223343},
pmid = {41302050},
issn = {2076-2615},
support = {D31-1381/S1-SAMA//Wallonie agriculture SPW/ ; },
abstract = {Hypoglycin A is a plant-derived protoxin that causes atypical myopathy in equids. In atypical myopathy-affected horses, metabolomic and microbiome studies have reported alterations in metabolic markers and faecal microbiota composition, pointing to a potential disruption of microbial homeostasis. However, in vivo observations are strongly confounded by host-related factors, underscoring the need for controlled in vitro approaches. To address this, we used an in vitro static batch fermentation model simulating the equine colon to investigate the direct effects of hypoglycin A on microbiota composition and activity. Faecal inocula from healthy horses were incubated in control and hypoglycin A-treated fermenters for 48 h, with serial analyses of hypoglycin A concentration, short-chain fatty acids, and 16S rRNA gene profiles. Hypoglycin A remained stable in the nutritive medium in the absence of microbiota, confirming that its degradation in inoculated fermenters was microbiota-dependent. The results showed significant microbial-associated hypoglycin A degradation without evidence of toxic metabolite formation. The analysis of α- and β-diversity revealed both an effect of incubation time, reflecting the natural temporal dynamics of microbial communities under batch fermentation, and a specific impact of hypoglycin A exposure, with certain taxa such as Paraclostridium being affected. This study provides the first in vitro evidence that the equine microbiota contributes to hypoglycin A degradation.},
}

@article {pmid41302043,
year = {2025},
author = {Zeng, L and Shi, L and Yang, Y and Zheng, D and Zhang, W and Yang, J and Qiao, M and Shi, H},
title = {Compositional Changes and Comparative Analysis of Oral Microbial Community During the Formation of Canine Dental Calculus.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/ani15223335},
pmid = {41302043},
issn = {2076-2615},
support = {2223001//the Talent Fund of China Agricultural University Veterinary Teaching Hospital/ ; },
abstract = {Periodontal disease remains a prevalent clinical condition in dogs, significantly impacting the quality of life of affected animals. Dental calculus is closely associated with periodontal disease, primarily because it serves as a reservoir for dental plaque and bacterial toxins, that contribute to gingival inflammation. To investigate the changes in the oral microbiome during the formation of dental calculus, a total of 30 dogs were enrolled and divided into three groups: healthy dogs (H, n = 10), provided tooth surface samples; dogs with dental plaque (P, n = 10) supplied plaque samples; and dogs with dental calculus (C, n = 10) provided calculus samples. DNA was subsequently extracted from all collected samples and subjected to PacBio sequencing. The results revealed significant differences in the composition and diversity of the oral microbiome between the plaque and calculus groups compared to the healthy group. As calculus gradually formed, the relative abundance of Pseudomonadota decreased significantly, while the proportions of Bacillota, Actinomycetota, Campylobacterota, and Thermodesulfobacteriota increased markedly. Bacteroides pyogenes and Peptostreptococcus canis were identified as potential biomarkers associated with calculus formation, whereas Conchiformibius steedae and Pasteurellaceae bacterium canine oral taxon 271 may serve as indicators of healthy periodontal tissue. Functional prediction analysis revealed a notable reduction in the ABC transporter pathway in the oral microbiota of dogs with dental calculus compared to the healthy group. In conclusion, our study has revealed the compositional changes in the oral microbial community and potential metabolic pathways during the formation of dental calculus in dogs. These findings provide a theoretical foundation for the identification of potential microbial biomarkers and for developing preventive and therapeutic strategies for canine periodontal disease.},
}

@article {pmid41302016,
year = {2025},
author = {Meng, F and Zhao, Y and Guo, Y and Guo, X and Zhang, Q and Wang, Z and Li, L and Hui, F and Tong, M and Yan, S},
title = {Rectal Microbiome Reveals the Improved Effect of Dietary Selenium Levels on Lactation Performance and Milk Fatty Acid Profiles in Lactating Donkeys.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/ani15223309},
pmid = {41302016},
issn = {2076-2615},
support = {32160794//National Natural Science Foundation of China/ ; },
abstract = {This study evaluated the effects of dietary selenium (Se) supplementation on lactation performance, milk fatty acid composition, and rectal microbiota and short-chain fatty acids in lactating Dezhou donkeys to determine the optimal dose. Twenty-four lactating Dezhou donkeys (estimated milk yield: 3.60 ± 0.84 kg/d; days in milk: 39.93 ± 7.02 d; body weight: 247.24 ± 26.27 kg; parity: 2.82 ± 0.48) were randomly divided into four groups (n = 6): CON (0 mg Se/kg DM), Se1 (0.15 mg Se/kg DM), Se2 (0.3 mg Se/kg DM), and Se3 (0.5 mg Se/kg DM), and were supplemented with Se yeast in the basal diet. The results showed that plasma Se concentrations increased dose-dependently. The Se2 group significantly increased milk yield, milk component yield, milk protein production efficiency, milk production efficiency, the digestibility of acid detergent fiber and neutral detergent fiber, protein biological value, and nitrogen metabolic rate, as well as the proportions of C18:1c9, C18:2c6, unsaturated fatty acids, monounsaturated fatty acids, polyunsaturated fatty acids, n-3 long-chain polyunsaturated fatty acids, the ratio of unsaturated to saturated fatty acids, the ratio of polyunsaturated to saturated fatty acids (P/S), desirable fatty acids, and (C18:0 + C18:1)/C16:0 in donkey milk, while decreasing the proportion of saturated fatty acids, atherogenicity index, and thrombogenic index. The Se2 group also increased acetate and butyrate in rectal feces, and promoted the growth of beneficial bacteria, including Christensenellaceae R-7 group, Lachnospiraceae XPB1014, and norank_f_Erysipelotrichaceae. In summary, the effects of Se supplementation were dose-dependent: 0.3 mg Se/kg DM improved milk performance and optimized milk fatty acid profiles by improving nutrient digestion and metabolism and modulating rectal bacteria structure, whereas 0.5 mg Se/kg DM showed no lactation benefits (with potential inhibitory effects) despite improving the P/S ratio and reducing the atherogenicity and thrombogenic indices.},
}

@article {pmid41302004,
year = {2025},
author = {Abarra, ST and Maulu, S and Odu-Onikosi, SG and Momoh, TA and Eynon, B and Emery, M and Rawling, M and Merrifield, DL},
title = {In Vitro and In Vivo Evaluation of Autochthonous Probiotics and Their Effects on the Mucosal Health of Nile Tilapia (Oreochromis niloticus).},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/ani15223296},
pmid = {41302004},
issn = {2076-2615},
support = {Foreign Graduate Scholarship//Department of Science and Technology/ ; },
abstract = {The host microbiome is a promising source of probiotics for aquaculture species including Nile tilapia. In this study, the probiotic potential of autochthonous bacterial isolates from Nile tilapia and carp mid-intestines were screened in vitro. Two isolates (C61 and T70), closely related to Bacillus subtilis, exhibited antagonistic activity against multiple pathogen species and demonstrated multiple digestive enzyme activities. Their antagonistic activity in Aeromonas hydrophila assays remained even under simulated intestinal juice (SIJ) exposure. Subsequently, C61 (PT1) and T70 (PT2) were added to experimental diets at log 7 CFU/g of diet, and fed to Nile tilapia (5.32 ± 0.12 g) for 40 days. There were no significant differences observed in the growth performance across treatments. Despite limited Bacillus intestinal recovery levels, 16S rRNA gene metabarcoding revealed subtle shifts in the intestinal microbial community composition of the probiotic-fed groups. In addition, the PT1 group showed significantly longer mucosal fold length, elevated intestinal and skin goblet cell levels, and higher skin goblet cell coverage compared to the control. These results indicate the potential benefits of the isolates as functional feed additives for enhancing the mucosal health of Nile tilapia, but their benefits were likely achieved through transient activity given the low level of Bacillus recovery in the intestine.},
}

@article {pmid41301981,
year = {2025},
author = {Luo, X and He, J and Luo, J and Xiong, H and Xiao, Y and Zhao, Y and Guo, X and Chen, D},
title = {Multi-Niche Microbiota of a Desert-Adapted Lizard: 16S rRNA Profiling of Teratoscincus roborowskii Endemic to the Turpan Depression in Northwest China.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/ani15223273},
pmid = {41301981},
issn = {2076-2615},
support = {2025ZNSFSC0249//Sichuan Science and Technology Program/ ; 31872959//National Natural Science Foundation of China/ ; 32470466//National Natural Science Foundation of China/ ; },
abstract = {The microbial communities of desert-dwelling reptiles, such as lizards, are vital for their health and adaptation, yet remain poorly understood. This study provides the first detailed analysis of the microbiome of the Turpan Wonder Gecko (Teratoscincus roborowskii), using 16S rRNA sequencing on samples from its gut, oral cavity and environment in China's Turpan Depression. The results showed distinct microbial profiles across these niches. Key findings include a highly diverse gut microbiota, primarily belonging to the phyla Bacteroidota and Bacillota, as well as thermophilic Thermodesulfobacteriota, which may enhance heat tolerance. The oral microbiota was rich in Pseudomonadota, likely aiding its omnivorous diet. Environmental samples were mostly Cyanobacteriota, typical of desert soils. Gut microbes appear to be specialized in carbohydrate metabolism, while oral microbes may assist in xenobiotic degradation. These results emphasize the important role that the gecko's microbial communities play in its survival in harsh desert conditions.},
}

@article {pmid41301944,
year = {2025},
author = {Yuan, Z and Fei, J and Li, S and Wu, Y and Liu, P},
title = {From Compensation to Collapse: UVB-Driven Disruption of Host-Microbiota Homeostasis Exacerbates Amphibian Ecological Risk.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/ani15223236},
pmid = {41301944},
issn = {2076-2615},
support = {KXB202310//the Scientific and Technological Innovation Ascend Plan of Harbin Normal University/ ; },
abstract = {The synergistic effects of stratospheric ozone depletion and climate change are intensifying surface ultraviolet-B (UVB) radiation, posing a severe threat to amphibians-one of the most endangered vertebrate groups globally. Xenopus laevis, with its cutaneous respiration and limited photoprotective mechanisms, exhibits high sensitivity to UVB, making it a suitable model for ecotoxicological studies. While UVB is known to cause DNA damage, immune suppression, and microbial dysbiosis, its mechanisms in multi-organ interactions, dose-response thresholds, and host-microbiome regulatory networks remain poorly understood. This study employed a gradient UVB exposure regime integrated with histopathology, oxidative stress assays, and 16S rRNA sequencing to systematically evaluate the effects of UVB on (1) cascade damage across skin, liver, and intestinal barriers; (2) immune cell distribution; (3) redox dynamics; and (4) microbial community structure and function. Our findings demonstrate that low-dose UVB activated compensatory antioxidant defenses without structural disruption, whereas exposure beyond a critical threshold induced nonlinear redox collapse, microbial dysbiosis, and multi-organ barrier failure, collectively exacerbating ecological adaptation risks. These results reveal a cross-scale mechanism by which UVB impairs amphibian health via disruption of host-microbe homeostasis, providing a conceptual and empirical framework for assessing species vulnerability under ongoing climate change.},
}

@article {pmid41301843,
year = {2025},
author = {Zhao, L},
title = {Microbiome Dysregulation and Inflammation: Key Players in Pulmonary Hypertension Pathophysiology.},
journal = {Biomedicines},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/biomedicines13112750},
pmid = {41301843},
issn = {2227-9059},
abstract = {Pulmonary hypertension (PH) is a fatal disease characterized by elevated pulmonary pressures, progressive pulmonary vascular remodeling, and right heart failure [...].},
}

@article {pmid41301831,
year = {2025},
author = {Lopetuso, LR and Murgiano, M and Mantuano, E and Schiavone, V and Costa, A and Mascianà, G and Bezzerri, V and Costa, G},
title = {The Molecular Landscape of Inflammation in Inflammatory Bowel Disease (IBD): Targets for Precision Medicine.},
journal = {Biomedicines},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/biomedicines13112738},
pmid = {41301831},
issn = {2227-9059},
abstract = {Inflammatory bowel diseases (IBDs), including Crohn's disease (CD) and ulcerative colitis (UC), are chronic immune-mediated disorders characterized by mucosal injury, cycles of inflammation and repair, and tissue damage. Persistent inflammation accelerates epithelial turnover, generates oxidative and replication stress, and remodels the stromal niche, contributing to the risk of colorectal cancer (CRC). Systematic dysplasia surveillance remains essential. Cellular senescence has emerged as a unifying mechanism linking inflammation, impaired epithelial repair, fibrosis, and neoplasia. In UC, p16/p21 upregulation, telomere erosion, and loss of lamin B1 accumulate and adopt a senescence-associated secretory phenotype (SASP) that perpetuates barrier dysfunction. In CD, senescence within stem and stromal compartments limits regeneration, promotes pro-fibrotic remodeling, and sustains cycles of injury and repair via chronic SASP signaling. IBD prevalence continues to rise from environmental factors, dietary changes, antibiotic exposures, and gut microbiota alterations. Pathogenesis integrates genetic factors (e.g., NOD2, IL23R, HLA, and ATG16L1 mutations), environmental modifiers, dysbiosis characterized by loss of short-chain fatty-acid-producing Gram-positive bacteria and expansion of Proteobacteria, and a dysregulated immune system. Therapeutic strategies have shifted toward targeted biologics and small molecules to promote mucosal healing. In this review, we recapitulate the mechanistic axes of inflammation, oxidative stress, and senescence in IBD and then critically evaluate emerging targeted therapies. Topics include anti-TNFα, integrin blockade, IL-12/23 and IL-23 inhibition, JAK inhibitors, S1P receptor modulators, microRNA modulation, senomorphics, mesenchymal cell therapy, and microbiome interventions. We endorse biomarker-guided therapy and propose future directions to break the SASP-driven inflammatory loop and mitigate long-term carcinogenic risk.},
}

@article {pmid41301759,
year = {2025},
author = {Laffusa, A and Burti, C and Viganò, C and Poggi, F and Grieco, L and Occhipinti, V and Greco, S and Orlando, S},
title = {Inflammatory Bowel Disease: Understanding Therapeutic Effects of Distinct Molecular Inhibitors as the Key to Current and Future Advanced Therapeutic Strategies.},
journal = {Biomedicines},
volume = {13},
number = {11},
pages = {},
doi = {10.3390/biomedicines13112667},
pmid = {41301759},
issn = {2227-9059},
abstract = {The pathogenesis of Inflammatory Bowel Disease is complex and not completely understood, resulting from multifactorial interactions between genetic predisposition, environmental triggers, and dysregulation of both innate and adaptive immune responses. Cytokines, produced by dysregulated immune cells, trigger chronic intestinal inflammation leading to tissue damage, carcinogenesis, and disease perpetuation. Current advanced therapies-including tumor necrosis factor (TNF)-α antagonists, adhesion and trafficking inhibitors (such as anti-integrin agents and sphingosine-1-phosphate receptor modulators), interleukin inhibitors, and Janus kinase inhibitors-have improved patient outcomes, but targeting a single inflammatory pathway is often insufficient for long-term disease control. To further improve therapeutic efficacy, novel approaches are under investigation, including advanced combination therapies that simultaneously inhibit multiple pro-inflammatory pathways and microbiome-based treatments to restore intestinal homeostasis. In this evolving therapeutic scenario, precision medicine and advanced combination therapies appear promising for breaking through the current therapeutic ceiling. This review highlights current knowledge on the role of cytokines in IBD pathogenesis and explores how their modulation can modify and control disease course.},
}

@article {pmid41301533,
year = {2025},
author = {Sabharwal, A and Haase, EM and Scannapieco, FA},
title = {Amylase Binding to Oral Streptococci: A Key Interaction for Human Oral Microbial Ecology, Adaptation and Fitness.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111616},
pmid = {41301533},
issn = {2218-273X},
support = {1R01DE022673-01/NH/NIH HHS/United States ; 1C06DC022673-18/NH/NIH HHS/United States ; },
mesh = {Humans ; *Mouth/microbiology ; *Streptococcus/metabolism/enzymology ; Biofilms/growth & development ; *Amylases/metabolism ; Bacterial Adhesion ; Adaptation, Physiological ; Microbiota ; },
abstract = {The interaction between human salivary alpha-amylase (HSAmy) and amylase-binding oral streptococci (ABS) helps determine the bacteria that colonize the oral cavity by establishing dental biofilms. Streptococci are important pioneer species of the oral cavity and influence oral health as well as common diseases such as dental caries. Various oral streptococcal species express distinct amylase-binding proteins, among which amylase-binding protein A (AbpA), encoded by the abpA gene in Streptococcus gordonii and several other species, which is the most extensively studied. Amylase binding facilitates microbial adhesion to host surfaces and biofilm formation and enables bacteria to harness the host's amylase enzymatic activity at their cell surface, enhancing their capacity to metabolize dietary starch for nutritional gain. Additionally, amylase binding may also influence bacterial cell division and stress tolerance by engaging novel bacterial signaling pathways. From an evolutionary perspective, both Neanderthals and modern humans exhibit functional adaptations in nutrient metabolism, including selection for salivary amylase-binding oral streptococci, highlighting the importance of microbial co-adaptation in response to host diet. Further research is warranted to elucidate the broader roles of amylase binding to bacteria in host-bacterial signaling, bacterial cell division and fitness and the evolutionary trajectory of the oral microbiome.},
}

Humans
*Mouth/microbiology
*Streptococcus/metabolism/enzymology
Biofilms/growth & development
*Amylases/metabolism
Bacterial Adhesion
Adaptation, Physiological
Microbiota

@article {pmid41301495,
year = {2025},
author = {Teslya, AV and Stepanov, AA and Poshvina, DV and Petrushin, IS and Vasilchenko, AS},
title = {From Lab to Field: Context-Dependent Impacts of Pseudomonas-Produced 2,4-Diacetylphloroglucinol on Soil Microbial Ecology.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111578},
pmid = {41301495},
issn = {2218-273X},
support = {19-76-30005//Russian Science Foundation/ ; FEVZ-2024-0005//The Ministry of Science and Higher Education of the Russian Federation/ ; },
mesh = {*Soil Microbiology ; *Phloroglucinol/analogs & derivatives/pharmacology/metabolism ; *Pseudomonas/metabolism ; Fungi/drug effects/genetics ; Bacteria/drug effects/genetics ; Microbiota/drug effects ; },
abstract = {The secondary metabolite 2,4-diacetylphloroglucinol (2,4-DAPG), which is produced by Pseudomonas bacteria, is a potent antimicrobial agent with well-documented properties that suppress phytopathogens. However, its broader ecological impact on soil microbial communities is not understood. Through a combination of controlled microcosm and field trials, we have demonstrated that the effects of 2,4-DAPG are highly context-dependent. Laboratory exposure (10 mg kg[-1]) altered the abundance of 8.53% of bacterial and 6.91% of fungal amplicon sequence variants, and simplified the bacterial co-occurrence networks (reduced number of nodes and links). In contrast, field conditions amplified bacterial sensitivity (the Shannon index decreased from 4.77 to 4.17, p < 0.05) but maintained fungal stability (Shannon index varied from 3.93 to 3.97, p > 0.05); these conditions affected a smaller proportion of fungal ASVs (4.23%). Taxonomic analysis revealed consistent suppression of fungi of the Mucoromycota (e.g., Mortierella) and context-dependent shifts in bacteria, with an enrichment of Bacillota (e.g., Bacillus, Paenibacillus) in the laboratory but not in the field. Enzymatic responses revealed a dose-dependent activation of the C-cycle, with up to 7.4-fold increases in the laboratory and up to a 10.5-fold increase in the field. P- and N- cycles showed more complex dynamics, with acid phosphatase activity increasing 3.8-fold in laboratory conditions and recovering from initial suppression to an increase of 144% in field conditions, while N-acetylglucosaminidase activity increased and L-leucine aminopeptidase decreased under laboratory conditions. Our results suggest that the response of microorganisms to 2,4-DAPG in natural soils is reduced, probably due to functional redundancy and pre-adaptation to abiotic stresses. This difference between laboratory and field studies warns against extrapolating data from controlled experiments to predict outcomes in agricultural ecosystems, and emphasizes the need for a context-specific evaluation of biocontrol agents.},
}

*Soil Microbiology
*Phloroglucinol/analogs & derivatives/pharmacology/metabolism
*Pseudomonas/metabolism
Fungi/drug effects/genetics
Bacteria/drug effects/genetics
Microbiota/drug effects

@article {pmid41301489,
year = {2025},
author = {Intonti, S and Olivieri, C and Reibaldi, M and Borrelli, E and Curcio, C and Conedera, FM},
title = {Translational Molecular and Fluid Biomarkers for Age-Related Macular Degeneration: Practical Insights from Animal Models and Humans.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111571},
pmid = {41301489},
issn = {2218-273X},
support = {PZ00P3_223803/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Humans ; *Biomarkers/metabolism ; Animals ; *Macular Degeneration/metabolism/diagnosis/pathology/genetics ; Disease Models, Animal ; Oxidative Stress ; Mice ; },
abstract = {Age-related macular degeneration (AMD) is a leading cause of irreversible central vision loss. Its pathogenesis is complex and multifactorial, involving genetic predisposition, inflammation, oxidative stress, and environmental influences, which underscores the need to better understand biomarkers associated with the disease. This review provides a comprehensive translational overview of biomarkers linked to both dry and wet forms of AMD by integrating findings from human studies and preclinical mouse models, including chemical, genetic, and laser-induced paradigms. It outlines key tissue, fluid, and systemic biomarkers related to oxidative stress, inflammation, complement activation, extracellular matrix remodeling, angiogenesis, and gut microbiota alterations. The main findings highlight similarities and differences between human AMD and animal models, identify challenges in biomarker validation, and emphasize the potential of combining biomarker profiles from ocular tissues, blood, tear fluid, aqueous and vitreous humor, and gut microbiome samples to improve early diagnosis, therapeutic monitoring, and personalized treatment strategies. These insights suggest that integrating experimental and clinical biomarker data could advance precision medicine in AMD, facilitating better early detection and individualized therapies. Future research should aim to bridge these datasets to optimize biomarker-driven approaches for AMD management.},
}

Humans
*Biomarkers/metabolism
Animals
*Macular Degeneration/metabolism/diagnosis/pathology/genetics
Disease Models, Animal
Oxidative Stress
Mice

@article {pmid41301464,
year = {2025},
author = {Cai, Y and Zhao, F and Cheng, X},
title = {Gut Microbiota and Ferroptosis in Colorectal Cancer: A Comprehensive Review of Mechanisms and Therapeutic Strategies to Overcome Immune Checkpoint Resistance.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111546},
pmid = {41301464},
issn = {2218-273X},
mesh = {Humans ; *Ferroptosis/drug effects ; *Gastrointestinal Microbiome/drug effects ; *Colorectal Neoplasms/microbiology/immunology/therapy/drug therapy/pathology/metabolism ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Animals ; *Drug Resistance, Neoplasm ; },
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide. Although immune checkpoint inhibitors (ICIs) have achieved striking clinical efficacy in the subset of CRCs with mismatch repair deficiency/high microsatellite instability (dMMR/MSI-H), the vast majority of patients-those with proficient mismatch repair/microsatellite-stable (pMMR/MSS) tumors-derive little benefit from current immunotherapies. Ferroptosis, an iron-dependent form of regulated cell death driven by lethal accumulation of lipid peroxides, has emerged as a promising antitumor mechanism that can interact with and modulate antitumor immunity. Concurrently, the gut microbiota exerts powerful control over host metabolism and immune tone through microbial community structure and metabolite production; accumulating evidence indicates that microbiota-derived factors can either sensitize tumors to ferroptosis (for example, via short-chain fatty acids) or confer resistance (for example, indole-3-acrylic acid produced by Peptostreptococcus anaerobius acting through the AHR→ALDH1A3→FSP1/CoQ axis). In this review we synthesize mechanistic data linking microbial ecology, iron and lipid metabolism, and immune regulation to ferroptotic vulnerability in CRC. We discuss translational strategies to exploit this "microbiota-ferroptosis" axis-including precision microbiome modulation, dietary interventions, pharmacologic ferroptosis inducers, and tumor-targeted delivery systems-and we outline biomarker frameworks and trial designs to evaluate combinations with ICIs. We also highlight major challenges, such as interindividual microbiome variability, potential collateral harm to ferroptosis-sensitive immune cells, adaptive antioxidant compensation (e.g., NRF2/FSP1 activation), and safety/regulatory issues for live biotherapeutics. In summary, this review highlights that targeting the microbiota-ferroptosis axis may represent a rational and potentially transformative approach to reprogramming the tumor microenvironment and overcoming immune checkpoint resistance in pMMR/MSS colorectal cancer; however, further research is essential to validate this concept and address existing challenges.},
}

Humans
*Ferroptosis/drug effects
*Gastrointestinal Microbiome/drug effects
*Colorectal Neoplasms/microbiology/immunology/therapy/drug therapy/pathology/metabolism
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Animals
*Drug Resistance, Neoplasm

@article {pmid41301443,
year = {2025},
author = {Papavassiliou, KA and Sofianidi, AA and Spiliopoulos, FG and Margoni, A and Papavassiliou, AG},
title = {Emerging Issues Regarding the Effects of the Microbiome on Lung Cancer Immunotherapy.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111525},
pmid = {41301443},
issn = {2218-273X},
mesh = {Humans ; *Lung Neoplasms/therapy/microbiology/immunology ; *Immunotherapy/methods ; *Microbiota/immunology ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Animals ; },
abstract = {Lung cancer remains the deadliest malignancy, with limited effective and long-term therapeutic options. Immunotherapy has revolutionized the therapeutic landscape of lung cancer. However, not everyone with lung cancer responds to immunotherapy, while, inpatients who temporarily derive clinical benefit, resistance eventually develops. The host microbiome has emerged as a pivotal player in cancer growth and progression. It has been implicated in the intricate connections between immune cells and tumor cells, ultimately augmenting immunotherapy efficacy in solid tumors, while simultaneously mitigating the immune-related adverse events associated with this type of treatment. Notably, lung cancer patients who obtain benefit from immunotherapy have been found to be colonized with specific bacterial populations, and it is this observation that the scientific community is trying to exploit, aspiring to improve lung cancer immunotherapy response rates. Delving deeper into the molecular mechanisms underpinning the effects of the microbiome on immunotherapy is an area that we should pay attention to if we want to utilize microbiome modulation in everyday clinical practice. Fecal microbiota transplantation, probiotics, targeted antibiotic interventions, and dietary modifications are among the strategies that are under investigation in clinical trials, with the ultimate endpoint of lengthening the life expectancy of lung cancer patients.},
}

Humans
*Lung Neoplasms/therapy/microbiology/immunology
*Immunotherapy/methods
*Microbiota/immunology
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Animals

@article {pmid41301434,
year = {2025},
author = {Shahamati, D and Akhavan, NS and Rosenkranz, SK},
title = {Postprandial Inflammation in Obesity: Dietary Determinants, Adipose Tissue Dysfunction and the Gut Microbiome.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111516},
pmid = {41301434},
issn = {2218-273X},
mesh = {Humans ; *Obesity/metabolism/microbiology/pathology ; *Inflammation/metabolism/pathology ; *Adipose Tissue/metabolism/pathology ; *Gastrointestinal Microbiome ; *Postprandial Period ; Animals ; Diet ; },
abstract = {Obesity is characterized by chronic low-grade inflammation that disrupts metabolic homeostasis and increases cardiometabolic risk. The postprandial period, during which individuals spend much of the day, is a critical window when nutrient absorption, lipid metabolism, and immune activation intersect. In obesity, dysfunctional adipose tissue and impaired gut barrier integrity amplify postprandial inflammatory responses through increased translocation of lipopolysaccharides and altered adipokine secretion. These processes converge on signaling pathways such as Toll-like receptor 4/nuclear factor-κB, c-Jun n-terminal kinase, and the NOD-like receptor family pyrin domain-containing protein 3 (NLRP3) inflammasome, leading to insulin resistance, endothelial dysfunction, and atherogenesis. This review synthesizes evidence on the interplay between gut-derived endotoxemia and adipose tissue dysfunction in postprandial inflammation. We further highlight the modulatory roles of dietary fat quality, plant-based dietary patterns, polyphenols, omega-3 fatty acids, dietary fiber, and nuclear receptor activation, particularly through peroxisome proliferator-activated receptors (PPARs). Emerging evidence indicates that nutritional and pharmacological strategies targeting these mechanisms can attenuate postprandial inflammation and improve metabolic outcomes. A combined approach integrating personalized nutrition, functional foods, and therapies targeting PPAR isoforms may represent a promising avenue for mitigating obesity-associated postprandial inflammation and long-term cardiometabolic complications.},
}

Humans
*Obesity/metabolism/microbiology/pathology
*Inflammation/metabolism/pathology
*Adipose Tissue/metabolism/pathology
*Gastrointestinal Microbiome
*Postprandial Period
Animals
Diet

@article {pmid41301403,
year = {2025},
author = {Zhang, S and Liu, X and Xu, S and Li, W and Song, J and Tian, Q and Du, Y},
title = {Multi-Omics Integration Reveals Electroacupuncture Ameliorates Cognitive Impairment in Alzheimer's Disease via Gut-Brain Axis.},
journal = {Biomolecules},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/biom15111486},
pmid = {41301403},
issn = {2218-273X},
support = {82374564//National Natural Science Foundation of China/ ; 81873380//National Natural Science Foundation of China/ ; 82074566//National Natural Science Foundation of China/ ; 2025AFD596//Hubei Provincial Joint Fund Project/ ; },
mesh = {Animals ; *Electroacupuncture/methods ; *Alzheimer Disease/therapy/metabolism/microbiology ; Mice ; *Gastrointestinal Microbiome ; *Cognitive Dysfunction/therapy/metabolism ; Male ; *Brain/metabolism ; Disease Models, Animal ; Metabolomics ; RNA, Ribosomal, 16S/genetics ; Metabolome ; *Brain-Gut Axis ; Multiomics ; },
abstract = {BACKGROUND: Alzheimer's disease (AD) lacks effective therapeutic strategies. Electroacupuncture (EA) offers promising neuroprotective effects, but its underlying mechanisms remain unclear.

OBJECTIVE: To explore the mechanisms of EA's neuroprotective effects on AD via microbiome and metabolome integration.

METHODS: Utilizing a well-established model of AD, Senescence-Accelerated Mouse Prone 8 (SAMP8), EA intervention was performed. 16S ribosomal RNA (rRNA) sequencing and serum metabolomics were conducted on SAMP8 mice, SAMP8 mice after EA intervention, and their normal control group Senescence-Accelerated Mouse Resistant 1 (SAMR1) mice.

RESULTS: SAMP8 mice were subjected to electroacupuncture (EA) treatment at the Baihui (GV20) and Shenshu (BL23) acupoints for 15 min daily over a period of four weeks. EA enhanced cognitive function and reduced neuronal damage in AD models. The treatment lowered pro-inflammatory cytokines (TNF-α, IL-1β) and AD-related pathologies (tau, Aβ1-42). EA also rebalanced gut microbiota by increasing beneficial Gastranaerophilales while decreasing harmful Proteobacteria. Additionally, it restored purine and phenylpropanoid metabolism by regulating key metabolites. Importantly, EA reduced levels of specific metabolites linked to pro-inflammatory bacteria (Sphingomonas, Massilia, Escherichia-Shigella), simultaneously decreasing their abundance. These findings highlight EA's multi-target effects on neuroinflammation, gut microbiota, and metabolic pathways in AD. Notably, the interactions between EA-regulated key metabolites and AD-related targets, predicted via PubChem and ChEMBL databases, remain computational and have not been validated by experimental studies.

CONCLUSIONS: EA exerts neuroprotective effects in AD via modulation of gut microbiota and metabolic pathways, representing a novel non-pharmacological therapeutic strategy.},
}

Animals
*Electroacupuncture/methods
*Alzheimer Disease/therapy/metabolism/microbiology
Mice
*Gastrointestinal Microbiome
*Cognitive Dysfunction/therapy/metabolism
Male
*Brain/metabolism
Disease Models, Animal
Metabolomics
RNA, Ribosomal, 16S/genetics
Metabolome
*Brain-Gut Axis
Multiomics

@article {pmid41300985,
year = {2025},
author = {De Lucia, SS and Nista, EC and Candelli, M and Archilei, S and Deutschbein, F and Capuano, E and Gasbarrini, A and Franceschi, F and Pignataro, G},
title = {Microbiota and Pancreatic Cancer: New Therapeutic Frontiers Between Engineered Microbes, Metabolites and Non-Bacterial Components.},
journal = {Cancers},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/cancers17223618},
pmid = {41300985},
issn = {2072-6694},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) remains one of the most aggressive and lethal human malignancies, with five-year survival rates showing only marginal improvement despite decades of intensive research. Its dismal prognosis reflects a combination of intrinsic biological aggressiveness, late clinical presentation, and marked resistance to standard therapies, underscoring the urgent need for innovative diagnostic and therapeutic approaches. Growing evidence indicates that the microbiome is a modifiable factor influencing the onset, progression, and treatment response of PDAC. Microbial communities originating from the gut, oral cavity, and even the tumor microenvironment can shape carcinogenic pathways, modulate immune activity, and alter the efficacy of chemotherapy and immunotherapy. In addition to bacteria, fungal and viral populations are emerging as relevant contributors within this complex ecosystem. This review provides a comprehensive overview of the current mechanistic and translational evidence linking the microbiome to PDAC biology and therapy. It further explores microbiota-targeted interventions-such as probiotics, postbiotics, engineered bacterial strains, bacteriophages, oncolytic viruses, and fecal microbiota transplantation-as promising adjuncts to conventional treatments. A deeper understanding of host-microbiome interactions could yield novel biomarkers and open innovative avenues for precision medicine in PDAC, ultimately improving patient outcomes and reshaping therapeutic paradigms. Integrating microbiome-based strategies into PDAC management may thus represent a crucial step toward more effective and personalized oncologic care.},
}

@article {pmid41300973,
year = {2025},
author = {Winslow, TB and Gupta, S and Vaddaraju, VS and Guercio, BJ and Sahasrabudhe, DM},
title = {The Microbiome and Genitourinary Cancers: A New Frontier.},
journal = {Cancers},
volume = {17},
number = {22},
pages = {},
doi = {10.3390/cancers17223606},
pmid = {41300973},
issn = {2072-6694},
abstract = {Introduction of immune checkpoint inhibitors and targeted agents has markedly improved outcomes and extended survival in urothelial and renal cell carcinoma. However, the substantial subset of cases are treatment-resistant. Emerging strategies aim to enhance the effectiveness of immunotherapy. One area of growing interest and promise is the microbiome. The microbiome plays a complex and dynamic role in regulating the immune system, and represents a new frontier as a promising target for modulating response to immunotherapy. This review summarizes recent advances in our understanding of the microbiome, its interactions with immunotherapy, novel avenues for microbiome modification, and potential implications for the treatment of urothelial and renal cell carcinoma.},
}

@article {pmid41300898,
year = {2025},
author = {Grigore, I and Ciobotaru, OR and Hînganu, D and Gurau, G and Stamate, E and Tutunaru, D and Gavril, RS and Ciobotaru, OC and Hînganu, MV},
title = {Lipid, Metabolomic and Gut Microbiome Profiles in Long-Term-Hospitalized Cardiac Patients-An Observational and Retrospective Study.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {22},
pages = {},
doi = {10.3390/diagnostics15222874},
pmid = {41300898},
issn = {2075-4418},
abstract = {Background/Objectives: Long-term hospitalization in cardiac patients is associated with significant metabolic and microbial alterations that may influence disease progression and prognosis. Although lipid imbalances, metabolomic shifts, and gut microbiome dysbiosis have each been linked individually to cardiovascular outcomes, their integrated evaluation in long-term-hospitalized patients remains underexplored. Methods: We conducted a retrospective observational study including 51 cardiac patients hospitalized for more than 25 days, compared with a control group of 41 patients hospitalized for short and intermediate durations (3-24 days). Clinical and demographic data were collected, alongside lipid profiling, metabolomic assessment through liquid chromatography-mass spectrometry (LC-MS), and gut microbiome analysis using GI360™ sequencing. Ethical approval was obtained, and all data were anonymized. Lipid-related findings are exploratory due to the small number of complete measurements. Results: Preliminary lipid trends were characterized by higher levels of LDL, triglycerides, and Lp(a), and lower HDL, in the long-term group. Metabolomic analyses revealed decreased energy-related metabolites (ATP, phosphocreatine ratio), altered amino acid patterns, and increased ketone utilization. Gut microbiome evaluation demonstrated a significant increase in dysbiosis index, with reduced diversity and dominance of potentially pathogenic taxa. These findings were correlated with clinical severity scores. Cross-domain relationships are exploratory and based on associative profiling rather than deep integrative modelling. Conclusions: Long-term hospitalization in cardiac patients is associated with distinct lipid, metabolomic, and gut microbiome profiles that may serve as predictive biomarkers of adverse outcomes. Future studies should validate these findings in larger cohorts and explore their integration into personalized management strategies.},
}

@article {pmid41300565,
year = {2025},
author = {Stanciu, OO and Moga, A and Balanescu, L and Balanescu, R and Andriescu, M},
title = {Continuous Antibiotic Prophylaxis for Vesicoureteral Reflux: Impact on the Pediatric Microbiome-A Systematic Review.},
journal = {Children (Basel, Switzerland)},
volume = {12},
number = {11},
pages = {},
doi = {10.3390/children12111446},
pmid = {41300565},
issn = {2227-9067},
abstract = {Background: Continuous antibiotic prophylaxis (CAP) is widely used in infants with vesicoureteral reflux (VUR) to prevent recurrent urinary tract infections and renal scarring. However, this practice entails prolonged low-dose antibiotic exposure during a critical period of microbiome establishment, potentially influencing long-term microbial and immune development. Methods: A systematic review was conducted according to PRISMA 2020 guidelines. PubMed, Embase, Scopus, Web of Science, and the Cochrane Library were searched up to September 2025 for studies evaluating gut or urinary microbiome changes in children receiving CAP for VUR. Eligible studies included human participants under 18 years with microbiome outcomes assessed by sequencing or culture-based methods. Results: Twenty-one records were identified, and four studies met inclusion criteria-three observational microbiome studies and one randomized controlled trial. CAP preserved overall microbial alpha diversity but induced compositional changes, notably enrichment of Enterobacteriaceae and reduction in Bifidobacteriaceae. The included RCT confirmed reduced UTI recurrence but increased antimicrobial resistance and non-E. coli infections. Conclusions: CAP in early life maintains microbial diversity but alters microbiota composition and resistance profiles. Identifying these shifts may support individualized prophylaxis strategies and microbiome-preserving interventions to balance infection prevention with ecological safety in infancy.},
}

@article {pmid41300483,
year = {2025},
author = {Kipp, ZA and Pauss, SN and Martinez, GJ and Hinds, TD and Lee, WH},
title = {Bilirubin Hepatic and Intestinal Transport and Catabolism: Physiology, Pathophysiology, and Benefits.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {11},
pages = {},
doi = {10.3390/antiox14111326},
pmid = {41300483},
issn = {2076-3921},
support = {1R01DK121797-01/NH/NIH HHS/United States ; R01DA058933//National Institute of Health/ ; R01HL174521//National Institute of Health/ ; F31HL170972//National Institute of Health/ ; 25PRE1374495//American Heart Association/ ; },
abstract = {Bilirubin, a metabolite derived from heme degradation, has traditionally been regarded as a waste product and a marker of liver injury. However, increasing evidence suggests that bilirubin also functions as a hormone, and reduced levels are associated with metabolic dysfunction. Studies have shown a strong association between low circulating bilirubin levels and an increased risk of metabolic disorders and cardiovascular disease. To advance bilirubin-based treatment strategies, it is essential to elucidate the mechanisms underlying bilirubin transport and metabolism. Therefore, we provide an in-depth discussion of bilirubin production and its subsequent fates, with a particular focus on the transport between the liver and the intestine. We describe the molecular players involved in heme degradation and biliverdin formation, leading to bilirubin production, followed by its transport from the bloodstream to hepatocytes and from the liver to the intestine. We discuss intestinal bilirubin catabolism, including the microbiome generation of urobilinogen, urobilin, and other metabolites. Finally, we discuss how bilirubin clearance and catabolism intersect with its metabolic effects, highlighting potential therapeutic targets. By integrating these aspects, this review provides a comprehensive understanding of bilirubin's physiological importance, intestinal transport, and breakdown, as well as insights into novel strategies for treating hypobilirubinemia-associated disorders.},
}