@article {pmid41484402,
year = {2026},
author = {González, R and Castelló-Sanjuán, M and Romoli, O and Blanc, H and Kobayashi, H and Nigg, J and Saleh, MC},
title = {Microbiome composition modulates the lethal outcome of Drosophila A virus infection.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-025-06042-8},
pmid = {41484402},
issn = {1420-9071},
support = {ANR-23-CE15-0038-01//Agence Nationale de la Recherche/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; 101024099//H2020 Marie Skłodowska-Curie Actions/ ; },
abstract = {Host-associated microbiomes can strongly influence viral infection outcomes, yet how minor variations in commensal bacterial composition modulate viral pathogenesis remain poorly understood. Here, we used Drosophila melanogaster to investigate how bacterial microbiome composition affects pathogenesis of enteric RNA viruses. Lactiplantibacillus plantarum supplementation increased bacterial microbiome diversity without altering total bacterial load, while Acetobacter pomorum supplementation had minimal impact on the bacterial microbiome. L. plantarum-enriched flies exhibited an additional ~ 15% reduction in lifespan from Drosophila A virus (DAV) infection despite showing reduced viral protein accumulation and similar viral RNA levels. The reduction in tolerance to viral infection required live bacteria and was observed only for DAV, as no change in mortality was observed with Nora virus or Drosophila C virus infections. Mechanistic investigations revealed that tolerance reduction occurs independently of transcriptional immune responses, as DAV-infected flies showed similar transcriptional profiles regardless of bacterial microbiome composition. Intestinal barrier function assays demonstrated that a large number of L. plantarum-supplemented flies died before developing signs of gut barrier disruption, suggesting that extra-intestinal mechanisms contribute to mortality; this interpretation is further supported by similar levels of intestinal damage markers observed in virus-infected flies under both microbiome conditions. Viral genomic sequencing ruled out microbiome-driven selection of more pathogenic viral variants, as no adaptive mutations were observed between microbiome conditions that could account for the differential pathogenesis. These findings describe how subtle shifts in microbiome composition modulate viral infection outcomes through pathways that operate independently of canonical immune responses, viral evolution, and intestinal damage.},
}

@article {pmid41484272,
year = {2026},
author = {Liu, X and Zou, Y and Jin, C and Wang, Y and Zhang, J and Yan, M and Xie, Y and Ding, M and Wang, K and Liu, L and Ding, C and Chen, X},
title = {Viral infections are associated with apical periodontitis: A meta-analysis of prevalence, clinical symptoms, and lesion sizes across 31 clinical studies.},
journal = {Clinical oral investigations},
volume = {30},
number = {1},
pages = {37},
pmid = {41484272},
issn = {1436-3771},
support = {HB2023093//Top Talent Support Program for young and middle-aged people of Wuxi Health Committee/ ; A20210056//Health and Science Project of Hangzhou/ ; 2023WJC034//Hangzhou Biological Medicine and Health Industry Development Support Science and Technology Project/ ; 2021WJCY131//Hangzhou Biological Medicine and Health Industry Development Support Science and Technology Project/ ; 2024ZL724//Zhejiang Science and Technology Program of Chinese Medicine/ ; 20211231Y028//Guided Project of Science and Technology of Hangzhou/ ; },
mesh = {Humans ; *Periapical Periodontitis/virology/epidemiology/pathology ; Prevalence ; *Virus Diseases/complications/epidemiology ; },
abstract = {OBJECTIVE: Bacteria and viruses are components of the oral microbiome and are linked to various oral diseases. Clinical observations indicate a higher prevalence of apical periodontitis (AP) during viral epidemics. However, research on this association is limited. This meta-analysis aimed to explore the relationship between viral infections and AP.

METHODS: This study adhered to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. Relevant studies were identified through systematic database searches, and data were extracted for eligible studies. Three validated quality assessment tools were used to ensure rigor. The pooled odds ratio (OR) with 95% confidence interval (CI) was calculated to quantify the strength of the association.

RESULTS: Out of 427 screened records, 31 studies comprising 1,341,636 participants met the inclusion criteria. The meta-analysis revealed that the prevalence of AP was 2.78 times higher in patients with viral infections compared to controls (95% CI = 1.88-4.12, p < 0.001). Infected individuals demonstrated more severe clinical symptoms (OR = 3.49, 95% CI = 2.07-5.90, p < 0.001) and significantly larger periapical lesions (OR = 3.84, 95% CI = 1.08-13.67, p < 0.05).

CONCLUSIONS: The evidence suggests a significant association between viral infections and AP, particularly in cases of viral co-infections.

CLINICAL RELEVANCE: These findings suggest that evaluating viral infections, particularly herpesviruses, could inform the clinical management of AP. However, further research is required to establish causality.},
}

Humans
*Periapical Periodontitis/virology/epidemiology/pathology
Prevalence
*Virus Diseases/complications/epidemiology

@article {pmid41484074,
year = {2026},
author = {de Molon, RS and Vernal, R and Oliveira, GE and Steffens, JP and Ervolino, E and Theodoro, LH and van den Beucken, JJJP and Tetradis, S},
title = {Inflammatory bone loss and signaling pathways in periodontitis: mechanistic insights and emerging therapeutic strategies.},
journal = {Bone research},
volume = {14},
number = {1},
pages = {1},
pmid = {41484074},
issn = {2095-4700},
mesh = {Humans ; *Periodontitis/pathology/metabolism/therapy/complications ; *Signal Transduction ; Animals ; *Inflammation/pathology ; Osteoclasts/pathology/metabolism ; *Bone Resorption/pathology/metabolism ; Osteogenesis ; },
abstract = {Bone resorption is a vital physiological process that enables skeletal remodeling, maintenance, and adaptation to mechanical forces throughout life. While tightly regulated under the physiological state, its dysregulation contributes to pathological conditions such as osteoporosis, rheumatoid arthritis, and periodontitis. Periodontitis is a highly prevalent chronic inflammatory disease driven by dysbiotic biofilms that disrupt the oral microbiome, leading to the progressive breakdown of the periodontal ligament, cementum, and alveolar bone and ultimately resulting in tooth loss. This review outlines the molecular and cellular mechanisms underlying periodontitis, focusing on osteoclastogenesis, the differentiation and activation of osteoclasts, the primary mediators of bone resorption. Key transcriptional regulators, including NFATc1, c-Fos, and c-Src are discussed alongside major signaling pathways such as Mitogen Activated Protein Kinase (MAPK), Janus Tyrosine Kinase/Signal Transducer and Activator of Transcription (JAK/STAT), Nuclear Factor Kappa B (NF-κB), and Phosphoinositide 3-kinase (PI3K)/Akt, to elucidate their roles in the initiation and progression of periodontal bone loss. These pathways orchestrate the inflammatory response and osteoclast activity, underscoring their relevance in periodontitis and other osteolytic conditions. Hallmark features of periodontitis, including chronic inflammation, immune dysregulation, and tissue destruction are highlighted, with emphasis on current and emerging therapeutic strategies targeting these molecular pathways. Special attention is given to small molecules, biologics, and natural compounds that have the potential to modulate key signaling pathways. Although advances in understanding these mechanisms have identified promising therapeutic targets, translation into effective clinical interventions remains challenging. Continued research into regulating bone-resorptive signaling pathways is essential for developing more effective treatments for periodontitis and related inflammatory bone diseases.},
}

Humans
*Periodontitis/pathology/metabolism/therapy/complications
*Signal Transduction
Animals
*Inflammation/pathology
Osteoclasts/pathology/metabolism
*Bone Resorption/pathology/metabolism
Osteogenesis

@article {pmid41484033,
year = {2026},
author = {An, Y and E, P},
title = {Oral butyrate in IBD: From enterotype stratification to a multi-omic and long-term clinical dialogue.},
journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dld.2025.12.020},
pmid = {41484033},
issn = {1878-3562},
}

@article {pmid41484024,
year = {2025},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and De Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Gut microbiome profiles and associated functional pathways are linked to Mediterranean diet adherence and blood glucose control in adults with type 1 diabetes mellitus.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104487},
doi = {10.1016/j.numecd.2025.104487},
pmid = {41484024},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: The Mediterranean diet (MD) has been associated with better glycaemic control in children with type 1 diabetes mellitus (T1DM) and favourable microbiome profiles in healthy individuals. However, it remains unclear whether MD adherence is associated with glycaemic control via microbiome. This study examined the relationships among MD adherence, gut microbiome, and glycaemic control in adults with T1DM and assessed the microbiome's ability to predict clinical and dietary outcomes.

METHODS AND RESULTS: In a cross-sectional study of 253 adults with T1DM, dietary intake was assessed using the EPIC food frequency questionnaire, and MD adherence was measured using the rMED score. Participants were stratified by adherence level (low, medium, high). Glycaemic control was evaluated using HbA1c and CGM metrics. Shotgun metagenomic sequencing of stool samples (n = 103) assessed the gut microbiome. Statistical analyses included ANOVA, PERMANOVA, LEfSe, and machine learning modeling. Higher MD adherence was associated with lower HbA1c levels (7.1 % vs 7.7 %; p < 0.001), greater time in range (67.0 % vs 59.4 %; p-trend = 0.03), and higher HDL cholesterol (1.62 vs 1.39 mmol/L; p = 0.01). High MD adherence was linked to a greater abundance of bacterial species such as Faecalibacterium prausnitzii. Both high MD adherence and lower HbA1c were associated with distinct microbiome functional pathways. Microbiome-based machine learning models predicted dietary patterns and clinical metrics.

CONCLUSIONS: In adults with T1DM, greater MD adherence is associated with better glycaemic control and a favourable gut microbiome. Specific microbial pathways may underlie these associations. Integrating diet and microbiome data supports personalized care. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}

@article {pmid41483804,
year = {2026},
author = {Psarrakis, C and Tziolos, NR and Matzarakis, V and Kumar, V and Stylianakis, E and Sidiropoulou, C and Tasouli, E and Iliopoulou, K and Samarkos, M and Metallidis, S and Georgiadou, S and Akinosoglou, K and Bolanou, A and Hatziagelaki, E and Kostaki, A and Panagopoulos, P and Toutouzas, K and Milionis, H and Adamis, G and Poulakou, G and Lada, M and Skoutelis, A and Alexiou, Z and Symbardi, S and Chrysos, G and Netea, MG and Giamarellos-Bourboulis, EJ},
title = {A randomized controlled trial of precision bezlotoxumab treatment for Clostridioides difficile infection.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102533},
doi = {10.1016/j.xcrm.2025.102533},
pmid = {41483804},
issn = {2666-3791},
abstract = {Early risk recognition for organ dysfunction and death by Clostridioides difficile infection (CDI) is an unmet need. A prediction score is developed in the BEYOND study (ClinicalTrials.gov; NCT02573571, NCT04725123, and NCT05304715). At the first stage, using 153 patients and 150 comparators, the BEYOND score was developed integrating hemoglobin; blood urea; blood interleukin-8; carriage of G alleles of rs2091172; and presence of Terrisporobacter glycolicus, Enterococcus avium, and Anaerovorax odorimutans in the stool. The score had 84.6% sensitivity and 95.8% specificity for unfavorable outcomes. At the second stage, a double-blind randomized controlled trial was performed, and 44 patients at high-risk by BEYOND score were treated with standard-of-care plus Bezlotoxumab or placebo. The primary endpoint was the incidence of organ dysfunction, CDI relapse, and/or death. This endpoint was met in 72.7% of patients in the placebo arm and 31.8% in the Bezlotoxumab arm (p = 0.015). Results suggest that BEYOND score can detect early risk in patients with CDI.},
}

@article {pmid41483682,
year = {2026},
author = {Viglino, J and Perea, L and Garcia-Nuñez, M and Rodrigo-Troyano, A and Torrego, A and Domínguez-Alvarez, M and Villar, J and Carrizosa, X and Quero, S and Gabaldon, T and Willis, JR and Saus, E and Gea, J and Santos, S and Camps, P and Agustí, A and Monso, E and Sibila, O and Faner, R},
title = {Characterisation of the gut-lung axis microbiome in clinically stable patients with chronic obstructive pulmonary disease.},
journal = {EBioMedicine},
volume = {123},
number = {},
pages = {106099},
doi = {10.1016/j.ebiom.2025.106099},
pmid = {41483682},
issn = {2352-3964},
abstract = {BACKGROUND: Airway and gut dysbiosis have been reported in Chronic Obstructive Pulmonary Disease (COPD); however, their relationship and association with clinical features remain poorly understood. We aimed to characterise the lung and gut microbiome in patients with stable COPD and controls.

METHODS: Prospective, multicentre, longitudinal and controlled study of n = 60 stable patients with COPD and n = 30 controls. In them, we analysed 16S rRNA-seq in oropharyngeal (OP) swabs, sputum, bronchoalveolar lavage fluid (BALF) and stool. Weighted gene co-expression network analysis (WGCNA) was employed in each sample type to identify modules of co-abundant bacteria associated with clinical traits.

FINDINGS: We found that the microbiome in airway and stool samples was highly dissimilar both in patients and controls, with 0.37% of this diversity associated to COPD. The microbiome taxa associated with COPD in OP swabs and sputum were highly similar, but different from BALF, suggesting that OP swabs can be a surrogate sample of sputum. Finally, using WGCNA, we identified: (a) 5 modules in OP swabs and 3 in sputum associated with FEV1, but some of them were also associated with exacerbations, dyspnoea and inhaled steroid (ICS) use; (b) In BALF 4 modules associated with FEV1 and dyspnoea, and 2 modules with ICS; and, finally, (c) in stool, 1 module related to FEV1, 1 to exacerbations and 3 with ICS.

INTERPRETATION: The gut and lung microbiomes in patients with COPD are distinct, but both clinically relevant as both present bacterial associations with airflow limitation, exacerbation history, and ICS use.

FUNDING: ISC-III PI24/00476. FRPA.2014, ICREA-2024.},
}

@article {pmid41483516,
year = {2025},
author = {Li, Z and Li, J and Shen, J and Zeng, Q and Lü, Y and Zheng, Y and Nie, H and Su, S},
title = {Tetracycline-induced alterations of gut microbiota and metabolism exacerbate imidacloprid susceptibility in honey bees (Apis mellifera).},
journal = {Journal of hazardous materials},
volume = {502},
number = {},
pages = {140996},
doi = {10.1016/j.jhazmat.2025.140996},
pmid = {41483516},
issn = {1873-3336},
abstract = {The honey bee (Apis mellifera) plays a vital role in global pollination, yet its health is increasingly threatened by multiple environmental stressors. Among these, the molecular interactions between gut microbiota disruption and pesticide exposure remains insufficiently understood. Here, we showed that tetracycline-induced gut microbiota dysbiosis significantly increased bee susceptibility to imidacloprid, leading to premature mortality. Microbiota-depleted bees also exhibited higher mortality under imidacloprid stress, confirming the protective role of a stable gut community. Taxonomic and functional analysis revealed pronounced shifts in bacterial composition, notably the reduction of Gilliamella and Bartonella and the enrichment of Lactobacillus and Commensalibacter, accompanied by broad perturbations in amino acid and carbohydrate metabolism in dysbiotic bees exposed to imidacloprid. Key metabolites with antioxidant and protective functions, including alanyl-glutamine, serotonin, and shikimic acid, were markedly reduced in the gut microbiota dysbiosis-imidacloprid group and correlated with changes in core bacterial taxa. Consistently, immune, detoxification, and nutritional genes were downregulated in bees with disturbed microbiota, indicating weakened antioxidant defense and metabolic capacity. Notably, dietary supplementation with alanyl-glutamine mitigated imidacloprid-induced mortality in honey bees, suggesting that restoring microbiota-derived metabolic functions could enhance host resilience towards imidacloprid toxicity. These findings provide direct evidence that gut microbiota integrity is critical for mitigating imidacloprid stress, and that disturbances in microbial balance heighten honey bee vulnerability to imidacloprid. This work underscores the ecological risk of combined antibiotic-pesticide exposure and emphasizes the microbiome's role as a key mediator of pollinator resilience.},
}

@article {pmid41483182,
year = {2026},
author = {Caviedes-Triana, K and Vivero-Gómez, R and Duque-Granda, D and Junca, H and Cadavid-Restrepo, G and Moreno-Herrera, CX},
title = {Structure and Diversity of the Microbiome in Amazonian Sand Flies: Insights into Vector-Microbe Interactions.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-025-02663-5},
pmid = {41483182},
issn = {1432-184X},
support = {Scholarship Program of Ministerio de Ciencia, Tecnología e Innovación, Call 15, for Human Capital Development in the context of the Bicentennial and the 2021-2022 Biennial Plan.//Ministerio de Ciencia, Tecnología e Innovación/ ; Hermes 57545//Universidad Nacional de Colombia/ ; },
abstract = {This study uses high-throughput sequencing of the 16 S rRNA gene and specific PCR to analyze the microbiome and identify secondary endosymbionts in sand flies from the Amazon region, important vectors of parasitic and viral diseases. Specimens of Psychodopygus, Trichophoromyia, Nyssomyia, Trichopygomyia and Brumptomyia were collected and analyzed. The results revealed that the richness, diversity, and composition of the microbiome are influenced by several factors, such as insect species specific composition, and insect sex. The core microbiome community was represented by 18 genera, with Novosphingobium, Cutibacterium, Methylobacterium and Staphylococcus being the most prevalent. The highest diversity at the genus level was observed in sand flies of epidemiological relevance as Psychodopygus and Nyssomyia, dominated by Novosphingobium (66.5%), Cutibacterium (29.4%) and Methylobacterium (20.4%), while in non-vectors such as Trichophoromyia, Delftia predominated (59.9%). Endosymbiont analysis showed a high prevalence of Cardinium (20%) and Wolbachia (33%), as well as the presence of Spiroplasma, Arsenophonus and Rickettsia. In addition, some bacterial genera related to the inhibition of parasite development, which have entomopathogenic activity and are involved in the degradation of insecticides were identified. Our results are relevant and contribute to the knowledge of the characterization of the microbiome and the endosymbionts in leishmaniasis vectors in the Amazon region and show promise for improving vector management, highlighting the importance of investigating their interaction with pathogens and their impact on vector biology.},
}

@article {pmid41482938,
year = {2026},
author = {Jin, N and Chen, Y and Luo, H and Su, Y and Weng, Y and Lin, X and Zheng, T and Li, B and Liu, T and Chen, J},
title = {Long-term management of psoriasis recurrence via modulation of cutaneous microbiome: synergistic topical therapy with blue light and aptamer-functionalized curcumin formulation.},
journal = {Drug delivery},
volume = {33},
number = {1},
pages = {2610532},
doi = {10.1080/10717544.2025.2610532},
pmid = {41482938},
issn = {1521-0464},
mesh = {Animals ; *Curcumin/administration & dosage/pharmacology/chemistry ; *Psoriasis/drug therapy/microbiology/therapy ; Mice ; *Microbiota/drug effects ; Disease Models, Animal ; Imiquimod ; *Skin/microbiology/drug effects ; *Aptamers, Nucleotide/administration & dosage/chemistry ; Recurrence ; Mice, Inbred BALB C ; Silicon Dioxide/chemistry ; Interleukin-17/metabolism ; Male ; Female ; Blue Light ; },
abstract = {The recurrence following the discontinuation of medication is a formidable challenge in managing psoriasis. Changes in the microbiome accompany the onset of psoriasis relapse, highlighting a potential therapeutic modality. To evaluate the superiority of the topical administration of aptamer-functionalized curcumin mesoporous silica (Apt-GA+Cur@μmS) plus blue light (BL) in restoring dysbiosis and intervening in recurrence in a murine model, a psoriasis relapse murine model with double imiquimod induction was established. With a BL-responsive shell, Apt-GA+Cur@μmS released curcumin (Cur) to assist BL to improve the preventative and therapeutic effects in the psoriasis relapse murine model, as evidenced by the psoriasis area and severity index, histology, splenic index, and dorsal IL-17A level. We also observed a negative correlation between splenic nitric oxide (NO) levels and the splenic index, indicating a possible mechanism by which Apt-GA+Cur@μmS&BL may function in the treatment of splenomegaly. Treatment with Apt-GA+Cur@μmS&BL exhibited a higher alpha diversity than the model group, with levels similar to those of healthy mice, indicating that this combination could adjust the composition of the dorsal microbiome to a healthier state. A reduction in the combined relative abundance of Staphylococcus, Streptococcus, and Corynebacterium as well as restoration of dysbiosis was also verified through 16S rDNA gene sequencing in vivo. Collectively, BL and Apt-GA+Cur@μmS cotherapy alleviates psoriasiform lesions in a double imiquimod-induced murine model by inhibiting IL-17A and increasing splenic NO. Additionally, this cotherapy restores the eubiosis of the dorsal lesions. Thus, it is a promising and innovative therapeutic modality for psoriasis inflammation alleviation and recurrence intervention.},
}

Animals
*Curcumin/administration & dosage/pharmacology/chemistry
*Psoriasis/drug therapy/microbiology/therapy
Mice
*Microbiota/drug effects
Disease Models, Animal
Imiquimod
*Skin/microbiology/drug effects
*Aptamers, Nucleotide/administration & dosage/chemistry
Recurrence
Mice, Inbred BALB C
Silicon Dioxide/chemistry
Interleukin-17/metabolism
Male
Female
Blue Light

@article {pmid41482665,
year = {2026},
author = {Trischler, R and Müller, V},
title = {Formate as electron carrier in the gut acetogen Blautia luti: a model for electron transfer in the gut microbiome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2609406},
doi = {10.1080/19490976.2025.2609406},
pmid = {41482665},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome ; *Formates/metabolism ; Humans ; Electron Transport ; *Clostridiales/metabolism/genetics ; Fermentation ; Formate Dehydrogenases/metabolism/genetics ; Acetates/metabolism ; Succinic Acid/metabolism ; Glucose/metabolism ; Bacterial Proteins/metabolism/genetics ; },
abstract = {Species of the genus Blautia are commonly found in the human gut and are known to be beneficial for the human well-being. However, only little is known about the physiology and the specific role of Blautia species in the human gut. In this study, we investigated the heterotrophic metabolism of the formate dehydrogenase lacking gut acetogen Blautia luti. We identified acetate, succinate, lactate, formate, and hydrogen as end products of sugar fermentation. Interestingly, formate is produced by the pyruvate-formate lyase reaction and used as electron acceptor in the Wood-Ljungdahl pathway of CO2 fixation. Thus, formate connects the oxidative branch of glucose metabolism with the reductive branch. The use of formate as an intraspecies electron carrier seems to be common in gut acetogens. This study highlights the role of formate as electron carrier in the gut microbiome and improves our understanding of the physiology of Blautia species in the human gut. It also introduces B. luti as potential candidate for biotechnological applications due to the production of highly desired succinate.},
}

*Gastrointestinal Microbiome
*Formates/metabolism
Humans
Electron Transport
*Clostridiales/metabolism/genetics
Fermentation
Formate Dehydrogenases/metabolism/genetics
Acetates/metabolism
Succinic Acid/metabolism
Glucose/metabolism
Bacterial Proteins/metabolism/genetics

@article {pmid41482646,
year = {2026},
author = {Levine, J and Thomas, SC and Xu, F and Isbiroglu, A and Zanganeh, R and Barazani, L and Vardhan, M and Hwang, S and Persaud, JK and Thakor, N and Joseph, S and Trasande, L and Saxena, D},
title = {Microbial signature of pediatric Crohn's disease: Differentiation from functional gastrointestinal disorders and relationship with increased disease activity.},
journal = {Physiological reports},
volume = {14},
number = {1},
pages = {e70665},
pmid = {41482646},
issn = {2051-817X},
support = {1911-03329//Leona M. and Harry B. Helmsley Charitable Trust (Helmsley)/ ; },
mesh = {Humans ; *Crohn Disease/microbiology/diagnosis ; Male ; Female ; Child ; *Gastrointestinal Microbiome ; Feces/microbiology ; Adolescent ; Bacteria/classification/genetics ; *Gastrointestinal Diseases/microbiology/diagnosis ; },
abstract = {The prevalence and incidence of Crohn's disease (CD) in pediatric populations have been steadily increasing. Growing evidence suggests that gut microbiomal community differences play a critical role in the pathogenesis of CD. Additionally, the clinical course of patients with CD is unpredictable, making treatment decisions challenging. We investigated the fecal microbiome of newly diagnosed, treatment-naïve pediatric CD patients (n = 43) compared to age- and sex-matched controls with other functional gastrointestinal disorders (n = 139). We also correlated microbial changes with CD disease activity, measured by the Pediatric Crohn's Disease Activity Index (PCDAI). Our results showed that microbial richness and diversity were significantly lower in CD patients. Furthermore, taxonomic analysis revealed an enrichment in pro-inflammatory bacteria (Fusobacteria and Proteobacteria) and depletion in favorable bacteria (Firmicutes and Verrucomicrobia). Higher PCDAI scores were linked to the enrichment of genera harboring pro-inflammatory taxa (Hungatella and Veillonella) and decreased abundance of genera harboring protective taxa (Lachnospiraceae). Our study underscores the potential of fecal microbiome profiling as an effective tool for understanding CD pathogenesis, identifying microbial biomarkers, and predicting disease activity for treatment response. This, in turn, can help to improve personalized treatment and management strategies in pediatric CD.},
}

Humans
*Crohn Disease/microbiology/diagnosis
Male
Female
Child
*Gastrointestinal Microbiome
Feces/microbiology
Adolescent
Bacteria/classification/genetics
*Gastrointestinal Diseases/microbiology/diagnosis

@article {pmid41482560,
year = {2026},
author = {Chakaroun, RM and Pradhan, M and Björnson, E and Arvidsson, D and Fridolfsson, J and Gummesson, A and Schoeler, M and Mitteregger, M and Smith, GJ and Larsson, I and Börjesson, M and Blüher, M and Uhlén, M and Stumvoll, M and Bergström, G and Tremaroli, V and Bäckhed, F},
title = {Multi-omic definition of metabolic obesity through adipose tissue-microbiome interactions.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41482560},
issn = {1546-170X},
support = {2017.0026//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 2017.0026//Diabetesfonden (Stiftelsen Svenska Diabetesförbundets Forskningsfond)/ ; 20210366//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; 20240882//Hjärt-Lungfonden (Swedish Heart-Lung Foundation)/ ; NNF15OC0016798//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF21OC0070298//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF24OC0092455//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 17CVD01//Fondation Leducq/ ; ERC-2022-ADG 101096705//Fondation Leducq/ ; 2019-01599//Vetenskapsrådet (Swedish Research Council)/ ; EXC3105/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC3105/1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {Obesity's metabolic heterogeneity is not fully captured by body mass index (BMI). Here we show that deep multi-omics phenotyping of 1,408 individuals defines a metabolome-informed obesity metric (metBMI) that captures adipose tissue-related dysfunction across organ systems. In an external cohort (n = 466), metBMI explained 52% of BMI variance and more accurately reflected adiposity than other omics models. Individuals with higher-than-expected metBMI had 2-5-fold higher odds of fatty liver disease, diabetes, severe visceral fat accumulation and attenuation, insulin resistance, hyperinsulinemia and inflammation and, in bariatric surgery (n = 75), achieved 30% less weight loss. This obesogenic signature aligned with reduced microbiome richness, altered ecology and functional potential. A 66-metabolite panel retained 38.6% explanatory power, with 90% covarying with the microbiome. Mediation analysis revealed a bidirectional, metabolite-centered host-microbiome axis, mediated by lipids, amino acids and diet-derived metabolites. These findings define an adipose-linked, microbiome-connected metabolic signature that outperforms BMI in stratifying cardiometabolic risk and guiding precision interventions.},
}

@article {pmid41482527,
year = {2026},
author = {Riaz, N and Alban, TJ and Haddad, RI and Saul, M and Makarov, V and Zhu, Y and Cohen, EEW and Ferris, RL and Chang, PM and Lin, JC and Psyrri, A and Parthasarathy, PB and Novaj, A and Gawali, M and Hoen, D and Hamilton, P and Silver, NL and Juric, I and Chawla, D and Gradissimo, A and Ko, J and McGrail, DJ and Davis, CB and Lee, NY and Chan, TA},
title = {Tumor ecosystem and microbiome features associated with efficacy and resistance to avelumab plus chemoradiotherapy in head and neck cancer.},
journal = {Nature cancer},
volume = {},
number = {},
pages = {},
pmid = {41482527},
issn = {2662-1347},
abstract = {Immune checkpoint blockade-based multimodal therapy is widely used across oncology; yet drivers of resistance in most cancer types are not well understood. Here, we comprehensively characterized the tumor genome, microenvironment and microbiome in a phase 3 international randomized trial (NCT02952586) to identify factors that shape outcomes to anti-PD-L1 avelumab plus standard-of-care chemoradiotherapy versus placebo/chemoradiotherapy in individuals with locally advanced head and neck cancer. Patients receiving avelumab whose tumors contained distinct immunologic and genetic features had superior outcomes compared to those receiving placebo. By contrast, patients with increased myeloid/neutrophil activities had worse outcomes with avelumab than those treated with placebo. Strikingly, these tumors possessed telltale intratumoral bacteria, elevated tumor-associated neutrophils, high systemic neutrophil-to-lymphocyte ratios and suppressed adaptive immunity. We define tumor ecosystems associated with benefit to chemoimmunotherapy. Our data demonstrate how intratumoral bacteria affect immune checkpoint blockade response within a randomized trial. These discoveries enhance our understanding of combination immunotherapy, provide a useful multiomic resource and identify unanticipated interactions that may guide future therapeutic strategies.},
}

@article {pmid41482480,
year = {2026},
author = {McKenzie, J and Carter, C and Jackson, MM and Singanayagam, A and Shah, A},
title = {Mechanisms driving immunopathogenesis of viral exacerbations in chronic respiratory disease.},
journal = {Thorax},
volume = {},
number = {},
pages = {},
doi = {10.1136/thorax-2024-222169},
pmid = {41482480},
issn = {1468-3296},
abstract = {BACKGROUND: Exacerbations are major causes of morbidity in individuals with chronic respiratory diseases such as chronic obstructive pulmonary disease, asthma and bronchiectasis. Increasing evidence implicates respiratory viruses as predominant triggers, though the underlying immunopathogenic mechanisms remain poorly understood.

NARRATIVE: This review synthesises current knowledge on the interplay between viral pathogens at the airway epithelial barrier, including structural and immunological mechanisms that may dysregulate antiviral immunity in chronic respiratory diseases. Furthermore, we discuss how perturbations in the respiratory microbiome, characterised by reduced microbial diversity, can modulate host antiviral immune defences.

CONCLUSIONS: Collectively, these interconnected factors create a permissive environment predisposing to viral infection and exacerbations in chronic respiratory diseases. Understanding the complex interactions between airway structure, interferon-mediated antiviral responses, inflammation and microbiota is essential for developing targeted therapies to effectively manage virus-induced exacerbations and reduce disease burden.},
}

@article {pmid41482458,
year = {2026},
author = {Zhou, CB and Zhao, LC and Qin, Y and Yu, J and Li, W and Feng, Q and Tong, X and Abuduaini, R and Lu, SY and Tang, H and Zhang, YX and Cui, Y and Xiao, L and Song, LH and Ni, LK and Wu, K and Zhong, H and Jiang, YC and Zou, Y and Leng, XX and Wang, M and Zhao, WY and Wang, CJ and Liu, Q and Zhang, JQ and Hu, C and Chen, YX and Yao, YF and Zhu, S and Fang, JY},
title = {Streptococcus anginosus-derived methionine promotes gastric cancer progression.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336966},
pmid = {41482458},
issn = {1468-3288},
abstract = {BACKGROUND: Streptococcus anginosus has been linked with an increasing risk of gastric cancer (GC) and recognised as a signature for GC screening.

OBJECTIVE: To investigate the promotional effect of S. anginosus in terms of its metabolic interactions with the host.

DESIGN: We used the functional profiles of shotgun metagenomic sequencing from stools to detect bioactive molecules relevant to S. anginosus. In vivo and in vitro experiments were used to validate the facilitation of S. anginosus to GC progression. S. anginosus clinical strains were isolated and cultivated from cancerous tissues to verify its promotion of GC via methionine production. S. anginosus ΔmetE mutant strains were constructed to confirm the critical role of metE in methionine biosynthesis.

RESULTS: We verified S. anginosus facilitated GC progression in vivo and in vitro. Our functional analysis of metagenomes revealed a significant enrichment of bacterial methionine biosynthesis pathways in GC patients with high S. anginosus abundance. Methionine, identified here as one of the primary microbial metabolites derived from S. anginosus, contributed to GC progression in humans and mice. S. anginosus strains from cancerous tissues were found to promote GC via methionine production. We further observed a higher abundance and prevalence of metE gene in cancer stool metagenomes. By constructing an S. anginosus ΔmetE mutant strain, we confirmed the critical role of metE in methionine biosynthesis.

CONCLUSION: Our results elucidate the role of S. anginosus-derived methionine in GC progression, shedding light on intricate metabolic interplay between S. anginosus and host.},
}

@article {pmid41482415,
year = {2026},
author = {Tomuța, RA and Gîtea, MF and Ghitea, MC and Ghitea, EC and Ghitea, TC and Banica, F},
title = {Nutritional Assessment of Pesticide-associated Metabolic Stress in Plant-based Diets.},
journal = {In vivo (Athens, Greece)},
volume = {40},
number = {1},
pages = {136-150},
pmid = {41482415},
issn = {1791-7549},
mesh = {Humans ; Oxidative Stress/drug effects ; Male ; Female ; *Pesticides/adverse effects/toxicity ; Biomarkers ; Adult ; *Nutrition Assessment ; Middle Aged ; Metabolomics/methods ; *Stress, Physiological/drug effects ; Fruit/chemistry ; Vegetables/chemistry ; Diet, Plant-Based ; },
abstract = {BACKGROUND/AIM: Chronic low-dose pesticide exposure through high fruit and vegetable consumption is an underappreciated risk factor for metabolic dysfunction. While plant-based diets provide antioxidants and polyphenols, co-exposure to pesticide residues and heavy metals may induce subtle but clinically relevant biochemical disruptions.

MATERIALS AND METHODS: We analyzed the detailed metabolomic organic acid profiles from 26 individuals reporting high intake of conventionally grown fruits and vegetables. Dietary modeling was performed to estimate daily polyphenol intake, while metabolomic data were evaluated for markers of detoxification stress, oxidative damage, mitochondrial function, gut dysbiosis, and heavy metal burden.

RESULTS: Both profiles revealed reproducible patterns of metabolic disturbance, including elevated methylmalonic acid, formiminoglutamic acid, and xanthurenic acid (suggestive of methylation and B-vitamin deficits); increased lipid peroxides and 8-OHdG (indicative of systemic oxidative stress); raised Krebs cycle intermediates and β-hydroxybutyrate (suggesting mitochondrial dysfunction); mild to moderate dysbiosis markers and evidence of fungal overgrowth; and elevated mercury levels exceeding reference thresholds. Despite estimated high polyphenol intake (2.5-3.5 g/day), antioxidant biomarkers remained elevated, supporting the hypothesis of pesticide-induced oxidative burden.

CONCLUSION: These findings suggest that chronic dietary pesticide exposure - even at regulatory-compliant levels - may produce a consistent metabolomic signature, particularly when at least five different pesticide, herbicide, or fungicide residues are simultaneously detected, highlighting the potential for cumulative biological effects characterized by oxidative stress, detoxification pathway strain, gut microbiome disruption, and mitochondrial impairment. This underscores the need for integrated dietary strategies to reduce contaminant intake and highlights the importance of further cohort studies to clarify health impacts and guide nutritional interventions.},
}

Humans
Oxidative Stress/drug effects
Male
Female
*Pesticides/adverse effects/toxicity
Biomarkers
Adult
*Nutrition Assessment
Middle Aged
Metabolomics/methods
*Stress, Physiological/drug effects
Fruit/chemistry
Vegetables/chemistry
Diet, Plant-Based

@article {pmid41482260,
year = {2025},
author = {Ticinesi, A and Zuliani, G and Spaggiari, R and Volpato, S and Maggi, S and Franceschi, C},
title = {The social microbiome of older people.},
journal = {Ageing research reviews},
volume = {},
number = {},
pages = {103008},
doi = {10.1016/j.arr.2025.103008},
pmid = {41482260},
issn = {1872-9649},
abstract = {The human gut microbiome (GM) is increasingly recognized as one of the main systems influencing the aging trajectory. Age-related dysbiosis, with imbalance between symbionts and pathobionts, can in fact fuel chronic inflammation (inflammaging) and promote frailty. In older individuals, GM composition is characterized by marked inter-individual variability and consistently influenced by environmental exposures. Studies conducted in animals and closed human communities suggest that social contacts are associated with horizontal transmission of commensal bacteria, enhancing biodiversity and preventing dysbiosis. Recent studies also suggest transmission of intestinal commensal bacteria from animals to humans sharing the same household. Bacterial populations residing on environmental surfaces may also have an influence on GM composition. In this framework, impoverishment of social relationships in older individuals may not be only associated with cognitive and emotional disengagement, but also with unfavorable changes in GM composition, driven by isolation and top-down neuromodulation of intestinal function. In fact, studies conducted during forced social distancing in the COVID-19 pandemic show GM changes pointing towards dysbiosis. Therefore, the detrimental consequences of social isolation for health outcomes of older individuals, including frailty progression towards disability, could be at least partly mediated by GM dysbiosis. Conversely, interventions aimed at restoring sociality, including animal-assisted activities, could expose older individuals to a range of novel bacterial species helping to counteract GM dysbiosis. This perspective article critically discusses the concept of social microbiome, its possible relevance for maintenance of good health in human beings, and its implications for the care of older patients.},
}

@article {pmid41482235,
year = {2025},
author = {Chambial, P and Thakur, N and Kumar, U and Gupta, S},
title = {The Mediating Role of the Gut Microbiome in the Nutritional Prevention of Cancer.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101301},
doi = {10.1016/j.tjnut.2025.101301},
pmid = {41482235},
issn = {1541-6100},
abstract = {The concept of food as medicine is gaining renewed importance in oncology, with growing recognition that diet is not only supportive care but a mechanistically informed intervention for cancer treatment. However, the biological basis linking nutrition to cancer outcomes has remained incomplete until recent advances positioned the gut microbiome as the missing link. Recent research has highlighted the gut microbiome as a key mediator, acting as a biochemical and immunological bridge that transforms dietary compounds into metabolites, influencing inflammation, immune function, and carcinogenesis. This perspective shifts nutrition from a supportive measure to an active, evidence-based strategy in cancer prevention. In this review, we highlight how specific foods, nutrients, and microbial consortia contribute to anti-cancer effects, while also identifying research gaps related to causality, multi-omics integration, and the need to account for global dietary and genetic diversity.},
}

@article {pmid41482230,
year = {2025},
author = {Goand, UK and Paudel, D and Koehle, AM and Hao, F and Nguyen, LV and Yalavarthi, G and Tian, S and Rajakaruna, S and Robert, CEM and da Silva, IV and Chassaing, B and Patterson, AD and Castro, R and Singh, V},
title = {Invited: Longitudinal assessment of diets with varying carbohydrate-to-fat ratios and fiber supplementation on immunometabolic markers, liver function, and gut microbiome.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101285},
doi = {10.1016/j.tjnut.2025.101285},
pmid = {41482230},
issn = {1541-6100},
abstract = {The proportions of macronutrients and fiber in the diet influence host metabolism and the development of metabolic dysfunction-associated steatotic liver disease (MASLD). However, it remains unclear how early shifts in immune, metabolic and liver function markers occur upon consuming diets with markedly different proportions of carbohydrates and fats such as the ketogenic diet (KD) and the high-carbohydrate diet (HCD) and whether these diets exert differential effects on these markers under lean and obese conditions. Moreover, the potential for prebiotic fiber supplementation to alter or mitigate the metabolic consequences of the KD has not been established. To address these questions, we conducted longitudinal assessments at 2-, 4-, 8-, and 16-weeks post-intervention in lean C57BL/6 mice, which revealed that diets rich in fat (high fat (HFD) and KD) induced obesity and hyperglycemia compared to the baseline chow diet. KD resulted in nutritional ketosis as early as two-weeks post-feeding; however, it impaired metabolic and liver function starting from week 2. Following the 16-week intervention, we observed that the fat-rich diets (HFD & KD), but not the HCD, promoted hepatic steatosis, inflammation, and fibrosis, as assessed by [1]H-NMR, quantitative PCR, and histology, respectively. Next, we found that incorporating inulin into the KD (KD-F) partly mitigated the adverse immunometabolic effects of the KD. In the HFD-induced obesity cohort, intervention with HCD and KD-F improved immunometabolic and liver function markers. The HCD showed the most pronounced benefits as early as two weeks following the diet switch. Microbiome analysis revealed reduced bacterial richness across all experimental diets (HCD, KD, and KD-F) compared to standard chow. Collectively, the present study highlights that high fat intake, but not high-carbohydrate consumption negatively impacts metabolic and liver health in lean mice. The incorporation of dietary fiber into a KD may enhance its metabolic effects while preserving the therapeutic benefits of ketogenesis.},
}

@article {pmid41481471,
year = {2026},
author = {Regan, MD and Chiang, E and Grahn, M and Tonelli, M and Assadi-Porter, FM and Suen, G and Carey, HV},
title = {Host-microbiome mutualism drives urea carbon salvage and acetogenesis during hibernation.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {1},
pages = {e2518978123},
doi = {10.1073/pnas.2518978123},
pmid = {41481471},
issn = {1091-6490},
support = {IOS-1558044//NSF (NSF)/ ; P41GM136463//HHS | NIH (NIH)/ ; DGE-1747503//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; RGPIN-2021-03109//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; 21HLSRM06//Canadian Space Agency (CSA)/ ; },
mesh = {Animals ; *Hibernation/physiology ; *Urea/metabolism ; *Sciuridae/microbiology/physiology/metabolism ; *Carbon/metabolism ; *Acetates/metabolism ; *Gastrointestinal Microbiome/physiology ; *Symbiosis/physiology ; Acetic Acid/metabolism ; Fatty Acids, Volatile/metabolism ; *Host Microbial Interactions/physiology ; },
abstract = {Hibernation is a seasonal survival strategy employed by certain mammals that, through torpor use, reduces overall energy expenditure and permits long-term fasting. Although fasting solves the challenge of winter food scarcity, it also removes dietary carbon, a critical biomolecular building block. Here, we demonstrate a process of urea carbon salvage (UCS) in hibernating 13-lined ground squirrels, whereby urea carbon is reclaimed through gut microbial ureolysis and used in reductive acetogenesis to produce acetate, a short-chain fatty acid (SCFA) of major value to the host and its gut microbiota. We find that urea carbon incorporation into acetate is more efficient during hibernation than the summer active season and that while both host and gut microbes oxidize acetate for energy supply throughout the year, the host's ability to absorb and oxidize acetate is highest during hibernation. Metagenomic analysis of the gut microbiome indicates that genes involved in the degradation of gut mucins, an abundant endogenous nutrient, are retained during hibernation. The hydrogen disposal associated with reductive acetogenesis from urea carbon helps facilitate this mucin degradation by providing a luminal environment that sustains fermentation, thereby generating SCFAs and other metabolites usable by both the host and its gut microbes. Our findings introduce UCS as a mechanism that enables hibernating squirrels and their gut microbes to exploit two key endogenous nutrient sources-urea and mucins-in the resource-limited hibernation season.},
}

Animals
*Hibernation/physiology
*Urea/metabolism
*Sciuridae/microbiology/physiology/metabolism
*Carbon/metabolism
*Acetates/metabolism
*Gastrointestinal Microbiome/physiology
*Symbiosis/physiology
Acetic Acid/metabolism
Fatty Acids, Volatile/metabolism
*Host Microbial Interactions/physiology

@article {pmid41481427,
year = {2026},
author = {Wang, J and Zi, F and Liu, W and Liu, C and Zhang, Z and Kong, L and Xu, X and Wei, J and Chen, T and Li, J},
title = {Clostridium butyricum alleviates multiple myeloma by remodeling the bone marrow microenvironment and inhibiting PI3K/AKT pathway through the gut‒bone axis.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2609455},
doi = {10.1080/19490976.2025.2609455},
pmid = {41481427},
issn = {1949-0984},
mesh = {*Clostridium butyricum/physiology/metabolism ; Animals ; *Multiple Myeloma/microbiology/therapy/metabolism/pathology ; Humans ; *Gastrointestinal Microbiome/physiology ; Mice ; Phosphatidylinositol 3-Kinases/metabolism/genetics ; *Proto-Oncogene Proteins c-akt/metabolism/genetics ; Butyrates/metabolism ; Fecal Microbiota Transplantation ; Male ; *Bone Marrow/metabolism/pathology ; Signal Transduction ; Tumor Microenvironment ; Dysbiosis/microbiology ; Female ; Th17 Cells/immunology ; },
abstract = {Emerging evidence reveals a strong connection between the gut microbiota and cancer. However, the exact role of gut microbiota dysbiosis in multiple myeloma (MM) is poorly understood, and the therapeutic potential of microbiota-targeted interventions represents a promising strategy that demands urgent mechanistic and translational investigation. First, we conducted a comprehensive microbiome-metabolite analysis between MM patients and healthy individuals. The result revealed a marked compositional difference characterized by reduced abundances of butyrate-producing bacteria and diminished butyrate levels in the MM cohort. Subsequent fecal microbiota transplantation demonstrated that the gut microbiota critically modulates MM progression, with healthy donor-derived microbiota reducing the tumor burden and concomitantly elevating serum butyrate. Furthermore, through function-based culturomics screening, Clostridium butyricum (C. butyricum) was identified as a key butyrate-producing specialist. C. butyricum or its metabolite butyrate significantly reduced the systemic tumor burden in 5TGM1 mice. Notably, C. butyricum and butyrate alleviated bone marrow inflammation and osteolytic lesions by suppressing Th17 cells and IL-17 levels in the bone marrow. Moreover, cellular assays and transcriptome sequencing further revealed that butyrate could induce MM cells' apoptosis via HDAC inhibition-mediated upregulation of PPARγ, leading to sequential suppression of the PI3K/AKT pathway and antiapoptotic BCL-2 expression. This apoptotic signaling cascade was reversed by PPARγ antagonism. The direct antitumor effect was further confirmed in M-NSG mice. Our research systematically verifies the specific role of the gut microbiota in MM and provides the first evidence of the immune and molecular mechanisms by which C. butyricum alleviates MM progression, offering preclinical support for probiotic-based therapies against MM.},
}

*Clostridium butyricum/physiology/metabolism
Animals
*Multiple Myeloma/microbiology/therapy/metabolism/pathology
Humans
*Gastrointestinal Microbiome/physiology
Mice
Phosphatidylinositol 3-Kinases/metabolism/genetics
*Proto-Oncogene Proteins c-akt/metabolism/genetics
Butyrates/metabolism
Fecal Microbiota Transplantation
Male
*Bone Marrow/metabolism/pathology
Signal Transduction
Tumor Microenvironment
Dysbiosis/microbiology
Female
Th17 Cells/immunology

@article {pmid41481332,
year = {2026},
author = {Wall, H and Ivarsson, E and Sun, L and Boyner, M and Naghizadeh, M and Dalgaard, TS and Wattrang, E},
title = {Early access to feed, water and Neurospora intermedia in broiler starter diet (part II) - caecal microbiota, antibody production and blood leukocyte counts.},
journal = {British poultry science},
volume = {},
number = {},
pages = {1-11},
doi = {10.1080/00071668.2025.2595642},
pmid = {41481332},
issn = {1466-1799},
abstract = {1. This study examined the effects of providing feed and water immediately post hatch in combination with inclusion of Neurospora intermedia biomass in chick starter diet, as a source of protein and bioactive compounds. Variables monitored were caecal microbiota, total levels of IgY, specific antibody responses to vaccination and blood leukocyte counts.2. Ross 308 chicks were subjected to two hatching treatments - immediate access to feed and water, or delayed access at 48 h. In addition, three starter diets were fed until d 10: a control diet (C), a diet with inclusion of 10% N. intermedia (N) or diet N followed by diet C (NC).3. Chicks were vaccinated against avian pneumovirus (APV) and focal birds were repeatedly blood sampled for quantification of total IgY and antibodies specific to APV in serum. Birds fed starter diet C were sampled for measures of blood leukocyte counts. Caecal microbiota were studied in birds sacrificed on d 5, 9 and 43, respectively.4. With age, microbial richness in caeca increased and there was a shift in composition, but no effects of hatching treatment or starter diet were observed.5. Neither the starter diet nor the hatching treatment affected the total IgY in serum or specific antibody responses to APV vaccination. Late-fed chicks had a significant decrease in the total amount of IgY in serum from d 2 to d 8, likely a consequence of dehydration at d 2. Early feeding did not affect any of the leukocyte populations monitored.6. In conclusion, there were no effects of early feeding or inclusion of N. intermedia on gut microbiome or the immune traits monitored. However, the absence of adverse effects of a starter diet with the fungal biomass suggested that N. intermedia is a source of high-quality protein.},
}

@article {pmid41481156,
year = {2026},
author = {Jones, EV and Wang, Y and Wei, W and Reed, JC and Chaudhari, SN and Li, DK and Boursier, J and Lang, S and Demir, M and Diehl, AM and Allegretti, AS and Schnabl, B and Chung, RT and Devlin, AS},
title = {Bile salt hydrolase activity as a rational target for MASLD therapy.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2608437},
doi = {10.1080/19490976.2025.2608437},
pmid = {41481156},
issn = {1949-0984},
mesh = {Humans ; Bile Acids and Salts/metabolism ; *Amidohydrolases/metabolism/antagonists & inhibitors/genetics ; Feces/microbiology/chemistry ; Gastrointestinal Microbiome/drug effects ; *Bacteria/enzymology/isolation & purification/genetics/classification/drug effects ; Male ; Female ; Middle Aged ; Bacterial Proteins/metabolism/antagonists & inhibitors/genetics ; Enzyme Inhibitors/pharmacology ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most prevalent chronic liver disease in the United States, yet therapeutic options remain limited. Emerging evidence implicates the gut‒liver axis and intestinal permeability in disease pathogenesis. Previous studies in animal models and human cell culture indicated that bile salt hydrolases (BSHs), which are gut bacterial enzymes that deconjugate host-derived bile acids, damage intestinal barrier integrity and cause liver damage through the generation of unconjugated bile acids (UBAs). However, the relevance of these findings to MASLD patients is unknown. Here, we demonstrate that BSH activity is elevated in fecal samples from MASLD patients with advanced liver fibrosis and correlates with reduced fecal bile acid levels, which is consistent with a proposed model of increased intestinal permeability during MASLD progression. Through anaerobic culturing and activity-guided screening, we identify diverse BSH-active bacteria from patient fecal samples, suggesting broad microbial contributions to bile acid deconjugation in MASLD patients. Importantly, small-molecule BSH inhibitors suppressed BSH activity in both fecal communities and monocultures from MASLD patients without affecting bacterial viability. These findings indicate that BSH activity is a microbial function associated with MASLD progression and suggest that BSH inhibitors could be developed as a microbiome-targeted strategy for MASLD treatment.},
}

Humans
Bile Acids and Salts/metabolism
*Amidohydrolases/metabolism/antagonists & inhibitors/genetics
Feces/microbiology/chemistry
Gastrointestinal Microbiome/drug effects
*Bacteria/enzymology/isolation & purification/genetics/classification/drug effects
Male
Female
Middle Aged
Bacterial Proteins/metabolism/antagonists & inhibitors/genetics
Enzyme Inhibitors/pharmacology

@article {pmid41480755,
year = {2026},
author = {Lorsch, ZS and Liddle, RA},
title = {Mechanisms and clinical implications of gut-brain interactions.},
journal = {The Journal of clinical investigation},
volume = {136},
number = {1},
pages = {},
pmid = {41480755},
issn = {1558-8238},
mesh = {Humans ; Animals ; *Brain/metabolism ; *Gastrointestinal Microbiome ; *Brain-Gut Axis ; Glucagon-Like Peptide-1 Receptor ; Obesity/metabolism ; Irritable Bowel Syndrome/metabolism/physiopathology ; Glucagon-Like Peptide-1 Receptor Agonists ; },
abstract = {Connections between the digestive system and the brain have been postulated for over 2000 years. Despite this, only recently have specific mechanisms of gut-brain interaction been identified. Due in large part to increased interest in the microbiome, the wide use of incretin-based therapies (i.e., glucagon-like peptide 1 [GLP-1] receptor agonists), technological advancements, increased understanding of neuroimmunology, and the identification of a direct enteroendocrine cell-neural circuit, research in the past 10 years has made it abundantly clear that the gut-brain connection plays a role both in clinical disease as well as the actions of therapeutics. In this Review, we describe mechanisms by which the gut and brain communicate and highlight human and animal studies that implicate changes in gut-brain communication in disease states in gastroenterology, neurology, psychiatry, and endocrinology. Furthermore, we define how GLP-1 receptor agonists for obesity and guanylyl cyclase C agonists for irritable bowel syndrome leverage gut-brain mechanisms to improve patient outcomes. This Review illustrates the critical nature of gut-brain communication in human disease and the potential to target gut-brain pathways for therapeutic benefit.},
}

Humans
Animals
*Brain/metabolism
*Gastrointestinal Microbiome
*Brain-Gut Axis
Glucagon-Like Peptide-1 Receptor
Obesity/metabolism
Irritable Bowel Syndrome/metabolism/physiopathology
Glucagon-Like Peptide-1 Receptor Agonists

@article {pmid41480620,
year = {2025},
author = {Rodriguez, MT and Olmstead, SJ and McLaurin, KA and Mactutus, CF and Booze, RM},
title = {S-Equol: a novel therapeutic for HIV-1-associated gastrointestinal dysbiosis.},
journal = {NeuroImmune pharmacology and therapeutics},
volume = {4},
number = {4},
pages = {325-337},
pmid = {41480620},
issn = {2750-6665},
abstract = {OBJECTIVE: HIV-1 infection affects approximately 38.4 million people around the world. The advent of combination anti-retroviral therapy (cART) has greatly improved the quality of life of infected individuals; however, roughly 50 % of these individuals will still experience HIV-1-associated neurocognitive disorders (HAND). Additionally, the gastrointestinal microbiome has been reported to be dysbiotic in HIV-1 infected individuals, regardless of adherence to cART. Current research has pointed to the gut-brain-microbiota axis as a potential target to treat both cognitive deficits and microbial changes. The present study investigated S-Equol (SE) as a potential therapeutic for HAND by modulating the gastrointestinal microbiome.

METHODS: The study included 21 HIV-1 Tg rats and 21 F344 control animals to test the effect 0.2 mg SE has on cocaine-maintained responding on a PR schedule of reinforcement.

RESULTS: Gastrointestinal microbiome alterations between genotypes were found at the phylum and genus level, regardless of treatment group, and SE treatment had both main effects and interactions with genotype. Prevotella_UCG_001 was significantly associated with lever presses for drug, suggesting an effect on motivation for cocaine. Alloprevotella was found to significantly differentiate between genotype by treatment effects, indicating that SE differently affects genotypes.

CONCLUSIONS: SE may provide a novel adjuvant treatment in addition to cART for HIV-1-associated dysbiosis and associated neurocognitive dysfunction.},
}

@article {pmid41480617,
year = {2025},
author = {Abu, YF and Tao, J and Jayakumar, A and Hussain, H and Paidas, M and Roy, S},
title = {Maternal opioid use is associated with altered placental bacterial DNA and activation of immune-apoptotic pathways.},
journal = {NeuroImmune pharmacology and therapeutics},
volume = {4},
number = {4},
pages = {353-362},
pmid = {41480617},
issn = {2750-6665},
abstract = {OBJECTIVES: Opioid use during pregnancy is associated with adverse perinatal outcomes, but its effects on placental biology are not well understood. Because the placenta plays a vital role in fetal development and immune regulation, we examined how maternal opioid exposure influences microbial DNA signatures and immune gene expression in the placenta.

METHODS: Placentas from opioid-exposed and control C57 BL/6 female mice were analyzed through 16S rRNA gene sequencing, bulk RNA sequencing and pathway enrichment analysis.

RESULTS: Opioid-exposed placentas showed altered microbial DNA profiles, including increased α-diversity and enrichment of Staphylococcus spp. Transcriptomic analysis revealed 357 differentially expressed genes, emphasizing immune pathways, including dendritic cell-NK cell crosstalk, immunogenic cell death, and cytokine storm signaling. STAT3 signaling and heparan sulfate biosynthesis were downregulated. Pathways related to apoptosis, cytotoxicity, and neonatal death were upregulated.

CONCLUSIONS: Maternal opioid exposure may disrupt placental microbial and immune environments, potentially leading to structural compromise through immune-mediated cellular apoptosis.},
}

@article {pmid41480369,
year = {2025},
author = {Qin, S and Guo, S and Tan, X and Li, K and Huang, J},
title = {Research progress of gut microbiota and its metabolites in polycystic ovary syndrome.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1700191},
pmid = {41480369},
issn = {1664-2392},
mesh = {Humans ; *Polycystic Ovary Syndrome/metabolism/microbiology ; *Gastrointestinal Microbiome/physiology ; Female ; Animals ; },
abstract = {Polycystic ovary syndrome (PCOS) ranks among the most widespread endocrine and metabolic conditions affecting women of childbearing age, but its specific pathogenesis remains unknown. More and more evidence indicates that PCOS may be a complex polymorphic disease, influenced by epigenetic and environmental factors, including diet and lifestyle. This review focuses on the role of the gut microbiota and its metabolites in PCOS, a topic that has gained significant attention recently due to the established link between the gut microbiome and metabolic disorders.},
}

Humans
*Polycystic Ovary Syndrome/metabolism/microbiology
*Gastrointestinal Microbiome/physiology
Female
Animals

@article {pmid41480316,
year = {2025},
author = {Majeed, AA and Butt, AS},
title = {Gut microbiota: An overlooked target in dyslipidemia management.},
journal = {World journal of gastroenterology},
volume = {31},
number = {48},
pages = {113178},
pmid = {41480316},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/physiology/immunology ; *Dyslipidemias/therapy/microbiology/metabolism ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; Lipid Metabolism ; Cardiovascular Diseases/prevention & control ; Bile Acids and Salts/metabolism ; Circadian Rhythm ; },
abstract = {With the global rise in sedentary lifestyles, obesity, and unhealthy dietary patterns, dyslipidemia has emerged as a leading modifiable risk factor for atherosclerotic cardiovascular disease. Beyond host genetics and diet, the gut microbiota has gained recognition as a critical regulator of lipid homeostasis through mechanisms involving bile acid metabolism, short-chain fatty acid signaling, and microbial modulation of inflammation. Lv et al provide a comprehensive synthesis of the diet microbe-lipid axis and therapeutic strategies, including probiotics, prebiotics, and fecal microbiota transplantation. In this correspondence, we expand on their framework by highlighting underexplored yet clinically relevant dimensions, including circadian rhythm alignment, pharmacotherapy microbe crosstalk, population-specific microbial signatures, and functional microbial phenotyping. Addressing these overlooked aspects could accelerate the translation of microbiome science into precision dyslipidemia management, with the potential to improve cardiovascular outcomes worldwide.},
}

Humans
*Gastrointestinal Microbiome/drug effects/physiology/immunology
*Dyslipidemias/therapy/microbiology/metabolism
Probiotics/therapeutic use
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
Lipid Metabolism
Cardiovascular Diseases/prevention & control
Bile Acids and Salts/metabolism
Circadian Rhythm

@article {pmid41480270,
year = {2025},
author = {Bustos-Caparros, E and Viver, T and Gago, JF and Venter, SN and Bosch, R and Konstantinidis, KT and Rodriguez-R, LM and Rossello-Mora, R},
title = {Uneven sequencing (coverage) depth can bias microbial intraspecies diversity estimates and how to account for it.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf228},
pmid = {41480270},
issn = {2730-6151},
abstract = {An unbiased and accurate estimation of intraspecies diversity, i.e. the extent of genetic diversity within species (or microdiversity), is crucial for clinical and environmental microbiome studies. Although it is well appreciated that sequencing depth (or coverage depth) below 10X can provide biased estimates of microdiversity, typically underestimating diversity due to the random sampling of alleles, there is a widely accepted convention that microdiversity estimates tend to be relatively stable at sequencing depth exceeding 10X. Therefore, discarding species with <10X or rarefying to 10-20X sequencing depth are generally used to compare microdiversity among taxa and samples. Our findings showed that these biases may persist even at depth levels above 50-200X for all popular sequencing platforms, including Illumina, PacBio, and Oxford Nanopore. The biases mostly, but not always, represent an underestimation of diversity and were attributable to the incomplete recovery of Single Nucleotide Variants (SNVs) at lower sequencing depth levels. To address this issue, we recommend using rarefaction-based approaches to standardize data at least 50X, and ideally at 200X sequencing depth, which reduces differences between observed and expected microdiversity values to <0.5%. Furthermore, the Average Nucleotide Identity of reads (ANIr) metric is significantly less sensitive to sequencing depth variability than nucleotide diversity (π), making it a robust alternative for estimating microdiversity at sequencing depth close or exceeding 10X, without a need to rarefying data. Therefore, the sequencing depth thresholds proposed herein provide a more standardized framework for direct comparisons of microdiversity across samples and studies.},
}

@article {pmid41480268,
year = {2025},
author = {Wang, Y and Lejoly, JDM and Berlinches de Gea, A and van den Elsen, S and Veen, GFC and Geisen, S},
title = {Protist size-dependent shifts of bacterial communities can reduce litter decomposition.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf231},
pmid = {41480268},
issn = {2730-6151},
abstract = {Microbial-mediated litter decomposition drives carbon and nutrient cycling. This process can be top-down regulated by microbiome predators, particularly the diverse protists. Size has been suggested to determine predation impacts, but how protists of different size categories affect microbial-mediated litter decomposition remains unknown. Using a litter decomposition experiment with three protist size categories, we investigated protist size-dependent effects on microbial-driven litter decomposition. We found that protists of the large-size category created more structurally similar bacterial communities compared to the no-protist control. These protists of the large size category also reduced litter mass loss by 40%, while increasing microbial respiration by 17% compared to the no-protist control after five weeks of decomposition. In contrast, protists of the small-size category and protists of the medium-size category had no measurable impact on bacterial communities, litter mass loss, or microbial respiration. Random forest analysis identified Streptomyces as a major contributor to litter mass loss (explained 8% of litter mass), while the potential protist symbionts Taonella and Reyranella explained 8% and 6% of microbial respiration, respectively. These likely predation-resistant bacterial taxa were primarily enriched by protists of the large-size category. Our results indicate that protists, especially large ones, can alter litter decomposition by shaping microbiome composition. Future studies on litter decomposition and carbon cycling should incorporate protists and their traits, particularly size, to enhance our understanding of global carbon and nutrient cycling.},
}

@article {pmid41480266,
year = {2025},
author = {Li, HR and Wang, ZQ and Zhang, XY and Ullah, Y and Yuan, R and Zhao, JY and Xu, X and Luo, X and Zhang, W},
title = {Oral microbiome is related to lepidopteran herbivore performance by lignin degradation.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf229},
pmid = {41480266},
issn = {2730-6151},
abstract = {Microorganisms associated with insects play crucial roles in mediating the host plant adaptation of their insect hosts. Although oral microbiota are the primary interface with ingested plant material, we still poorly understand their diversity, their function, and their ecological relationship with insect performance. Here, we investigated the diversity and function of the oral microbiota in two generalist lepidopteran pests (Spodoptera litura and Spodoptera frugiperda) feeding across three host plants (bok choy, peanut, and maize). Plant species significantly influenced the diversity and composition of oral microbiota in both S. litura and S. frugiperda. Oral microbial communities from insects feeding on bok choy exhibited significantly higher Sobs richness and Shannon diversity compared to those with peanut or maize plants. Community-level analysis revealed overlapping enriched oral taxa-including Brevibacterium, Staphylococcus, Microbacterium, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Brachybacterium, and Rhodococcus-that were enriched in both insect species when consuming bok choy. In contrast, they accumulated distinct bacterial taxa emerged when feeding on peanut and maize. Microbial ligninolysis capacity within the oral microbiota showed positive associations with leaf lignin content and herbivore performance. This functional trait primarily associated with Brevibacterium and Rhodococcus taxa. Accordingly, two isolated strains, Brevibacterium sedimins OS20 and Rhodococcus sp. OS5 demonstrated effective lignin degradation capacity, achieving 41.01% and 17.62% lignin loss in litter, respectively, after 60 days in microcosm experiments. Overall, host plants shape the diversity and composition of insect oral microbiota. Crucially, microbial ligninolysis capacity and leaf lignin content positively correlated with herbivore performance. This study provides novel insights into the function of oral microbiota in plant-insect interactions, potentially informing the complex multitrophic relationships underlying coevolutionary dynamics.},
}

@article {pmid41480264,
year = {2025},
author = {Kok, PJR and Urbaniak, M},
title = {Lost paradise-anthropogenic pressure alters microbial functional diversity in an endangered endemic toad-habitat system.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf239},
pmid = {41480264},
issn = {2730-6151},
abstract = {Tourism-driven human activity is increasingly disrupting fragile and once-pristine ecosystems worldwide, as evidenced by coral reef degradation in the Great Barrier Reef, vegetation loss in the Himalayas, and, as demonstrated in this study, microbial shifts in isolated highland habitats such as tepui summits. Integrating field-based ecological, microbiological, and conservation perspectives, this study provides novel insights into how anthropogenic disturbance-particularly tourism-affects microbial functional diversity across interconnected environmental (soil) and host-associated (amphibian skin and faeces) compartments in a globally unique and poorly studied highland ecosystem, the summit of Roraima-tepui in Venezuela. Our results provide clear evidence that anthropogenic disturbance on the summit of Roraima-tepui reduces microbial functional diversity-by 59% in soil and by 21% and 14% in the skin and faecal microbiomes of the (near)endemic toad Oreophrynella quelchii, respectively-compared to pristine sites. Our findings raise significant concern, as alterations in microbial composition and functions could disrupt host immunity and disease resistance in this unique, insular, and ecologically fragile ecosystem, particularly given the recent detection of anthropogenic pathogen incursion in amphibian communities. Our results stress the need to better understand the link between the observed shift in the skin microbiome's functional profiles in O. quelchii at summit sites most impacted by tourism and the recent emergence of the fungal pathogen Batrachochytrium dendrobatidis in the same environmental context. Our findings underscore the urgent need to mitigate human-induced pressures threatening the ecological integrity of the summit of Roraima-tepui, one of the world's most fragile and irreplaceable montane habitats.},
}

@article {pmid41480259,
year = {2025},
author = {Bachtiar, E and Bachtiar, BM and Tahapary, DL and Fath, T and Theodora, CF and Haerani, N and Shahab, SN and Soeroso, Y and Wildan, A and Runtu, FMJG and Tadjoedin, FM and Ayuningtyas, D},
title = {Salivary microbiome and periodontopathogen/denitrifying bacteria associated with gingivitis and periodontitis in people with type 2-diabetes.},
journal = {F1000Research},
volume = {14},
number = {},
pages = {297},
pmid = {41480259},
issn = {2046-1402},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/complications ; *Saliva/microbiology ; *Periodontitis/microbiology/complications ; *Microbiota ; *Gingivitis/microbiology/complications ; Adult ; Male ; Female ; *Bacteria/metabolism/genetics ; Young Adult ; Nitrites/metabolism ; Nitrates/metabolism ; },
abstract = {BACKGROUND: Despite diabetes mellitus and periodontal diseases are mutually exclusive, little is known about particular types of bacteria that may have exacerbated the development of diabetics' periodontal inflammation. The purpose of this study was to descriptively characterize and explore the differences in the salivary microbiomes of individuals with type 2 diabetes (20-40 years old) who had gingivitis or periodontitis to those who did not. Additionally, we evaluated the descriptive relationship between the relative abundance of periodontopathogens and nitrate-reducing bacteria in their salivary microbiome.

METHODS: Saliva was collected from all participants. Genomic DNA was isolated and pooled in equimolar quantities from all individuals within each group to create three pooled libraries: type 2 diabetes (T2DM) patients without periodontal disease (G1), T2DM patients with gingivitis (G2), and T2DM patients with periodontitis (G3). Sequencing was performed using Oxford Nanopore MinION Technology. The relative abundance and bacterial diversity were measured using bioinformatic methods, and all analyses of sequencing data were strictly descriptive and exploratory. Salivary nitrite/nitrate concentrations were measured on individual, un-pooled samples.

RESULTS: The salivary microbiota among people with type 2 diabetes and periodontal disease (G2; G3) was observed to have greater bacterial diversity and abundance than that of patients without periodontal disease (G1), according to descriptive alpha-diversity analysis. The G3 group exhibited the largest relative abundance of Porphyromonas gingivalis, a key periodontopathogen. Descriptive analysis also suggested that periodontopathic bacteria and nitrate-reducing bacteria have different community structures across the groups. Furthermore, comparison of individual salivary samples showed that nitrite/nitrate concentration was significantly lower in the G3 group compared to the G1 group (p< 0.05).

CONCLUSION: Results of this exploratory study suggest that the relationship between periodontopathic and denitrifying bacteria in the salivary microbiome varies among those with type 2 diabetes mellitus who also have gingivitis or periodontitis. These distinct microbial features observed may be microbiological characteristics associated with the progression of periodontal disease in this population, warranting further validation as potential indicators for early management.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/complications
*Saliva/microbiology
*Periodontitis/microbiology/complications
*Microbiota
*Gingivitis/microbiology/complications
Adult
Male
Female
*Bacteria/metabolism/genetics
Young Adult
Nitrites/metabolism
Nitrates/metabolism

@article {pmid41480207,
year = {2025},
author = {Song, S and Xu, LS and Wang, LQ and Zhou, X and Jiang, X and Li, CP},
title = {Tumor-resident microorganisms as clinical biomarkers in primary liver cancer: A systematic review of current evidence.},
journal = {World journal of gastrointestinal oncology},
volume = {17},
number = {12},
pages = {112936},
pmid = {41480207},
issn = {1948-5204},
abstract = {BACKGROUND: Hepatic malignancies represent the sixth most prevalent cancer globally, with emerging evidence revealing that intratumoral microbes actively modulate carcinogenesis through immunomodulation and metabolic reprogramming. Recent high-throughput sequencing technologies have identified taxonomically diverse microbial communities within tumor tissues, challenging traditional sterility paradigms. Germ-free mouse models have established causal relationships between gut microbiota and hepatocarcinogenesis. However, comprehensive evaluation of intratumoral microbiota as clinical biomarkers remains limited, necessitating systematic analysis of their diagnostic, prognostic, and therapeutic applications in hepatic malignancies.

AIM: To systematically analyze intratumoral microbes as biomarkers for hepatic malignancies diagnosis, prognosis, and treatment response.

METHODS: We conducted a systematic literature search in PubMed from inception to July 2025 using keywords combining hepatic malignancies, intratumoral microbiota, and biomarkers. Inclusion criteria encompassed human studies examining intratumoral microbial communities with biomarker applications. Exclusion criteria included animal-only studies, reviews, and research focusing solely on gut microbiota. Data extraction focused on diagnostic accuracy, prognostic significance, therapeutic predictions, and underlying mechanisms. Study quality was assessed using Newcastle-Ottawa Scale, with scores ≥ 7 indicating high quality.

RESULTS: Twenty studies (sample sizes: 18-925 patients) examining hepatocellular carcinoma (80%) and intrahepatic cholangiocarcinoma (20%) were included. All studies achieved Newcastle-Ottawa Scale scores ≥ 6, with 60% scoring the maximum 9 points, indicating moderate-to-high quality. Studies predominantly employed 16S rRNA sequencing (100%) targeting V3-V4 regions, with complementary validation techniques including fluorescence in situ hybridization, quantitative PCR, and immunohistochemistry. Specific bacterial taxa demonstrated exceptional diagnostic accuracy [area under the curve (AUC) > 0.9] for tumor discrimination. Notably, Bacilli showed AUC = 0.943 in validation cohorts. Microbial diversity and specific genera (Methylobacterium, Akkermansia, Intestinimonas) showed consistent prognostic associations with survival outcomes, though relationships varied across cancer subtypes. Advanced risk stratification models incorporating multiple bacterial biomarkers showed independent predictive capacity through multivariable Cox regression. Mechanistic investigations revealed microbe-mediated oncogenic pathway activation, particularly NF-κB signaling, immune modulation through M2 macrophage polarization, and drug resistance mechanisms via autophagy regulation. Germ-free mouse models established causal relationships, demonstrating that specific bacterial communities, particularly Klebsiella pneumoniae, can autonomously initiate hepatocarcinogenesis through TLR4-dependent pathways.

CONCLUSION: Intratumoral microbes represent promising clinical biomarkers for hepatic malignancies across diagnostic, prognostic, and therapeutic applications. While standardization and multicenter validation remain essential prerequisites, mechanistic evidence from human and experimental studies positions microbiome-based biomarkers at the threshold of clinical translation.},
}

@article {pmid41480165,
year = {2025},
author = {Madarasz, B and Balazs, MA and Palfi, E and Konczos, J and Toth, A and Szentmartoni, G and Herold, Z and Dank, M},
title = {Ultra-processed foods and dietary habits of oncology patients: Risk factor or survival strategy.},
journal = {World journal of clinical oncology},
volume = {16},
number = {12},
pages = {111372},
pmid = {41480165},
issn = {2218-4333},
abstract = {The consumption of ultra-processed foods (UPFs) is continuously increasing, and there is growing evidence that these foods contribute to the development and progression of cancer. For oncology patients alone, maintaining nutritional status is crucial for tolerating treatments and improving survival. The aim of this paper is to review the role of UPFs in the diet of oncology patients, highlighting their potential health-damaging effects (e.g., increased inflammation, microbiome disruption, nutrient deficiencies) and potential benefits (e.g., easy accessibility, high energy content, specially formulated nutritional supplements) particularly in the context of addressing the energy and nutrient needs and nutritional challenges of patients experiencing cancer-related cachexia or anorexia. Using a literature review, we examine how the UPFs can impact oncology patients' health, supporting the quality of life and clinical outcomes of oncology patients.},
}

@article {pmid41480161,
year = {2025},
author = {Ansari, S and Ahmed, N},
title = {Pathogenicity of Helicobacter pylori-associated gastric cancer.},
journal = {World journal of clinical oncology},
volume = {16},
number = {12},
pages = {110909},
pmid = {41480161},
issn = {2218-4333},
abstract = {Gastric cancer (GC) is one of the leading causes of cancer-related deaths worldwide and ranks among the top five most common malignancies. Helicobacter pylori (H. pylori) infection is recognized as the primary risk factor, although gastric carcinogenesis also reflects complex interactions among bacterial virulence factors, host genetics, and the gastric microbiome. H. pylori harbors well-characterized proteins such as CagA, VacA, BabA, and SabA that enable persistent infection and fuel tumor initiation. Recent high-quality evidence from randomized trials and meta-analyses provide strong support that H. pylori eradication therapy substantially reduces cancer risk-even in those with established precancerous lesions such as intestinal metaplasia or dysplasia. Additionally, emerging research indicate that H. pylori may influence the tumor immune microenvironment, such as through altering programmed death ligand 1 expression-which could affect immunotherapy outcomes. This review presents a cohesive and updated perspective on H. pylori-driven GC, summarizing bacterial virulence, host predispositions, microbiome interactions, epigenetic changes like DNA repair gene methylation, and evolving therapeutic implications, all while illuminating current scientific debates and emerging directions.},
}

@article {pmid41480121,
year = {2025},
author = {Wang, Y and Wu, J and Wang, Y and Jiang, W and Wang, D and Zhao, J and Qin, X and Yuan, Y and Zhang, H and Wang, J and Zhen, J and Du, Y and Mu, X and Li, L and Wang, T and Zou, L and Fang, X and Sun, B and Li, H},
title = {Respiratory Microbiome in Elderly Patients on Prolonged Mechanical Ventilation: A Prospective Multi-Center Observational Study.},
journal = {Clinical interventions in aging},
volume = {20},
number = {},
pages = {2705-2716},
pmid = {41480121},
issn = {1178-1998},
mesh = {Humans ; Aged ; Male ; Female ; Prospective Studies ; *Pneumonia, Ventilator-Associated/microbiology/virology ; *Microbiota ; *Respiration, Artificial/adverse effects ; Aged, 80 and over ; Klebsiella pneumoniae/genetics/isolation & purification ; },
abstract = {PURPOSE: The purpose of this study was to explore dynamic changes of respiratory microbiome in elderly patients undergoing prolonged mechanical ventilation (PMV) by isothermal microfluidic amplification chip technology (IAMC).

METHODS: The study enrolled patients in six general hospitals in Beijing. Patients who developed Ventilator-associated pneumonia (VAP) within the observation period were enrolled in the VAP group, while those without VAP were categorized in non-VAP group. The study adopted IAMC technology to dynamically monitor the differences in the detection rates of bacteria, fungi, and viruses in the two groups. The conventional microbiological tests (CMT) were performed to clarify the correlation between KPC and drug resistance phenotype of K. pneumoniae.

RESULTS: Among 218 patients, 78 were diagnosed with VAP. The pulmonary microbiota composition of patients without VAP was relatively stable. Compared with the non-VAP group, the detection rates of Enterococcus faecalis, Epstein-Barr virus, and Herpes simplex virus were significantly increased in the VAP group, whereas those of Haemophilus influenzae and Serratia marcescens were significantly reduced. In the VAP group, the detection rates of Enterococcus faecalis and Epstein-Barr virus were higher after the occurrence of VAP than before. A high correlation was observed between the KPC genotype of K. pneumoniae and its resistance phenotype.

CONCLUSION: Viruses and Gut microbes might be closely related to the development of VAP in elderly undergoing PMV. The detection of the KPC gene of K. pneumoniae can guide antibiotic selection, and IAMC can aid in quickly identifying pathogens and facilitate targeted treatment.

ChiCTR2100051343.},
}

Humans
Aged
Male
Female
Prospective Studies
*Pneumonia, Ventilator-Associated/microbiology/virology
*Microbiota
*Respiration, Artificial/adverse effects
Aged, 80 and over
Klebsiella pneumoniae/genetics/isolation & purification

@article {pmid41480114,
year = {2025},
author = {Robayo-Cuevas, C and Junca, H and Uribe, S and Gómez-Palacio, A},
title = {Detection of endosymbiotic, environmental, and potential bacterial pathogens in diverse mosquito taxa from Colombian tropical forests using RNAseq.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1727830},
pmid = {41480114},
issn = {1664-302X},
abstract = {INTRODUCTION: Mosquitoes of the subfamily Culicinae transmit pathogens of major medical and veterinary importance, particularly in tropical regions where urbanization and ecological change promote arbovirus circulation. In Colombia, rural Culicinae species are diverse and harbor microbiomes that may influence vector competence, yet their bacterial communities remain poorly characterized.

METHODS: We characterized the bacterial microbiota of multiple Culicinae species and morphotypes collected from two rural localities in Antioquia, Colombia, using an integrated metagenomic approach. Ribosomal 16S rRNA sequences were extracted from total RNA-seq datasets to infer bacterial community composition and assess α- and β-diversity. Diversity metrics (Chao1 and Shannon indices), Discriminant Analysis of Principal Components (DAPC), and Bray-Curtis ordination were used to evaluate community structure. In parallel, de novo assembled contigs were taxonomically annotated against the NCBI NR bacterial database to obtain complementary taxonomic and functional insights.

RESULTS: Culex morphotypes exhibited the highest richness and evenness, whereas Aedes and Trichoprosopon showed lower diversity. Ordination and DAPC analyses revealed partial clustering by species and tribe. Both the 16S and assembly-based analyses showed complex bacterial assemblages dominated by Wolbachia (up to 60% of reads in several Aedes and Culex morphotypes), followed by environmental genera such as Pseudomonas and Acinetobacter (10-20%). Lower-abundance taxa of medical and veterinary importance-including Salmonella, Borrelia, and Clostridium (<5%)-were also detected. Bacterial community structure differed among mosquito species; Aedes albopictus was enriched in lactic acid bacteria, while Culex morphotypes exhibited broader environmental and endosymbiotic profiles.

DISCUSSION: This study provides the first comprehensive metagenomic description of bacterial communities associated with rural Culicinae mosquitoes in Colombia. The predominance of symbionts such as Wolbachia and Spiroplasma, coupled with distinct bacterial signatures among host species, highlights the ecological complexity of these microbiomes and their potential relevance for microbiome-based strategies in sustainable arboviral disease management.},
}

@article {pmid41480112,
year = {2025},
author = {Fu, J and Bu, G and Aimaier, S and Yang, Y and Bao, Z and Wulasihan, M},
title = {Sex-specific association between gut Faecalibacterium prausnitzii and hypertension in male individuals.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1683587},
pmid = {41480112},
issn = {1664-302X},
abstract = {OBJECTIVE: While gut microbiota (GM) dysbiosis has been implicated in hypertension, the sexassociated microbial signatures and their underlying mechanisms remain poorly understood, particularly in populations living in unique geographical and climatic conditions.

DESIGN: Through an integrated approach combining 16S rRNA sequencing, shotgun metagenomics, and serum metabolomics, we systematically investigated the sex-associated characteristics of the gut microbiota in hypertension among a cohort of 200 participants from Xinjiang.

METHODS: An initial cohort analysis identified Faecalibacterium as a male-associated biomarker for hypertension. Subsequent species-level characterization revealed that Faecalibacterium prausnitzii (F. prausnitzii) showed significant negative correlations with systolic blood pressure (SBP). This male-specific association was consistently observed across both 16S rRNA sequencing and shotgun metagenomic datasets. Then, our integrated analysis suggested a potential pathway through which F. prausnitzii may be linked to systolic blood pressure in male individuals, with N-phenylacetylglutamine (PAGln) identified as a potential mediating metabolite.

CONCLUSION: Our study establishes a microbe-metabolite-clinical trait axis in the pathophysiology of sex-associated hypertension and significantly advances our understanding of sex-driven host-microbe interactions.},
}

@article {pmid41480103,
year = {2025},
author = {Jobert, L and Vicheth, V and Czernic, P and Suong, M and Béna, G and Moulin, L},
title = {Rhizosphere legacy of leaf-diseased rice and its impact on next generation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1677271},
pmid = {41480103},
issn = {1664-302X},
abstract = {Plants interact continuously with the surrounding soil microbiota, shaping and being shaped by these communities over time, termed as the plant-soil feedback (PSF). As a result, plants can leave a biological imprint in the soil that affects the performance of subsequent plants, a phenomenon termed the soil-borne legacy. In this study, we investigated how the rhizosphere microbiota of rice plants exhibiting (or not) foliar disease symptoms in a Cambodian field was modified and influenced subsequent generation of plants. Based on a visual assessment of foliar symptoms, we collected and mixed the rhizospheres of plants classified as "diseased" or "healthy," respectively. These mixed rhizospheres were then used to sow new rice plants in controlled conditions, which were subsequently challenged with Xanthomonas oryzae pv. oryzae. Phenotypic analyses revealed that plants grown in the rhizosphere microbiota collected from diseased field plants were smaller, yet displayed smaller symptoms to foliar pathogens compared to those grown in the microbiota of healthy plants. Amplicon sequencing of roots and rhizospheres from field samples confirmed that diseased and healthy plants harbored distinct microbial communities. A dysbiotic rhizosphere was found to be present in leaf-diseased plants, in contrast to healthy ones. These differences were also detectable in the composite rhizosphere mixes, and persisted in the rhizospheres of a new generation of rice plants grown in these soils. This suggests a microbiota-driven legacy, wherein the health status of the previous generation shapes the microbial environment and influences plant phenotype in terms of growth and defense. Our results support the idea that leaf-diseased plants condition their rhizosphere microbiota thus influencing plant phenotype in the next generation. Understanding the impact of disease-induced microbial legacy on next generation plant phenotype is crucial for developing microbiome-based crop protection strategies.},
}

@article {pmid41480099,
year = {2025},
author = {Chen, Y and Li, X and Huang, R and Zhang, F and Ma, C},
title = {Changes in soil microbial community structure during the transformation from native soil to alfalfa cultivation soil in the Kunlun Mountain sand area, Xinjiang, China.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1702974},
pmid = {41480099},
issn = {1664-302X},
abstract = {Alfalfa cultivation is widely regarded as an effective biological approach for improving desertified and degraded soils. However, it remains unclear how this effect unfolds in high-altitude desert environments and how soil and plant microbiomes assemble when native soil (NS) host plants are replaced. In this study, we tested whether converting NS to alfalfa-cultivated soil (CS) affected the composition of soil microbial communities and changed microbial diversity. Specifically, alfalfa cultivation reshaped core microbial components, increasing beneficial bacteria such as Arthrobacter and Pseudomonas, potentially enhancing nutrient cycling and plant growth, while reducing certain decomposers (e.g., Bacteroides). Results indicated that alfalfa cultivation improved NS quality, and with longer planting time, promoted the recovery and homogenization of soil microbial diversity. This process was accompanied by the replenishment or exclusion of soil microorganisms. Soil organic matter and pH were identified as key drivers of microbial community change. Across 541 bacterial OTUs and 56 fungal OTUs were shared across NS, CS, and alfalfa rhizosphere soil (RS), this core microbiome accounted for a large proportion of reads (bacteria: 28.70%, fungi: 40.37%). Microbial network structure and interactions were more complex NS and RS than in CS, with bacterial interactions more pronounced than fungal ones. Overall, the transition from NS to CS via alfalfa planting positively affected local microbial diversity, and RS assembly was shaped by both recruitment and dispersal. This research highlights the potential of alfalfa to restore high-altitude desertified ecosystems by strengthening microbially mediated soil fertility and biogeochemical cycling, offering insights for sustainable land management in arid regions.},
}

@article {pmid41479870,
year = {2025},
author = {Ghosh, N and Sinha, K},
title = {Guardians within: Cross-talk between the gut microbiome and host immune system.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {16},
number = {4},
pages = {111245},
pmid = {41479870},
issn = {2150-5330},
abstract = {The gut microbiome, a complex ecosystem of trillions of microorganisms, plays a crucial role in immune system regulation and overall health. This review explores the intricate cross-talk between the gut microbiota and the host immune system, emphasizing how microbial communities shape immune cell differentiation, modulate inflammatory responses, and contribute to immune homeostasis. Key interactions between innate and adaptive immune cells - including macrophages, dendritic cells, natural killer cells, innate Lymphoid cells, T cells, and B cells - and gut microbiota-derived metabolites such as short-chain fatty acids are discussed. The role of commensal bacteria in neonatal immune system development, mucosal barrier integrity, and systemic immunity is highlighted, along with implications for autoimmune diseases, inflammatory conditions, and cancer immunotherapy. Recent advances in metagenomics, metabolomics, and single-cell sequencing have provided deeper insights into the microbiota-immune axis, opening new avenues for microbiome-based therapeutic strategies. Understanding these interactions paves the way for novel interventions targeting immune-mediated diseases and optimizing health through microbiome modulation.},
}

@article {pmid41479867,
year = {2025},
author = {Priyanka, P and Khullar, S and Singh, M and Morya, AK and Sharma, B and Periasamy, B and Moharana, B and Morya, R},
title = {Role of gut microbiomes in different ocular pathologies: A systematic review.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {16},
number = {4},
pages = {113488},
pmid = {41479867},
issn = {2150-5330},
abstract = {BACKGROUND: The gut microbiome is integral to human health, with emerging research underscoring its potential impact on ocular health through the gut-eye axis. Various ocular disorders, such as dry eye syndrome, retinal vascular diseases, macular degeneration, and glaucoma, may be influenced by gut dysbiosis, which could significantly contribute to their development and progression.

AIM: To evaluate the influence of the gut microbiome on the pathogenesis and progression of various ocular diseases.

METHODS: An extensive search of the scientific literature was undertaken by adhering to Preferred Reporting Items for Systematic Reviews & Meta-Analyses standards, using PubMed (MEDLINE), Scopus, EMBASE, and the Cochrane Library as sources to locate studies addressing the relationship between the gut microbiome and human health. To capture all relevant publications, search terms were systematically applied across these major databases, without limiting the search by language or publication date. Inclusion criteria covered randomized controlled trials, non-randomized controlled trial, prospective studies, cross-sectional studies, and case-control studies. Out of the 3077 articles, 36 full texts were included in the review.

RESULTS: Ocular health appears to be shaped by the gut microbial community through mechanisms such as immune regulation, preservation of the blood-retinal barrier, and the generation of protective metabolites. Disturbances in this microbial balance can provoke measurable alterations in host immunity, providing a plausible immunopathogenic pathway that connects intestinal dysbiosis with eye disease. Both laboratory models and early human data suggest that targeted interventions, including prebiotics, probiotics, synbiotics, and faecal microbiota transfer, hold therapeutic potential.

CONCLUSION: The gut-eye relationship reflects a multifaceted interaction in which the intestinal microbiome contributes to ocular health through complex biological pathways. Integrating microbiome assessments into diagnostic methods can revolutionize disease management through early detection and targeted interventions. Further, randomised controlled clinical trials are necessary for ocular diseases to prove causal relationships.},
}

@article {pmid41479866,
year = {2025},
author = {Dutta, AK and Vishruth, S and Kovi, SL and Dadhich, P and Polavarapu, J and Abraham, D},
title = {Gut microbiota as a potential predictor of therapeutic response in adults with Crohn's disease: A systematic review.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {16},
number = {4},
pages = {112961},
pmid = {41479866},
issn = {2150-5330},
abstract = {BACKGROUND: Various therapeutic options are available for the treatment of Crohn's disease (CD). About 30%-40% patients experience primary non-response, and 20%-30% secondary loss of response to biological therapy. Predicting therapeutic response is challenging and an area of active research. Gut microbiota has emerged as an important player in the pathogenesis of CD and also appears to be a promising biomarker for predicting therapeutic response.

AIM: To systematically review the literature on the current status of gut microbiota as a tool to predict response to treatment in adults with CD.

METHODS: We searched the literature database (PubMed, Scopus, and Cochrane database) from inception to August 2025. We screened for studies reporting on adult patients with CD receiving biologic or immunomodulator therapies, with baseline microbiome analyses performed prior to treatment. Papers reporting on baseline gut microbiota as a predictor of therapeutic response were finally included. The utility of bacterial diversity, microbial community structure, and the role of specific operational taxonomic units as biomarkers of therapeutic response was reviewed. The results were grouped based on the bacterial parameters studied and presented in separate tables. The quality of the included studies was assessed using the MINORS criteria. The review was registered prospectively in PROSPERO.

RESULTS: After applying the selection criteria, sixteen studies were included in this systematic review. The majority of the papers were from Europe and the United States. All except two papers assessed gut bacterial population using 16S rRNA gene sequencing. Ten of the sixteen studies were of high quality. Among the sixteen studies included, most identified an association between microbial taxa and treatment response, while the relation with alpha-diversity was inconsistent. The functional characteristics were reported in only four studies and were found to be useful. The best prediction was achieved when microbial characteristics were combined with clinical and other parameters, with area under the curve values up to 0.96.

CONCLUSION: The overall results suggest good performance of microbial parameters as a novel biomarker of therapeutic response. However, there are variations across individual studies, probably related to the methodology of assessing microbial communities and the therapeutic agent used. Future multicenter studies integrating microbial, clinical, and metabolomic data are warranted to develop predictive models for personalized therapy in CD.},
}

@article {pmid41479772,
year = {2025},
author = {Jiang, C and Ma, J and Mu, J and Fu, Y and Zhao, Y and You, Y and Cui, Z and Guo, C},
title = {Biological relationship between Parkinson's disease and gallstone disease.},
journal = {Neuroprotection (Chichester, England)},
volume = {3},
number = {4},
pages = {322-335},
pmid = {41479772},
issn = {2770-730X},
abstract = {Compelling evidence indicates a significant connection between dysfunction of the gastrointestinal tract, the gut microbiome, and Parkinson's disease (PD), which aligns with the notion of the "gut-brain axis". While the exact mechanisms involved in gut-brain interactions are still not fully understood, the high incidence of gastrointestinal symptoms during the early stages of PD aids in the development of diagnostic biomarkers and prospective disease-modifying therapies. Importantly, a number of studies have revealed a possible association between gallstone disease (GD) and PD; nevertheless, the exploration of diverse risk factors and the theory suggesting that the onset of PD might be associated with GD requires further investigation. This review aims to explore the evidence that connects alterations in GD with PD, emphasizing mechanisms that promote gut dysbiosis, the gut-brain connection, changes in lipid profiles, genetic and dietary influences, as well as neuroinflammation. Furthermore, we assess the potential implementation of innovative therapeutic strategies, including probiotic treatments and gut microbiota transplantation, in patients with PD. Although the evidence supports an association between PD and GD, causality remains to be established. Prospective cohort studies are needed to determine whether gallstones represent a prodromal marker or a causal risk factor for PD, and to validate these pathways as novel diagnostic and therapeutic targets for PD.},
}

@article {pmid41479668,
year = {2025},
author = {Vázquez-Frias, R and Vinderola, G and Abreu Y Abreu, AT and Angulo, D and Giler-Párraga, N and Ladino, L and Ortiz, C and Pereira, S and Bustamante, JP},
title = {Postbiotics in pediatric clinical practice: position paper from Special Group of Latin American Society of Pediatric Gastroenterology, Hepatology and Nutrition (LASPGHAN).},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1716791},
pmid = {41479668},
issn = {2296-861X},
abstract = {Postbiotics, defined by the ISAPP as preparations of inanimate microorganisms and/or their components that confer health benefits, represent a promising category of microbiome-derived solutions. This position paper highlights their clinical relevance, particularly in pediatrics, while addressing key aspects of definition, safety, quality, and strain-level specificity. Evidence supports the use of Lactobacillus LB -including L. fermentum CNCM I-2998 and L. delbrueckii subsp. lactis CNCM I-4831- in reducing the duration and severity of acute diarrhea in children. Other strains, such as Bifidobacterium breve C50, Streptococcus thermophilus 065, Lacticaseibacillus paracasei CBA L74, Lactiplantibacillus plantarum LPL28, and Ligilactobacillus salivarius AP-32, show promise in preventing infections, supporting oral health, and modulating immune responses. Additional postbiotics, including Limosilactobacillus reuteri DSM 17648, expand their potential into metabolic and gastrointestinal disorders. Collectively, postbiotics emerge as clinically valuable interventions, bridging science and medical practice.},
}

@article {pmid41479564,
year = {2025},
author = {N Kukaev, E and Tokareva, AO and Krogh-Jensen, OA and Lenyushkina, AA and Starodubtseva, NL},
title = {Gut Microbiota and Short-Chain Fatty Acids in the Pathogenesis of Necrotizing Enterocolitis in Very Preterm Infants.},
journal = {Acta naturae},
volume = {17},
number = {4},
pages = {38-51},
pmid = {41479564},
issn = {2075-8251},
abstract = {The development of a symbiotic gut ecosystem is a crucial step in postnatal adaptation. The gut microbiome of very preterm infants is characterized by an overall instability, reduced microbial diversity, and a predominance of Gram-negative Proteobacteria, all factors associated with an increased risk of necrotizing enterocolitis (NEC). Short-chain fatty acids (SCFAs) are the key bacterial metabolites that are essential for maintaining intestinal homeostasis, supporting immune development, enhancing intestinal barrier integrity, and reducing inflammation. This review examines the role of gut microbiota and SCFAs in neonatal NEC, with a focus on potential diagnostic and therapeutic strategies. Clinical studies have consistently demonstrated a significant decrease in total SCFA levels and individual bacterial metabolites in preterm infants with NEC. This finding has been corroborated by various experimental models. Clarification of the role of SCFAs in NEC pathogenesis, determination of their diagnostic utility, and assessment of the feasibility of developing comprehensive pro- and postbiotic formulations require multi-center, multi-omics investigations that include a large cohort of very preterm infants.},
}

@article {pmid41479542,
year = {2025},
author = {Nath, S and Weyrich, LS and Guzzo, G and Hedges, J and Tamrakar, M and Kapellas, K and Jamieson, L},
title = {The sociobiome-oral microbiome mediates dental caries among Indigenous Australians.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1721183},
pmid = {41479542},
issn = {2235-2988},
mesh = {Humans ; *Dental Caries/microbiology/epidemiology ; Saliva/microbiology ; *Microbiota ; Female ; Male ; Adult ; Cross-Sectional Studies ; Australia/epidemiology ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Young Adult ; Socioeconomic Factors ; Dental Plaque/microbiology ; Aged ; Adolescent ; *Mouth/microbiology ; Oral Health ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: The sociobiome refers to the social and socioeconomic conditions that shape human microbial communities, linking structural inequities to biological changes in the microbiome. The aim of this study was to examine how individual and neighbourhood socioeconomic status (SES) are associated with the oral microbiota and dental caries in Indigenous Australian adults.

METHODS: This cross-sectional study involved 100 Indigenous Australian participants aged ≥ 18 years and was embedded within a decolonising, community-based participatory research framework. Demographic, socioeconomic, and oral health behaviour data were collected, followed by a dental examination and collection of saliva and plaque samples. The samples were analysed using 16S rRNA amplicon sequencing, and alpha and beta diversity, redundancy analysis, and differential abundance analysis were conducted. Mediation models were used to examine associations between income (Healthcare card ownership), education (≤ secondary), the oral microbiome, and dental caries.

RESULTS: The microbiome analyses showed saliva had higher alpha diversity (p < 0.01), and beta diversity was significantly different between saliva and plaque (adonis p < 0.001). In saliva, alpha diversity was lower with advancing age, secondary education, income, Healthcare card ownership, and dental caries presence. Beta diversity in saliva microbiome composition showed a stronger association with SES than plaque, with income source (R²=3.8%, p < 0.01), education (R²=2.0%, p < 0.01), and dental caries (R²=2.2%, p < 0.01). Differential abundance analysis showed that the Rikenellaceae RC9 gut group, F0058, Fillifactor, and Treponema were elevated in the low-SES and caries groups. Mediation analysis showed that 75% of the impact of low income on caries was mediated via microbiome shifts, compared with 21% for education, highlighting the strong role of oral microbiome alterations in SES-driven caries risk.

CONCLUSION: Socioeconomic disadvantage is associated with variations in the oral microbiome, and these microbial patterns may explain the link between lower income and dental health caries. Saliva may serve as a sensitive biomarker of socioeconomic gradients in oral health. These findings support integrated approaches that address structural determinants of disadvantage alongside microbiome-informed preventive strategies when tackling oral health inequities in Indigenous populations.},
}

Humans
*Dental Caries/microbiology/epidemiology
Saliva/microbiology
*Microbiota
Female
Male
Adult
Cross-Sectional Studies
Australia/epidemiology
Middle Aged
RNA, Ribosomal, 16S/genetics
Young Adult
Socioeconomic Factors
Dental Plaque/microbiology
Aged
Adolescent
*Mouth/microbiology
Oral Health
Bacteria/classification/genetics

@article {pmid41479540,
year = {2025},
author = {Kong, Z and He, Y and Xue, J and Chen, Z and Gui, Y and Wu, J and Chen, X},
title = {Plant growth-promoting bacteria (PGPB) inoculants enhance the bacterial network connectivity more than non-PGPB in heavy metal-contaminated soil.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1717976},
pmid = {41479540},
issn = {1664-462X},
abstract = {Optimizing the performance of plant growth-promoting bacteria (PGPB) inoculants in phytoremediation requires a deeper understanding of their interactions with the indigenous soil microbiome. However, current knowledge is particularly limited regarding how PGPB versus non-PGPB inoculants interact with indigenous microbes and establish colonization persistence in the rhizosphere. In this study, we employed amplicon sequencing to compare the impacts of PGPB versus non-PGPB inoculants on the indigenous rhizosphere and bulk soil microbiome of Indian mustard in heavy metal-contaminated soil, and their interactions within the indigenous bacterial networks. Our results showed that both PGPB and non-PGPB inoculants significantly altered the composition and diversity of the rhizosphere microbiome. However, only PGPB inoculants enhanced the complexity and stability of bacterial co-occurrence networks. PGPB inoculants not only maintained rhizosphere persistence but also actively integrated into the network, enhancing associations with indigenous bacterial taxa. Notably, they established enhanced co-occurrence associations with native bacterial taxa characterized as potential PGPB, including Lysinimonas, Sinomonas, Nocardioides, Actinoalloteichus, Amycolatopsis, Bradyrhizobium, Novosphingobium etc., and these interactions were predominantly positive. These findings highlight the important role of PGPB versus non-PGPB inoculants in reshaping the rhizosphere microbiome under heavy metal stress, indicating a potential approach for improving phytoremediation efficiency by fostering a more resilient and cooperative soil microbiome.},
}

@article {pmid41479529,
year = {2025},
author = {Punnuri, SM and Thudi, M and Mir, RR},
title = {Editorial: Genetics and genomics of emerging and multifactorial stresses affecting plant survival and associated plant microbiomes.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1738816},
pmid = {41479529},
issn = {1664-462X},
}

@article {pmid41479404,
year = {2025},
author = {Wang, D and Yu, L and Lu, Q and Han, M and Wang, B and Peng, X and Yue, M and Li, Y},
title = {Oral pretreatment with Escherichia coli Nissle 1917 enhances the host's defense against influenza A virus infection.},
journal = {mLife},
volume = {4},
number = {6},
pages = {666-682},
pmid = {41479404},
issn = {2770-100X},
abstract = {Influenza A viruses (IAVs) pose a significant threat to global health, causing annual epidemics and occasional pandemics with substantial morbidity and mortality. Despite the availability of vaccines and antiviral therapies, the development of novel preventive and therapeutic strategies remains a critical research focus. In this study, we evaluated the protective effects of orally administering Escherichia coli Nissle 1917 in IAV-infected mice and elucidated its mechanisms of action by analyzing cecal microbiota and plasm metabolome profiles. Oral administration of E. coli Nissle 1917 alleviated respiratory symptoms, reduced weight loss, and mitigated pathological injury in mice infected with H9N2 or H1N1 IAV. These protective effects were mediated through the modulation of gut microbiota diversity, which increased the abundance of Bacteroides and Akkermansia, correlating with elevated pipecolic acid levels and ultimately aiding in defense against IAV infection in mice. Notably, we identified that the circulating metabolic molecule pipecolic acid plays a significant role in fighting IAV infection. Our findings suggest the potential usefulness of E. coli Nissle 1917 or pipecolic acid in influenza prevention.},
}

@article {pmid41479117,
year = {2026},
author = {Attar, R and Hamid, A and Dar, LS and Normakhamatov, N and Farooqi, AA},
title = {Silhouette of Probiotics in the Regulation of miRNAs and lncRNAs in Carcinogenesis and Metastasis: Is It a Silver Lining or a Cross to Bear.},
journal = {Experientia supplementum (2012)},
volume = {115},
number = {},
pages = {243-251},
pmid = {41479117},
issn = {1664-431X},
mesh = {*Probiotics/therapeutic use ; *RNA, Long Noncoding/genetics ; Humans ; Animals ; *MicroRNAs/genetics ; *Carcinogenesis/genetics/drug effects ; *Neoplasms/genetics/pathology/microbiology ; Neoplasm Metastasis ; Gene Expression Regulation, Neoplastic/drug effects ; },
abstract = {Cancer is a genomically complex and multifaceted disease. Wealth of information distilled through decades of high-throughput research has revealed a broad spectrum of oncogenic signaling cascades, immunological evasion, and drug resistance, which play a steering role in carcinogenesis and metastasis. Noncoding RNAs have also emerged as key players in the regulation of multiple stages of cancer progression and metastatic spread of cancer cells to secondary sites. The concept of probiotics has started to gain limelight due to its ability to pharmacologically modulate the host microbiome and the immunological responses. The genomics era has provided impetus for the discovery and characterization of bacterial probiotic effector molecules that stimulate specific responses. We have witnessed an exponential increase in the seminal studies which provided proof-of-concept about the mechanistic regulation of cell signaling pathways and noncoding RNAs by probiotics. These exciting and groundbreaking studies ignited an outburst of data generated using several "omics" technologies. In this chapter, we have provided a summary of seminal studies associated with the anticancer and antimetastatic role of probiotics in animal models. However, circumstantial evidence has also underlined tumor-promoting role of probiotics in animal model studies. Therefore, there is a need to scrupulously reinterpret the existing pieces of evidence related to conflicting data about pro-tumorigenic and tumor-inhibitory roles of probiotics. We also critically summarized how probiotics modulated noncoding RNAs to prevent/inhibit cancer progression. Surprisingly, probiotics-mediated regulation of noncoding RNAs has not been comprehensively explored in different cancers. In accordance with this approach, in-depth analysis of target long noncoding RNAs and circular RNAs by probiotics will allow the researchers to develop near-to-complete signaling landscape to reap the full benefits of the medicinal significance of probiotics.},
}

*Probiotics/therapeutic use
*RNA, Long Noncoding/genetics
Humans
Animals
*MicroRNAs/genetics
*Carcinogenesis/genetics/drug effects
*Neoplasms/genetics/pathology/microbiology
Neoplasm Metastasis
Gene Expression Regulation, Neoplastic/drug effects

@article {pmid41360887,
year = {2025},
author = {Le Lay, A and Brial, F and Rouch, C and Shao, X and Bourgey, M and Sonomura, K and Ou, H and Ghezzal, S and Vincent, M and Rugard, M and Audouze, K and Ragoussis, J and Matsuda, F and Bourque, G and Grundberg, E and Lathrop, M and Magnan, C and Gauguier, D},
title = {Gastrectomy promoted diabetes remission involves the molecular clock and epigenetic mechanisms in a rat model of lean type 2 diabetes.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {96},
pmid = {41360887},
issn = {2045-2322},
support = {DIABETOMARKERS//Institut National de la Santé et de la Recherche Médicale/ ; EpiTriO, ANR-15-EPIG-0002-05//Agence Nationale de la Recherche/ ; },
abstract = {UNLABELLED: Bariatric surgery results in type 2 diabetes (T2D) improvement. To identify mechanisms associated with gastrectomy-promoted T2D remission in lean individuals, we performed pathophysiological, behavioural and molecular (liver transcriptome, metabolome and lipidome) investigations in the Goto-Kakizaki (GK) model of spontaneously-occurring non-obese T2D following vertical sleeve gastrectomy (VSG) or sham operation. VSG resulted in sustained reduction in hyperglycemia and changes in nycthemeral feeding patterns and activity. Liver transcriptome and lipidome profiling pointed to changes in the expression of genes involved in inflammation, PPAR signalling and fatty acid metabolism, and in the regulation of phosphatidylcholine and lysophosphatidylethanolamine classes. Deeper analysis revealed altered expression of genes involved in histone methylation and co-ordinately differential transcription of key regulators of the molecular clock (Clock, Arntl/Bmal1, Per1, Per2, Per3). In addition to previously reported changes in bile acid metabolism and gut microbiome in this model of VSG, our findings underline the multiple biological mechanisms associated with diabetes remission following VSG and suggest a contribution of chronobiology and epigenetic processes in the long-term therapeutic consequences of VSG in the context of polygenic non-obese T2D.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-29273-y.},
}

@article {pmid41316248,
year = {2025},
author = {Wang, L and Wang, L and Liu, M and Yuan, Q and Cheng, L and Chen, H and Mao, S and Li, S and Yan, Q and Xing, G and Zheng, N},
title = {Characterization of the gut virome in patients with nonalcoholic fatty liver disease.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {6},
pmid = {41316248},
issn = {1479-5876},
abstract = {BACKGROUND: Nonalcoholic fatty liver disease (NAFLD) is a prevalent metabolic disorder with complex gut microbiome involvement. While bacterial dysbiosis in NAFLD has been widely studied, the role of the gut virome remains largely unexplored.

METHODS: We profiled gut viral communities from 90 NAFLD patients and 90 non-NAFLD controls using whole-metagenome shotgun sequencing. Viral taxonomic composition, host associations, and functional gene repertoires were analyzed. Serum metabolomic data were integrated to assess virus–metabolite interactions, and random forest models were constructed to evaluate the diagnostic potential of viral signatures.

RESULTS: Overall viral diversity showed no significant differences between NAFLD and controls, but subtle compositional shifts were detected at the vOTU level, with 105 viruses enriched in NAFLD and 185 in non-NAFLD individuals. NAFLD-enriched phages primarily targeted Bacteroides, whereas non-NAFLD-enriched phages were associated with beneficial genera such as Faecalibacterium, Oscillibacter, and Prevotella. Functional annotation revealed a reorganization of viral gene repertoires: genes involved in DNA recombination and horizontal transfer (e.g. int, recD) were depleted, while those related to host interaction and stress response (e.g. xerD, dnaK, hipB) were enriched in NAFLD, indicating enhanced viral persistence and host communication. Serum metabolomic profiling identified 8 differential metabolites, and correlation analysis linked specific vOTUs with altered metabolic pathways. A random forest model based on viral features achieved an AUC of 0.758, outperforming the bacterial model, while integration of viral and bacterial features further improved prediction (AUC = 0.837).

CONCLUSION: The gut virome in NAFLD undergoes compositional and functional remodeling characterized by a shift toward host-adaptive, metabolically interactive viral communities. These viral alterations are closely associated with host metabolic changes and demonstrate strong diagnostic potential. Our findings highlight the virome as an overlooked yet critical component of the gut ecosystem in NAFLD pathogenesis and as a promising source of noninvasive biomarkers for disease prediction and monitoring.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-025-07443-w.},
}

@article {pmid41479039,
year = {2026},
author = {Elbrashy, MM and Farouk, S and Hamdy, NM and Metwally, H and Bader El Din, NG},
title = {Unlocking the Epigenetic Landscape of Colorectal Cancer: A Step Toward Epigenetics to Precision.},
journal = {Sub-cellular biochemistry},
volume = {114},
number = {},
pages = {183-236},
pmid = {41479039},
issn = {0306-0225},
mesh = {Humans ; *Colorectal Neoplasms/genetics/pathology/metabolism ; *Epigenesis, Genetic ; *DNA Methylation ; *Gene Expression Regulation, Neoplastic ; MicroRNAs/genetics/metabolism ; Biomarkers, Tumor/genetics ; Precision Medicine ; },
abstract = {Epigenetic modifications function as central controllers of gene expression in cancer, coordinating crucial cellular activities that trigger the initiation and progression of the tumor, besides their importance in therapeutic response. These modifications can control the gene expression without changing the sequence of DNA. In colorectal cancer (CRC), these alterations involving DNA methylation, histone modifications, chromatin rearrangement, and noncoding ribonucleic acids play a significant role in the pathogenesis of CRC. Abnormal DNA methylation silences the tumor suppressor genes, meanwhile leading to the instability of the genome via reduction of the whole methylation. Specific methylation signatures, such as CpG islands, help in categorizing the subtypes of the tumor and predicting the clinical outcomes. In addition, histone-modifying enzymes, including enhancer of zeste homolog 2 and histone deacetylases, are frequently uncontrolled in cancer, leading to alterations in gene expression. Moreover, small regulatory ribonucleic acids such as microRNA-21 and microRNA-143 contribute to the complex networks that regulate cell survival and growth. Collectively, these epigenetic alterations trigger the transition from benign growth to malignant cancer by continuously suppressing crucial genes. Furthermore, the epigenetic markers can be detected in blood and stool specimens, offering promising tools for the early detection of cancer. The major obstacle in cancer treatment is the resistance to chemotherapy drugs, which is mainly caused by epigenetic modifications in cancer cells. Therefore, the new therapeutic ways target the modifications that occur in DNA methylation and histone, mostly in conjunction with conventional therapies. As the metabolites produced by the gut microbiome can alter the host epigenetics, they can promote cancer development. Promising technologies help in the concise proofreading of epigenetic marks, and advanced single-cell analysis is paving the way for personalized treatment approaches. This cutting-edge knowledge of epigenetic regulation mechanisms offers new prospects for enhancing diagnosis, prognosis, and targeted therapies in colorectal cancer.},
}

Humans
*Colorectal Neoplasms/genetics/pathology/metabolism
*Epigenesis, Genetic
*DNA Methylation
*Gene Expression Regulation, Neoplastic
MicroRNAs/genetics/metabolism
Biomarkers, Tumor/genetics
Precision Medicine

@article {pmid41479037,
year = {2026},
author = {El-Daly, SM and Fayed, B and Talaat, RM and Gouhar, SA and Fahmy, CA and El-Jawad, AMA and Hamdy, NM and Abd Elmageed, ZY},
title = {The Intricate Interplay of Noncoding RNAs and the Gut Microbiome in Gastrointestinal and Endocrine-Related Cancers.},
journal = {Sub-cellular biochemistry},
volume = {114},
number = {},
pages = {61-121},
pmid = {41479037},
issn = {0306-0225},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Gastrointestinal Neoplasms/microbiology/genetics/pathology/metabolism ; *RNA, Untranslated/genetics/metabolism ; *Endocrine Gland Neoplasms/microbiology/genetics/metabolism/pathology ; Dysbiosis/microbiology/genetics ; Animals ; },
abstract = {The human gut microbiome and noncoding RNAs (ncRNAs) represent interconnected regulatory networks that profoundly influence cancer development, particularly in gastrointestinal and endocrine-related malignancies. This chapter delineates the intricate interplay of microbiome-ncRNA crosstalk in the context of gastrointestinal and endocrine-related cancers.The chapter begins with a comprehensive overview of the taxonomic and functional landscape of the healthy adult gut microbiome. The gut microbiome, comprising trillions of microorganisms, plays a crucial role in endocrine regulation through hormone metabolism, synthesis of bioactive compounds, and modulation of immune responses, thereby establishing a critical crosstalk with the host endocrine system. Dysbiosis, or microbial imbalance, has been linked to endocrine dysfunction and the pathogenesis of various diseases, including gastrointestinal and endocrine-related cancers.We then elucidate the classifications of noncoding RNAs and their function as key molecular regulators in cellular communication, gene expression, and disease progression. NcRNAs contribute significantly to the development and progression of endocrine-related malignancies. The intricate crosstalk between the gut microbiome and host ncRNAs demonstrates how gut dysbiosis can disrupt host ncRNA expression patterns, thereby affecting oncogenic pathways, immune surveillance, and metabolic reprogramming linked to tumor initiation, progression, and metastasis. Conversely, host-derived ncRNAs, secreted into the gut lumen, can directly shape microbial gene expression. In this section, we explore how dysregulation of this axis contributes to carcinogenesis through the promotion of chronic inflammation, epithelial barrier dysfunction, and oncogenic signaling. Therapeutic strategies targeting this interplay, including probiotics, prebiotics, fecal microbiota transplantation, and dietary interventions, are introduced in the context of restoring microbial balance.This comprehensive chapter provides crucial insights into the molecular mechanisms governing microbiome-ncRNA interactions and their implications for cancer biology, offering new perspectives for therapeutic interventions in gastrointestinal and endocrine-related malignancies.},
}

Humans
*Gastrointestinal Microbiome
*Gastrointestinal Neoplasms/microbiology/genetics/pathology/metabolism
*RNA, Untranslated/genetics/metabolism
*Endocrine Gland Neoplasms/microbiology/genetics/metabolism/pathology
Dysbiosis/microbiology/genetics
Animals

@article {pmid41478928,
year = {2026},
author = {de Brito, CB and de Amorim-Santos, BM and Souza, DG},
title = {Handling and Experimentation with Germ-Free Mice.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2993},
number = {},
pages = {1-8},
pmid = {41478928},
issn = {1940-6029},
mesh = {Animals ; *Germ-Free Life ; Mice ; *Gastrointestinal Microbiome ; },
abstract = {Immediately after birth, mammals are largely colonized by microorganisms, with the gastrointestinal tract being the most commonly colonized organ. Over the years, several studies have shown that the intestinal microbiota is important for various physiological functions of the host. Gnotobiotic animal models are frequently used to better understand how the microbiota influences health and disease scenarios. Among gnotobiotic models, germ-free (GF) animals were first used in 1895, but it was not until 60 years later that germ-free colonies were suitable for large-scale experiments. The use of GF mice is an interesting and rich tool for studying the microbiome. However, their maintenance is a complex process that needs to be done carefully. In this chapter, we describe step by step how to manage and manipulate the gut microbiota of GF mice.},
}

Animals
*Germ-Free Life
Mice
*Gastrointestinal Microbiome

@article {pmid41478687,
year = {2026},
author = {Wang, G and Liu, Y and Ma, F and Qiu, W},
title = {Insights into meat-microbiome interactions: from community assembly to meat spoilage.},
journal = {Food microbiology},
volume = {136},
number = {},
pages = {105010},
doi = {10.1016/j.fm.2025.105010},
pmid = {41478687},
issn = {1095-9998},
mesh = {*Meat/microbiology ; *Microbiota ; Animals ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Food Microbiology ; Microbial Interactions ; Ecosystem ; },
abstract = {Meat spoilage represents a critical challenge in food security and sustainability. Although extensive research has characterized meat microbiota composition and identified specific spoilage organisms, comprehensive understanding of the complex ecological dynamics within meat microbiomes remains limited. This review critically examines current knowledge of meat-associated microbiomes by applying an ecological perspective to address four key questions: the functional roles assigned to microorganisms during community assembly, microbial colonization and adaptation mechanisms in meat ecosystems, nutrient utilization patterns driving metabolic activities and ecological interactions, and microbial interaction effects on community ecology and functional outcomes. Through systematic exploration of these questions, we reveal that meat spoilage is determined by community dynamics and functional activities of entire microbial ecosystems rather than individual species alone. Our analysis identifies critical research gaps including inadequate understanding of core and keystone taxa contributions, limited exploration of microbial interactions, and insufficient integration of multi-omics approaches with ecological modeling. Based on these findings, future practical applications should focus on ecology-guided preservatives that target key spoilage pathways and predictive models integrating metabolic fluxes with environmental parameters. This comprehensive paradigm shift from composition-focused to function-oriented research will enhance theoretical understanding and provide practical insights for more effective spoilage control in the food industry.},
}

*Meat/microbiology
*Microbiota
Animals
*Bacteria/classification/genetics/isolation & purification/metabolism
Food Microbiology
Microbial Interactions
Ecosystem

@article {pmid41478678,
year = {2026},
author = {Wang, Y and He, L and Hu, X and Guan, Y and Chen, X and Du, J and Chen, J and Ma, C and Ye, L},
title = {Metagenomic and culture-based genomics reveal virulence and resistance risks in Manila clam microbiomes.},
journal = {Food microbiology},
volume = {136},
number = {},
pages = {105001},
doi = {10.1016/j.fm.2025.105001},
pmid = {41478678},
issn = {1095-9998},
mesh = {Animals ; *Bivalvia/microbiology ; Metagenomics ; *Bacteria/genetics/isolation & purification/pathogenicity/drug effects/classification ; *Microbiota ; Virulence Factors/genetics ; Anti-Bacterial Agents/pharmacology ; Virulence ; Genomics ; *Drug Resistance, Bacterial ; Vibrio/genetics/pathogenicity/isolation & purification/drug effects ; Shellfish/microbiology ; Phylogeny ; },
abstract = {Bivalves are important aquaculture products whose safety is shaped by their microbiomes. Here, we present the first comprehensive characterization of Manila clam (Ruditapes philippinarum) microbiomes using both shotgun metagenomics (6 clams) and culture-based genomics (169 isolates, 40 draft genomes), integrating community, functional, and antimicrobial resistance profiling. Communities were dominated by Proteobacteria (99.3-99.9 %), with Pseudoalteromonas and Vibrio collectively accounting for 74.9-99.7 % and showing strong inverse correlations, defining Pseudoalteromonas-dominated, Vibrio-dominated, and mixed states. Species richness ranged from 22 to 180 per sample. Recognized human pathogens occurred at low abundance (<0.3 %), including Vibrio parahaemolyticus, Vibrio alginolyticus, and Photobacterium damselae, while opportunistic vibrios expanded in some clams (e.g., Vibrio cyclitrophicus 57.9 %). We reconstructed 34 high-quality MAGs, seven resolved to species (Pseudoalteromonas tetraodonis, V. cyclitrophicus, Shewanella aquimarina), alongside unclassified lineages. Metagenomes encoded 14 virulence-factor categories with 2281 subtypes, and isolate genomes added 93 further subtypes, including high-virulence loci in Escherichia coli and type III secretion genes in V. parahaemolyticus. Resistomes spanned 18 antibiotic classes with 511 subtypes; isolates contributed 22 additional antibiotic resistance genes(ARGs), including extended-spectrum β-lactamases (blaCTX-M-102) and blaNDM-1. Four carbapenemase-producing isolates (three Shewanella algae, one V. parahaemolyticus) carried blaNDM-1 on IncC plasmids, with the V. parahaemolyticus plasmid transferable to E. coli. Two P. tetraodonis MAGs encoded RiPP-like and terpene biosynthetic clusters plus phage-defense systems, consistent with Vibrio suppression. These findings demonstrate that clam microbiomes fluctuate between protective (Pseudoalteromonas) and pathogenic (Vibrio-Shewanella) states, providing a first integrated framework for assessing microbial risk, antimicrobial resistance, and food safety interventions in bivalve aquaculture.},
}

Animals
*Bivalvia/microbiology
Metagenomics
*Bacteria/genetics/isolation & purification/pathogenicity/drug effects/classification
*Microbiota
Virulence Factors/genetics
Anti-Bacterial Agents/pharmacology
Virulence
Genomics
*Drug Resistance, Bacterial
Vibrio/genetics/pathogenicity/isolation & purification/drug effects
Shellfish/microbiology
Phylogeny

@article {pmid41478594,
year = {2025},
author = {Lee, DY and Liu, J and Lee, SJ and Lamichhane, G and Swayze, A and Zhang, G and Kim, TY and Egan, JM and Kim, Y},
title = {Bioconverted red ginseng protects liver functions and alters insulin homeostasis-associated gut microbiome composition in aged mice.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101310},
doi = {10.1016/j.tjnut.2025.101310},
pmid = {41478594},
issn = {1541-6100},
abstract = {BACKGROUND: Aging is associated with progressive functional deteriorations that affect the metabolic dysfunction in the liver and the alteration of the gut microbial environment. Red ginseng (RG) is one of the widely investigated ginseng products known for its anti-aging properties, derived from its unique bioactive compounds known as ginsenosides.

OBJECTIVE: This study aimed to discover the potential anti-aging effects of bioconverted red ginseng (BRG), a new RG product applied with enzymatic treatments, using an aged mouse model.

METHODS: Two different interventional regimes were employed: oral gavage administration and ad libitum intervention. For oral gavage study, 9-week-old (Young) and 18-month-old (Old) mice were orally injected with either distilled water or 300 mg/kg BRG for 4 weeks (n = 10 per group). For ad libitum study, 19-month-old mice were fed with a normal chow diet (NCD), NCD with 150 mg/kg BRG (BRG-Low; NCD+BRGL), or NCD with 300 mg/kg BRG (BRG-High; NCD+BRGH) for 14 weeks (n = 9-10 per group). Liver tissues were harvested from each group for RNA sequencing, immunoblotting, and mRNA expression analyses. Fecal samples were collected and 16S rRNA sequencing was conducted to profile gut microbiome composition.

RESULTS: The 4-week BRG administration provided potential modulations in hepatic gene expression profiling in terms of mitigating age-driven liver cholestasis, as well as positive alterations in the gut microbial structure and composition. Moreover, the 14-week BRG supplementation protected insulin homeostasis through activating the hepatic protein kinase B (AKT)/mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway and inhibiting glycogen synthase kinase (GSK)-3β in aged mice. In the meantime, BRG consumption altered insulin homeostasis-related microbiome structures by not only reducing the Firmicute/Bacteroidetes (F/B) ratio and relative abundance of opportunistic taxa, including Erysipelotrichaceae, but also increasing the enrichment of commensal bacteria, such as Muribaculaceae.

CONCLUSIONS: Taken together, this study highlights that BRG could be a promising anti-aging functional food substance by maintaining insulin homeostasis and the gut microbial equilibrium.},
}

@article {pmid41478407,
year = {2025},
author = {Ribeiro, BE and Schmukler de Lima, I and Cristina da Silva E Souza, K and Bittencourt Rosas, SL and Santana, PT and Amaral, G and Machado, JC and Pereira de Oliveira, R and Leal, C and Thompson, C and Thompson, F and Lima Castelo-Branco, MT and Coutinho-Silva, R and Pereira de Souza, HS},
title = {The P2X7 receptor promotes intestinal fibrosis by modulating the gut microbiota and the inflammasome.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101718},
doi = {10.1016/j.jcmgh.2025.101718},
pmid = {41478407},
issn = {2352-345X},
abstract = {BACKGROUND AND AIMS: Considering the role of the P2X7 receptor in intestinal inflammation, we examined its potential involvement in fibrosis development.

METHODS: Colonic biopsies from patients with inflammatory bowel disease (IBD) were analyzed via double immunofluorescence under confocal microscopy. Colon fibroblasts were used to analyze P2X7 receptor modulation and chemotaxis. Experimental chronic colitis was induced with three cycles of oral dextran sodium sulfate (DSS) treatment in P2X7[+/+] and P2X7[-/-] mice. The mice were evaluated via follow-up video endoscopy with an endoluminal ultrasound biomicroscopic (eUBM) system, histological scoring, immunohistochemistry, cytokine measurement in colon explants, gene expression analysis of P2X7 signaling targets via qRT‒PCR, and microbiome composition analysis.

RESULTS: Colocalization studies revealed a greater density of P2X7[+]/α-SMA[+] cells in colon sections from patients than in those from controls, especially in patients with Crohn's disease (p<0.05). Activation of the ATP-P2X7 pathway in human fibroblasts increased cell migration, calcium influx, and collagen production. Video colonoscopy with the eUBM system revealed significantly more inflammation, with greater wall thickness and stiffness, in P2X7[+/+]- mice than in P2X7[-/-] and P2X7[+/+] mice treated with A740003 (a P2X7-selective inhibitor). P2X7[+/+] mice exhibited increased caspase-1 and NLRP3 expression, as well as NF-κB and ERK activation, accompanied by decreased PPARγ expression. In the supernatants of colon explants, TNF-α, IL-1β, IFN-γ, TGF-β, IL-10, and collagen production were increased in P2X7[+/+] mice. Various microbial changes were observed in P2X7[-/-] and P2X7[+/+] mice.

CONCLUSION: Regulatory mechanisms downstream of P2X7, combined with signals from a dysbiotic microbiota, activate intracellular signaling pathways and the inflammasome, leading to intestinal inflammation and promoting fibrogenesis.},
}

@article {pmid41478323,
year = {2025},
author = {Li, R and Liu, S and Zhang, H and Huang, X and Qian, W and Han, D and Wang, F and Feng, Z and Zhang, T and Lin, H and Li, H},
title = {Prevotella copri leads to colonic barrier dysfunction via the succinate receptor 1-FoxM1-IL-6 axis.},
journal = {Biochimica et biophysica acta. Molecular cell research},
volume = {},
number = {},
pages = {120099},
doi = {10.1016/j.bbamcr.2025.120099},
pmid = {41478323},
issn = {1879-2596},
abstract = {Prevotella copri, a key commensal bacterium in the human gut microbiome, exhibits both positive and negative abundance correlations with various disorders. Although multiple studies have suggested an association between P. copri and intestinal pathologies, the mechanistic basis remains elusive. In this study, we examined P. copri's effects on colonic physiology in healthy mice, revealing its capacity to compromise intestinal barrier integrity. This was demonstrated through downregulation of colonic tight junction proteins (Occludin and ZO-1) and elevated serum levels of gut permeability markers (LPS and D-LA). We identified succinate as the primary microbial metabolite mediating P. copri's barrier-disrupting effects, with succinate receptor 1 (SUCNR1) being essential for this pathological process. Notably, both P. copri colonization and succinate administration activated the IL-6-STAT3 signaling pathway, leading to transcriptional suppression of the tight junction-related gene, Occludin. Through mechanistic studies, we identified Forkhead box M1 (FoxM1) as a crucial transcription factor regulating P. copri- or succinate-induced Il-6 expression. Clinical relevance was established through human cohort analyses showing significant positive correlations between fecal succinate levels and plasma markers of gut permeability. These findings elucidate a novel mechanistic pathway through which P. copri impairs colonic function, suggesting therapeutic potential in colitis through strategies targeting either P. copri abundance or microbial succinate production.},
}

@article {pmid41478268,
year = {2025},
author = {Chen, J and Xu, J and Xu, J and Xu, F and Gong, F and Xiao, P and Ma, H and Zhang, Q and Feng, J and Min, Y},
title = {Gut microbiota-derived propionic acid mitigates age-related albumen quality deterioration by modulating magnum functions.},
journal = {Poultry science},
volume = {105},
number = {3},
pages = {106357},
doi = {10.1016/j.psj.2025.106357},
pmid = {41478268},
issn = {1525-3171},
abstract = {The declined albumen quality during the late laying phase is associated with age-related magnum dysfunction, in which to the roles of gut microbiota is unclear. This study aimed to elucidate the relationship between gut microbiota and magnum function, and its impact on albumen quality. Hy-Line Brown layers at peak (30 wk) and late (70 wk) laying phases were compared to assess age-related changes in albumen quality, magnum function, and gut microbiota. Fecal microbiota transplantation (FMT) from peak- to late-phase hens was conducted to assess functional effects. Microbiome and metabolome analyses were then integrated to identify key bacterial taxa and metabolites. The role of the leading candidate metabolite was further validated through dietary supplementation. Results showed that late-phase hens exhibited significant reductions in albumen height, magnum mucosal fold height, and tubular gland diameter (P < 0.05), alongside gut microbial dysbiosis. FMT from peak-phase donors effectively reversed age-related declines in magnum histomorphology and albumen height in late-phase hens. It also up-regulated the expression of barrier function genes (Claudin-1, ZO-2, MUC2, AGR2) and magnum secretory markers (OVOA), while down-regulating pro-inflammatory cytokines (IL-4, IFN-γ) (P < 0.05). Microbial analysis identified Anaerotruncus as the only genus consistently enriched following FMT and positively correlated with improved albumen height and magnum morphology. Metabolomic analysis revealed that propionic acid was the top metabolite associated with Anaerotruncus abundance. Crucially, dietary supplementation with sodium propionate recapitulated the key benefits of FMT. In summary, our findings revealed a gut microbiota-oviduct axis through which microbiota from peak-laying hens ameliorate age-related magnum decline and improve albumen quality in aging hens.},
}

@article {pmid41478129,
year = {2025},
author = {Baharaghdam, S and Karimi, S and Farahani, ME and Aghebati-Maleki, L and Yousefi, M},
title = {Endometrial immune profile: A predictor of pregnancy success.},
journal = {Reproductive biology},
volume = {26},
number = {1},
pages = {101174},
doi = {10.1016/j.repbio.2025.101174},
pmid = {41478129},
issn = {2300-732X},
abstract = {The likelihood of a successful pregnancy is influenced by a set of variables that influence endometrial receptivity, including hormonal, genetic, metabolic, age, lifestyle, and immunological factors. Among these, the endometrial immune profile has received particular attention as a critical actor of implantation and embryo tolerance. Dynamic fluctuations in immune cell populations-such as macrophages, dendritic cells, uterine natural killer cells, and regulatory T cells-across the menstrual cycle might significantly affect the endometrium's capacity to support successful implantation. Recent evidence highlights that disruptions in the quantity, phenotype, or function of these immune cells contribute to impaired endometrial receptivity in infertility-related disorders, including recurrent implantation failure, recurrent pregnancy loss, endometriosis, and polycystic ovary syndrome. This review provides a comprehensive assessment of immune cell composition and function in the healthy endometrium compared to pathological conditions, emphasizing how immune dysregulation may impair pregnancy. Furthermore, we evaluate both current and emerging diagnostic modalities-from immunohistochemistry and flow cytometry to high-resolution single-cell transcriptomics-and endometrial microbiome impact on immune profiling that enables more precise characterization of immune profile dysregulation, alongside established and investigational therapies, with particular attention to their efficacy and mechanistic rationale. By integrating these insights, a clinically oriented framework can be provided to guide the development of personalized diagnostic algorithms and targeted immune-based therapies that, ultimately, could lead to improved implantation rates and live birth outcomes in individuals facing infertility disorders with immunological causes.},
}

@article {pmid41478124,
year = {2025},
author = {Xing, W and Gai, X and Cheng, X and Fang, Z and Chen, G},
title = {Rhizosphere microbiome drives Betula luminifera adaptation to antimony mining sites through functional traits and transcriptional reprogramming.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140972},
doi = {10.1016/j.jhazmat.2025.140972},
pmid = {41478124},
issn = {1873-3336},
abstract = {Rhizosphere microbiome are pivotal for plant adaptation to extreme environments. However, the regulatory mechanisms underlying their control of the ecological adaptation of native woody plants in mining areas remain unclear. Here, we integrated metagenomic and transcriptomic analyses to elucidate how the rhizosphere microbiome facilitates Betula luminifera adaptation to antimony (Sb) mining sites. Under sterile conditions, B. luminifera from mining sites prioritized shoot growth, whereas control-origin seedlings favored root development. Microbial inoculation mitigated this growth dichotomy, balancing above- and belowground biomass allocation. Notably, B. luminifera from control sites upregulated antioxidant biosynthesis genes (α- and β-tocopherol pathways), while B. luminifera from mining sites enhanced lignin synthesis under Sb stress. After inoculation with rhizosphere microbiome from the mining-site, genes related to Sb/As resistance (ACR3, arsB/C) and soil nutrient cycle (narG, phnM) were significantly enriched in the rhizosphere of B. luminifera, which were contributed by Proteobacteria and Actinobacteria. Transcriptional profiling revealed that microbial inoculation triggered systemic upregulation of phytohormone-related genes (auxin, cytokinin, abscisic acid), enhancing stress resilience and growth. These findings unveil a synergistic plant-microbe adaptation mechanism in Sb polluted soils in mining sites, highlighting microbial-mediated trait trade-offs and transcriptional plasticity as drivers of ecological success in extreme environments.},
}

@article {pmid41477949,
year = {2025},
author = {Li, W and Song, X and Wang, Y and Wen, D and Zhou, Y and Zhang, D},
title = {Iron-manganese inputs shape the coupling between deposit morphology and microbiome during the early-stage corrosion on cement mortar-lined pipe walls under drinking-water conditions.},
journal = {Journal of environmental management},
volume = {398},
number = {},
pages = {128468},
doi = {10.1016/j.jenvman.2025.128468},
pmid = {41477949},
issn = {1095-8630},
abstract = {Maintaining water quality in drinking water distribution systems (DWDSs) requires resilient pipe-wall interfaces, yet the build-up of iron (Fe) and manganese (Mn), the most common metals in DWDSs, often initiates deposit growth and triggers discoloration events. However, the physicochemical impacts of early Fe-Mn deposition on pipe-wall surfaces have not been systematically elucidated. To elucidate their mechanistic role in the onset of scale development, self-designed electrodes were employed to monitor the electrochemical behavior of cement mortar-lined pipe surfaces under controlled Fe-Mn dosing (50-200 μg/L Fe with 10 μg/L Mn). Results showed that a dosing condition of 100 μg/L Fe with 10 μg/L Mn produced compact and adherent deposits with high charge-transfer resistance (Rct = 1.33 × 10[6] Ω) and low corrosion current density (icor = 3.68 × 10[-5] mA/cm[2]). This condition was attributed to cohesive biofilms dominated by Pseudomonas with co-dominant Hydrogenophaga and Sphingomonas, which, through assimilation-centered carbon and nitrogen pathways, secreted abundant extracellular polymeric substances, associated with minimized particulate metal accumulation in bulk water. In contrast, excessive Fe input (200 μg/L) generated scale-like, metal-oxide-bearing deposits accompanied by elevated Fe-Al contents, reduced Rct = 2.97 × 10[5] Ω, higher icor = 1.70 × 10[-4] mA/cm[2] and metabolically diverse but weakly coordinated microbial communities. These results demonstrate that Fe-Mn-regulated morphology-microbiome coupling shapes early-stage corrosion behavior and that appropriate Fe-Mn levels are essential for promoting stable deposits and supporting long-term drinking-water safety.},
}

@article {pmid41477864,
year = {2026},
author = {Favela, A and Kent, AD and Sible, CN and Flint-Garcia, S and Klimasmith, IM and Mujjabi, C and Raglin, SS and Below, FE and Bohn, MO},
title = {Lost and found: Rediscovering microbiome-associated phenotypes that reshape agricultural sustainability.},
journal = {Science advances},
volume = {12},
number = {1},
pages = {eaed3360},
pmid = {41477864},
issn = {2375-2548},
mesh = {*Microbiota ; Phenotype ; *Agriculture/methods ; *Zea mays/microbiology/genetics/growth & development ; Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; Crops, Agricultural/microbiology ; Nitrogen/metabolism ; Nitrification ; },
abstract = {Modern agriculture faces an urgent need to improve nutrient use efficiency while reducing environmental impacts. Here, we show that ancestral traits controlling rhizosphere microbiome functions can be reintroduced into elite maize through targeted teosinte introgressions. Using near-isogenic lines, we mapped microbiome-associated phenotypes (MAPs) derived from teosinte that suppress nitrification and denitrification-key microbial processes contributing to nitrogen loss. These introgressions altered root exudate chemistry, resulting in distinct microbial assemblies and enhanced nitrogen retention. We identified candidate loci and exudate metabolites responsible for suppressive activity and demonstrated their functional effects in vitro. These findings reveal a genetic and biochemical basis for rewilding microbiome-mediated ecosystem services in crops, offering a scalable path toward sustainable nutrient management in global agriculture.},
}

*Microbiota
Phenotype
*Agriculture/methods
*Zea mays/microbiology/genetics/growth & development
Rhizosphere
Soil Microbiology
Plant Roots/microbiology
Crops, Agricultural/microbiology
Nitrogen/metabolism
Nitrification

@article {pmid41477781,
year = {2025},
author = {Garashchenko, NE and Smurova, NE and Semenova, NV and Belkova, NL and Nemchenko, UM and Klimenko, ES and Zugeeva, RE and Kolesnikov, SI and Madaeva, IM and Kolesnikova, LI},
title = {[Gut microbiome and sleep disturbances in menopause.].},
journal = {Advances in gerontology = Uspekhi gerontologii},
volume = {38},
number = {4},
pages = {562-570},
pmid = {41477781},
issn = {1561-9125},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; Middle Aged ; *Menopause/physiology ; *Sleep Wake Disorders/microbiology/diagnosis/physiopathology ; Surveys and Questionnaires ; Sleep Quality ; },
abstract = {The paper presents the results of the gut microbiota study in menopausal women with sleep disorders based on different assessments of sleep quality. The study involved 96 menopausal women. Sleep quality was assessed using three questionnaires: the Insomnia Severity Index (ISI), the Pittsburgh Sleep Quality Index (PSQI), and the Epworth Sleepiness Scale. The qualitative and quantitative composition of the microbiota was assessed using microbiological and molecular genetic methods. In the group with sleep disorders (according to PSQI), molecular genetic analysis of the microbiome revealed an increased content of Enterococcus spp. (p=0,03), Clostridium perfringens (p=0,01), and Shigella spp. (p=0,04). Compared to the control, with moderate sleep disorders (according to the ISI questionnaire), the content of Clostridium perfringens was increased (p=0,02). According to the Epworth scale, a higher content of Bifidobacterium spp. (p=0,04), Prevotella spp. (p=0,02) and Eubacterium rectale (p=0,04) was noted in the group with excessive daytime sleepiness compared to the control. Thus, in menopausal women, the composition and structure of the gut microbiota are associated with sleep disorders.},
}

Humans
Female
*Gastrointestinal Microbiome/physiology
Middle Aged
*Menopause/physiology
*Sleep Wake Disorders/microbiology/diagnosis/physiopathology
Surveys and Questionnaires
Sleep Quality

@article {pmid41477766,
year = {2025},
author = {Mirji, G and Bhat, SA and El Sayed, M and Reiser, SK and Gavara, SP and Ye, Y and Miyamoto, T and Zhang, W and Vogel, P and Cassel, J and Liu, Q and Goldman, AR and Kossenkov, A and Zhang, N and Shinde, RS},
title = {Aromatic microbial metabolite hippuric acid enhances inflammatory responses in macrophages via TLR-MyD88 signaling and lipid remodeling.},
journal = {Cell reports},
volume = {45},
number = {1},
pages = {116749},
doi = {10.1016/j.celrep.2025.116749},
pmid = {41477766},
issn = {2211-1247},
abstract = {The gut microbiome produces diverse metabolites shaping immunity, yet their pro-inflammatory potential remains unclear. Using untargeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) metabolomics, we identified hippuric acid-an aromatic, microbe-derived metabolite-as a potent enhancer of inflammatory responses during Escherichia coli infection. Hippuric acid administration heightened inflammation, activated innate immune cells, and reduced survival in infected mice. In vitro, hippuric acid selectively potentiated M1-like (lipopolysaccharide [LPS] or LPS+interferon gamma [IFNγ]) macrophage pro-inflammatory responses but had no effect on M2-like (interleukin [IL]-4) polarization. It enhanced responses to myeloid differentiation primary response 88 (MyD88)-dependent Toll-like receptor (TLR) ligands but not TRIF-, STING-, or NOD2-mediated stimuli. Genetic deletion of MyD88 abolished hippuric-acid-induced pro-inflammatory responses. Transcriptomic and lipidomic analyses revealed increased cholesterol biosynthesis and lipid accumulation, while reducing cellular cholesterol blunted the pro-inflammatory effects of hippuric acid. Notably, hippuric acid also enhanced pro-inflammatory responses in human macrophages, and its elevated levels correlated with sepsis mortality, linking microbial metabolism, lipid remodeling, and innate immunity.},
}

@article {pmid41477725,
year = {2026},
author = {Chan, NSL and Cross, C and Prestidge, CA and Wardill, HR and Bowen, J and Joyce, P},
title = {The resilient microbiome: how baseline gut microbial composition influences response to cancer treatment.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-18},
doi = {10.1080/1040841X.2025.2610215},
pmid = {41477725},
issn = {1549-7828},
abstract = {The human gut microbiome is increasingly recognized as a key modulator of health and disease, with growing evidence supporting its influence on responses to cancer therapy. An important aspect of this relationship is gut microbial resilience, defined as the ability of the microbiome to recover its ecological equilibrium following disruption. Individual variations in microbial composition significantly influence resilience and, consequently, personalized responses to cancer treatments. However, the underlying functional characteristics of a resilient microbiome remain incompletely understood. Identifying specific microbial profiles with greater resilience to cancer therapies could improve the ability to predict treatment responses and mitigate adverse events. However, despite growing interest, a lack of longitudinal and mechanistic studies currently limits their clinical translation. This review examines current literature on gut microbiome compositions and individual treatment response to cancer therapy, with a focus on microbial features linked to resilience which could enable prediction of adverse response. While the use of microbial metabolites as predictive biomarkers (e.g. short-chain fatty acids and bile acids) is promising, further longitudinal and interventional studies are essential to support clinical application. Establishing specific microbial and metabolite profiles that promote resilience is essential to advance this emerging field of personalized gut-microbiome therapy.},
}

@article {pmid41477720,
year = {2025},
author = {Kurnosov, AS and Linde, NN and Molodtsova, PA and Glazunova, EV and Moskalenko, AM and Sheptulina, AF and Bodunova, NA and Zlobovskaya, OA},
title = {[Comparative Evaluation of DNA Extraction Methods from Fecal Samples: Statistical Analysis of Commercial Kits and Laboratory Protocols Using Real-Time PCR Data].},
journal = {Molekuliarnaia biologiia},
volume = {59},
number = {6},
pages = {1002-1021},
doi = {10.7868/S3034555325060104},
pmid = {41477720},
issn = {0026-8984},
mesh = {*Feces/microbiology/chemistry ; Humans ; *DNA, Bacterial/isolation & purification/genetics ; *Real-Time Polymerase Chain Reaction/methods ; *Gastrointestinal Microbiome/genetics ; Reagent Kits, Diagnostic ; *Gram-Negative Bacteria/genetics/isolation & purification ; *Gram-Positive Bacteria/genetics/isolation & purification ; },
abstract = {The emergence of new data on the association between the composition of the intestinal microbiota and various human diseases has generated increasing interest in microbiome research. In this context, selection of the DNA extraction method represents a critical stage in the design of the experiment, significantly affecting the reliability and reproducibility of results. This study presents a comparative analysis of 12 DNA extraction methods, including nine commercial kits and three laboratory protocols. We evaluated the taxonomic representation, including Gram-positive (Lactobacillaceae, Coprococcus spp., Streptococcus sp., Clostridium leptum) and Gram-negative bacteria (Enterobacteriaceae, Akkermansia muciniphila, Fusobacterium nucleatum, Bacteroides fragilis). The extraction efficiency was assessed by the DNA yield, expressed in GE/pL of eluate or in GE/-µL of feces, as well as by the frequency of low-abundance taxa loss. Clustering of the methods according to the type of lysis was demonstrated: mechanical lysis provided stable and high DNA yields, particularly for Gram-positive bacteria, while chemical and enzymatic methods showed lower efficiency. We determined that the lysis type and pre-processing of intact fecal samples are the key factors affecting the DNA extraction efficiency and preservation of the native taxonomic profile. The best results were demonstrated by the QIAamp® PowerFecal® Pro DNA Kit (Qiagen) and the combination of AmpliTest UniProb + AmpliTest RIBO-prep kits (Center for Strategic Planning, Federal Medical-Biological Agency, Russia), both of which outperformed other methods in terms of DNA yield. The QIAamp® Fast DNA Stool Mini Kit (Qiagen) showed minimal losses of low-abundance taxa. These findings can be used for the standardization of gut microbiota DNA extraction methodologies and the development of domestic protocols.},
}

*Feces/microbiology/chemistry
Humans
*DNA, Bacterial/isolation & purification/genetics
*Real-Time Polymerase Chain Reaction/methods
*Gastrointestinal Microbiome/genetics
Reagent Kits, Diagnostic
*Gram-Negative Bacteria/genetics/isolation & purification
*Gram-Positive Bacteria/genetics/isolation & purification

@article {pmid41477712,
year = {2025},
author = {Glazunova, EV and Kurnosov, AS and Molodtsova, PA and Moskalenko, AM and Makarov, VV and Zlobovskaya, OA},
title = {[Gut Microbiota in Colorectal Cancer Carcinogenesis: The Evolution of Hypotheses].},
journal = {Molekuliarnaia biologiia},
volume = {59},
number = {6},
pages = {891-908},
doi = {10.7868/S3034555325060029},
pmid = {41477712},
issn = {0026-8984},
mesh = {*Colorectal Neoplasms/microbiology/pathology ; Humans ; *Gastrointestinal Microbiome ; *Carcinogenesis/pathology/genetics ; Animals ; *Dysbiosis/microbiology ; },
abstract = {Colorectal cancer remains one of the leading causes of cancer-related mortality, highlighting the importance of optimizing approaches for its early diagnosis and therapy. One promising area in this field is the investigation of the role of the gut microbiome in the initiation and progression of colorectal cancer. This review examines three principal hypotheses explaining the contribution of microbiota to carcinogenesis: the "Alpha-bug", the "Keystone pathogen", and the "Driver-Passenger" models. We analyze data on the mechanisms of microbiota-tumor cells interactions, including the induction of inflammation, genotoxicity, and disruption of the intestinal barrier function. Findings are also presented indicating that certain microorganisms previously considered markers of the advanced stages may possess pro-oncogenic properties, thereby refining existing carcinogenesis models. Overall, the data suggest that the microbiota and its dysbiotic alterations can be considered potential targets for colorectal cancer diagnosis and therapy.},
}

*Colorectal Neoplasms/microbiology/pathology
Humans
*Gastrointestinal Microbiome
*Carcinogenesis/pathology/genetics
Animals
*Dysbiosis/microbiology

@article {pmid41477689,
year = {2026},
author = {Chen, F and Sun, T and Song, H},
title = {Advances in Chemically Modified Polysaccharides with Enhanced Hypoglycemic Bioactivity.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c08511},
pmid = {41477689},
issn = {1520-5118},
abstract = {Polysaccharides are natural biopolymers with diverse bioactivities, but their clinical use in diabetes is restricted by poor solubility and bioavailability. Chemical modification provides an effective strategy to optimize polysaccharide structures, thereby enhancing their physicochemical properties and biological functions. This review summarized major chemical modification methods, focusing on introducing functional groups to sites such as hydroxyl, carboxyl, aldehyde, and amino groups. These modifications influence molecular weight distribution, monosaccharide composition, glycosidic linkage, solubility, and thermal stability, thereby modulating biological activities. Enhanced hypoglycemic effects of chemically modified polysaccharides were extensively discussed, emphasizing mechanisms such as suppression of digestive enzyme activities and the prevention of advanced glycation end-product generation, improvement of oxidative stress, improvement of gut microbiome and maintenance of gut health, and anti-inflammatory actions. This review underscored the potential of chemically modified polysaccharides as functional antidiabetic agents and advocated for further mechanistic studies and scalable, environmentally friendly modification techniques to advance their applications.},
}

@article {pmid41477501,
year = {2025},
author = {Govindharaj, GP and Choudhary, JS and Panda, RM and Basana-Gowda, G and Annamalai, M and Patil, N and Khan, RM and Banra, S and Srivastava, K and Mohapatra, SD},
title = {Bacterial communities in Nilaparvata lugens (Stål) (Hemiptera: Delphacidae) showed significant variation among the developmental stages with functional diversity.},
journal = {Heliyon},
volume = {11},
number = {4},
pages = {e42776},
pmid = {41477501},
issn = {2405-8440},
abstract = {Nilaparvata lugens, a major rice pest, hosts an essential microbiome, yet its dynamic changes across developmental stages remain poorly understood. This study analyzed the bacterial community across developmental stages using V3-V4 amplicon sequences of 16S rRNA gene. The microbiome was classified into 20 phyla, 38 classes, 77 orders, 155 families, and 273 genera, with Proteobacteria, Firmicutes, and Bacteroidetes dominating phyla. Families Morganellaceae, Enterobacteriaceae, and Moraxellaceae were prevalent across all stages, while Anaplamataceae was dominant in all the developmental stages except males. Key genera included Arsenophonous (5 %), Bacillus (5 %), and Acinetobacter (3 %), with Wolbachia (11 %) abundant in all developmental stages except in males. The shared operational taxonomic units (OTUs) between the developmental stages of N. lugens were only 40 OTUs, and higher unique OTUs were found in the late instar stage (89 OTUs), and the lowest unique OTUs were found at the male stage (64 OTUs). Functional prediction indicated roles in carbohydrate, amino acid, and energy metabolism, as well as membrane transport, signaling, DNA replication and repair. These findings highlight stage-specific microbiome variations, laying the foundation for microbiome-based pest management techniques.},
}

@article {pmid41477359,
year = {2025},
author = {Lee, YR and Park, JH and Yoo, HH and Choi, I and Park, HY},
title = {Standardization of Fecal Metabolomics Using Microbiome Preservation Kits: Implications for Multiomics Integration.},
journal = {International journal of analytical chemistry},
volume = {2025},
number = {},
pages = {8551545},
pmid = {41477359},
issn = {1687-8760},
abstract = {With the advancement of multiomics technologies and cohort study designs, integrative omics research is increasingly applied to human health and nutrition. However, optimal storage and preprocessing of labile biological samples, particularly feces, remain challenging. In this study, we systematically evaluated three normalization methods-wet weight, dry weight, and protein quantification-for quantitative metabolomic profiling of fecal samples, using 41 metabolites. Fresh fecal samples from three healthy individuals showed high reproducibility, with 24 metabolites exhibiting a coefficient of variation (CV) below 30 for both wet and dry weight normalization. Fecal samples from 20 obese patients collected using the OMNIgene·GUT kit demonstrated improved reproducibility with wet weight normalization (20 metabolites, CV < 30) and protein quantification normalization (19 metabolites, CV < 30), whereas dry weight normalization yielded no metabolites meeting the CV < 30 criterion. Direct analysis of the kit solution without a drying step further enhanced chromatographic clarity, highlighting practical considerations for large-scale studies. Overall, wet weight normalization consistently minimized variation across sample types, providing a robust and standardized framework for fecal metabolite profiling. These findings demonstrate that the OMNIgene·GUT kit is compatible with broad-spectrum metabolomic analyses and support its integration into multiomics workflows. By establishing reproducible normalization protocols, this study provides the foundation for accurate, comparable, and scalable fecal metabolomics in both clinical and nutritional research settings.},
}

@article {pmid41477198,
year = {2025},
author = {Feng, X and Song, W and Ren, X and Xu, Z and Li, C and Feng, M and Wang, N},
title = {Microbial influences on HPV infection and cervical carcinogenesis: emerging evidence from the vaginal microbiome.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1733315},
pmid = {41477198},
issn = {1664-302X},
abstract = {Microbial communities play a vital role in the human defense system, existing symbiotically with us, contributing to metabolic processes, and strengthening immune defenses against pathogens. A diverse bacterial population in the vagina contributes to maintaining dynamic homeostasis, with their interactions playing a critical role in determining health or disease status. The balanced vaginal microbiota, dominated by Lactobacilli, helps maintain vaginal pH, converts glycogen to lactic acid, and produces bacteriocins and hydrogen peroxide (H2O2), all contributing to its protective functions. On the other hand, an abnormal vaginal microbial composition, characterized by a decrease in beneficial microorganisms, heightens the risk of gynecological diseases such as bacterial vaginosis (BV), sexually transmitted infections, human papillomavirus (HPV) infections, and cervical cancer due to persistent infections. Variation in microbial composition is influenced by factors such as racial background, ethnicity, pregnancy, hormonal fluctuations, sexual behavior, personal hygiene practices, and various physiological conditions. This review aims to offer a detailed overview of the existing literature, focusing on the complex interplay between vaginal microbiota and gynecological conditions such as HPV infection. Our goal is to provide valuable insights that can inform future clinical strategies and interventions.},
}

@article {pmid41477061,
year = {2025},
author = {Zhong, D and Sun, Y and Zhao, L and Hu, Z and Li, G and Li, H and Xie, Z},
title = {Interplay between aging and metabolic diseases: from molecular mechanisms to therapeutic horizons.},
journal = {Medical review (2021)},
volume = {5},
number = {6},
pages = {477-489},
pmid = {41477061},
issn = {2749-9642},
abstract = {Aging and metabolic diseases are intricately linked through bidirectional molecular mechanisms that foster a harmful cycle of physiological decline. This cycle is driven by several key factors, including altered nutrient sensing, mitochondrial dysfunction, cellular senescence, chronic inflammation, epigenetic modifications, circadian rhythm disruptions, and imbalances in the gut microbiota. Emerging interventions targeting this aging-metabolism axis hold significant promise for extending healthspan. These approaches include the use of pharmacological mimetics, senolytics, multi-omics strategies, and microbiome modulation, all of which aim to restore metabolic homeostasis and mitigate age-related pathologies. However, several challenges remain in translating these strategies into clinical practice. These include the need for tissue-specific targeting, ensuring the long-term safety of interventions, and addressing socioeconomic disparities in healthcare access. Future research efforts are focusing on integrating multi-omic technologies, organoid and human cellular models, and developing equitable precision medicine frameworks. These initiatives aim to extend healthspan and reduce the global impact of aging-related metabolic diseases.},
}

@article {pmid41477025,
year = {2025},
author = {Miao, H and Wang, Z and Chen, S and Wang, J and Ma, H and Liu, Y and Yang, H and Guo, Z and Wang, J and Cui, P},
title = {Application of machine learning in the discovery of antimicrobial peptides: exploring their potential for ulcerative colitis therapy.},
journal = {eGastroenterology},
volume = {3},
number = {4},
pages = {e100253},
pmid = {41477025},
issn = {2976-7296},
abstract = {BACKGROUND: Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease with complex aetiology and limited treatment options. Antimicrobial peptides (AMPs), as endogenous immune effectors, have recently emerged as promising therapeutic agents in UC. However, systematic identification and functional evaluation of AMPs remain underexplored. We aimed to discover novel AMPs with potential therapeutic efficacy in UC by leveraging machine learning-based prediction and validating their impact in an experimental colitis model.

METHODS: We established a machine learning-driven pipeline to predict candidate AMPs based on their structural and functional features. Top-ranked peptides were synthesised and subjected to in vitro antibacterial assays and proteolytic stability tests. Their therapeutic potential was evaluated using a dextran sulfate sodium (DSS)-induced colitis mouse model, assessing clinical indicators, histopathology, inflammatory markers and gut microbiota alterations. Metagenomic and metabolomic analyses provided insights into microbial community dynamics and metabolic pathways. To probe the role of gut microbes in AMP-mediated gut homeostasis, we conducted Akkermansia (A.) muciniphila replenishment experiments.

RESULTS: Several AMPs identified by machine learning exhibited potent antimicrobial activity and resistance to proteolytic degradation. In vivo, AMP administration ameliorated DSS-induced colitis symptoms, including body weight loss, Disease Activity Index and histological damage. Treatment also modulated the gut microbiome, increasing the abundance of A. muciniphila and restoring microbial balance. Functional metagenomic profiling revealed enrichment of genes involved in mucosal barrier protection and immunoregulation. These findings were supported by improved inflammatory cytokine profiles and enhanced epithelial integrity.

CONCLUSIONS: Our findings demonstrate that machine learning-guided discovery of AMPs is a viable approach to identify promising therapeutic agents for UC. By integrating multi-omics analyses, we reveal potential microbiota-mediated mechanisms underlying AMP efficacy. These insights provide a strong foundation for advancing AMP-based strategies in UC management.},
}

@article {pmid41476963,
year = {2025},
author = {Ma, S and Zheng, L and Zhuang, X and Wang, M and Zou, Y},
title = {Pathogenic mechanisms and therapeutic potential of the microbiome in premature ovarian insufficiency.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1734367},
pmid = {41476963},
issn = {1664-3224},
mesh = {Humans ; *Primary Ovarian Insufficiency/therapy/microbiology/metabolism/etiology ; Female ; Animals ; *Microbiota ; Ovary/metabolism/microbiology ; Probiotics/therapeutic use ; },
abstract = {The postponement of childbearing age has become a global issue. Factors such as increased work pressures on women and environmental changes have led to a rising incidence and younger onset of premature ovarian insufficiency (POI). POI not only impacts patients' reproductive function but also heightens the risk of depression, anxiety, cognitive decline, premature mortality, osteoporosis, and cardiovascular disease. Exploring effective prevention and treatment strategies for POI can slow ovarian ageing and safeguard female reproductive health. Microbiome research confirms that most human tissues and organs form dynamic, interactive systems with symbiotic microbes that play a crucial role in female reproductive function. Previous studies on the microbiome and female reproductive health have rarely focused on POI. The proposed 'Microbiota-Ovary Axis' aims to establish an integrated regulatory framework. This theoretical model systematically elucidates how microbial signals influence ovarian function through four core pathways: the hypothalamic-pituitary-ovarian (HPO) axis, metabolism and endocrine regulation, immunoregulation, and oxidative stress. Evaluating the efficacy of dietary modifications, probiotics, and microbiota transplantation in animal models and preliminary clinical studies will establish a robust theoretical foundation for developing microbiota-targeted innovative diagnostic and therapeutic strategies for POI, thereby enhancing reproductive health throughout the female lifespan.},
}

Humans
*Primary Ovarian Insufficiency/therapy/microbiology/metabolism/etiology
Female
Animals
*Microbiota
Ovary/metabolism/microbiology
Probiotics/therapeutic use

@article {pmid41476768,
year = {2025},
author = {Dommer, AC and Amaro, RE and Prather, KA},
title = {Understanding Aerosol-Mediated Disease Transmission.},
journal = {ACS central science},
volume = {11},
number = {12},
pages = {2319-2328},
pmid = {41476768},
issn = {2374-7943},
abstract = {This Outlook aims to update the longstanding treatment of airborne disease transmission through an interdisciplinary lens combining biology, surface chemistry, and aerosol physics, drawing parallels between environmental and human-generated infectious aerosols and examining their effects on human and ecosystem health. By recasting the lung surface as a dynamic interface akin to the ocean surface, this Outlook illustrates the importance of a multidisciplinary approach to elucidate the mechanisms of disease transmission at a depth that enables practical mitigation strategies. The urgency of this analysis is motivated by the evolving nature of airborne pathogens of concern, such as SARS-CoV-2 and influenza, and the global impact of dynamic environments on the poorly understood airborne microbiome.},
}

@article {pmid41476253,
year = {2025},
author = {Kvitne, KE and Zuffa, S and Charron-Lamoureux, V and Mohanty, I and Patan, A and Mannochio-Russo, H and Zemlin, J and Burnett, LA and Zhang, LS and Cecala, MC and Ersoz, C and Connelly, JA and Halasa, N and Nicholson, M and Dorrestein, PC and Tsunoda, SM and Markle, J},
title = {Fecal microbial and metabolic signatures in children with very early onset inflammatory bowel disease.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-025-00899-0},
pmid = {41476253},
issn = {2055-5008},
support = {5P30HD106451-03//NICHD/NIH/ ; 5P30HD106451-03//NICHD/NIH/ ; 5P30HD106451-03//NICHD/NIH/ ; P50HD106463/HD/NICHD NIH HHS/United States ; },
abstract = {Very early onset inflammatory bowel disease (VEO-IBD) is a clinically distinct form of IBD manifesting in children before the age of six years. Disease in these children is especially severe and often refractory to treatment. While previous studies have investigated changes in the fecal microbiome and metabolome in adult and pediatric IBD, insights in VEO-IBD remain limited. This multi-omics analysis reveals changes in the fecal microbiome and metabolome in children diagnosed with VEO-IBD compared with age- and sexmatched healthy controls. Untargeted metabolomics analysis identified a depletion of short-chain N-acyl lipids and an enrichment of dipeptides, tripeptides, and oxo bile acids in children with VEO-IBD. Differential abundance analysis of 16S rRNA sequencing data showed lower abundance of beneficial bacteria such as Bifidobacterium and Blautia, and higher abundance of Lachnospira, Veillonella, and Bacteroides in VEO-IBD. Multi-omics integration revealed associations between the altered gut microbiome composition and metabolic dysregulation, specifically for the N-acyl lipids. This study offers unique insight into fecal microbial and metabolic signatures in VEO-IBD, paving the way for a better understanding of disease patterns and thereby more effective treatment strategies.},
}

@article {pmid41476057,
year = {2025},
author = {Wu, Y and Wong, O and Chen, S and Wang, Y and Lu, W and Cheung, CP and Ching, JYL and Cheong, PK and Chan, S and Leung, P and Chan, FKL and Su, Q and Ng, SC},
title = {Distinct diet-microbiome associations in autism spectrum disorder.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-67711-7},
pmid = {41476057},
issn = {2041-1723},
abstract = {Autism spectrum disorder (ASD) is linked to both altered gut microbiota and unhealthy diets; however, the mechanistic connections remain elusive. In this study, we conducted a systematic analysis of fecal microbiome metagenomic data, paired with granular dietary assessments and phenotypic profiles, across a cohort of 818 children (462 with ASD, 356 without ASD; mean age = 8.4 years; 27.3% female). By integrating dietary indices, nutrient intake, and food additive exposures, we uncovered ASD-specific linkages to the microbiome. Poor dietary quality correlated with aggregated core autistic symptoms, gastrointestinal complications, and atypical eating behaviors. Notably, children with ASD exhibited a more pronounced diet-microbiome interaction network compared to neurotypical peers, suggesting heightened microbial sensitivity to nutritional inputs. Furthermore, synthetic emulsifiers-specifically polysorbate-80 and carrageenan-were associated with disrupted microbial connectivity in ASD, a phenomenon attenuated in neurotypical children. Our findings elucidate the mechanistic links between dietary factors-particularly synthetic food additives-and microbiome dysregulation in ASD, urging a re-evaluation of dietary guidelines for ASD populations and laying the groundwork for personalized nutritional strategies.},
}

@article {pmid41475989,
year = {2025},
author = {Liu, YH and Peng, P and Hung, WC and Wu, PH and Kao, CY and Wu, PY and Huang, JC and Chen, SC and Kuo, CH},
title = {Gut microbiota profiles by LDL-C target achievement in statin-treated patients: A cross-sectional study.},
journal = {Nutrition, metabolism, and cardiovascular diseases : NMCD},
volume = {},
number = {},
pages = {104465},
doi = {10.1016/j.numecd.2025.104465},
pmid = {41475989},
issn = {1590-3729},
abstract = {BACKGROUND AND AIMS: Hyperlipidemia is linked to gut microbiota alterations, but the impact of statins on the gut microbiome remains unclear, especially concerning different low-density lipoprotein cholesterol (LDL-C) targets. This study explores gut microbiome changes in chronic disease patients under varying LDL-C targets with statin therapy.

METHODS AND RESULTS: A total of 125 patients (77 males and 48 females) diagnosed with chronic diseases, specifically diabetes mellitus (87 %), hypertension (74 %), and chronic kidney disease (48 %), were recruited. Fecal samples were collected from the participants to analyze the composition of the gut microbiota using Illumina sequencing of the 16S ribosomal ribonucleic acid gene. The patients were divided into two groups according to LDL-C level, including 57 patients in the LDL-C target-achieved group (LDL-C < 70 mg/dL), and 68 in the LDL-C target-not-achieved group (LDL-C ≥ 70 mg/dL). There were no significant differences in microbial species diversity (Chao1 index and Shannon index), beta diversity and microbial dysbiosis index between the two groups. However, a distinct microbial community structure was found in the LDL-C target-achieved group, with decreased abundances at the genus level of Barnesiella, Coprococcus 1, Flavonifractor, Odoribacter and Coprobacter.

CONCLUSION: No significant difference in alpha diversity, beta diversity, and microbial dysbiosis index were found between the LDL-C target-achieved and target-not-achieved groups. However, the LDL-C target-achieved group was associated with a significant reduction in short-chain fatty acid-producing bacteria, including taxa Barnesiella, Coprococcus 1, Flavonifractor and Odoribacter.},
}

@article {pmid41475718,
year = {2026},
author = {Zavagna, L and Alfano, A and Bianchi, M and Di Meo, C and Fusco, A and Esin, S and Batoni, G and Donnarumma, G and Schiraldi, C and Danti, S},
title = {Gellan gum electrohydrodynamic microencapsulation of probiotics for intestine-targeted delivery.},
journal = {Carbohydrate polymers},
volume = {375},
number = {},
pages = {124742},
doi = {10.1016/j.carbpol.2025.124742},
pmid = {41475718},
issn = {1879-1344},
mesh = {*Probiotics/chemistry/pharmacology/administration & dosage ; *Polysaccharides, Bacterial/chemistry ; Humans ; Caco-2 Cells ; Limosilactobacillus fermentum/chemistry ; Drug Compounding/methods ; Escherichia coli/drug effects ; Intestines/microbiology ; Particle Size ; *Anti-Bacterial Agents/pharmacology/chemistry ; Microspheres ; Drug Delivery Systems ; Hydrogen-Ion Concentration ; },
abstract = {Microencapsulation is a promising strategy to improve time-stability, viability and targeted delivery of probiotics, thus enhancing their beneficial roles in the intestine. However, areas of improvement persist, including optimal viability protection during storage and gastrointestinal (GI) transit, control over encapsulation and targeted release. Due to pH-responsiveness, gellan gum (GG) could be ideal to face some of these criticalities. In this study, we set-up a robust electrohydrodynamic (EHD) microdripping process to produce GG microparticles (GGMs) encapsulating Limolactobacillus fermentum. By varying GG concentration, flow rate and applied voltage, the optimized EHD parameters led to highly monodisperse microbeads with controlled morphology. Successful encapsulation of L. fermentum in GGMs was obtained at concentrations of 10[6] CFU/mL and 10[9] CFU/mL, leading to 300 ± 40 μm and 450 ± 100 μm particle sizes, with encapsulation efficiency of 94 ± 6 % and 99 ± 1 %, respectively. GGMs demonstrated post-encapsulation probiotic viability with lactic acid production. Freeze-dried formulations were lasting under storage until 3 months and resulted stable under GI-simulated conditions. Their bioactive properties were demonstrated by antimicrobial efficacy against Escherichia coli and enhanced defensin expression in Caco-2 intestinal cells. Overall, EHD microdripping was a versatile and robust platform useful in functional foods and gut microbiome engineering.},
}

*Probiotics/chemistry/pharmacology/administration & dosage
*Polysaccharides, Bacterial/chemistry
Humans
Caco-2 Cells
Limosilactobacillus fermentum/chemistry
Drug Compounding/methods
Escherichia coli/drug effects
Intestines/microbiology
Particle Size
*Anti-Bacterial Agents/pharmacology/chemistry
Microspheres
Drug Delivery Systems
Hydrogen-Ion Concentration

@article {pmid41475684,
year = {2025},
author = {Yamoah, JAA and Kwofie, KD and Akorli, J and Ladzekpo, D and Kawada, H and Boateng, KY and Beyuo, J and Keleve, A and Danquah, JB and Tawiah-Mensah, C and Ansah-Owusu, J and Dadzie, SK and Wallace, PA and Tsuji, N and Hatta, T},
title = {Beyond the usual suspects: Uncovering less-recognized pathogenic bacteria in Ghanaian blood-feeding Amblyomma variegatum ticks using 16S rRNA amplicon sequencing.},
journal = {Parasitology international},
volume = {112},
number = {},
pages = {103228},
doi = {10.1016/j.parint.2025.103228},
pmid = {41475684},
issn = {1873-0329},
abstract = {Ticks are important vectors of bacterial pathogens affecting both human and animal health. In Ghana, Amblyomma variegatum is the predominant cattle-infesting tick, yet most studies have focused on a limited range of well-characterized pathogens, potentially overlooking a broader diversity of less-recognized, emerging, or opportunistic bacteria. In this study, we used 16S rRNA amplicon sequencing to characterize the bacteriome of partially blood-fed Am. variegatum ticks, with emphasis on underexplored taxa. As ticks were blood-fed at the time of collection, some detected microorganisms may represent transient, host-derived bacteria rather than endogenous tick microbiota; therefore, findings should also be interpreted within the context of xenosurveillance. Partially-fed ticks were collected from cattle across three ecological zones within Ghana's Greater Accra Region. 11 Am. variegatum ticks, confirmed through both morphological and molecular analyses, were subjected to high-throughput sequencing, and bacterial diversity and composition were analysed using established bioinformatics tools. Sequencing generated over 1.75 million high-quality reads and 3172 amplicon sequence variants. Five dominant bacterial phyla were detected, with Actinomycetota and Bacillota being the most abundant. While Rickettsia spp. were prevalent in some samples, Anaplasma and Coxiella, two commonly studied tick-borne bacteria, were not detected. Several less-recognized or opportunistic species, including multidrug-resistant Corynebacterium resistens and bovine-associated Porphyromonas levii, were identified at high relative abundance. These findings suggest that Am. variegatum may harbor a broader range of bacterial taxa than previously recognized. Incorporating such neglected microorganisms into a One Health tick-surveillance framework may improve disease risk assessment and guide public and animal health interventions in the region.},
}

@article {pmid41475679,
year = {2025},
author = {Morel, C and Li, R and Luces, CF and Brougham, MFH and Pascual-Gazquez, JF and Iniesta, RR and Torquati, L},
title = {Interventions targeting the gut microbiome to improve cancer treatment outcomes and their gastrointestinal side effects: a systematic review and meta-analysis.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101300},
doi = {10.1016/j.tjnut.2025.101300},
pmid = {41475679},
issn = {1541-6100},
abstract = {BACKGROUND: Improvements in cancer treatment are essential to reduce premature mortality. Emerging evidence highlights the role of the gut microbiome (GM) in influencing treatment responses and modulating gastrointestinal adverse events (GIAEs). Because cancer therapy disrupts GM composition, restoring gut health may help mitigate side effects and support gut-associated immunity.

OBJECTIVE: This study aims to systematically evaluate and assess the effectiveness of GM interventions on the occurrence of GIAEs and clinical responses to cancer treatment.

METHODS: Three databases (PubMed, Web of Science, Cochrane Library) were systematically searched up to February 2025 for studies assessing gut microbiome interventions during cancer treatment. Risk of bias was evaluated using the EPHPP Quality Assessment Tool. Meta-analyses were conducted in Stata 18® using random-effects models to estimate the pooled relative risk of GM interventions on GIAEs (primary outcome) and objective disease response rates (secondary outcome).

RESULTS: Fifty-six studies were included in the systematic review and forty were meta-analysed (n=37 for GIAE outcomes, n=8 for treatment response). GM interventions reduced the overall risk of GIAEs (RR = 0.59, 95% CI = 0.53, 0.65, I[2] = 76.8%; 95% PI = 0.32, 1.08), including diarrhoea, constipation, nausea, and vomiting, but with considerable heterogeneity between studies. There was insufficient evidence to suggest improvements in objective disease response rates (RR = 1.06, 95% CI = 0.93, 1.20; I[2] = 0%; 95% PI = 0.93, 1.20).

CONCLUSION: GM interventions show promise in improving cancer care by reducing GIAEs, though evidence for direct effects on treatment response remains limited. Standardising intervention protocols and outcome reporting in future RCTs is essential to strengthen the evidence base and guide clinical recommendations.

PROSPERO REGISTRATION: Registration number: CRD42023443332 LINK TO PROTOCOL: Https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42023443332.},
}

@article {pmid41475610,
year = {2025},
author = {Xie, Y and Jiang, C and Xu, S and Zhou, H and Wang, P and Yang, Y and Hou, X and Zheng, X and Zhuang, X},
title = {Application and mechanisms of wastewater load regulation for enhanced partial denitrification in constructed wetlands: From microbiome structure to single-cell functional validation.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {133899},
doi = {10.1016/j.biortech.2025.133899},
pmid = {41475610},
issn = {1873-2976},
abstract = {Achieving robust nitrogen removal in constructed wetlands (CWs) is often hindered by the inhibitory effects of high pollutant loads on microbial activity. This study validates that influent load regulation is a pivotal strategy for engineering a partial denitrification (PD)-dominant microbial ecosystem, effectively overcoming such limitations. Comparing low-load (LL), medium-load (ML), and high-load (HL) conditions, the LL group achieved superior total nitrogen removal (up to 97.11%), outperforming the ML and HL groups by 9.28% and 16.21%, respectively. The underlying mechanism involves the alleviation of free ammonia (FA) inhibition at lower loads, which permitted the enrichment of crucial PD-related genera like Pseudomonas and Flavobacterium. This engineered community structure facilitated the stable production of nitrite, a key substrate that subsequently fueled downstream processes such as anammox and DAMO, thereby creating a synergistic nitrogen removal network. Consequently, our findings confirm that managing influent load is a critical and practical method for engineering a stable, PD-dominant microbial ecosystem to achieve robust and sustainable nitrogen removal in CWs.},
}

@article {pmid41475548,
year = {2025},
author = {Borgini, S and Pasveer, E and Petre, C and Iorga, BI and Vertommen, D and Remaut, H and Collet, JF and Lauber, F},
title = {Identification of receptor-binding domains of Bacteroidales antibacterial pore-forming toxins.},
journal = {The Journal of biological chemistry},
volume = {},
number = {},
pages = {111113},
doi = {10.1016/j.jbc.2025.111113},
pmid = {41475548},
issn = {1083-351X},
abstract = {Bacteroidales are abundant Gram-negative bacteria present in the gut microbiota of most animals, including humans, where they carry out vital functions for host health. To thrive in this competitive environment, Bacteroidales use sophisticated weapons to outmatch competitors. Among these, BSAPs (Bacteroidales Secreted Antimicrobial Proteins) represent a novel class of bactericidal pore-forming toxins that are highly specific to their receptor, typically targeting only a single membrane protein or lipopolysaccharide. The molecular determinants conferring this high selectivity remain unknown. In this study, we therefore investigated the model protein BSAP-1 and determined which of its domains is involved in providing receptor specificity. We demonstrate that receptor recognition is entirely driven by the C-terminal domain (CTD) of BSAP-1 using a combination of in vivo competition assays, in vitro protein binding studies and mutational analysis. Specifically, we show that deletion of the CTD abrogates BSAP-1 bactericidal activity by preventing receptor binding, while grafting the CTD to unrelated carrier proteins enables CTD-driven interaction with the BSAP-1 receptor. Combining structural investigation of a BSAP-1-receptor complex with mutational analysis, we unveil that this interaction is driven by electrostatic interactions. Building upon this discovery, we show that BSAPs can be categorized according to the structure of their CTD, suggesting a strong CTD structure/receptor type correlation. In summary, our research demonstrates that BSAP receptor recognition is driven by their CTD and paves the way for future applications.},
}

@article {pmid41475542,
year = {2025},
author = {Nayak, A and Bera, S and Purohit, S and Jain, CK},
title = {Gut Microbiota Mediated Neuroinflammation in Psychiatric Disorders: Current Perspectives and Challenges.},
journal = {Behavioural brain research},
volume = {},
number = {},
pages = {116019},
doi = {10.1016/j.bbr.2025.116019},
pmid = {41475542},
issn = {1872-7549},
abstract = {Psychiatric disorders remain a major global health concern, with complex diagnostic criteria and a lack of clear biological markers that continue to challenge therapeutic strategies. Current treatment methods, such as psychotherapy, brain stimulation therapy, and pharmacological interventions, often come with their own set of side effects, thus warranting the need to explore alternative approaches. Emerging research highlights the gut brain axis (GBA) and gut microbiota (GM) as key modulators of brain health and disease. Dysbiosis, a disruption in gut microbial composition, can influence blood brain barrier (BBB) integrity, immune signaling, and microbial metabolite production, collectively modulating neuroimmune homeostasis and contributing to the onset of neuroinflammation. While growing preclinical and clinical evidence links altered GM to depression, anxiety, schizophrenia, bipolar disorder (BD), and autism spectrum disorder (ASD), causal relationships remain incompletely defined. This review examines the established and emerging mechanisms connecting the GM to neuroinflammation underlying psychiatric disorders and evaluates current microbiome targeted interventions, such as diet based strategies, probiotics, next generation probiotics (NGPs), and fecal microbiota transplantation (FMT). We also discuss speculative microbiome engineering approaches and highlight translational limitations that must be addressed before clinical implementation. A holistic approach integrating these strategies with conventional psychiatric treatments could facilitate more effective and personalized interventions.},
}

@article {pmid41475424,
year = {2025},
author = {Ranson, HJ and Ye, Y-S and Petukhova, VZ and Green-Saxena, A and He, R and Sun, J and Godugu, B and Sanchez, LM and Wu, Q and Rowley, DC},
title = {Lipopeptides and antibiotics from a marine Bacillus pumilus mediate a potential "catch and kill" effect on pathogenetic Vibrio parahaemolyticus.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0144025},
doi = {10.1128/msystems.01440-25},
pmid = {41475424},
issn = {2379-5077},
abstract = {UNLABELLED: Bacteria produce a diverse range of specialized metabolites that influence the health and behavior of neighboring cells and, therefore, have potential applications in treating diseases. Deciphering the intended ecological functions of specialized metabolites is challenging due to the small scales at which these interactions occur and the complexity of unraveling simultaneous responses to multiple signals. In this study, we investigated the chemical interactions between two marine bacterial colonies, Vibrio parahaemolyticus PSU5429 and Bacillus pumilus YP001. When the two bacteria were grown in proximity on agar, V. parahaemolyticus exhibited swarming motility toward B. pumilus, but close approach to the B. pumilus colony was impeded by a zone of inhibition. Matrix-assisted laser desorption/ionization time-of-flight imaging mass spectrometry (MALDI-TOF IMS) suggested that lipopeptides produced by Bacillus induced swarming motility, a finding corroborated by genomic and chemical analyses of YP001. Based on activity and metabolomics guidance, the antibiotic amicoumacin B was found to be responsible for the observed antibiosis, while swarming motility by V. parahaemolyticus was induced by lipopeptides and two lipoamides. In this scenario, lipopeptide production by the Bacillus colony induces the Vibrio colony to swarm toward a lysis zone, resulting in a possible "catch and kill" effect. These results demonstrate the complexity of behaviors and outcomes exhibited by microbes under the simultaneous influence of different allelochemicals, suggesting possible interplays between antibiotics and compounds that induce motility.

IMPORTANCE: Microbes communicate and compete using small molecules, yet linking specific metabolites to visible behaviors is difficult. We combine imaging mass spectrometry, genomics, analytical chemistry, and bioassays to decode an interaction between a marine Bacillus and the pathogen Vibrio parahaemolyticus. Surfactin-like lipopeptides act at a distance to stimulate Vibrio swarming and draw cells toward the colony. Amicoumacin B accumulates at the interface and halts growth, yielding a simple "catch and kill" outcome. This study shows that the spatial localization of natural products shapes microbial behavior on surfaces and provides a general, scalable workflow that maps chemistry to phenotype. Beyond this case, the approach can be applied broadly to understand and, ultimately, tune microbial interactions relevant to marine ecosystems, aquaculture health, and microbiome engineering.},
}

@article {pmid41475279,
year = {2025},
author = {Singh, G and Ansari, S and Yadav, S and Aran, KR},
title = {Gut microbiota's role in NAFLD- and HBV/HCV-related hepatocellular carcinoma: Mechanisms and therapeutic implications.},
journal = {Microbial pathogenesis},
volume = {211},
number = {},
pages = {108273},
doi = {10.1016/j.micpath.2025.108273},
pmid = {41475279},
issn = {1096-1208},
abstract = {Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality globally and has been closely linked to chronic liver conditions, such as viral hepatitis and non-alcoholic fatty liver disease. Recent research has demonstrated that the gut microbiota significantly impacts the gut-liver axis, a crucial aspect of the pathophysiology of HCC. This review emphasizes the mechanisms by which gut dysbiosis contributes to liver inflammation, fibrosis, and tumor formation. In NAFLD-related HCC, modification in the microbiota composition facilitates intestinal barrier dysfunction, endotoxemia, and metabolic disturbances. In HCC associated with HBV/HCV, the microbiome modulates immune surveillance and viral persistence. Shared pathogenic pathways, such as LPS-TLR4 signaling, bile acid dysregulation, and immunosuppressive microenvironments, highlight the role of microbial imbalance across varied etiologies. We also discuss how antibiotics, diet, probiotics, and postbiotics influence gut-liver homeostasis, as well as their therapeutic potential in primary and secondary prevention and treatment of HCC. Short-chain fatty acids and valeric acid are examples of postbiotics with anti-inflammatory and pro-apoptotic anti-IBD effects, while fecal microbiota transplantation and dietary modulation have shown potential in improving outcomes. The review also identifies significant research gaps, particularly in establishing causality, understanding intrahepatic metastasis, and investigating the roles of the fungal and viral microbiome (mycobiome and virome). Finally, the incorporation of microbiome-based interventions into clinical practice could represent an effective future strategy for risk stratification, prevention, and adjuvant therapy of HCC. Future studies focusing on longitudinal analysis, mechanistic validation, and multi-kingdom profiling are essential for translating microbiome research into effective clinical applications.},
}

@article {pmid41475232,
year = {2025},
author = {Lehmann, K and Arachchige, DE and Lehmann, R and Overholt, WA and Küsel, K and Totsche, KU},
title = {Neglected but pivotal: Complex matter dynamics in the aeration zone contribute to groundwater quality evolution.},
journal = {Water research},
volume = {291},
number = {},
pages = {125287},
doi = {10.1016/j.watres.2025.125287},
pmid = {41475232},
issn = {1879-2448},
abstract = {Fluid and matter dynamics in thick aeration zones of topographic highs are insufficiently understood, particularly in their role for groundwater quality evolution and subsurface ecosystem functioning. We apply novel drainage collectors, installed in sub-horizontal boreholes, to fill the observational gap of bedrock percolates. In the Hainich Critical Zone Exploratory, 20 spatially distributed collectors act as a super-collector for percolates from the highly geodiverse aeration zone, complementing a lysimeter and well network. For over 3 years, we investigated percolate volume, quality, and controlling factors. 65% of the annual percolation flux occurred during winter. Of this, extreme rainfall (33%) and snowmelt events (25%) together accounted for 58%, depending on the recent past of subsurface moisture conditions. Collectors captured 13% of topsoil seepage, with soil thickness, sub-season, slope, and fracture properties as major factors. The mobile percolate inventory showed strong seasonality, driven by weather conditions. The solute signature differed markedly from that of soil seepage, more closely resembling groundwater. Winter high-flows translocated most of the organic carbon and a broad spectrum of mineral particles, up to 160 µm large mineral-organic aggregates, and bioparticles. Bacterial diversity suggests a distinct aeration-zone microbiome adapted to fluctuating habitat conditions, serving as a dispersal source for phreatic communities. Our findings showcase complex dynamics between matter sources, transformations, and sinks. Weather extremes affect the formation and transport of matter through regolith and bedrock. Increasing above- and belowground effects of climate change could thus impair subsurface services, including the provision of high-quality groundwater. We advocate considering thick recharge-area aeration zones as key compartments for subsurface life and for the evolution of groundwater quality.},
}

@article {pmid41475022,
year = {2025},
author = {Chen, N and Pang, D and Shang, H},
title = {Akkermansia muciniphila: A double-edged sword in life-stage-specific nutritional modulation of Parkinson's disease via the gut-brain axis.},
journal = {Microbiological research},
volume = {305},
number = {},
pages = {128436},
doi = {10.1016/j.micres.2025.128436},
pmid = {41475022},
issn = {1618-0623},
abstract = {The gut mucin specialist Akkermansia muciniphila (A. muciniphila) exhibits a paradoxical duality in PD, showing both positive and negative correlations with motor and non-motor symptoms across distinct PD subtypes. This enigmatic role is further complicated by its dynamic lifespan trajectory: colonizing early life, peaking in adulthood, declining with aging, yet resurging in longevity cohorts. This review synthesizes evidence on A. muciniphila's structural components, its divergent associations with PD phenotypes, and the dietary and host factors shaping its abundance from gestation to senescence. We propose a lifespan-targeted intervention model that strategically modulates A. muciniphila, which could concurrently mitigate PD progression and promote healthy aging. We suggest suppressing its neurotoxic pathways in susceptible individuals while enhancing its beneficial functions in the aging process. Reconciling this microbial Janus face may pave the way for novel microbiome-based precision therapeutics against neurodegeneration.},
}

@article {pmid41474788,
year = {2025},
author = {Wong, KX and Chen, ST and Ong, JJ and Gan, WY and Abdul Murad, NA and Chong, CW and Ramzi, NH},
title = {Exploring gut microbiome and nutritional status among children with Autism Spectrum Disorder (MY-ASD Microbiome): A study protocol.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0338801},
pmid = {41474788},
issn = {1932-6203},
mesh = {Humans ; *Autism Spectrum Disorder/microbiology ; *Gastrointestinal Microbiome ; Child ; Male ; Child, Preschool ; *Nutritional Status ; Case-Control Studies ; Feces/microbiology ; Saliva/microbiology ; Malaysia ; Female ; },
abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterised by persistent deficits in social communication and the presence of restricted, repetitive behaviours or interests. Previous literature has identified a link between the gut and ASD; however, the underlying mechanisms remain unclear. Gut microbiota dysbiosis has been extensively reported in cohort studies of ASD, and specific microbial metabolites or by-products may serve as potential biomarkers for ASD. Additionally, children with ASD often exhibit food refusal, have a limited food repertoire and display a tendency to consume the same foods frequently; thus, these behaviours increase their risk of malnutrition (over-nutrition or under-nutrition) compared to typically developing (TD) healthy children. This study primarily aims to identify oral and gut microbiota among children with ASD and TD healthy children. The secondary aim is to determine the associations between oral and gut microbiota with nutritional status among children with ASD. The findings will enhance understanding of the aetiology of ASD and inform early intervention strategies to mitigate disease severity and early identification of malnutrition in genetically at-risk children.

METHODS AND ANALYSIS: This observational, age-matched, case-control study is conducted in Malaysia among 40 male children with ASD and age-matched with 40 TD healthy controls aged 4-10 years. The dependent variables include the microbiota profile, identified through metagenomic sequencing analysis of saliva and faecal samples, and autism severity, assessed through validated questionnaires. Independent variables include nutritional status, determined through Subjective Global Nutrition Assessment (SGNA), anthropometry and dietary measurements, gastrointestinal symptoms, eating behaviour, behavioural profile, and sleep quality. Data collection is expected to be completed by June 2026. The study nature may limit causality establishment. Analyses will use chi-square/ANOVA for group comparisons, SparCC for microbiota correlations, and mixed-effects logistic regression to model associations.

CONCLUSION: This study advances understanding of ASD-related microbiota, guiding personalised nutrition and precision healthcare in Malaysia.},
}

Humans
*Autism Spectrum Disorder/microbiology
*Gastrointestinal Microbiome
Child
Male
Child, Preschool
*Nutritional Status
Case-Control Studies
Feces/microbiology
Saliva/microbiology
Malaysia
Female

@article {pmid41474687,
year = {2025},
author = {Abulaiti, A and Yu, H and Ma, J and Wuji, A and Chi, H},
title = {Advancement on the Association between Gut Microbiota and Autism Spectrum Disorder in Children.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-24},
doi = {10.1159/000549716},
pmid = {41474687},
issn = {1421-9697},
abstract = {Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder characterized by deficits in social interaction, communication, and the presence of restricted, repetitive behaviors. The rising global prevalence of ASD suggests a multifactorial etiology involving genetic, environmental, and neurodevelopmental factors. This review explores the establishment of the early-life microbiome, highlighting rapid microbial colonization from maternal and environmental sources. Emerging evidence indicates that delivery mode and infant feeding practices may influence ASD susceptibility. Although the concept of a sterile intrauterine environment remains debated, its investigation is valuable. The bidirectional "microbiota-gut-brain axis" has emerged as a critical pathway linking gut microbiota and brain function, offering potential therapeutic targets for ASD. Dietary patterns in children with ASD are often characterized by selectivity and restriction, which may disrupt gut microbiota composition and exacerbate gastrointestinal symptoms, thereby increasing ASD risk. Nutritional interventions and early behavioral therapies are thus essential. The gluten-free, casein-free (GFCF) diet remains controversial, with inconsistent evidence regarding its efficacy. Probiotic supplementation shows strain-specific effects, necessitating rigorous evaluation before clinical application. Given the heterogeneity of ASD, pharmacological treatments have shown limited universal efficacy. This review provides a comprehensive analysis of the interplay between diet, gastrointestinal symptoms, and ASD, evaluates the gut-brain axis as a mechanistic framework, and assesses the therapeutic potential of microbial interventions, including probiotics, prebiotics, and fecal microbiota transplantation (FMT). While promising findings have emerged, further well-designed clinical studies are needed to elucidate the complex etiology of ASD and validate therapeutic strategies.},
}

@article {pmid41474588,
year = {2025},
author = {Rattanapitoon, NK and Thanchonnang, C and Rattanapitoon, SK},
title = {Exploring the gut-biliary microbiome axis in Opisthorchis viverrini-associated cholangiocarcinoma: An overlooked pathogenic interface.},
journal = {Journal of cancer research and therapeutics},
volume = {21},
number = {7},
pages = {1464-1465},
doi = {10.4103/jcrt.jcrt_1012_25},
pmid = {41474588},
issn = {1998-4138},
}

@article {pmid41474487,
year = {2025},
author = {Mukhanbetzhanov, N and Zhetkenev, S and Vinogradova, E and Sergazy, S and Jarmukhanov, Z and Issilbayeva, A and Kossumov, A and Kassenova, A and Mukhametuly, B and Kenessarin, M and Zhumadilov, K and Stepanenko, V and Bogacheva, V and Petukhov, A and Sato, H and Endo, S and Fujimoto, N and Hoshi, M},
title = {Multicompartmental analysis of microbiome alterations under radiation stress.},
journal = {AMB Express},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13568-025-02002-4},
pmid = {41474487},
issn = {2191-0855},
support = {(Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; (Grant No. AP09057915)//Science Committee of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
}

@article {pmid41474484,
year = {2025},
author = {Kinkpe, L and Solomon, AI and Niu, Y and Goswami, N and Ikele, CM and Hu, D and Abdessan, R and Zhigang, H and Xia, W},
title = {A guide to network analysis, multi-omics integration, and applications in livestock microbiome research.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {1},
pages = {17},
pmid = {41474484},
issn = {1573-0972},
support = {2023YFD1300300//National Key Research and Development Program of China/ ; (CARS-42-2)//China Agriculture Research System of MOF and MARA/ ; },
mesh = {Animals ; *Livestock/microbiology ; *Gastrointestinal Microbiome ; *Genomics/methods ; *Microbiota ; Computational Biology/methods ; Machine Learning ; Multiomics ; },
abstract = {The function of the livestock gut microbiome in driving animal growth, health, and methane emissions is controlled by networks of interactions among microbes. A major challenge is to move beyond simply listing microbial members to understanding these interaction networks, which determine how the community functions as a whole. This review synthesizes how network analysis, combined with multi-omics data, can meet this challenge. We focus on the critical task of identifying keystone species, the disproportionately influential microbes that direct processes like fiber digestion and immune function, yet are often missed by standard surveys. We evaluate a progression of methods, from identifying correlated species to building models that integrate genomic, metabolic, and host data. This integration is key to separating true ecological relationships from statistical noise and to linking microbial presence to function. We highlight how computational techniques like metabolic modeling and machine learning are turning networks into predictive tools. Finally, we outline the path forward: field-ready studies that track microbiomes over time, the development of livestock-specific metabolic models, and analytical standards that will allow research to translate into practical strategies. The goal is to provide a framework for using network science to actively manage the microbiome, enhancing sustainable livestock production.},
}

Animals
*Livestock/microbiology
*Gastrointestinal Microbiome
*Genomics/methods
*Microbiota
Computational Biology/methods
Machine Learning
Multiomics

@article {pmid41474336,
year = {2025},
author = {Vazquez-Munoz, R and Ranjan, A and Bertolini, M and Thompson, A and Mosharaf Ghahfarokhy, P and Harnden, A and Nobile, CJ and Sobue, T and Vera-Licona, P and Dongari-Bagtzoglou, A},
title = {Enterococcus faecalis induces H2O2-mediated epithelial cell death and enhances Candida albicans virulence in oropharyngeal candidiasis.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0082225},
doi = {10.1128/msphere.00822-25},
pmid = {41474336},
issn = {2379-5042},
abstract = {UNLABELLED: In immunosuppressed humans with oropharyngeal candidiasis (OPC) and in mice with experimental OPC, Candida albicans infection is associated with a bacterial imbalance characterized by significantly reduced oral microbiome diversity and the expansion of enterococcal and streptococcal species, which may exacerbate oral mucosal pathology. In this study, we applied an unbiased genome-wide transcriptomic profiling approach to shed further mechanistic light on the role of indigenous enterococcal communities in mucosal infection in a mouse model of cancer chemotherapy-associated OPC. Transcriptomic profiling of tongue tissues revealed a wide-ranging, barrier-compromising molecular activity of resident enterococci that explains the previously observed attenuation of fungal mucosal invasion with antibiotic treatment in this mouse model. Mechanistically, we validated the pathogenic potential of resident bacteria by showing that enterococci isolated from mice with OPC produce hydrogen peroxide (H2O2) and induce oral epithelial cell death through apoptosis and necrosis in vitro. We also discovered that C. albicans increased enterococcal H2O2 production. These findings uncover a novel mechanism of pathogenic synergy between C. albicans and Enterococcus faecalis, which may be responsible for increased epithelial barrier damage and mucosal invasion by C. albicans hyphae during cancer chemotherapy.

IMPORTANCE: Chemotherapy-induced mucosal barrier injury and immune suppression increase susceptibility to oropharyngeal candidiasis (OPC), a debilitating fungal infection. Our study uncovers a previously unknown pathogenic interaction between Candida albicans and Enterococcus faecalis, by showing that indigenous enterococci produce H2O2, which contributes to oral epithelial cell death during fungal infection. By integrating transcriptomics with functional assays, we demonstrate that enterococci compromise epithelial integrity independently of fungal burdens, highlighting the role of the bacterial microbiota in driving tissue damage. These findings emphasize the need to consider bacterial-fungal interactions in managing OPC and suggest that targeting the microbial crosstalk could be a promising adjunctive strategy in immunocompromised hosts.},
}