@article {pmid40707722,
year = {2025},
author = {Mangnier, L and Bodein, A and Mariaz, M and Mathieu, A and Scott-Boyer, MP and Vashist, N and Bramble, MS and Droit, A},
title = {A systematic benchmark of integrative strategies for microbiome-metabolome data.},
journal = {Communications biology},
volume = {8},
number = {1},
pages = {1100},
pmid = {40707722},
issn = {2399-3642},
mesh = {Humans ; *Metabolomics/methods ; *Metabolome ; *Gastrointestinal Microbiome ; Benchmarking ; *Metagenomics/methods ; *Microbiota ; Computational Biology/methods ; },
abstract = {The rapid advancement of high-throughput sequencing technologies has enabled the integration of various omic layers into computational frameworks. Among these, metagenomics and metabolomics are increasingly studied for their roles in complex diseases. However, no standard currently exists for jointly integrating microbiome and metabolome datasets within statistical models. We benchmarked nineteen integrative methods to disentangle the relationships between microorganisms and metabolites. These methods address key research goals, including global associations, data summarization, individual associations, and feature selection. Through realistic simulations, we identified the best-performing methods and validated them on real gut microbiome datasets, revealing complementary biological processes across the two omic layers. Practical guidelines are provided for specific scientific questions and data types. This work establishes a foundation for research standards in metagenomics-metabolomics integration and supports future methodological developments, while also providing guidance for designing optimal analytical strategies tailored to specific integration questions.},
}

Humans
*Metabolomics/methods
*Metabolome
*Gastrointestinal Microbiome
Benchmarking
*Metagenomics/methods
*Microbiota
Computational Biology/methods

@article {pmid40707563,
year = {2025},
author = {Jørgensen, AB and Almer, L and Brandstrup, B and Friis-Hansen, L},
title = {Fecal microbiomes from screening sampling tubes are stable despite varying sampling and storage conditions.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26951},
pmid = {40707563},
issn = {2045-2322},
support = {R374-A22413//The Danish Cancer Society/ ; R22A613//The Health Science Research Foundation of Region Zealand, Denmark/ ; },
mesh = {Humans ; *Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; *Specimen Handling/methods ; *Gastrointestinal Microbiome/genetics ; Adult ; *Bacteria/genetics/classification/isolation & purification ; DNA, Bacterial/genetics ; Male ; Colorectal Neoplasms/diagnosis ; Female ; Early Detection of Cancer ; *Microbiota ; Middle Aged ; },
abstract = {Residual material from fecal immunochemical test (FIT) tubes, commonly used in colorectal cancer screening programs, offers a valuable resource for large-scale gut microbiome studies. With recent advances in sequencing technologies, sequencing the full-length bacterial 16S ribosomal gene is now feasible. In this study, we evaluated the impact of pre-analytical handling conditions on microbiome profiling using FIT samples. Stool samples from eight healthy adults were subjected to various short-term (+ 20 °C) and long-term (-18 °C or -80 °C) storage conditions prior to DNA extraction. We also investigated the effects of sampling variation and the presence of buffer medium. Full-length 16S rRNA gene amplicons were generated and sequenced using Oxford Nanopore Technology to characterize the microbiome composition. Despite variations in sampling and storage conditions, microbiome richness, Shannon diversity, and individual characteristics were preserved, demonstrating the robustness of microbiomes extracted from FIT tubes. However, some variations were noted, such as increased amounts of collagenase-producing bacteria from 0.2 to 0.6% to 1.7-2.6% in samples stored at +20 °C for 4-10 days. Despite unsupervised and varying sampling and storage conditions, the fecal 16S rRNA microbiomes remained representative and robust. These findings support the usability of FIT samples for large-scale population microbiome research.},
}

Humans
*Feces/microbiology
RNA, Ribosomal, 16S/genetics
*Specimen Handling/methods
*Gastrointestinal Microbiome/genetics
Adult
*Bacteria/genetics/classification/isolation & purification
DNA, Bacterial/genetics
Male
Colorectal Neoplasms/diagnosis
Female
Early Detection of Cancer
*Microbiota
Middle Aged

@article {pmid40707505,
year = {2025},
author = {Verdoodt, F and Hesta, M and Goossens, E and Van Immerseel, F and Molina, J and Van Ham, L and Vanhaecke, L and Hemeryck, LY and Bhatti, SFM},
title = {The fecal metabolome and microbiome are altered in dogs with idiopathic epilepsy compared to healthy dogs.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27024},
pmid = {40707505},
issn = {2045-2322},
support = {1S71421N//Fonds Wetenschappelijk Onderzoek/ ; 1297623N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {Animals ; Dogs ; *Feces/microbiology/chemistry ; *Metabolome ; *Epilepsy/veterinary/metabolism/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; *Dog Diseases/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Idiopathic epilepsy (IE) is the most common chronic neurological disease in dogs, and a natural animal model for human epilepsy types with genetic and unknown etiology. The microbiota-gut-brain axis (MGBA) is a promising target for improving brain health in individuals where brain function is hampered. It's role in the pathophysiology of epilepsy remains however unclear. We aimed to identify differences in fecal metabolome and microbiome between healthy and dogs with IE. To this purpose, fecal samples of healthy (n = 39) and dogs with IE (n = 49) were metabolically profiled (n = 148 metabolites) and fingerprinted (n = 3690 features) using liquid chromatography coupled to mass spectrometry, and the bacterial phylogeny examined using 16 S rRNA sequencing. Dogs with IE were categorized as drug-resistant (DR) (n = 27) or mild phenotype (MP) (n = 22). In dogs with DR IE compared to healthy, fecal metabolites such as histamine (P = 0.022) and microbiome genera such as Escherichia-Shigella (P = 0.021) increased, associated with a proinflammatory environment. In dogs with MP IE compared to healthy, alterations associated with anti-inflammatory properties, such as increased fecal serotonin (P = 0.034) and Blautia hominis (P = 0.012) were revealed. Overall, a role for the MGBA communication in canine IE was established.},
}

Animals
Dogs
*Feces/microbiology/chemistry
*Metabolome
*Epilepsy/veterinary/metabolism/microbiology
*Gastrointestinal Microbiome
Male
Female
*Dog Diseases/microbiology/metabolism
RNA, Ribosomal, 16S/genetics

@article {pmid40707492,
year = {2025},
author = {Villette, R and Novikova, PV and Laczny, CC and Mollenhauer, B and May, P and Wilmes, P},
title = {Human gut microbiome gene co-expression network reveals a loss in taxonomic and functional diversity in Parkinson's disease.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {142},
pmid = {40707492},
issn = {2055-5008},
support = {863664//HORIZON EUROPE European Research Council/ ; 863664//HORIZON EUROPE European Research Council/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; CORE/16/BM/11333923//Fonds National de la Recherche Luxembourg/ ; },
mesh = {*Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Gene Regulatory Networks ; Metagenomics ; Gene Expression Profiling ; Male ; Female ; Aged ; Middle Aged ; },
abstract = {Gut microbiome alterations are linked to various diseases, including neurodegeneration, but their ecological and functional impacts remain unclear. Using integrated multi-omics (metagenomics and metatranscriptomics), we analyse microbiome gene co-expression networks in Parkinson's disease (PD) and healthy controls (HC). We observe a significant depletion of hub genes in PD, including genes involved in secondary bile acid biosynthesis, bacterial microcompartments (BMCs), polysaccharides transport and flagellar assembly (FA). Blautia, Roseburia, Faecalibacterium and Anaerobutyricum genera are the main contributors to these functions, showing significantly lower expression in PD. Additionally, we identify a strong correlation between BMC and FA expression, and an apparent dysregulation in cross-feeding between commensals in PD. Finally, PD also exhibits reduced gene expression diversity compared to HC, whereby higher gene expression correlates with greater diversity. We identify disruptions in gut metabolic functions, at both taxonomic and functional level, and microbiome-wide ecological features, highlighting targets for future gut microbiome restoration efforts.},
}

*Parkinson Disease/microbiology
*Gastrointestinal Microbiome/genetics
Humans
*Bacteria/classification/genetics/isolation & purification/metabolism
*Gene Regulatory Networks
Metagenomics
Gene Expression Profiling
Male
Female
Aged
Middle Aged

@article {pmid40707377,
year = {2025},
author = {Yan, MX and Wang, YQ and Shen, LJ and Zhang, Z},
title = {[Research progress on biomarkers for proficient mismatch repair/microsatellite stable colorectal cancer in the immunotherapy era].},
journal = {Zhonghua wei chang wai ke za zhi = Chinese journal of gastrointestinal surgery},
volume = {28},
number = {7},
pages = {796-803},
doi = {10.3760/cma.j.cn441530-20250226-00072},
pmid = {40707377},
issn = {1671-0274},
support = {82473237//National Natural Science Foundation of China/ ; Y-Young2022-0092//Beijing Xisike Clinical Oncology Research Foundation/ ; },
mesh = {Humans ; *Colorectal Neoplasms/genetics/therapy ; *Immunotherapy ; Microsatellite Instability ; *Biomarkers, Tumor ; B7-H1 Antigen ; *DNA Mismatch Repair ; Immune Checkpoint Inhibitors/therapeutic use ; Precision Medicine ; Mutation ; },
abstract = {Immunotherapy based on immune checkpoint inhibitor (ICI) has shown remarkable efficacy in the treatment of microsatellite instability (MSI)-high CRC. However, the monotherapy of ICI in microsatellite stable (MSS) CRC has not been satisfactory. Some patients with MSS CRC can benefit from various combination immunotherapy regimens. Identifying appropriate biomarkers to select MSS-type CRC patients who will benefit from ICI treatment prior to therapy initiation and dynamically monitoring treatment efficacy during the therapeutic course have become crucial components of precision medicine in clinical practice. This article reviews the current research status of traditional biomarkers such as tumor mutation burden (TMB) and PD-L1 expression. It also explores the latest research progress and clinical translation potential of emerging biomarkers, including POLE/POLD1 mutations, immune score, circulating tumor DNA, and gut microbiome. Furthermore, it addresses the challenges in the clinical application of biomarkers, such as the controversy over TMB cutoff values and the heterogeneity of PD-L1 expression. Finally, it outlines future research directions with the aim of providing a basis for clinical decision-making in immunotherapy and facilitating the realization of precision medicine.},
}

Humans
*Colorectal Neoplasms/genetics/therapy
*Immunotherapy
Microsatellite Instability
*Biomarkers, Tumor
B7-H1 Antigen
*DNA Mismatch Repair
Immune Checkpoint Inhibitors/therapeutic use
Precision Medicine
Mutation

@article {pmid40707147,
year = {2025},
author = {Prop, J and De Vos van Steenwijk, P and Lardenoije, CMJG and Cremers, NAJ and Morre, SA and Mongula, J},
title = {Effect of medical-grade honey (L-Mesitran) for cervical intraepithelial neoplasia II: protocol for a multicentre cohort pilot study (HONEY FOR CIN II study).},
journal = {BMJ open},
volume = {15},
number = {7},
pages = {e104585},
doi = {10.1136/bmjopen-2025-104585},
pmid = {40707147},
issn = {2044-6055},
mesh = {Female ; Humans ; *Uterine Cervical Dysplasia/virology/therapy/drug therapy ; Pilot Projects ; *Honey ; *Uterine Cervical Neoplasms/virology/therapy/drug therapy ; *Papillomavirus Infections/complications ; Adult ; Multicenter Studies as Topic ; Administration, Intravaginal ; Middle Aged ; },
abstract = {INTRODUCTION: High-grade squamous intraepithelial lesions are caused by persistent high-risk human papillomavirus (hr-HPV) infections and are subdivided into cervical intraepithelial neoplasia (CIN) lesions: CIN II (moderate) and CIN III (severe). Current treatment options for CIN II include large loop excision of the transformation zone, imiquimod and expectant management. Each treatment option has its drawbacks, and therefore, a non-invasive treatment is desirable. Preliminary evidence shows that medical-grade honey (MGH) has antiviral activity and might be able to modulate the vaginal microbiome, reduce local inflammation or directly influence the intralesional immune response within cervical tissues. Therefore, this study aims to investigate the possible effect of MGH on hr-HPV clearance and to investigate the possible underlying mechanisms contributing to the regression of CIN II lesions.

METHODS AND ANALYSIS: This study is performed in the Zuyderland Medical Centre and Maastricht University Medical Centre+. A total of 60 eligible women with newly histologically confirmed CIN II will receive MGH (L-Mesitran Soft) for intravaginal use for 6 months. The primary objective is to investigate the effect of MGH on the hr-HPV clearance after 6 months. Secondary aims are the effect of MGH on the regression of CIN II lesions, clearance of hr-HPV at 12 and 24 months and the role of the vaginal microbiome, local immune system and intravaginal inflammatory status in response to MGH. Moreover, data on quality of life, side effects and compliance will be collected.

ETHICS AND DISSEMINATION: Ethical approval from the Medical Ethics Review Committee of the Zuyderland Medical Centre Heerlen has been obtained (NL86044.096.24 on 24 April 2024). The results will be presented to researchers and healthcare professionals through conferences, meetings and publications in international journals.

TRIAL REGISTRATION NUMBER: NCT06219018.},
}

Female
Humans
*Uterine Cervical Dysplasia/virology/therapy/drug therapy
Pilot Projects
*Honey
*Uterine Cervical Neoplasms/virology/therapy/drug therapy
*Papillomavirus Infections/complications
Adult
Multicenter Studies as Topic
Administration, Intravaginal
Middle Aged

@article {pmid40707016,
year = {2025},
author = {Gang, H and Wei, J and McFarland, LV and Zahra, R and Saez, ME and Blanco-Rojo, R and Millette, M},
title = {Impact of Heyndrickxia (Bacillus) coagulans GBI-30, 6086 (BC30) probiotic on gastrointestinal function in healthy adults: a randomised controlled trial.},
journal = {Beneficial microbes},
volume = {},
number = {},
pages = {1-18},
doi = {10.1163/18762891-bja00084},
pmid = {40707016},
issn = {1876-2891},
abstract = {Many healthy people complain of functional gastrointestinal (GI) tract symptoms that do not fit diagnostic criteria for established diseases. Disrupted intestinal microbiomes are associated with these functional conditions, thus the use of beneficial bacteria shown to restore the protective microbiome may be useful. Our aims were to determine if Heyndrickxia (Bacillus) coagulans GBI-30, 6086 (BC30) would improve GI functions in healthy adults living in China and to determine its effect on the GI microbiome. Healthy adults (n = 111, 18-65 years old) with functional GI complaints were enrolled in a prospective, double-blind trial and randomised (by random number table) to either BC30 (1 × 109/day) or placebo for four weeks. Outcomes were analysed by ANOVA or the Wilcoxon tests or with mixed regression models. Functional GI symptoms improved significantly in adults given BC30 compared to placebo: increase in number of stools/week (P = 0.036), improved fecal consistency (P < 0.001) and fewer participants had constipation (P < 0.001). Four weeks of BC30 increased intestinal Bacteroides levels and reduced Clostridium, Blautia, Ruminococcus levels but did not otherwise alter the general microbiome. BC30 significantly improved GI functions in healthy adults in China, with minor modifications of the fecal microbiome and was well-tolerated. The trial was registered at ClinicalTrials.gov (NCT06644001).},
}

@article {pmid40706956,
year = {2025},
author = {Sanjeevi, N and Dreisbach, C and Peddada, S and Siega-Riz, AM and Fouladi, F and Nansel, T},
title = {Prospective associations of breastfeeding parents' postpartum dietary intake with infant gut microbiome at 6 months in the Pregnancy Eating Attributes Study.},
journal = {Journal of the Academy of Nutrition and Dietetics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jand.2025.07.005},
pmid = {40706956},
issn = {2212-2672},
abstract = {BACKGROUND: Oligosaccharides in breast milk facilitate colonization of infant gut microbiota that reduce the risk of metabolic disorders. Although diet influences human milk composition, no study to date has examined the association of breastfeeding parents' dietary intake, exclusively during the postpartum period, with infant gastrointestinal microbiome.

OBJECTIVE: To examine the relationship of postpartum diet quality of the breastfeeding parent, as measured by Healthy Eating Index-2015 (HEI-2015), with 6-month infant gut microbiota.

DESIGN: A secondary data analysis of a prospective pregnancy cohort participating in the Pregnancy Eating Attributes Study in North Carolina.

PARTICIPANTS/SETTINGS: Of 458 participants enrolled from November 2014 through October 2016, this study included 103 breastfeeding parent-infant dyads. Dietary recalls collected at 4-6 weeks and 23-31 weeks postpartum estimated diet quality. Infants were classified into one of the following groups based on their feeding exposures at 6 months: 1) breastmilk only; 2) breastmilk and solids; 3) breastmilk and formula (with/without solids).

MAIN OUTCOME MEASURES: Infant rectal swabs, collected 23-31 weeks following delivery, were used for deoxyribonucleic acid extraction and sequencing. The paired-end FASTQ files were input into Just A Microbiology System pipeline.

STATISTICAL ANALYSES: Multivariate linear models examined relationships between HEI-2015 components and abundances of infant microbial taxa in the full sample and by feeding groups.

RESULTS: In the overall sample, higher breastfeeding parents' total HEI-2015 score was associated with lower abundance of Campylobacter hominis (β = -0.0012, SE = 0.0003, p < .001, FDR q-value=0.002) and Acidaminococcus (Unclassified) (β = -0.0012, SE = 0.0003, p < .001, FDR q-value=0.002). Among infants exclusively fed breastmilk, higher HEI-2015 total protein foods score was associated with lower abundance of Streptococcus (unclassified) (β = -0.078, SE = 0.012, p < .001, FDR q-value=<0.001) and Anaerococcus tetradius (β = -0.014, SE = 0.003, p < .001, FDR q-value=0.043). Among infants fed breastmilk and solid foods, higher HEI-2015 refined grain score was associated with lower abundance of Clostridiaceae (β = -0.002, SE = 0.0004, p < .001, FDR q-value=0.013). Among infants fed breastmilk and formula, higher HEI-2015 total protein foods score was associated with lower abundance of Atopobium (Unclassified) (β = -0.01, SE = 0.004, p < .001, FDR q-value= 0.04).

CONCLUSIONS: Higher breastfeeding parents' HEI-2015 scores were associated with lower abundance of gut microbial genera that have been previously implicated in inflammation. Findings suggest the potential of the parent's dietary intake during breastfeeding to support the development of infant gut microbiome associated with favorable short- and long-term health outcomes.},
}

@article {pmid40706943,
year = {2025},
author = {Wang, B and Xie, G and Zhang, H and Zhao, Y and Sun, Y and Yuan, H and Cai, L and Li, X and Wang, W and Hu, C},
title = {Combined effects of microplastics and copper on antioxidant capacity, gut microbiome, and metabolomics of Pseudorasbora parva.},
journal = {Comparative biochemistry and physiology. Toxicology & pharmacology : CBP},
volume = {},
number = {},
pages = {110295},
doi = {10.1016/j.cbpc.2025.110295},
pmid = {40706943},
issn = {1532-0456},
abstract = {Microplastics (MPs) and metal pollutants such as copper (Cu) are common pollutants in aquatic environments worldwide, posing a potential threat to the health of aquatic organisms and ecosystems. In this study, we investigated the effects of single and combined exposures of MPs (1 mg/L) and Cu (50 μg/L) on the antioxidant capacity, histopathology, gut microbiota, and metabolomics of Pseudorasbora parva which was used as a model organism. Results showed that exposure to both Cu and MPs in combination reduced Cu accumulation in tissues, mitigating the effects of Cu-induced oxidative damage. Histopathological analysis revealed that combined exposures resulted in lower levels of tissue damage than exposure to Cu alone, as evidenced by reduced leukocyte infiltration in hepatocytes, the mitigation of intestinal mucosal damage and improved gill filament epithelial cell integrity. Gut microbial community analysis showed that higher Cu concentrations significantly increased the abundance of Fusobacteriota and Cetobacterium. Metabolomics analysis revealed that in the group exposed to both Cu and MPs, compared to the Cu group, the metabolism of nucleotides, pyrimidine and glycerophospholipids was upregulated, enhancing cellular repair and defense, while the downregulation of other pathways reduced energy expenditure and prevented reaction excess. This study demonstrated that P. parva responded to multiple pollutant stress through a complex range of metabolic regulatory mechanisms, providing novel insights into the molecular response mechanisms of aquatic organisms to the combined stress of multiple pollutants, which is of great significance for aquatic ecological risk assessments.},
}

@article {pmid40706870,
year = {2025},
author = {Søndergaard Knudsen, MJ and Jensen, FH and Cecilia Rubin, IM and Petersen, AM},
title = {Chicken or egg - the role of dysbiosis in intestinal carriage of carbapenemase-producing Enterobacterales.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2025.06.018},
pmid = {40706870},
issn = {1532-2939},
abstract = {BACKGROUND: We aimed to determine whether intestinal dysbiosis is associated with intestinal carriage of carbapenemase-producing Enterobacterales (CPE). As secondary aims, we investigated treatment with antibiotics, and hospitalisation prior to study inclusion.

METHODS: We conducted a systematic review of the PubMed, EMBASE and Cochrane databases in September 2024, and we included studies, where the authors compared microbiome analysis of CPE carriers with microbiome analysis of non-carriers.

RESULTS: Our search in the PubMed, EMBASE and Cochrane databases resulted in 1,812 records. After removing duplicates, and non-eligible records based on title and abstract screening, we managed to retrieve 67 records for full-text screening. Of these, four studies were included in the systematic review including 140 CPE carriers and 141 controls. In three studies the authors found dysbiosis in the group of CPE carriers, and in the fourth study they found a decrease in diversity in CPE carriers compared with healthy adults, however there was no decrease in diversity compared with hospitalized non-carriers.

CONCLUSION: In this systematic review, we have discovered an association between intestinal dysbiosis and intestinal carriage of CPE. Nonetheless, the potential influence of antibiotic treatment on this result cannot be dismissed.},
}

@article {pmid40706730,
year = {2025},
author = {Iacucci, M and Nardone, OM and Ditonno, I and Capobianco, I and Pugliano, CL and Maeda, Y and Majumder, S and Zammarchi, I and Santacroce, G and Ghosh, S},
title = {Advancing Inflammatory Bowel Disease-driven Colorectal Cancer Management: Molecular Insights and Endoscopic Breakthroughs Towards Precision Medicine.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2025.06.035},
pmid = {40706730},
issn = {1542-7714},
abstract = {Colorectal cancer (CRC) is a serious complication of inflammatory bowel disease (IBD), significantly contributing to increased mortality and healthcare burden. While advances in IBD management have led to a decline in CRC incidence, it remains a major clinical concern. Recent breakthroughs in advanced imaging, molecular diagnostics, and artificial intelligence (AI) are poised to revolutionize precision medicine in IBD-associated CRC, potentially reducing neoplastic risk and improving patient outcomes. This review explores emerging concepts in colitis-associated cancer pathogenesis, including the intricate interplay between diet, microbiome alterations, and intestinal barrier dysfunction in CRC progression. Additionally, it highlights cutting-edge diagnostic and assessment techniques, such as ultra-high magnification endoscopy, and new spatial biology platforms for assessing intestinal barrier integrity and molecular biomarkers like miRNAs and liquid biopsy. The future of IBD-related CRC management will incorporate a holistic, multi-integrated approach, combining AI-driven diagnostics, omics data integration, endoscopic and surgical innovations and nanotechnology-based therapies. This paradigm shift aims to enhance precision medicine, promoting organ-sparing approaches, improved diagnostics, and personalized cancer treatment with the potential to reduce CRC risk.},
}

@article {pmid40706714,
year = {2025},
author = {Verma, B and Kumar, N and Ashique, S and Debnath, B and Garg, A and Mishra, N and Mojgani, N and Kaurav, M and Gupta, M and Bhowmick, M and Taghizadeh-Hesary, F},
title = {Probiotics: An Adjuvant Treatment Strategy for Chronic Respiratory Diseases.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {108268},
doi = {10.1016/j.rmed.2025.108268},
pmid = {40706714},
issn = {1532-3064},
abstract = {Chronic respiratory disease is considered by reduced airflow and heightened airway inflammation, a pattern that has progressively increased in past few decades. Currently, chronic respiratory disease is considered one of the main leading causes of death worldwide. The gut-lung axis, which connects these two organs, facilitates bidirectional communication and may be influenced by microbiome populations in the context of disease interactions. The human microbiome, particularly in the gastrointestinal tract is thought to play a pivotal role in affecting diseases and maintaining homeostasis. Dysbiosis, defined as an imbalance in the gut microbiota, is associated with an elevated risk of lung infections. Studies have shown that modifying the gut microbiota by the use of probiotics, prebiotics, and synbiotics can reduce the duration and extent of respiratory infections. Probiotics have been observed to significantly alter serum cytokine and IgE levels in allergic conditions, as well as reduce eosinophilia in individuals with asthma. However, there has been no discernible improvement in clinical symptoms, although this approach may diminish eosinophilia in chronic obstructive pulmonary disease (COPD) patients and mitigate serum cytokine and IgE levels. Several factors such as illness severity, treatment duration, patient-specific, environmental characteristics, and treatment regimen seem to influence the effectiveness of these interventions. Research indicates that direct interaction and colonization of respiratory epithelial cells by probiotic microbes can enhance the success of intranasal probiotic delivery compared to oral administration. Although allergic rhinitis is a chronic inflammatory ailment, nasal probiotics have been utilized to address acute infections and respiratory disorders, offering a promising therapeutic avenue for a range of chronic inflammatory conditions.},
}

@article {pmid40706674,
year = {2025},
author = {Ivan, FX and Aogáin, MM and Ali, NABM and Tiew, PY and Poh, TY and Setyawati, MI and Bello, D and Demokritou, P and Ng, KW and Chotirmall, SH},
title = {Occupational exposure to printer toner-emitted nanoparticles at printing facilities influences air and airway microbiomes.},
journal = {NanoImpact},
volume = {},
number = {},
pages = {100575},
doi = {10.1016/j.impact.2025.100575},
pmid = {40706674},
issn = {2452-0748},
abstract = {Workplace exposure to printer toner-emitted nanoparticles at commercial printing facilities poses respiratory health risks to workers on the printing floor, however, its impact on environmental and airway microbiomes and how this relates to worker health remains unknown. To investigate this, we prospectively evaluated five printing centres in Singapore, collecting air samples from office areas and printing floors and airway specimens from workers stationed in office or printing floor areas. All specimens were subjected to targeted amplicon sequencing to determine bacteriome and mycobiome profiles. Relationships between nanoparticle exposure levels, air and airway microbiomes were assessed. We reveal that nanoparticle exposure at printing facilities was significantly associated with shifts in air microbiome profiles in high-exposure printing areas relative to low-exposure office areas. Microbiome correlates of indoor air chemical exposures, mainly polycyclic aromatic hydrocarbons (PAHs) and trace elements, were identified. Lung function and airway microbiomes were influenced by nanoparticle exposure where printing floor workers demonstrate reduced lung function, independent of exposure level, with airway microbiomes characterized by enrichment of Chryseobacterium, Porphyromonas and Candida. Assessment of potential air-airway microbial crossover at each site, accounting for nanoparticle exposure levels, reveals significant increases in bacterial but not fungal crossover in printing floor workers. Taken together, this study demonstrates altered environmental and airway microbiomes at commercial printing facilities and in printing floor workers. Further research is needed to assess the long-term health impacts of such exposure including the potential for microbial profiling in printing facility design and operation.},
}

@article {pmid40706658,
year = {2025},
author = {Nezamzadeh, F and Masroor, A and Esmaeilkhani, A and Bialvaei, AZ},
title = {Exploring the complex interplay: insulin resistance and gut microbiome dysbiosis in multiple sclerosis.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.07.024},
pmid = {40706658},
issn = {1873-7544},
abstract = {Multiple sclerosis (MS) is a progressive, autoimmune demyelinating disorder of the central nervous system (CNS), characterized by neurological impairments driven by complex interactions between genetic, immunological, and environmental factors. While the individual roles of insulin resistance (IR) and gut microbiome dysbiosis in MS have been explored, their synergistic interaction remains under-investigated. In this novel integrative review, we comprehensively examine the bidirectional crosstalk between IR and gut microbiota alterations, highlighting shared inflammatory and metabolic pathways; such as NLRP3 inflammasome activation, Th17/Treg imbalance, and blood-brain barrier disruption; that underpin neuroinflammation in MS. We identify emerging evidence suggesting that concurrent modulation of both IR and microbial composition may offer a more effective therapeutic strategy than targeting each independently. Furthermore, we propose a framework for personalized, microbiota-informed metabolic interventions (e.g., "probiotic-metformin combinatorial strategies"), grounded in recent findings from multi-omics studies and experimental autoimmune encephalomyelitis (EAE) models. This review aims to bridge existing knowledge gaps, provide a unified perspective on metabolic-immune-microbial interplay in MS, and stimulate new research directions toward holistic and precision medicine approaches for disease prevention and management.},
}

@article {pmid40706488,
year = {2025},
author = {Tong, Y and Wang, Y and Zhang, J and Guo, Y and Yuan, T and Chen, H and Zhang, H and Zhan, K and Zhao, L and Ma, Q and Huang, S},
title = {Comprehensive study on the impact of ginger extract on laying performance, egg quality, inflammatory responses, intestinal barrier function, and cecal microbiome and resistome in laying hens.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105448},
doi = {10.1016/j.psj.2025.105448},
pmid = {40706488},
issn = {1525-3171},
abstract = {Experimental models have been extensively used to explore the effects of ginger extract (GE) on oxidative stress and immune response. However, the influence of GE dietary supplementation on gut microbial composition, function, and the resistome in laying hens remains not fully understood. This research investigated the impact of GE supplementation on laying performance, egg quality, metabolism, inflammation, and the gut microbiome and resistome in laying hens. Thirty healthy, 35-week-old Jingfen No.6 laying hens with consistent body weight and laying rate were randomly allocated to either the control group (Con; basal diet) or the ginger extract supplementation group (Con-G; basal diet with 5 g/kg GE), each with fifteen replicates (one hen per replicate). The pre-feeding period lasted one week, followed by an eight-week trial. The results revealed that average laying rate (P = 0.051) and egg mass (P < 0.05) significantly increased, while feed conversion efficiency improved (P < 0.05) in the GE-supplemented group during the study period. Additionally, egg quality, host metabolism, serum antioxidant levels, and histological assessments of the jejunum, ileum, and cecum tissues were positively affected by GE (P < 0.05). Notably, GE supplementation significantly decreased (P < 0.05) serum pro-inflammatory cytokines (IL-6, IL-1β, and TNF-α) and increased (P < 0.05) IgA, IgG, and IL-10 levels. LEfSe analysis revealed that the relative abundance of genera such as Ligilactobacillus salivarius, Limosilactobacillus vaginalis, Butyricimonas virosa, and Limosilactobacillus alvi were significantly increased (P < 0.05) in the Con-G group. Furthermore, ginger extract significantly enhanced (P < 0.05) the production of short-chain fatty acids(including acetate, propionate, butyrate, isovalerate, valerate, and lactate) in the cecum, modulated the expression profile of antibiotic resistance genes in the intestines of laying hens, and inhibited pathogen colonization. The study concludes that ginger extract supplementation in laying hen diets improves laying performance, egg quality, host metabolism, and immune responses, positively alters gut microbiota composition and functionality, and modulates the poultry resistome. Metagenomic analysis underscores the potential of GE as a safe and effective additive.},
}

@article {pmid40706398,
year = {2025},
author = {Pérez, AE and Guillemi, EC and Abuin-Denis, L and Piloto-Sardiñas, E and Obregon, D and Pin Viso, N and Sarmiento, N and Cabezas-Cruz, A and Farber, MD},
title = {Anaplasma marginale modulates the microbiota of Rhipicephalus microplus organs involved in pathogen transmission.},
journal = {Ticks and tick-borne diseases},
volume = {16},
number = {5},
pages = {102522},
doi = {10.1016/j.ttbdis.2025.102522},
pmid = {40706398},
issn = {1877-9603},
abstract = {The cattle tick Rhipicephalus microplus is a vector for Anaplasma marginale in tropical and subtropical regions worldwide. The study of pathogen-microbiome-vector interactions at the tick organ scale is a promising area of development, unraveling control strategies for tick-borne diseases. Our study focused on how A. marginale infection affects the bacterial community within the salivary glands and ovaries of R. microplus. Engorged female ticks collected from cattle in a disease-endemic area of Argentina were further classified based on whether they were infected with A. marginale by targeting the msp1β gene through PCR diagnosis in tissue samples. We included negative control samples throughout the study. We analyzed the bacterial communities in tick tissues by sequencing the 16S rRNA V3-V4 region. Our results revealed significant differences in community composition between infected and uninfected samples. Sphingomonadaceae was identified as a predominant taxon in uninfected salivary glands and ovaries. Additionally, we constructed co-occurrence networks to study interactions within the microbial communities. It is noteworthy that A. marginale infection led to an increase in network complexity in the salivary glands, exerting the opposite effect on the ovaries. These findings reinforced the hypothesis that A. marginale impacts the microbiota of R. microplus at an organ-specific level.},
}

@article {pmid40706155,
year = {2025},
author = {Wang, YC and He, LY and Wu, HY and Qiao, LK and Huang, Z and Bai, H and Gao, FZ and Shi, YJ and Zhao, JL and Liu, YS and Ying, GG},
title = {High-risk plasmid-borne resistance genes from swine farm environments infiltrate deep soil and interact with the human gut microbiome via horizontal transfer.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139281},
doi = {10.1016/j.jhazmat.2025.139281},
pmid = {40706155},
issn = {1873-3336},
abstract = {Swine farms serve as critical reservoirs of antibiotic resistance genes (ARGs), yet the frequency of horizontal gene transfer (HGT) remains poorly understood. In this study, we explored the gene exchange within the "swine farm-human-pig" network and assessed its risks. We identified 16,612 plasmid contigs from 107 field samples, revealing a significant presence of previously uncharacterized plasmid types. Notably, 52.88 % of acquired ARGs were located on plasmids, with 71.22 % containing at least one mobile genetic element (MGE). We quantified HGTs at the microbial community level among the human gut, pig gut, and swine farm environments. Among 4687 metagenome-assembled genomes (MAGs), 3008 were involved in 11,250 HGTs. HGT linkages were most frequently identified between microbial genomes from the swine farm and the human gut microbiome. ARGs were involved in 91 HGT events, with 645 events linked to MGEs and 16 related to virulence factors, suggesting potential cross-species transmission of clinical pathogens. The detection of 32 Rank I ARGs and the identification of increased resistome risks underscore the extensive dispersion of livestock-related contaminants into more distant environmental compartments. This study elucidates the complexities of gene exchange networks in swine farm environments, underscoring the urgent need for strategies to mitigate risks associated with the antibiotic resistome.},
}

@article {pmid40706019,
year = {2025},
author = {Bui, G and Marco, ML},
title = {Impact of Fermented Dairy on Gastrointestinal Health and Associated Biomarkers.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf114},
pmid = {40706019},
issn = {1753-4887},
support = {//National Dairy Council/ ; },
abstract = {In this narrative review, we examined observational and randomized controlled trials investigating the effects of fermented dairy foods, including yogurt, fermented milk, kefir, and cheese, on gastrointestinal (GI) symptoms and/or GI biomarkers of health. Studies that recorded GI symptoms such as intestinal discomfort, flatulence, gastroenteritis, diarrhea, and constipation were included. GI health biomarkers encompassed measurements of intestinal integrity or permeability (eg, endotoxemia, zonulin, 2-arachidonoylglycerol), immune responses (eg, TNFα, IL-6, high-sensitivity CRP [hs-CRP], IFNγ, IL-1β, CCL5, TGFβ, IL-10, secretory IgA, α- and β-defensin, and LL-37), fecal microbiota, and fecal short-chain fatty acids (SCFAs). Studies on probiotic-containing fermented dairy foods were included if the primary focus was the fermented dairy food, not specific probiotic strains. Thirty-seven reports met the inclusion criteria and encompassed studies on healthy children, healthy adults, or individuals with underlying conditions. Twenty-one of these studies included fermented dairy products with probiotic strains. No study reported a harmful impact of fermented dairy on gut health. Ten studies reported no benefit of fermented dairy on GI symptoms or immune biomarkers compared with milk or when no dairy was consumed. The remaining studies described significant changes in one or more gut symptoms or biomarkers with fermented dairy intake. Improvements in GI symptoms, such as abdominal pain or discomfort, flatulence, constipation, and IBS severity, were found in most studies for which such symptoms were assessed. Reductions in intestinal inflammatory markers, specifically serum TNFα levels, were found to be associated with fermented dairy intake. In several trials, significant alterations to the gut microbiota or increased levels of fecal SCFAs following fermented dairy intake were measured, but not all of those studies incorporated clinically relevant outcomes. New investigations evaluating the impact of fermented dairy on gut health should build upon the findings of these prior studies, considering target populations, underlying health conditions, and relevant gut health end points.},
}

@article {pmid40705888,
year = {2025},
author = {Wang, G and van der Putten, WH and Klironomos, J and Zhang, F and Zhang, J},
title = {Steering plant-soil feedback for sustainable agriculture.},
journal = {Science (New York, N.Y.)},
volume = {389},
number = {6758},
pages = {eads2506},
doi = {10.1126/science.ads2506},
pmid = {40705888},
issn = {1095-9203},
mesh = {*Soil/chemistry ; *Agriculture/methods ; *Crops, Agricultural/growth & development/microbiology ; Soil Microbiology ; Rhizosphere ; Microbiota ; Climate Change ; },
abstract = {The challenge of producing food at low monetary cost comes with high environmental impacts as yield maximization by excessive fertilization and chemical pest control drive farmers away from using the natural multifunctional potential of soils. We show how the ecological concept of plant-soil feedback can be used to restore the capacity of agricultural soils to provide nutrients, suppress pathogens, and enhance crop resilience sustainably. We review how recent advances in molecular and multiomic methods, soil management, and crop diversification reduce negative and promote positive plant-soil feedback, emphasizing the need for rhizosphere microbiome engineering and soil restoration strategies. Applying nature-based plant-soil feedback principles would enhance transformation to more sustainable agricultural practices that secure food production by restoring natural soil functions, while simultaneously mitigating climate change.},
}

*Soil/chemistry
*Agriculture/methods
*Crops, Agricultural/growth & development/microbiology
Soil Microbiology
Rhizosphere
Microbiota
Climate Change

@article {pmid40705807,
year = {2025},
author = {Bobowik, K and Fachrul, M and Crenna Darusallam, C and Kusuma, P and Sudoyo, H and Febinia, CA and Malik, SG and Wells, CA and Gallego Romero, I},
title = {Whole blood transcriptomics analysis of Indonesians reveals translocated and pathogenic microbiota in blood.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0328788},
doi = {10.1371/journal.pone.0328788},
pmid = {40705807},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; Indonesia/epidemiology ; Female ; Male ; *Transcriptome ; Adult ; Gene Expression Profiling ; Malaria/epidemiology/blood/microbiology ; Middle Aged ; Plasmodium/genetics/isolation & purification ; Southeast Asian People ; },
abstract = {Pathogens found within local environments are a major cause of morbidity and mortality. This is particularly true in Indonesia, where infectious diseases such as malaria or dengue are a significant part of the disease burden. Unequal investment in medical funding throughout Indonesia, particularly in rural areas, has resulted in under-reporting of cases, making surveillance challenging. Here, we use transcriptome data from 117 healthy individuals living on the islands of Mentawai, Sumba, and the Indonesian side of New Guinea Island to explore which pathogens are present within whole blood. We identified diverse microbial taxa in RNA-sequencing data from whole blood but found no evidence of a consistent core microbiome across the Indonesian cohort. Yet, Flaviviridae and Plasmodium stood out as the most predominantly abundant taxa, particularly in samples from the easternmost island within our Indonesian dataset. The high prevalence of Plasmodium, the pathogen responsible for malaria, aligns with epidemiological data showing that the Indonesian part of New Guinea has the country's highest malaria rates. We also compare the Indonesian data to two other cohorts from Mali and UK and find a distinct microbiome profile for each group. Higher levels of dissimilarity were found between UK cohort (urban) compared to Indonesian and Malian cohorts (rural), where the former also have significantly lower within-population dissimilarity. This study provides a framework for RNA-seq as a possible retrospective surveillance tool and an insight to what makes up the transient human blood microbiome.},
}

Humans
*Microbiota/genetics
Indonesia/epidemiology
Female
Male
*Transcriptome
Adult
Gene Expression Profiling
Malaria/epidemiology/blood/microbiology
Middle Aged
Plasmodium/genetics/isolation & purification
Southeast Asian People

@article {pmid40705717,
year = {2025},
author = {Korczyńska, L and Dąbrowska, M and Kulecka, M and Olcha, P and Łoziński, T and Brązert, M and Ostrowski, J and Hennig, EE and Ciebiera, M and Zeber-Lubecka, N},
title = {Increased gut microbiota diversity in women with uterine fibroids: Insights from a pilot study on gut and reproductive tract microbiota.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0327177},
doi = {10.1371/journal.pone.0327177},
pmid = {40705717},
issn = {1932-6203},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; Pilot Projects ; *Leiomyoma/microbiology ; Adult ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Vagina/microbiology ; Feces/microbiology ; },
abstract = {Uterine fibroids (UFs) are still mysterious lesions, they are influenced by hormonal imbalances and chronic inflammation, with recent emerging evidence suggesting a role for microbiota. While gastrointestinal and vaginal microbiota in UF patients have been moderately explored, this study uniquely examines endometrial microbiota in women with UFs. Aim of this study was to investigate the microbiota composition in the uterine cavity, cervix and stool using 16S rRNA bacterial gene sequencing, alongside the concentration of bacterial metabolites in stool samples, comparing women with UFs to a control group. Results revealed no statistically significant differences in α- and β-diversity in cervical swab and endometrial tissue samples between patients with UFs and controls. However, detailed analyses highlighted the overrepresentation of Lactobacillus iners in cervical samples of patients with UFs, a species often associated with vaginal dysbiosis. Gut microbiota analysis demonstrated increased Shannon index measured α-diversity in patients with UFs, yet no differences in richness or β-diversity. While short-chain fatty acids (SCFAs) modulate inflammation and immunity, this study found no significant differences in SCFA or amino acid levels, though trends warrant further investigation. The small sample size and microbiota variability limited statistical significance, emphasizing the need for larger studies to unravel microbiota's complex role in UF pathogenesis. In conclusion, the study underscores microbiota's potential impact on gynecological health and highlights avenues for future research, including microbiome-targeted therapies for UFs and related disorders.},
}

Humans
Female
*Gastrointestinal Microbiome/genetics
Pilot Projects
*Leiomyoma/microbiology
Adult
RNA, Ribosomal, 16S/genetics
Middle Aged
Vagina/microbiology
Feces/microbiology

@article {pmid40705553,
year = {2025},
author = {Baidoo, N and Sanger, GJ},
title = {The Ageing of the Human Lower Bowel.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {86},
number = {7},
pages = {1-16},
doi = {10.12968/hmed.2024.0734},
pmid = {40705553},
issn = {1750-8460},
mesh = {Humans ; *Aging/physiology ; Constipation/physiopathology ; *Colon/physiopathology/pathology ; Gastrointestinal Motility/physiology ; Intestinal Mucosa/physiopathology ; Abdominal Pain/physiopathology ; },
abstract = {Older people suffer a greater number of disorders of the gastrointestinal tract, including chronic constipation and faecal incontinence. In this review, we examine the age-related degenerative changes that have been identified in the lower bowel of humans. Firstly, older individuals may experience less abdominal pain and a lower incidence of gut-brain disorders that are defined partly by abdominal pain (e.g., irritable bowel syndrome); the causes are unclear. Secondly, an age-dependent reduction in mucosal barrier functions may follow a decline in intestinal stem cell activity, a reduced density of tight junction proteins linking epithelial cells and a decline in mucus layer thickness. This allows antigenic and toxic material to enter the wall of the colon. Thirdly, degenerative changes within the wall of the colon occur in both the ascending and descending regions, but the ascending colon appears most vulnerable. Here, there is reduced cholinergic neuromuscular function (potentially reducing colonic motility), perhaps because of dysfunctional nerve axon transport, and associated senescence-like activity. These changes lower the 'intestinal reserve', that is the capacity of neuromuscular functions to absorb other 'life events' that affect bowel motility (e.g., changes in lifestyle or eating habits, medications that affect neuromuscular functions and diseases such as diverticulosis) without generating symptoms such as constipation. When combined, symptoms are more likely to develop.},
}

Humans
*Aging/physiology
Constipation/physiopathology
*Colon/physiopathology/pathology
Gastrointestinal Motility/physiology
Intestinal Mucosa/physiopathology
Abdominal Pain/physiopathology

@article {pmid40705167,
year = {2025},
author = {Gdanetz, K and Noel, ZA and Saville, K and Marsh, T and Scribner, KT and Trail, F},
title = {Eukaryotic Microbiome of Lake Sturgeon Eggs, and Identification of Chemical Thresholds for Infection Control.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {80},
pmid = {40705167},
issn = {1432-184X},
mesh = {Animals ; *Fishes/microbiology ; *Microbiota/drug effects ; Lakes/microbiology ; *Fish Diseases/microbiology/prevention & control/parasitology ; *Ovum/microbiology ; *Fungi/isolation & purification/classification/drug effects/genetics ; Oomycetes/drug effects/isolation & purification ; Aquaculture ; *Eukaryota/isolation & purification/classification/drug effects/genetics ; },
abstract = {Eukaryotic microorganisms are an important, but understudied, component of freshwater aquatic ecosystems, and are significant sources of mortality in early life stages of fishes in natural and aquaculture systems. The eukaryotic microbiome colonizing egg surfaces of the lake sturgeon (Acipenser fulvescens) was characterized from eggs collected in natural stream habitats and a streamside hatchery in the Cheboygan River watershed in MI, USA. The taxonomic diversity of members of the Kingdoms Fungi and Stramenopile associated with infections of lake sturgeon eggs during spawning is contributing to lake sturgeon mortality in the hatchery. Characterization of the microbial communities from deposited eggs demonstrated heavy influence of spawning location on the diversity of Pythium, an Oomycete predominating in the microbiome. The Ascomycota also had a strong and distinguishing presence, with members of the Dothidiales found only on eggs from the streamside hatchery. Aureobasidium pullulans, a ubiquitous pigmented yeast, was present in the greatest numbers of egg samples, and Helotiales were found only on samples from the Black River. Independent isolates were collected from egg surfaces and tested for chemical sensitivity to the oomicides ethaboxam and mefenoxam, which are used for control of Oomycete agricultural pathogens. Ethaboxam inhibited mycelial growth almost completely for all Saprolegnia strains tested, while mefenoxam, at 20 × strength, was largely ineffective. Water prevents the natural inactivation of mefenoxam by light, thus is not advisable in aquatic systems, where it could accumulate. Alternatively, ethaboxam may be a nonpersistent, welcome control option for these fish pathogens.},
}

Animals
*Fishes/microbiology
*Microbiota/drug effects
Lakes/microbiology
*Fish Diseases/microbiology/prevention & control/parasitology
*Ovum/microbiology
*Fungi/isolation & purification/classification/drug effects/genetics
Oomycetes/drug effects/isolation & purification
Aquaculture
*Eukaryota/isolation & purification/classification/drug effects/genetics

@article {pmid40705071,
year = {2025},
author = {Zhao, Y and Liu, X and Song, P and Chen, Q and Yang, X and Yu, W},
title = {Advances in the Relationship Between Skin Tumor Occurrence, Development, Prognosis, and the Human Microbiome.},
journal = {Current microbiology},
volume = {82},
number = {9},
pages = {408},
pmid = {40705071},
issn = {1432-0991},
mesh = {Humans ; *Microbiota ; *Skin Neoplasms/microbiology/pathology/therapy/diagnosis ; Prognosis ; Tumor Microenvironment ; Bacteria/classification/isolation & purification/genetics ; Skin/microbiology ; },
abstract = {The human microbiome, including bacteria, fungi, and viruses, is widely distributed on the skin, in the oral cavity, in the gastrointestinal tract, and is also present in tumors. It is closely associated with the occurrence, development, and treatment of skin cancers and contributes to the formation of the tumor microenvironment. This review provides a detailed overview of the composition and origin of microorganisms in different types of skin tumors, focuses on the roles and mechanisms of microbiome in skin cancer, discusses their applications in the treatment of skin tumors, and outlines future research directions.},
}

Humans
*Microbiota
*Skin Neoplasms/microbiology/pathology/therapy/diagnosis
Prognosis
Tumor Microenvironment
Bacteria/classification/isolation & purification/genetics
Skin/microbiology

@article {pmid40704918,
year = {2025},
author = {Pan, J and Tian, X and Wu, K and Ji, J and Dong, M and Sun, T and Lv, D and Yao, P and Lv, L and Yao, H},
title = {Gut microbiota-associated non-cholesterol sterol dysregulation modulates immune reconstitution during antiretroviral therapy in people living with HIV.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0140425},
doi = {10.1128/spectrum.01404-25},
pmid = {40704918},
issn = {2165-0497},
abstract = {Non-cholesterol sterol metabolism plays a crucial role in immune regulation. However, the non-cholesterol sterol profiles, its association with gut dysbiosis, and its impact on the CD4[+] T cell recovery in people living with HIV (PLWH) are yet to be elucidated. In this study, we recruited 37 PLWH and 50 healthy controls to characterize non-cholesterol sterol profiles and gut microbiota composition using targeted liquid chromatography-mass spectrometry and metagenomic analysis. Correlations between sterol profiles and immune cell subsets were assessed. In vitro peripheral blood mononuclear cell (PBMC) model was used to validate key findings. We identified a distinct dysregulation of non-cholesterol sterol metabolism in PLWH, characterized by elevated levels of cholesterol precursors and metabolites and depleted levels of plant sterols, which were linked to gut dysbiosis. Our study results highlighted Oscillibacter spp. as the key regulator of sterol metabolism. Specifically, plant sterols (e.g., brassicasterol and campesterol) were found to be associated with impaired CD4[+] T cell recovery during antiretroviral therapy (ART). These findings were validated using ex vivo PBMC models, which revealed that brassicasterol stimulates T cell abnormal activation and pro-inflammatory cytokine release, whereas lathosterol dampens immune activation and inflammation. In summary, our study highlights the interplay between gut dysbiosis and sterol dysregulation in PLWH, demonstrating that higher brassicasterol levels impair immune recovery post-ART by promoting CD4[+] T cell hyperactivation. Hence, targeting microbial sterol metabolism-through Oscillibacter spp. enrichment or plant sterol modulation-may offer novel therapeutic strategies to optimize ART outcomes by balancing immune activation and resolution.IMPORTANCEThis study is the first to integrate non-cholesterol sterol profiling with gut microbiota analysis in people living with HIV (PLWH), uncovering a unique sterol dysregulation characterized by elevated cholesterol precursors and depleted plant sterols in this population. We demonstrate that Oscillibacter spp. were associated with these metabolic shifts and that specific sterols differentially affect immune recovery: plant sterols such as brassicasterol impede CD4[+] T cell restoration by promoting hyperactivation, whereas the cholesterol derivative lathosterol mitigates inflammation and supports immune reconstitution. These insights reveal novel microbiome-sterol interactions that can be leveraged to develop targeted microbiome- and sterol-based interventions aimed at enhancing antiretroviral therapy efficacy and long-term immune health in PLWH.},
}

@article {pmid40704792,
year = {2025},
author = {Zhang, M and Zhang, C and Ramos, A and Whitaker, RJ and Whiteley, M},
title = {Conserved cross-domain protein-to-mRNA ratios enable proteome prediction in microbes.},
journal = {mBio},
volume = {},
number = {},
pages = {e0141125},
doi = {10.1128/mbio.01411-25},
pmid = {40704792},
issn = {2150-7511},
abstract = {UNLABELLED: Microbial communities are often studied by measuring gene expression (mRNA levels), but translating these data into functional insights is challenging because mRNA abundance does not always predict protein levels. Here, we present a strategy to bridge this gap by deriving gene-specific RNA-to-protein conversion factors that improve the prediction of protein abundance from transcriptomic data. Using paired mRNA-protein data sets from seven bacteria and one archaeon, we identified orthologous genes where mRNA levels poorly predicted protein abundance, yet each gene's protein-to-RNA ratio was consistent across these diverse organisms. Applying the resulting conversion factors to mRNA levels dramatically improved protein abundance predictions, even when the conversion factors were obtained from distantly related species. Remarkably, conversion factors derived from bacteria also enhanced protein prediction in an archaeon, demonstrating the robustness of this approach. This cross-domain framework enables more accurate functional inference in microbiomes without requiring organism-specific proteomic data, offering a powerful new tool for microbial ecology, systems biology, and functional genomics.

IMPORTANCE: Deciphering the biology of natural microbial communities is limited by the lack of functional data. While transcriptomics enables gene expression profiling, mRNA levels often fail to predict protein abundance, the primary indicator of microbial function. Prior studies addressed this by calculating RNA-to-protein (RTP) conversion factors using conserved protein-to-RNA (ptr) ratios across bacterial strains, but their cross-species and cross-domain utility remained unknown. We generated comprehensive transcriptomic and proteomic data sets from seven bacteria and one archaeon spanning diverse metabolisms and ecological niches. We identified orthologous genes with conserved ptr ratios, enabling the discovery of RTP conversion factors that significantly improved protein prediction from mRNA, even between distant species and domains. This reveals previously unrecognized conservation in ptr ratios across domains and eliminates the need for paired proteomic data in many cases. Our approach offers a broadly applicable framework to enhance functional prediction in microbiomes using only transcriptomic data.},
}

@article {pmid40704791,
year = {2025},
author = {Reasoner, SA and Francis, J and Hadjifrangiskou, M},
title = {The urinary microbiome: the next frontier of bacterial ecology.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0010525},
doi = {10.1128/jb.00105-25},
pmid = {40704791},
issn = {1098-5530},
abstract = {The human urinary tract, once presumed to be sterile, has emerged as a new frontier of microbial ecology. Recent advancements in high-throughput sequencing technologies have revealed the complexity and diversity of microbial communities that reside within the urinary tract. This mini-review discusses the prominent bacteria identified in the urinary microbiome and their correlations with various urologic conditions. This review serves to summarize the current state of urobiome research and chart a path for ongoing discovery. Additionally, we address the methodological challenges in urinary microbiome research, emphasizing the need for standardization in study protocols and the refinement of bioinformatics tools. We highlight that although differences in urobiome composition have been described for various urologic diseases. Similarly, the pathophysiologic source and consequences of those differences remain uncertain. We outline the steps to move urobiome research from descriptive to mechanistic studies, emphasizing rigorous study design, integrating multi-omics approaches, and developing robust model systems for experimental investigation. Finally, we outline critical questions for future investigation aimed at elucidating the intricate connections between the urinary microbiome and host health.},
}

@article {pmid40704596,
year = {2025},
author = {Zhang, X and Pu, R and Zhang, C and Zhan, M and Chen, L and Ma, L and Chen, H},
title = {Engineered Probiotic Hydrogel Alleviates Vaginitis via Antimicrobial and Anti-inflammatory Pathways.},
journal = {ACS applied bio materials},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsabm.5c00766},
pmid = {40704596},
issn = {2576-6422},
abstract = {Vulvovaginal candidiasis (VVC), primarily caused by Candida albicans, is a prevalent infection that presents significant clinical challenges. Current antifungal treatments have limitations, including a narrow antimicrobial spectrum and a lack of anti-inflammatory effects. To address these limitations, we genetically modified Bacillus subtilis to produce high-molecular-weight hyaluronic acid (HMHA) for sustained local delivery of antimicrobial peptides (AMP) and HMHA at the infection site. The engineered Bacillus subtilis (B. sub@HMHA) hydrogel exhibited both antifungal and vaginal microbiome-modulating activities. Specifically, AMP effectively inhibited the growth of fungi and bacteria, while HMHA modulated local inflammatory responses, improving the vaginal microenvironment. By targeting both the infection and chronic inflammation, this probiotic hydrogel may help reduce recurrence rates and promote tissue repair, offering a promising alternative therapy for VVC.},
}

@article {pmid40704481,
year = {2025},
author = {Xiao, YY and Ma, YY and Zhang, YB and Chen, C and Meng, Y and Zhao, MY},
title = {Advances in Influencing Mechanisms and Therapeutic Effects of Bacteriophages on Cancer.},
journal = {Zhongguo yi xue ke xue yuan xue bao. Acta Academiae Medicinae Sinicae},
volume = {47},
number = {3},
pages = {470-477},
doi = {10.3881/j.issn.1000-503X.16282},
pmid = {40704481},
issn = {1000-503X},
mesh = {Humans ; *Neoplasms/therapy ; *Bacteriophages ; *Phage Therapy ; Microbiota ; },
abstract = {Cancer brings about an enormous threat to human health,making the exploration of its mechanisms and therapeutic strategies a current focal point and challenge in research.Bacteriophages are integral components of the human microbiome,and studies have shown their influences on tumor growth and metastasis and their pivotal role in cancer treatment.This article elucidates the mechanisms by which bacteriophages impact the occurrence and development of cancer from their interactions with cancer cells,effects on bacteria,and influence on the immune system.Additionally,it explores bacteriophage-based strategies in cancer treatment and their potential in this field.This article aims to bring new thoughts and insights to the research in this field.},
}

Humans
*Neoplasms/therapy
*Bacteriophages
*Phage Therapy
Microbiota

@article {pmid40704429,
year = {2025},
author = {Mercer, SD and McBain, AJ and O'Neill, C},
title = {The Skin Microbiome, Microbial Metabolites and the Epidermal Response to Ultraviolet Radiation-Towards Next Generation Suncare.},
journal = {Experimental dermatology},
volume = {34},
number = {7},
pages = {e70142},
doi = {10.1111/exd.70142},
pmid = {40704429},
issn = {1600-0625},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
mesh = {Humans ; *Ultraviolet Rays/adverse effects ; *Microbiota/radiation effects ; *Skin/microbiology/radiation effects/metabolism ; Animals ; *Epidermis/radiation effects/metabolism/microbiology ; Mice ; Skin Microbiome ; },
abstract = {Ultraviolet radiation (UVR) presents one of the greatest challenges to human skin, with numerous studies documenting its effects on skin physiology. Recently, growing recognition of the microbiome's crucial role in skin health has led to investigations on how UVR influences skin-microbiome interactions. Research in mice suggests that the microbiome plays a key role in regulating the skin's response to UVR, impacting inflammation, immune function, and keratinocyte differentiation. These effects may be mediated by microbial metabolites (MM), yet the impact of UVR on microbial metabolism and its subsequent effects on skin health remains poorly understood. Some studies suggest that UVR exposure may modify the composition of the microbiome, which could, in turn, alter the microbial metabolome. This viewpoint reviews the current literature regarding the interplay between the skin, its microbiome, and UVR, and speculates on how UVR-induced changes to microbial composition and metabolism might affect skin health. Furthermore, future areas of research that should be considered and the potential of MM in next generation suncare, cosmetics and therapeutics will be highlighted.},
}

Humans
*Ultraviolet Rays/adverse effects
*Microbiota/radiation effects
*Skin/microbiology/radiation effects/metabolism
Animals
*Epidermis/radiation effects/metabolism/microbiology
Mice
Skin Microbiome

@article {pmid40704428,
year = {2025},
author = {Wu, F and Tilbrook, A and Maloney, SK and Blache, D},
title = {The intricate relationship between stress and animal welfare: from historical perspective to new avenues.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.70057},
pmid = {40704428},
issn = {1469-185X},
support = {KYCX24_3808//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; //International Academic Exchange Fund for Graduate Students of Yangzhou University, Jiangsu, P.R. China/ ; },
abstract = {We discuss the intricate relationship between the evolution of the concept of stress and the development of the concept of animal welfare. After a brief review of the main concepts of animal welfare, we analyse important steps in the evolution of the concept of stress, starting from the mechanistic approach of the General Adaptation Syndrome to the recent integrative allostatic theory. We show how, over time, each concept of stress has informed the development of the concept of animal welfare. We discuss the role of emotions and affective states in the response of animals to challenges and how psychological stress is integral to the welfare of animals. Lastly, we discuss briefly the potential role of the gut-brain axis in both the concept of stress and the concept of welfare.},
}

@article {pmid40704320,
year = {2025},
author = {Yin, H and Qiu, Y and Gan, C and Zhou, Y and Chen, T and Liang, M},
title = {The association between a dietary index for the gut microbiota and frailty in older adults: emphasising the mediating role of inflammatory indicators.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1562278},
pmid = {40704320},
issn = {2296-861X},
abstract = {BACKGROUND: The dietary index for the gut microbiota (DI-GM) is a novel indicator of gut microbiome health, and its association with frailty remains unknown.

METHODS: We recruited participants from the 2007-2020 National Health and Nutrition Examination Survey (NHANES). Restricted cubic splines (RCSs) and multifactorial logistic regression were employed to investigate the relationship between the DI-GM and frailty. A mediation analysis was conducted to evaluate the mediating role of inflammatory markers. Stratification and sensitivity analyses were performed to evaluate the consistency of this association.

RESULTS: A total of 4,578 eligible individuals were screened, with a frailty prevalence of 35.50%. After adjusting for all of the covariates, each unit increase in the DI-GM was associated with a 6% decrease in the prevalence of frailty (OR = 0.94; 95% CI: 0.89, 0.99; p = 0.020). Furthermore, participants in the highest tertile of the DI-GM were significantly less likely to be frail than were those in the lowest tertile (OR = 0.70; 95% CI: 0.53, 0.91; p = 0.008). Mediation analysis revealed that inflammatory biomarkers significantly mediated the association between the DI-GM and frailty, with percentages of 16.47% for the neutrophil-to-lymphocyte ratio (NLR), 14.59% for the systemic inflammation response index (SIRI), and 11.13% for the systemic immune-inflammation index (SII). This negative relationship remained robust across subgroups and in the sensitivity analyses.

CONCLUSION: An elevated DI-GM, which reflects a healthier microbiota state, was associated with a reduced prevalence of frailty. This relationship was partially mediated through inflammatory biomarkers.},
}

@article {pmid40704094,
year = {2025},
author = {Chawla, M and Lavania, M and Sahu, N and Banerjee, D and Singh, N and Lal, B},
title = {In-situ bio-stimulation for enhanced biological methane production and its effect on the microbiome of CBM wells in Raniganj block, India.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1571653},
pmid = {40704094},
issn = {2296-4185},
abstract = {Microbially enhanced coalbed methane production (MeCBM) is a way towards translation of the recent momentum of the high demand for renewable energy into operational capacity. The present study demonstrates the enhancement of biogenic methane in coalbed methane (CBM) wells of an Indian coal reservoir via in-situ biostimulation. A laboratory-scale strategy was previously developed to understand and enhance the microbial processes for the bioconversion of coal to methane before transferring it to the field. The quantitative measurement of gas production after the industrial-scale microbial stimulation job carried out at the EOGEPL Raniganj block indicated upto a four-fold enhancement in methane production, with the best results observed in Well-B, from a baseline production of 117.04 standard cubic meters per day (scmd) to 461.38 scmd, followed by Well-E, with an increase from 210.93 scmd to 385.19 scmd, and Well-C, with an increase from 514.22 scmd to 670.22 scmd. Molecular and isotopic compositions of the gases collected by post-nutrient injection have been studied and the results indicate the occurrence of secondary microbial gas. The 16s rRNA amplicon sequencing analysis of formation water samples post-nutrient injection, and its comparison with previously published pre-injection microbial community analysis gives an insight into the impact of the microbial stimulation on the indigenous microbiome of the CBM wells. The present study provides a framework for understanding the effects of in-situ biostimulation via nutrient amendment in a coal reservoir. Further, the findings of the study will help to implement methane enhancement strategy via biostimulation on a wider range of coal fields to enhance its commercial potential.},
}

@article {pmid40703984,
year = {2024},
author = {Lee, HA},
title = {Pathogenesis and management of metabolic dysfunction-associated steatohepatitis-related hepatocellular carcinoma: a narrative review.},
journal = {Ewha medical journal},
volume = {47},
number = {4},
pages = {e65},
pmid = {40703984},
issn = {2234-2591},
abstract = {Metabolic dysfunction-associated steatohepatitis (MASH) is increasingly recognized as a leading cause of hepatocellular carcinoma (HCC), the third-leading cause of cancer mortality worldwide, driven by the global obesity epidemic. Projected to become the primary cause of HCC by 2030, MASH-HCC presents unique clinical challenges. This review examines its clinical management, including surveillance strategies and treatment advances, and discusses prospects to overcome existing challenges. MASH-HCC accounts for 10%-20% of HCC cases, particularly in Western countries, with a rising incidence due to obesity. Risk factors include cirrhosis, diabetes, obesity, alcohol, smoking, genetic polymorphisms (e.g., PNPLA3), and microbiome alterations. The pathogenesis involves fibrosis, immune dysfunction (e.g., T-cell impairment), and molecular changes. Prevention focuses on lifestyle modifications. Surveillance in patients with MASH cirrhosis is crucial but is hindered by poor ultrasound sensitivity in obese patients, necessitating alternative methods. Treatment mirrors that of other HCC types, but comorbidities and potentially reduced efficacy of immunotherapy necessitate tailored approaches. MASH is becoming the leading cause of HCC, necessitating lifestyle interventions for prevention. Improved surveillance and early detection are critical but challenging due to obesity-related factors. Treatments align with those for other HCC types, but comorbidities and potential differences in immunotherapy efficacy due to T-cell dysfunction require careful consideration. Key needs include identifying molecular drivers in non-cirrhotic metabolic dysfunction-associated steatotic liver disease, developing preventive therapies, refining surveillance methods, and tailoring treatments. Trials should specifically report MASH-HCC outcomes to enable personalized therapies. Further research is needed to understand T-cell dysfunction, optimize immunotherapies, and identify predictive biomarkers.},
}

@article {pmid40703844,
year = {2025},
author = {Annegowda, VM and Satelur, KP and Shekar, BCT and Rao, K},
title = {Detection and quantification of Fusobacterium nucleatum and Porphyromonas gingivalis in salivary samples of gutka and non-gutka users- 'A pilot study'.},
journal = {Journal of oral and maxillofacial pathology : JOMFP},
volume = {29},
number = {2},
pages = {206-211},
pmid = {40703844},
issn = {0973-029X},
abstract = {CONTEXT: Gutka, a form of smokeless tobacco, is widely consumed and has been associated with adverse oral health effects, including changes in the oral microbiome. Fusobacterium nucleatum and Porphyromonas gingivalis are prominent oral pathogens linked to periodontal diseases and oral carcinogenesis. The study aims to understand the microbial profile of gutka users by analysing salivary samples.

METHODS AND MATERIAL: This pilot study was conducted on 20 participants (Healthy individuals, gutka users with premalignant lesion and frank cancer). Unstimulated saliva samples were collected under aseptic conditions. Samples were cultured on selective media for F. nucleatum and P. gingivalis under anaerobic conditions. Colony morphology was used to identify and quantify the isolates. Statistical analysis compared the bacterial counts between the two groups. Statistical analysis T-tests and ANOVA were used.

RESULTS: Both F. nucleatum and P. gingivalis were isolated in higher proportions among gutka users. The mean colony-forming unit (CFU) count of F. nucleatum was significantly higher in gutka users compared to non-users. Similarly, P. gingivalis counts were elevated in gutka users CFU/ml) compared to non-users. The difference was statistically significant (P < 0.05).

CONCLUSION: Gutka consumption is associated with increased salivary levels of Fusobacterium nucleatum and Porphyromonas gingivalis. These findings emphasize the role of smokeless tobacco in altering the oral microbiome and its potential contribution to oral diseases.},
}

@article {pmid40703671,
year = {2025},
author = {Wang, Y and Lu, J and Dai, W and Yang, S},
title = {Jian-Pi-Yi-Shen formula improves kidney function by regulating gut microbiome in rats with chronic kidney disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1526863},
pmid = {40703671},
issn = {2235-2988},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Renal Insufficiency, Chronic/drug therapy/microbiology ; *Drugs, Chinese Herbal/pharmacology/administration & dosage ; Rats ; *Kidney/drug effects/physiopathology ; Disease Models, Animal ; Feces/microbiology ; Male ; Creatinine/blood ; Rats, Sprague-Dawley ; Metagenomics ; Medicine, Chinese Traditional ; },
abstract = {INTRODUCTION: Recent studies have underscored the role of interactions between Traditional Chinese Medicine (TCM) and the gut microbiome (GM) in mediating therapeutic effects. Jian-Pi-Yi-Shen Formula (JPYSF) has shown efficacy in ameliorating chronic kidney disease (CKD) symptoms, but its mechanisms via GM modulation remain unclear.

METHODS: In this study, 8-week-old rats were assigned to three groups after a two-week acclimation: C (normal diet for six weeks), M (adenine diet for four weeks then normal diet for two weeks), and T (same as M, with JPYSF administered during the final three weeks). Fecal samples were collected at three timepoints (T1: post-acclimation; T2: after three weeks on respective diets; T3: after three weeks of JPYSF treatment) for metagenomic sequencing. Serum creatinine (SCR) was measured at T2 and T3.

RESULTS: At T2, adenine-fed rats showed elevated SCR (C: 28.4 ± 1.5 µmol/L; M: 189.6 ± 25.8µmol/L; T: 186.4 ± 32.5µmol/L; p < 0.001). By T3, SCR decreased more in T (86.0 ± 14.9µmol/L) than in M (119.6 ± 16.3µmol/L; p = 0.012), with C remaining stable (30.8 ± 4.4µmol/L). Adenine feeding induced significant GM shifts, evidenced by increased Aitchison distance (p < 0.01) and altered co-abundance interaction groups (CIGs): CIG3, 6, 9, 10 increased; CIG1, 2, 4, 12 decreased (all p < 0.05). After JPYSF treatment, only CIG4 significantly rebounded (T3 vs. M, p = 0.0079), and T3-T1 dissimilarity was lower in T than M (p < 0.05). SCR levels were significantly lower in T than M after returning to a normal diet, suggesting a renoprotective effect of JPYSF. Co-occurrence analysis linked SCR positively with toxin-associated CIGs (CIG3, 6, 7, 9, 10) and pathways (purine metabolism, toluene degradation), and negatively with CIG4.

DISCUSSION: These results demonstrate that JPYSF lowers SCR and selectively modulates GM modules, particularly CIG4, which inversely correlates with uremic toxin-producing pathways, suggesting improved renal function and specific gut microbiota modulation in CKD rats.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Renal Insufficiency, Chronic/drug therapy/microbiology
*Drugs, Chinese Herbal/pharmacology/administration & dosage
Rats
*Kidney/drug effects/physiopathology
Disease Models, Animal
Feces/microbiology
Male
Creatinine/blood
Rats, Sprague-Dawley
Metagenomics
Medicine, Chinese Traditional

@article {pmid40703572,
year = {2025},
author = {Banks, WA},
title = {Synergies from a distance: Inspirations from the struggles of Dr James M Krueger.},
journal = {Neurobiology of sleep and circadian rhythms},
volume = {18},
number = {Suppl},
pages = {100114},
pmid = {40703572},
issn = {2451-9944},
abstract = {In this article for Dr Krueger's Festschrift, I trace how his early career influenced many aspects in the fields of sleep, neuroimmunology, and the microbiome. Mostly, however, I trace how his career and interests intertwined with those of Abba J. Kastin and mine and how he exerted a profound influence on the direction of our studies. Dr. Krueger, while developing his career as a sleep researcher, encountered resistance to his work that required two major paradigm shifts: 1) that bacterial products could affect sleep and 2) that small peptides can cross the blood-brain barrier (BBB) in sufficient amounts to affect brain functioning. Dr Kastin had also shown that small peptides administered peripherally could affect brain function and postulated that this was because they could cross the BBB. Our efforts to determine whether peptides could or could not cross the BBB were bolstered by Dr Krueger's exemplary struggles.},
}

@article {pmid40703518,
year = {2025},
author = {Wang, Z and Feng, S and Yao, X and Zhao, R and Li, Y and Zheng, M and Li, Z and Wang, Y},
title = {Molecular pathology of lymphoma and its treatment strategies: from mechanistic elucidation to precision medicine.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1620895},
pmid = {40703518},
issn = {1664-3224},
mesh = {Humans ; *Precision Medicine/methods ; *Lymphoma/therapy/genetics/pathology/etiology/diagnosis ; Tumor Microenvironment ; Mutation ; Biomarkers, Tumor/genetics ; Epigenesis, Genetic ; Animals ; },
abstract = {Lymphoma is a highly heterogeneous hematologic malignancy characterized by intricate molecular and pathological mechanisms. Key mechanisms contributing to its complexity include malignant clonal evolution driven by somatic mutations, epigenetic modifications affecting gene regulation and cellular behavior, and dynamic tumor microenvironment remodeling. These factors collectively undermine the efficacy of conventional therapeutic strategies. Differences in the molecular mechanisms of different subtypes lead to heterogeneity in treatment response and recurrence of drug resistance. Current and future investigative priorities emphasize molecular stratification, precision diagnosis and therapeutic strategies, advancement of novel diagnostic tools, and the implementation of artificial intelligence (AI) for integrative analysis of high-dimensional biological data. Moreover, emerging areas such as microbiome-targeted interventions are being explored to improve clinical outcomes and support the evolution of precision oncology in lymphoma treatment.},
}

Humans
*Precision Medicine/methods
*Lymphoma/therapy/genetics/pathology/etiology/diagnosis
Tumor Microenvironment
Mutation
Biomarkers, Tumor/genetics
Epigenesis, Genetic
Animals

@article {pmid40703452,
year = {2025},
author = {Park, SY and Lee, YQ and Kim, D and Sung, DK and Kim, KS and Lee, JS and Cho, JY and Lee, W and Sung, SI and Lee, DY},
title = {Deciphering dynamic antibiotics-microbiome-metabolome interactions in preterm infants using systems biology.},
journal = {iScience},
volume = {28},
number = {8},
pages = {113038},
pmid = {40703452},
issn = {2589-0042},
abstract = {Preterm infants are frequently administered antibiotics to prevent infections, yet their impact on the developing gut microbiota and metabolome remains complex and clinically significant. To systematically assess these effects, we analyzed longitudinal stool samples from 54 extremely- and very-low-birthweight infants by integrating clinical data, 16S rRNA-based microbiome profiling, targeted metabolomics, and community-scale metabolic modeling. Antibiotic exposure disrupted microbial diversity, depleted beneficial taxa, and altered metabolites such as short-chain fatty acids (SCFAs) and bile acids. Class-specific antibiotic effects were observed, with cephalosporins promoting Staphylococcus dominance and potentially reducing bile acid diversity. Necrotizing enterocolitis (NEC) samples showed SCFAs depletion and enrichment of antibiotic-resistant genera. In silico models further identified microbial contributors to SCFAs production and recapitulated metabolite trends. These findings demonstrate how antibiotic regimens can perturb the neonatal gut ecosystem and highlight the need for precision antibiotic stewardship to preserve microbiome-derived metabolic functions and reduce disease risk in preterm infants.},
}

@article {pmid40703243,
year = {2025},
author = {Zhu, J and Fu, Y and Olovo, CV and Xu, J and Wu, Q and Wei, W and Jiang, K and Zheng, X},
title = {The influence of gut microbiota on the gut-brain-kidney axis and its implications for chronic kidney disease.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1535356},
pmid = {40703243},
issn = {1664-302X},
abstract = {The gut-brain-kidney axis represents a dynamic interplay among the gut microbiota, renal function, and neurological processes, emerging as a critical factor in chronic kidney disease (CKD) pathophysiology. This paper reviews recent data on the mechanisms and pathways that integrate gut-brain-kidney signaling and communication, advances in our understanding of this axis, and potential diagnostic and prognostic biomarkers and interventions for CKD. Literature search was conducted on PubMed, Scopus, Web of Science, and Embase using a combination of the keywords gut microbiota, gut microbiome, gut-brain axis, gut-kidney axis, gut-brain-kidney axis, chronic kidney disease, dysbiosis, therapy, metabolites, and neuroinflammation." Relevant studies were selected and synthesized in this narrative review. Gut dysbiosis, characterized by microbial composition and function alterations, contributes to systemic inflammation and metabolic imbalances, exacerbating CKD progression. Uremic toxins such as indoxyl sulfate and p-cresyl sulfate, derived from microbial metabolism, impair kidney function and disrupt neurocognitive health via oxidative stress and neuroinflammation, highlighting the interconnectedness of these systems. Recent advances in high-throughput sequencing and metabolomics have elucidated mechanisms linking gut microbiota and associated metabolites to kidney and brain health, revealing the role of microbial diversity and metabolite profiles in disease outcomes. Studies demonstrate that probiotics, prebiotics, and dietary interventions targeting the gut microbiota can modulate systemic inflammation and reduce uremic toxin levels, offering therapeutic potential. Understanding the bidirectional signaling within the gut-brain-kidney axis opens avenues for novel biomarkers and interventions in CKD management.},
}

@article {pmid40703238,
year = {2025},
author = {Rangasamy, K and Saleh, AM},
title = {Bio-priming of tomato seedlings with bacterial consortium against Fusarium oxysporum: a study on morphological parameters and molecular profiling.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1606896},
pmid = {40703238},
issn = {1664-302X},
abstract = {Soil-borne diseases significantly threaten global crop production, resulting in substantial economic losses. Among these, Fusarium oxysporum, a major pathogen responsible for wilt in the root zones, severely affects tomato (Solanum lycopersicum), a widely consumed yet vulnerable vegetable. Conventional management strategies rely on fungicides and synthetic chemicals, which pose environmental and health risks, prompting the exploration of safer alternatives such as plant growth-promoting rhizobacteria (PGRP). In this study, we investigated the efficacy of two bacterial isolates, Pseudomonas aeruginosa VITK-1 and Burkholderia cepacia VITK-3, both individually and as a consortium, in the presence of Fusarium oxysporum under greenhouse conditions. In vitro assays revealed that the isolates inhibited Fusarium oxysporum, with rates ranging from 64.1 to 76.5%. Additionally, significant inhibition was observed against Ralstonia solanacearum, Septoria protearum (57.2%), Verticillium dahlia (88.5 to 81%), and Cercospora canescens (66.1 to 47.7%) in vitro. Both strains produced bioactive compounds against the test pathogens and formed biofilms, which enhanced plant growth and suppressed phytopathogens. Consortium treatment with Fusarium oxysporum significantly improved tomato seedlings' antioxidant activity, including superoxide dismutase (SOD), catalase (CAT), phenolic, and flavonoid content, along with enhanced physiological parameters. Gene expression analysis confirmed the up-regulation of defense-related genes, while metagenomic profiling indicated improvements in the soil microbial community under consortium treatment with Fusarium oxysporum compared to individual treatments and untreated controls. These findings underscore the potential of bacterial consortia as effective biocontrol agents that promote plant health and soil microbiome integrity.},
}

@article {pmid40703237,
year = {2025},
author = {Xu, D and Peng, C and Si, G and Xu, X and Zhao, S and You, C and Zhou, W},
title = {Soil microbiome dysbiosis and rhizosphere metabolic dysfunction drive continuous cropping obstacles of Codonopsis tangshen.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1628234},
pmid = {40703237},
issn = {1664-302X},
abstract = {Successive monocropping of Codonopsis tangshen causes continuous cropping obstacles, impairing growth, yield, and quality. To investigate the soil environmental and microbial changes caused by these obstacles, we collected both continuous cropping (C-crop) and non-continuous cropping (NC-crop) soil for analysis. We employed high-throughput sequencing, Biolog-ECO microplate, and metabolomics technology to evaluate microbial diversity, community structure, and carbon source utilization efficiency. Compared with NC-crop, C-crop decreased the yield and polysaccharide content of C. tangshen by 40.47 and 29.4%, respectively. Continuous cropping significantly altered soil physicochemical properties and metabolomes, driving distinct shifts in microbial community structure and impairing carbon utilization efficiency. Microbial carbon use efficiency was positively correlated with key soil bacteria and fungi. However, their abundance decreased significantly under continuous cropping, ultimately disrupting soil carbon cycling. Moreover, key bacterial (e.g., Flavobacterium, Lysobacter, Pseudomonas, Burkholderia) and fungal genera (e.g., Ophiosphaerella, Dactylonectria, Humicola) showed strong correlations with critical soil physicochemical properties, microbial carbohydrate metabolism, and rhizosphere metabolite profiles. The reduced abundance of these microbes disrupted soil nutrient balance and microbial activity, potentially contributing to C. tangshen continuous cropping obstacles. This study contributes to the understanding of the mechanisms underlying continuous cropping obstacles in C. tangshen and lays the foundation for developing strategies to alleviate these obstacles.},
}

@article {pmid40703235,
year = {2025},
author = {Pan, J and Huang, MD and Wang, J and Zhao, JX and Yang, B and Yang, HH and Huang, JS and Su, YL and Song, XR and Wang, WG and Bu, LD},
title = {Unraveling the microbiome-aroma Nexus: a metagenomic and volatile compound analysis of Yunnan cigars.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1597501},
pmid = {40703235},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding how microbial communities influence aroma profiles is critical to improving cigar quality. However, comparative studies examining the microbiome-aroma nexus across major cigar-producing regions remain limited.

METHODS: We integrated high-throughput metagenomic sequencing with volatile organic compound (VOC) profiling to investigate microbial community structure and aroma compounds in four Yunnan cigars and two Cuban cigars.

RESULTS: Bacillus spp. was consistently dominant across all samples, while Yunnan cigars exhibited higher microbial diversity. A total of 121 VOCs were detected, with nicotine, ylangene, δ-elemene, (R,S)-anatabine, and phenethyl alcohol identified as key aroma components. Nicotine, accounting for 29.7-55.0% of total VOC content, was positively correlated with Enterobacter and Escherichia, and negatively with Corynebacterium and Brachybacterium. Ylangene showed strong positive associations with Brachybacterium and Yaniella. After FDR correction, 26 differential VOCs were identified across cigar groups. KEGG pathway analysis revealed functional enrichment in carbohydrate, amino acid, and lipid metabolism. Principal component analysis indicated that the aroma complexity of certain Yunnan cigars, particularly YX4, approached that of Cuban cigars.

DISCUSSION: Our findings demonstrate that region-specific fermentation microbiota are intricately linked to the production of key VOCs. This work provides a scientific framework for optimizing cigar fermentation through microbial regulation and supports the potential for targeted microbial inoculation to enhance sensory quality and global competitiveness.},
}

@article {pmid40703234,
year = {2025},
author = {Lv, C and Wang, Z and Li, Z and Shi, X and Xiao, M and Xu, Y},
title = {Formation, architecture, and persistence of oral biofilms: recent scientific discoveries and new strategies for their regulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1602962},
pmid = {40703234},
issn = {1664-302X},
abstract = {Complex microbial interactions occur on the surfaces within the oral cavity, where biofilms form highly organized ecosystems composed of diverse microbial communities and their metabolic products. These biofilms, typically located on the tooth surface or within the gingival sulcus, play a crucial role in both oral and systemic health. Recent studies have significantly improved our understanding of the mechanisms of biofilm formation, their structural characteristics, and their persistence over time. However, the intricate interactions between biofilms and the host, as well as their contributions to both local (e.g., dental caries and periodontitis) and systemic conditions, remain only partially understood. This mini-review summarizes recent scientific progress on the formation, structural dynamics, and ecological functions of oral biofilms. It also highlights emerging strategies for modulating biofilm composition and activity, the regulatory systems governing these interactions, and potential directions for microbiome-based therapies in future research.},
}

@article {pmid40702575,
year = {2025},
author = {Rubio-Garcia, A and E C Luiken, R and Marcelino, I and W A Rossen, J and H van Zeijl, J and A Wagenaar, J and L Zomer, A},
title = {Antimicrobial treatment affects the microbiome and resistome of both treated and untreated rehabilitating harbour seals (Phoca vitulina).},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {77},
pmid = {40702575},
issn = {2524-4671},
support = {202085/WT_/Wellcome Trust/United Kingdom ; 202085/WT_/Wellcome Trust/United Kingdom ; },
}

@article {pmid40702553,
year = {2025},
author = {Martí-Carreras, J and Carrasco, M and Noguera-Julian, M and Francino, O and Leal, RO and Ferrer, L and Oliva, G and Molina, J and Roura, X},
title = {Effects of meglumine antimoniate and allopurinol treatment on the fecal microbiome profile in dogs with leishmaniosis.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {78},
pmid = {40702553},
issn = {2524-4671},
abstract = {BACKGROUND: The combination of meglumine antimoniate and allopurinol is considered one of the most effective treatments for canine leishmaniosis caused by Leishmania infantum. This study investigated the effects of this treatment on the gut microbiome of 10 dogs from Spain, Portugal, and Italy via fecal shotgun metagenomic sequencing over six months.

METHODS: Dogs were sampled at baseline (BL), after one month of combined treatment with meglumine antimoniate and allopurinol (M1) and after six months of allopurinol treatment (M6). Fecal samples had their total DNA extracted and sequenced by Illumina sequencing. Posteriorly, a microbiome analysis was conducted to analyze bacterial abundance, diversity and enrichment.

RESULTS: The gut microbiome of Leishmania-infected dogs (BL) is dominated by Prevotella, Collinsella, Bacteroides, and Blautia, with individual variability being the primary determinant of microbiome composition. No significant changes in alpha diversity (Shannon index, gene number) or beta diversity (Bray-Curtis dissimilarity, UniFrac distance) were detected between pre- and post-treatment time points, suggesting that treatment with meglumine antimoniate and allopurinol does not disrupt the gut microbiota. Minor trends in taxonomic shifts were noted, with slight increases in Bifidobacterium pseudocantenulatum, Collinsella tanakaei, and Slackia piriformis after treatment, but these changes were not statistically significant after correction for multiple testing. Linear discriminant analysis and multivariable modeling confirmed that the microbial community structure was resilient to treatment effects. Individual-specific microbiome differences in diversity accounted for 52% of the observed variability, underscoring the personalized nature of the gut microbiota in dogs. Importantly, no adverse microbiome disruptions were detected, even with prolonged allopurinol use.

CONCLUSIONS: This study highlights the robustness of the canine gut microbiome during antileishmanial therapy and highlights the use of meglumine antimoniate and allopurinol without compromising gut microbial diversity or health. Further studies with larger cohorts are recommended to confirm these findings and explore the functional roles of the gut microbiota in modulating immune responses in Leishmania-infected dogs.},
}

@article {pmid40702530,
year = {2025},
author = {Kanamori, D and Fujii, T and Yoshida, M and Ito, R and Sakai, A and Takahashi, H and Kuramitsu, K and Funasaka, K and Ohno, E and Hirooka, Y and Tochio, T},
title = {Oral care for intubated patients in the intensive care unit: examination of bacterial count and microbiota.},
journal = {Critical care (London, England)},
volume = {29},
number = {1},
pages = {320},
pmid = {40702530},
issn = {1466-609X},
support = {24K13251//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; Intensive Care Units/organization & administration/statistics & numerical data ; Male ; Female ; Middle Aged ; *Oral Hygiene/methods/standards ; Pneumonia, Ventilator-Associated/prevention & control ; Aged ; *Microbiota/physiology ; *Intubation, Intratracheal/adverse effects/methods ; *Bacterial Load/methods ; Mouth/microbiology ; Adult ; },
abstract = {BACKGROUND: Ventilator-associated pneumonia (VAP) after tracheal intubation is a major infectious complication in patients in the intensive care unit (ICU), with an incidence of 8-28%. Oral care in the ICU is essential; however, the presence of an intubation tube and restricted mouth opening cause complications. A healthy commensal microflora in the oral cavity resists colonization by respiratory pathogens, and poor oral hygiene may increase the risk for VAP. In this study, we examined the effectiveness of oral care on oral bacterial counts and microbial diversity in patients admitted to the ICU.

METHODS: Fifteen ICU patients were included in this study. Oral microbiome samples were collected by swabbing the surface of the tongue. Oral bacterial counts were measured at four time points: before and after oral care, both pre- and post-extubation. Additionally, microbiome analysis was conducted twice: once before oral care pre-extubation, and once before oral care post-extubation. Oral bacterial counts were assessed using a bacterial counter, and microbiome analysis was performed through 16S rRNA gene amplicon sequencing.

RESULTS: Oral bacterial counts significantly decreased after oral care at both pre- and post-extubation time points. Microbiome analysis revealed significant differences in alpha diversity pre- and post-extubation samples. Samples post extubation were less diverse.

CONCLUSIONS: This study demonstrates that oral care effectively reduces bacterial counts in ICU patients, both pre- and post-extubation. Microbiome analysis revealed shifts in microbial diversity, suggesting that the oral microbiota was disrupted during intubation. Given the risk of VAP, oral care may play an important role to prevent VAP in ICU settings.},
}

Humans
Intensive Care Units/organization & administration/statistics & numerical data
Male
Female
Middle Aged
*Oral Hygiene/methods/standards
Pneumonia, Ventilator-Associated/prevention & control
Aged
*Microbiota/physiology
*Intubation, Intratracheal/adverse effects/methods
*Bacterial Load/methods
Mouth/microbiology
Adult

@article {pmid40702391,
year = {2025},
author = {Krishnappa, C and Sahu, KP and Ashajyothi, M and Kumar, M and Reddy, B and Kumar, A},
title = {Dysbiosis of the rice leaf phyllomicrobiome induced by Magnaporthe oryzae infection: evidence from metabarcoding and microbiome imprinting.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {},
number = {},
pages = {},
pmid = {40702391},
issn = {1618-1905},
abstract = {Rice blast, caused by Magnaporthe oryzae, remains a major constraint to global rice production, typically presenting as necrotic lesions on infected leaves. To investigate the bacterial communities associated with these lesions, we employed a novel "Microbiome Imprinting-Metabarcoding" approach, which generated comprehensive microbial datasets (203.34 Mb) from two blast-infected rice cultivars, aromatic Pusa Basmati 1 (PB1) and non-aromatic VL Dhan 85. Metabarcoding analysis revealed the consistent presence of several dominant bacterial genera, including Pantoea, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pseudomonas, and Chryseobacterium, across both cultivars. Notably, bacterial diversity was reduced in blast lesions compared to healthy phylloplane tissues. Lesion samples comprised 28 genera (Shannon Diversity Index: 1.66; Chao1 richness: 326.86), whereas healthy leaves harbored 48 genera (Shannon Diversity Index: 1.98; Chao1 richness: 361.82). Linear discriminant effect size (LEfSe) analysis identified specific genera such as Bifidobacterium, Desemzia, Acidovorax, and Mucilaginibacter that were uniquely associated with the dysbiotic microbial communities in infected tissues. Core microbiome analysis further revealed ten genera shared between both cultivars, with Pantoea and Allorhizobium emerging as the most abundant. These findings offer new insights into the composition and dynamics of lesion-associated bacterial communities in rice blast and highlight potential microbial targets for the development of improved disease management strategies.},
}

@article {pmid40702285,
year = {2025},
author = {Liu, R and Zhu, Z and Zhu, Y and Lin, X and Li, H and Wang, T and Zheng, J and Li, M and Zhao, Z and Xu, Y and Lu, J and Wang, W and Ning, G and Bi, Y and Hu, W and Xu, M},
title = {Identification of gut microbiota causally associated with aging and longevity and mediation roles of the cerebrospinal fluid proteins: proteomic genetic evidence from Mendelian randomization.},
journal = {GeroScience},
volume = {},
number = {},
pages = {},
pmid = {40702285},
issn = {2509-2723},
support = {82270859//National Natural Science Foundation of China/ ; 82470887//National Natural Science Foundation of China/ ; 82088102//National Natural Science Foundation of China/ ; 91857205//National Natural Science Foundation of China/ ; 2024ZD0531501//National Science and Technology Major Project/ ; 2023ZD0508901//National Science and Technology Major Project/ ; 2023ZD0508902//National Science and Technology Major Project/ ; },
abstract = {Gut microbiota (GM) is implicated in aging biology, yet its dual regulatory role in the distinct yet interconnected processes of lifespan extension and aging remains poorly understood. This study employed genetic approaches to identify GM taxa exerting causal effects on longevity and aging and assess the mediation role of cerebrospinal fluid (CSF) proteins. We leveraged summary statistics of the GM taxa (207 taxa, 7738 participants from the Dutch Microbiome Project), the CSF proteins (7008 aptamers, 3506 participants), and the longevity and aging phenotypes (UK Biobank, Longevity Genomics, and Edinburgh DataShare) from the largest genome-wide association studies so far. We performed bidirectional Mendelian randomization (MR) to explore causal relationships between GM and longevity and aging and two mediation analyses, the two-step MR and the multivariable MR (MVMR), to discover potential mediating proteins. Nine taxa exhibited causal associations with longevity-related phenotypes, such as the Bacteroides vulgatus and Blautia. Three taxa demonstrated causal associations with aging-related phenotypes, such as Streptococcus. Among them, Streptococcus was causally associated with aging (β = 0.3310, P = 0.0019) and lifespan-shortening (β = - 0.0247, P = 0.0184), while Bacteroides vulgatus associated with aging (β = 0.3884, P = 0.0204) and lifespan-promoting (β = 0.0354, P = 0.0198). Mediation MR analysis found that CSF protein CD28 mediated the causal effects of Streptococcus on longevity (mediation proportion 11.7%, P = 0.0394). These findings establish genetic links between GM, CSF proteins, and longevity and aging-related outcomes, advancing gut-brain axis understanding while offering insights for future mechanistic exploration and clinical investigation.},
}

@article {pmid40703684,
year = {2024},
author = {Joo, SK and Kim, W},
title = {Sex differences in metabolic dysfunction-associated steatotic liver disease: a narrative review.},
journal = {Ewha medical journal},
volume = {47},
number = {2},
pages = {e17},
pmid = {40703684},
issn = {2234-2591},
abstract = {Understanding the effects of sex and sex differences on liver health and disease is crucial for individualized healthcare and informed decision-making for patients with liver disease. The impact of sex on liver disease varies according to its etiology. Women have a lower prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) than men. However, postmenopausal women face a higher risk of advanced liver fibrosis due to hormonal influences. Sex differences affect the pathogenesis of MASLD, which involves a complex process involving several factors such as hormones, obesity, and the gut microbiome. Furthermore, sex-related differences in the development of MASLDrelated hepatocellular carcinoma have been observed. The sex-specific characteristics of MASLD necessitate an individualized management approach based on scientific evidence. However, research in this area has been lacking. This article reviews the current understanding of sex differences in MASLD.},
}

@article {pmid40702063,
year = {2025},
author = {Senkus, KE and Azrad, M and Bolland, A and Park, HA and Tice, JR and Zhang, M and Liu, T and Blood, AB and Van Der Pol, W and Morrow, C and Crowe-White, KM},
title = {Functional mouth rinse containing inorganic nitrate and antioxidants bolsters the enterosalivary pathway and lowers blood pressure in Wistar rats.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26827},
pmid = {40702063},
issn = {2045-2322},
mesh = {Animals ; *Nitrates/pharmacology/administration & dosage ; *Mouthwashes/pharmacology ; Rats, Wistar ; *Blood Pressure/drug effects ; *Antioxidants/pharmacology/administration & dosage ; Male ; Rats ; Saliva/chemistry/metabolism ; Nitrites ; Chlorhexidine/pharmacology ; },
abstract = {The enterosalivary pathway generates systemic nitric oxide from dietary nitrate for vasodilation and blood pressure (BP) regulation, but standard antibacterial mouth rinses may disrupt this process. This study evaluated a bioactive mouth rinse infused with inorganic nitrate and antioxidants on mechanistic and clinical measures of the enterosalivary pathway, vascular health, and oral microbiome compared to an antibacterial mouth rinse containing chlorhexidine (CHX). Nine-week-old male Wistar rats were randomized to the bioactive or CHX rinse administered twice daily for one week. Systolic (SBP) and diastolic BP (DBP) were measured using tail cuff plethysmography. Blood and salivary nitrate and nitrite concentrations were determined by ozone-based chemiluminescence. Oral microbiome was assessed by 16S rRNA V4 gene amplicon sequencing. From baseline to week one, favorable changes in SBP (p = 0.008) and DBP (p = 0.016) were observed in the bioactive group compared to the CHX group. Blood and salivary nitrate and salivary nitrite concentrations (p < 0.05) were higher in the bioactive group. Compared to the CHX group, the bioactive group had significantly greater mean relative abundance of genera with established nitrate-/nitrite-reducing properties. Results suggest mouth rinse infused with inorganic nitrate and antioxidants favorably modulates the oral microbiome to support the enterosalivary pathway while reducing BP over one week.},
}

Animals
*Nitrates/pharmacology/administration & dosage
*Mouthwashes/pharmacology
Rats, Wistar
*Blood Pressure/drug effects
*Antioxidants/pharmacology/administration & dosage
Male
Rats
Saliva/chemistry/metabolism
Nitrites
Chlorhexidine/pharmacology

@article {pmid40701150,
year = {2025},
author = {Cho, HS and Yoo, JS and Song, X and Goh, B and Diallo, A and Lee, J and Son, S and Hwang, YS and Park, SB and Oh, SF and Kasper, DL},
title = {Structure of gut microbial glycolipid modulates host inflammatory response.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.05.016},
pmid = {40701150},
issn = {1097-4172},
abstract = {Commensals are constantly shaping the host's immunological landscape. Lipopolysaccharides found in gram-negative microbes have a terminal lipid A in their outer membrane. Here, we report that structural variations in symbiotic lipid A lead to divergent immune responses with each lipid A structure, eliciting effects distinct from those induced by classical lipid A. Certain lipid A structures can induce a sustained interferon (IFN)-β response orchestrated by Cdc42-facilitated Toll-like receptor 4 (TLR4) endocytosis and lipid droplet (LD) formation. This lipid A-directed IFN-β response is paramount for colon RORγt[+] regulatory T cell (Treg) induction while simultaneously suppressing colonic TH17 cells and controlling gut inflammation. Intriguingly, the quantitatively dominant penta-acylated lipid A species in Bacteroidetes fails to elicit an IFN-β response. Instead, a less abundant tetra-acylated lipid A species sustainably induces IFN-β, thereby contributing to RORγt[+] Treg homeostasis. Nuances in symbiont lipid A structure contribute to maintaining potent regulation of Tregs to maintain a healthy endobiotic balance.},
}

@article {pmid40701130,
year = {2025},
author = {Sun, YL and Guo, Y and Yu Wang, X and Zhang, YS and Jin, XQ and Zheng, J and Chen, Y and Cheng, X and Guo, YH and Li, XM and Gao, J and Chen, LD and Feng, XD},
title = {Elimination of gut microbiota hinders the therapeutic effect of amentoflavone on respiratory syncytial virus-induced lung inflammation injury by regulating innate immunity.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {145},
number = {},
pages = {157033},
doi = {10.1016/j.phymed.2025.157033},
pmid = {40701130},
issn = {1618-095X},
abstract = {BACKGROUND: Respiratory syncytial virus (RSV) is a major cause of bronchiolitis and pneumonia in infants and the elderly. Currently, there are no approved RSV-specific therapeutic small molecules available. Amentoflavone (AMF) is a well-known biflavone occurring in many plant spp with potential antiviral activities against RSV. However, the underlying mechanism remains unclear.

PURPOSE: In this study, we aimed to investigate the potential of AMF in treating RSV-induced lung inflammation injury, along with the mechanism underlying its effects, focusing on the roles of gut microbiota and innate immune response.

STUDY DESIGN AND METHODS: Nasal inoculation of RSV was performed on BALB/C mice to induce lung inflammation injury, followed by treatments with AMF and the positive control drug ribavirin. In addition, the mice were treated with antibiotics for 14 days to eliminate the gut microbiota and establish a model of pseudo-sterile gut, before receiving AMF drug intervention. Various techniques, including histological assays, TCID50 assays, immunofluorescence staining, immunohistochemical staining, qRT-PCR, western blotting, untargeted metabolomics, targeted metabolomics, molecular docking simulation, and molecular dynamics simulation, were utilized to determine the potential mechanisms underlying AMF's therapeutic effects in RSV-induced lung inflammation injury, as well as the role of gut microbiota in this process.

RESULTS: AMF effectively inhibited RSV replication, reduced virus titer, and alleviated RSV-induced lung inflammation injury. AMF exerted antiviral effects and protected lung tissue from RSV damage by activating innate immune signaling pathways. Specifically, AMF enhanced the RIG-I-MAVS signaling pathway, leading to increased release of type I interferons (IFNs). These type I IFNs interact with the interferon receptor (IFNAR) to induce the expression of interferon-stimulated genes (ISGs), which are crucial for inhibiting RSV replication. In addition, we found that AMF was metabolized by gut microbiota to produce desaminotyrosine (DAT), a compound that interacts with IFNAR and increases the levels of ISG products. Upon the elimination of gut microbiota, DAT levels were significantly reduced, decreasing the effectiveness of AMF in the treatment of RSV-induced lung inflammation injury. This study uniquely reveals multifaceted antiviral strategy of AMF, directly engaging the RIG-I-MAVS pathway while also utilizing gut microbiota metabolism to generate the IFNAR agonist DAT, representing a novel interplay between the compound, host immunity, and the microbiome. Furthermore, our metabolomic data suggested AMF significantly modulates host metabolic pathways, potentially contributing to the enhanced antiviral state.

CONCLUSION: The effects of AMF in treating RSV-induced lung inflammation injury are achieved through the activation of innate immune responses and modulation of host-microbiota metabolic interactions. Based on its novel mechanism involving concurrent direct immune activation and microbiota-dependent metabolic potentiation of IFN signaling, AMF demonstrates significant activity against RSV and can be considered a potential therapeutic agent. Furthermore, gut microbiota plays a crucial, mechanistically defined role in this antiviral process and is an essential component of the antiviral effect of AMF, highlighting the host-metabolism-immunity axis as a promising therapeutic target.},
}

@article {pmid40701110,
year = {2025},
author = {Cambon, MC and Xu, X and Kovács, ÁT and Gomes, SI and McDonald, JE},
title = {Synthetic microbial communities for studying and engineering the tree microbiome: challenges and opportunities.},
journal = {Current opinion in microbiology},
volume = {87},
number = {},
pages = {102636},
doi = {10.1016/j.mib.2025.102636},
pmid = {40701110},
issn = {1879-0364},
abstract = {Trees are essential to ecosystems in both natural and urban environments, yet they are increasingly threatened by abiotic and biotic stresses linked to climate change and human activities. The use of microbial-based approaches and microbiome engineering to safeguard plants and crop production is promising, but their application in trees raises specific challenges. Here, we review knowledge on the tree microbiome and outline opportunities to leverage tree-associated microbial communities. We describe the specific challenges inherent to working with tree species and highlight how Synthetic Microbial Communities (SynComs) can be used to study and engineer tree microbiomes. Finally, we propose that future research priorities include (1) developing model tree systems for experimental work, (2) obtaining tree-specific culture collections and SynComs, and (3) optimising methods for tree SynCom inoculation. Unlocking these methodological challenges will enable us to realise the potential of the tree microbiome and address global challenges in tree health and the provision of ecosystem services.},
}

@article {pmid40701105,
year = {2025},
author = {Wang, Q and Tong, M and Wang, R and Meng, Q and Zhou, Y and Shi, A and Wang, S and Liu, X and Wei, L and Chu, J and Yao, X},
title = {Silicon regulates microplastic-induced phytotoxicity and its detoxification mechanism: A plant-microbe perspective.},
journal = {Journal of hazardous materials},
volume = {496},
number = {},
pages = {139325},
doi = {10.1016/j.jhazmat.2025.139325},
pmid = {40701105},
issn = {1873-3336},
abstract = {Microplastics (MP) threaten agricultural ecosystems by altering soil properties and plant-microbe interactions. This study examined polyethylene microplastics (PE-MP) and silicon (Si) effects on kale growth, soil enzymes, and rhizosphere microbiota. PE-MP reduced kale shoot and root biomass by 11 % and 27 %, respectively, and shifted soil properties (e.g., increased pH, decreased potassium). Si increased biomass by 16 % (shoot) and 25 % (root) versus CK and alleviated PE-MP-induced enzyme inhibition. PE-MP suppressed carbon-cycle enzymes (sucrase, S-β-glucosidase) but enhanced nitrogen-cycle enzymes (urease, N-acetyl-β-D-glucosidase). Si restored sucrase and boosted alkaline phosphatase activity. PE-MP enriched stress-tolerant Proteobacteria and Actinobacteria, while Si promoted beneficial taxa (e.g., Sphingomonas) and mitigated declines in Acidobacteriota and Gemmatimonadota. Co-occurrence networks linked bacterial ASVs to plant physiology, showing Si enhances microbial interactions for nutrient cycling. Si mitigates PE-MP stress via microbial restructuring and enzyme regulation, offering strategies for crop resilience in contaminated soils.},
}

@article {pmid40701002,
year = {2025},
author = {Sun, H and Hu, Z and Li, Z and Xiong, X and Gu, T and Xu, W and Chen, L and Tian, Y and Li, G and Zeng, T and Lu, L and Shi, F},
title = {Investigating the correlation between phenotype, cecal microbiome, and serum metabolome in laying ducks with different shell strength.},
journal = {Poultry science},
volume = {104},
number = {10},
pages = {105558},
doi = {10.1016/j.psj.2025.105558},
pmid = {40701002},
issn = {1525-3171},
abstract = {Eggshell quality plays a critical role in the poultry industry, influencing both biological and economic outcomes. However, the factors determining eggshell strength in egg-laying ducks remain poorly understood. This study sought to explore phenotypic variations, gut microbiota composition, and serum metabolites in ducks with differing eggshell strengths to identify key microbial and metabolic factors affecting shell integrity. Over four weeks of continuous feeding, 525 eggs were collected over two days and assessed for quality. Ducks were ranked based on shell strength and classified into high eggshell strength (HEG) and low eggshell strength (LEG) groups, with 12 ducks selected from each group (24 total) for analysis of phenotypic traits, gut microbiota, and serum metabolomics. The results revealed that sharp apex thickness, medium zone thickness, and blunt apex thickness were significantly greater in the HEG group than in the LEG group (P < 0.01). Additionally, shell-breaking strength was markedly higher in HEG ducks (P < 0.01). The HEG group also exhibited significantly higher levels of superoxide dismutase (P < 0.01), catalase (P < 0.01), and total antioxidant capacity (P < 0.05) compared to the LEG group. Conversely, HEG ducks had significantly lower levels of malondialdehyde (P < 0.01), indicating reduced oxidative stress. Microbiological analysis of cecal contents showed higher Chao1 and Faith_pd indices in the HEG group (P < 0.05), while Goods coverage indices were elevated in the LEG group (P < 0.01). The abundances of Firmicutes_A, Desulfobacterota_I, Phocaeicola_A, and Phascolarctobacterium_A were higher in the HEG group (P < 0.05), whereas Prevotella abundance was greater in the LEG group (P < 0.05). Serum metabolomics revealed 1,099 differentially accumulated metabolites between the groups, with 198 metabolites up-regulated and 131 down-regulated in the LEG group (P < 0.05). KEGG pathway enrichment analysis identified six metabolites enriched in carbon metabolism and three in cation uptake pathways. These findings suggest that differences in eggshell quality and serum antioxidant capacity in Shanma ducks during peak laying may result from the modulation of gut microbiota and metabolites. This hypothesis is supported by the correlation between Firmicutes_A, Prevotella, and the metabolic pathways related to carbon metabolism and mineral absorption. These results provide a theoretical foundation for future duck breeding and selection efforts.},
}

@article {pmid40700711,
year = {2025},
author = {Tan, Z and Yang, C and Zhao, Y and Yang, X and Li, T},
title = {Interactional Effects of Food Macronutrients with Gut Microbiome: Implications for Host Health and Risk.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c04034},
pmid = {40700711},
issn = {1520-5118},
abstract = {Macronutrients in the diet (e.g., carbohydrates, proteins, and lipids) that are rarely absorbed in the small intestine can typically traverse to the colon where they are metabolized by the gut microbiota to produce a spectrum of beneficial or detrimental metabolites. These gut-microbiota-dependent small-molecule metabolites are subsequently absorbed by the intestinal mucosa to participate in various physiological responses. Notably, succinate as a star dicarboxylic acid metabolite stemming from microbial fermentation of nondigestible carbohydrates regulates blood glucose homeostasis by promoting intestinal gluconeogenesis while inhibiting hepatic gluconeogenesis. Furthermore, protein- or tryptophan-derived indole metabolites have emerged as a promising target for modulating neuropathic diseases. Fascinatingly, the linkage between gut microbiota and lncRNA Snhg9 introduces a novel promising dimension for modulating lipid absorption, metabolism, and storage. Ongoing advancements in elucidating the interplay between macronutrients, gut microbiota, and host health may facilitate the development of gut microbiota-directed clinical precision nutrition strategies through intake of tailored macronutrients.},
}

@article {pmid40700054,
year = {2025},
author = {Estela-Zape, JL and Sanclemente-Cardoza, V and Espinosa-Cifuentes, MA and Ordoñez-Mora, LT},
title = {Impact of Invasive Mechanical Ventilation on the Lung Microbiome.},
journal = {Advances in respiratory medicine},
volume = {93},
number = {4},
pages = {},
doi = {10.3390/arm93040023},
pmid = {40700054},
issn = {2543-6031},
support = {01-2025//Universidad Santiago de Cali/ ; },
mesh = {Humans ; *Respiration, Artificial/adverse effects/methods ; *Microbiota ; *Lung/microbiology ; COVID-19/therapy ; SARS-CoV-2 ; },
abstract = {The lung microbiota is integral to maintaining microenvironmental homeostasis, influencing immune regulation, host defense against pathogens, and overall respiratory health. The dynamic interplay among the lung microbiota emphasizes their significance in shaping the respiratory milieu and potential impact on diverse pulmonary affections. This investigation aimed to identify the effects of invasive mechanical ventilation on the lung microbiome. Materials and Methods: A systematic review was conducted with registration number CRD42023461618, based on a search of PubMed, SCOPUS, and Web of Science databases, in line with the PRISMA guidelines. To achieve this, "(mechanical ventilation) AND (microbiota)" was used as the search term, replicable across all databases. The closing date of the search was 12 March 2025, and the evidence was scored using the MINORS scale. Results: A total of 16 studies were included, with patients aged 13.6 months to 76 years, predominantly male (64.2%). Common ICU admission diagnoses requiring invasive mechanical ventilation (IMV) included pneumonia, acute respiratory failure, and COVID-19. IMV was associated with reduced lung microbiota diversity and an increased prevalence of pathogenic bacteria, including Prevotella, Streptococcus, Staphylococcus, Pseudomonas, and Acinetobacter. The most frequently used antibiotics were cephalosporins, aminoglycosides, and penicillins. IMV-induced pulmonary dysbiosis correlated with higher infection risk and mortality, particularly in pneumonia and COVID-19 cases. Factors such as antimicrobial therapy, enteral nutrition, and systemic inflammation contributed to these alterations. Conclusions: Invasive mechanical ventilation has been associated with the development of alterations in the respiratory microbiome, resulting in reduced diversity of lung microorganisms.},
}

Humans
*Respiration, Artificial/adverse effects/methods
*Microbiota
*Lung/microbiology
COVID-19/therapy
SARS-CoV-2

@article {pmid40699951,
year = {2025},
author = {Cho, S and Jung, Y and Oh, HS and Yum, J and Song, S and Jeong, J and Ha, WS and Kim, KM and Kim, WJ and Chu, MK},
title = {Oral and Gut Dysbiosis in Migraine: Oral Microbial Signatures as Biomarkers of Migraine.},
journal = {Neurology(R) neuroimmunology & neuroinflammation},
volume = {12},
number = {5},
pages = {e200437},
doi = {10.1212/NXI.0000000000200437},
pmid = {40699951},
issn = {2332-7812},
mesh = {Humans ; *Migraine Disorders/microbiology/diagnosis ; *Dysbiosis/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; Adult ; Biomarkers/analysis ; Cross-Sectional Studies ; Case-Control Studies ; Middle Aged ; *Mouth/microbiology ; Saliva/microbiology ; },
abstract = {BACKGROUND AND OBJECTIVES: Emerging evidence suggests that oral health conditions may exacerbate migraine, and saliva is a potential source of biomarkers for migraine. The 3-way interaction of the oral-gut-brain axis has been implicated in several neurologic disorders, but has rarely been studied in migraine. This study examined the oral and gut microbiomes simultaneously and identified several key oral microbes that may influence migraine.

METHODS: In this cross-sectional case-control study, participants were divided into 3 groups: episodic migraine (n = 55), chronic migraine (n = 55), and healthy control (HC) (n = 55). Demographic and clinical characteristics; lifestyle factors; and biological samples including saliva, stool, and blood were collected. Composition, function, and community type of the oral and gut microbiomes were compared among the 3 groups.

RESULTS: Oral dysbiosis was more pronounced than gut dysbiosis in the migraine groups, with 13 oral genera significantly enriched or depleted compared with HCs. The migraine groups showed increased abundance of Gemella, Streptococcus, Granulicatella, and Rothia and decreased abundance of Alloprevotella, Veillonella, Haemophilus, Selenomonas, Campylobacter, Cardiobacterium, Megasphaera, and Kingella after adjustment for demographic and lifestyle factors including diet. The enriched oral genera within the migraine groups were associated with carbohydrate metabolic pathways, whereas the depleted oral genera were associated with pathways related to nitrogen. A significant proportion of the oral microbial signatures of migraine included genera capable of reducing nitrate and/or nitrite. Some of these oral microbial signatures of migraine had a relative abundance that was positively or negatively associated with the number of headache days per 30 days and formed distinct microbial clusters in both the oral cavity and gut. Machine learning classifiers using the oral microbiome effectively classified migraine status, with an area under the receiver-operating characteristic curve of 0.83-0.88.

DISCUSSION: Our findings suggest that oral dysbiosis may be involved in the development of migraine and highlight specific oral microbes as potential diagnostic biomarkers and therapeutic targets for migraine.},
}

Humans
*Migraine Disorders/microbiology/diagnosis
*Dysbiosis/microbiology
Female
Male
*Gastrointestinal Microbiome/physiology
Adult
Biomarkers/analysis
Cross-Sectional Studies
Case-Control Studies
Middle Aged
*Mouth/microbiology
Saliva/microbiology

@article {pmid40699823,
year = {2025},
author = {Borozan, S and Fernandez, CJ and Samee, A and Pappachan, JM},
title = {Gut-Adipose Tissue Axis and Metabolic Health.},
journal = {Current issues in molecular biology},
volume = {47},
number = {6},
pages = {},
doi = {10.3390/cimb47060424},
pmid = {40699823},
issn = {1467-3045},
abstract = {The gut-adipose tissue axis plays a crucial role in metabolic health. It is a two-way communication pathway between the gastrointestinal tract and adipose tissue. This axis influences physiological processes vital for maintaining metabolic health, including energy homeostasis, lipid metabolism, and inflammation. Emerging research suggests that the gut microbiota, composed of trillions of microorganisms residing in the intestines, significantly impacts this axis by modulating host metabolism. An imbalance in the gut microbiota (dysbiosis) has been linked to obesity, insulin resistance, and other metabolic disorders. Innovative therapeutic strategies and dietary interventions aimed at modulating the gut-adipose tissue axis have shown encouraging results in improving metabolic health. A deeper critical understanding of the gut-adipose tissue axis is, therefore, essential in understanding the pathophysiology of metabolic disorders so that targeted interventions can be developed to prevent and treat these metabolic disorders. This article highlights the need for integrative approaches that consider both gastrointestinal and adipose functions in metabolic health management.},
}

@article {pmid40699813,
year = {2025},
author = {Kim, J and Jung, S and Kim, G and Kim, J and Son, B and Shin, H},
title = {Modulation of Gut Microbiota by Cacao: Insights from an In Vitro Model.},
journal = {Current issues in molecular biology},
volume = {47},
number = {6},
pages = {},
doi = {10.3390/cimb47060414},
pmid = {40699813},
issn = {1467-3045},
support = {2024ER211400//Korea National Institute of Health/ ; NRF-2022M3A9I5082349//National Research Foundation of Korea/ ; RS-2024-00358007//National Research Foundation of Korea/ ; },
abstract = {Natural products play a pivotal role in human health by exerting bioactive effects, including the modulation of the gut microbiome. Cacao, a widely consumed natural product, is rich in polyphenols and dietary fiber, which may influence microbial composition and metabolic functions. However, its effects on the gut microbiota remain poorly understood, particularly regarding inter-individual differences. This study investigated the impact of cacao on gut microbiota using an in vitro fecal incubation model with samples from healthy Korean adults. Our findings classified the gut microbiota of Korean individuals into two distinct enterotypes: Bacteroides and Prevotella. In the Bacteroides enterotype, cacao treatment significantly increased the relative abundance of beneficial bacterial genera, including Roseburia, Lachnospiraceae NK4A136, Faecalibacterium, and Agathobacter. Conversely, in the Prevotella enterotype, cacao treatment was associated with an increase in the relative abundance of Prevotella; however, the small sample size and community shifts during incubation limited the robustness of this observation. Functional predictions based on KEGG pathways further revealed enterotype-specific differences. In the Bacteroides enterotype, the cacao-treated group exhibited enhanced pathways associated with starch, sucrose, galactose, and thiamine metabolism, which was not observed in the Prevotella enterotype. These findings suggest a potential role for cacao as a gut microbiome modulator, highlighting its possible utility in microbiome-targeted dietary interventions and therapeutic strategies.},
}

@article {pmid40699562,
year = {2025},
author = {Zhang, L and Ji, M and Li, N and Yu, J and Yan, G and Di, Y and Zhang, Y and Liu, Q and Sun, L and Liu, X and Wang, Y},
title = {Synergy of secoisolariciresinol diglucoside and fructooligosaccharide in enhancement of the intestinal mucus barrier by relieving ER stress and regulating the gut microbiome.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo01526j},
pmid = {40699562},
issn = {2042-650X},
abstract = {The impairment of the intestinal barrier and the high incidence of gastrointestinal diseases can be caused by poor dietary patterns, such as long-term high-fat diets. The mucous layer, composed of mucin-2-based glycoproteins, is important for the intestinal barrier. Mucins are secreted by the goblet cells (GC), which are highly sensitive to endoplasmic reticulum (ER) stress. Therefore, promoting mucin synthesis and secretion by relieving ER stress is an effective way to enhance the intestinal mucus barrier. On the other hand, mucins are influenced by the gut microbiome. Mucin-associated bacteria can degrade mucins and then stimulate goblet cells to secrete mucin. Secoisolariciresinol diglucoside (SDG) has been reported to relieve ER stress and improve the gut barrier. As a prebiotic, fructooligosaccharide (FOS) has the potential to regulate intestinal flora. In the present study, we investigated the synergistic effect of SDG and FOS on the improvement of the intestinal mucus barrier in high-fat mice. It was found that both SDG and FOS alleviated histological damage in the colon, inhibited mRNA expression of proinflammatory cytokines, and improved the mucosal barrier. Notably, the synergistic treatment exhibited a better effect. Goblet cell differentiation was promoted, consistent with the relief of ER stress, and SDG might be superior in this process. FOS primarily regulated the gut microbiota, enriched mucus-associated bacteria, and increased the content of metabolite short-chain fatty acids (SCFAs). The simultaneous treatment displayed a synergistic effect. The results indicated that the synergistic treatment had a stronger effect on enhancing the intestinal mucus barrier from dual approaches of relieving ER stress and regulating gut microbiota. This study provides a novel viewpoint and strategy for improving intestinal health.},
}

@article {pmid40699436,
year = {2025},
author = {Ding, G and Weng, W and Feng, X and Gao, Y and Zhang, Y},
title = {Rhizosphere microbiota adaptation under blueberry cultivation: modified paddy soil versus acidic red soil.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {9},
pages = {119},
pmid = {40699436},
issn = {1572-9699},
support = {2024CSJZN1200//The Yangtze River Delta Science and Technology Innovation Community Joint Basic Research Project/ ; 2024CSJZN1200//The Yangtze River Delta Science and Technology Innovation Community Joint Basic Research Project/ ; 2024CSJZN1200//The Yangtze River Delta Science and Technology Innovation Community Joint Basic Research Project/ ; 2024CSJZN1200//The Yangtze River Delta Science and Technology Innovation Community Joint Basic Research Project/ ; 2024CSJZN1200//The Yangtze River Delta Science and Technology Innovation Community Joint Basic Research Project/ ; HXXM2022129 & HXXM2023075//Horizontal Development Project of Hefei Normal University/ ; HXXM2022129 & HXXM2023075//Horizontal Development Project of Hefei Normal University/ ; HXXM2022129 & HXXM2023075//Horizontal Development Project of Hefei Normal University/ ; HXXM2022129 & HXXM2023075//Horizontal Development Project of Hefei Normal University/ ; HXXM2022129 & HXXM2023075//Horizontal Development Project of Hefei Normal University/ ; },
mesh = {*Rhizosphere ; *Soil Microbiology ; *Blueberry Plants/microbiology/growth & development ; *Soil/chemistry ; *Microbiota ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Hydrogen-Ion Concentration ; *Adaptation, Physiological ; Phylogeny ; },
abstract = {Although rhizosphere microbiota play pivotal roles in the adaptation of blueberry to acidic soils, their adaptation to contrasting soil types remains unexplored. Herein, rhizosphere soils from modified paddy and red soil plantations were analysed via 16S sequencing, core microbiome identification and KEGG pathway mapping. These analyses revealed that modified paddy soil exhibited higher α-diversity (Shannon index: p = 0.037) than red soil. The analysis of β-diversity confirmed significant divergence between the red soil rhizosphere communities and their bulk soil counterparts (p < 0.05), whereas the modified paddy soil communities remained structurally stable. Core OTU analysis identified 96 shared taxa (18.2% of total OTUs) across soils. The red soil rhizosphere microbes prioritised energy-yielding pathways (e.g. glucose-1-phosphate and sucrose degradation) that are critical for fruit cell wall synthesis. The modified paddy soil communities favoured glycogen degradation, reflecting the existence of resource competition under acidic stress. This study aimed to characterize the rhizosphere microbiota of blueberries cultivated in two distinct acidic soil types (modified paddy soil and red soil), identify core microbiome members, and elucidate their functional adaptations, thereby emphasising the importance of tailored microbial management during soil modification strategies (e.g. paddy soil acidification) to meet plant growth requirements.},
}

*Rhizosphere
*Soil Microbiology
*Blueberry Plants/microbiology/growth & development
*Soil/chemistry
*Microbiota
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Hydrogen-Ion Concentration
*Adaptation, Physiological
Phylogeny

@article {pmid40699254,
year = {2025},
author = {Samuels, THA and Warrell, CE},
title = {Travellers' diarrhoea - solidifying our knowledgebase.},
journal = {Current opinion in infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/QCO.0000000000001131},
pmid = {40699254},
issn = {1473-6527},
abstract = {PURPOSE OF REVIEW: Travellers' diarrhoea remains one of the most common diseases amongst international travellers. However, significant uncertainty remains about the most effective strategies for its prevention and management. This review summarises recent advances in travellers' diarrhoea epidemiology, diagnostics, and management, focusing on new severity definitions, the impact of molecular diagnostics, antimicrobial resistance, and postinfectious sequelae.

RECENT FINDINGS: The incidence of travellers' diarrhoea remains substantial although much of this is attributable to mild disease. Viral travellers' diarrhoea is more frequently recognised due to the improved sensitivity of molecular diagnostics. Advances in microbiome research reveal both acute and persistent disruption to the microbiota following travellers' diarrhoea and antibiotic use. New severity definitions incorporating functional impairment offer improved clinical relevance but consensus over use remains lacking. Nonabsorptive antibiotics and probiotics show promise for treatment and prevention, but antimicrobial resistance continues to rise. Postinfectious irritable bowel syndrome (IBS) significantly impacts the recovery of some travellers' diarrhoea patients.

SUMMARY: Consensus on severity definitions is needed to support successful research into new vaccines and therapeutics. Surveillance of resistance, research into microbiome disruption and recovery, and development of vaccines and probiotics are key priorities. Better pathophysiological understanding and new intervention strategies are required to help alleviate the suffering of post-travellers' diarrhoea IBS.},
}

@article {pmid40699244,
year = {2025},
author = {Bei, Q and Zhang, J and Huang, Q and Yang, C and Li, Y and Mu, R and Shu, D and Dai, Y and Megharaj, M and He, W and Tian, H},
title = {Rhizosphere Microbiome-Root Exudate Synergy in Pteris vittata: Coordinated Arsenic Speciation and Multielement Metabolic Coupling Drive Hyperaccumulation Efficiency.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {79},
pmid = {40699244},
issn = {1432-184X},
support = {2023YFD1700102//the National Key R&D Program of China/ ; 2024NC-ZDCYL-02-14//the Key R&D Program of Shaanxi Province/ ; 2025JC-QYCX-034//Frontier Exploration Project (Innovative Exploration Category)/ ; },
mesh = {*Arsenic/metabolism ; *Rhizosphere ; *Pteris/microbiology/metabolism ; *Plant Roots/microbiology/metabolism ; *Microbiota ; Soil Microbiology ; Bacteria/metabolism/classification/genetics/isolation & purification ; *Soil Pollutants/metabolism ; Biodegradation, Environmental ; Fungi/metabolism/classification/genetics/isolation & purification ; *Plant Exudates/metabolism ; Soil/chemistry ; },
abstract = {Rhizosphere microorganisms play a pivotal role in enhancing the arsenic (As) remediation efficiency of Pteris vittata. However, the interactions among rhizosphere microorganisms, root exudates, and As, as well as their influence on As uptake by Pteris vittata at different As concentrations, remain poorly understood. This study systematically elucidates the molecular-ecological mechanisms through which Pteris vittata facilitates arsenic (As) remediation within a multidimensional interaction network. It was found that the rhizosphere microbial community was dominated by Proteobacteria, Acidobacteriota, and Ascomycota, with 44 bacterial and 10 fungal genera identified as genetically conserved core microorganisms. Microbial-mediated arsenic (As) methylation and reduction processes, coupled with metabolic pathways such as carbon fixation, sulfur oxidation, and phosphorus mineralization, contribute to the formation of an "As-multielement cycling" synergy. This synergy drives As speciation transformation and enhances plant uptake. Root exudates, such as L-phenylalanine and citric acid, enhance arsenic (As) activation and detoxification by selectively recruiting functional microbes, including Sphingomonas carrying arsC. The resulting metabolite profiles exhibit soil-specific response patterns. High As stress shifted microbial community assembly from stochastic to deterministic processes while maintaining remediation efficiency through enhanced fungal network stability (increased average connectivity). These findings reveal the dual "genetic conservation-environmental adaptation" regulatory strategy of Pteris vittata, providing both theoretical and practical foundations for designing targeted rhizosphere microecological technologies to enhance the phytoremediation of arsenic (As)-contaminated soils.},
}

*Arsenic/metabolism
*Rhizosphere
*Pteris/microbiology/metabolism
*Plant Roots/microbiology/metabolism
*Microbiota
Soil Microbiology
Bacteria/metabolism/classification/genetics/isolation & purification
*Soil Pollutants/metabolism
Biodegradation, Environmental
Fungi/metabolism/classification/genetics/isolation & purification
*Plant Exudates/metabolism
Soil/chemistry

@article {pmid40699220,
year = {2025},
author = {Baltazar, E and Leitão, R and Rodrigues, S and Figueira, D and Garcia, E and Costa, J},
title = {Monilinia fructicola as a Driver of Fungal Dysbiosis and Microbial Network Disruption in Prunus persica.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-02-25-0062-R},
pmid = {40699220},
issn = {0031-949X},
abstract = {Fungal community dynamics play a fundamental role in plant health, influencing resilience, disease progression, and ecosystem stability. Monilinia fructicola, a quarantine pathogen affecting Prunus persica, is hypothesized to drive fungal dysbiosis by altering microbial diversity, ecological interactions and functional roles. In this study, its impact on fungal community composition, trophic dynamics, and network structure was investigated using ITS metabarcoding and high-throughput sequencing of flowers and branches from infected and non-infected P. persica trees were analysed. Results showed a pathogen-induced shift, most pronounced in flowers, where M. fructicola increased richness (Chao1), diversity (Shannon), and dominance (Simpson). In wood samples, increased dominance suggested pathogen-associated ecological filtering. Network analysis demonstrated that M. fruticola disrupts fungal connectivity, leading to fragmentation of microbial interactions, reduced network complexity, and increased modularity - indicative of weakened ecological cohesion. Shifts in fungal primary lifestyles further suggested that M. fructicola accelerates tissue decomposition and induces an imbalance in functional guilds, potentially facilitating secondary infections. Taxonomic restructuring was marked by the decline of dominant genera and the emergence of stress-adapted or pathogen-associated taxa. The isolation of Epicoccum nigrum, a known biocontrol agent, highlights its potential as a nature-based solution for disease management. Overall, these findings identify M. fructicola as a driver of fungal dysbiosis in P. persica, with cascading effects on microbial function, network resilience, and plant health. Understanding these pathogen-induced shifts is essential to inform sustainable microbiome-based approaches to disease management.},
}

@article {pmid40699006,
year = {2025},
author = {Nauwynck, W and Faust, K and Boon, N},
title = {Droplet microfluidics for single-cell studies: a frontier in ecological understanding of microbiomes.},
journal = {FEMS microbiology reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsre/fuaf032},
pmid = {40699006},
issn = {1574-6976},
abstract = {Recent advances in single-cell technologies have profoundly impacted our understanding of microbial communities-shedding light on cell-to-cell variability in gene expression, regulatory dynamics and metabolic potential. These approaches have shown that microbial populations are more heterogeneous and functionally complex than previously thought. However, direct probing of single-cell physiology-arguably more ecologically relevant by focusing on functional traits such as growth, metabolic activity, and enzymatic activity-remains underexplored. Droplet microfluidics provides a practical and high-throughput approach to address this gap, allowing functional characterization of individual microbial cells within complex communities and offering new opportunities to study ecological processes at high resolution. In this review we look at the state of droplet microfluidics for single-cell microbial ecology. We revisit the fundamentals of microbial droplet workflows, we overview the current capabilities of droplet microfluidics that exist for microbial ecology and we look at the phenomena these workflows have uncovered and understanding they have generated. Finally, we integrate these capabilities to envision future droplet workflows that could enhance our understanding of single-cell physiology and discuss the fundamental limitations that go together with the droplet format.},
}

@article {pmid40698987,
year = {2025},
author = {Tong, X},
title = {Asian bat skin mycobiome maintains defense against Pseudogymnoascus destructans during hibernation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0061125},
doi = {10.1128/spectrum.00611-25},
pmid = {40698987},
issn = {2165-0497},
abstract = {Since its discovery in 2006, white-nose syndrome (WNS), caused by the fungus Pseudogymnoascus destructans, has devastated North American bat populations (W. F. Frick, J. F. Pollock, A. C. Hicks, K. E. Langwig, et al., Science 329:679-682, 2010, https://doi.org/10.1126/science.1188594). In contrast, certain Asian bats, such as Rhinolophus ferrumequinum (greater horseshoe bat), exhibit significant resistance, prompting research into the mechanisms behind this resilience. A recent study by H. Leng, A. Li, Z. Li, J. R. Hoyt, et al. (Microbiol Spectr 13:e02233-24, 2025, https://doi.org/10.1128/spectrum.02233-24) explored fungal community dynamics on R. ferrumequinum skin and in their cave environment during hibernation using ITS amplicon sequencing and ecological modeling. The authors identified Debaryomyces as a dominant, potentially protective skin-associated fungus. This work provides fresh insights into microbe-mediated resistance in bats and highlights microbiome-based strategies as a promising avenue for WNS mitigation.},
}

@article {pmid40698936,
year = {2025},
author = {Maghini, DG and Kiguchi, Y and Darling, AE and Monahan, LG and Halpern, AL and Burke, CM and Jaeger, E and Statham, A and Truong, T and Ying, K and Bruinsma, SP and Schroth, GP and Bhatt, AS},
title = {Illumina complete long read assay yields contiguous bacterial genomes from human gut metagenomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0153124},
doi = {10.1128/msystems.01531-24},
pmid = {40698936},
issn = {2379-5077},
abstract = {Metagenomics enables direct investigation of the gene content and potential functions of gut bacteria without isolation and culture. However, metagenome-assembled genomes are often incomplete and have low contiguity due to challenges in assembling repeated genomic elements. Long-read sequencing approaches have successfully yielded circular bacterial genomes directly from metagenomes, but these approaches require high DNA input and can have high error rates. Illumina has recently launched the Illumina Complete Long Read (ICLR) assay, a new approach for generating kilobase-scale reads with low DNA input requirements and high accuracy. Here, we evaluate the performance of ICLR sequencing for gut metagenomics for the first time. We sequenced a microbial mock community and 10 human gut microbiome samples with standard, shotgun 2 × 150 paired-end sequencing, ICLR sequencing, and nanopore long-read sequencing and compared performance in read lengths, assembly contiguity, and bin quality. We find that ICLR human metagenomic assemblies have higher N50 (119.5 ± 24.8 kilobases) than short read assemblies (9.9 ± 4.5 kilobases; P = 0.002), and comparable N50 to nanopore assemblies (91.0 ± 43.8 kilobases; P = 0.32). Additionally, we find that ICLR draft microbial genomes are more complete (94.0% ± 20.6%) than nanopore draft genomes (85.9% ± 23.0%; P ≤ 0.001), and that nanopore draft genomes have truncated gene lengths (924.6 ± 114.7 base pairs) relative to ICLR genomes (954.6 ± 71.5 base pairs; P ≤ 0.001). Overall, we find that ICLR sequencing is a promising method for the accurate assembly of microbial genomes from gut metagenomes.IMPORTANCEMetagenomic sequencing allows scientists to directly measure the genome content and structure of microbes residing in complex microbial communities. Traditional short-read metagenomic sequencing methods often yield fragmented genomes, whereas advanced long-read sequencing methods improve genome assembly quality but often suffer from high error rates and are logistically limited due to high input requirements. A new method, the Illumina Complete Long Read (ICLR) assay, is capable of generating highly accurate kilobase-scale sequencing reads with minimal input material. To evaluate the utility of ICLR in metagenomic contexts, we applied short-read, long-read, and ICLR methods to simple and complex microbial communities. We found that ICLR outperforms short-read methods and yields comparable metagenomic assemblies to standard long-read approaches while requiring less input material. Overall, ICLR represents an additional option for assembling complete genomes from complex metagenomes.},
}

@article {pmid40698931,
year = {2025},
author = {Salbreiter, M and Wagenhaus, A and Rösch, P and Popp, J},
title = {p-Cresol and C. difficile: A Love-Hate Story Revealed by Raman Spectroscopy.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c02927},
pmid = {40698931},
issn = {1520-6882},
abstract = {Clostridioides difficile is known to produce p-cresol, a phenolic compound with selective antimicrobial properties, which may contribute to its competitive advantage within the gut microbiome. In this study, we investigated the interaction between Clostrioides difficile and Escherichia coli in coculture to assess the role of p-cresol in modulating interspecies dynamics. Raman spectroscopy was employed as a label-free, nondestructive analytical technique to profile the molecular signatures of both species in mono- and coculture. Excitation wavelengths at 244 and 532 nm were used to enhance complementary vibrational features, including those associated with aromatic compounds like p-cresol. Our results demonstrate distinct spectral changes in coculture conditions suggesting the involvement of p-cresol and its impact on the biochemical composition of E. coli. This dual-wavelength Raman approach offers a powerful means of characterizing microbial interactions and identifying metabolic markers that may drive microbial competition and survival.},
}

@article {pmid40698890,
year = {2025},
author = {Pezzuto, JM},
title = {Perspective: Are Grapes Worthy of the Moniker Superfood?.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c05738},
pmid = {40698890},
issn = {1520-5118},
abstract = {Superfood, an au courant word in the American vernacular, refers to mainstream foods that are basically individual components of the Mediterranean diet, i.e., berries, fish, olive oil, cruciferous vegetables, legumes, etc., and perceived as "healthy." There is no regulation; the main source of information is the Internet. Blueberries and strawberries are generally featured as superior. However, when tested as a whole food in human beings, grapes modulate the gut microbiome, the metabolome and gene expression, and there are associated health benefits. Thus, based on actual scientific data, grapes have earned what should be a prominent position in the superfood family.},
}

@article {pmid40698849,
year = {2025},
author = {Siggers, JA and Sturchio, MA and Gordon, L and Mead, S and Smith, MD and Knapp, AK},
title = {Environmental Heterogeneity Imposed by Photovoltaic Array Alters Grassland Soil Microbial Communities.},
journal = {Global change biology},
volume = {31},
number = {7},
pages = {e70376},
doi = {10.1111/gcb.70376},
pmid = {40698849},
issn = {1365-2486},
support = {//Colorado State University/ ; //Graduate Degree Program in Ecology, Colorado State University/ ; 2021-68012-35898//National Institute of Food and Agriculture/ ; COL0-2019-08309//National Institute of Food and Agriculture/ ; },
mesh = {*Soil Microbiology ; *Grassland ; *Microbiota ; *Soil/chemistry ; *Solar Energy ; },
abstract = {The rapid expansion of photovoltaic (PV) energy production has generated concern over its potential ecosystem impacts. PV arrays induce unique microenvironmental conditions by altering resource availability and substantially impacting aboveground processes. However, the belowground consequences of PV development are understudied, limiting our understanding of overall ecosystem impacts. Here, we paired soil physiochemical, molecular, and functional analyses with aboveground measures to assess plant-soil-microbial responses to distinct microsites beneath a single-axis tracking PV system in a semi-arid C3 grassland. We hypothesized that each PV microsite would harbor a unique suite of soil physiochemical properties and microbiomes. We found only subtle differences in soil organic matter and pH, corresponding with aboveground productivity patterns, but other physiochemical properties remained unchanged. However, soil microbial community structure and function differed markedly across PV microsites and from a reference grassland plot. Within the array, microbial decomposition rates were highest where plant productivity and organic matter were greatest, but surprisingly lowest where soil moisture remained elevated throughout the growing season. Overall, these findings suggest that PV arrays create disparate patterns of soil microbial community structure and function, which may feedback to influence overall ecosystem functionality. Coarse measures of soil physiochemical properties, such as total carbon, may overlook key impacts of PV development.},
}

*Soil Microbiology
*Grassland
*Microbiota
*Soil/chemistry
*Solar Energy

@article {pmid40698780,
year = {2025},
author = {Stollewerk, A and Kratina, P and Sentis, A and Chaparro-Pedraza, C and Decaestecker, E and De Meester, L and Eyice, O and Govaert, L and Jones, JI and Laforsch, C and Madeira, C and Narwani, A and Oostra, V and Raeymaekers, JAM and Rossberg, AG and Schott, M and Stoks, R and van Velzen, E and Boukal, D},
title = {Plasticity in climate change responses.},
journal = {Biological reviews of the Cambridge Philosophical Society},
volume = {},
number = {},
pages = {},
doi = {10.1111/brv.70056},
pmid = {40698780},
issn = {1469-185X},
support = {21-29169S//Grant Agency of the Czech Republic/ ; ANR-19-CE02-0001-01//Agence Nationale de la Recherche/ ; CEECIND/01526/2018//Fundação para a Ciência e Tecnologia/ ; PTDC/BIA-BMA/1494/2020//Fundação para a Ciência e Tecnologia/ ; UIDP/04378/2020//Fundação para a Ciência e Tecnologia/ ; UUIDB/04378/2020//Fundação para a Ciência e Tecnologia/ ; LA/P/0140/2020//Fundação para a Ciência e Tecnologia/ ; MR/V024744/2//UK Research & Innovation/ ; 511084840//Deutsche Forschungsgemeinschaft/ ; C16/2017/002//KU Leuven Research Council/ ; C16/2023/007//KU Leuven Research Council/ ; NE/Y001184/1//Natural Environment Research Council/ ; },
abstract = {Recent research has shown that climate change can both induce and modulate the expression of plastic traits but our understanding of the role of phenotypic plasticity as an adaptive response to climate change is limited. In this review, we dissect the mechanisms and impact of phenotypic plasticity as a response to accumulating climatic pressures on the individual, species and community levels. (i) We discuss how plasticity can affect individuals, populations and community dynamics and how climate change can alter the role of plasticity. We hypothesise that some pathways to phenotypic plasticity such as irreversible and anticipatory organismal responses will be reduced under increasing climate change. (ii) We then propose an integrated conceptual framework for studying phenotypic plasticity to advance our understanding of the feedbacks between the different levels of biological organisation. (iii) By formulating as yet unaddressed research questions within and across levels of biological organisation, we aim to instigate new research on phenotypic plasticity and its role in climate change responses.},
}

@article {pmid40698732,
year = {2025},
author = {Vimalesvaran, S and Abdulla, MA and Kyrana, E},
title = {Gut Microbiome in Liver Transplantation: From Preoperative Status to Posttransplant Outcomes.},
journal = {Pediatric transplantation},
volume = {29},
number = {5},
pages = {e70128},
doi = {10.1111/petr.70128},
pmid = {40698732},
issn = {1399-3046},
mesh = {Humans ; *Liver Transplantation ; *Gastrointestinal Microbiome ; *Postoperative Complications/microbiology ; Dysbiosis ; *End Stage Liver Disease/surgery ; Treatment Outcome ; Preoperative Period ; Graft Rejection ; },
abstract = {Liver transplantation remains the gold standard treatment for patients with end-stage liver disease. Despite significant improvement in surgical care and postoperative medical care, complications in the posttransplant period remain a concern. Graft rejection due to immunological factors is associated with increased morbidity and mortality. Infectious complications also have a major impact on patient outcomes. There is growing evidence about the role of the gut microbiome in the perioperative liver transplant course and the impact on patient outcomes in liver transplantation. These patients often already have gut dysbiosis at the time of liver transplantation due to their severe underlying disease and the use of repeated antibiotic courses. In this comprehensive review, we compile the current evidence for the role of the gut microbiome during the liver transplantation period.},
}

Humans
*Liver Transplantation
*Gastrointestinal Microbiome
*Postoperative Complications/microbiology
Dysbiosis
*End Stage Liver Disease/surgery
Treatment Outcome
Preoperative Period
Graft Rejection

@article {pmid40698647,
year = {2025},
author = {Relaño de la Guía, E and Cueva, C and Molinero, N and Ruano, A and Motilva, MJ and Bartolomé, B and Moreno-Arribas, MV},
title = {May Sulfites in Wine Affect Gut Microbiota? An In Vitro Study of Their Digestion and Interplay with Wine Polyphenols.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c02710},
pmid = {40698647},
issn = {1520-5118},
abstract = {Sulfites are widely used in the wine industry, but their human health effects remain debated. This study is the first to investigate the interaction between wine sulfites and gut microbiota under simulated gastrointestinal conditions. Using the simgi model, red and synthetic wines─with and without SO2 (200 mg/L)─underwent gastrointestinal digestion and colonic fermentation with fecal microbiota from three healthy donors (n = 3). SO2-treated wines slightly modified gut microbiota composition, decreasing beneficial bacteria like Bacteroides and Ruminococcus, while increasing Coprococcus and pro-inflammatory Escherichia/Shigella, although the overall microbiome of each individual seems to condition its resilience toward SO2. These effects were partially mitigated in red wine, suggesting a protective role of wine polyphenols. Additionally, SO2 treatment in red wines enhanced phenolic metabolism at the gut level, increasing low-molecular-weight phenolic compounds, such as valerolactones, bioavailable in the small intestine and colon. For instance, 5-(3',4'-dihydroxyphenyl)-γ-valerolactone concentrations were consistently higher in SO2-treated red wine (0.86-1.28 mg/L) than in the untreated wine (<0.78 mg/L) after 6 h of fermentation. This pioneering study reveals a complex interplay between sulfites, wine components, and gut microbiota, with potential health implications, especially for sulfite-sensitive individuals.},
}

@article {pmid40698515,
year = {2025},
author = {Hossain, MS and Amin, MA and Islam, S and Imam, H and Das, LC and Mahmud, S},
title = {Analyzing the Challenges and Opportunities Associated With Harnessing New Antibiotics From the Fungal Microbiome.},
journal = {MicrobiologyOpen},
volume = {14},
number = {4},
pages = {e70034},
doi = {10.1002/mbo3.70034},
pmid = {40698515},
issn = {2045-8827},
support = {//The authors received no specific funding for this work./ ; },
mesh = {*Fungi/metabolism/genetics ; *Anti-Bacterial Agents/biosynthesis/isolation & purification ; *Mycobiome ; *Microbiota ; Fermentation ; Drug Discovery/methods ; },
abstract = {The rapid rise in antibiotic resistance is a critical global health issue, and few new classes of antibiotics have been discovered since 1990 compared to the antibiotic's golden era between 1950 and 1970. However, developing new antimicrobial compounds faces many challenges, improvements in cultivation methods, genetic engineering, and advanced technologies are opening new paths for discovering and producing effective antibiotics. This study focuses on the fungal microbiome as a promising source of new antibiotics. We explored historical developments and advanced genetic techniques to reveal the potential of fungi in antibiotic production. Although isolating and scaling up fungal antibiotic production presents challenges, innovative approaches like in situ separation during fermentation can effectively address these issues. Our research highlights the importance of understanding fungal communication and metabolite sharing to enhance antibiotic yields and the connection of cutting-edge technologies in accelerating the discovery and optimization of antibiotic-producing fungi. By focusing on these technical aspects and fostering teamwork across various fields, this study aims to overcome current obstacles, and advance the development of antibiotic production technologies.},
}

*Fungi/metabolism/genetics
*Anti-Bacterial Agents/biosynthesis/isolation & purification
*Mycobiome
*Microbiota
Fermentation
Drug Discovery/methods

@article {pmid40698485,
year = {2025},
author = {Kalra, S and Verma, M and Kapoor, N},
title = {The 4BE quinqunx: A model for obesity pathogenesis.},
journal = {JPMA. The Journal of the Pakistan Medical Association..},
volume = {75},
number = {6},
pages = {1002-1003},
doi = {10.47391/JPMA.25-46},
pmid = {40698485},
issn = {0030-9982},
mesh = {Humans ; *Obesity/etiology/physiopathology ; Gastrointestinal Microbiome ; Adipose Tissue ; Brain/physiopathology ; },
abstract = {For obesity management to be effective, one must appreciate its causes and consequences. To do so, the seemingly complex science of obesity must be made simpler. A model which helps us explain its causes, contributory factors, as well as potential corrective measures, is needed. We share the 4BE winged quincunx model of obesity etiopathogenesis. Four central players - the Brain, Bowel, Beta/alpha cell and Bulk (adipose tissue)- form a causative quadruple, with four wings- Environmental determinants, Endocrine factors, Enteric microbiome and Extraneous limitations. The centre of the quincunx is occupied, in a stylish manner, by the ABC of weight management: Attitude, Behaviour and Choices. The 4BE concept makes it easy for health care professionals to understand, and explain, obesity.},
}

Humans
*Obesity/etiology/physiopathology
Gastrointestinal Microbiome
Adipose Tissue
Brain/physiopathology

@article {pmid40698372,
year = {2025},
author = {Xie, Z and Zheng, S and Yang, S and Tang, Y and Yu, H and Chang, Y and Zhu, Y and Zhan, X and Zeng, G and Chen, H},
title = {Comparative analysis of fruit microbiota and metabolites in two bayberry cultivars: implications for fruit quality and postharvest disease control.},
journal = {Food chemistry: X},
volume = {29},
number = {},
pages = {102773},
pmid = {40698372},
issn = {2590-1575},
abstract = {The fruit microbiome is crucial for fruit quality and postharvest characteristic. This study characterized the microbiome and metabolome of two bayberry cultivars (Myrica rubra cv. DongKui and Dingao) across three orchardsusing high-throughput sequencing and GC-MS metabolomics. The results indicated Dongkui showed lower microbial diversity dominated by Hyphozyma and Papiliotrema and bacterial genus 1174_901_12, whereas Dingao exhibited greater microbial diversity with Hannaella, Uwebraunia, and Pantoea. Fungal diversity was cultivar-dependent, while bacterial composition varied by orchard. Metabolomics revealed higher amino acid in Dingao and elevated myricetin in Dongkui correlating with microbiome differencs. GC-MS identified 16 differntial metabolites between cultivars, linked to microbial variations. Notably, core microbiome analysis identified Aureobasidium as a potential biocontrol agent. However, Dingao hosted more phytopathogens (Colletotrichum, Uwebraunia), implying heightened disease susceptibility and the need for targeted postharvest interventions. These findings provide insights for improving bayberry quality and developing microbiome-based strategies for crop improvement and preservation.},
}

@article {pmid40698332,
year = {2025},
author = {Kamenova, S and Albon, SD and Loe, LE and Irvine, RJ and Langvatn, R and Gusarova, G and de Muinck, EJ and Trosvik, P},
title = {Arctic Greening Drives Changes in the Diet and Gut Microbiome of a Large Herbivore With Consequences for Body Mass.},
journal = {Ecology and evolution},
volume = {15},
number = {7},
pages = {e71731},
pmid = {40698332},
issn = {2045-7758},
abstract = {Rapid climate warming is 'greening' the tundra, reflecting a higher plant biomass, particularly of deciduous shrubs and grasses. However, the consequences of these changes for herbivore nutrition are unclear. Although, the gut microbiome mediates nutrient metabolism, and hence herbivores' capacity to adapt to dietary change, few studies have investigated the effect of annual changes in the diet-gut microbiome nexus on fitness-related traits. In a model system, the Svalbard reindeer, a species experiencing the greatest rate of climate warming on Earth, we investigate how changes in diet and the gut microbiome impact reindeer body mass. Using high-resolution DNA metabarcoding, we assessed diet and gut microbiome bacterial composition in rumen samples from animals culled in October from 1998 to 2004 in four different valleys. Overall diet diversity and grass relative reads abundance (RRA) were significantly higher following warmer summers, while the RRA of the dwarf shrub Salix polaris increased with the maximum normalised difference vegetation index (NDVI), our measure of annual biomass. Autumn body mass, a strong proxy of fitness in Svalbard reindeer, was significantly, positively correlated with Salix RRA, most pronounced in females that had reproduced, and by that depleted body reserves. Multivariate analyses revealed a highly significant relationship between diet and microbiome composition at the individual level. This included a significant positive correlation between Salix and bacterial diversity. However, a structural equation model revealed that the direct path effect of Salix on reindeer body mass was stronger than the indirect path effect, mediated through the gut microbiome. Our results suggest that climate-driven Arctic greening may have implications for herbivore body mass, operating through a change in diet composition. These findings reveal some of the mechanistic underpinnings of Arctic warming on herbivore populations and highlight the importance of the diet-gut microbiome nexus in facilitating species resilience to rapid climate change.},
}

@article {pmid40698196,
year = {2025},
author = {Luo, L and Wang, Z and Yan, X and Ye, C and Hao, J and Liu, X and Zhu, S and Yang, M},
title = {Diversified alternaria pathogenicity alters plant-soil feedbacks through leaf-root-microbiome dynamics in agroforestry systems.},
journal = {Horticulture research},
volume = {12},
number = {8},
pages = {uhaf137},
pmid = {40698196},
issn = {2662-6810},
abstract = {Interspecific interactions including plant-plant, plant-microbe, and plant-insect are the important elements to drive the positive plant-soil feedback for maintaining ecosystem stability in biodiversity ecosystems. Yet, the role of diversified foliar pathogens in biodiversity system in influencing the plant-soil feedback (PSF) has often been underestimated. Here, we assessed the effects of foliar Alternaria panax pathogenicity diversity from agroforestry system on PSF and rhizosphere microbial community. We show that a moderate intensity of foliar pathogen infection by A. panax could activate jasmonic acid (JA)-mediated defense from shoots to roots. This activation enhanced the synthesis and secretion of 2-aminoethanesulfonic acid into the rhizosphere for a disease-suppressive rhizo-microbiota assembly, contributing to positive PSF. However, excessive foliar pathogen infection allocated JA-mediated defense only in leaf and disrupted this rhizomicrobial enrichment, resulting negative PSF. This study enhances the understanding of the ecological roles of foliar pathogen within agroforestry systems and provides an insight into agricultural sustainability.},
}

@article {pmid40698186,
year = {2025},
author = {Lukács, AF and Herczeg, G and Kovács, GM},
title = {Effects of dark septate endophytic fungi on the performance of non-mycorrhizal cabbage plants under normal and low water conditions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1593265},
pmid = {40698186},
issn = {1664-302X},
abstract = {Drought, a major consequence of global environmental change, poses a serious threat to both natural and agricultural ecosystems. Root-associated fungi, particularly the widely distributed dark septate endophytes (DSE), are key components of the plant microbiome and can influence host plant performance in various ways. We conducted two manipulative experiments using two model DSE species from a semiarid habitat to investigate their effects on a non-mycorrhizal host plant (cabbage) under both normal and reduced water supply conditions. The positive effects of Periconia were limited-it not only increased root biomass but also reduced water potential and soil moisture under normal watering conditions. In contrast, Cadophora significantly increased shoot biomass (by up to 50%) and root biomass in one experiment. However, this was also associated with a decline in plant water potential, particularly at the cost of reduced plant water status, and their effects varied on the same host. Interestingly, autoclaved inoculum, also had positive effects on plant growth. Our findings highlight the potential role of symbiotic DSE fungi in mitigating drought stress and suggest their promise as biotechnological tools for addressing the increasing challenges posed by drought.},
}

@article {pmid40698182,
year = {2025},
author = {Cano-Argüelles, AL and Abuin-Denis, L and Obregon, D and Mateos-Hernandez, L and Maître, A and Piloto-Sardiñas, E and Wu-Chuang, A and Tonnerre, P and Cabezas-Cruz, A},
title = {Why the Jenner/Pasteur paradigm is insufficient for controlling vector-borne diseases and the role of microbiota-mediated interactions.},
journal = {Current research in parasitology & vector-borne diseases},
volume = {8},
number = {},
pages = {100291},
pmid = {40698182},
issn = {2667-114X},
abstract = {Vaccination campaigns have profoundly influenced the dynamics of infectious diseases, acting as one of the largest ecological experiments in history. By vaccinating billions across decades, we have imposed powerful selective pressures on pathogens, illuminating their ability to adapt, evade, or persist. Rooted in the Jenner/Pasteur paradigm - where exposure to an antigen induces protective immunity - vaccines have revealed how pathogens differ in their ecological susceptibility to immunity. Using this framework, pathogens can be categorized based on their strategies to endure, from those limited by direct immunity to those relying on antigenic variation, chronic infection, or reservoirs. Vector-borne pathogens (VBPs) present a set of challenges to vaccination efforts due to their complex life cycles, stage-specific antigen expression, and reliance on arthropod vectors for transmission. These pathogens not only evade host immunity but also adapt to selective pressures within the vector's microbiome and immune system. Such complexity often places VBPs beyond the scope of traditional vaccine paradigms, requiring alternative strategies such as transmission-blocking and vector-targeted vaccines. This review explores these insights, examining the interplay between vaccination, pathogen ecology, and evolution - with special emphasis on VBPs - to guide future strategies in vector-borne disease (VBD) control.},
}

@article {pmid40698041,
year = {2025},
author = {Liu, S and Cheng, L and Li, S},
title = {Characteristics of Gut Microbiota in Patients with Polycystic Ovary Syndrome and Its Association with Metabolic Abnormalities: A Review.},
journal = {International journal of women's health},
volume = {17},
number = {},
pages = {2165-2174},
pmid = {40698041},
issn = {1179-1411},
abstract = {Polycystic Ovary Syndrome (PCOS) is a prevalent endocrine disorder that has garnered attention in recent years for its intricate relationship with gut microbiota, which plays a significant role in the metabolic abnormalities associated with this condition. This review focuses on the characteristics of gut microbiota in polycystic ovary syndrome (PCOS). By analyzing current literature, we will focus on the alterations in gut microbiota composition, influential factors, and the pathophysiological mechanisms linking gut microbiota and PCOS, diagnostic approaches, therapeutic strategies, as well as controversies and future directions in this field are discussed. Understanding these relationships may provide insights into the disease mechanism and highlight novel treatment strategies for managing PCOS.},
}

@article {pmid40697984,
year = {2025},
author = {Hebbar, P and Han, OB and Yan, NX and Kay, D and Chu, KY and Woon, JS and Lun, PK and Kabekkodu, SP and Prasad, ASB and Prakash, B and Nograles, N and Kanakal, MM and Goodson, M and Nagaraja, S and Mascarenhas, R},
title = {Characterization of microbiome diversity unveils substantial microbial variation in mangrove soil sediments from coastal regions of Malaysia.},
journal = {Access microbiology},
volume = {7},
number = {6},
pages = {},
pmid = {40697984},
issn = {2516-8290},
abstract = {The mangrove ecosystems are of great ecological importance found in tropical and subtropical coasts, including Malaysia. The microbial communities in the mangrove sediments play an indispensable role in maintaining homeostasis and supporting biodiversity. However, mangroves are facing various threats due to increasing anthropogenic activities. Thus, it is important to monitor the microbial community to improve our understanding of anthropogenic pressure on reshaping these ecosystems. This study examines the microbial community diversity in mangrove sediments of southern peninsular Malaysia. High-throughput MinION sequencing of the 16S rRNA gene was performed to compare the soil microbiome diversity in 35 samples from 8 different mangroves representing Sungai Sedili Kecil and Sungai Sedili Besar that flow into the South China Sea; Sungai Pulai, Sungai Melayu, Sungai Danga, Sungai Skudai and Sungai Johor that join the Straits of Johor; and Pulau Kukup from the Straits of Malacca. The metagenomic classification performed with 16S rRNA showed 2,573 taxa comprising 32 phyla. Total abundance analysis showed Pseudomonadota (67-69%), Bacteroidota (6-8%), Bacillota (5-8%), Campylobacterota (4-5%), Acidobacteriota (3-4%), Planctomycetota (2-4%) and Actinomycetota (1-2%) as the relatively common phyla. Alpha diversity indices revealed significantly higher richness in samples from mangroves of the South China Sea. Further, the 'Shannon' index showed a significant difference in diversity between Sungai Melayu and Sungai Pulai. Higher abundance of Burkholderiaceae, Bacillaceae and Enterobacteriaceae suggests a difference in the microbial community structure. This study stands as the first comprehensive analysis of microbial communities for future monitoring and conservation in these mangroves.},
}

@article {pmid40697638,
year = {2025},
author = {Guo, Y and Mao, Y and Zhao, S and Yang, F and Yu, Y and Chen, C and Yang, M and Wang, J},
title = {Analysis of microbial aerosols diversity in cattle farms in Ningxia.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1542971},
pmid = {40697638},
issn = {2297-1769},
abstract = {INTRODUCTION: Beef cattle farming, a key industry in Ningxia Hui Autonomous Region, has intensified, raising public health concerns due to bioaerosol emissions. However, the distribution characteristics of these bioaerosols remain poorly understood.

METHODS: We characterized bacterial communities in bioaerosols from beef cattle pens across five Ningxia regions-Guyuan (G), Yinchuan (Y), Shizuishan (S), Zhongwei (Z), and Wuzhong (W)-and compared two rearing scales: smallholder farms (S) and large-scale farms (L). Using filter membrane sampling and 16S rRNA gene sequencing, we analyzed bacterial abundance and diversity.

RESULTS AND DISCUSSION: Regional differences significantly influenced bacterial abundance (p < 0.05), whereas rearing scales had minimal impact. We identified 45,486 operational taxonomic units (OTUs), of which 423 were shared across all samples, constituting a core microbiome that accounted for 46% of total sequences. Co-occurrence network analysis revealed greater microbial interaction complexity in regionally distinct samples. Our results elucidate the distribution of bioaerosol-borne microbial communities in cattle farms, highlighting potential transmission pathways of airborne microorganisms and informing strategies to mitigate exposure risks for livestock and workers.},
}

@article {pmid40697195,
year = {2025},
author = {Shea, MK and Lynch, SD and Brinkley, TE and Kritchevsky, SB},
title = {Nutrition and Aging Biology: Summary of a Research Centers Collaborative Network Workshop and Research Needs.},
journal = {Current developments in nutrition},
volume = {9},
number = {7},
pages = {107485},
pmid = {40697195},
issn = {2475-2991},
abstract = {As the global population of older adults increases, identifying strategies that modify biological aging has become an increasing priority for improving health span and lifespan. When coupled with the growing epidemic of overweight and obesity, nutritional strategies have garnered considerable research attention due to their potential to modulate both aging and metabolism at the cellular and molecular levels. Several key nutritional influences are currently being studied for their effects on aging biology, including caloric restriction, protein restriction, time-restricted eating, ketosis, and the gut microbiome. Of particular relevance is the role of dietary interventions in older adults with obesity, which must carefully balance the cardiometabolic benefits of weight loss with the unintended musculoskeletal losses, including muscle and bone mass. To discuss these critical issues, the Research Centers Collaborative Network sponsored a 1.5-d multidisciplinary workshop bringing together basic, clinical, and translational scientists in the fields of nutrition and aging biology. This meeting included sessions on calorie and protein restriction, timing of food intake, the gut microbiome, and obesity treatment for older adults. The agenda and recordings are archived at https://www.rccn-aging.org/nutrition-and-aging-biology. In this article, we describe the workshop's themes and discussions and highlight research gaps that, if filled, will considerably advance our understanding of the role of nutrition in healthy aging.},
}

@article {pmid40697099,
year = {2025},
author = {Zhang, Y and Tu, M and Long, P and Zheng, J and Du, G and Xiao, S and Gao, C},
title = {Efficacy of probiotics pretreatment in Helicobacter pylori eradication therapy: a systematic review and meta-analysis of clinical outcomes.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2533431},
doi = {10.1080/07853890.2025.2533431},
pmid = {40697099},
issn = {1365-2060},
mesh = {*Probiotics/therapeutic use/administration & dosage ; Humans ; *Helicobacter Infections/therapy/microbiology/drug therapy ; *Helicobacter pylori/drug effects ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; Gastrointestinal Microbiome/drug effects ; Randomized Controlled Trials as Topic ; },
abstract = {BACKGROUND: Probiotics inhibit Helicobacter pylori (H. pylori) growth and alter gut microbiome, in addition to alleviating the side effects of H. pylori eradication. It has also been reported that H. pylori be eradicated after fecal microbiota transplantation in some cases. However, whether probiotics used before H. pylori eradication improves the eradication rate remains unclear. This study evaluates their role through a systematic review and meta-analysis.

METHODS: We searched PubMed, EMBASE, the Cochrane Library, and the Conference Proceedings Citation Index up to January 31, 2024, to identify randomized controlled studies (RCTs) assessing the efficacy of probiotics used before H. pylori eradication. Meta-analyses of eradication rates were performed.

RESULTS: Twelve eligible RCTs with 2,144 participants were included. The intention-to-treat analysis revealed that the overall eradication rate of H. pylori was higher in the probiotics pretreatment group compared to the control group (80.34% vs. 70.49%), with a risk ratio (RR) of 1.14 (95% CI: 1.08 to 1.19; I[2] = 36%) and side effects were less (16.0% vs. 28.3%, RR = 0.59, 95% CI 0.41 to 0.84). The per-protocol analysis yielded similar results (86.43% vs. 76.88%, RR = 1.12, 95% CI: 1.08 to 1.17; I[2] = 57%). Subgroup analyses, considering factors like geographic location, eradication regimens, and probiotic combinations, consistently confirmed the benefits. Finally, probiotics pretreatment durations of 14 days or more, as well as the study designs pre vs. free and pre and combine vs. free, demonstrated significant effects. Shorter durations and other study designs with fewer studies did not show significant effects.

CONCLUSION: There is moderate to high evidence to suggest that probiotics pretreatment improves H. pylori eradication rate and reduces side effects. These findings highlight the potential value of gut microbiome modulation in H. pylori treatment and offer a new direction for addressing the challenges of antibiotic resistance and treatment failure.},
}

*Probiotics/therapeutic use/administration & dosage
Humans
*Helicobacter Infections/therapy/microbiology/drug therapy
*Helicobacter pylori/drug effects
Anti-Bacterial Agents/therapeutic use
Treatment Outcome
Gastrointestinal Microbiome/drug effects
Randomized Controlled Trials as Topic

@article {pmid40696831,
year = {2025},
author = {Wyatt-Johnson, SK and Desai, JM and Wireman, A and Eipers, P and Morrow, C and Vornhagen, J and Brutkiewicz, RR},
title = {The MR1/MAIT cell axis impacts the gut-brain axis through both cognition and microbial community structure in 5XFAD mice.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {7},
pages = {e70493},
doi = {10.1002/alz.70493},
pmid = {40696831},
issn = {1552-5279},
support = {R21 AG071269-01/NH/NIH HHS/United States ; TL1TR002531/NH/NIH HHS/United States ; AARGD-NTF-22-928436//Alzheimer's Association Research/ ; T32-AI-060519//National Institutes of Health, National Center for Advancing Translational Sciences, Clinical, and Translational Sciences/ ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Histocompatibility Antigens Class I/genetics/metabolism ; *Brain ; *Cognition/physiology ; *Alzheimer Disease/microbiology ; Male ; Mice, Knockout ; Disease Models, Animal ; *Mucosal-Associated Invariant T Cells/metabolism ; Female ; *Minor Histocompatibility Antigens/genetics/metabolism ; Mice, Transgenic ; Feces/microbiology ; },
abstract = {INTRODUCTION: Mucosal-associated invariant T (MAIT) cells recognize microbial antigens presented by major histocompatibility complex class I-like molecule (MR1) and are elevated in Alzheimer's disease (AD) model mouse brains; MAIT cell-deficient AD mice have reduced brain pathology, supporting the importance of the gut-brain axis in AD. How the MR1/MAIT cell axis impacts cognition and the microbiome remains unknown.

METHODS: Novel object recognition/placement, Y-maze, and Barnes maze were used to determine memory changes in wild-type (WT), MR1 KO, 5XFAD, and 5XFAD/MR1 KO mice. Fecal samples were analyzed using 16S rRNA gene amplicon sequencing.

RESULTS: 5XFAD/MR1KO mice did not display the cognitive deficits observed in 5XFAD. There were relative abundance differences in the fecal microbiota between 5XFAD and 5XFAD/MR1 KO mice, and male 5XFAD/MR1 KO mice had increased microbiome alpha diversity compared to 5XFAD mice.

DISCUSSION: Our data suggest that the MR1/MAIT cell axis negatively affects cognition and impacts gut microbiome diversity. These results further support a detrimental role for the MR1/MAIT cell axis in AD.

HIGHLIGHTS: 5XFAD mice lacking major histocompatibility complex, class I-related (MR1) and mucosal-associated invariant T (MAIT) cells had no deficits in recognition memory. Compared to 5XFAD, there was improved learning in the Barnes maze by female 5XFAD/MR1 knock-out (KO) mice. There was an increased abundance of Campylobacterota in male 5XFAD/MR1 KO versus 5XFAD mice. Six of nine linear discriminant analysis effect size-identified distinguishing features were higher in 5XFAD/MR1 KO mice.},
}

Animals
Mice
*Gastrointestinal Microbiome
*Histocompatibility Antigens Class I/genetics/metabolism
*Brain
*Cognition/physiology
*Alzheimer Disease/microbiology
Male
Mice, Knockout
Disease Models, Animal
*Mucosal-Associated Invariant T Cells/metabolism
Female
*Minor Histocompatibility Antigens/genetics/metabolism
Mice, Transgenic
Feces/microbiology

@article {pmid40696806,
year = {2025},
author = {Bridgman, SL and Drall, KM and Lau, AA and Tun, HM and Morales-Lizcano, NP and Huynh, HQ and Mandhane, PJ and Moraes, TJ and Simons, E and Turvey, SE and Subbarao, P and Scott, JA and Kozyrskyj, AL},
title = {Infant Acid-Suppressant Medication, C. difficile Colonisation, and Childhood Body Mass Index in a Canadian Cohort.},
journal = {Acta paediatrica (Oslo, Norway : 1992)},
volume = {},
number = {},
pages = {},
doi = {10.1111/apa.70243},
pmid = {40696806},
issn = {1651-2227},
support = {227312/CAPMC/CIHR/Canada ; },
abstract = {AIM: To determine relationships between paediatric use of acid-suppressive medications (ASMs) (proton pump inhibitors (PPI) and histamine-2 receptor antagonists (H2RA)) and preschool body mass index (BMI) and mediation by C. difficile colonisation.

METHODS: ASMs were parent-reported at age 3, 6 and 12 months in 1025 infants from the CHILD Cohort Study. Targeted qPCR for C. difficile was conducted in stool collected at 3 months, and age/sex adjusted BMI-z scores were calculated at age 5 years. ASM use and BMI-z score associations were assessed by regression, and mediation analyses were conducted.

RESULTS: Approximately 4% of infants received H2RAs, most before age 3 months. C. difficile colonisation was twice as likely in 3-month-old infants receiving H2RAs (OR: 2.27, 95% CI: 1.13-4.51) and was associated with higher BMI-z scores at age 5 years (β: 0.31, 95% CI: 0.16, 0.46). Mediation models showed an indirect positive effect of H2RA use on 5-year BMI-z scores, mediated through C. difficile colonisation (β: 0.065, 95% CI: 0.01, 0.13).

CONCLUSIONS: We found evidence of increased preschool BMI following H2RA use in infants that was mediated through C. difficile colonisation. Further study on ASM use in infancy, the gut microbiome, and pathways to body weight health outcomes is warranted.},
}

@article {pmid40696591,
year = {2025},
author = {Zhang, M and Fan, L and Li, J},
title = {Prediction of calcium oxalate kidney stones: A comprehensive analysis of clinical and gut microbiome characteristics.},
journal = {Medicine},
volume = {104},
number = {29},
pages = {e43103},
doi = {10.1097/MD.0000000000043103},
pmid = {40696591},
issn = {1536-5964},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Calcium Oxalate/analysis ; *Kidney Calculi/microbiology/urine ; Female ; Male ; Middle Aged ; Adult ; Case-Control Studies ; RNA, Ribosomal, 16S ; Body Mass Index ; Hydrogen-Ion Concentration ; Oxalobacter formigenes ; },
abstract = {In recent years, the role of the gut microbiome in stone formation has gained increasing attention. Specifically, certain gut microbes that metabolize oxalate may regulate oxalate levels in the body, thereby influencing the occurrence of kidney stones. This study aims to investigate the clinical characteristics of calcium oxalate stone patients, the composition of their gut microbiome, and the relationship between these factors and stone formation. This study included 159 calcium oxalate stone patients (case group) and 141 healthy controls (control group). Clinical data were collected to analyze differences in body mass index, urinary metabolic markers (urinary oxalate, calcium, and pH), and other indicators between the 2 groups. High-throughput 16S rRNA sequencing was used to compare the diversity and composition of the gut microbiome. Further, correlations between the gut microbiome and clinical metabolic indicators were analyzed, and a risk prediction model for calcium oxalate stones was developed based on clinical and gut microbiome characteristics. Significant differences in body mass index, urinary oxalate concentration, urinary calcium concentration, and urinary pH were observed between the case and control groups. Gut microbiome diversity analysis revealed that the Shannon and Chao1 indices were lower in the case group, and significant differences in microbiome composition were found. The abundance of Proteobacteria and Firmicutes changed significantly, with a notable decrease in Oxalobacter formigenes and an increase in Escherichia-Shigella species in the case group. Correlation analysis showed a negative correlation between O formigenes abundance and urinary oxalate concentration, and a negative correlation between Escherichia-Shigella and urinary pH. The random forest prediction model exhibited high predictive accuracy (area under the receiver operating characteristic curve = 0.90). The formation of calcium oxalate stones is closely related to the structure and function of the gut microbiome, particularly with the reduced abundance of the oxalate-degrading bacterium O formigenes. Gut microbiome imbalance may influence stone formation through various mechanisms. This study provides new theoretical insights for the early prediction, prevention, and treatment of calcium oxalate stones.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Calcium Oxalate/analysis
*Kidney Calculi/microbiology/urine
Female
Male
Middle Aged
Adult
Case-Control Studies
RNA, Ribosomal, 16S
Body Mass Index
Hydrogen-Ion Concentration
Oxalobacter formigenes

@article {pmid40696495,
year = {2025},
author = {Nambiar, G and Appleyard, SA and Wos-Oxley, ML and Afonso, LOB and Oxley, APA},
title = {Frozen in time: using museomics to investigate the gut bacteriome of fish from the Gulf of Carpentaria.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70155},
pmid = {40696495},
issn = {1095-8649},
support = {//School of Life and Environmental Sciences, Deakin University/ ; //CSIRO/ ; },
abstract = {Archival fish collections are not only an important resource for informing systematic and taxonomic research, but also for elucidating the diversity of microorganisms that colonise the body surfaces of fish and which interact with the host to drive health and fitness (as the 'microbiome'). Effectively 'frozen in time', these specimens act as potential host-microbiome time capsules, enabling the opportunity to gain valuable insights into their dynamics, although to date they have been underutilised. Here, whole frozen archived specimens from seven well-represented fish species (belonging to the Labridae and Platycephalidae) collected from the Gulf of Carpentaria off the northern coast of Australia and stored in the Australian National Fish Collection for 11 years were evaluated for determining their suitability for fish gut bacteriome investigations. DNA yield and quality were assessed from extracts obtained from samples of the gastrointestinal tract (from thawed specimens) and the 16S rRNA gene sequenced using the Illumina platform to determine the core and unique gut bacteriome constituents of these fish species. High-quality bacterial DNA from frozen specimens produced comparable numbers of sequence reads and bacterial amplicon sequence variants to contemporary studies and identified some unique and common constituents across the two fish families, notably members belonging to the Gammaproteobacteria as well as putative symbionts belonging to the genus Epulopiscium. This study highlights for the first time the relevance of frozen specimens for gut bacteriome investigations and provides a baseline for future comparative investigations of contemporary specimens.},
}

@article {pmid40696437,
year = {2025},
author = {Ashton, PM and Mageiros, L and Meiring, JE and Chunga-Chirambo, A and Khanam, F and Dongol, S and Banda, H and Karkey, A and Preciado-Llanes, L and Thomaides-Brears, H and Gibani, M and Rajib, NH and Rahman, N and Biswas, PK and Bhuiyan, MAI and Kay, S and Auger, K and Seret, O and Thomson, NR and Pollard, AJ and Baker, S and Basnyat, B and Clemens, JD and Dolecek, C and Dunstan, SJ and Dougan, G and Heyderman, RS and Pitzer, VE and Qadri, F and Gordon, MA and Holt, KE and Darton, TC and , },
title = {Interplay between the gut microbiome and typhoid fever: insights from endemic countries and a controlled human infection model.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {168},
pmid = {40696437},
issn = {2049-2618},
mesh = {Humans ; *Typhoid Fever/microbiology/epidemiology ; *Gastrointestinal Microbiome ; *Salmonella typhi/pathogenicity ; Prospective Studies ; Male ; Female ; Malawi/epidemiology ; Adult ; Bangladesh/epidemiology ; Nepal/epidemiology ; Adolescent ; Child ; Feces/microbiology ; Young Adult ; Endemic Diseases ; Fatty Acids, Volatile/metabolism ; Middle Aged ; Child, Preschool ; },
abstract = {BACKGROUND: Typhoid fever is a systemic infection caused by Salmonella enterica serovar Typhi (S. Typhi) invasion from the gut lumen. Transmission between people occurs through ingestion of contaminated food and water, particularly in settings with poor water and sanitation infrastructure, resulting in over 10 million illnesses annually. As the pathogen invades via the gastrointestinal tract, it is plausible that the gut microbiome may influence the outcome of S. Typhi exposure. There is some evidence that bacteria producing short-chain fatty acids (SCFAs) may create an environment unfavourable to invasive Salmonella, but data from humans is limited.

METHODS: To investigate the association between the gut microbiome and typhoid fever, we analysed samples collected from three all-age cohorts enrolled in a prospective surveillance study conducted across three settings where typhoid fever is endemic (Dhaka, Bangladesh; Blantyre, Malawi; and Kathmandu, Nepal). Cohorts consisted of acute typhoid fever patients (n = 92), asymptomatic household contacts of typhoid fever patients (representing individuals who were likely exposed to S. Typhi but did not develop the disease, n = 97) and asymptomatic serosurvey participants with high Vi antibody titres (representing individuals who were exposed to S. Typhi and may be carriers, n = 69). The stool microbiomes of each cohort were characterised using shotgun metagenomics, and bacterial diversity, composition and function were compared.

RESULTS: We identified 4 bacterial species that were significantly lower in abundance in typhoid fever patients compared with household contacts (i.e. probably exposed), in two of the three participant populations (Bangladesh and Malawi). These bacteria may represent taxa that provide protection against the development of clinical infection upon exposure to S. Typhi and include the inflammation-associated species Prevotella copri clade A and Haemophilus parainfluenzae. Our functional analysis identified 28 specific metabolic gene clusters (MGCs) negatively associated with typhoid fever in Bangladesh and Malawi, including seven MGCs involved in SCFA metabolism. The putative protection provided by microbiome SCFA metabolism was supported by data from a controlled human infection model conducted in a UK population, in which participants who did not develop typhoid fever following ingestion of S. Typhi had a higher abundance of a putative SCFA-metabolising MGC (q-value = 0.22).

CONCLUSIONS: This study identified the same protective associations between taxonomic and functional microbiota characteristics and non-susceptibility to typhoid fever across multiple human populations. Future research should explore the potential functional role of SCFAs and inflammation-associated bacteria in resistance to S. Typhi and other enteric infections. Video Abstract.},
}

Humans
*Typhoid Fever/microbiology/epidemiology
*Gastrointestinal Microbiome
*Salmonella typhi/pathogenicity
Prospective Studies
Male
Female
Malawi/epidemiology
Adult
Bangladesh/epidemiology
Nepal/epidemiology
Adolescent
Child
Feces/microbiology
Young Adult
Endemic Diseases
Fatty Acids, Volatile/metabolism
Middle Aged
Child, Preschool

@article {pmid40696369,
year = {2025},
author = {Song, S and Wen, X and Chen, F and Li, J and Shi, K and Lou, Y and Xu, A and Wen, C and Shao, T},
title = {Qu-zhuo-tong-bi decoction exerts gouty arthritis therapy by skewing macrophage polarization through butanoate metabolism.},
journal = {Chinese medicine},
volume = {20},
number = {1},
pages = {115},
pmid = {40696369},
issn = {1749-8546},
support = {82274302//National Natural Science Foundation of China/ ; 82074248//National Natural Science Foundation of China/ ; 2023C03040//Key Research and Development Program of Zhejiang Province/ ; },
abstract = {BACKGROUND: Qu-zhuo-tong-bi decoction (QZTBD), a traditional Chinese medicine (TCM), has demonstrated efficacy in the treatment of gouty arthritis. However, to date, the precise pharmacological mechanisms remain unclear.

PURPOSE: The study aims to ascertain the therapeutic effects and the underlying mechanisms of QZTBD in the treatment of gouty arthritis.

METHODS: The efficacy and safety of different doses of QZTBD were investigated in Uox-KO mice. Candidate active ingredients were identified using UHPLC-MS/MS. The potential therapeutic pathways of the active ingredients were predicted through network pharmacology. The mechanisms of QZTBD in alleviating gouty arthritis were explored via comprehensive analyses of gut microbiota, combined with RT-qPCR, western blot, immunofluorescence, ELISA, flow cytometry, and Seahorse assay. Fecal microbiota transplantation (FMT), bacterial culture experiment, butyrate-producing bacteria (BPB) and butyrate administration, and 2-DG intervention were conducted to explore the roles of BPB and butanoate metabolism in gout progression and therapeutic mechanisms of QZTBD. In vitro studies further validated the regulatory effects of butyrate and QZTBD on macrophage polarization through glycolysis modulation.

RESULTS: 18.0 g/kg/d of QZTBD effectively alleviated the symptoms of gouty arthritis with excellent hepatic and renal safety. UHPLC-MS/MS analysis and network pharmacology revealed that QZTBD exerts its effects on butanoate metabolism during gouty arthritis inflammation. QZTBD treatment increased the abundance of BPB, the levels of serum and colon butyrate, and the expression levels of Buk and But. The transplantation of QZTBD-treated microbiota reproduced the therapeutic effects of QZTBD. M1 macrophage polarization was suppressed after QZTBD intervention. The administration of BPB and butyrate attenuated gouty arthritis and orchestrated macrophage polarization. Inhibition of glycolysis regulated the phenotype of macrophage and attenuated inflammatory processes. In vitro analysis unveiled that QZTBD and butyrate modulated glycolysis to regulate macrophage polarization, thereby alleviating gouty arthritis.

CONCLUSION: QZTBD targeted butanoate metabolism to regulate macrophage polarization, thereby effectively alleviating intestinal inflammation and restoring immune homeostasis in gouty arthritis. These findings establish a mechanistic foundation for developing precision therapeutic strategies leveraging QZTBD to combat gouty arthritis.},
}

@article {pmid40696355,
year = {2025},
author = {Dutta, B and Tripathy, A and Archana, PR and Kamath, SU},
title = {Unraveling the complexities of diet induced obesity and glucolipid dysfunction in metabolic syndrome.},
journal = {Diabetology & metabolic syndrome},
volume = {17},
number = {1},
pages = {292},
pmid = {40696355},
issn = {1758-5996},
abstract = {The consumption of a high-fat high-calorie diet with or without fructose (western or cafeteria diet) increases body mass due to calorie excess, inducing glucolipid metabolism dysfunctions culminating in development of unhealthy obesity and metabolic syndrome (MetS). Understanding the sequelae of events that translates caloric excess to the development of MetS symptoms interlinking metabolic interrelationship between organs is paramount in the development of new treatment strategies. This review aims to create a compendium of evidence from mammalian studies (rodents, humans) to elucidate the metabolic changes induced by overnutrition. This review explores gut microbiome alterations, gut barrier dysfunctions, and immune dysregulation induced by a high-fat diet that changes gut tryptophan and biliary metabolism, which, with concomitant elevations in free fatty acids and ceramides, promote insulin insensitivity. Immunometabolic alteration induce adipose tissue dysfunction, which alters the secretion of adipokines and lipid metabolites that contribute to dyslipidemia, hepatosteatosis, cardiovascular dysfunction, and endocrine disruption. This review provides insights into the mechanism underlying unhealthy adipose expansion, shedding light on some of the exosome-mediated epigenomic alterations affecting obesity or MetS pathogenesis, which may help in the future design of microRNA biomarkers. The review also highlights areas where more supportive evidence may be needed to elucidate metabolic syndrome pathogenesis.},
}

@article {pmid40696300,
year = {2025},
author = {Giese, M and Stefani, E and Larger, S and Pindo, M and Farneti, B and Ajelli, M and Cattani, M and Delgado-Baquerizo, M and Giongo, L and Coleine, C and Donati, C},
title = {The blueberry phyllosphere microbiota: tissue-specific core communities and their stability across cultivars and years.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {947},
pmid = {40696300},
issn = {1471-2229},
mesh = {*Blueberry Plants/microbiology ; *Microbiota ; Fruit/microbiology ; *Plant Leaves/microbiology ; Bacteria/classification/genetics/isolation & purification ; Fungi/genetics/classification/isolation & purification ; },
abstract = {Blueberries are critical for food production due to their widespread consumption and nutritional value. Beyond agriculture, wild Vaccinium species play essential ecological roles, including supporting pollinators and enhancing soil health. This dual importance underscores their relevance to both food security and ecosystem sustainability. The fruit-associated microbiome, both internal and surface-dwelling, includes a wide range of microorganisms. These microbial communities play a dual role: they influence fruit quality (e.g., taste, texture, shelf life) and are also involved in the degradation processes that occur during fruit senescence or postharvest storage.". Despite their importance, the specific factors shaping the microbiomes of blueberry fruits, as well as their relationship with other above-ground parts of the plant and their stability over different years, remain poorly understood. We conducted a field experiment to characterize the taxonomic composition of fungal and bacterial communities colonizing the leaves and the surface and pulp of fruits on a collection of 10 different cultivars of blueberry over two years. Independently from the sampling time, pulp of the fruit, surface and leaves harbor specific and distinct microbiomes. A major factor determining the microbiome of blueberry fruits and leaves was plant cultivar, followed by tissue. We further identified the core microbiome for each plant tissue and demonstrated that core taxa account for the dominant fraction of the microbiota of each plant. As trade and production of blueberries is expanding, our results provide a foundation for advancing the development of targeted microbiome management strategies, with potential applications in enhancing plant health and productivity.},
}

*Blueberry Plants/microbiology
*Microbiota
Fruit/microbiology
*Plant Leaves/microbiology
Bacteria/classification/genetics/isolation & purification
Fungi/genetics/classification/isolation & purification

@article {pmid40696219,
year = {2025},
author = {Pawluski, JL and Kacimi, K and Zhang, C and Guillot, L and Guidice, AL and Charlier, TD and Lonstein, JS},
title = {Reproductive experience influences the effects of Lactocaseibacillus rhamnosus HN001 on gut microbiota and hippocampal plasticity in female rats.},
journal = {Journal of neuroendocrinology},
volume = {},
number = {},
pages = {e70068},
doi = {10.1111/jne.70068},
pmid = {40696219},
issn = {1365-2826},
support = {//Biostime Institute of Nutrition and Care Geneva/ ; },
abstract = {There is increasing interest in the role of probiotics in supporting maternal well-being throughout female reproduction. However, it remains largely unknown whether the brain of a female with reproductive experience responds differently to probiotics compared to females without reproductive experience. Reproduction involves remarkable neuroplasticity; therefore, we hypothesized that reproducing females are particularly susceptible to the effects of probiotic treatment. Groups of early pregnant or age-matched virgin female Long-Evans rats were administered the probiotic, Lactocaseibacillus rhamnosus HN001 (HN001), in their drinking water or given untreated water for 30 days. To measure changes in gut microbiota, fecal samples were taken regularly. Brains were analyzed at the end of treatment to quantify hippocampal cells containing the neurogenesis marker doublecortin, the synaptic marker synaptophysin, and the microglial activation marker Iba1. For dams, an offspring retrieval test was performed. Main findings show that HN001 administration lowers Bacteroidota abundance in the gut regardless of reproductive experience. In HN001-treated dams there was an increase in the number of times offspring were carried and this was negatively correlated with Bacteroidota abundance in the dam's gut. HN001-treated dams also had more immature neurons in the hippocampus and more thick-type microglial cells in the dorsal hippocampus compared to control dams. HN001-treated females, regardless of reproductive experience, had lower density of synaptophysin immunoreactivity in the CA1, and more thick-type microglia cells in the ventral hippocampus, compared to control females. These results indicate that the probiotic, HN001, alters female rat maternal behavior, plasticity in the hippocampus, and the gut microbiota abundance, with some effects being influenced by reproductive experience.},
}

@article {pmid40695901,
year = {2025},
author = {Awad, N and Larson, PJ and Sissoko, CA and Bond, LL and Dion, GR},
title = {Metagenomic whole genome shotgun analysis of the airway microbiome in laryngotracheal stenosis: a pilot study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {26570},
pmid = {40695901},
issn = {2045-2322},
mesh = {Humans ; Pilot Projects ; *Microbiota/genetics ; *Laryngostenosis/microbiology ; *Tracheal Stenosis/microbiology ; Male ; Female ; Middle Aged ; *Metagenomics/methods ; Aged ; Metagenome ; Adult ; Tracheostomy ; Whole Genome Sequencing ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; },
abstract = {The airway microbiome has been implicated in the pathogenesis of laryngotracheal stenosis (LTS), yet prior studies using 16 S rRNA sequencing have limited sub-genus level resolution. Metagenomic whole genome shotgun sequencing (mWGS) allows for strain-level taxonomic and functional genomic analysis, providing detailed insights into specific organisms and pathways. A pilot study was conducted to explore the advantages and challenges of mWGS in investigating the airway metagenome in LTS. mWGS was conducted on 12 intraoperative swab samples from 8 LTS patients, divided into tracheostomy-dependent (n = 3) and non-tracheostomy (n = 5) groups, and 4 controls. Patient comorbidities, antibiotic use, and medications were documented. Biobakery workflows were used for taxonomic and functional profiling. Species-specific reference databases were constructed for 6 abundant species for strain-level analyses. LTS samples had decreased taxonomic diversity and were dominated by species with previously described roles in other chronic inflammatory processes such as Staphylococcus aureus, Streptococcus parasanguinis, Streptococcus mitis, and Corynebacterium pseudogenitalium. LTS samples were enriched for pathways involved in fatty acid biosynthesis and formaldehyde metabolism. Our results identified tracheostomy as an important potential confounder in airway metagenomics but show mWGS techniques are promising in uncovering microbiota correlates in LTS that could reveal disease-specific biomarkers, comorbidity links, and therapeutic targets.},
}

Humans
Pilot Projects
*Microbiota/genetics
*Laryngostenosis/microbiology
*Tracheal Stenosis/microbiology
Male
Female
Middle Aged
*Metagenomics/methods
Aged
Metagenome
Adult
Tracheostomy
Whole Genome Sequencing
RNA, Ribosomal, 16S/genetics
Shotgun Sequencing

@article {pmid40695592,
year = {2025},
author = {Welsch, EC and Barron, M and Storage, KM and Kazen, AB and Aboulalazm, FA and Kirby, J and Kindel, TL},
title = {Gut microbiome and bile acid changes after male rodent sleeve gastrectomy: what comes first?.},
journal = {American journal of physiology. Regulatory, integrative and comparative physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpregu.00297.2024},
pmid = {40695592},
issn = {1522-1490},
support = {R01HL158900//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; HL072483//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; Clowes Career Development Award//American College of Surgeons (ACS)/ ; },
abstract = {Background Understanding how a sleeve gastrectomy (SG) achieves metabolic improvement is challenging due to the complex relationship between the liver, bile acid (BA) pool, and gut microbiome. We hypothesized that SG alters the gut microbiome which then increases the BA pool leading to metabolic efficacy. Methods We performed fecal material transfer (FMT) from SG or sham mice to surgically-naïve mice with an intact microbiome. We evaluated the effect of surgery and FMT on BA-related liver enzymes, BA concentrations, and gut microbiome composition via 16s and metagenomic analysis. Results SG significantly deflected weight gain compared to sham surgery, 5±2 g vs 10±3 g respectively (p= 0.004). SG significantly increased the BA pool and decreased liver transcription of slc10a1 (p=0.04) and cyp8b1 (p=0.03). Random forest analysis identified several features with significantly increased relative abundance in SG compared to sham mice including Lactobacillus. Examination of metabolic profiles with metagenomic analysis revealed a BA salt hydrolase produced by the Ligilactobacillus species. FMT of SG stool to surgically-naïve mice significantly decreased the BA pool compared to sham FMT (p=0.034). Unlike SG surgery, we found no effect of SG or sham FMT on bile acid related enzymes in the liver after 14 weeks of treatment. Conclusion Overall, we propose that the metabolic benefits of SG surgery are related to decreased liver transcription of cyp8b1and slc10a1 with subsequent increases in the systemic and enterohepatic BA pool including LCA. The gut microbiome adapts to the altered BA pool with associated increases in Ligilactobacillus and bile salt hydrolase production.},
}

@article {pmid40695364,
year = {2025},
author = {Kabil, A and Liu, LT and Xu, C and Nayyar, N and Gonzalez, L and Chopra, S and Brassard, J and Beaulieu, MJ and Li, Y and Damji, A and Zandstra, PW and Blanchet, MR and Hughes, MR and McNagny, KM},
title = {Microbial dysbiosis sculpts a systemic ILC3/IL-17 axis governing lung inflammatory responses.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.mucimm.2025.07.002},
pmid = {40695364},
issn = {1935-3456},
abstract = {Advancements in vaccination and sanitation have significantly reduced the prevalence and burden of infectious diseases; however, these benefits have coincided with a marked rise in autoimmune and allergic disorders. Recent studies have investigated these linked trends through the lens of host-microbiome alterations, proposing these shifts as a potential explanatory mechanism. Previously, we demonstrated that vancomycin-induced depletion of short-chain fatty acid (SCFA)-producing bacteria results in hyperactivation of ILC2s and exacerbated allergic responses. Here we investigate the effects of low-dose streptomycin on innate and adaptive immune cell populations and their activation states. Although streptomycin-treated mice exhibit normal allergic responses, they display heightened susceptibility to Th1/Th17-mediated disease, specifically hypersensitivity pneumonitis (HP). This is characterized by a two-fold increase in ILC3s and Th17 cells in the lungs, alongside activation of antigen-presenting cells (APCs) at steady state-an effect that is further amplified upon exposure to HP-inducing agents. Shotgun metagenomic analysis revealed that streptomycin-induced dysbiosis reduces microbial diversity, depletes bile acid-metabolizing bacteria, and enriches for metabolic pathways involved in branched-chain amino acid biosynthesis, including leucine-a known activator of mTORC1. Strikingly, administration of the secondary bile acid metabolite isolithocholic acid (an inverse agonist of RORγt), or an IL-23 neutralizing antibody, reverses the enhanced susceptibility to HP. Inhibition of mTORC1 significantly reduced Th17/ILC3 responses and histopathology. Our findings underscore microbial equilibrium as a key determinant of susceptibility to HP and uncover a positive feedback loop between IL and 23-producing APCs and ILC3/Th17 cells that mechanistically links dysbiosis to sustained type 3 inflammation, and we identify a simple, actionable means of intervention.},
}

@article {pmid40695291,
year = {2025},
author = {Perl, M and Fante, MA and Herfeld, K and Scherer, JN and Poeck, H and Thiele Orberg, E},
title = {Microbiota-derived metabolites: Key modulators of cancer immunotherapies.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100773},
doi = {10.1016/j.medj.2025.100773},
pmid = {40695291},
issn = {2666-6340},
abstract = {The human gut microbiome shapes local and systemic immune responses and influences cancer immunotherapy outcomes. Microbial metabolites, including short-chain and branched-chain fatty acids, bile acids, tryptophan derivatives, and others, influence anti-tumor immunity by modulating immune cells, tumor growth, and the tumor microenvironment. These metabolites impact the efficacy of immune checkpoint inhibitors, allogeneic stem cell transplantation, chimeric antigen receptor T cell therapies, and immune-related adverse events. However, interindividual microbiome variability, antibiotic exposure, and the context-dependent pro- and anti-inflammatory effects of metabolites present significant challenges for clinical translation. Microbiome-based therapies, including live biotherapeutic products, dietary modifications (such as prebiotics), and synthetic metabolite compounds (postbiotics), are being developed for use in combination with immunotherapy. This review outlines how metabolites influence immunotherapy outcomes and discusses translational approaches to harness them for clinical practice. Future research should focus on validating metabolite-based biomarkers and tailoring metabolite-based interventions to enhance efficacy and reduce toxicity across different immunotherapies.},
}