@article {pmid41344748,
year = {2025},
author = {Suzuki, T and Ding, H and Yuan, F and Li, Y and Ren, J and Zhan, H and Israr, MZ and Sun, X and Qiu, Z and Sheng, H},
title = {Association of Gut Microbiome Biomarkers With Mortality in Chinese Patients With Acute/Worsening Heart Failure.},
journal = {JACC. Asia},
volume = {5},
number = {12},
pages = {1634-1637},
doi = {10.1016/j.jacasi.2025.09.023},
pmid = {41344748},
issn = {2772-3747},
}

@article {pmid41344619,
year = {2025},
author = {Li, Y and Li, T and Zhang, Y and Wang, Y and Wu, G and Tan, Y},
title = {Microbial metabolites in the gut-brain axis: their impact on depression pathophysiology and treatment.},
journal = {Neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neuroscience.2025.12.002},
pmid = {41344619},
issn = {1873-7544},
abstract = {Gut microbiota influences major depressive disorder (MDD) via the microbiota-gut-brain axis through various metabolites, but a systematic understanding of their neuroregulatory mechanisms is lacking. This review categorizes gut microbial metabolites according to their metabolic origin and physiological function, clarifies their roles in depression-related neurobiological processes, and explores their therapeutic potential. Following PRISMA-ScR guidelines, a scoping review screened 1,249 records from five databases (2020-2025), including 23 studies on tryptophan metabolism, short-chain fatty acids (SCFAs), gamma-aminobutyric acid (GABA), and other metabolites that regulate depression-related neurobiological pathways; tryptophan metabolism affects serotonin/kynurenine pathways, causing neuroinflammation and neurotransmitter imbalance; SCFAs(primarily butyrate, less so propionate) modulate gene expression, neuroinflammation, and microglial function as histone deacetylase (HDAC) inhibitors; GABA-producing bacteria influence synaptic plasticity and suppress hypothalamic-pituitary-adrenal (HPA) axis hyperactivity; and other metabolites (e.g., homovanillic acid and β-hydroxybutyrate) have neuroprotective effects and affect neurotransmitter dynamics. Notably, this review advances the field via an integrative cross-pathway perspective, a critical appraisal of evidence strength across animal/human studies, and translational implications. Microbiome-modifying interventions (like probiotics, prebiotics, and dietary changes, are promising in animal models for correcting metabolite dysregulation and alleviating depressive symptoms.},
}

@article {pmid41344580,
year = {2025},
author = {Tariq, F and Zhao, L and Hussain, S and Riaz, MW and Wu, C and Zhang, J and Li, P and Gowda, M and Nair, SK and Prasanna, BM and Zhang, X and Wang, X and Gangurde, SS},
title = {Plasticity and adaptive architecture of roots for enhanced salinity tolerance in crops.},
journal = {Biotechnology advances},
volume = {},
number = {},
pages = {108773},
doi = {10.1016/j.biotechadv.2025.108773},
pmid = {41344580},
issn = {1873-1899},
abstract = {Soil salinization poses a major challenge to global food security, affecting over one billion hectares of arable land and severely constraining crop productivity. As the primary interface between plants and soil, roots play a pivotal role in sensing and adapting to salinity stress through remarkable structural and functional plasticity. This review integrates recent advances in root system architecture (RSA) dynamics, suberin biosynthesis, hormonal regulation, and microbiome interactions to elucidate how plants achieve salinity resilience. We discuss key genes and regulatory modules controlling primary root elongation, lateral root patterning, and barrier formation, emphasizing transcriptional networks involving MYB, NAC, and WRKY families and their coordination with ABA, auxin, and ethylene signaling. Special attention is given to the biosynthesis and deposition of suberin as a dynamic ion-selective barrier governed by hormonal crosstalk and lipid metabolism. We further highlight how beneficial microbes such as Azospirillum, Bacillus, and arbuscular mycorrhizal fungi enhance salt tolerance by modulating phytohormones, antioxidant systems, and ionic homeostasis. Integrating multi-omics and CRISPR-based tools with microbiome engineering offers new avenues to design salt-resilient root ideotypes. We propose a conceptual framework linking molecular regulation, hormonal dynamics, and rhizosphere ecology to root system plasticity, providing a blueprint for engineering next-generation crops capable of maintaining growth and productivity in saline environments.},
}

@article {pmid41344505,
year = {2025},
author = {Rizwan, A and Karim, S and Andrabi, IL and Mushtaq, M and Farooqi, H},
title = {Fermentation Alters the Anticancer Properties of Dietary Polyphenols in Pulses.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tjnut.2025.11.023},
pmid = {41344505},
issn = {1541-6100},
abstract = {Pulses are a rich dietary source of polyphenols, compounds increasingly known for their role in disease prevention and overall health. Recent advances show that fermentation can not only improve the bioavailability of pulse polyphenols but can also generate new metabolites. This review explores how these fermentation-driven molecular transformations enhance the anticancer effect of pulse polyphenol, highlighting newly identified microbial metabolite pathways. We also describe how fermented polyphenols interact with the gut microbiome, influencing pathways linked to cancer. Looking ahead, precision fermentation and multi-omics profiling promise to accelerate the development of next-generation functional foods and support cancer therapeutics, bridging the gap between laboratory innovation and clinical application.},
}

@article {pmid41344385,
year = {2025},
author = {Piccolo, L and Sligar, K and Kuster, A},
title = {Reevaluating Neonatal Erythromycin Prophylaxis Policy Amid Advances in Sexually Transmitted Infection Screening, Antenatal Treatment, and Antibiotic Stewardship.},
journal = {Journal of obstetric, gynecologic, and neonatal nursing : JOGNN},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jogn.2025.11.003},
pmid = {41344385},
issn = {1552-6909},
abstract = {Long-standing mandates in the United States require universal ophthalmic prophylaxis with erythromycin for all neonates, although recent evidence has led to reconsideration of this practice. This intervention was originally adopted to prevent blindness caused by Neisseria gonorrhoeae (gonococcal ophthalmia neonatorum, GON) and Chlamydia trachomatis (chlamydial ophthalmia neonatorum, CON). Today, however, prenatal screening and treatment have rendered such infections rare at birth. Current population data indicate that GON is exceedingly uncommon in the United States and that erythromycin is ineffective at preventing CON. Moreover, concerns regarding antimicrobial resistance, medication shortages, and early microbiome disruption call into question the rationale for maintaining this policy. In this analysis, we integrate contemporary epidemiologic and policy evidence to support the conclusion that continuing universal prophylaxis provides minimal clinical benefit, exposes newborns to unnecessary antibiotics, and conflicts with modern principles of antibiotic stewardship. Risk-based prevention models already adopted in many high-income countries offer a safer and more evidence-aligned alternative. Nurses are uniquely positioned to lead this transition through patient education, antibiotic stewardship, and advocacy for evidence-based neonatal care.},
}

@article {pmid41344333,
year = {2025},
author = {Cao, Y and Bowker, MA and Feng, Y and Delgado-Baquerizo, M and Xiao, B},
title = {The Great Wall of China harbors a diverse and protective biocrust microbiome.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.087},
pmid = {41344333},
issn = {1879-0445},
abstract = {The Great Wall of China, one of the most emblematic human heritage sites ever built, is largely covered by a living skin that has a potentially distinct microbiome compared with bare wall surfaces. However, the structure and function of this microbiome remain virtually unknown, which hampers any effort to understand the impacts of this microbiome on the long-term conservation of the Great Wall. Here, we investigated the microbiome of the Great Wall at six sampling sites along a 600-km section, which stretches across arid and semiarid climates and is covered by a mosaic of biological soil crusts (biocrusts) and exposed wall surfaces. We hypothesized that these biocrusts could establish a unique microhabitat and support a microbiome with a community structure and function potentially distinct from those on bare walls, thereby modulating the biodeterioration processes affecting the Great Wall. Our findings revealed that biocrust-covered sections exhibited a 12%-62% increase in abundance, diversity, and co-occurrence network complexity for bacterial and fungal communities compared with bare walls. Further metagenomic analyses indicated that the biocrust cover enhanced the abundance of overall functional genes and stress-resistance pathways within the microbiome by 4%-15%, while decreasing the metabolic pathways linked to heritage biodeterioration. Aridity was an additional determinant of the microbiome. Our work serves as a critical step toward understanding the microbiome of the Great Wall, which contributes to conserving this unparalleled human monument for future generations.},
}

@article {pmid41344294,
year = {2025},
author = {Sazykina, M and Lanovaya, O and Barabashin, T and Azhogina, T and Klimova, M and Karchava, S and Khmelevtsova, L and Khammami, M and Polinichenko, A and Sazykin, I},
title = {Ecotoxicity and antibiotic resistance genes in hydrobionts of the Azov Sea.},
journal = {Marine environmental research},
volume = {214},
number = {},
pages = {107759},
doi = {10.1016/j.marenvres.2025.107759},
pmid = {41344294},
issn = {1879-0291},
abstract = {Antimicrobial resistance is a major global health problem. Natural ecosystems, especially aquatic environments and aquatic animals, are important reservoirs of ARGs and antibiotic-resistant bacteria (ARB). The presence of ARGs in the microbiome of seafood may lead to their transfer to human bacteria. While most ARG research focus on water and sediments, the role of aquatic organisms (fish, shellfish, jellyfish) as reservoirs and vectors of ARGs is poorly understood. The aim of this work is to assess ARGs distribution in bacteria associated with aquatic organisms in different ecological niches of the Azov Sea (mollusks, jellyfish and fish) using PCR analysis and to study toxicity of aquatic organisms' tissues using a battery of whole-cell bacterial lux-biosensors, as well as to search for a correlation between samples toxicity and ARGs content in them. We also evaluate the potential relationship between toxicity levels in aquatic organisms, the frequency of ARGs and mobile genetic elements (MGEs) detected. In the course of the work, it was found that the most common are the genes that determine resistance to monobactams blaCTX-M and carbapenems blaVIM-1. Microbial communities of mollusks and fish are characterized by gill bacteria being more contaminated with ARGs than the gut microbiome, which is due to the constant and direct contact of the gill epithelium with polluted aquatic environment. Statistical analysis revealed a positive link between the toxicity of the organs in which the bacteria are localized and the presence of a number of ARGs was found; these findings highlight that tissue toxicity caused by endogenous toxins or external xenobiotic pollutants creates an unfavorable internal environment. A correlation was also discovered between the content of individual genes, which probably indicates their colocalization on the same mobile elements of the genome. This information may be useful for better understanding the spread of antimicrobial resistance genes in aquatic animals.},
}

@article {pmid41344253,
year = {2025},
author = {Zhao, Y and An, J and Wang, Y and Chang, J and Zeng, H and Liu, S and Ding, Y and Zhou, X and Jia, S},
title = {Mechanistic insights into ozone-slurry ice synergy for preserving the quality of Litopenaeus vannamei during chilled storage.},
journal = {Food chemistry},
volume = {499},
number = {},
pages = {147318},
doi = {10.1016/j.foodchem.2025.147318},
pmid = {41344253},
issn = {1873-7072},
abstract = {Rapid post-harvest deterioration of Litopenaeus vannamei during chilled storage limits its economic value. Here, we assessed the combined treatment of ozone and slurry ice (referred to as SIO) as a preservation strategy at 4 °C, integrating physicochemical, structural and microbiome analyses. Compared with conventional icing, SIO markedly suppressed increases in total volatile basic nitrogen, K value, and total viable count. Meanwhile, SIO preserved inosine monophosphate by inhibiting acid phosphatase activity, while mitigating protein degradation to maintain myofibrillar integrity. High-throughput sequencing revealed that SIO decreased the relative abundance of Cupriavidus, and suppressed the proliferation of spoilage-associated genera Psychrobacter, Vibrio, and Shewanella. The K value in the CK group exceeded 60 % by day 5, whereas SIO postponed this threshold to day 7, effectively extending shelf life by 2 days. These findings demonstrate that SIO provides synergistic microbial suppression and biochemical stabilization, offering a scalable, residue-free approach for maintaining the quality of seafood.},
}

@article {pmid41344097,
year = {2025},
author = {Montoro-Dasi, L and Lorenzo-Rebenaque, L and Marco-Fuertes, A and Sisquella, L and Gomez, M and Soler, P and Marco-Jiménez, F and Marin, C},
title = {Dual Salmonella vaccination attenuates microbiota dysbiosis and enhances microbiota functionality in poultry challenged with S. Typhimurium.},
journal = {Poultry science},
volume = {105},
number = {1},
pages = {106140},
doi = {10.1016/j.psj.2025.106140},
pmid = {41344097},
issn = {1525-3171},
abstract = {Salmonella is a leading cause of gastrointestinal illness and foodborne outbreaks worldwide, with poultry products such as eggs as the primary source of infection. In this context, live attenuated vaccines play a critical role in reducing the risk of infection in poultry flocks. However, their impact on the gut microbiota remains poorly understood. Thus, the aim of this study was to evaluate the effects of a live attenuated combined vaccine against Salmonella Enteritidis and Salmonella Typhimurium on the gut microbiota of chicks challenged with S. Typhimurium, including the study of microbial balance and functionality. The trial involved 40 specific pathogen-free chicks, divided into vaccinated and control groups, all challenged with S. Typhimurium at 14 days of age. Afterwards, caecal content of 10 animals per group was collected at 7 and 14 days post infection. Then, the composition, diversity and functionality of the microbiota were analyzed using 16S rRNA sequencing and bioinformatic analysis. The results of the taxonomic analysis revealed 1,261 bacterial taxa, with Firmicutes and Proteobacteria as the dominant phyla. In addition, vaccination resulted in significant changes in microbiota composition, with marked differences in microbial diversity between groups. PLS-DA and Bayesian analysis identified key species such as Clostridium innocuum in vaccinated chicks and Eubacterium coprostanoligenes in the control group. Results also showed that vaccination promoted the growth of beneficial genera such as Lactobacillus and Blautia, which was associated with reduced Salmonella colonization and shedding. Alpha diversity analysis revealed significantly higher microbial richness and evenness in the control group. Finally, functional annotation revealed shared microbial functions between the groups, with potentially pathogenic bacteria, including Salmonella, present in both. These results suggest that vaccination improves microbiota stability and supports the protective role of beneficial bacteria against Salmonella, highlighting the importance of vaccination in improving poultry health and pathogen control throughout the food chain.},
}

@article {pmid41343929,
year = {2025},
author = {Jemimah, S and Majdalawieh, AF and Hamad, M and Mahasneh, AA},
title = {Differential analysis of microbial profiles in colorectal cancer reveals modulations corresponding to immune subtypes.},
journal = {Computers in biology and medicine},
volume = {200},
number = {},
pages = {111346},
doi = {10.1016/j.compbiomed.2025.111346},
pmid = {41343929},
issn = {1879-0534},
abstract = {The proximity of the gut microbiome to the tumor microenvironment (TME) in colorectal cancer (CRC) presents a unique ecological niche. A systematic study of tumor-microbiome interactions will facilitate a deeper understanding of the heterogeneity in immune response and clinical outcomes in CRC. Previous studies have identified specific microbial species such as Fusobacterium nucleatum, pks[+] Escherichia coli, and enterotoxigenic Bacteroides fragilis as contributors to CRC initiation and progression. However, the extent to which interactions between the microbiome and immune landscape affect prognosis and tumor heterogeneity remains poorly understood. To address this, immune subtypes from The Cancer Genome Atlas (TCGA) were integrated with microbial profiles from The Cancer Microbiome Atlas (TCMA) to examine the relationship between immune subtypes and the tumor microbiome in CRC. A cohort of 631 TCGA CRC cases with clinical, microbial and immune subtype data was analyzed. Differential abundance analysis indicated significant associations between specific taxa and immune subtypes. We demonstrate that pathogenic genera such as Selenomonas, Butyricimonas and Centipeda are significantly enriched (padjusted < 0.05) in the C2 IFN-ɣ dominant subtype. Our findings show that the abundance of pathogenic genera may play a critical role in driving the paradoxically poorer survival observed in CRC patients with the C2 subtype.},
}

@article {pmid41343559,
year = {2025},
author = {George, NA and Bradford, L and Hinz, A and El Kadi, M and Xing, L and Doukhanine, E and MacFadden, DR and Nott, C and Fralick, M and Kassen, R and Wong, A and Hug, LA},
title = {SARS-CoV-2 detection is independent of microbiome composition on surfaces in a major Ontario hospital.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0326403},
doi = {10.1371/journal.pone.0326403},
pmid = {41343559},
issn = {1932-6203},
mesh = {Ontario/epidemiology ; *COVID-19/epidemiology/virology/diagnosis/microbiology ; *SARS-CoV-2/isolation & purification/genetics ; Humans ; *Microbiota ; Hospitals ; },
abstract = {The SARS-CoV-2 pandemic has resulted in considerable mortality in hospital settings. Built environment surveillance can provide a non-invasive indicator of SARS-CoV-2 status in hospitals, but we have a limited understanding of SARS-CoV-2's microbial co-associations in the built environment, including any potential co-occurrence dynamics with pathogenic and antimicrobial-resistant microorganisms. Here we examine the microbial communities on floors and elevator buttons across several locations in two major tertiary-care Ontario hospitals during a surge in SARS-CoV-2 cases in 2020. Total microbial community composition, prevalence and type of detected antimicrobial resistance genes, and virulence factor distributions were governed by sample source rather than SARS-CoV-2 detection status. Fifteen microorganisms were identified as indicator species associated with positive SARS-CoV-2 signal, including three opportunistic pathogens (i.e., two Corynebacterium sp. and a Sutterella sp). Key clinically relevant antimicrobial resistance genes showed varying prevalence across sites within the hospital, suggesting that our workflow could inform resistance burden in hospitals. Overall, these results indicate limited or only weak interactions between microbiome composition and SARS-CoV-2 detection status in the hospital built environment.},
}

Ontario/epidemiology
*COVID-19/epidemiology/virology/diagnosis/microbiology
*SARS-CoV-2/isolation & purification/genetics
Humans
*Microbiota
Hospitals

@article {pmid41343511,
year = {2025},
author = {Mahalak, KK and Narrowe, AB and Liu, L and Firrman, J and Lemons, JMS and Van den Abbeele, P and Baudot, A and Yao, Y and Li, Y and Yu, L},
title = {The ex vivo effects of ethanolic extractions of black cumin seed, turmeric root, and Ceylon cinnamon bark on the human gut microbiota.},
journal = {PloS one},
volume = {20},
number = {12},
pages = {e0334824},
doi = {10.1371/journal.pone.0334824},
pmid = {41343511},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Plant Extracts/pharmacology/chemistry ; *Curcuma/chemistry ; *Cinnamomum zeylanicum/chemistry ; Plant Roots/chemistry ; Plant Bark/chemistry ; Male ; Adult ; Seeds/chemistry ; Fatty Acids, Volatile/metabolism ; Ethanol/chemistry ; Female ; *Nigella sativa/chemistry ; },
abstract = {Black cumin, turmeric root, and Ceylon cinnamon bark are spices that have been used for both culinary purposes and in traditional medicine practices. These spices are frequently connected with providing antidiabetic, antimicrobial, anti-inflammatory, and gastroprotective properties. However, most studies on potential health effects have not been performed in humans. Since many of the health effect claims relate to gastrointestinal health, we explored the impact of black cumin extract (BCE), turmeric root extract (TRE), and Ceylon cinnamon extract (CCE) on the human gut microbiota ex vivo using the SIFR® technology. The impact on the gut microbiota were determined using shotgun sequencing and flow cytometry, while the health-related short-chain fatty acids (SCFA) were analyzed to assess the metabolic output. While TRE and CCE had very little effect on the gut microbiota, BCE significantly increased acetate (+ 8.7mM), butyrate (+1.3mM), and propionate (+3mM) production. This related to specific increases of Alistipes onderdonkii, Alistipes shahii and particularly Candidatus Cibiobacter qucibialis, CCE and TRE increased the health related Faecalibacterium prausnitzii and Dysosmobacter welbionis, respectively, with CCE also increasing Enterococcus and Veillonella species. Overall, these findings indicate these spices may have an impact on the human gut microbiome that could explain their purported health effects.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Plant Extracts/pharmacology/chemistry
*Curcuma/chemistry
*Cinnamomum zeylanicum/chemistry
Plant Roots/chemistry
Plant Bark/chemistry
Male
Adult
Seeds/chemistry
Fatty Acids, Volatile/metabolism
Ethanol/chemistry
Female
*Nigella sativa/chemistry

@article {pmid41343437,
year = {2025},
author = {Ramírez-Larrota, JS and Juyoux, P and Guerra, P and Eckhard, U and Gomis-Rüth, FX},
title = {Correction: Biochemical and structural characterization of the human gut microbiome metallopeptidase IgAse provides insight into its unique specificity for the Fab' region of IgA1 and IgA2.},
journal = {PLoS pathogens},
volume = {21},
number = {12},
pages = {e1013742},
doi = {10.1371/journal.ppat.1013742},
pmid = {41343437},
issn = {1553-7374},
abstract = {[This corrects the article DOI: 10.1371/journal.ppat.1013292.].},
}

@article {pmid41343181,
year = {2025},
author = {Roth, TD and Russo-Savage, L and Bahojb Habibyan, Y and Keenan, CM and Wallace, LE and Nasser, Y and Mawe, GM and Lavoie, B and Sharkey, KA},
title = {Microbial dysbiosis alters serotonin signaling in a post-inflammatory murine model of visceral pain.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00240.2025},
pmid = {41343181},
issn = {1522-1547},
support = {FDN148380//Canadian Institutes of Health Research (CIHR)/ ; DK113800//HHS | National Institutes of Health (NIH)/ ; AT011203//HHS | National Institutes of Health (NIH)/ ; },
abstract = {Serotonin (5-HT) is a multifunctional signaling molecule in the gastrointestinal (GI) tract. 5-HT synthesis is regulated by the gut microbiota. Microbial dysbiosis has been implicated in visceral pain and persistent alterations in gut function that occur following inflammation. Here we tested the hypothesis that alterations in gut microbiota in a post-inflammatory model of visceral pain contribute to dysregulated 5-HT signaling. We used mice treated with dextran sodium sulfate (DSS) 42 days earlier (post-colitis) or untreated mice as donors for fecal microbiota transplants (FMTs) into germ-free mice to explore changes in enterochromaffin (EC) cell populations, expression of 5-HT synthesis, transport, and degradation genes, levels of 5-HT and its major metabolite, 5-hydroxyindoleacetic acid (5-HIAA), and 5-HT release. Significant differences were observed in EC cells, Tph1, Slc6a4, and Maoa gene expression, 5-HT and 5-HIAA levels and 5-HT release between germ-free mice and mice receiving an FMT from either control or post-colitis donor mice. We observed no differences in the total number of EC cells, Tph1, or Slc6a4 gene expression of mice after FMT from post-colitis or control mice. However, there was a significant increase in Maoa gene expression in the terminal ileum, an increased 5-HIAA/5-HT ratio in the proximal colon and reduced 5-HT release to mechanical and chemical stimulation in the proximal and distal colon after FMT from post-colitis mice. Collectively, these findings provide additional evidence that the gut microbiota regulates 5-HT signaling. Moreover, they reveal functional changes in EC cell sensitivity in the presence of an altered microbiota after recovery from inflammation.},
}

@article {pmid41342934,
year = {2025},
author = {Bell, W and Jennings, A and Bondonno, NP and Franke, A and Bang, C and Both, M and Kassubek, J and Müller, HP and Borggrefe, J and Lieb, W and Kühn, T and Cassidy, A},
title = {The gut microbiome mediates the association between a flavonoid-rich diet and MASLD in a population-level analysis.},
journal = {European journal of nutrition},
volume = {65},
number = {1},
pages = {1},
pmid = {41342934},
issn = {1436-6215},
support = {22/CC/11147//Co-Centre for Sustainable Food Systems/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Flavonoids/administration & dosage ; Male ; Cross-Sectional Studies ; Female ; *Diet/methods ; Middle Aged ; *Fatty Liver/microbiology/prevention & control/epidemiology ; Adult ; Aged ; },
abstract = {PURPOSE: A growing body of evidence suggests diets rich in flavonoids may protect against metabolic-dysfunction associated steatotic liver disease (MASLD) development and progression. As the gut microbiome is important in the biotransformation of flavonoids to their constituent bioactive metabolites, studies on the potential mediating role of the gut microbiome in the association between dietary flavonoid intakes and MASLD are warranted but lacking. Thus, this study aims to examine the associations between a diet rich in flavonoids and MASLD, and assess the potential mediating role of the gut microbiome.

METHODS: In a cross-sectional analysis (n = 531), using the FlavoDiet score (FDS), we assessed the association between a flavonoid-rich diet and MASLD (ascertained by magnetic resonance imaging) using multivariable logistic and linear regression. Additionally, we used mediation analysis to identify and assess potential 16S-derived gut microbiome mediators.

RESULTS: Each doubling of the FDS was associated with a 27% lower odds of MASLD (OR: 0.73 [95% CI 0.54-0.98], p = 0.04) after multivariable adjustment. 9.2% of this association was mediated by a greater abundance of the genus Eisenbergiella (indirect effect ß = - 0.006 [95% CI - 0.019, to - 0.000], p = 0.04).

CONCLUSION: These findings suggest that a flavonoid-rich diet is associated with better liver health, and that the abundance of the Eisenbergiella taxa may in part explain the association between a flavonoid-rich diet and MASLD.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Flavonoids/administration & dosage
Male
Cross-Sectional Studies
Female
*Diet/methods
Middle Aged
*Fatty Liver/microbiology/prevention & control/epidemiology
Adult
Aged

@article {pmid41342739,
year = {2025},
author = {Shah, UA and Cogrossi, LL and Garces, JJ and Policastro, A and Castro, F and Derkach, A and Fei, T and DeWolf, S and Grioni, M and Sisti, S and Blaslov, J and Adintori, PA and Hosszu, KK and McAvoy, D and Baichoo, M and Cross, JR and Paredes, J and Anuraj, A and Raj, SS and Pohl, C and Zordan, P and Zinsmeyer, V and Jesus Faustino Ramos, RJ and Lorenzoni, M and Gipson, B and Maclachlan, KH and Gradissimo, A and Boiocchi, L and Aleynick, N and Marchigiani, C and Pagani, S and Salehi, E and Koche, RP and Chaligne, R and Block, T and Korde, N and Tan, CR and Hultcrantz, M and Hassoun, H and Shah, GL and Scordo, M and Lahoud, OB and Chung, DJ and Landau, HJ and Peled, JU and Clementi, N and Chesi, M and Bergsagel, PL and Mailankody, S and Pollak, MN and D'Souza, A and Landgren, O and Chimonas, S and Giralt, SA and Usmani, SZ and Iyengar, NM and Lesokhin, AM and van den Brink, MRM and Bellone, M},
title = {A High-Fiber Plant-Based Diet in Myeloma Precursor Disorders - Results from the NUTRIVENTION Clinical Trial and Preclinical Vk*MYC Model.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-25-1101},
pmid = {41342739},
issn = {2159-8290},
abstract = {Consumption of a western diet and high body mass index (BMI) are risk factors for progression from pre-malignant phenotypes to multiple myeloma, a hematologic cancer. In the NUTRIVENTION trial (NCT04920084), we administered a high-fiber, plant-based diet (meals for 12 weeks, coaching for 24 weeks) to 23 participants with myeloma precursor states and elevated BMI. The intervention was feasible, improved quality of life and modifiable risk factors: metabolic (BMI, insulin resistance), microbiome (diversity, composition), and immune (inflammation, monocyte subsets). Disease-progression trajectory improved (n=2) or was stable. Findings were translated to Vk*MYC mice modeling the myeloma-precursor state, in which a high-fiber diet delayed disease progression through improved metabolism and microbiome composition leading to increased short-chain fatty acid production that reinvigorated anti-tumor immunity and inhibited tumor growth. These effects from fiber consumption were independent of calorie restriction and weight loss. A high-fiber diet is a low-risk intervention that may delay progression to myeloma.},
}

@article {pmid41342539,
year = {2025},
author = {Song, W and Zhang, S and Perez, M and Li, J and Ma, H and Thomas, T and Qiu, J-W and Qian, P-Y},
title = {Distinct patterns of microbial association across deep-sea corals from the Western Pacific Magellan Seamounts.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0209325},
doi = {10.1128/spectrum.02093-25},
pmid = {41342539},
issn = {2165-0497},
abstract = {Ahermatypic corals are common inhabitants in the Magellan Seamounts of the Western Pacific Ocean, yet their microbiomes are largely unexplored. In the present study, we used 16S rRNA gene amplicon sequencing targeting the V4 variable region to characterize the microbiomes of 30 deep-sea coral samples from 9 coral families collected from this area, including members of the families Schizopathidae, Victorgorgiidae, and Chrysogorgiidae, whose microbiomes had not been previously described. Our analyses revealed distinct patterns of microbial association between the coral families, with most coral samples being dominated by single amplicon sequence variants belonging to 11 prokaryotic genera. Ammonia-oxidizing archaea of the genus Nitrosopumilus were abundant exclusively in schizopathid corals, with relative 16S rRNA gene read abundances ranging from 29.4% to 99.8%. In contrast, Nitrosopumilus was either absent or constituted no more than 5.3% of the reads in the remaining coral families. This may be attributed to the catabolism of the protein-rich zooplankton preferred by schizopathid corals, which could, in turn, facilitate ammonia-driven carbon fixation within the holobiont. Three cladopathid corals hosted abundant sequences of two distantly related bacteria capable of utilizing nitric oxide, which could be used by the symbionts either to generate oxygen for aerobic metabolisms or be reduced as a defense against the host's antibacterial activity. The distinct patterns of microbial association between coral taxa indicate that the microbiomes have differential roles in the adaptation of the hosts to specific ecological niches in the deep-sea environments.IMPORTANCEMicrobiomes play crucial roles in host development, physiology, and health, especially in the deep-sea environments. In this study, we collected 30 deep-sea corals from the Western Pacific Magellan Seamounts at depths ranging from 805 to 5,572 m. These samples spanned nine coral families, including three whose microbiomes have not been previously described. Our analyses revealed distinct patterns of microbial association between coral taxa. A majority of the deep-sea corals were dominated by single microbial species, indicating strong selection for certain microbial symbionts and thus functions, such as chemolithoautotrophy, the production of oxygen or secondary metabolites. Furthermore, we observed an overwhelming dominance of sequences from the ammonia-oxidizing archaeal genus Nitrosopumilus exclusively in black corals from the family Schizopathidae, a phenomenon not previously reported. This may be attributed to the catabolism of the protein-rich zooplankton preferred by the schizopathid corals, which could, in turn, facilitate ammonia-driven carbon fixation within the coral holobiont.},
}

@article {pmid41342438,
year = {2025},
author = {Yaqoob, A and Sharif, MK and Haider, U and Feng, Q},
title = {Quercetin Modulates Gut Microbiome and Immune Response to Mitigate Arsenic-Induced Toxicity: Insights From a Microbiome-Immune Study.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70330},
doi = {10.1002/mnfr.70330},
pmid = {41342438},
issn = {1613-4133},
abstract = {Arsenic exposure from contaminated food and water is a global nutritional issue. Nutritional interventions indicate that dietary polyphenols, such as quercetin, may reduce these toxic effects via antioxidant and immunomodulatory properties. This study examined the protective effect of quercetin against arsenic-induced toxicity in a Wistar rat model. Twenty-four adult Wistar rats were divided into four groups as follows: control (G0), arsenic-exposed (G1; 5 mg/kg/day NaAsO2), quercetin-treated (G2; approximately 50 mg/kg/day), and co-treated (G3; arsenic + quercetin). Over 28 days, catalase (CAT), glutathione peroxidase (GPx), glutathione S-transferase (GST), superoxide dismutase (SOD), cytokine gene expression (IL-1β, IL-6, TNF-α, IL-4, IL-10, TGF-β), claudin, occludin (CLDN1, OCLN), and fecal microbial profiles (q-PCR, diversity index) were assessed. Our results demonstrate that arsenic exposure significantly reduces antioxidant enzyme levels, elevates pro-inflammatory cytokines, disrupts tight junction protein expression, and causes dysbiosis and proliferation of Proteobacteria and E. coli, ultimately damaging intestinal structure. Quercetin treatment, especially in G3, restored antioxidant levels, balanced cytokine profiles, normalized tight junction gene expression, and maintained gut microbial diversity. Histopathological and correlation analyses also confirmed structural and functional recovery of gut tissues. These findings support quercetin's potential as a dietary intervention to counteract heavy metal-induced gut disorders, reinforcing its nutritional relevance in environmental toxins.},
}

@article {pmid41342432,
year = {2026},
author = {Gonciarz, M and Wiatrak, B and Lombard, I and Konecki, Ł and Sarbinowska, J},
title = {Therapeutic Potential of Melatonin in Gastrointestinal Cancers: Molecular Mechanisms, Preclinical Evidence and Clinical Implications.},
journal = {Journal of pineal research},
volume = {78},
number = {1},
pages = {e70101},
doi = {10.1111/jpi.70101},
pmid = {41342432},
issn = {1600-079X},
support = {//The authors received no specific funding for this work./ ; },
mesh = {*Melatonin/therapeutic use/pharmacology ; Humans ; Animals ; *Gastrointestinal Neoplasms/drug therapy/metabolism ; },
abstract = {Gastrointestinal (GI) cancers remain a leading cause of global morbidity and mortality, necessitating novel therapeutic strategies. Melatonin (MEL), an indoleamine with pleiotropic biological activities, has emerged as a promising adjuvant in oncology due to its antiproliferative, proapoptotic, and antioxidant properties. This review synthesizes current evidence on MEL's molecular mechanisms in GI carcinogenesis, including modulation of NF-κB, PI3K/AKT, and Wnt/β-catenin pathways, suppression of reactive oxygen species (ROS), and regulation of circadian rhythm-related genes (e.g., CLOCK, BMAL1). Preclinical studies demonstrate that MEL enhances chemoradiotherapy efficacy-reducing tumor volume by 70% in murine colorectal models and decreasing 5-fluorouracil (5-FU) resistance via miR-532-3p/β-catenin axis modulation. Clinical trials report a 23%-41% risk reduction in colorectal cancer among shift workers with MEL supplementation and a 53% decrease in radiotherapy-induced oral mucositis. Despite promising data, limitations persist: fewer than 15% of clinical trials focus on GI cancers, dosing remains unstandardized (10-40 mg/day), and molecular heterogeneity (e.g., KRAS mutations in pancreatic cancer) may limit therapeutic responses. Future research must prioritize phase III trials, chronotherapy optimization, and biomarker-driven approaches, including MT1/MT2 receptor expression and microbiome profiling. Given its low toxicity and putative synergy with immunotherapies, MEL should be regarded as an adjunct under investigation rather than an established option; to date, no GI-specific phase III randomized trials exist, and clinical signals come primarily from small, heterogeneous cohorts. Dosing is unstandardized and limited by low oral bioavailability (first-pass) and possible pharmacogenomic variability.},
}

*Melatonin/therapeutic use/pharmacology
Humans
Animals
*Gastrointestinal Neoplasms/drug therapy/metabolism

@article {pmid41342428,
year = {2026},
author = {Astan, R},
title = {Gut microbiome-metabolome interplay in nondipper hypertension: pathophysiological insights and clinical perspectives.},
journal = {Journal of hypertension},
volume = {44},
number = {1},
pages = {231-232},
doi = {10.1097/HJH.0000000000004170},
pmid = {41342428},
issn = {1473-5598},
}

@article {pmid41342427,
year = {2026},
author = {Ozbek, DA and Altun, B},
title = {Reply to correspondence 'Gut microbiome-metabolome interplay in nondipper hypertension: pathophysiological insights and clinical perspectives'.},
journal = {Journal of hypertension},
volume = {44},
number = {1},
pages = {231},
pmid = {41342427},
issn = {1473-5598},
}

@article {pmid41342324,
year = {2025},
author = {Silber, JL and Norman, JM and Kanno, T and Crossette, EM and Szabady, R and Menon, R and Marko, M and Hao, LY and Tomsho, L and Bhagat, S and Yuan, A and Olle, B and Lamousé-Smith, E},
title = {A randomized, double-blind, placebo-controlled, single- and multiple-dose phase 1 study of VE202, a defined bacterial consortium for treatment of inflammatory bowel disease: safety and colonization dynamics of a novel live biotherapeutic product in healthy adults.},
journal = {European journal of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MEG.0000000000003098},
pmid = {41342324},
issn = {1473-5687},
abstract = {OBJECTIVES: VE202 is an oral, defined 16-strain bacterial consortium with properties that may diminish dysbiosis and alleviate symptoms of inflammatory bowel disease. This phase 1 study evaluated VE202 safety and tolerability and assessed strain colonization.

METHODS: Thirty-one healthy adults received oral vancomycin 125 mg four times daily for 5 days to decrease gut microbial burden, followed by a single dose of VE202 at 1 × 109 or 1 × 1010 colony-forming units (CFUs), or 14-days of the lower dose (1.4 × 1010 total CFU). Adverse events were monitored through week 12, with follow-up at week 24. Stool was collected for VE202 strain detection and abundance during screening and pretreatment, day 2, day 4, day 7, day 14, week 4, week 8, week 12, and optionally at week 24.

RESULTS: VE202 and vancomycin pretreatment were well tolerated. Among VE202 recipients, the most frequent adverse events (>20% of subjects) were abdominal discomfort, diarrhea, headache, and fatigue. Most treatment-related adverse events were gastrointestinal. Two serious adverse events were reported; these were not treatment-related and occurred weeks after dosing completion. VE202 strain detection and relative abundance in the vancomycin-perturbed gut occurred as soon as day 2, sustained through 2 weeks postdosing, then declined slowly but remained substantially above baseline through week 24. Colonization was dose- and duration-dependent, with 14-day dosing providing more durable VE202 colonization.

CONCLUSION: VE202 was well tolerated. Following antibiotic pretreatment, rapid and durable gut colonization of VE202 strains was observed, most significantly in participants administered multiple doses (NCT03931447).},
}

@article {pmid41341909,
year = {2025},
author = {Yang, L and Wang, Y and Yuan, L and Tang, W},
title = {Advances in research on congenital and hereditary intestinal diseases: From molecular mechanisms to precision medicine.},
journal = {Intractable & rare diseases research},
volume = {14},
number = {4},
pages = {258-265},
pmid = {41341909},
issn = {2186-3644},
abstract = {Congenital and hereditary intestinal diseases are a group of major disorders caused by gene mutations or embryonic developmental anomalies and are characterized by diverse clinical manifestations and complex management. This review systematically explores the molecular genetic basis and pathogenic mechanisms of common intestinal diseases, including familial adenomatous polyposis (FAP), Peutz-Jeghers syndrome (PJS), Lynch syndrome (LS), Hirschsprung disease (HSCR), congenital short bowel syndrome (SBS), and cystic fibrosis (CF). It focuses on cross-disease commonalities in translational research frontiers such as gene-environment interactions, organoid-based precision medicine, the immune microenvironment, and metabolic and microbiome remodeling. The review also forecasts future directions, including gene therapy, targeted drugs, and other cutting-edge research advances.},
}

@article {pmid41341501,
year = {2025},
author = {Deng, X and Wu, X and Wang, R and Qiao, X and Cao, T and Xu, Y and Jin, Q and Jia, L and Liang, W},
title = {Gut microbiota-based biomarkers for precision subtype classification and mechanistic understanding of biliary and hyperlipidemic acute pancreatitis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1695811},
pmid = {41341501},
issn = {1664-302X},
abstract = {BACKGROUND: Acute pancreatitis (AP) is an inflammatory disorder with distinct etiological subtypes, yet the role of gut microbiota in disease pathogenesis remains poorly understood. We hypothesized that biliary acute pancreatitis (BAP) and hyperlipidemic acute pancreatitis (HLAP) exhibit etiology-specific gut microbiota signatures that correlate with disease severity and metabolic dysfunction.

METHODS: We conducted a cross-sectional study in which stool samples were collected from 20 BAP patients, 20 HLAP patients, and 20 healthy controls (HC) for 16S rRNA gene sequencing to compare gut microbiota profiles among the three groups. Microbial diversity, taxonomy, and functional genes were analyzed using bioinformatics pipelines. Clinical-microbial correlations were assessed, and the construction of RF and logistic regression models evaluated diagnostic biomarker potential.

RESULTS: Both AP groups showed significantly reduced microbial diversity compared to controls, with HLAP patients exhibiting more severe dysbiosis. HLAP patients showed enrichment of pro-inflammatory taxa, including Escherichia-Shigella and Collinsella, alongside depletion of beneficial genera Faecalibacterium and Bifidobacterium. As a key SCFA-producing genus, Faecalibacterium exhibited comprehensive correlations with inflammatory markers, pancreatic enzymes, and lipid profiles in Spearman correlation analysis. Functional analysis revealed compromised short-chain fatty acid biosynthesis capacity, as evidenced by significant downregulation of acetate (ackA, pta) and butyrate (buk, but) synthesis genes in AP patients, which may have partially mediated the observed differences in microbiota composition. Furthermore, our findings reveal that multi-species biomarker panels provide superior diagnostic performance compared to single-species predictors for BAP and HLAP subtype classification.

CONCLUSION: BAP and HLAP patients exhibit distinct gut microbiota signatures with progressive dysbiosis, functional impairment, and strong host associations. These findings establish a novel framework linking gut microbial composition to AP pathophysiology, providing insights for microbiome-targeted precision medicine strategies.},
}

@article {pmid41341495,
year = {2025},
author = {Rana, TS and Bansode, RR and Rana, JP and Williams, LL},
title = {A systematic review: polyphenol's effect on food allergy via microbiome modulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1673472},
pmid = {41341495},
issn = {1664-302X},
abstract = {INTRODUCTION: Food allergy is an increasing health concern worldwide. Microbes, food allergies, and polyphenols are found to be interrelated. However, studies relating polyphenols' effect on food allergy via microbiome modulation are scarce, and there is a lack of common signature microbiome modulation patterns. Thus, this review aims to summarize the effect of polyphenols on food allergy via microbiome modulation.

METHODS: Research articles were searched from Scopus, PubMed, ScienceDirect, and Web of Science database. The in vivo and in vitro studies were assessed via SYRCLE risk of bias and modified CONSORT checklist, respectively. The population characteristics and experimental details were extracted, and the data were synthesized narratively.

RESULTS: The included studies were free of selective reporting of results. The allergy of egg (ovalbumin), milk (𝛽-lactoglobulin), soybean (𝛽-conglycinin), and shrimp allergy contributed to 54%, 23%, 15%, and 8% of the total included studies, respectively. The used compounds were a different source or types of polyphenols such as cocoa, cyanidin-3-O-glucoside (C3G), avenanthramide's (AVA), rosmarinic acid (RA), neohesperidin, and fermented apple juice for egg allergy, luteolin, and green tea polyphenol (GTP) for soybean allergy, and flavonoids (Luteolin, myricetin and hyperoside), ferulic acid, and luteolin for milk allergy. Allergies of milk, egg, wheat, and shrimp occurred with the reduction of Lactobacillus, Alistipes, Odaribactor, Akkermansia, Bacteroides, and Lachnospiraceae_NK4A136_group and an increase of Prevotella, Alloprevotella, Faecalibaculum, Helicobactor, Blautia, Clostridium, and Staphylococcus. The polyphenols modulated these microbes in order to attenuate the food allergies.

DISCUSSION: The types of polyphenols, food allergies, animal model used, and taxonomic resolution of the microbiome studies lead to variation in the results. Thus, by increasing the studies on effect of polyphenols on individual food allergies, and combining with higher taxonomic resolution techniques such as shotgun metagenomics along with metabolomics would increase reliability of the results of the future studies.},
}

@article {pmid41341407,
year = {2025},
author = {Arshad, MT and Maqsood, S and Hossain, MS and Awlqadr, FH and Rauf, A and Ullah, I and Ikram, A and Bibi, A and Mukhtar, S and Abdullahi, MA},
title = {Integrating Microbiomes for Regenerative Food Systems: Recent Insights, Implementations, and Emerging Trends.},
journal = {Food science & nutrition},
volume = {13},
number = {12},
pages = {e71312},
pmid = {41341407},
issn = {2048-7177},
abstract = {Microbiomes play a central role in food science by influencing food quality, safety, sustainability, and human health. This review brings together contemporary advancements in the understanding and use of microbiomes in the food system, with a focus on sustainable agriculture, fermentation, food safety, and nutrition. We discuss both traditional approaches (e.g., natural fermentation and soil management) and new high-tech strategies, including precision microbiome engineering, synthetic biology, and machine learning. The major applications under consideration are microbiome-based food preservation, biofertilisers and biopesticides, waste valorisation, and alternative protein production. The socioeconomic context is also being considered, recognizing that while recent advances are more pragmatic in high-income countries, traditional and low-input approaches are still critical in low- and middle-income country (LMIC) settings. The emphasis in this review is laid on food science and food systems, and nutrition and health effects are considered as downstream consequences. The readership includes food scientists, microbiologists, agricultural researchers, and policy decision-makers who care about the integration of microbiome science into resilient and sustainable food systems. By presenting a fair representation of standard and advanced microbiome techniques, this review delineates the prospects and challenges in the application of microbial communities in shaping the future of food.},
}

@article {pmid41341259,
year = {2025},
author = {Wang, Y},
title = {Linear Dimensionality Reduction Methods for Analyzing Structured Biomedical Data: Existing Research and Future Opportunities.},
journal = {Wiley interdisciplinary reviews. Computational statistics},
volume = {17},
number = {3},
pages = {e70045},
pmid = {41341259},
issn = {1939-5108},
abstract = {High-dimensional biomedical data often exhibit complex structural features that challenge traditional analytical methods. These features include distributional structures, such as count and sparse data in single-cell RNA-seq studies; correlation structures among biomarkers, such as phylogenetic relationships in microbiome studies; and correlation structures among samples, such as spatial correlations in spatial transcriptomics. Dimensionality reduction methods that account for these structures are essential for extracting biologically meaningful insights. This article provides a selected review of existing linear dimensionality reduction methods for both supervised and unsupervised analysis of structured data. Leveraging a unified framework based on low-rank-plus-noise models, we conduct theoretical and numerical comparisons of these methods. Our review aims to equip researchers with a deeper understanding of the strengths and limitations of various structured dimensionality reduction techniques, aiding in the selection of the most suitable approach for their data. Finally, this review highlights several promising directions for future research, offering opportunities for advancements in dimensionality reduction methods tailored to the unique complexities of structured biomedical data. This article is categorized under: Statistical Learning and Exploratory Methods of the Data Sciences > Modeling MethodsStatistical and Graphical Methods of Data Analysis > Multivariate AnalysisStatistical and Graphical Methods of Data Analysis > Dimension Reduction.},
}

@article {pmid41341205,
year = {2025},
author = {Yue, Z and Li, C and Yan, F and Guan, S and Fan, Y and Chen, X},
title = {The oral microbiome in aging: a window into health and longevity.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2589648},
pmid = {41341205},
issn = {2000-2297},
abstract = {BACKGROUND: Aging is characterized by progressive physiological decline and increased susceptibility to age-related diseases. The oral microbiome, a complex community of microorganisms, has been increasingly recognized as a potential key player in the aging process.

OBJECTIVE: This review aims to explore and summarize the relationship between the oral microbiome and aging, with a specific focus on contrasting microbial changes in healthy and unhealthy aging populations.

DESIGN: We conducted a comprehensive review of the current literature to synthesize evidence on oral microbiome shifts during aging, the influencing factors, associations with age-related conditions, and potential interventions.

RESULTS: Evidence indicates that the composition of the oral microbiome changes with age, although findings on diversity are inconsistent, with reports of both increases and decreases in older adults. These shifts are influenced by factors such as diet, oral hygiene, and immune function. Unhealthy aging, including conditions like frailty, neurodegenerative diseases, and sarcopenia, is associated with distinct oral dysbiosis. Potential mechanisms linking the oral microbiome to aging include chronic inflammation and immunosenescence. Interventions targeting the oral microbiome, such as probiotics and dietary modifications, show promise in promoting healthspan.

CONCLUSIONS: The oral microbiome is significantly altered during aging and is implicated in age-related health status. It represents a promising target for strategies aimed at promoting healthy aging. Future research should prioritize elucidating the functional mechanisms of oral microbiota and developing targeted microbiome-based interventions.},
}

@article {pmid41340927,
year = {2025},
author = {Samuel David, AV and María Del Rocío, PR},
title = {Termites and their gut microbiome in animal nutrition: Advances and biotechnological applications.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {23},
number = {},
pages = {527-534},
pmid = {41340927},
issn = {2405-6383},
abstract = {Since the late 20th century, termites have attracted attention due to the vast potential of their gut microbiome and digestive enzymes, which enable them to efficiently degrade lignocellulosic biomass, making them a promising resource for animal nutrition, particularly for recovering fibrous waste. Termite gastrointestinal symbionts and enzymes are highly effective at decomposing plant fiber, thus positioning them as natural bioreactors with significant biotechnological potential. This review examines the evolving applications of termites in animal feed, including their incorporation as protein sources in diets for monogastric animals and fish, as well as the utilization of bacteria, fungi, and enzymes derived from their guts as additives to enhance the digestibility of agricultural byproducts in both ruminants and non-ruminants. Furthermore, recent developments have demonstrated the identification and heterologous expression of lignocellulolytic enzymes and metabolites with prebiotic and detoxifying properties. The diversity of termite species offers an exceptional source of microbial communities. These communities highly adaptable to various fibrous substrates due to their diet, which enhances their potential despite existing limitations in cultivation and process standardization. However, their gut microbiota remains an untapped resource with immense potential to improve feed efficiency, promote sustainability, and reduce reliance on conventional inputs. It is concluded that at larger scale in vivo studies are needed to fully realize the potential of these symbiotic systems in animal nutrition.},
}

@article {pmid41340567,
year = {2025},
author = {Ouradova, A and Ferrero, G and Bratova, M and Daskova, N and Bohdanecka, A and Dohnalova, K and Heczkova, M and Chalupsky, K and Kralova, M and Kuzma, M and Modos, I and Tichanek, F and Najmanova, L and Pardini, B and Pelantová, H and Tarallo, S and Videnska, P and Gojda, J and Naccarati, A and Cahova, M},
title = {A vegan diet signature from a multi-omics study on different European populations is related to favorable metabolic outcomes.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2593050},
doi = {10.1080/19490976.2025.2593050},
pmid = {41340567},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Vegan ; Male ; Female ; Adult ; Czech Republic ; Cross-Sectional Studies ; *Metabolome ; Middle Aged ; Italy ; *Bacteria/classification/metabolism/genetics/isolation & purification ; Vegans ; Metagenome ; Multiomics ; },
abstract = {Vegan and omnivorous diets differ markedly in composition, but their effects on the gut microbiome, metabolome, and lipidome across populations remain insufficiently characterized. While both diet and country of origin influence these molecular layers, the relative contribution of diet versus country-specific factors has not yet been systematically evaluated within a multi-omics framework.In this cross-sectional, bicentric, observational study, we profiled healthy vegans (n = 100) and omnivores (n = 73) from the Czech Republic and Italy using integrated microbiome, metabolome, and lipidome analyses. Findings were subsequently validated in an independent cohort (n = 142).Significant differences across all omics layers were observed for both country and diet. The predictive models confirmed diet-associated separation, with validation cohort AUCs of 0.99 (lipidome), 0.89 (metabolome), and 0.87 (microbiome). Functional metagenome analysis revealed enrichment of amino acid biosynthesis, inositol degradation, and the pentose phosphate pathway in vegans, while omnivores presented greater potential for amino acid fermentation, fatty acid biosynthesis, and propanoate metabolism. Linear models identified a robust, country-independent "vegan signature" consisting of 27 lipid metabolites, five non-lipid metabolites, and 11 bacterial species. Several lipid features associated with an omnivorous diet were inversely related to the duration of vegan diet adherence. Some of the vegan-associated metabolites and bacteria have been previously linked to favorable cardiometabolic profiles, although causality remains to be established.These findings demonstrate that vegan diets are associated with reproducible, country-independent molecular and microbial signatures. Our results highlight diet-driven shifts in host-microbiota interactions and provide a framework for understanding how dietary patterns relate to host-microbiota interactions.},
}

Humans
*Gastrointestinal Microbiome
*Diet, Vegan
Male
Female
Adult
Czech Republic
Cross-Sectional Studies
*Metabolome
Middle Aged
Italy
*Bacteria/classification/metabolism/genetics/isolation & purification
Vegans
Metagenome
Multiomics

@article {pmid41340403,
year = {2025},
author = {Park, J and Cheon, JH},
title = {The epidemiology of inflammatory bowel disease: exploring the impacts of environmental factors.},
journal = {The Korean journal of internal medicine},
volume = {},
number = {},
pages = {},
doi = {10.3904/kjim.2025.083},
pmid = {41340403},
issn = {2005-6648},
abstract = {Inflammatory bowel diseases (IBD), such as ulcerative colitis and Crohn's disease, are distinct chronic immune-mediated intestinal inflammatory disorders. The pathogenesis of IBD is complex and involves a combination of genetic and environmental factors, the gut microbiome, and the host immune system. Despite significant progress in identifying the genetic factors of IBD, the increasing IBD incidence in recent decades, along with findings from immigrant and twin studies, suggest the involvement of environmental factors on IBD susceptibility. In this review, we summarize various up-to-date environmental factors, including early-life influences; diet, food, and nutritional exposures; urbanization and air pollution; smoking; appendectomy; medications; psychological stress; sleep; and latitude and geography.},
}

@article {pmid41340205,
year = {2025},
author = {Chakraborty, S and Guo, Z},
title = {Invisible contaminants, irreversible consequences? LDPE residues twist the Arabidopsis holobiome.},
journal = {Journal of experimental botany},
volume = {76},
number = {22},
pages = {6569-6572},
doi = {10.1093/jxb/eraf388},
pmid = {41340205},
issn = {1460-2431},
support = {NE/B000187/1//UKRI NERC Independent Research Fellowship/ ; EP/X525662/1//Engineering and Physical Sciences Research Council/ ; 202106300062//China Scholarship Council/ ; },
}

@article {pmid41340173,
year = {2025},
author = {Zhang, X and Dong, TS and Gee, GC and Kilpatrick, LA and Beltran-Sanchez, H and Wang, MC and Vaughan, A and Church, A},
title = {Social bonds and health: exploring the impact of social relations on oxytocin and brain-gut communication in shaping obesity.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2566978},
doi = {10.1080/19490976.2025.2566978},
pmid = {41340173},
issn = {1949-0984},
mesh = {Humans ; *Oxytocin/blood ; *Obesity/psychology/microbiology/metabolism ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/physiology ; *Brain/physiology/metabolism ; Body Mass Index ; Feeding Behavior/psychology ; Middle Aged ; Young Adult ; *Brain-Gut Axis ; *Interpersonal Relations ; },
abstract = {Social relationships play a crucial role in shaping health. To better understand the underlying mechanisms, we explored the independent and interactive effects of perceived emotional support (PES) and marital status on body mass index (BMI), eating behaviors, brain reactivity to food images, plasma oxytocin, and alterations in the brain-gut microbiome (BGM) system. Brain responses to food stimuli, fecal metabolites, and plasma oxytocin levels were measured in 94 participants. Structural equation modeling was used to determine the integrated pathways linking social factors to obesity-related outcomes. Marital status and PES interact and independently influence lower BMI, healthier eating behaviors, increased oxytocin levels, food-cue reactivity in frontal brain regions involved in craving inhibition and executive control, and tryptophan-pathway metabolites related to inflammation, immune regulation, and energy homeostasis. These findings suggest that supportive human relationships, particularly high-quality marital bonds, may regulate obesity risk through oxytocin-mediated alterations in brain and gut pathways.},
}

Humans
*Oxytocin/blood
*Obesity/psychology/microbiology/metabolism
Male
Female
Adult
*Gastrointestinal Microbiome/physiology
*Brain/physiology/metabolism
Body Mass Index
Feeding Behavior/psychology
Middle Aged
Young Adult
*Brain-Gut Axis
*Interpersonal Relations

@article {pmid41340151,
year = {2025},
author = {Kropp, DR and Glover, ME and Samanta, R and Unroe, KA and Clinton, SM and Hodes, GE},
title = {Perinatal citalopram exposure alters the gut composition and microbial metabolic profiles of Sprague-Dawley rat dams and female offspring but not male offspring.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-025-00794-5},
pmid = {41340151},
issn = {2042-6410},
support = {R01MH105447-01/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Selective serotonin reuptake inhibitors are widely prescribed during pregnancy. Their main route of administration is through the gut. However, their impact on the maternal and offspring gut microbiome and microbial metabolic pathways remains poorly understood. This study used metagenomic shotgun sequencing to examine the effects of perinatal citalopram exposure in rat dams and their offspring on gut composition and downstream metabolic pathways.

METHODS: We treated pregnant and nursing rat dams with either citalopram or vehicle (water). Their feces were collected, DNA from these samples was extracted and then sequenced using shotgun metagenomic sequencing. The BioBakery suite of microbiome analysis tools was utilized in tandem with RStudio to analyze the gut composition and microbial metabolic pathways of the rat dams and their offspring.

RESULTS: Pregnant and nursing dams treated with citalopram exhibited marked shifts in microbial community structure, including phylum-level alterations in Proteobacteria and Defferibacteria. Citalopram treated dams displayed significantly altered beta diversity. Species level alterations due to treatment were composed of five significantly altered microbes, two of which belong to the Proteobacteria phylum. These changes were highly diverse and were not congruent with microbe-level alterations observed in offspring. Alpha diversity of microbial metabolic pathways was compared using the Gini-Simpson index, which was significantly increased in dams suggesting greater metabolic functional diversity with age. Female offspring perinatally exposed to citalopram showed significant changes in gut beta diversity, with seven significant alterations at the microbe level. These microbial shifts were accompanied by twenty-one significantly altered microbial metabolic pathways. In contrast, male offspring showed no significant differences in microbial composition or beta diversity and only minor metabolic changes.

CONCLUSIONS: These findings demonstrate that maternal citalopram exposure during pregnancy and lactation has lasting, sex-specific impacts on the offspring's gut microbiome and microbial metabolic pathways. The pronounced alterations in female, but not male offspring, suggest that host sex may be a critical determinant in the developmental response to citalopram exposure. This work underscores the value of metagenomic approaches in uncovering complex host-microbiome interactions and highlights the need to consider offspring sex in evaluating the safety and long-term effects of antidepressant use during pregnancy.},
}

@article {pmid41340133,
year = {2025},
author = {Abavisani, M and Sajjadi, SM and Ebadpour, N and Karav, S and Sahebkar, A},
title = {Gut microbiota-cholesterol crosstalk in cardiovascular diseases: mechanisms, metabolites, and therapeutic modulation.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-025-01051-7},
pmid = {41340133},
issn = {1743-7075},
abstract = {Cardiovascular diseases (CVD) are one of the leading causes of death worldwide. Genetic factors, and various environmental factors, including nutrition and the composition of the gut microbiota, have been identified as important factors in the initiation of CVD. Among them, the pivotal role of the gut microbiota in modulating cholesterol metabolism and influencing cardiovascular outcomes has recently been highlighted. Extensive research has confirmed that the gut microbiota has direct and indirect regulatory effects on host cholesterol homeostasis. Recent studies have shown that the microbiota can influence blood cholesterol levels and thus the risk of CVD through various pathways, such as the production of certain metabolites such as bile acids (BAs), SCFAs, and TMAO, the activation of nuclear and membrane-bound receptors such as farnesoid X receptor (FXR), the regulation of gene expression involved in lipid metabolism and inflammatory responses, as well as microbial enzymatic pathways. These complex regulatory mechanisms make the gut microbiota a potential therapeutic target in cholesterol-related diseases and CVD. Microbiota-modulating strategies, including the use of probiotics, prebiotics, fecal microbiota transplantation (FMT), and selective antibiotics, have shown beneficial effects in previous studies. In this regard, in this study, we conducted an in-depth investigation of the regulatory effect of intestinal microbiota on cholesterol metabolism and their impact on the development and progression of atherosclerosis and CVD, and described potential therapeutic pathways based on the regulation of intestinal microbiota in CVD.},
}

@article {pmid41340088,
year = {2025},
author = {Hu, J and Guo, P and Yu, J and Zhang, T and Yang, X},
title = {Oral and fecal microbiota in Chinese adults with obesity reveal potential niche-specific microbiota associated with obesity.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04561-9},
pmid = {41340088},
issn = {1471-2180},
abstract = {BACKGROUND: Obesity has emerged as a global health crisis. Increasing evidence suggests that imbalances in gut and oral microbiota are linked to obesity, with specific microbial profiles influencing metabolic dysfunction and weight gain. Given the distinct ecological niches and the importance of gut and oral microbiota in obesity, this study analyzed both oral and fecal microbiota in adults with obesity, aiming to identify potential niche-specific microbial signatures associated with the condition.

RESULTS: The comparison of fecal and oral microbiota communities between individuals with obesity and non-obese controls revealed significant differences in microbial composition and diversity. The predominant genera identified in both sample types were Prevotella, Faecalibacterium, Streptococcus, and Porphyromonas. A notable restructuring of microbial communities was observed between fecal and oral samples, regardless of obesity status. Furthermore, obesity-associated changes in microbial co-occurrence networks were found to be niche-specific, with reduced modularity in stool samples. In contrast, saliva microbial networks appeared to be more compartmentalized than those in stool. MaAsLin 3 and ANCOM-BC2 analyses identified five niche-specific taxa associated with obesity. These included positive associations in saliva with Granulicatella sp902479935, Lancefieldella sp938036925, Peptostreptococcus stomatis, Rothia sp916715725, as well as a negative association in saliva with Faecalibacterium sp934503275. Mediation analysis indicated that the second principal component partially mediated these effects, with Lancefieldella sp938036925 and others serving as positive contributors. The taxa Wolinella, Phocaeicola, and Bulleidia, which exhibited high abundance in saliva, were consistently selected by all machine learning models.

CONCLUSIONS: This study contributes to the growing body of literature investigating the relationship between obesity and microbial communities. Using 16 S rRNA gene amplicon sequencing, we characterized distinct microbial compositions in both saliva and fecal samples from individuals with obesity compared to normal-weight controls within a defined geographic population. The results suggest that the salivary microbiome may contain potential associative biomarkers indicative of obesity risk, warranting further in-depth investigation.},
}

@article {pmid41340070,
year = {2025},
author = {Jeilu, O and Sumner, JT and Moghadam, AA and Thompson, KN and Huttenhower, C and Catlett, C and Hartmann, EM},
title = {Metagenomic profiling of airborne microbial communities from aircraft filters and face masks.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {249},
pmid = {41340070},
issn = {2049-2618},
mesh = {*Air Microbiology ; *Metagenomics/methods ; Humans ; *Bacteria/genetics/classification/isolation & purification ; *Aircraft ; *Masks/microbiology ; *Microbiota/genetics ; *Air Filters/microbiology ; Metagenome ; },
abstract = {BACKGROUND: Airborne microbial communities, although often challenging to study due to low biomass, play crucial roles in public health and pathogen transmission. Through shotgun metagenomics, this study utilizes non-invasive air sampling of face masks and aircraft cabin filters to investigate microbial diversity in environments with frequent human interactions, including hospitals and airplanes. A comprehensive sampling and analysis workflow was developed, incorporating environmental and enrichment protocols to enhance microbial DNA recovery and diversity profiling.

RESULTS: Despite limitations in biomass, optimized extraction methods allowed for the successful identification of 407 species, with dominant taxa including Cutibacterium acnes, Staphylococcus epidermidis, Sphingomonas hankookensis, and Methylobacterium radiotolerans. Enrichment processing resulted in greater metagenome-assembled genome (MAG) recovery and higher antimicrobial resistance gene (ARG) identification.

CONCLUSIONS: The findings highlight the presence of ARGs in high-occupancy public spaces, suggesting the importance of monitoring and the potential for mitigating airborne transmission risks in such environments. This study demonstrates the utility of combining environmental and enrichment sampling to capture comprehensive microbial and ARG profiles in confined spaces, providing a framework for enhanced pathogen monitoring in public health contexts. Video Abstract.},
}

*Air Microbiology
*Metagenomics/methods
Humans
*Bacteria/genetics/classification/isolation & purification
*Aircraft
*Masks/microbiology
*Microbiota/genetics
*Air Filters/microbiology
Metagenome

@article {pmid41340067,
year = {2025},
author = {Parmar, A and Nigam, SK and Cai, K and Falah, K and Ermakov, VS and Wang, K and Ferguson, CJ},
title = {Developmentally dynamic chromatin state at loci regulating organ crosstalk by remote sensing and signaling.},
journal = {Epigenetics & chromatin},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13072-025-00648-9},
pmid = {41340067},
issn = {1756-8935},
support = {R01DK109392/DK/NIDDK NIH HHS/United States ; },
abstract = {BACKGROUND: Interorgan communication, metabolite regulation and drug handling require fine-tuned small molecule transport across membranes. The Remote Sensing and Signaling (RSS) theory, which has found applicability in chronic kidney disease and uric acid disorders, emphasizes the central role of solute carrier (SLC) and ATP-binding cassette (ABC) transporters, enzymes and transcription factors in organ crosstalk. Based on prior network biology studies, ~ 1000 protein-coding genes are predicted to mediate RSS. This gene set largely overlaps with genes that are important for absorption, digestion, metabolism and excretion (ADME) of small molecules. However, it is not known how epigenetic regulation of these loci changes during the development of the liver and kidney, which control the small molecule composition of the blood, or the brain, whose physiology relies upon this process. Epigenetic regulation of these genes is also critical for understanding pharmacokinetics.

RESULTS: We profiled chromatin state at 1034 RSS/ADME genes in the mouse kidney, liver and brain at the embryonic and adult stages. Using the high-resolution chromatin mapping method CUT&RUN, we examined the activating histone modifications H3K4me3, H3K27ac and H3K9ac, and the repressive modification H3K27me3. Activating modifications were most dynamic at the chromatin level in the liver and least dynamic in the brain. Acetylated histone modifications were more dynamic overall than methylation marks in all three tissues. Hierarchical clustering demonstrated that a subset of RSS/ADME genes undergoes a coordinated program of activation during kidney and liver development that correlates with changes in transcript abundance.

CONCLUSIONS: Defining the changes in chromatin that occur after birth within this gene set provides insight into tissue-specific regulation of RSS. Our findings carry implications for how the body acquires autonomous functionality through organ crosstalk mediated by transport of endogenous small molecules. Given their critical roles in ADME as well as handling of exogenous toxins, medications and metabolites derived from the gut microbiome, our analysis has ramifications for both precision pharmacology and diseases such as chronic kidney disease, metabolic syndrome and gout, in which dysregulation of RSS drives pathophysiology.},
}

@article {pmid41339959,
year = {2025},
author = {McAdams, ZL and Campbell, EJ and Dorfmeyer, RA and Turner, G and Shaffer, S and Ford, T and Lawson, J and Terry, J and Raju, M and Coghill, L and Cresci, L and Lascola, K and Pridgen, T and Blikslager, A and Barrell, E and Banse, H and Paul, L and Gillen, A and Nott, S and VandeCandelaere, M and van Galen, G and Townsend, KS and Martin, LM and Johnson, PJ and Ericsson, AC},
title = {A novel dataset of 2,362 equine fecal microbiomes from veterinary teaching hospitals across three countries reveals effects of geography and disease.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {124},
pmid = {41339959},
issn = {2524-4671},
abstract = {BACKGROUND: Horses and other equids are reliant on the gut microbiome for health, and studies have reported associations between certain clinical conditions and features of the fecal microbiome. However, research to date on the equine fecal microbiome has often relied on small sample sizes collected from single and relatively localized geographic regions. Previous work also largely employs single timepoint analyses, or horses selected based on limited health criteria.

RESULTS: To address these limitations and expand our understanding of the core microbiome in health, and the changes associated with adverse outcomes, the Equine Gut Group (EGG) has collected and performed 16S rRNA sequencing on 2,362 fecal samples from 1,190 healthy and affected horses. This resource of 16S rRNA sequencing data with accompanying demographic and clinical metadata represent a diverse equine population in health and disease. We identified features making up the core microbiome of healthy equids and metadata factors influencing the relative abundance of those features. We then identified microbial markers of acute gastrointestinal disease at the community and taxonomic levels.

CONCLUSIONS: Here we present the EGG database and demonstrate its utility in characterizing the equine microbiome in health and acute gastrointestinal disease. The EGG 16S rRNA database is a valuable resource to study the equine microbiome and its role in equine health.},
}

@article {pmid41339940,
year = {2025},
author = {Parwin, N and Dixit, S and Das, S and Sahoo, RK and Subudhi, E},
title = {Metagenomic analysis of microbiome spatial dynamics in urban river confluence affected by city wastewater.},
journal = {Genomics & informatics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s44342-025-00054-3},
pmid = {41339940},
issn = {1598-866X},
abstract = {BACKGROUND: Environmental pollutants have a profound impact on microbial dynamics. This study highlights the influence of anthropogenic activity on the shift in bacterial diversity in the catchment area compared to upstream and downstream at Kathajodi, using a metagenomic approach for the first time in River Kathajodi.

METHODS: Water samples were collected from upstream, catchment, and downstream locations and transported at 4°C to the laboratory for DNA extraction, library preparation, sequencing, and physicochemical analysis employing inductively coupled plasma. The extracted DNA was sequenced via the Illumina HiSeq platform and analyzed through MG-RAST for taxonomic and functional classification using KEGG and COG annotations. Statistical diversity analysis, including rarefaction curves, alpha- and beta-diversity indices, and Venn diagrams, provided insights into microbial composition and community variations across sites.

RESULTS: A significant abundance of pollution indicator members of phylum Bacteroidetes (29.82%) in the catchment (CM), highly contaminated with metals, fecal, and other organic pollutants, could be attributed to their high metabolic capabilities to degrade them. The pristine upstream (US) exhibited an abundance of Shewanella (25.04%), Pseudomonas (17.35%), and Synechococcus (5.62%). The CM, influenced by high anthropogenic activity, showed higher abundances of Flavobacterium (5.20%), Arcobacter (4.05%), and Bacteroides (3.88%). In contrast, downstream (DS), with fewer anthropogenic activities, displayed higher abundances of Aeromonas (4.40%), Acidovorax (0.52%), and Acidimicrobium (0.32%). The highest bacterial diversity of CM could be due to the influence of the physicochemical properties of city waste effluent. From the Venn diagram, 73 common OTUs at the genera level were observed in all three sites, which indicates that the native microflora of the river water niche remains unaffected irrespective of the temporary changes in the vicinity. The functional profiling through KEGG and COG revealed that CM was enriched in carbohydrate metabolism (12.11%), while DS exhibited higher contributions to amino acid metabolism, along with the highest relative abundance of general function prediction (R) (12.89%), all indicative of stress adaptation and metabolic flexibility under polluted conditions. The clean upstream is home to oxygen-loving helpful bacteria, the catchment supports nutrient-hungry and sewage-linked microbes, while the downstream is dominated by metal-tolerant and possibly harmful bacteria, showing the clear impact of human activities along the river.

CONCLUSIONS: The marked shift in bacterial diversity between US, CM, and DS regions highlights the ecological consequences of anthropogenic impact. These findings emphasize the need for effective environmental management to safeguard water quality and prevent undesirable health issues.},
}

@article {pmid41339867,
year = {2025},
author = {Chen, YT and Sui, J and Yang, Y and Zhang, H and Wesselius, A and Shen, Y and Qin, QR and Sun, GJ and Wang, SK and Wang, XD and Wang, S and Li, WC and Cheng, KK and James, ND and Bryan, RT and Zeegers, MP and Chen, L and Xia, H and Yu, EY},
title = {Integration of gut microbiome and lipid metabolism reveals the anti-cancer effects of pentadecanoic acid on bladder cancer.},
journal = {BMC medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12916-025-04554-5},
pmid = {41339867},
issn = {1741-7015},
support = {82574191; 82204033//National Natural Science Foundation of China/ ; BK20220826//Natural Science Foundation of Jiangsu Province/ ; 2242022R10062/3225002202A1//Fundamental Research Funds for the Central Universities/ ; 2242023R40031//Zhishan Young Scholar Award at the Southeast University/ ; AHWJ2023A20172; AHWJ2023BAa20055//The Scientific Research Project for Health Commission of Anhui Province/ ; 2024AH050663//Natural Science Research Project of Anhui Educational Committee/ ; SSCBS20220169//Jiangsu Provincial Double-Innovation Doctor Program/ ; },
abstract = {BACKGROUND: Pentadecanoic acid (PEA), an odd-chain fatty acid derived from diet by the gut microbiome, has garnered increasing attention for its systemic health-promoting properties. Its potential role in bladder cancer (BC) occurrence and invasion, however, remains unclear.

METHODS: Large-scale cohorts' analyses were performed to assess the association between dietary PEA and BC occurrence and invasion. In vitro and in vivo experiments, including EJ and T24 BC cell assays and a BBN-induced mouse model, were conducted to experimentally assess the impact of PEA on BC. Serum proteomics, gut microbiome, and targeted fecal lipidomics analyses were employed to explore the underlying mechanisms.

RESULTS: Dietary PEA was negatively associated with BC occurrence and invasion in cohort analyses. PEA suppressed EJ and T24 BC cell migration, invasion, and proliferation, while inhibiting BC development in a BBN-induced mouse model. In vivo serum proteomics identified differentially expressed lipid-related proteins (e.g., Apoe and Apob) following PEA treatment, implicating its modulation of lipid metabolism pathways. Considering the essential role of the gut-bladder axis, the gut microbiome analysis exhibited that PEA markedly altered bacteria (e.g., g_Alistipes) and fungi (e.g., o_Erysiphales, g_Teberdinia, and g_Gibberella), with concomitant lipid metabolism changes. Furthermore, targeted fecal lipidomics demonstrated the shifts in key lipids, such as phosphatidylethanolamines (PE) involved in essential lipid clusters, suggesting regulation by gut microbiome linked to BC development.

CONCLUSIONS: Collectively, our findings demonstrate that PEA mitigates BC by reshaping the gut microbiome and modulating lipid metabolism, providing new insights into its molecular and therapeutic potential.},
}

@article {pmid41339801,
year = {2025},
author = {Yang, T and Wang, Y and Zhang, Y and Liu, C and Zeng, Y and Shi, P and Zhou, J and Li, Y and Wei, H},
title = {Haemophilus influenzae dominance in fungal ball microbiome revealed through multi-niche metagenomic sequencing.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04546-8},
pmid = {41339801},
issn = {1471-2180},
support = {7222026//Natural Science Foundation of Beijing Municipality/ ; },
abstract = {OBJECTIVE: This study employed metagenomic sequencing to characterize the sinonasal microbiome in patients with unilateral maxillary sinus fungal ball (MSFB), with specific emphasis on bacterial-fungal interactions and functional pathways implicated in fungal ball pathogenesis.

METHODS: The study enrolled 30 MSFB patients and 30 healthy controls. Nasal secretion samples were obtained from three anatomical sites in MSFB cases: fungal ball cavity (FC), affected middle nasal meatus (AM), and contralateral unaffected middle nasal meatus (UM). And in the control group, samples were obtained from the healthy middle nasal meatus (HM). Metagenomic sequencing of microbial DNA was performed using the Illumina Novaseq platform. Taxonomic and functional analyses were conducted using Kraken2, Bracken, and HUMAnN2.

RESULTS: Bacteria dominated the microbiome in the FC group (98.53%), with Haemophilus influenzae identified as a key biomarker (LDA score > 5). A negative correlation between H. influenzae and Aspergillus flavus was observed in the FC group (r = -0.46, P = 0.013). Functional pathways enriched in the FC group included amino acid biosynthesis (map00290), lipopolysaccharide biosynthesis (map00540), and fatty acid biosynthesis (map00061), supporting H. influenzae survival and immune modulation. FC microbiota showed reduced diversity and distinct composition compared to other groups (PERMANOVA, P < 0.001). No significant differences were found in the composition of the microbiota between the bilateral middle nasal meatus groups of MSFB.

CONCLUSION: This study highlights H. influenzae as a critical bacterial biomarker in MSFB. The inverse relationship between H. influenzae and A. flavus may suggest competitive or immune-mediated interactions. These findings advance understanding of non-invasive fungal sinusitis. Future validation in larger fungal ball cohorts or invasive fungal sinusitis is warranted.},
}

@article {pmid41339745,
year = {2025},
author = {Zhang, L and Marfil-Sánchez, A and Kuo, TH and Seelbinder, B and van Dam, L and Depetris-Chauvin, A and Jahn, LJ and Sommer, MOA and Zimmermann, M and Ni, Y and Panagiotou, G},
title = {Gut microbiome-mediated transformation of dietary phytonutrients is associated with health outcomes.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41339745},
issn = {2058-5276},
support = {Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; Germany's Excellence Strategy (EXC 2051) project ID 390713860//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; "PerMiCCion" project (Project ID 01KD2101A)//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; Excellent Young Scientists Fund (project ID 24HAA01325)//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Food, especially plant-based diet, has complex chemical diversity. However, large-scale phytonutrient-metabolizing activities of gut bacteria are largely unknown. Here we integrated and systematically analysed multiple databases containing information on enzymatic reactions and food health benefits, and 3,068 global public human microbiomes. Transformation of 775 phytonutrients from edible plants was associated with enzymes encoded by diverse gut microbes. In vitro assays validated the biotransformation activity of gut species, for example, Eubacterium ramulus. The biotransformation of phytonutrients demonstrated high interpersonal and geographical variability. Machine learning models based on 2,486 public case-control microbiomes, using the abundances of enzymes associated with modification of phytonutrients present in health-associated foods, discriminated the health status of individuals in multiple disease contexts, suggesting altered biotransformation potential in disease. We validated the association of microbiome-encoded enzymes with the anti-inflammatory activity of common edible plants by combining metagenomics and metatranscriptomics analysis in specific-pathogen-free and germ-free mice. These findings have implications for designing precise, personalized diets to guide an individual towards a healthy state.},
}

@article {pmid41339732,
year = {2025},
author = {Vogel, SC and Querdasi, FR and Callaghan, BL and Brito, NH},
title = {Examining associations among caregiver stress, social support, and the infant gut microbiota.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-025-30553-w},
pmid = {41339732},
issn = {2045-2322},
abstract = {Maternal stress is a growing societal concern, with implications for both maternal wellbeing and infant development. One of the mechanisms by which maternal stress is thought to impact infant development is by shaping the development of the infant gut microbiome. Here, we examined how measures of maternal stress and social support were associated with alpha diversity, beta diversity, and relative abundance of individual bacterial taxa in the gut microbiota at 12 months of age in a community-based sample of infants and their biological mothers (n = 34) from New York. Maternal social support was negatively associated with alpha diversity of the infant gut microbiota and was associated with abundance of bacteria from several genera. We did not find associations between caregiver perceived stress and markers of infant gut microbiota diversity or composition. Results suggest that greater social support for new parents may be associated with infant health via changes in the diversity and composition of the infant gut microbiota.},
}

@article {pmid41339713,
year = {2025},
author = {Valdin, H and Gray, B and Cook, G and Creamer, M and Yu, L and LeBlanc, Z},
title = {Primary Prevention of Clostridioides difficile Infection With Oral Vancomycin in Pediatric Hematopoietic Stem Cell Transplant Patients.},
journal = {Pediatric transplantation},
volume = {29},
number = {8},
pages = {e70246},
doi = {10.1111/petr.70246},
pmid = {41339713},
issn = {1399-3046},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation ; *Vancomycin/administration & dosage/therapeutic use ; Retrospective Studies ; Female ; *Clostridium Infections/prevention & control/epidemiology ; Male ; Child ; *Anti-Bacterial Agents/administration & dosage/therapeutic use ; Child, Preschool ; Adolescent ; Administration, Oral ; Incidence ; Infant ; *Antibiotic Prophylaxis/methods ; *Primary Prevention/methods ; Clostridioides difficile ; *Postoperative Complications/prevention & control ; },
abstract = {BACKGROUND: Clostridioides difficile infection (CDI) poses a significant risk to pediatric hematopoietic stem cell transplant (HSCT) due to microbiome disruption, mucosal injury, and graft versus host disease (GVHD). While oral vancomycin prophylaxis (OVP) is effective for preventing recurrent CDI, evidence for its role in preventing initial infection is limited. Our institution employs empiric OVP during the first HSCT admission to prevent initial CDI.

OBJECTIVES: We sought to describe the incidence of CDI among pediatric HSCT recipients receiving OVP and to evaluate secondary outcomes related to OVP exposure.

METHODS: We conducted a single center, retrospective observational study of 84 pediatric HSCT recipients at our institution receiving OVP during their initial transplant admission. Chart review captured demographics, transplant information, and clinical outcomes. The primary outcome was CDI incidence during hospitalization. Secondary outcomes included VRE infections, refractory CDI following cessation of OVP, and acute GI GVHD.

RESULTS: Only one patient developed CDI (1.19%) while on OVP, despite universal exposure to high-risk antibiotics among the entire cohort. No VRE infections were observed. Rates of GI aGVHD were consistent with national averages. Nine patients (10.7%) developed CDI after discontinuing OVP, all managed with standard treatment.

CONCLUSION: Empiric OVP during pediatric HSCT hospitalization was associated with a markedly low CDI incidence. Despite theoretical risks of microbiome disruption, no adverse effects were identified in this cohort, including long-term follow-up beyond 5 years. These findings support the safety and potential efficacy of OVP as primary CDI prophylaxis in pediatric HSCT patients.},
}

Humans
*Hematopoietic Stem Cell Transplantation
*Vancomycin/administration & dosage/therapeutic use
Retrospective Studies
Female
*Clostridium Infections/prevention & control/epidemiology
Male
Child
*Anti-Bacterial Agents/administration & dosage/therapeutic use
Child, Preschool
Adolescent
Administration, Oral
Incidence
Infant
*Antibiotic Prophylaxis/methods
*Primary Prevention/methods
Clostridioides difficile
*Postoperative Complications/prevention & control

@article {pmid41339624,
year = {2025},
author = {Lamichhane, S and Dickens, AM and Buchacher, T and Lou, T and Charron-Lamoureux, V and Kattelus, R and Karmacharya, P and da Silva, LP and Kråkström, M and Rasool, O and Sen, P and Walker, C and Patan, A and Gentry, EC and Zuffa, S and Arzoomand, A and Lakshmikanth, T and Mikeš, J and Mebrahtu, A and Vatanen, T and Raffatellu, M and Zengler, K and Hyötyläinen, T and Xavier, RJ and Brodin, P and Lahesmaa, R and Dorrestein, PC and Knip, M and Orešič, M},
title = {Microbiome-derived bile acid signatures in early life and their association with islet autoimmunity.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-025-66619-6},
pmid = {41339624},
issn = {2041-1723},
support = {363417//Academy of Finland (Suomen Akatemia)/ ; },
abstract = {Emerging studies reveal that gut microbes can conjugate diverse amino acids to bile acids, known as microbially conjugated bile acids. However, their regulation and health effects remain unclear. Here, we analyzed early-life microbially conjugated bile acid patterns and their link to islet autoimmunity. We quantified 110 microbial bile acids in 303 stool samples collected longitudinally (3-36 months) from children who developed one or more islet autoantibodies and controls who remained autoantibody-negative. We identified distinct age-dependent trajectories of these bile acid amidates and correlated them with gut microbiome composition. We found that altered levels of ursodeoxycholic and deoxycholic acid conjugates were linked to islet autoimmunity as well as modulated monocyte activation in response to immunostimulatory lipopolysaccharide and Th17/Treg cell balance. These findings suggest that microbially conjugated bile acids influence immune development and type 1 diabetes risk.},
}

@article {pmid41339536,
year = {2025},
author = {Oikonomou, P and Akhoundi, FH and Olfati, N and Litvan, I},
title = {Characteristics and mechanisms of cognitive impairment in Parkinson disease.},
journal = {Nature reviews. Neurology},
volume = {},
number = {},
pages = {},
pmid = {41339536},
issn = {1759-4766},
abstract = {Cognitive impairment in people with Parkinson disease (PD) imposes a substantial societal burden: PD affects over 1% of the population aged 65 years and older, and 24-31% of individuals with this condition develop dementia and another 26% present with mild cognitive impairment. Given the increasing prevalence of PD in light of an ageing population, the challenge of PD-associated cognitive impairment is likely to intensify. In this Review, we highlight the latest research advances in PD-associated cognitive impairment, emphasizing emerging mechanistic insights and new biomarkers. We outline the epidemiology and natural history of cognitive decline in PD, focusing on prodromal stages and the closely related spectrum of Lewy body dementia. We discuss key pathophysiological factors and mechanisms, including aggregation and prion-like propagation of α-synuclein; co-pathologies; synaptic dysfunction; genetics; neuroinflammation; mitochondrial dysfunction; oxidative stress; microbiome alterations; degeneration of cholinergic and monoaminergic systems; autonomic dysfunction; altered neuronal network activity; and glymphatic impairment. We consider how advances in fluid and neuroimaging biomarkers, together with preclinical disease models and pathological studies, are providing insights into these mechanisms. A deeper understanding of the multifaceted pathophysiology of PD-associated cognitive impairment will help us to explain the heterogeneity of cognitive profiles and disease progression in PD, providing a foundation for personalized disease-modifying treatments.},
}

@article {pmid41339503,
year = {2025},
author = {Liu, X and Geng, A and Xia, M and Lan, J and Wu, H and Zhou, Z and Huang, F and He, Y and Lei, T and Hur, J and Guo, K and Yu, X and Zhou, X},
title = {Alterations in short-chain fatty acid-associated gut microbiota and tight junction integrity in adolescent major depressive disorder.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-025-03743-3},
pmid = {41339503},
issn = {2158-3188},
support = {2022ZD0212900//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 82271565//National Natural Science Foundation of China (National Science Foundation of China)/ ; CSTB2024NSCQ-LZX0060//Natural Science Foundation of Chongqing (Natural Science Foundation of Chongqing Municipality)/ ; W0045//Chongqing Medical University (CQMU)/ ; },
abstract = {Major depressive disorder (MDD) often begins during adolescence, a critical developmental period during which nearly 50% of lifetime cases emerge. Despite its high prevalence and impact, objective diagnostic biomarkers for adolescent MDD remain limited, particularly those related to gut microbiota. Our study examined potential co-diagnostic biomarkers from peripheral blood and fecal samples in adolescents with MDD. We enrolled drug-naïve adolescents with first-episode MDD (n = 46, aged ≤18 years, 71.74% female) and age-/sex-matched healthy controls (HCs, n = 44). The levels of tight junction proteins (Claudin-5, Zonulin, FABP) and inflammatory biomarkers (IL-6, IL-8, TNF-α, and CRP) were markedly elevated in the plasma of adolescents with MDD, indicating gut barrier dysfunction and systemic inflammation. The microbiome in MDD patients exhibited a lower Firmicutes-to-Bacteroidetes ratio. At the genus level, Intestinimonas and Barnesiella were significantly enriched, while Dialister and Collinsella were considerably reduced. Integrating Collinsella abundance with tight junction proteins and inflammatory markers significantly improved diagnostic performance, achieving an area under the curve (AUC) of 0.964. Moreover, Collinsella negatively correlated with sex, Claudin-5, and TNF-α. Claudin-5 was strongly associated with short-chain fatty acids (SCFAs)-related pathways, including alanine, aspartate, glutamate metabolism, D-glutamine and D-glutamate metabolism, and autophagy regulation. Treatment of Caco-2 cells with propionate and butyrate confirmed the regulatory effects of SCFAs on tight junction biomarkers. These findings suggest the interplay between gut dysbiosis, barrier dysfunction, and inflammation in adolescent MDD and support microbiota-host biomarkers as a promising strategy for improving MDD diagnostic precision.},
}

@article {pmid41331614,
year = {2025},
author = {Yu, H and Zhang, Y and Yang, D and Luo, H and Zhou, Y},
title = {Advances in capsule-based fecal microbiota transplantation: clinical applications and innovations.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1370},
pmid = {41331614},
issn = {1479-5876},
support = {LTGD23C040008//Zhejiang Provincial Natural Science Foundation of China/ ; LBY23H200006//Natural Science Foundation of Hebei Province/ ; 2023020612//Ningbo Top Medical and Health Research Program/ ; 2023-S013//Ningbo Public Welfare Project/ ; 06-445-1211//Talent Initiation Program of the High-Level University Development Project at Guangzhou Medical University/ ; },
abstract = {Capsule-based fecal microbiota transplantation (cFMT) has emerged as a vital tool for modulating gut dysbiosis for therapeutic intervention. This noninvasive alternative to traditional FMT avoids procedural invasiveness while offering logistical advantages in terms of storage, administration, and patient compliance. This review evaluates cFMT as a transformative approach across diverse diseases. Notably, cFMT demonstrates robust efficacy in restoring the microbial balance in Clostridioides difficile infection (CDI), inflammatory bowel disease (IBD), and multidrug-resistant infections, with outcomes comparable to those of conventional methods. It also alleviates symptoms and enhances microbiota diversity in small intestinal bacterial overgrowth (SIBO). However, the clinical benefits remain inconsistent for individuals with in irritable bowel syndrome (IBS) and functional constipation (FC), despite alterations in gut microbial diversity. Emerging applications highlight the potential of cFMT metabolic disorders (e.g., obesity and hypertension) via the modulation of gut-derived metabolites and neuropsychiatric conditions (e.g., depression and autism) through gut–brain axis signaling, in addition to chronic kidney disease and hepatic encephalopathy. Challenges such as donor variability, standardization gaps, and transient adverse effects hinder widespread adoption. Further advancements, including targeted colon-release formulations, synthetic microbial consortia, and single-cell delivery systems, could improve precision and scalability. Despite its transformative potential, the clinical adoption of cFMT hinges on rigorous quality control, mechanistic insights, and long-term safety data. In recent years, the United States Food and Drug Administration (FDA) has officially approved the oral microbiome therapy Vowst for marketing. This marked the gradual transition of fecal microbiota transplantation (FMT)-related therapies from clinical research to standardized clinical application, and at the same time, Vowst has become the world’s first oral fecal microbiome therapy approved by the FDA. This review highlights the role of cFMT in microbiota-targeted therapies while advocating for innovation to address current limitations and expand its therapeutic scope.},
}

@article {pmid41280017,
year = {2025},
author = {Guitor, AK and Wang, S and Tuck, OT and Firek, B and Mostacci, N and Jauhal, A and Chen, LX and Dziegiel, AH and Baker, S and Duong, VT and Mather, AE and Corander, J and Kantele, A and Shenhav, L and Hilty, M and Morowitz, MJ and Sachdeva, R and Banfield, JF},
title = {Megaplasmids associate with Escherichia coli and other Enterobacteriaceae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {41280017},
issn = {2692-8205},
abstract = {Humans and animals are ubiquitously colonized by Enterobacteriaceae, a bacterial family that contains both commensals and clinically significant pathogens. Here, we report Enterobacteriaceae megaplasmids of up to 1.58 Mbp in length in infant and adult guts, and other microbiomes. Of 19 complete plasmid genomes, one was reconstructed from an E. coli isolate; others were linked to species of Citrobacter and Enterobacter via analysis of genome modification patterns. The detection of related plasmids in different Enterobacteriaceae, conjugation machinery, and more diverse modified motifs in certain plasmids compared to hosts suggests that these elements are self-transmissible, with a broad host range. The plasmids encode multi-drug efflux systems and potential secreted effectors. Up to 208 tRNAs are encoded and include sequence variants that may counter tRNA-centric defense mechanisms. Overall, the vast megaplasmid coding capacity may broaden host range, increase competitiveness, control invasion by other elements, and counter programmed cell death.},
}

@article {pmid41339392,
year = {2025},
author = {Muratore, E and Conti, G and Fabbrini, M and Zama, D and Decembrino, N and Muggeo, P and Mura, R and Perruccio, K and Leardini, D and Barone, M and Zecca, M and Cesaro, S and Brigidi, P and Turroni, S and Masetti, R},
title = {Distinct functional and compositional properties in the gut microbiome of children with acute lymphoblastic leukaemia identified by shotgun metagenomics.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {43082},
pmid = {41339392},
issn = {2045-2322},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; Child ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology ; Male ; Female ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; Adolescent ; Bacteria/genetics/classification ; Case-Control Studies ; },
abstract = {Acute lymphoblastic leukaemia (ALL) represents the most common childhood malignancy, and emerging evidence underscores the impact of the gut microbiome (GM) on its pathogenesis. In this study, we used shotgun metagenomics to investigate the GM of 30 ALL patients at diagnosis-19 with B-ALL and 11 with T-ALL-and compared them to 176 healthy controls (HCs). When considered as a single ALL group versus HCs, clear compositional differences emerged: ALL patients exhibited higher relative abundances of Enterococcus faecium, oral commensals such as Rothia dentocariosa, and multiple opportunistic species, whereas HCs were enriched in short-chain fatty acid producers like Anaerostipes hadrus and Intestinibacter bartlettii. Functionally, the ALL GM relied more on protein and amino acid catabolism, while HCs possessed enhanced pathways for carbohydrate and folate metabolism. These findings broadly align with 16S rRNA-based analyses from previous publications, though some discrepancies highlight differences in technique-driven resolution. In contrast, comparing the two major molecular phenotypes-B-ALL and T-ALL-revealed only minimal taxonomic and functional differences, primarily confined to BAs metabolism pathways. Overall, our results indicate that children with ALL at the time of diagnosis already display a dysbiotic signature, bolstering the notion that a disturbance in GM development during childhood may be linked to the multistep pathogenesis model of ALL.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
Child
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/microbiology
Male
Female
Child, Preschool
RNA, Ribosomal, 16S/genetics
Adolescent
Bacteria/genetics/classification
Case-Control Studies

@article {pmid41339319,
year = {2025},
author = {Harrison, LC and Allnutt, TR and Hanieh, S and Roth-Schulze, AJ and Ngui, KM and Stone, NL and Bandala-Sanchez, E and Backshell, L and Gurruwiwi, G and Gondarra, V and Couper, JJ and Craig, ME and Davis, EA and Huynh, T and Soldatos, G and Wentworth, JM and Vuillermin, P and Penno, MAS and Biggs, BA and , },
title = {Indigenous infants in remote Australia retain an ancestral gut microbiome despite encroaching Westernization.},
journal = {Nature communications},
volume = {16},
number = {1},
pages = {9904},
pmid = {41339319},
issn = {2041-1723},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Infant ; Australia ; Female ; Male ; Bacteria/genetics/classification/isolation & purification ; Feces/microbiology ; Infant, Newborn ; Indigenous Peoples ; Metagenome ; },
abstract = {Studies of traditional Indigenous compared to 'Western' gut microbiomes are underrepresented, and lacking in young children, limiting knowledge of early-life microbiomes in different cultural contexts. Here we analyze the gut metagenomes of 50 Indigenous Australian infants (median age }

Humans
*Gastrointestinal Microbiome/genetics
Infant
Australia
Female
Male
Bacteria/genetics/classification/isolation & purification
Feces/microbiology
Infant, Newborn
Indigenous Peoples
Metagenome

@article {pmid41339176,
year = {2025},
author = {Khan, S and Zobairi, A and Pouwels, S and Celik, A and Ugale, S and Parmar, C},
title = {Theories and concepts of physiological mechanisms in metabolic and bariatric surgery, beyond restriction and malabsorption: a narrative review.},
journal = {Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.soard.2025.10.017},
pmid = {41339176},
issn = {1878-7533},
abstract = {Metabolic and Bariatric surgery (MBS) has become an essential treatment for severe obesity and associated comorbidities, particularly type 2 diabetes mellitus (T2DM), with substantial benefits in weight loss, improved glycemic control, and cardiovascular risk reduction. The International Diabetes Federation (IDF) recognizes MBS as an effective option for individuals with obesity with T2DM due to its ability to improve insulin sensitivity and lower inflammation. These surgeries induce metabolic improvements through distinct mechanisms that affect gut hormone secretion, nutrient absorption, and energy balance. These interventions modulate key gut hormones like glucagon-like peptide-1 (GLP-1), ghrelin, and leptin, which influence appetite, glucose metabolism, and fat storage. Moreover, MBS alters the gut microbiome, contributing to enhanced metabolic function and the resolution of obesity-related conditions. Theories such as the Foregut-Hindgut Hypothesis, Ileal Brake Mechanism, and Gastric Center Hypothesis further try explain these metabolic changes. Understanding these theories and the physiological alterations they provoke is crucial for optimizing patient care and advancing the future of obesity treatments, offering insights into mechanisms that go beyond simple weight loss to address complex metabolic disorders.},
}

@article {pmid41338872,
year = {2025},
author = {Soule, K and Nelson, N and Wiemels, J and Gallant, R},
title = {Impact of infection and microbial exposures on pediatric cancer.},
journal = {Current problems in pediatric and adolescent health care},
volume = {55},
number = {9},
pages = {101819},
doi = {10.1016/j.cppeds.2025.101819},
pmid = {41338872},
issn = {1538-3199},
mesh = {Humans ; Child ; *Neoplasms/epidemiology/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; Environmental Exposure/adverse effects ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/epidemiology/immunology ; Female ; Incidence ; },
abstract = {The etiology of pediatric cancer is likely multifactorial including a combination of genetic alterations and environmental exposures. Infection and antigenic exposures have been identified as contributors to the development of pediatric cancers particularly acute lymphoblastic leukemia (ALL), the most common pediatric malignancy. Viral infections such as Epstein-Barr virus (EBV) and human papilloma virus (HPV) have a well-established association with Hodgkin lymphoma (EBV), Burkitt lymphoma (EBV), and head and neck cancers (HPV). More recent evidence suggests CMV is associated with glioblastoma multiforme and ALL. The incidence of pediatric cancer is much lower than the incidence of these viral infections, indicating that there are likely other factors at play. Aside from these specific viral infections, antigenic exposures in general have been associated with pediatric cancers as well. Early life antigenic exposures are known to impact the gut microbiome which is a crucial component to developing a competent immune system. Higher microbial exposure in early life, such as vaginal delivery (versus cesarean delivery), daycare attendance, and breastfeeding have been associated with lower incidence of pediatric ALL, and this effect is hypothesized to be mediated by the gut microbiome. In this review, we highlight the association between infection, antigenic exposures, and pediatric cancer and potential underlying mechanisms that facilitate this association.},
}

Humans
Child
*Neoplasms/epidemiology/microbiology/immunology
*Gastrointestinal Microbiome/immunology
Environmental Exposure/adverse effects
*Precursor Cell Lymphoblastic Leukemia-Lymphoma/epidemiology/immunology
Female
Incidence

@article {pmid41338496,
year = {2025},
author = {Sheridan, L and Hutton, P and Noble, G and Nobari, B},
title = {An in vitro investigation into the effects of postbiotic supplementation on stabilising equine hindgut pH.},
journal = {Journal of equine veterinary science},
volume = {},
number = {},
pages = {105746},
doi = {10.1016/j.jevs.2025.105746},
pmid = {41338496},
issn = {0737-0806},
abstract = {BACKGROUND: Dysbiosis of the intestinal microbiome is a precursor to hindgut acidosis. As microbial diversity and fermentation are influenced by diet, including a postbiotic could help maintain healthy gastrointestinal microbes and reduce acidosis risk.

AIMS/OBJECTIVES: It was hypothesised that including a postbiotic in batch culture would reduce the degree of pH decline and lactate accumulation during fermentation.

METHODS: In vitro batch cultures with faecal inoculant were prepared with either low starch (LS) or high glucose (G) substrate to represent normal and acidic fermentation. Saccharomyces cerevisiae derived postbiotic was added at 280 μg (T1), corresponding to the recommended daily feeding rate for a 500 kg horse adjusted to the dry matter of the incubated substrate, and 560 μg (T2), representing twice this rate, and incubated for 48 h to assess effects on pH, gas, volatile fatty acids (VFAs), ammonia (NH₃), and D-lactate production.

RESULTS: Substrate G showed a faster decline in pH (P <0.001) than LS at 6 and 12 h post incubation. Postbiotic concentration had a positive linear relationship with pH in G and observed higher (P <0.001) pH for T1 at 6 h, and T2 at 6 and 12 h. Production of propionic, and acetic acids was increased (P <0.001) with postbiotic at 12 h and 36 h, and butyric acid at 36 h (P = 0.05). D-lactate production was greater in G than LS (P <0.001) at 12 h and lower at 36 h (P <0.001). Postbiotics reduced lactate at 12 and 36 h (P <0.001) in LS.

CONCLUSION: The addition of postbiotic could reduce the severity of pH decline in high non-structural carbohydrate rations and increase VFAs, however acidosis was not prevented.},
}

@article {pmid41337904,
year = {2025},
author = {Niu, X and Ma, L and Zhou, Z and Li, Y and Shi, A and Weng, L and Xing, H},
title = {Composition of gut microbiota and alcohol-related liver disease: A systematic review and meta-analysis.},
journal = {Drug and alcohol dependence},
volume = {278},
number = {},
pages = {112988},
doi = {10.1016/j.drugalcdep.2025.112988},
pmid = {41337904},
issn = {1879-0046},
abstract = {BACKGROUND AND OBJECTIVES: The intestinal microbiome has been identified as a key factor influencing the development and prognosis of alcohol-related liver disease (ARLD). This article aims to systematically review and meta-analyze the alterations in the gut microbiome associated with ARLD, providing a comprehensive overview of these changes.

METHODS: PubMed, Embase, and Web of Science databases were systematically searched from January 1, 2015, to September 1, 2024, with the search limited to studies published in English and Chinese. Articles meeting the inclusion criteria-providing gut microbiota analysis and reporting changes in diversity and abundance-were selected through a two-stage screening process. Data extraction was conducted independently by two reviewers to ensure accuracy and reliability.

RESULTS: We compared gut microbiota differences between ARLD patients and healthy individuals, focusing on α-diversity, β-diversity, and microbial abundance. Among 17 studies, α-diversity indices showed a significant decrease in Shannon index (SMD=-0.63, 95 % CI= [-1.40, -0.14]), p < 0.001), Chao1 (SMD=-1.20, 95 % CI= [-1.67, -0.74], p = 0.022), and OTUs (SMD=-1.14, 95 % CI= [-1.55, -0.73], p = 0.010), with no significant differences observed in Simpson index, ACE, inverse Simpson, or Pielou evenness. Of 21 studies on β-diversity, 16 reported significant differences between ARLD and healthy controls. Most findings indicate a reduction in anti-inflammatory microorganisms and an enrichment of pro-inflammatory microorganisms in ARLD patients.

CONCLUSION: The study revealed that intestinal microbiome changes in ARLD patients are characterized by decreased microbial diversity, a reduction in anti-inflammatory microbiota, and an enrichment of pro-inflammatory bacteria. These findings highlight the intestinal microbiome as a promising target for potential ARLD treatment strategies.},
}

@article {pmid41338335,
year = {2025},
author = {Ono, N and Ito, Y and Aoki, S and Shiohama, A and Sasaki, T and Kurokawa, R and Suda, W and Amagai, M and Kubo, A},
title = {Microbial Dysbiosis and Foot Odor in Nagashima-Type Palmoplantar Keratosis: Improvement with Topical Benzoyl Peroxide.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.11.011},
pmid = {41338335},
issn = {1523-1747},
abstract = {Nagashima-type palmoplantar keratosis (NPPK; also referred to as SERPINB7-palmoplantar epidermal differentiation disorder) is the most common form of palmoplantar keratoderma in East Asia. It is characterized by erythematous hyperkeratosis, palmoplantar hyperhidrosis, and a distinctive foot odor that significantly impairs quality of life. In this study, we aimed to clarify the etiology of this odor by investigating the plantar microbiome and evaluating the therapeutic effects of topical benzoyl peroxide (BPO). Compared with healthy controls, individuals with NPPK exhibited significantly higher objective odor scores, increased bacterial load, especially in the intertoe area, and reduced microbial diversity. Corynebacterium and Staphylococcus were the predominant dysbiotic flora species. The topical application of BPO significantly reduced foot odor and bacterial load, increased microbial diversity, and selectively decreased Corynebacterium abundance, particularly that of C. tuberculostearicum. These changes correlate with the species-specific susceptibility of skin-resident bacteria to BPO. Our findings suggest that microbial dysbiosis, especially the overgrowth of Corynebacterium species, is central to the pathogenesis of foot odor in NPPK. Topical BPO is a promising therapeutic intervention for mitigating dysbiosis and its associated foot odor. This study highlights the potential of microbiome-targeted therapies for symptom relief in inherited skin disorders such as NPPK.},
}

@article {pmid41338170,
year = {2025},
author = {Egea, LG and Jiménez-Ramos, R and Rodríguez-Arias, L and Infantes, E},
title = {Successive stressors alter microbiome composition and reduce resilience in the eelgrass Zostera marina.},
journal = {Marine environmental research},
volume = {214},
number = {},
pages = {107748},
doi = {10.1016/j.marenvres.2025.107748},
pmid = {41338170},
issn = {1879-0291},
abstract = {Seagrass meadows are among the most threatened ecosystems worldwide, facing multiple anthropogenic stressors that often occur in succession. While plant-physiological responses to multiple stressors are well documented, the role of microbial symbionts in mediating consecutive stressors events remains poorly understood. Using a mesocosm experiment, Zostera marina (eelgrass) was exposed to sequential stressors: nutrient enriched sediments (NE; 70 mg of total N per 100 gDW sediment[-1] for 28 days), followed by a simulated marine heatwave (MHW, 23.3 °C for 15 days) and subsequent storm event (25 cm/s flow, 12 days). Nutrient enrichment resulted in a microbiome shift, specifically a 49.2-fold enrichment of sulfur-oxidizing Arcobacteraceae and a 4.7-fold increase in Sulfurimonadaceae, suggesting possible microbiome-mediated responses mitigating sulfide toxicity. In contrast, warming responses were primarily physiological: aboveground biomass increased by 41.5 % and net production increased by 37.1 % (mg FW shoot[-1] day[-1]), with synergistic effects under combined enrichment and heat stress (up to 175 % higher production), indicating that temperature outweighs nutrient stress. Storm exposure triggered a 114 % increase in belowground biomass via root elongation, which increases the resilience of these plants to higher flow velocities, but this acclimation was diminished by 51 % in plants previously exposed to the MHW, indicating environmental legacy effects. Our results demonstrate that eelgrass resilience depends critically on stressors sequence, where legacy effects alter both plant-microbe interactions and physiological responses. These findings emphasize the need to incorporate both a consecutive-stressor approach and microbiome dynamics into seagrass research and conservation strategies under climate change.},
}

@article {pmid41338072,
year = {2025},
author = {Jose, S and Lohith Kumar, DH and Malla, MA and Featherston, J and Bux, F and Kumari, S},
title = {Insights into microbial community, nitrogen‑phosphorus metabolism from metagenomic and metabolomic analysis of microalgal-cyanobacterial consortium-based bioinoculants.},
journal = {The Science of the total environment},
volume = {1009},
number = {},
pages = {181092},
doi = {10.1016/j.scitotenv.2025.181092},
pmid = {41338072},
issn = {1879-1026},
abstract = {The intensification of agriculture through chemical fertilizers has led to severe environmental consequences. This study provides a comprehensive investigation on chemical fertilizer, vermiculite and on microalgal-cyanobacterial consortia (bioinoculants) influencing soil microbial community. Chemical fertilizer application significantly altered the microbial community, suppressing the dominant phylum Proteobacteria to 48.3 % abundance from 60.9 % in the control soil. The bioinoculant treatments maintained a high Proteobacteria abundance (58.9 %-59.7 %) and fostered a growth-oriented, anabolic strategy. The 50:50 mix treatment uniquely promoted the fungal phylum Basidiomycota to 18.2 % abundance and showed the highest investment in the Glycolysis/Gluconeogenesis pathway (23.0 %). Chemical fertilizer treatment upregulated genes for rapid nitrogen assimilation (glnA, Log2FC = 0.60) and phosphorus starvation response (phoB, Log2FC = 0.65; pstS, Log2FC = 0.83). The enhanced energy production and conversion (11.83 %), amino acid transport and metabolism (11.20 %), and fatty acid biosynthesis (45.3 %) was observed in bioinoculant treatment. Unlike chemical fertilizer treatment, bioinoculant treatment led to the accumulation of the osmoprotectant trehalose and structural membrane lipids, while the 50:50 mix was uniquely characterized by a higher abundance of xylose. These findings demonstrate that the microalgal-cyanobacterial consortium can enhance nutrient recycling, and potentially boost soil health by reshaping the soil microbiome and metabolic functions, offering a promising strategy for sustainable agriculture.},
}

@article {pmid41337959,
year = {2025},
author = {Dong, D and Xie, Z and Wang, B and Ou, W and Tang, Y and Yang, J and Guo, Y and Fa, X},
title = {Effects of a forage-native multi-PGPM consortium symbiotic system on rhizosphere ecology and microbial regulation for remediating PAHs-contaminated very-high-altitude coal mines.},
journal = {Journal of hazardous materials},
volume = {501},
number = {},
pages = {140653},
doi = {10.1016/j.jhazmat.2025.140653},
pmid = {41337959},
issn = {1873-3336},
abstract = {The very-high-altitude coal mines face polycyclic aromatic hydrocarbons (PAHs) pollution, yet studies on microbial degradation of PAHs in this region remain scarce. In this study, a native multi-plant growth-promoting microorganism consortium (N-M-PGPM-C, comprising four Tibetan Plateau strains: Trichoderma, Bacillus, Pseudomonas, and Floccularia luteovirens) was constructed. Their effects on forage growth, PAHs degradation, rhizosphere microbes, and soil metabolites were systematically investigated via high-throughput sequencing and LC-MS/MS metabolomics. The results showed that the N-M-PGPM-C significantly improved forage growth (93.81 %-120.05 % increase in dry weight compared to single PGPM treatment), degraded aromatic compounds in the rhizosphere soil, and enriched seven plant-beneficial microorganisms (e.g., Lysinibacillus, Solibacillus). In addition, it promoted the colonization and proliferation of two strains from the N-M-PGPM-C (i.e., Trichoderma by 3.20-fold and Bacillus by 9.41-fold) by reshaping the rhizosphere microbial community. According to the metabolomic analysis, the N-M-PGPM-C modulated 114 metabolites, enriching pathways for bisphenol, toluene, and benzoate degradation. The metabolite 2'-deoxyguanosine was strongly correlated with the enrichment of seven plant-beneficial microorganisms such as Lysinibacillus and Solibacillus and synergized with Trichoderma and Bacillus. Laboratory validations confirmed that Trichoderma and Bacillus possess intrinsic PAH-degrading capabilities, and exogenous application of 2'-deoxyguanosine significantly alleviated PAH stress in forages. These findings reveal the mechanism by which the N-M-PGPM-C remediates PAH contamination through the forage- native multi-PGPM consortium symbiotic system, providing a promising strategy for ecological restoration in the very-high-altitude regions.},
}

@article {pmid41337711,
year = {2025},
author = {Babu, R and Kaur, M and Sharma, S and Sureshan, CS and Garg, R and Baweja, S and Rastogi, M and Singh, SP and Varshney, M and Patil, NS and Pamecha, V and Sarin, SK and Bihari, C},
title = {Baseline oral microbiome associated with post-living donor liver transplant early complications within 6 months.},
journal = {Liver transplantation : official publication of the American Association for the Study of Liver Diseases and the International Liver Transplantation Society},
volume = {},
number = {},
pages = {},
doi = {10.1097/LVT.0000000000000779},
pmid = {41337711},
issn = {1527-6473},
abstract = {BACKGROUND AND AIMS: Oral dysbiosis noted in chronic liver disease (CLD). This may play a role in post-liver transplantation (LT) outcomes. This study aimed to assess the baseline oral microbiome and its association with early complications (EC) within 6 months after liver transplantation (LT).

METHODS: This prospective longitudinal study included 94 CLD recipients (CR) and their living donors. Patients were managed with a standardized immunosuppressive regimen and monitored for 6 months post-LT EC rejection, infection, biliary complications (BCs), and death. Pre- and post-LT saliva samples were processed for bacterial sequencing, qPCR validation, and cytokine profiling. The association between microbial abundance and EC was assessed.

RESULTS: At baseline, CR exhibited a lower Bacteroidota and a higher abundance of Bacillota compared to donors. Streptococcaceae and Veillonellaceae were enriched in CR compared to their respective donors (p<0.05, each). On follow-up, post-LT early complications were noted in 35/94 patients. Prominent Bacillota, Bacteroidetes, and Actinomycetota were noted at baseline in those who developed rejection, infection, and BC, respectively. Species-level analysis, followed by qPCR validation, revealed complication-specific baseline microbial signatures: E. marmotae (FC 3.9) for rejection, P. salivae (FC 71) for infections, and Rothia (FC 301) and Lactobacillus rhamnosus (FC 51) in BC. The baseline enrichment of Prevotella_7_sp2, Klebsiella pneumoniae, and Staphylococcus was associated with sepsis-related mortality. Recipients with post-LT EC showed pro-inflammatory links (Prevotella with IL-2, Streptococcus with IL-8).

CONCLUSION: Baseline oral microbiome profiles were differentially abundant among individuals who developed post-LT early complications. Incorporating microbial signatures may enable noninvasive risk stratification after LT.},
}

@article {pmid41337660,
year = {2025},
author = {Silva, IB and Puig-Domingo, M},
title = {The impact of thyroid disorders on the gut microbiome: emerging mechanisms and clinical relevance.},
journal = {Archives of endocrinology and metabolism},
volume = {70},
number = {Spe1},
pages = {e250075},
doi = {10.20945/2359-4292-2025-0075},
pmid = {41337660},
issn = {2359-4292},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Thyroid Diseases/microbiology/immunology/metabolism ; Dysbiosis/microbiology/immunology ; Thyroid Gland/metabolism/immunology ; Animals ; Clinical Relevance ; },
abstract = {The thyroid-gut axis represents a dynamic interaction between the intestinal microbiota and thyroid function, with growing evidence linking gut dysbiosis to thyroid diseases. The gut microbiome, comprising over 100 trillion microorganisms, influences immune modulation, iodine metabolism, and thyroid hormone regulation. Short-chain fatty acids, produced by beneficial gut bacteria, support immune homeostasis and thyroid function, while pathogenic bacteria and lipopolysaccharides trigger inflammatory pathways that impair thyroid activity. Alterations in gut microbiota composition have been associated with autoimmune thyroid diseases, including Hashimoto's thyroiditis and Graves' disease. Dysbiosis increases intestinal permeability, antigen exposure, and immune activation, exacerbating thyroid autoimmunity. A reduction in short-chain fatty acids-producing bacteria weakens immune tolerance, promoting inflammatory cytokine release and autoantibody production. Recent studies highlight microbial metabolites such as tryptophan derivatives and their role in immune regulation. Gut dysbiosis is also implicated in thyroid nodules and cancer. Decreased butyrate-producing bacteria and increased inflammatory bacterial taxa have been observed in thyroid malignancies. Microbiota influence iodine and selenium bioavailability, essential for thyroid hormone synthesis, and modulate sodium-iodide symporter expression, affecting thyroid cancer response to radioactive iodine therapy. Microbiome-targeted interventions, including probiotics, prebiotics, dietary modifications, and fecal microbiota transplantation, may restore microbial balance, enhance immune regulation, and improve thyroid treatments. This review synthesizes our current understanding of the thyroid-gut axis, indicating that the intestinal microbiota and its metabolites may act directly or indirectly on the thyroid gland, highlighting potential clinical implications and paving the way for therapeutic strategies targeting the intestinal microbiota.},
}

Humans
*Gastrointestinal Microbiome/physiology/immunology
*Thyroid Diseases/microbiology/immunology/metabolism
Dysbiosis/microbiology/immunology
Thyroid Gland/metabolism/immunology
Animals
Clinical Relevance

@article {pmid41337497,
year = {2025},
author = {Camara, PEAS and Gonçalves, VN and Pellizzari, FM and Lopes, FAC and Convey, P and Ramada, MHS and Paiva, TDS and Carvalho-Silva, M and Rosa, LH},
title = {Eukaryotic diversity associated with the phycosphere of the seaweed Ulvaria obscura (Kützing) Gayral (Chlorophyta, Ulvophyceae) in the Svalbard Archipelago, Arctic region assessed using DNA metabarcoding.},
journal = {Anais da Academia Brasileira de Ciencias},
volume = {97},
number = {4},
pages = {e20240808},
doi = {10.1590/0001-3765202520240808},
pmid = {41337497},
issn = {1678-2690},
mesh = {*DNA Barcoding, Taxonomic/methods ; *Biodiversity ; *Seaweed/classification ; Arctic Regions ; Svalbard ; *Chlorophyta/classification/genetics ; },
abstract = {Microorganisms often occur in association with macroalgae, with the term "phycosphere" referring to the seaweed surface where they may be present. Phycosphere represents a poorly explored niche of marine diversity, especially in the polar regions. DNA metabarcoding provides a new and accessible method for the detection of DNA from different organisms, especially applicable for poorly known groups where taxonomic expertise is limited or unavailable. In this study we used DNA metabarcoding to provide an initial survey of eukaryotic communities associated with marine macroalgae obtained from the shores of Svalbard. Samples of Ulvaria obscura were sequenced and the DNA reads found were assigned to 75 taxa of six Kingdoms and 17 phyla: Chromista (Ciliophora, Haptophyta, Ochrophyta, Oomycota and Chrysophyta), Fungi (Ascomycota, Basidiomycota, Chytridiomycota, Mortierellomycota and Rozellomycota), Holozoa (Ichthyosporia), Metazoa (Cnidaria), Protozoa (Cercozoa, Discosea and Heterolobosea) and Viridiplantae (Bryophyta and Chlorophyta). The most abundant group was Viridiplantae, followed by Fungi. Our environmental DNA study confirmed that the phycosphere of U. obscura shelters a rich and complex microbiome, suggesting that Arctic macroalgae provide a hotspot of currently undescribed polar biodiversity. Additionally, our results were obtained during the first official Brazilian Arctic expedition, representing a historic step for the Brazilian Antarctic Program (PROANTAR).},
}

*DNA Barcoding, Taxonomic/methods
*Biodiversity
*Seaweed/classification
Arctic Regions
Svalbard
*Chlorophyta/classification/genetics

@article {pmid41336154,
year = {2025},
author = {Zhan, B and He, D and Yang, X and Zhang, Z and Yan, S},
title = {FNatPred: A Data-Driven Approach for Distinguishing Between NAT and Tumor on the Fungal Microbiome.},
journal = {IEEE transactions on computational biology and bioinformatics},
volume = {PP},
number = {},
pages = {},
doi = {10.1109/TCBBIO.2025.3639775},
pmid = {41336154},
issn = {2998-4165},
abstract = {OBJECTIVE: The role of fungal microbiota in human carcinogenesis remains largely uncharacterized. Recent evidence suggests normal adjacent tissue (NAT) represents an intermediate state between healthy and malignant tissues, highlighting its potential for early cancer detection. Discriminating fungal compositional profiles between tumor and NAT is thus critical for elucidating fungal involvement in oncogenesis. However, the high similarity between tumor and NAT mycobiota poses significant analytical challenges.

METHOD: To overcome this limitation, we developed a two-level ensemble discriminative model. Base-level classifiers, trained using rigorously filtered fungal microbiota data (based on prevalence, abundance, and quality metrics) via Random Forest, generate initial predictions. A meta-level classifier then integrates these base predictions, transforming high-dimensional, sparse fungal feature data into a low-dimensional, dense representation optimized for discrimination. Model implementation and analysis code are available at: https://github.com/cskyan/FNatPred.

RESULTS: Our approach achieved clear separation between tumor and NAT mycobiomes across multiple cancer types, with particularly pronounced discrimination in colorectal cancer (CRC). The proposed model significantly outperformed existing methods in tumor-NAT classification, demonstrating an average AUC improvement of approximately 10%.},
}

@article {pmid41335478,
year = {2025},
author = {Yin, C and Xu, L and Wei, Z and Zhao, Y and Bai, R and Gao, G and Fan, Y and Li, Y and Sun, W and Li, X and Pi, Y},
title = {Gut microbiota and bile acid profiles in purebred vs. crossbred sows: links to oxidative stress and inflammation in late gestation.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001579},
pmid = {41335478},
issn = {2057-5858},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Oxidative Stress ; Female ; Pregnancy ; *Bile Acids and Salts/metabolism/analysis ; Swine/microbiology ; *Inflammation/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology/chemistry ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Understanding the interactions between gut microbiota, bile acid (BA) metabolism and systemic health is critical for supporting gestational physiological stability in sows, especially during the physiologically demanding late gestation period. Although physiological advantages vary by breed in late-gestation sows, the microbiota-related mechanisms underlying these differences remain poorly understood. This study compared serum antioxidant enzyme activity, oxidative damage markers, inflammatory cytokine levels, gut microbiota composition (analysed via 16S rRNA sequencing), and BA profiles (assessed through targeted metabolomics) between purebred large white (LW) and large white×landrace (LW×LR) crossbred sows during late gestation. Results showed that LW×LR crossbred sows exhibited significantly higher serum superoxide dismutase (SOD) activity and IL-10 levels, alongside reduced IL-6 levels (P<0.05), indicating enhanced antioxidant and anti-inflammatory capacity. Gut microbiota analysis revealed greater alpha diversity (Shannon indices) and a lower Simpson index, along with distinct beta diversity (P<0.05) in crossbred sows, with notable enrichment of functional taxa such as Treponema and Prevotella. Additionally, faecal concentrations of modified BAs, specifically 3-oxolithocholic acid and 7-ketolithocholic acid, were significantly elevated, correlating with increased abundance of gut microbiota encoding BA: Na[+] symporter (BASS family) proteins, as well as the increased 7-α-hydroxysteroid dehydrogenase activity (P<0.05). In contrast, LW sows exhibited enrichment of Terrisporobacter and Clostridium sensu stricto 1, alongside accumulation of primary (e.g. chenodeoxycholic acid) and unconjugated BAs (e.g. deoxycholic acid) (P<0.05). Correlation analysis demonstrated that the accumulation of Terrisporobacter and primary BAs was positively correlated with exacerbation of inflammation. In conclusion, under intensive production conditions, significant differences in the gut microbiota-BA axis between LW and LW×LR crossbred sows may underlie variations in oxidative stress and inflammatory status during late pregnancy. These findings provide valuable insights into microbiome-BA-host associations underlying the physiological advantages (enhanced antioxidant and anti-inflammatory capacity) of crossbred sows.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Oxidative Stress
Female
Pregnancy
*Bile Acids and Salts/metabolism/analysis
Swine/microbiology
*Inflammation/metabolism/microbiology
RNA, Ribosomal, 16S/genetics
Feces/microbiology/chemistry
Bacteria/classification/genetics/isolation & purification

@article {pmid41335477,
year = {2025},
author = {Riskumäki, M and Ruuskanen, MO and Mäenpää, K and Ruokolainen, L and Mäkelä, MJ and Jousilahti, P and Vartiainen, E and Ottman, N and Laatikainen, T and Haahtela, T and Alenius, H and Fyhrquist, N and Sinkko, H},
title = {Shotgun metagenomics reveals distinct skin microbial species in allergen-sensitized individuals.},
journal = {Microbial genomics},
volume = {11},
number = {12},
pages = {},
doi = {10.1099/mgen.0.001527},
pmid = {41335477},
issn = {2057-5858},
mesh = {Humans ; *Metagenomics/methods ; *Allergens/immunology ; *Skin/microbiology/virology ; Finland ; Adolescent ; *Microbiota/genetics ; Male ; Russia ; Female ; *Hypersensitivity/microbiology/immunology ; Malassezia/genetics/isolation & purification ; Immunoglobulin E/immunology ; Bacteria/genetics/classification ; Child ; },
abstract = {The Karelian region, which spans the border between Finland and Russia, presents distinct environmental exposures and lifestyles on either side of the governmental border. In the more urbanized Finnish Karelia, allergic diseases are markedly more prevalent than in the more rural Russian Karelia. Prior studies, based on amplicon sequencing, have demonstrated major differences in skin microbiotas between the two populations. However, compositional differences in microbiota between sensitized and non-sensitized (NS) individuals have not been characterized. Here, in a selected population of 112 allergen-sensitized and NS adolescents, we used shotgun metagenomics to characterize the prokaryotic, eukaryotic and viral species in the skin potentially involved in allergic sensitization via distinct environmental exposures. In the more urban Finnish Karelia, the microbiome species composition was associated with IgE-mediated allergen sensitization status, while in the more rural Russian Karelia, the composition was associated with exposure to furry pets. Finnish participants showing high IgE-mediated sensitization to common allergens (allergen-specific IgE >7.5 kU/L) had less Cutibacterium acnes and Malassezia in their skin and displayed weaker interconnectedness of the microbial co-occurrence network compared with NS participants. Moreover, Malassezia restricta strain-level differences were related to allergen sensitization in both Finnish and Russian participants. In summary, we found distinct skin microbiomes between allergen-sensitized and NS participants and tracked the bacterial and fungal species associated with the degree of allergic sensitization in the more urbanized part of the Karelian region. These findings provide new insights into the factors that shape the human skin microbiome and influence allergic diseases.},
}

Humans
*Metagenomics/methods
*Allergens/immunology
*Skin/microbiology/virology
Finland
Adolescent
*Microbiota/genetics
Male
Russia
Female
*Hypersensitivity/microbiology/immunology
Malassezia/genetics/isolation & purification
Immunoglobulin E/immunology
Bacteria/genetics/classification
Child

@article {pmid41335295,
year = {2025},
author = {Jayanandan, M and Veeraraghavan, VP and Govindarajan, S and Mariyappa Subramani, S},
title = {Development of oral dysbiosis following use of antimicrobial mouthwashes: a systematic review.},
journal = {Odontology},
volume = {},
number = {},
pages = {},
pmid = {41335295},
issn = {1618-1255},
abstract = {The oral microbiome maintains the oral and systemic health. The extensive use of antimicrobial mouthwashes to control biofilm-related diseases has increased the concerns about their effect on microbial ecology. Specific formulations may cause microbial shifts which influences both the oral and systemic physiology in an individual. This systematic review evaluates the oral dysbiosis development after antimicrobial mouthwash use and correlates the microbial changes with clinical and systemic outcomes. A comprehensive search in various databases like PubMed, Scopus, etc. (till March 2025) was done. It identified 14 relevant studies from a total of 681 screened records. Risk of bias was assessed using ROB2, ROBINS-I, CRIS, and NOS tools, with data extracted on microbial diversity, taxonomic changes, nitrate reduction capacity, and antibiotic resistance. The findings showed that chlorhexidine caused the greatest dysbiosis and reduces the microbial diversity by 40-60%, with increasing Streptococcus spp. two-to-threefold, and elevating antibiotic resistance gene prevalence. Cetylpyridinium chloride and polyhexamethylene biguanide showed milder effects, thus preserving 70-80% of commensals, while herbal and plant-based rinses (o-cymen-5-ol, StellaLife®, Rosella) reduced pathogens by 25-40% without disrupting the balance. Fluoride-arginine formulations promote beneficial bacteria by 30-50% but marginally upregulated resistance genes, whereas mechanical hygiene methods maintained over 90% microbial diversity. Suppression of nitrate-reducing bacteria was associated with reduced nitric oxide bioavailability, potentially increasing vascular and cognitive risks. Hence, antimicrobial mouthwashes especially chlorhexidine induces significant dysbiotic shifts, while herbal, postbiotic, and mechanical alternatives demonstrate safer, microbiome thereby preserving the effects which is suitable for long-term oral health maintenance.},
}

@article {pmid41335130,
year = {2025},
author = {Wang, K and Xu, Z and Ma, J and Zheng, M and Zhang, Y and Lin, Z and Ji, T},
title = {Evaluating preservation effects on honeybee gut microbiota inocula.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0275425},
doi = {10.1128/spectrum.02754-25},
pmid = {41335130},
issn = {2165-0497},
abstract = {UNLABELLED: The honeybee (Apis mellifera) gut microbiota serves as a model for host-microbe studies, as germ-free bees enable a relatively sterile system. Fresh gut homogenates are optimal for colonization, but immediate use may be limited by practical considerations, such as pathogen screening and the need to minimize repeated preparation for animal welfare. In this study, we systematically evaluated how short-term preservation conditions influence the colonization efficiency and structural integrity of the honeybee gut microbiota. Gut homogenates were prepared and either used immediately, refrigerated for one day or three days, or frozen for seven days with or without glycerol, before being fed to germ-free bees. Colonization outcomes were assessed by combining absolute quantification of bacterial 16S ribosomal RNA gene copy numbers with diversity indices and community composition analyses. Survival rates of inoculated bees did not differ significantly among treatments, but bees receiving inocula refrigerated for three days showed reduced gut mass, suggesting compromised microbial activity. Absolute quantification revealed that total bacterial loads were broadly maintained, yet taxon-specific responses varied, with Gilliamella showing marked sensitivity to freezing. Discrepancies between relative and absolute measurements highlighted the importance of absolute quantification for accurately evaluating colonization. Overall, inocula retained the ability to establish the characteristic core microbiota under all preservation conditions. Notably, refrigeration for one day preserved community features without any detectable differences from freshly prepared inocula, whereas longer refrigeration and freezing introduced measurable perturbations. These results provide methodological guidance for honeybee microbiota transplantation experiments and underscore the necessity of absolute quantification in microbiome research.

IMPORTANCE: The gut microbes of honeybees are essential for their nutrition, immunity, and overall health. To study these microbes, scientists often use germ-free bees colonized with gut communities from donor bees. Fresh preparations are ideal, but repeated preparation is time-consuming, requires pathogen checks, and may involve sacrificing many bees. In this study, we tested practical preservation methods and found that both refrigerated and frozen samples retained the ability to colonize germ-free bees. However, one day of refrigeration preserved microbial abundance and composition most similar to fresh samples, whereas longer refrigeration and freezing introduced detectable changes. These findings provide researchers with clear guidance for preparing standardized microbial inocula while also minimizing repeated dissection of donor bees, thereby improving both experimental reproducibility and animal welfare.},
}

@article {pmid41335096,
year = {2025},
author = {Ji, X and Qian, Q and Zhang, H and Cai, Q and Zhang, K and Xiao, J and Jiang, X and Li, M},
title = {ResMicroDb: a comprehensive database and analysis platform for the human respiratory microbiome.},
journal = {Nucleic acids research},
volume = {},
number = {},
pages = {},
doi = {10.1093/nar/gkaf1194},
pmid = {41335096},
issn = {1362-4962},
support = {2024YFC2607900//National Key R&D Program of China/ ; 2022YFA1304300//National Key R&D Program of China/ ; 2024YFC2607900//National Key R&D Program of China/ ; 32300078//National Natural Science Foundation of China/ ; XDA0460404//Chinese Academy of Sciences/ ; XDA0460202//Chinese Academy of Sciences/ ; },
abstract = {The respiratory microbiome plays an important role in maintaining human health. Despite the rapid growth of literature and publicly accessible data on the respiratory microbiome, a large-scale, well-curated database is still lacking. Here, we introduced ResMicroDb, a comprehensive database and analysis platform for the human respiratory microbiome. ResMicroDb contains 106 464 samples from 514 projects, spanning 10 sample sites, 72 sample types, and 146 phenotypes. Notably, it includes ~7-fold more respiratory samples than existing multi-body-site resources. To improve the reusability and accessibility of data, a standardized bioinformatics pipeline was employed to generate taxonomic profiles, and 32 metadata fields were manually curated. ResMicroDb also provides 11 908 microbe-disease associations, identified from 132 case-control studies, to deepen the understanding of microbiome-disease relationships. Additionally, ResMicroDb offers three tools for in-depth analysis: "Microbiome Composition" for visualizing taxonomic profiles of user-selected samples; "Sample Similarity Search" for inferring the characteristics of new samples by comparing them to the database based on similarity; and "Cross-study Analysis" for identifying common and specific microbial characteristics across cohorts, phenotypes and sample sites. ResMicroDb serves as a versatile and valuable resource for advancing a broad spectrum of respiratory microbiome research and clinical relevance. ResMicroDb is freely accessed at https://resmicrodb.cncb.ac.cn.},
}

@article {pmid41334942,
year = {2025},
author = {Butorac, K and Banić, M and Zucko, J and Leboš Pavunc, A and Novak, J and Jerić, I and Balog, T and Kralj, M and Penava, L and Ceilinger, M and Šušković, J and Kos, B},
title = {Modulation of the Gut Microbiota of Diabetes-Induced Mice Through Curcumin-Enriched Dietary Fibers Intervention.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70350},
doi = {10.1002/mnfr.70350},
pmid = {41334942},
issn = {1613-4133},
support = {IP-2019-04-2237//Hrvatska Zaklada za Znanost/ ; IP-2024-05-6548//Hrvatska Zaklada za Znanost/ ; KK.01.1.1.01.0002//European Commission/ ; OP KK.01.1.1.07.0040//European Commission/ ; },
abstract = {This study aimed to investigate the effect of innovative dietary fiber mixtures, comprised predominantly of resistant dextrin together with insoluble citrus fibers, fructooligosaccharides, long-chain inulin, and gum arabic, with or without curcumin or resveratrol/grape seed extract, on the intestinal microbiota of a mouse model with T2DM. The applied innovative formulations resulted in the desired changes in the distribution of gut microbiome species associated with T2DM, as revealed by QIIME2 and additionally confirmed by ANCOM. This effect was particularly pronounced in the curcumin-supplemented formulation, as evident from the enrichment of the Verrucomicrobiota representative Akkermansia muciniphila and short-chain fatty acid producers Faecalibaculum and Dubosiella, while also leading to a decrease in Patescibacteria, as well as Chlamydia muridarum, Desulfovibrio, Candidatus Saccharimonas, and Alistipes species. The administration of the examined innovative dietary fiber formulations statistically reduced the alpha diversity and altered the beta diversity of the gut microbiota in a mouse model with T2DM, in terms of abundance and presence of species analyzed with MicrobiomeAnalyst. Due to the strong influence on the composition of the gut microbiota, the innovative dietary formulations can be further evaluated for inclusion in food for special medical purposes specifically designed for the dietary management of diabetes.},
}

@article {pmid41334921,
year = {2025},
author = {Marinos, G and Zimmermann, J and Taubenheim, J and Kaleta, C},
title = {Virtual Colon: spatiotemporal modeling of metabolic interactions in a computational colonic environment.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0139125},
doi = {10.1128/msystems.01391-25},
pmid = {41334921},
issn = {2379-5077},
abstract = {Host-microbial metabolic interactions have been recognized as an essential factor in host health and disease. Genome-scale metabolic modeling approaches have made important contributions to our understanding of the interactions in such communities. One particular such modeling approach is BacArena, in which metabolic models grow, reproduce, and interact as independent agents in a spatiotemporal metabolic environment. Here, we present a modeling application of BacArena, a virtual colonic environment, which reveals spatiotemporal metabolic interactions in a computational colonic environment. This environment resembles the crypt space together with the mucus layers, the lumen, and fluid dynamics. Our proof-of-principle experiments include mono-colonization simulations of context-specific colonic cells and simulations of context-specific colonic cells with the SIHUMIx minimal model microbiome. Our simulations propose host-microbial and microbial-microbial interactions that can be verified based on the literature. Most importantly, the Virtual Colon offers visualization of interactions through time and space, adding another dimension to the genome-scale metabolic modeling approaches. Lastly, like BacArena, it is freely available and can be easily adapted to model other spatially structured environments (http://www.github.com/maringos/VirtualColon).IMPORTANCEInteractions between the human body and gut microbes are crucial for health and disease. We present the Virtual Colon, an extension of the individual-based microbiome modeling approach BacArena that mimics key features of the colon, including the crypts, mucus layers, lumen, and fluid flow. Using this model, we simulate gut environments including host cells with bacterial species alone and with a simplified gut microbiota (SIHUMIx). These simulations reveal patterns of host-microbe and microbe-microbe interactions that align with known findings. A key strength of the Virtual Colon is its ability to show how interactions unfold over time and space, offering new insights beyond traditional modeling approaches. The Virtual Colon is freely available and can be adapted to other structured biological environments (http://www.github.com/maringos/VirtualColon).},
}

@article {pmid41334892,
year = {2025},
author = {Bhatnagar, M and Burney, R and Bedawi, EO},
title = {Managing treatment failure in pleural infection.},
journal = {Expert review of respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1080/17476348.2025.2600106},
pmid = {41334892},
issn = {1747-6356},
abstract = {INTRODUCTION: Pleural infection is a common condition associated with significant morbidity, mortality, and prolonged hospital stay. Whilst antibiotics and chest tube drainage comprise initial management, over one-third of patients experience medical treatment failure, necessitating intrapleural enzyme therapy (IET) or surgery. This review examines advances in diagnosis and management of treatment failure in pleural infection.

AREAS COVERED: A literature search of PubMed, Embase, and Cochrane Library (January 2005- April 2025) was performed using keywords related to pleural infection, diagnostics, biomarkers, and treatment interventions. Treatment failure emerged as a multifactorial process involving delayed presentation, structural and physiological barriers such as increased pleural fluid viscosity, septation formation, pleural thickening, and biofilm development, alongside host factors and microbiological complexity. We review current strategies including antibiotics, chest tube drainage, IET (tPA + DNase), and surgical options, alongside emerging modalities such as next-generation sequencing, pleural biopsy, medical thoracoscopy, saline irrigation, and indwelling catheters.

EXPERT OPINION: Early identification of treatment failure within 48 hours is crucial for guiding escalation. A precision medicine approach integrating microbiological, radiological, and host-response data may redefine standards of care and improve outcomes. Future priorities include early risk stratification, biomarker-guided therapy, microbiome-informed antibiotic strategies, and improving global access to effective treatments.},
}

@article {pmid41334814,
year = {2025},
author = {López-Gutiérrez, JC and López-Hernández, D and Toro, M},
title = {Arbuscular Mycorrhizal Fungi and Phosphorus-mobilizing Microorganisms Mediate Organic Phosphorus Cycling in Tropical Savanna Soils.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnaf135},
pmid = {41334814},
issn = {1574-6968},
abstract = {In highly weathered tropical soils, organic phosphorus (Po) constitutes a primordial reservoir for plant P-nutrition. We studied the dynamics of Po fractions, soil phosphatase activity and P-mobilizing microflora in root compartments of non-mycorrhizal (rhizosphere and bulk soil) and mycorrhizal (mycorrhizosphere and hyphosphere) Urochloa brizantha plants growing in rhizoboxes with a low P-sorbing Entisol and a high P-sorbing Ultisol from native neotropical savannas. Inoculation with native arbuscular mycorrhizal fungi resulted in an improvement in plant P-status, particularly in the high P-sorbing soil, that coincided with transformations in more recalcitrant P fractions, a higher phosphatase activity and a higher proportion of P-solubilizing and P-mineralizing organisms in mycorrhizal compartments. We provide evidence for a mycorrhizospheric effect in low P-fertility soils that allows plants to access specific P-pools via symbiosis with arbuscular mycorrhizal fungi.},
}

@article {pmid41334655,
year = {2025},
author = {Zhang, K and Dong, H and Bian, T},
title = {Multi-omics integration and precision medicine in chronic prostatitis: from molecular mechanisms to clinical translation.},
journal = {Systems biology in reproductive medicine},
volume = {71},
number = {1},
pages = {618-629},
doi = {10.1080/19396368.2025.2586609},
pmid = {41334655},
issn = {1939-6376},
mesh = {Humans ; *Prostatitis/therapy/genetics/diagnosis/metabolism/microbiology ; Male ; *Precision Medicine ; Chronic Disease ; *Proteomics ; *Genomics ; *Metabolomics ; Translational Research, Biomedical ; Animals ; Multiomics ; },
abstract = {Chronic prostatitis (CP) imposes a considerable global disease burden, with notable regional disparities in China and significant associated healthcare costs. Traditional classification systems, particularly type III subtypes, are hindered by high symptom heterogeneity and low treatment response rates. Recent advances in multi-omics approaches have elucidated the molecular mechanisms underlying CP, including genomic and epigenetic regulation, transcriptomic and immune microenvironment interactions, metabolomic and microbiome interplay, as well as proteomic and neural remodeling. Precision diagnostic techniques are evolving, integrating multi-omics biomarkers, imaging, and functional assessments for molecular subtyping and clinical translation. Targeted therapeutic strategies are emerging, focusing on immune microenvironment modulation, neuro-immune cross-intervention, and microbiome modulation. However, challenges in clinical translation remain, including technical bottlenecks in integrating dynamic multi-omics data and limitations of animal models. To address these issues, complementary strategies between real-world evidence and traditional randomized controlled trials are proposed. Looking forward, future directions include the development of AI-driven multimodal high-precision diagnostic systems and innovative combination therapies involving targeted, immunotherapeutic, and neuro-stimulatory approaches.},
}

Humans
*Prostatitis/therapy/genetics/diagnosis/metabolism/microbiology
Male
*Precision Medicine
Chronic Disease
*Proteomics
*Genomics
*Metabolomics
Translational Research, Biomedical
Animals
Multiomics

@article {pmid41334604,
year = {2025},
author = {Cui, X and Ding, Z and Ji, Y and Wang, X and Wang, Y and Yuan, Z and Zhang, Y and Liu, K and Liu, Y},
title = {The combination of gut microbiota and metabolomics reveals the effects of polysaccharides from Schisandra chinensis on microbiota and metabolic profile in Alzheimer's disease rats.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70361},
pmid = {41334604},
issn = {1097-0010},
support = {//National Natural Science Foundation of China Young Scientists Fund/ ; },
abstract = {BACKGROUND: Polysaccharide from Schisandra chinensis (SPJ) can attenuate the progression of Alzheimer's disease (AD) by regulating changes in gut microbiota and its metabolites, but the mechanism of action is unclear. This study aimed to investigate the anti-AD effects and regulatory mechanisms of SPJ in an Aβ25-35-induced AD model from the perspective of the 'microbe-gut-brain' axis.

RESULTS: The results showed that SPJ improved spatial learning memory ability, pathological changes in the hippocampal CA1 region and intestinal barrier integrity, and modulated the composition and abundance of gut microbiota in AD rats. Meanwhile, SPJ also regulated phenylalanine, tyrosine, and tryptophan biosynthesis, and linoleic acid, α-linolenic acid, phenylalanine, and arachidonic acid metabolism in AD rats. Furthermore, correlation analysis revealed a correlation between gut microbes and metabolites.

CONCLUSION: In short, via the 'microbe-gut-brain' axis, SPJ ameliorates cognitive deficits, spatial memory loss, and neuroinflammation in AD rats. © 2025 Society of Chemical Industry.},
}

@article {pmid41334554,
year = {2025},
author = {Nabthonglang, J and Gomez, A and Rutschke, S and Santativongchai, P and Kosonsiriluk, S and Studniski, M and Wileman, B and Navanukraw, C and Boukherroub, K},
title = {Effect of bardoxolone methyl on the lower reproductive tract microbiome in turkey breeder hens.},
journal = {Frontiers in physiology},
volume = {16},
number = {},
pages = {1703742},
pmid = {41334554},
issn = {1664-042X},
abstract = {INTRODUCTION: Fertility decline in aging turkey breeder hens is associated with reduced sperm storage in the uterovaginal junction (UVJ), inflammation, oxidative stress, and tissue aging. The mucosal microbiome is an important contributor to subfertility, with shifts in immune function, inflammation, and oxidative stress linked to microbial changes. Bardoxolone methyl, a potent activator of the nuclear erythroid 2-related factor 2 (NRF2) pathway, enhances antioxidant defenses and reduces inflammation. This study investigated if bardoxolone methyl treatment alters the microbial composition and diversity of the UVJ and vagina in turkey hens.

METHODS: Forty turkey hens (59 weeks old) were randomly assigned to a bardoxolone methyl group (n = 20) or a control group (n = 20). Birds received intramuscular tail injections of bardoxolone methyl or vehicle, every other day for two weeks. Swabs from the UVJ and vagina (VAG) were collected for 16S rRNA sequencing. Microbial diversity, differential taxonomic composition, and predicted functional pathways were assessed using QIIME2, PICRUSt2, and R-based statistical packages. Microbiome profiles revealed significant differences between UVJ and VAG communities.

RESULTS: The VAG showed higher bacterial richness, while both sites were dominated by Firmicutes, Proteobacteria, Thermoproteota, and Actinobacteriota phyla, indicator species analyses identified enrichment of Staphylococcus and Escherichia in UVJ, and Lactobacillaceae in VAG. Bardoxolone methyl did not significantly alter global alpha diversity but selectively modulated unweighted beta diversity and low-abundance taxa, enriching Corynebacterium in UVJ and rare taxa like Armatimonadota and Omnitrophota in the VAG. Functional predictions indicated bardoxolone methyl's association with enrichment of pathways including energy metabolism, nucleotide biosynthesis, protein quality control, and redox balance, particularly in the UVJ.

DISCUSSION: This study provides the first characterization of the turkey lower reproductive tract microbiome, revealing tissue-specific communities and functional profiles between the UVJ and vagina. Bardoxolone methyl treatment did not alter overall microbial diversity, but selectively enriched low-abundance taxa and metabolic pathways related to energy metabolism, nucleotide biosynthesis, and stress resilience, particularly in the UVJ. These findings indicate that bardoxolone methyl treatment can finetune microbial functional capacity without destabilizing overall community structure. The results also highlight the importance of considering tissue-specific differences and functional potential when investigating reproductive function.},
}

@article {pmid41334445,
year = {2025},
author = {Jing, M and Jiang, Y},
title = {Microbiome-mediated crosstalk between T2DM and MASLD: a translational review focused on function.},
journal = {Frontiers in endocrinology},
volume = {16},
number = {},
pages = {1677175},
pmid = {41334445},
issn = {1664-2392},
mesh = {Humans ; *Diabetes Mellitus, Type 2/microbiology/metabolism/complications ; *Gastrointestinal Microbiome/physiology ; Animals ; *Non-alcoholic Fatty Liver Disease/microbiology/metabolism ; *Fatty Liver/microbiology/metabolism ; },
abstract = {Type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated steatotic liver disease (MASLD) frequently co-occur and aggravate one another through shared pathways of insulin resistance, low-grade inflammation and disordered lipid handling. Framing their interaction through the gut-liver-pancreas axis, this review synthesizes recent progress with a function-first emphasis, moving beyond taxonomic lists to the microbial outputs most consistently linked to dual metabolic-hepatic endpoints. We summarize how short-chain fatty acids (SCFAs), bile acids (BAs), lipopolysaccharide (LPS) and other microbe-associated molecular patterns, branched-chain amino-acid (BCAA) catabolites, trimethylamine N-oxide (TMAO) and endogenous ethanol reach the liver via portal inflow or the enterohepatic BA cycle and act on epithelial, immune and endocrine interfaces, including the farnesoid X receptor (FXR), G-protein-coupled BA receptor 1 (TGR5) and fibroblast growth factor 19/15 signaling. Mechanistic routes-barrier dysfunction and endotoxaemia; SCFA signaling with effects on enteroendocrine tone and substrate flux; BA remodeling that resets hepatic and pancreatic set-points; and nitrogen/choline and ethanol pathways that promote lipotoxic injury-offer biologically coherent explanations for parallel trajectories of hyperglycemia and steatosis/inflammation. We appraise therapeutic modulation spanning diet and fermentable substrates, live biotherapeutics/postbiotics, BA-targeting drugs, fecal microbiota transplantation and metabolic/bariatric surgery, and we outline clinically actionable biomarker opportunities using function-based panels (fermentative capacity, BA transformation, inflammatory ligands, nitrogen/methyl flux) integrated with host metabolites and genetics for diagnosis, risk stratification and response prediction. By advocating standardized reporting, careful control of diet/medications and composite metabolic-hepatic endpoints in prospective trials, this review provides a practical framework to accelerate translation from association to targeted prevention and therapy that improves glycemic control and MASLD activity in parallel.},
}

Humans
*Diabetes Mellitus, Type 2/microbiology/metabolism/complications
*Gastrointestinal Microbiome/physiology
Animals
*Non-alcoholic Fatty Liver Disease/microbiology/metabolism
*Fatty Liver/microbiology/metabolism

@article {pmid41334216,
year = {2025},
author = {Szabó, S and Kovács-Weber, M and Pap, TI and Dolányi, Á and Pajor, F and Bodnár, Á and Vajda, T and Heincinger, M and Szabó, RT},
title = {Effect of postbiotics on the production parameters of rearing goose.},
journal = {Veterinary and animal science},
volume = {30},
number = {},
pages = {100541},
pmid = {41334216},
issn = {2451-943X},
abstract = {Our aim was to measure the mortality, live body weight, feed conversion, intake and detect the weight and stiffness of the liver, liver colour, breast and thigh weight as an effect of the dry form of Burain® postbiotic supplementation in rearing goose. The goslings were allocated into 5 equal groups: control (without supplementation), group 1 (1 g/kg postbiotic during the starter and grower period), group 2 (2 g/kg postbiotic during the starter and grower period), group 3 (0.2 g/kg postbiotic during the starter and grower period), group 4 (1 g/kg postbiotic during the starter period). Granulated feed and drinking water were provided ad libitum to all rearing goose. Supplementation significantly increased body weight in group 2 (6321.84±664.9 g) on week 8. Group 2 showed a significantly reduced feed conversion ratio (1.51±0.04), while groups 1 and 4 exhibited significantly lower daily feed intake than the control during the starter phase. There were no significant differences among groups in foie gras parameters or in thigh and breast weights. The liver weight and stiffness were found to be significantly positively correlated in each treatment group. The supplementation made a significant difference in the parameters of b* and L* for liver colour, but not for a* values. The impact of postbiotic supplementation in the rearing period is extended to weeks. Further investigations are needed to connect information from rearing to the fattening phase and the gut microbiome in goose.},
}

@article {pmid41334169,
year = {2025},
author = {Kashyap, AS and Manzar, N and Chaudhary, P and Ali, S},
title = {Editorial: Unravelling microbial interactions in plant health and disease dynamics.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1716380},
doi = {10.3389/fmicb.2025.1716380},
pmid = {41334169},
issn = {1664-302X},
}

@article {pmid41334162,
year = {2025},
author = {Elbehiry, A and Marzouk, E and Abalkhail, A},
title = {Antimicrobial resistance at a turning point: microbial drivers, one health, and global futures.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1698809},
pmid = {41334162},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is a major health threat of the 21st century, undermining the effectiveness of modern medical interventions and reversing decades of progress in infection control. Its drivers include microbial evolution, horizontal gene transfer, inappropriate use in human and veterinary medicine, agricultural practices, environmental reservoirs, and uneven regulation. This review integrates microbial, clinical, and environmental perspectives within a One Health framework. At the microbial level, resistance arises through mutation, gene transfer, and biofilm-associated tolerance, with soil, wastewater, and wildlife serving as conduits for spreading resistance elements. Advances in diagnostics-including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), whole-genome sequencing (WGS), digital PCR, and CRISPR-based assays are transforming detection and surveillance, but deployment remains uneven, particularly in low- and middle-income countries. Antimicrobial stewardship now extends beyond hospitals, supported by decision support systems, artificial intelligence (AI), and community programs; however, gaps in surveillance capacity and policy implementation continue to limit impact. One Health linkages connect agricultural use, wastewater, and wildlife exposure with human risk, embedding clinical decisions within ecological and veterinary contexts. Persistent gaps include fragmented regulation, limited involvement of microbiologists in policy development, and weak incentives for antibiotic innovation. Priority directions include biomarker-guided prescribing, CRISPR-directed antimicrobials, microbiome-sparing therapeutics, and genomics-informed surveillance that integrates clinical and environmental data. Positioning the clinical microbiology laboratory as an operational hub can align rapid diagnostics, interpretive reporting, antimicrobial stewardship, and integrated surveillance (GLASS, EARS-Net, NARMS, and wastewater/wildlife monitoring) on a common platform. Clear reporting triggers and concise case vignettes can translate laboratory results into actionable bedside decisions and policy measures across diverse resource settings, with measurable benefits for patient outcomes and public health.},
}

@article {pmid41333884,
year = {2025},
author = {Sousa, LM and Izquierdo, VS and Cappellozza, BI and Moriel, P},
title = {Maternal supplementation with Bacillus-based direct-fed microbials altered the maternal and offspring fecal microbiome.},
journal = {Translational animal science},
volume = {9},
number = {},
pages = {txaf145},
pmid = {41333884},
issn = {2573-2102},
abstract = {This study evaluated the effects of maternal supplementation of a Bacillus-based direct-fed microbial (DFM) on fecal microbiome of heifer-calf pairs. At the start of the study (day 0), 72 pregnant Brangus crossbred beef heifers (20 to 22 mo of age) were stratified by body weight (BW; 431 ± 31 kg) and body condition score (BCS; 6.0 ± 0.36) and randomly allocated into 1 of 12 bahiagrass pastures (1 ha and 6 heifers/pasture). Treatments were assigned to pastures and consisted of heifers supplemented with 1 kg/hd/d of soybean hulls added (BAC) or not (CON) with DFM containing Bacillus subtilis 810 and B. licheniformis 809 (3 g/hd/d; 6.6 × 10[9] colony forming unit; Bovacillus; Novonesis, Lyngby, Denmark) from day 0 to 242 (139 ± 4 d prepartum to 104 ± 4 d postpartum). Calves were early weaned on day 242 and then allocated to drylot pens and fed the same diet until day 319. On days 271 and 287, calves were vaccinated against pathogens associated with bovine respiratory disease. Fecal samples were collected from 3 heifers per pasture on days 0, 90 and 180 and from 2 to 3 calves per pen on days 242 and 272. Shannon and Simpson diversity indexes tended to be greater (P = 0.09) for BAC vs. CON heifers. Clostridium and Blautia relative abundances on day 90 and average Mogibacterium relative abundance were lower (P ≤ 0.03) for BAC vs. CON heifers, whereas Bacteroides and Porphyromonas relative abundances tended (P ≤ 0.08) to be greater for BAC vs. CON heifers. Shannon diversity index did not differ (P ≥ 0.14) between CON and BAC calves, whereas Simpson diversity index remained constant (P = 0.98) for CON calves from day 242 to 272 but increased (P = 0.02) for BAC calves from day 242 to 272. Effects of maternal treatment × day tended (P = 0.06) to be detected for Paraprevotella genus, which Paraprevotella relative abundance on day 242 was lower (P = 0.05) for BAC vs. CON calves on day 242, and did not differ (P = 0.89) between treatments on day 272. Relative abundance of Bacteroides was greater (P = 0.01), whereas Slackia was lower (P < 0.01) for BAC vs. CON calves. Blautia, Butyrivibrio, and Methanobrevibacter relative abundance tended (P = 0.08) to be lower for BAC vs. CON calves. In conclusion, exclusive maternal supplementation with a Bacillus-based DFM during gestation and early lactation modulated the fecal microbiota of both heifers and their offspring.},
}

@article {pmid41333806,
year = {2025},
author = {Al Bataineh, MT and Dash, NR and Mysara, M and Saeed, O and Alkhayyal, N and Talaat, IM and Bendardaf, R and Saber-Ayad, M},
title = {Metagenomic analysis of gut microbiota in colorectal adenocarcinoma in the MENA region.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1634631},
pmid = {41333806},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Male ; Female ; Middle Aged ; *Adenocarcinoma/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Aged ; DNA, Bacterial/genetics/chemistry ; Middle East ; Feces/microbiology ; Phylogeny ; DNA, Ribosomal/genetics/chemistry ; },
abstract = {BACKGROUND: Growing evidence suggests that gut microbiota plays a role in the development of colorectal cancer (CRC), and a few bacterial strains have been linked to carcinogenesis. Contrary to the Western population, the relationship between pro-cancer microorganisms and CRC among Middle Eastern individuals remains largely unexplored. Ninety-eight samples from Middle Eastern individuals with and without CRC were subjected to microbial profiling based on the 16S rRNA gene.

RESULTS: The CRC group exhibited a more complex gut microbiota with clusters that were significantly distinct from those of the control group. The taxonomic orders Caulobacterales, Rhizobiales, Sphingomonadales, and Burkholderiales, along with the genera Recibecterium and Sphingobium, were overrepresented in the CRC samples based on differential abundance testing between the CRC and control groups. Utilizing 16S-based functional prediction, we identified a significant enrichment of pathways vital for pentose and glucuronate interconversions, metabolism of terpenoids and polyketides, spliceosome, and dTMP kinase pathways within the CRC group. Moreover, we observed a link between Herbaspirillum huttiense and the pathways regulating the actin cytoskeleton; this intriguing connection may provide insights into the molecular mechanisms underlying cytoskeletal rearrangement and carcinogenesis triggered by H. huttiense.

CONCLUSIONS: The findings of this study support the connection between gut microbiota and the development of CRC and highlight region-specific microbial signatures that may serve as non-invasive diagnostic biomarkers or predictive tools for early screening in Middle Eastern populations, where CRC is increasingly diagnosed at advanced stages. These insights could inform the development of microbiome-based screening panels and personalized prevention strategies adapted to the MENA region's unique genetic, dietary, and environmental profiles.},
}

Humans
*Colorectal Neoplasms/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
*Metagenomics
Male
Female
Middle Aged
*Adenocarcinoma/microbiology
*Bacteria/classification/genetics/isolation & purification
Aged
DNA, Bacterial/genetics/chemistry
Middle East
Feces/microbiology
Phylogeny
DNA, Ribosomal/genetics/chemistry

@article {pmid41333804,
year = {2025},
author = {Waechter, C and Wilkens, JN and Fehse, L and Heider, D and Sassani, K and Chatzis, G and Weyand, S and Pankuweit, S and Luesebrink, U and Soufi, M and Pöling, J and Braun, T and Ausbuettel, F and Ruppert, V},
title = {Comparative analysis of full-length 16s ribosomal RNA gene sequencing in human oropharyngeal swabs using primer sets with different degrees of degeneracy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1658615},
pmid = {41333804},
issn = {2235-2988},
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Oropharynx/microbiology ; *Microbiota/genetics ; *DNA Primers/genetics ; *Bacteria/genetics/classification/isolation & purification ; Sequence Analysis, DNA/methods ; DNA, Bacterial/genetics ; Saliva/microbiology ; },
abstract = {BACKGROUND: Full-length 16S rRNA gene sequencing using nanopore technology has become increasingly relevant for profiling complex microbial communities, including the human oral microbiome. Primer selection plays a critical role in amplification bias and taxonomic resolution, yet remains insufficiently investigated for oropharyngeal samples.

METHODS: We conducted a comparative analysis of two primer sets with differing degrees of degeneracy - Oxford Nanopores (ONT) standard 27F primer (27F-I) and a more degenerate variant (27F-II) - for full-length 16S rRNA gene sequencing of 80 human oropharyngeal swab samples using ONTs MinION Mk1C. Alpha diversity and taxonomic profiles were statistically compared between primer sets and benchmarked against a large-scale salivary microbiome dataset (n=1,989) from healthy individuals.

RESULTS: Primer choice significantly impacted microbial community composition and diversity. The more degenerate primer set 27F-II yielded significantly higher alpha diversity (Shannon index: 2.684 vs. 1.850; p < 0.001) and detected a broader range of taxa across all phyla. The taxonomic profiles generated with 27F-II strongly correlated with the reference dataset (Pearson's r = 0.86, p < 0.0001), whereas profiles generated with 27F-I showed weak correlation (r = 0.49, p = 0.06). 27F-I overrepresented Proteobacteria and underrepresented key genera such as Prevotella, Faecalibacterium, and Porphyromonas.

CONCLUSION: Our findings demonstrate that primer degeneracy has a substantial effect on taxonomic resolution and biodiversity estimates in oropharyngeal 16S rRNA gene sequencing. The more degenerate 27F-II primer set seams to more faithfully captures the complexity of the human oropharyngeal microbiome and aligns more closely with population-level reference data. These results underscore the importance of careful primer selection and support the adoption of degenerate primers as a methodological standard in nanopore-based oral microbiome research.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Oropharynx/microbiology
*Microbiota/genetics
*DNA Primers/genetics
*Bacteria/genetics/classification/isolation & purification
Sequence Analysis, DNA/methods
DNA, Bacterial/genetics
Saliva/microbiology

@article {pmid41333317,
year = {2025},
author = {Ullah, S and Wu, C and Zou, X and Zhong, Y and Ahmad, A and Jan, AU and Cong, Y and Chen, Y and Li, L},
title = {Understanding microbiota-driven oncogenesis: The role of metabolites in tumorigenesis.},
journal = {iScience},
volume = {28},
number = {12},
pages = {113945},
pmid = {41333317},
issn = {2589-0042},
abstract = {The gut microbiota profoundly influence human health through its composition and metabolic activity, which are shaped by diet and host factors. Disruption of this equilibrium, known as dysbiosis, has been implicated in cancer development. Microbial metabolites act as key mediators connecting the gut microbiome to tumor progression by altering the tumor microenvironment and modulating signaling pathways in tumor and immune cells. This review examines the mechanistic links between the gut microbiota, its metabolites, and tumorigenesis, emphasizing how microbial metabolism of host- and diet-derived compounds affects oncogenic and genotoxic processes in colorectal cancer (CRC). It also explores how dietary and host factors modulate microbial composition and function, influencing cancer susceptibility. Understanding these interconnected processes provides conceptual insight into the microbiota-cancer axis and highlights opportunities for microbiome-targeted interventions in cancer prevention and therapy.},
}

@article {pmid41333064,
year = {2025},
author = {Zhao, B and Sun, J and Xiang, L and Su, Z},
title = {Exercise as a modulator of gut microbiota for improvement of sleep quality: a narrative review.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1639099},
pmid = {41333064},
issn = {1662-4548},
abstract = {Sleep quality is a cornerstone of physical and mental well-being, yet millions of individuals worldwide suffer from chronic sleep disturbances. Recent developments in microbiome research have shown that the microbiota-gut-brain axis regulates sleep by two-way communication between the gut and brain. Exercise is well-documented for its beneficial impact on sleep, yet emerging evidence indicates that one mechanism by which it achieves this may involve the modulation of gut microbiota. This narrative review examines the developing triadic relationship among exercise, gut microbiota, and sleep. It examines how exercise influences microbial diversity, the production of sleep-related metabolites like serotonin, GABA, and SCFAs, and immune responses that collectively shape sleep architecture. Additionally, the review highlights physiological factors influenced by exercise-such as gut motility, intestinal barrier function, and bile acid metabolism-that may impact the gut ecosystem and, in turn, sleep. Although encouraging results, deficiencies persist in our comprehension of the specific mechanisms connecting these domains. This review underscores the need for interdisciplinary research and suggests that targeting the gut microbiota via customized exercise interventions presents a promising, non-pharmacological strategy for enhancing sleep quality.},
}

@article {pmid41332906,
year = {2025},
author = {Zhao, Z and Lu, L and Yi, Y and Gao, N and Hu, J and Han, G and Ma, X},
title = {Gut microbiota signature in a cohort of Chinese patients with rosacea.},
journal = {Biochemistry and biophysics reports},
volume = {44},
number = {},
pages = {102361},
pmid = {41332906},
issn = {2405-5808},
abstract = {BACKGROUND: Rosacea is a chronic inflammatory skin disease characterized by diverse symptoms and variable clinical progression, which can significantly impair patients' quality of life and mental health. The exact etiology of rosacea remains elusive. It has been hypothesized that specific microorganisms may trigger symptom onset and play crucial roles in the pathogenesis of the disease.

OBJECTIVE: We performed a case-control study to investigate the gut microbiome of rosacea patients compared to controls matched by age, sex in China.

METHODS: The study cohort comprised eight patients diagnosed with rosacea and eight age- and sex-matched healthy controls residing in Beijing. Metagenomic sequencing was performed using on a llumina Novaseq 6000 platform. Hospital Anxiety and Depression Scale was used to evaluate the severity of anxiety and depression of rosacea patients. Skindex-16 score was used to assess dermatology-specific health-related quality of life (HrQoL) in patients with rosacea. The clinical evaluation of acne was done using the ECLA score.

RESULTS: The rosacea patients showed higher HADS and Skindex-16 score (15.375 ± 1.302 and 46 ± 9.75 respectively) vs healthy controls (3.425 ± 1.308 and 0 respectively). A clear distinction was observed between the rosacea group and the control group, characterized by a significant increase in the abundance of Turicibacter_sp._TJ11, Turicibacter_sp._H121,Turicibacter_sp._TA25,Turicibacter_sp._T129,Ruminococcus_sp._AF18-22,Ruminococcus_sp._CAG:379,Ruminococcus_sp._AM2829LB,Ruminococcus_callidus, Ruminococcus_sp._AM36-18,Ruminococcus_sp._AF43-11,Ruminococcus_sp._AM28-41,Streptococcus sp. 23.2,Streptococcus infantarius, Streptococcus vestibularis, Streptococcus salivarius, Streptococcus gordonii, Clostridium_sp._CAG:798, Clostridium_tertium, Alistipes_sp._Z76 and Lachnospiraceae_bacterium_XBB2008in the rosacea group. In contrast, reduced levels were detected in the rosacea group for Clostridium_sp._AF12-41, Clostridium_sp._CAG:299, Clostridium_sp._OM05-5BH,Clostridium_sp._AF24-2LB, Clostridium_sp._AM18-55, Clostridium_sp._CAG:43, Clostridium_sp._OM047,Clostridium_sp._TF1113AC,Clostridium_sp._OF134,Clostridium_disporicum, Butyrivibrio_sp._CB08,Butyrivibrio_sp._INlla14, Roseburia_sp._CAG:50 (p < 0.05). Pearson correlation analysis revealed that Gemmiger_sp._An120 was positively correlated with Skindex-16 and negatively correlated with ECLA score (P < 0.05). Clostridium_sp._CAG:299 was negatively correlated with HADS scores and positive correlation with ECLA score (P < 0.05). KEGG pathway analysis found KO05034, KO04024 and KO00920 pathways exhibited increased activity in the Rosacea group (P < 0.05).

CONCLUSIONS: The gut microbiota in individuals with rosacea displayed changed from that of healthy control. These microbial alterations may contribute to the pathogenesis of rosacea through multiple mechanisms, including impairment of the intestinal barrier function, induction of pro-inflammatory cytokine release, and modulation of neurotransmitter synthesis. By integrating taxonomic shifts with functional alterations, this study provides deeper insights into the gut ecosystem changes associated with systemic inflammation in rosacea.},
}

@article {pmid41332831,
year = {2025},
author = {Armet, AM and Li, F and Deehan, EC and Nikolaeva, DD and Delannoy-Bruno, O and Siegwald, L and Berger, B and Castelli, KM and Rodionov, DA and Arzamasov, AA and Liu, J and Seethaler, B and Cole, JL and Nguyen, KN and Jin, M and Zhao, YY and Sharma, AM and Curtis, JM and Proctor, SD and Bischoff, SC and Wismer, WV and Osterman, AL and Bakal, JA and Greiner, R and Field, CJ and Knights, D and Prado, CM and Walter, J},
title = {Mechanistic insights into microbiome-dependent and personalized responses to dietary fibre in a randomized controlled trial.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.20.25340625},
pmid = {41332831},
abstract = {Dietary fiber supplementation can reduce cardiometabolic risk, but its effective use is limited by incomplete understanding of fibre-microbiome interactions and highly individualized responses. We tested acacia gum (AG; fermentable fibre), resistant starch type 4 (RS4; fermentable fibre), and microcrystalline cellulose (MCC; non-fermentable control fibre) in a six-week randomized trial in adults with excess body weight. Multi-omics profiling revealed distinct, structure-specific microbiota and short-chain fatty acid shifts with AG and RS4, which were not directly linked to physiological outcomes. Improvements in inflammation, gut barrier function, and satiety occurred across all arms, indicating fermentation-independent effects. AG reduced plasma ghrelin, linked to microbial carbohydrate-active enzyme genes targeting its structures. Machine-learning models predicted individualized, fiber-specific effects on blood pressure (AG) and C-reactive protein (RS4) from microbial pathways and fecal bile acids. These findings delineate fermentation-dependent and independent mechanisms of fibre action and provide a mechanistic basis for personalized fibre supplementation. Trial registration: ClinicalTrials.gov NCT02322112.},
}

@article {pmid41332770,
year = {2025},
author = {Anton, L and Kholod, O and Phatate, R and Ferguson, B and Klohonatz, K and Goods, BA and Gerson, KD},
title = {Multiomic analysis reveals that polyamines alter G. vaginalis -induced cervicovaginal epithelial cell dysfunction.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.20.689523},
pmid = {41332770},
issn = {2692-8205},
abstract = {An anaerobe-dominant, Lactobacillus -deplete cervicovaginal microbiome is associated with adverse reproductive outcomes. Gardnerella vaginalis , a common cervicovaginal anaerobe, alters cervicovaginal epithelial cell function, resulting in inflammatory immune responses and epithelial barrier breakdown. Specific host-microbial mechanisms inducing this epithelial dysfunction remain unknown. Here we show microbe-specific alterations in cervicovaginal epithelial cell metabolite profiles where G. vaginalis , but not Lactobacillus crispatus , increases polyamine biosynthesis. Pretreatment with polyamines (putrescine, spermidine and spermine) globally shifts G. vaginalis -induced transcriptomic profiles. Alterations in transcripts encoding enzymes responsible for polyamine synthesis and catabolism provides further evidence that G. vaginalis modifies polyamine biosynthesis. Additionally, polyamine-mediated transcriptomic changes include genes related to bacterial defense, inflammation, and epigenetic processes. Polyamines mitigate G. vaginalis -induced inflammatory responses through reduction of cytokines, chemokines, and matrix metalloproteinases. The ability of cervicovaginal metabolites to alter microbe-mediated changes in epithelial cell function suggests that metabolite-microbe interactions are critical mediators of epithelial defense against a Lactobacillus -deplete microbiota.},
}

@article {pmid41332743,
year = {2025},
author = {Patan, A and Xing, S and Charron-Lamoureux, V and Hu, Z and Deleray, V and Agongo, J and El Abiead, Y and Mannochio-Russo, H and Mohanty, I and Gouda, H and Zemlin, J and Rajkumar, P and Lee, C and Leanos, D and Weimann, N and Tsuda, W and Giddings, S and Bui, T and Kvitne, KE and Zhao, HN and Zuffa, S and Nguyen, V and Andrade, A and Gonçalves Nunes, WD and Caraballo-Rodríguez, AM and Caetano David, L and Carver, J and Bandeira, N and Wang, M and Burnett, LA and Siegel, D and Dorrestein, PC},
title = {Charting the Undiscovered Metabolome with Synthetic Multiplexing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.18.689170},
pmid = {41332743},
issn = {2692-8205},
abstract = {In untargeted metabolomics, reference MS/MS libraries are essential for structural annotation, yet currently explain only 6.9% of the more than 1.7 billion MS/MS spectra in public repositories. We hypothesized that many unannotated features arise from simple, biologically plausible transformations of endogenous and exposure-derived compounds. To test this, we created a reference resource by synthesizing over 100,000 compounds using multiplexed reactions that mimic such biochemical transformations. 91% of the compounds synthesized are absent from existing structural databases. Through improvements in the construction of the computational infrastructure that enables pan repository-scale MS/MS comparisons, searching this biologically inspired MS/MS library increased the overall reference-based match rate by 17.4%, yielding over 60 million new matches and raising the global pan-repository MS/MS annotation rate to 8.1%. By facilitating structural hypotheses for previously uncharacterized MS/MS data, this framework expands the accessible detectable biochemical landscape across human, animal, plant, and microbial systems, revealing previously undescribed metabolites such as ibuprofen-carnitine and 5-ASA-phenylpropionic acid conjugates arising from drug-host and host-microbiome co-metabolism.},
}

@article {pmid41332636,
year = {2025},
author = {Donado, CEP and Liu, S and Seravalli, J and Auchtung, JM and Rose, DJ},
title = {Cadmium toxicity to the human gut microbiome varies depending on composition.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.19.689308},
pmid = {41332636},
issn = {2692-8205},
abstract = {UNLABELLED: Cadmium (Cd) is a toxic heavy metal with detrimental impacts on the gut microbiota. We investigated the compositional and functional effects of acute Cd exposure on human fecal microbiotas using 24-hour in vitro cultures from 21 healthy adult donors. Regression analysis of butyrate production in the absence (Cd-) versus presence (Cd+) of Cd identified three categories of microbial responses: sensitive, intermediate, and resilient. Under Cd stress, sensitive microbiomes exhibited significant decreases in butyrate [-3.22±0.96 log 2 (Cd+/Cd-), p=0.001] coupled with elevated acetate [1.53±1.83 log 2 (Cd+/Cd-), p=0.003] and lactate [1.86±0.95 log 2 (Cd+/Cd-), p=0.001] production. In contrast, resilient microbiomes did not show significant changes in butyrate [0.22±0.43 log 2 (Cd+/Cd-), p=0.59] or acetate [-0.18±0.35 log 2 (Cd+/Cd-), p=0.26] and exhibited attenuated increases in lactate compared with sensitive microbiomes [0.45±0.43 versus 1.86±0.95 log 2 (Cd+/Cd-), p=0.002]. Sensitive microbiomes had a larger shift in global microbiota composition under Cd stress than resilient microbiomes (weighted UniFrac distance: 0.098±0.026 versus 0.073±0.035, p=0.04). Several genera were significantly different between sensitive and resilient communities after exposure to Cd, but the most striking was Anaerostipes (7.15 centered-log-ratio difference, Cd+/Cd-, q<0.001). Network analysis revealed a significantly greater disruption of microbial interactions in sensitive communities compared with resilient (χ [2] = 9.21, p = 0.002). Multivariable Association with Linear Models revealed that, in resilient communities, butyrate production was primarily associated with Faecalibacterium in the absence of Cd (q<0.001) and Anaerostipes in the presence of Cd (q=0.005). These findings highlight distinct gut microbial responses to acute Cd exposure and provide a foundation to investigate microbiota features underlying Cd sensitivity or resilience.

IMPORTANCE: Cadmium is a widespread environmental contaminant that reaches the human intestine, where it can disrupt the gut microbial community and negatively impact digestive and systemic health. However, this study demonstrates that human gut microbiomes vary in their responses to cadmium exposure: sensitive communities exhibit losses of beneficial organisms, particularly butyrate-producing taxa that contribute to intestinal integrity and metabolic balance, whereas resilient communities retain microorganisms with this key functional capacity. This work advances our understanding of how gut microbial functions may mitigate the adverse effects of cadmium exposure by identifying the compositional features that distinguish sensitive from resilient microbiomes. These findings highlight the importance of elucidating microbiome-mediated mechanisms that help sustain host health and lay the groundwork for deeper mechanistic studies aimed at mitigating cadmium toxicity.},
}

@article {pmid41332528,
year = {2025},
author = {Aufiero, MA and Hohl, TM},
title = {Antibiotic-induced microbiota disruption impairs neutrophil-mediated immunity to respiratory Aspergillus fumigatus infection in mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.18.689104},
pmid = {41332528},
issn = {2692-8205},
abstract = {UNLABELLED: Aspergillus fumigatus is an environmental mold that forms ubiquitous airborne conidia and can cause life-threatening infections in immunocompromised individuals. Invasive aspergillosis occurs in patients with quantitative or qualitative neutrophil defects, who often receive systemic antibiotics to prevent or manage bacterial infections. Antibiotic-induced bacterial dysbiosis has been linked to impaired neutrophil bactericidal activity and to intestinal commensal bacteria escape during systemic candidiasis, though it remains unclear whether receipt of antibacterial antibiotics impairs neutrophil-dependent defenses against inhaled mold pathogens in the lung. Herein, we measured the outcome of Aspergillus challenge in C57BL/6J mice that were treated with different antibiotics in the drinking water for three weeks prior to experimental infection. We found that ampicillin but not neomycin or vancomycin treatment significantly increased murine mortality and lung fungal burden. The heightened susceptibility was associated with impaired fungal killing by lung-infiltrating neutrophils and monocytes, as well as reduced neutrophil production of NADPH oxidase 2 (NOX2)-dependent reactive oxygen species (ROS). These findings demonstrate that systemic antibiotic treatment can compromise pulmonary anti- Aspergillus immunity and suggest that the host microbiota can enhance neutrophil fungicidal activity by promoting NOX2-mediated ROS production.

IMPORTANCE: Aspergillus fumigatus is an environmental mold that causes invasive pulmonary disease in immunocompromised individuals. Owing to limited diagnostic tools, a narrow arsenal of effective treatments, and rising antifungal resistance, the World Health Organization (WHO) has designated Aspergillus as a critical priority fungal pathogen, highlighting the urgent need for further research. Patients with compromised immunity often receive broad-spectrum antibiotics to prevent or treat opportunistic infections, leading to significant disruption of the resident commensal microbiota. This antibiotic-induced dysbiosis has been linked to Clostridium difficile colitis and to intestinal overgrowth of vancomycin-resistant Enterococcus and Candida parapsilosis , preceding bloodstream infection. However, the impact of antibiotic treatment on susceptibility to invasive pulmonary aspergillosis remains undefined. In this study, we found that oral treatment with ampicillin, but not neomycin or vancomycin, significantly increased mortality in mice following Aspergillus infection. Neutrophils from the lungs of ampicillin-treated mice also showed markedly impaired fungal killing. These findings raise the possibility that preserving microbiome integrity during antibiotic treatment could enhance immune protection against invasive aspergillosis in at-risk patient groups.},
}

@article {pmid41332522,
year = {2025},
author = {Salman, T and Luo, Z and Johnson, D and Noorani, AA and Wan, Z and Bordieanu, B and Ye, ZW and Penrod, RD and Xian, H and Fitting, S and Kalivas, PW and Jiang, W},
title = {Cannabis-enriched oral Actinomyces induces anxiety-like behavior via impairing mitochondria and GABA signaling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.11.21.689724},
pmid = {41332522},
issn = {2692-8205},
abstract = {UNLABELLED: The human oral microbiome is increasingly recognized as a contributor to brain health, yet its mechanisms remain unclear. Our previous work revealed that oral Actinomyces species was enriched in chronic cannabis smokers. Here, we show oral inoculation of cannabis use-associated Actinomyces species, especially A. meyeri , to wild-type C57BL/6 mice leads to anxiety-like behaviors, non-region-specific microglia activation, mitochondrial dysfunction, and reduced GABAergic neurotransmission, without evidence of bacterial translocation to the brain, neuroinflammation, and memory decline. Notably, Actinomyces species-producing metabolites, i.e., arginine and argininosuccinate, were increased in both oral swabs and brain following inoculation in vivo . These Actinomyces species-producing metabolites induced mitochondrial dysfunction and oxidative stress in neurons in vitro , indicating a neuropathogenic role and aligning with reduced GABAergic neurotransmission in vivo. Together, these results suggest that oral cannabis-associated dysbiosis impacts behavior through mitochondrial stress and impaired inhibitory signaling, indicating the oral-brain metabolic axis is potentially consequential in neuropsychiatric disorders.

TEASER: Chronic heavy cannabis use-enriched oral bacteria can drive anxiety and neuropathogenesis in mice.

HIGHLIGHTS: Cannabis-associated oral Actinomyces enrichment induces anxiety-like behavior in miceMicroglial activation occurs without neuroinflammation (IL-1β, TNF-α, and IL-6)Mitochondrial hyperactivation and reduced inhibitory GABAergic signaling.},
}

@article {pmid41332499,
year = {2025},
author = {Feng, X and Gan, X and Ren, B and Wan, Z and Wang, Y and Gao, X and Zhu, Z},
title = {Spatial and temporal dynamic changes of oral microbiome in removable partial denture wearers: a longitudinal study using full-length 16S rRNA sequencing.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2589655},
pmid = {41332499},
issn = {2000-2297},
abstract = {OBJECTIVE: This longitudinal study aimed to characterize the spatial and temporal dynamics of oral microbiome colonization on removable partial dentures (RPDs) and corresponding dental surfaces at species-level resolution, to elucidate ecological succession patterns and identify potential pathogenic colonizers.

METHODS: We conducted a longitudinal study of 10 participants requiring RPDs. Plaque samples were collected from four sites at five time points. The microbial communities were profiled using PacBio full-length 16S rRNA sequencing, enabling high accuracy taxonomic assignment to the species level. Bioinformatic analyses included alpha/beta diversity, LEfSe, and PICRUSt2 functional prediction.

RESULTS: Significant differences in microbial composition were observed between RPD and dental plaques, despite similar alpha diversity. Temporal analysis revealed a progressive decrease in RPD plaque diversity. Notably, the potential respiratory pathogen Klebsiella pneumoniae was detected in early RPD biofilms. A three-stage ecological succession model for RPD biofilm was proposed, initiating with acidogenic pioneers, followed by functional amplification of taxa involved in extracellular polysaccharide production, and culminating in a stable, acid-tolerant community.

CONCLUSION: This study provides a species-level understanding of microbiome changes associated with RPDs, confirms differences between RPD plaque and dental plaque, proposes a succession model for RPD-associated bacteria, and determines key turning points and potential pathogens.},
}

@article {pmid41332420,
year = {2025},
author = {Wang, X and Wang, Q and Guo, X and Tong, P and Li, C and Zhou, D and Yin, F},
title = {Regulating effects of hydroxytyrosol acyl esters with different acyl chain lengths and isomers on gut microbiota: insights from in vitro gastrointestinal digestion, fecal fermentation and Lactobacillus fermentation.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70360},
pmid = {41332420},
issn = {1097-0010},
support = {//Dalian Outstanding Youth Science and Technology Talent Project (2023RY018)/ ; //The National Natural Science Foundation of China (32472260)/ ; },
abstract = {BACKGROUND: Phenolic compounds are increasingly recognized for their diverse health benefits, particularly their potent antioxidant capacities. To enhance its lipophilicity, stability and bioavailability, hydroxytyrosol has been successfully esterified with various alkyl chains lengths and different isomers (branched-chain and straight-chain), forming hydroxytyrosol-fatty acid acyl esters (Hty-Es). These synthesized Hty-Es, have garnered significant interest and are widely explored in fields such as food preservation because of their superior antioxidant properties. However, little is known about the digestion, fermentation characteristics and the effects on the intestinal microbiota in vitro.

RESULTS: This study evaluated the influence of hydroxytyrosol (HTy) esterified with fatty acids of varying chain lengths (C2:0, C3:0, C4:0n, C4:0i, C6:0, C8:0, C12:0, C14:0 and C16:0) on polyphenol sustained-release properties and gut microbiota modulation during simulated in vitro digestion, fecal fermentation and Lactobacillus fermentation. The findings demonstrated partial hydrolysis of HTy-Es in both simulated gastric fluid and intestinal fluid to slowly release a small amount of polyphenols, suggesting their potential to reach the colon and cecum. Analysis of fermented fecal samples revealed that HTy-Es supplementation modulated microbiota composition, elevating the diversity of Actinobacteriota, Firmicutes and Bacteroidetes, whereas it decreased the diversity of Desulfobacterota, Actinobacteriota, Chloroflexi and Verrucomicrobiota. At the genus level, the growth of detrimental genera (Escherichia shigella) was successfully suppressed. Notably, HTy-Es with distinct acyl chain lengths and isomer configurations exhibited divergent effects on polyphenol bioaccessibility and gut microbiome diversity, underscoring their structure-dependent functional potential for health applications.

CONCLUSION: Conclusively, the slow release of fatty acids and HTy clearly demonstrated that HTy-Es would be an effective approach for enhancing the beneficial health effects of fatty acids and HTy. © 2025 Society of Chemical Industry.},
}

@article {pmid41332240,
year = {2025},
author = {Chua, W and Hei, Y and Koh, LF and Yap, BLH and Saw, HL and Fernandes, THM and da Silva, EB and Goh, S and Dawson, TL and O'Donoghue, AJ and Common, JE and Li, H},
title = {Aspartyl protease MfSAP2 is a key virulence factor in mycelial form of skin fungi Malassezia furfur.},
journal = {The Biochemical journal},
volume = {},
number = {},
pages = {},
doi = {10.1042/BCJ20253109},
pmid = {41332240},
issn = {1470-8728},
support = {H18/01/a0/016//Agency for Science, Technology and Research/ ; MOH-000612-00//Ministry of Health -Singapore/ ; },
abstract = {Malassezia is the dominant genus of fungi residing on human skin and is associated with both healthy skin and many dermatological conditions. Among these skin diseases, pityriasis versicolor (PV) has strong etiological connections with Malassezia. In the hyper or hypo-pigmented scales of PV patients, Malassezia is enriched in its mycelial form which is rarely present on healthy skin. How these Malassezia hyphae contribute to disease pathology in PV is unknown. In this study, we observed a distinct shift in the extracellular proteolytic activity when Malassezia furfur transitions from yeast to hyphae. We identified that the expression of the aspartyl protease MfSAP2 is dramatically upregulated at both the mRNA and protein level when M. furfur is in the mycelial form. We determined the protease substrate specificity and observed that MfSAP2 can degrade corneodesmosome proteins, which are intercellular adhesive proteins between corneocytes in the stratum corneum. In a 3D human skin model with MfSAP2 treatment, we observed clear degradation of corneodesmosin, a component of the corneodesmosome. Taken together, our study demonstrates that a secreted protease is a key virulence factor associated with M. furfur mycelium and is potentially involved in the disease pathogenesis of PV.},
}

@article {pmid41331985,
year = {2025},
author = {Lopez-Oliva, I and Chapple, IL and Paropkari, A and Saraswat, S and Sharma, P and Serban, S and de Pablo, P and Raza, K and Filer, A and Dietrich, T and Grant, M and Kumar, PS},
title = {Dysbiosis-Mediated Inflammation: A Pathophysiological Link Between Rheumatoid Arthritis and Periodontitis.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70063},
pmid = {41331985},
issn = {1600-051X},
support = {R01 DE022579/DE/NIDCR NIH HHS/United States ; U01 CA188250/CA/NCI NIH HHS/United States ; PB-PG-0609-19100//Department of Health, Social Services and Public Safety, UK Government/ ; DRF-2014-07-109//Department of Health, Social Services and Public Safety, UK Government/ ; PDF-2014-07-055//Department of Health, Social Services and Public Safety, UK Government/ ; //Department of Health, Social Services and Public Safety, UK Government/ ; },
abstract = {AIM: To explore mechanistic links between rheumatoid arthritis (RA) and periodontitis (PD) through the lens of subgingival microbial dysbiosis-mediated inflammation.

METHODS: Subgingival plaque from 100 volunteers with RA and PD (RAPD), 22 with RA (RAnoPD), 18 with PD (PDnoRA) and 19 healthy controls (noRAnoPD) was analysed using 16S-amplicon sequencing, semi-quantitative bead-based flow cytometry to measure crevicular fluid cytokines and ELISA to quantify antibodies to oral pathogens and systemic inflammatory markers in serum. The RAPD group had been randomised to receive intensive non-surgical periodontal therapy (PMPR) or oral hygiene alone and reviewed at 3 and 6 months in our previously reported study.

RESULTS: Subgingival microbial dysbiosis, as evidenced by higher species richness, alpha-diversity and higher levels of known and putative periodontal pathobionts, was evident at baseline in RAnoPD, RAPD and PDnoRA. Higher serum antibodies to oral pathogens were recorded in RAPD. PMPR restored host-microbial homeostasis in RAPD within 3 months. Significant decreases in serum antibodies to microbial antigens and clinical measures of RA activity were seen after 3 and 6 months in the PMPR group but not controls.

CONCLUSIONS: We demonstrate a mutualistic influence of RA and PD, beginning with RA-induced dysbiosis of the periodontal microbiome, progressing to periodontal inflammation and culminating in PD-driven exacerbation of systemic inflammation.},
}

@article {pmid41331872,
year = {2025},
author = {Zhu, L and Hu, J and Li, J and Qu, X and Zhou, X and Gan, G and Liu, Y and Liu, S and Chen, X},
title = {Sini San ameliorates symptoms of depression by modulating gut microbiota structure, Tryptophan metabolism, and short-chain fatty acid levels.},
journal = {BMC complementary medicine and therapies},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12906-025-05190-5},
pmid = {41331872},
issn = {2662-7671},
support = {82004253//National Natural Science Foundation of China/ ; 82004253//National Natural Science Foundation of China/ ; 82004253//National Natural Science Foundation of China/ ; 82004253//National Natural Science Foundation of China/ ; 82004253//National Natural Science Foundation of China/ ; [2023] No.2//Key Discipline Construction Project of Traditional Chinese Medicine in Hubei Province-Febrile Diseases/ ; 2023AFD146//Natural Science Foundation of Hubei Province/ ; 2023AFD146//Natural Science Foundation of Hubei Province/ ; 2023AFD146//Natural Science Foundation of Hubei Province/ ; WJ2023Z002//the Key Scientific Research Project of Hubei Provincial Health and Wellness Commission/ ; },
abstract = {BACKGROUND: Sini San (SNS) is a traditional Chinese medicinal formulation originating from the "Treatise on Febrile Diseases", an ancient text that has been historically employed for treating depression. However, the underlying mechanisms by which SNS potentially ameliorates symptoms of depression remain unclear. This study aimed to elucidate the role of gut microbiota in tryptophan metabolism and examine the involvement of short-chain fatty acids (SCFAs) in the putative antidepressant effects of SNS.

METHODS: A rat model of depression using chronic unpredictable mild stress (CUMS) was established through simultaneous modeling and treatment for six consecutive weeks. The possible therapeutic effect of SNS on CUMS-induced rats was thoroughly assessed using body weight measurements, open-field tests, and sucrose preference tests. Alterations in rat gut microbiota were analyzed using full-length 16 S rRNA third-generation sequencing. Furthermore, metabolomic analysis was performed on fecal samples. An enzyme-linked immunosorbent assay (ELISA) was used to quantify tryptophan (Trp), serotonin (5-HT), and kynurenine (Kyn) in the hippocampal and colonic tissues. Reverse transcription quantitative PCR (RT-qPCR) was used to measure the mRNA levels of TPH-1 and TPH-2 in hippocampal and colonic tissues. Immunofluorescence was used to assess hippocampal IDO-1 and IBA-1 expression. Finally, gas chromatography-mass spectrometry (GC-MS) was used to analyze the SCFAs content in fecal samples.

RESULTS: Administration of SNS significantly alleviated depressive symptoms induced by CUMS, as demonstrated by increased body weight, improved sucrose preference, and a statistically significant decrease in immobility time during the forced swim test (P < 0.05). The Shannon and Simpson indices were elevated following SNS treatment, signifying an enhancement in both the quantity and variety of the gut microbiota. Analysis using 16 S rRNA gene sequencing revealed that SNS influenced the composition of the gut microbiome, favorably increasing the presence of beneficial bacteria, such as Firmicutes, Lactobacillaceae, Ruminococcaceae, and Oscillospiraceae, while simultaneously decreasing the levels of potentially detrimental bacteria, such as Muribaculaceae, Prevotellaceae, Lachnospiraceae, and Alloprevotella. Fecal metabolomic studies identified 87 metabolites, of which 57 were differentially expressed, most notably l-tryptophan and phenylalanine. These metabolites were primarily linked to 15 metabolic pathways, with notable enrichment in the biosynthetic pathways of phenylalanine, tyrosine, and tryptophan, as well as the metabolic pathways of arachidonic acid and phenylalanine. Metabolomic profiling indicated that SNS stimulated the kynurenine pathway, leading to increased levels of metabolites with antidepressant properties, such as Trp, 5-HT, and Kyn, in both hippocampal and colonic tissues. In addition, SNS promoted the synthesis of SCFAs, particularly butyrate and propionate, which are known for their neuroprotective properties.

CONCLUSIONS: The present study suggests that the antidepressant effects of SNS can be attributed to its ability to modulate the structure of the gut microbiota, consequently regulating tryptophan metabolism and SCFA levels, which ultimately ameliorate symptoms of depression. These findings provide experimental evidence supporting the concept of the brain-gut axis in depression treatment and lay a foundation for further investigation of the underlying antidepressant mechanisms of the SNS.},
}

@article {pmid41331870,
year = {2025},
author = {Chen, M and Wang, J and Yang, Y and He, Y and Li, L},
title = {The interplay of estrogen, gut microbiome, and bone immunity in osteoporosis.},
journal = {Cell communication and signaling : CCS},
volume = {23},
number = {1},
pages = {516},
pmid = {41331870},
issn = {1478-811X},
support = {CSTB2023NSCQ-MSX0956//Natural Science Foundation of Chongqing/ ; 2023B23//Teaching Research Proiect of Army Medical University/ ; 2022YQB033//Xingiao hospital Young DoctIncubation Program/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Osteoporosis/immunology/microbiology/metabolism/pathology ; *Estrogens/metabolism ; *Bone and Bones/immunology ; Animals ; },
abstract = {Osteoporosis is a global health concern arising from estrogen deficiency, intestinal dysbiosis, and dysregulation of the bone immune system. The absence of estrogen after menopause created environmental changes within the gut, where the microbial growth of the body was disturbed by the endocrine hormone, and inflammation increases due to the gut-bone axis, which leads to heightened bone loss. The gut microbiota, composed of bacteria and their metabolites such as short-chain fatty acids, play a crucial role in bone immune regulation by modulating immune cell function, influencing bone cell activity, and mediating epigenetic modifications. Malfunction of this system, characterized by the activation of immune cells and the imbalance of cytokines, also leads to the development of osteoporosis. Treatment strategies involved the regulation of the dysbiosis of the gut microbiota, reposition estrogen to the body, and immune modulation. The future direction should be the clarification of these interactions between estrogen and intestinal microflora, identification of new therapeutic targets, and personalization of osteoporosis management.},
}

Humans
*Gastrointestinal Microbiome
*Osteoporosis/immunology/microbiology/metabolism/pathology
*Estrogens/metabolism
*Bone and Bones/immunology
Animals

@article {pmid41331711,
year = {2025},
author = {Lee, SH and Ha, NG and Jang, YH},
title = {Unraveling the Pathogenesis of Asian Atopic Dermatitis: Key Characteristics and Insights.},
journal = {Annals of dermatology},
volume = {37},
number = {6},
pages = {317-326},
doi = {10.5021/ad.25.008},
pmid = {41331711},
issn = {2005-3894},
support = {20023929/MOTIE/Ministry of Trade, Industry and Energy/Korea ; /SCH/Soonchunhyang University/Korea ; },
abstract = {Atopic dermatitis (AD) is a chronic skin condition influenced by genetic, environmental, and immune factors, with notable ethnic variations in its prevalence and mechanisms. In Asian populations, distinct immunopathogenic features include the significant roles of helper (Th) 17 and Th22 cytokine pathways, differing from other ethnic groups. Key genetic variations related to immune regulation and skin barrier function are more prevalent in Asians. Microbiome studies reveal the role of Staphylococcus aureus in AD skin and emerging microbial species linked to microbiome dysbiosis and the gut-skin axis. Environmental factors like pollution and fine dust further exacerbate symptoms in Asia. This study consolidates findings to highlight the genetic, immunological, microbiome, and environmental factors contributing to AD's unique characteristics in Asians. Tailored treatment approaches are essential for improving outcomes and management of AD in diverse populations.},
}

@article {pmid41331700,
year = {2025},
author = {Borum, LS and Bartolomaeus, TUP and Lamont, RF and Bagge, JR and Markó, L and Vinter, CA and Löber, U and Dechend, R and Forslund-Startceva, SK and Joergensen, JS},
title = {Probiotic ice cream influences gut and vaginal microbiota in women at high risk of preterm birth: a randomized controlled study.},
journal = {Maternal health, neonatology and perinatology},
volume = {11},
number = {1},
pages = {43},
pmid = {41331700},
issn = {2054-958X},
abstract = {BACKGROUND: Research into probiotic use in pregnancy typically focuses on general probiotic strains. We instead investigated the relation between intake of ice cream with vaginal commensal probiotics (L. crispatus, L. gasseri, L. jensenii, L. rhamnosus GR-1; these may govern a stable microbiota and may carry beneficial functions in the vagina), throughout pregnancy, and the impact on gut and vaginal microbiomes, in women at high risk of preterm birth.

METHODS: This was a randomised controlled feasibility trial where the impact on gut and vaginal microbiomes was assessed by using 16 S rRNA gene sequencing and qPCR. In total 43 pregnant women were randomized, with 29 assigned to the intervention group and 14 to the control group. Both groups provided vaginal and rectal swabs by self-sampling at gestational time points. Pregnancy outcomes were registered through hospital records, and ice cream adherence and study experience was recorded.

RESULTS: We observed statistically significant gut and vaginal Lactobacillus increase during first half of pregnancy in all women with a continued increase in the second half in women compliant with the intervention. L. crispatus was found more often in the intervention group, and L. gasseri, L. jensenii and L. rhamnosus GR-1 in the ice cream could be recovered in both rectal and vaginal samples. Finally, vaginal Prevotella spp, as well as gut Gardnerella and Atopobium spp, significantly decreased upon intervention. Adherence to the intervention varied but gradually decreased throughout the study with 30.4% displaying excellent adherence in the first time period.

CONCLUSIONS: We conclude that vaginal commensal probiotics administered in ice cream can be an effective method of optimizing the vaginal and intestinal health in pregnant women at high risk of preterm birth when administered regularly. We give recommendations for future studies.

TRIAL REGISTRATION: Clinicaltrials.gov registration number 18/27209. Date of registration 03/25/2019. Date of first enrolment 04/08/2019.},
}