@article {pmid40324150,
year = {2025},
author = {Sudermann, MA and Hua, GKH and Kurth, EG and LeBoldus, JM and Chang, JH and Dung, JKS},
title = {Treatment with the Antimicrobial Product Diallyl Disulfide Is Associated with Major Changes to Soil Microbiota.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-11-24-0366-SC},
pmid = {40324150},
issn = {0031-949X},
abstract = {Natural products derived from Allium spp., such as garlic oil, garlic powder, and diallyl disulfide (DADS), are strong elicitors of sclerotia germination in the fungus Sclerotium cepivorum (syn. Stromatinia cepivora), the causal agent of Allium white rot. However, these compounds can also have broad antimicrobial activity against a wide range of bacteria, oomycetes, and other fungi when they are applied to soil. The objective of this study was to determine the potential impacts that DADS application has on soil microbial communities. DADS was applied to two soil types and incubated under aerobic and anaerobic conditions. Metabarcodes for bacterial, fungal, and oomycete communities were analyzed to identify changes. A significant effect of DADS treatment on the overall compositions of bacterial, fungal, and oomycete communities was observed compared to the mock-treated control. Soil type and incubation conditions did not have a significant effect on soil microbial communities and significant interactions were not observed with DADS treatment in this study. Potential changes in soil microbial communities should be considered when applying DADS to field soils.},
}

@article {pmid40324108,
year = {2025},
author = {Zegeye, FD and Straumfors, A and Lei, P and Graff, P and Samulin Erdem, J and Afanou, AK},
title = {Microbial exposure and diversity in Norwegian shrimp processing plants.},
journal = {Journal of occupational and environmental hygiene},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/15459624.2025.2491488},
pmid = {40324108},
issn = {1545-9632},
abstract = {Seafood processing workers have a high prevalence of respiratory symptoms and occupational asthma, primarily attributed to allergenic protein exposure. However, exposure to airborne microorganisms from raw materials can also contribute to allergic sensitization and other respiratory ailments. This study aimed to assess microbial exposure in shrimp processing plants and identify susceptible work tasks. Full-shift personal air samples were collected from two Norwegian shrimp processing plants across five distinct work processes: thawing, truck driving, cooking-peeling (technician), packing, and flour production. The samples were analyzed for the presence of endotoxin, Toll-Like Receptor (TLR) activation, bacterial and fungal DNA copies, and microbial composition. Endotoxin levels were generally low, with only one sample (98 EU/m[3]) exceeding the recommended occupational exposure limit (OEL). A significant TLR2 activation was observed among thawers, indicating the presence of microbial ligands capable of triggering an immune response. The median bacterial (75 × 10[3] DNA copies/m[3]) and fungal (3,301 × 10[3] DNA copies/m[3]) exposure were highest among the flour production workers, while the lowest bacterial and fungal exposure was among packers (1.5 × 10[3] DNA copies/m[3]) and technicians (337 DNA copies/m[3]), respectively. Several bacterial and fungal species were identified, including ten allergenic and sixteen pathogenic species. Sporobolomyces roseus and Saccharomyces cerevisiae were the two most frequently identified allergenic fungal species. Among the pathogenic bacterial species, Prevotella nigrescens and Roseomonas gilardii were the two most detected species. While the pathogenic species were identified mainly in the packing, truck driving, and flour production work processes, most of the allergenic species were found in all work processes. Altogether, work processes before the cooking of shrimp (thawing and truck driving) had higher endotoxin, bacterial load, and species richness than after cooking, suggesting that these work tasks are susceptible to bacterial exposure and that the cooking process significantly reduces bacterial exposure. By shedding light on microbial exposure and identifying high-exposure work tasks, this study enables the development of targeted interventions and implementation of measures for the prevention of occupational diseases.},
}

@article {pmid40324037,
year = {2025},
author = {Klukoska, M and Ramji, N and Muñoz Bodnar, A and Hu, P and Ye, H and Xie, S and Li, L and Ashe, J and Reichling, T and Wang, J and Milleman, K and Milleman, J},
title = {Clinical effects of stannous fluoride dentifrice on peri-implant mucositis, plaque microbiome, and oxidative stress.},
journal = {American journal of dentistry},
volume = {38},
number = {2},
pages = {59-66},
pmid = {40324037},
issn = {0894-8275},
mesh = {Humans ; *Oxidative Stress/drug effects ; *Tin Fluorides/therapeutic use ; Female ; Male ; *Dental Plaque/microbiology ; Middle Aged ; *Microbiota/drug effects ; Adult ; *Dentifrices/therapeutic use ; *Peri-Implantitis/microbiology/prevention & control/drug therapy ; Periodontal Index ; Biomarkers/analysis ; *Dental Implants/adverse effects ; *Mucositis/drug therapy ; Aged ; Gingival Crevicular Fluid/microbiology ; },
abstract = {PURPOSE: This single-center, single-treatment, 4-week study evaluated the efficacy of a stannous fluoride (SnF2) dentifrice in reducing peri-implant mucositis while assessing changes in biomarkers and the oral microbiome profile.

METHODS: 24 healthy participants 18 years of age or older with osseointegrated implants were included, with 19 participants having mucositis and five without mucositis. The non-mucositis participants served as a reference group for microbiome and biomarker assessments (baseline comparison). All participants used the same 0.454% SnF₂ dentifrice (Crest Pro-Health Sensitive and Enamel Shield) and a soft manual toothbrush twice daily throughout the study. Participants received Modified Gingival Index (MGI) and Gingival Bleeding Index (GBI) assessments at Baseline - Day 1 and at Week 4 - Day 1. Subgingival plaque and peri-implant crevicular fluid (PICF) were collected on Baseline - Day 2 and Week 4 - Day 2 for oxidative stress markers, bacterial endotoxins, proinflammatory cytokines and 16S analysis.

RESULTS: After 4 weeks, participants with mucositis experienced a significant reduction from baseline in MGI and GBI scores (63.4% and 79.3%, respectively) and in the number of bleeding sites (72.5% based on GBI analysis). Microbiome analysis of subgingival plaque showed that mucositis was associated with a higher relative abundance of disease-associated genera (Fusobacterium, Porphyromonas, Treponema, and Prevotella) and a lower relative abundance of commensal genera (Rothia and Actinomyces). Alpha diversity was higher in the mucositis group compared to the non-mucositis group at baseline. By Week 4, the profile of participants with mucositis had shifted to align more closely with that of non-mucositis participants. Participants with mucositis showed significant reduction in biomarkers related to bacterial insult, plaque virulence, oxidative stress, and inflammation. Simulated pathway and process analysis revealed that multiple categories of genes were associated with a state of mucositis, and 4 weeks of use of the experimental dentifrice downregulated several virulence-associated genes.

CLINICAL SIGNIFICANCE: In participants with mucositis, use of a SnF₂ dentifrice for 4 weeks reduced clinical signs and key biomarkers of peri-implant inflammation and shifted the oral microbiome toward a healthier profile, highlighting the utility of SnF₂ dentifrice in the control of peri-implant mucositis.},
}

Humans
*Oxidative Stress/drug effects
*Tin Fluorides/therapeutic use
Female
Male
*Dental Plaque/microbiology
Middle Aged
*Microbiota/drug effects
Adult
*Dentifrices/therapeutic use
*Peri-Implantitis/microbiology/prevention & control/drug therapy
Periodontal Index
Biomarkers/analysis
*Dental Implants/adverse effects
*Mucositis/drug therapy
Aged
Gingival Crevicular Fluid/microbiology

@article {pmid40324006,
year = {2025},
author = {Ye, H and Meehan, D and Timmons, S and O'Toole, PW},
title = {Effects of Prebiotics and a Synthetic Microbiome Consortium on the Composition and Metabolites of the Elderly Gut Microbiota In Vitro.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c00364},
pmid = {40324006},
issn = {1520-5118},
abstract = {A 24 h artificial colon fermentation was performed to assess the effects of a prebiotic MIX and synthetic consortium (S7) on gut microbiota composition and microbial metabolite production in clinically stratified older adults (healthy and frail). Treatments included supplementation of the donor microbiota with a synthetic microbial consortium (S7), a prebiotic mix (MIX), and a combination of MIX and S7 (MIX+S7). The S7 treatment decreased the alpha diversity of long-stay-dwelling donor (LS, "frail") microbiota and increased the relative abundance of S7 taxa at 16 h. MIX alone caused the enrichment of reportedly beneficial genera such as Coprobacillus and Eubacterium in community-dwelling donor (CM, "healthy") microbiota and Citrobacter and Faecalibacterium in LS microbiota. The MIX+S7 treatment sustained higher overall S7 species richness and consortium taxon abundance at 24 h. Both MIX and MIX+S7 treatments enhanced short-chain acid production compared to control. These findings highlight the differential responses of microbiota from distinct elderly health strata to prebiotic and microbial consortia supplementation.},
}

@article {pmid40323787,
year = {2025},
author = {Silva, C and Puthanveetil, P and Oliveira, SD},
title = {Liver Bypass in the Development of Pathogen-associated Pulmonary Vascular Disease: Contribution of Mesocaval and Portosystemic Shunts.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00409.2024},
pmid = {40323787},
issn = {1522-1547},
support = {HL159037//HHS | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; CNPq 312051/2023-9//CNPq | Instituto Nacional de Ciência e Tecnologia da Criosfera (INCT da Criosfera)/ ; },
abstract = {Portosystemic and mesocaval shunts are aberrant vascular connections that bypass hepatic filtration, directly linking the portal to the systemic circulation. These shunts, whether congenital or acquired, play a pivotal role in the pathogenesis of schistosomiasis-associated pulmonary hypertension (Sch-PH) by facilitating the dissemination of pathogen-derived eggs and antigens from the guts and mesentery into the lungs. Beyond the translocation of Schistosoma mansoni eggs, emerging evidence implicates that gut-lung microbiome dysbiosis contributes to the development of pulmonary hypertension (PH) in the preclinical animal model of Sch-PH. Sch-PH emerges as a chronic complication of schistosomiasis and evolves silently, progressively increasing the mean pulmonary arterial pressure and vascular resistance, leading to right heart hypertrophy, failure, and significant morbidity and mortality. Chronic schistosomiasis is often linked to the development of portal hypertension, which significantly contributes to the formation of the porto/mesocaval shunt as a compensatory response that can have far-reaching implications on pulmonary vascular physiology. Additionally, portal hypertension compromises the integrity of the intestinal barrier, exacerbating peritoneal and mesenteric inflammation, potentially facilitating microbial and metabolite entrance into the systemic circulation.This article briefly discusses the mechanisms by which porto/mesocaval shunts contribute to PH, especially Group I PH, focusing on the interplay between portosystemic shunting, microbial translocation, and systemic dissemination of pro-inflammatory metabolites.},
}

@article {pmid40323603,
year = {2025},
author = {Chaturvedi, AK and Vogtmann, E and Shi, J and Yano, Y and Blaser, MJ and Bokulich, NA and Caporaso, JG and Gillison, ML and Graubard, BI and Hua, X and Hullings, AG and Kahle, L and Knight, R and Li, S and McLean, J and Purandare, V and Wan, Y and Freedman, ND and Abnet, CC},
title = {Oral Microbiome Profile of the US Population.},
journal = {JAMA network open},
volume = {8},
number = {5},
pages = {e258283},
doi = {10.1001/jamanetworkopen.2025.8283},
pmid = {40323603},
issn = {2574-3805},
mesh = {Humans ; Adult ; Male ; Female ; Middle Aged ; *Microbiota/genetics ; United States/epidemiology ; Cross-Sectional Studies ; *Mouth/microbiology ; Aged ; Young Adult ; Adolescent ; Nutrition Surveys ; RNA, Ribosomal, 16S ; },
abstract = {IMPORTANCE: The oral microbiome likely plays key roles in human health. Yet, population-representative characterizations are lacking.

OBJECTIVE: To characterize the composition, diversity, and correlates of the oral microbiome in US adults.

This cross-sectional study analyzed data from the population-representative National Health and Nutrition Examination Survey (NHANES) from 2009 to 2012. Microbiome data were made publicly available in 2024. NHANES participants were aged 18 to 69 years and provided oral rinse samples in 1 of 2 consecutive NHANES cycles (2009-2010 and 2011-2012).

EXPOSURES: Demographic, socioeconomic, behavioral, anthropometric, metabolic, and clinical characteristics.

MAIN OUTCOMES AND MEASURES: Oral microbiome measures, characterized through 16S ribosomal RNA gene sequencing, included α diversity (observed amplicon sequence variants [ASVs], Faith phylogenetic diversity, Shannon-Weiner Index, and Simpson Index); β diversity (unweighted UniFrac, weighted UniFrac, and Bray-Curtis dissimilarity); and prevalence and relative abundance at phylum level through genus level. Analyses accounted for the NHANES complex sample design.

RESULTS: This study included 8237 US adults aged 18 to 69 years, representing 202 314 000 individuals (102 813 000 men [50.8%]; mean [SD] age, 42.3 [14.4] years; 9.3% self-reported as Mexican American, 12.1% as non-Hispanic Black, 64.7% as non-Hispanic White, 5.9% as other Hispanic, and 8.1% as other non-Hispanic individuals). The oral microbiome encompassed 37 bacterial phyla, 99 classes, 212 orders, 446 families, and 1219 genera. Five phyla (Firmicutes, Actinobacteria, Bacteroidetes, Proteobacteria, and Fusobacteria) and 6 genera (Veillonella, Streptococcus, Prevotella 7, Rothia, Actinomyces, and Gemella) were present in nearly all US adults (weighted prevalence, >99%). These genera were the most abundant, accounting for 65.7% of total abundance. Observed ASVs showed a quadratic pattern with age (peak at 30 years), were similar by sex, significantly lower among non-Hispanic White individuals, and increased with greater body mass index (BMI), alcohol use, and periodontal disease severity. All covariates together accounted for a modest proportion of oral microbiome variability as measured by β diversity: R2 = 8.7% (95% CI, 8.4%-9.1%) for unweighted UniFrac, R2 = 7.2% (95% CI, 6.6%-7.7%) for weighted UniFrac, and R2 = 6.3% (95% CI, 3.1%-6.7%) for Bray-Curtis matrices. By contrast, relative abundance of a few genera explained a high percentage of variability in β diversity for weighted UniFrac: Aggregatibacter (R2 = 22.4%; 95% CI, 22.1%-22.8%), Lactococcus (R2 = 21.6%; 95% CI, 20.9%-22.3%), and Haemophilus (R2 = 18.4%; 95% CI, 18.1%-18.8%). Prevalence and relative abundance of numerous genera were associated with age, race and ethnicity, smoking, BMI categories, alcohol use, and periodontal disease severity.

CONCLUSIONS AND RELEVANCE: This cross-sectional study of the oral microbiome in US adults showed that a few genera were universally present and a different set of genera explained a high percentage of oral microbiome diversity across the population. This comprehensive characterization provides a contemporary reference standard for future studies.},
}

Humans
Adult
Male
Female
Middle Aged
*Microbiota/genetics
United States/epidemiology
Cross-Sectional Studies
*Mouth/microbiology
Aged
Young Adult
Adolescent
Nutrition Surveys
RNA, Ribosomal, 16S

@article {pmid40323507,
year = {2025},
author = {Wadan, AS and El-Aziz, MKA and Ellakwa, DE},
title = {The microbiota-gut-brain-axis theory: role of gut microbiota modulators (GMMs) in gastrointestinal, neurological, and mental health disorders.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {40323507},
issn = {1432-1912},
abstract = {The modulation of gut microbiota presents promising therapeutic possibilities for various health conditions, ranging from gastrointestinal infections to neurodegenerative and mental health disorders. Among the available interventions, gut microbiota modulators (GMMs) such as probiotics and prebiotics have demonstrated significant potential in infection prevention and neuroprotection. Despite these encouraging findings, the clinical application of GMMs remains challenging due to safety concerns and inconsistent effectiveness across diverse patient populations. These factors create substantial barriers to the widespread adoption of microbiota-based therapies in clinical practice. To overcome these challenges and fully leverage the therapeutic potential of microbiota modulation, this review explores the feasibility of repurposing GMMs for managing multiple health disorders. A broad spectrum of microbiota-targeted strategies is examined, including dietary modifications, fecal microbiota transplantation, bacteriophage therapy, microbiome engineering, and immune system modulation. A particularly innovative approach involves integrating GMMs with pharmaceutical delivery systems to enhance therapeutic efficacy while mitigating potential adverse effects. This integrative strategy underscores the pivotal role of the gut microbiome in health and disease, supporting the development of precision medicine tailored to individual patient needs. By combining GMMs with targeted delivery mechanisms, this approach not only improves treatment effectiveness but also addresses critical concerns regarding safety and patient variability. Furthermore, this review outlines future research directions within the rapidly evolving field of microbiota modulation, emphasizing the necessity of comprehensive clinical trials and long-term safety evaluations. By critically assessing both the challenges and opportunities associated with microbiota-based interventions, this study provides a strategic framework for translating experimental research into viable clinical applications. A holistic approach to gut microbiota modulation has the potential to redefine treatment paradigms, offering personalized therapeutic strategies for a wide range of disorders and advancing the broader field of precision medicine.},
}

@article {pmid40323477,
year = {2025},
author = {Kiran, NS and Chatterjee, A and Yashaswini, C and Deshmukh, R and Alsaidan, OA and Bhattacharya, S and Prajapati, BG},
title = {The gastrointestinal mycobiome in inflammation and cancer: unraveling fungal dysbiosis, pathogenesis, and therapeutic potential.},
journal = {Medical oncology (Northwood, London, England)},
volume = {42},
number = {6},
pages = {195},
pmid = {40323477},
issn = {1559-131X},
mesh = {Humans ; *Dysbiosis/microbiology ; *Mycobiome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; *Inflammation/microbiology ; *Gastrointestinal Neoplasms/microbiology ; Fungi/pathogenicity ; Animals ; },
abstract = {The gastrointestinal mycobiome, comprising diverse fungal species, plays a significant role in gastrointestinal carcinogenesis and inflammatory bowel disease (IBD) pathogenesis. Recent studies have demonstrated that dysbiosis of the gut mycobiome, characterized by an overrepresentation of pathogenic fungi such as Candida albicans and Aspergillus, correlates with increased inflammation and cancer risk. For instance, C. albicans has been shown to induce colonic inflammation through the activation of pattern recognition receptors and the release of pro-inflammatory cytokines, exacerbating IBD symptoms and potentially facilitating tumorigenesis. Additionally, metagenomic analyses have revealed distinct fungal signatures in colorectal cancer tissues compared to adjacent healthy tissues, highlighting the potential of fungi as biomarkers for disease progression. Mechanistically, gut fungi contribute to disease through biofilm formation, mycotoxin secretion (e.g., aflatoxins, candidalysin), pro-inflammatory cytokine induction (e.g., IL-1β, IL-17), and disruption of epithelial barriers-creating a tumor-promoting and inflammation-prone environment. Furthermore, the interplay between fungi and the bacterial microbiome can amplify inflammatory responses, contributing to chronic inflammation and cancer development. Fungal interactions with bacterial communities also play a synergistic role in shaping mucosal immune responses and enhancing disease severity in both cancer and IBD contexts. As research continues to elucidate these complex fungal-host and fungal-bacterial interactions, targeting the gut mycobiome may offer novel therapeutic avenues for managing IBD and gastrointestinal cancers, emphasizing the need for integrated, mechanistically informed approaches to microbiome research.},
}

Humans
*Dysbiosis/microbiology
*Mycobiome
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology
*Inflammation/microbiology
*Gastrointestinal Neoplasms/microbiology
Fungi/pathogenicity
Animals

@article {pmid40323435,
year = {2025},
author = {Reynolds, J and Yoon, JY},
title = {Fluorescence-based spectrometric and imaging methods and machine learning analyses for microbiota analysis.},
journal = {Mikrochimica acta},
volume = {192},
number = {6},
pages = {334},
pmid = {40323435},
issn = {1436-5073},
mesh = {*Machine Learning ; *Microbiota ; Humans ; Spectrometry, Fluorescence/methods ; *Bacteria/isolation & purification/genetics ; },
abstract = {Most microbiota determination (skin, gut, soil, etc.) are currently conducted in a laboratory using expensive equipment and lengthy procedures, including culture-dependent methods, nucleic acid amplifications (including quantitative PCR), DNA microarray, immunoassays, 16S rRNA sequencing, shotgun metagenomics, and sophisticated mass spectrometric methods. In situ and rapid analysis methods are desirable for fast turnaround time and low assay cost. Fluorescence identification of bacteria and their mixtures is emerging to meet this demand, thanks to the recent development in various machine learning methods. High-dimensional spectroscopic or microscopic imaging data can be obtained to identify the bacterial makeup and its implications for human health and the environment. For example, we can classify healthy versus non-healthy skin microbiome, inflammatory versus non-inflammatory gut microbiome, degraded versus non-degraded soil microbiome, etc. This tutorial summarizes the various machine-learning algorithms used in bacteria identification and microbiota determinations. It also summarizes the various fluorescence spectroscopic methods used to identify bacteria and their mixtures, including fluorescence lifetime spectroscopy, fluorescence resonance energy transfer (FRET), and synchronous fluorescence (SF) spectroscopy. Finally, various fluorescence microscopic imaging methods were summarized that have been used to identify bacteria and their mixtures, including epi-fluorescence microscopy, confocal microscopy, two-photon/multi-photon microscopy, and super-resolution imaging methods (STED, SIM, PALM, and STORM). Finally, it discusses how these methods can be applied to microbiota determinations, what can be demonstrated in the future, opportunities and challenges, and future directions.},
}

*Machine Learning
*Microbiota
Humans
Spectrometry, Fluorescence/methods
*Bacteria/isolation & purification/genetics

@article {pmid40323426,
year = {2025},
author = {Atuk Kahraman, T and Yılmaz, M and Aslan, K and Canatan, H and Kara, A and Nalbantoglu, OU and Gundogdu, A and Eken, A},
title = {Lycopene Supplemented Mediterranean Diet Ameliorates Experimental Autoimmune Encephalomyelitis (EAE) in Mice and Changes Intestinal Microbiome.},
journal = {Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology},
volume = {20},
number = {1},
pages = {50},
pmid = {40323426},
issn = {1557-1904},
mesh = {Animals ; *Lycopene/administration & dosage/pharmacology ; *Encephalomyelitis, Autoimmune, Experimental/diet therapy/immunology ; Female ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome/drug effects/physiology ; *Diet, Mediterranean ; *Dietary Supplements ; },
abstract = {This study aimed to determine the effects of the Mediterranean diet (MD) and lycopene on the development of EAE and on inflammatory markers. In the 43-day study, 72 female C57BL/6 mice were randomly divided into eight groups according to whether they were EAE or naive (control) mice, fed a Western diet or a MD, and whether they received lycopene. During the study, mice were fed ad libitum, and lycopene groups were given 10 mg/kg/day lycopene per mouse every other day for 28 days in oral gavage. The mice were scored for EAE, sacrificed and their spleen, lymph nodes, and spinal cords were removed. We observed slightly delayed EAE onset in the MD-Lyc group compared to the others, and the EAE clinical scores were also lower than in the other groups. T-cell counts in the spleen and lymph nodes of the MD-Lyc group were significantly lower than in other groups. The production of IFN-γ and IL-22 was higher than in the other groups. IL-17 A cytokine produced in the spleen was lower in the MD-Lyc group than in the other groups. In addition, the highest myelination score was seen in the MD-Lyc group. MD-Lyc group also had a unique microbiome profile compared with the remaining groups. In summary, MD and lycopene administration positively impacted EAE scores and myelination. However, more comprehensive studies at the in vitro and in vivo levels are needed to reveal the effect of this intervention on cell numbers in the CNS.},
}

Animals
*Lycopene/administration & dosage/pharmacology
*Encephalomyelitis, Autoimmune, Experimental/diet therapy/immunology
Female
Mice
Mice, Inbred C57BL
*Gastrointestinal Microbiome/drug effects/physiology
*Diet, Mediterranean
*Dietary Supplements

@article {pmid40323322,
year = {2025},
author = {Chen, X and Sui, Y and Gu, J and Wang, L and Sun, N},
title = {The Implication of The Vaginal Microbiome in Female Infertility and Assisted Conception Outcomes.},
journal = {Genomics, proteomics & bioinformatics},
volume = {},
number = {},
pages = {},
doi = {10.1093/gpbjnl/qzaf042},
pmid = {40323322},
issn = {2210-3244},
abstract = {The rise in infertility rates has prompted research into the impact of vaginal microbiota on female fertility and assisted reproduction technology (ART) success. Our study compares the vaginal microbiome of fertile and infertile women and explores its influence on ART outcomes. We analyzed vaginal secretions from 194 infertile women and 100 healthy controls at Shanghai Changzheng Hospital using polymerase chain reaction (PCR) to amplify the 16S rRNA V3-V4 region. A machine learning model predicted infertility based on genus abundances, and the PICRUSt algorithm predicted metabolic pathways related to infertility and ART outcome. The results showed women with infertility exhibited a significantly different vaginal microbial composition compared to healthy women, with the infertility group showing higher microbial diversity. Burkholderia, Pseudomonas, and Prevotella levels were significantly elevated in the vaginal microbiota of the infertility group, while Bifidobacterium and Lactobacillus abundances were reduced. Recurrent implantation failure (RIF) within the infertile population showed even higher diversity of vaginal microbiota, with specific genera such as Mobiluncus, Peptoniphilus, Prevotella, and Varibaculum being more abundant. Eleven metabolic pathways were associated with RIF and infertility, with Prevotella demonstrating stronger correlations. The present study provides insights into the differences in vaginal microbiome between healthy and infertile women, offering a new understanding of how vaginal microbiota may impact infertility and ART outcomes. Our findings underscore the significance of specific microbial taxa in women with RIF, suggesting avenues for targeted interventions to enhance embryo transplantation success rates.},
}

@article {pmid40323242,
year = {2025},
author = {Ofori-Kwafo, A and Sigdel, I and Al Mamun, E and Zubcevic, J and Tang, Y},
title = {Gut-on-a-chip platforms: Bridging in vitro and in vivo models for advanced gastrointestinal research.},
journal = {Physiological reports},
volume = {13},
number = {9},
pages = {e70356},
doi = {10.14814/phy2.70356},
pmid = {40323242},
issn = {2051-817X},
mesh = {Humans ; *Lab-On-A-Chip Devices ; *Gastrointestinal Tract/physiology ; Animals ; Gastrointestinal Diseases ; Gastrointestinal Microbiome ; },
abstract = {The gastrointestinal (GI) tract plays a critical role in nutrient absorption, immune responses, and overall health. Traditional models such as two-dimensional cell cultures have provided valuable insights but fail to replicate the dynamic and complex microenvironment of the human gut. Gut-on-a-chip platforms, which incorporate cells located in the gut into microfluidic devices that simulate peristaltic motion and fluid flow, represent a significant advancement in modeling GI physiology and diseases. This review discusses the evolution of gut-on-a-chip technology, from simple cellular mono-cultures models to more sophisticated systems incorporating bi-cultures and tri-cultures that enable studies of drug metabolism, disease modeling, and gut-microbiome interactions. Although challenges remain, including maintaining long-term cell viability and replicating immune responses, these platforms hold great potential for advancing personalized medicine and improving drug discovery efforts targeting gastrointestinal disorders.},
}

Humans
*Lab-On-A-Chip Devices
*Gastrointestinal Tract/physiology
Animals
Gastrointestinal Diseases
Gastrointestinal Microbiome

@article {pmid40323196,
year = {2025},
author = {Pramana, AAC and Xu, GB and Liang, S and Garcia Vazquez, EO and Allen, JM and Loman, B and Mei, W and Pan, YX and Chen, H},
title = {Gut Microbiota Dysbiosis in a Novel Mouse Model of Colitis Potentially Increases the Risk of Colorectal Cancer.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00040.2025},
pmid = {40323196},
issn = {1522-1547},
support = {ILLU-971351//USDA | National Institute of Food and Agriculture (NIFA)/ ; ILLU-698923//USDA | National Institute of Food and Agriculture (NIFA)/ ; Office of the Vice-Chancellor for Research//UofI | University of Illinois at Urbana-Champaign (UIUC)/ ; DNS vision 20/20//UofI | University of Illinois at Urbana-Champaign (UIUC)/ ; DNS Margin of Excellence//UofI | University of Illinois at Urbana-Champaign (UIUC)/ ; },
abstract = {This research investigates the gut microbiota profile in a novel mouse model of colitis with a specific knockout (KO) of the hnRNPI gene in intestinal epithelial cells. While the influence of gut microbiota on colitis pathophysiology in hnRNPI KO mice remains unexplored. To address this, we utilized 16S-rRNA gene amplicon sequencing to compare the gut microbiota between hnRNPI KO and wild-type (WT) mice at baseline and following dextran sodium sulfate (DSS) challenge. 16S-rRNA gene analysis revealed significant disparities in the gut microbiota between KO and WT mice. Notably, KO mice exhibited lower levels of Dubosiella sp. but higher levels of Paraclostridium bifermentans compared to WT mice. DSS challenge exacerbated colitis in KO mice and led to further alterations in gut microbiota diversity and composition. Specifically, the imbalance between Dubosiella sp. and P. bifermentans persisted in DSS-treated KO mice. Additionally, elevated levels of Clostridium paraputrificum and Lactococcus garvieae were detected in KO mice. Metabolomic analysis highlighted distinct bacterial metabolic profiles between cultured P. bifermentans and D. newyorkensis. P. bifermentans produced higher levels of glycocholate, urocanate, and deoxycholate, while D. newyorkensis predominantly produced n-formyltryptophan, indole-3-carboxaldehyde, and glycyl-L-norleucine. Comprehensive pathway analysis based on 16S-rRNA gene sequences revealed disturbances in several pathways, including those related to cancers, which were notably increased in hnRNPI KO mice after the DSS challenge. These findings underscore the disrupted microbiome balance in KO mice, particularly the altered levels of Dubosiella sp. and P. bifermentans, which may play a pivotal role in gut health and colitis development.},
}

@article {pmid40323127,
year = {2025},
author = {Almahal, ZH and Hasan, A and Razzak, SA and Nzila, A and Uddin, S},
title = {Molecular Perspective of Dietary Influences on the Gut Microbiome alongside Neurological Health: Exploring the Gut-Brain Axis.},
journal = {ACS chemical neuroscience},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschemneuro.5c00058},
pmid = {40323127},
issn = {1948-7193},
abstract = {Gut-brain axis, an intricate, two-way communication network between gut microorganisms and the central nervous system, plays a critical role in controlling brain function and thereby influencing mental health. Changes to this axis, frequently due to shifts in gut microbiota, can greatly affect brain function by hindering the creation of essential metabolites. This review examines new nutritional trends, including fermented foods and diets rich in prebiotics, that demonstrate the potential to improve microbial diversity and metabolic well-being. Although current studies emphasize possible advantages, most concentrate mainly on older populations, leaving research in younger groups limited. The field of nutritional psychiatry encounters difficulties due to the diversity in research methodologies and the intricacies of nutrient balance, potentially hindering prompt interventions. This review highlights the necessity for prolonged research to evaluate the effects of eating habits, especially regarding Western dietary patterns. Promising fields include the influence of the Mediterranean diet, the role of symbiotic and short-chain fatty acids (SCFAs), and the importance of high-fiber foods, polyphenols, and fruits and vegetables in enhancing mental health through gut-derived metabolites. We promote interdisciplinary methods that combine nutrition science, microbiology, and neurology to create tailored dietary recommendations focused on enhancing brain health.},
}

@article {pmid40323117,
year = {2025},
author = {Adli, DN and Sholikin, MM and Sitaresmi, PI and Ani Nurgiartiningsih, VM and Crooijmans, RPMA},
title = {Dose-Dependent Effects of Probiotics on the Reproductive Performance, Egg Characteristics, and Seminal Traits of Broiler Breeders: A Model-Based Meta-Analysis.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.14123},
pmid = {40323117},
issn = {1439-0396},
abstract = {Probiotics are increasingly used in poultry nutrition because of their potential to improve performance and reproductive outcomes. However, there is limited consensus on the effectiveness of different probiotic strains and formulations in broiler breeder hens. This meta-analysis aimed to evaluate the impact of various probiotics on broiler breeder performance and reproductive traits. A comprehensive data set on probiotic supplementation in poultry broiler breeder hens (of different strains) was compiled spanning the time period from 1990-2024. The effect size (Hedge's g) of probiotics was analysed to estimate the random and fixed effects of study variations. Among the rooster strains, the Hubbard strain presented a significant reduction in the number of dead sperm (p < 0.01). Moreover, multistrain probiotics were found to be more effective than single strains (p < 0.01). In hens, probiotics were associated with a significantly lower feed conversion ratio (FCR) (p < 0.001), as were improvements in the fertility and hatchability of settable eggs (p < 0.001). In particular, the addition of probiotics derived from Bacillus subtilis significantly increased fertility and hatchability (p < 0.001). In summary, both single-strain and multistrain probiotics significantly increase various reproductive and performance parameters in broiler breeders, with multistrain probiotics consistently showing superior effects across multiple areas. The inclusion of multistrain probiotics up to 1 g/kg generally yielded positive effects on several parameters in broiler breeder hens. These findings support the inclusion of probiotics, particularly multistrain formulations, to increase reproductive efficiency and performance in broiler breeders, providing a sustainable alternative to antibiotics.},
}

@article {pmid40323108,
year = {2025},
author = {Oz, A and Mairesse, O and Raikin, S and Hanani, H and Mor, H and Dafny Yelin, M and Sharon, I},
title = {Pear flower and leaf microbiome dynamics during the naturally occurring spread of Erwinia amylovora.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0001125},
doi = {10.1128/msphere.00011-25},
pmid = {40323108},
issn = {2379-5042},
abstract = {Erwinia amylovora is the causal pathogen of fire blight, a contagious disease that affects apple and pear trees and other members of the family Rosaceae. In this study, we investigated the community dynamics of the pear flower microbiome in an agricultural setting during the naturally occurring infection of E. amylovora. Five potential factors were considered: collection date, the flower's phenological stage, location on the tree, location within the orchard, and pear cultivar. The phenological stage and the collection date were identified as the most important factors associated with pear flower microbiome composition, while the location of the tree in the orchard and the flower's location on the tree had a marginal effect. The leaf microbiome reflected that of the abundant phenological stage on each date. The flower microbiome shifted toward E. amylovora dominating the community as time and phenological stages progressed, leading to a decreased community diversity. The E. amylovora population was represented almost exclusively by six amplicon sequence variants (ASVs) with similar proportions throughout the entire collection period. Other taxa, including Pseudomonas, Pantoea, Lactobacillus, and Sphingomonas, were represented by dozens of ASVs, and different succession patterns in their populations were observed. Some of the taxa identified include known antagonists to E. amylovora. Overall, our results suggest that flower physiology and the interaction with the environment are strongly associated with the pear flower microbiome and should be considered separately. Taxon-specific succession patterns under E. amylovora spread should be considered when choosing candidates for antagonist-based treatments for fire blight.IMPORTANCEThe spread of pathogens in plants is an important ecological phenomenon and has a significant economic impact on agriculture. Flowers serve as the entry point for E. amylovora, but members of the flower microbiome can inhibit or slow down the proliferation and penetration of the pathogen. Knowledge about leaf and flower microbiome response to the naturally occurring spread of E. amylovora is still lacking. The current study is the first to describe the Rosaceae flower microbiome dynamics during the naturally occurring infection of E. amylovora. Unlike previous studies, the study design enabled us to evaluate the contribution of five important environmental parameters to community composition. We identified different ASV succession patterns across different taxa in the flower consortia throughout the season. These results contribute to our understanding of plant microbial ecology during pathogen spread and can help improve biological treatments for fire blight.},
}

@article {pmid40323100,
year = {2025},
author = {Griggs, RG and Flörl, L and Swadener, M and Hernández-Velázquez, R and Mills, DA and Bokulich, NA},
title = {A tale of two vineyards: parsing site-specific differences in bacterial and fungal communities of wine grapes from proximal vineyards and their changes during processing in a single winery.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0052625},
doi = {10.1128/aem.00526-25},
pmid = {40323100},
issn = {1098-5336},
abstract = {Wine is a microbial product, naturally transformed through fermentation by a consortium of fungi and bacteria that originate from the vineyard and the cellar, in addition to any microorganisms that are intentionally inoculated. Previous work has shown that grapevine-associated microbiota follow distinct biogeographic patterns, associated with climate and soil properties, and that even neighboring vineyards can harbor distinct microbial communities, but it is unclear whether these differences persist when controlling for variations in farming practices, cultivar, and climate and whether site-specific microbial profiles change during processing in the winery. Here, we investigated the bacterial and fungal microbiota of fruits pre- and post-harvest from two neighboring vineyards planted to a single variety, geographically close to one another, and farmed the same way and then processed in a single winery. These communities underwent subtle changes during processing, yet retained distinct site-specific signatures, indicating the partial contribution of the winery environment to the microbiota of grape must and juice pre-fermentation. We also profiled the microbiota of key microbial sources in the winery environment, including fruit flies (Drosophila spp.) and processing equipment, demonstrating that the microbiota at these sites reflect contact with the plant material, harbor communities distinct from the fruit, and appear to partially contribute to the fermentation assemblage, especially via the contribution of fermentative yeasts that are rare or missing in the vineyard environment. These results bolster previous reports of site-specific microbial signatures in winegrowing and make a first estimation of the changes to the grape-associated microbiome during early processing.IMPORTANCENative wine fermentations are driven by microbes carried over from the vineyard or introduced in the winery. In this study, we tracked the microbiome dynamics of wine fermentations from two Chardonnay vineyards planted in close proximity in order to examine the relative contribution of vineyard- and winery-resident microbiota on microbial succession during wine fermentation. By tracking microbial changes from the vineyard to winery, we show that the winery environment, including processing equipment and fruit flies, contributes to the fermentation microbiome but does not override vineyard-specific microbial differences. These findings support the concept of microbial terroir and highlight the importance of vineyard microbiomes in shaping wine fermentation. This work advances our understanding of how microbial diversity influences wine production and provides insights into the ecological dynamics of fermentation. By identifying key microbial sources and their contributions, this study lays the groundwork for future research on microbiomes in viticulture and winemaking.},
}

@article {pmid40323071,
year = {2025},
author = {Zhao, Z and Yuan, Z and Li, Y and Huang, X},
title = {The Balance and Imbalance of Microbial Communities: Oral-Gut Microbiota and Colorectal Cancer.},
journal = {American journal of clinical oncology},
volume = {},
number = {},
pages = {},
doi = {10.1097/COC.0000000000001213},
pmid = {40323071},
issn = {1537-453X},
abstract = {The microbiome is a significant multimicrobial community that coexists with the human body in a symbiotic relationship. These microbial communities participate in mechanisms, such as defense against infections, absorption of nutrients, and maintenance of internal homeostasis. Although the microbiome is involved in physiological processes that are beneficial to host health, it can also lead to serious problems. Despite being far apart, the oral cavity and colon are both highly colonized by different microbial communities. Studies have shown that oral bacteria can migrate to and colonize the colon, which is most evident in diseases such as periodontitis. These oral pathogenic bacteria, which contain a large number of carcinogenic factors such as Fusobacterium nucleatum and Porphyromonas gingivalis, can penetrate the large intestine and cause intestinal microbial imbalance and dysfunction, thereby stimulating carcinogenesis. Increasing evidence suggests that oral microbiota, especially certain periodontal pathogens, may be used as biomarkers for colorectal cancer (CRC). Understanding the exact mechanisms of microbiome interactions and their impact on CRC will provide future opportunities for the prevention and treatment of colorectal cancer, and is an important prerequisite for its use as a precise noninvasive biomarker, which is crucial for the early detection of CRC. This review aims to summarize the current research status of oral microbiota, gut microbiota, and their association with CRC, and to evaluate the effectiveness of oral microbiome-derived biomarkers.},
}

@article {pmid40322851,
year = {2025},
author = {Zeng, Z and Li, M and Vannucci, M},
title = {Bayesian covariate-dependent graph learning with a dual group spike-and-slab prior.},
journal = {Biometrics},
volume = {81},
number = {2},
pages = {},
doi = {10.1093/biomtc/ujaf053},
pmid = {40322851},
issn = {1541-0420},
support = {2153704//DMS/NIGMS/ ; //National Science Foundation/ ; },
mesh = {Bayes Theorem ; Computer Simulation ; Humans ; *Models, Statistical ; Microbiota ; Algorithms ; },
abstract = {Covariate-dependent graph learning has gained increasing interest in the graphical modeling literature for the analysis of heterogeneous data. This task, however, poses challenges to modeling, computational efficiency, and interpretability. The parameter of interest can be naturally represented as a 3-dimensional array with elements that can be grouped according to 2 directions, corresponding to node level and covariate level, respectively. In this article, we propose a novel dual group spike-and-slab prior that enables multi-level selection at covariate-level and node-level, as well as individual (local) level sparsity. We introduce a nested strategy with specific choices to address distinct challenges posed by the various grouping directions. For posterior inference, we develop a full Gibbs sampler for all parameters, which mitigates the difficulties of parameter tuning often encountered in high-dimensional graphical models and facilitates routine implementation. Through simulation studies, we demonstrate that the proposed model outperforms existing methods in its accuracy of graph recovery. We show the practical utility of our model via an application to microbiome data where we seek to better understand the interactions among microbes as well as how these are affected by relevant covariates.},
}

Bayes Theorem
Computer Simulation
Humans
*Models, Statistical
Microbiota
Algorithms

@article {pmid40322848,
year = {2025},
author = {Wang, Z and Ling, W and Wang, T},
title = {A semiparametric quantile regression rank score test for zero-inflated data.},
journal = {Biometrics},
volume = {81},
number = {2},
pages = {},
doi = {10.1093/biomtc/ujaf050},
pmid = {40322848},
issn = {1541-0420},
support = {R01 HL155417/HL/NHLBI NIH HHS/United States ; R01GM151301/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; Computer Simulation ; *Models, Statistical ; Regression Analysis ; Data Interpretation, Statistical ; *Biometry/methods ; Gastrointestinal Microbiome ; },
abstract = {Zero-inflated data commonly arise in various fields, including economics, healthcare, and environmental sciences, where measurements frequently include an excess of zeros due to structural or sampling mechanisms. Traditional approaches, such as Zero-Inflated Poisson and Zero-Inflated Negative Binomial models, have been widely used to handle excess zeros in count data, but they rely on strong parametric assumptions that may not hold in complex real-world applications. In this paper, we propose a zero-inflated quantile single-index rank-score-based test (ZIQ-SIR) to detect associations between zero-inflated outcomes and covariates, particularly when nonlinear relationships are present. ZIQ-SIR offers a flexible, semi-parametric approach that accounts for the zero-inflated nature of the data and avoids the restrictive assumptions of traditional parametric models. Through simulations, we show that ZIQ-SIR outperforms existing methods by achieving higher power and better Type I error control, owing to its flexibility in modeling zero-inflated and overdispersed data. We apply our method to the real-world dataset: microbiome abundance from the Columbian Gut study. In this application, ZIQ-SIR identifies more significant associations than alternative approaches, while maintaining accurate type I error control.},
}

Humans
Computer Simulation
*Models, Statistical
Regression Analysis
Data Interpretation, Statistical
*Biometry/methods
Gastrointestinal Microbiome

@article {pmid40322723,
year = {2025},
author = {Cao, N and Lv, D and Liu, Y and Zhang, H and Zhang, X},
title = {Altered Gut Microbiota and Plasma Metabolome Profiles Characterize Depression Individuals with Ischemic Stroke: A Comparative Analysis.},
journal = {Neuropsychiatric disease and treatment},
volume = {21},
number = {},
pages = {973-987},
pmid = {40322723},
issn = {1176-6328},
abstract = {PURPOSE: Depression has been recognized as a significant risk factor for ischemic stroke (IS). This study aimed to describe gut microbiota differences between depression people with and without IS, thereby establishing the link between gut microbiota and an elevated risk of IS development in people with depression.

PEOPLE AND METHODS: This study included 30 hospitalized patients with comorbid depression and IS, and 30 age-/sex-matched patients with depression alone. We used two approaches: (1) genetic analysis techniques (16S rRNA gene sequencing) to map gut microbial ecosystems, and (2) broad-spectrum chemical (nontargeted metabolomics) analysis to detect blood metabolites.

RESULTS: Alpha (α)-diversity and beta (β)-diversity of people with depression, with or without IS, did not show significant differences between the two groups. The IS group showed increased levels of gut bacteria carrying pro-inflammatory molecules, specifically Gram-negative Enterobacteriaceae containing lipopolysaccharide (LPS) components, the Linear discriminant analysis (LDA) value =4.177, P=0.014. Alongside, the IS group reduced populations of beneficial microbes that produce butyric acid important for gut health, such as Acidaminococcaceae (LDA value =4.045, P=0.014), Roseburia (LDA value =3.894, P=0.007), and Fusicatenibacter (LDA value =3.345, P=0.012), compared to the non-IS group. 38 plasma metabolites with significant differences between people with IS and non-IS groups. The abundance of Alloprevotella and Bacteroides massiliensis was correlated with 9 and 4 metabolites, respectively.

CONCLUSION: This study highlighted that people with depression and IS exhibited distinct alterations in both their gut microbiome and metabolite profiles, in contrast to people with depression without IS. These findings may guide future interventions targeting gut microbiota to identify IS in depression people.},
}

@article {pmid40322049,
year = {2025},
author = {DeClercq, V and Wright, RJ and van Limbergen, J and Langille, MGI},
title = {Characterization of the salivary microbiome of adults with inflammatory bowel disease.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2499923},
pmid = {40322049},
issn = {2000-2297},
abstract = {BACKGROUND: Perturbations of the gut microbiota in patients with inflammatory bowel disease (IBD) have been extensively characterised, but changes to the oral microbiome remain understudied. This study aimed to evaluate the oral microbiome of adults with IBD and of matched controls.

METHODS: Saliva samples and data were obtained from a Canadian population cohort (n = 320). The salivary microbiome was characterised using 16S rRNA gene sequencing and examined for differences between control participants and those with IBD, as well as disease subcategories (Crohn's Disease and Ulcerative Colitis).

RESULTS: Alpha diversity was significantly lower in participants with IBD than controls in unadjusted models and many remained significant after adjusting for covariates. Significant differences in some beta diversity metrics between participants with IBD and controls were found, although these did not remain significant when adjusted for covariates. Ten genera were significantly differentially abundant between cases and controls. Veillonella and Streptococcus were both increased in abundance in IBD cases vs controls (25% vs 22% and 14% vs 12%, respectively).

CONCLUSION: These results showcase changes in oral microbial diversity and composition in those living with IBD and highlight the potential of using the salivary microbiome as a biomarker for screening or monitoring IBD.},
}

@article {pmid40321825,
year = {2025},
author = {Chakith M R, S and Pradeep, S and Gangadhar, M and Maheshwari N, C and Pasha, S and Kollur, SP and S, N and Shivamallu, C and Allur Mallanna, S},
title = {Advancements in understanding and treating psoriasis: a comprehensive review of pathophysiology, diagnosis, and therapeutic approaches.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e19325},
pmid = {40321825},
issn = {2167-8359},
mesh = {Humans ; *Psoriasis/diagnosis/therapy/physiopathology/epidemiology ; Quality of Life ; },
abstract = {Psoriasis is a chronic autoimmune disease affecting millions worldwide. This condition is characterized by scaly, red patches of skin that can be painful, itchy, and disfiguring. This non-contagious illness forms plaques and accelerates the dermal cell's life cycle. This review provides a comprehensive overview of the current knowledge on psoriasis, covering its definition, prevalence, causes, pathogenesis, clinical features, diagnosis, and treatment options. The psychosocial impact of psoriasis on patients and their coping mechanisms is also explored. Biologic agents, which target specific cytokines involved in psoriasis pathogenesis, have revolutionized psoriasis treatment and have significantly improved patient outcomes. However, effective and safe treatments for moderate to severe psoriasis are still needed. Future research directions include the development of biomarkers for predicting disease severity and treatment response, investigating new therapeutic targets like the microbiome and epigenetics, and leveraging advancements in technology and genomics for deeper insights into psoriasis pathogenesis and treatment. This study summarizes the key aspects of psoriasis, including its epidemiology, pathophysiology, clinical traits, disease burden, and management. However, further research is needed to improve treatment outcomes and enhance the quality of life for patients affected by this complex condition.},
}

Humans
*Psoriasis/diagnosis/therapy/physiopathology/epidemiology
Quality of Life

@article {pmid40321610,
year = {2025},
author = {Dong, Z and Zhang, R and Shen, L and Ji, HF and He, H and Ji, X and Zhao, L},
title = {Gut Microbiota and Immunoglobulin A Nephropathy: Exploration of Dietary Intervention and Treatment Strategies.},
journal = {Food science & nutrition},
volume = {13},
number = {5},
pages = {e70218},
pmid = {40321610},
issn = {2048-7177},
abstract = {Immunoglobulin A nephropathy (IgAN) is a primary glomerular disease characterized by the deposition of IgA. The pathogenesis of it is related to the dysbiosis of gut microbiota. Dysbiosis of gut microbiota influences mucosal immune response and systemic immune system, leading to glycosylation-deficient IgA1 (Gd-IgA1) increasing, which promotes the development of IgAN. Diet plays an important role in regulating gut microbiota and treating IgAN. In this review, we summarize the interplay between gut microbiota and IgAN, and their underlying mechanisms. We also describe the effects of dietary intake on IgAN, as well as the composition of gut microbiota. The progress on IgAN treatment mainly focuses on inhibiting or regulating the immune system. Moreover, therapeutic strategies related to gut microbiota such as dietary intervention, supplement of probiotics and prebiotics, as well as fecal microbiota transplantation (FMT) have shown the possibility of improving IgAN prognosis. Thus, exploration of the gut-kidney axis, the long-term effects of diet and microbiome is necessary to develop more effective treatment strategies.},
}

@article {pmid40321595,
year = {2025},
author = {Liu, H and Wang, T and Wu, J},
title = {Microbiome: A New Perspective on Immunotherapy for Metastatic Tumors.},
journal = {MedComm},
volume = {6},
number = {5},
pages = {e70185},
pmid = {40321595},
issn = {2688-2663},
}

@article {pmid40321366,
year = {2025},
author = {Khanna, S and Yoho, D and Van Handel, D and Clark, BJ and Awad, T and Guthmueller, B and Armandi, D and Knapple, W and Safdar, N and Baggott, B and Simon, K and Feuerstadt, P},
title = {Safety and effectiveness of fecal microbiota, live-jslm (REBYOTA[®]) administered by colonoscopy for prevention of recurrent Clostridioides difficile infection: 8-week results from CDI-SCOPE, a single-arm, phase IIIb trial.},
journal = {Therapeutic advances in gastroenterology},
volume = {18},
number = {},
pages = {17562848251339697},
pmid = {40321366},
issn = {1756-283X},
abstract = {BACKGROUND: Recurrent Clostridioides difficile infection (rCDI) occurs in up to 35% of patients with CDI, and further recurrence is common. Fecal microbiota, live-jslm (RBL) is safe and effective for preventing rCDI in adults following antibiotic treatment for rCDI when administered rectally. There is clinical interest in alternative routes of administration.

OBJECTIVES: CDI-SCOPE assessed the safety and clinical effectiveness of RBL when administered via colonoscopy to adults with rCDI.

DESIGN: Single-arm, exploratory phase IIIb trial conducted at 12 sites in the United States.

METHODS: Eligible adults with rCDI received one administration of RBL consisting of one 150-mL dose of RBL, delivered via colonoscopy to the right side of the colon. The primary endpoint assessed RBL-related treatment-emergent adverse events (TEAEs) within 8 weeks of RBL administration or until confirmed treatment failure. Secondary endpoints included treatment success (absence of CDI recurrence for 8 weeks following RBL administration), physician experience administering RBL via colonoscopy, and physician perception of participant benefit.

RESULTS: Of 54 participants screened, 41 were enrolled and received RBL via colonoscopy; 39 participants completed the 8-week visit. Five TEAEs in four participants (9.8%) were assessed as related to RBL, all of which were gastrointestinal and mild in severity. Overall, 18 participants (43.9%) experienced 33 TEAEs within 8 weeks, most of which were of mild (25/33; 75.8%) or moderate (5/33; 15.2%) severity. No TEAEs led to intensive care unit admission or death. Overall, 39 participants (95.1%) experienced treatment success; 2 participants (4.9%) withdrew consent and had an indeterminate outcome. Among physicians, 90.2% of investigators indicated a "positive" or "very positive" experience administering RBL by colonoscopy. All physicians assessed participant benefit as "much" or "very much" improved.

CONCLUSION: This single-arm study suggests RBL administered via colonoscopy is practical, safe, and effective for preventing CDI recurrence following antibiotic treatment in adults.

TRIAL REGISTRATION: ClinicalTrials.gov: NCT05831189.},
}

@article {pmid40321269,
year = {2025},
author = {Tronel, A and Roger-Margueritat, M and Plazy, C and Biennier, S and Craspay, A and Mohanty, I and Cools Portier, S and Laiola, M and Roeselers, G and Mathieu, N and Hupe, M and Dorrestein, PC and Alcaraz, JP and Martin, D and Cinquin, P and Silvent, AS and Giai, J and Proust, M and Soranzo, T and Buelow, E and Le Gouellec, A},
title = {Profiling the human luminal small intestinal microbiome using a novel ingestible medical device.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.18.25326056},
pmid = {40321269},
abstract = {The invasive nature of sample collection for studying the small intestinal (SI) microbiome often results in its poor characterization. This study evaluated a novel ingestible medical device (MD) for SI luminal sample collection. A monocentric interventional trial (NCT05477069) was conducted on 15 healthy subjects. Metagenomics, metabolomics and culturomics assessed the MD's effectiveness in characterizing the healthy SI microbiome and identifying potential biomarkers. The SI microbiota differed significantly from the fecal microbiota, displaying high inter-individual variability, lower species richness, and reduced alpha diversity. A combined untargeted and semi-targeted LC-MS/MS metabolomics approach identified a distinct SI metabolic footprint, with bile acids and amino acids being the most abundant classes of metabolites. Host and host/microbe-derived bile acids were particularly abundant in SI samples. The application of a fast culturomics approach to two SI samples enabled species-level characterization, resulting in the identification of 90 bacterial species, including five potential novel species. The present study demonstrates the efficacy of our novel sampling MD in enabling comprehensive SI microbiome analysis through an integrative multi-omics approach, allowing the identification of distinct microbiome signatures between SI and fecal samples.},
}

@article {pmid40320986,
year = {2025},
author = {da Silva Moreira, M and Schmitz, G and de Sá Alves, M and Mendes, MA and Alves, MGO and Alves, LAC and Dias, M and Bandeira, CM and Nepomuceno, GLJT and da Silva Martinho, H and Almeida, JD},
title = {Identification of Aerobic Salivary Microorganisms in Patients With Oral Squamous Cell Carcinoma Using MALDI-TOF MS: Preliminary Findings From a Pilot Study.},
journal = {Rapid communications in mass spectrometry : RCM},
volume = {39},
number = {15},
pages = {e10063},
pmid = {40320986},
issn = {1097-0231},
support = {2016/08633-0//São Paulo Research Foundation/ ; 311933/2021-1//National Council for Technological and Scientific Development (CNPq)/ ; 406761/2022-1//National Council for Technological and Scientific Development (CNPq)/ ; },
mesh = {Humans ; *Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Male ; *Saliva/microbiology ; *Mouth Neoplasms/microbiology ; Middle Aged ; Female ; Pilot Projects ; *Carcinoma, Squamous Cell/microbiology ; Microbiota ; Adult ; Aged ; *Bacteria, Aerobic/isolation & purification/classification ; },
abstract = {RATIONALE: Oral squamous cell carcinoma (OSCC) is a multifactorial disease, and emerging evidence links the oral microbiome to its development. Rapid, noninvasive identification of salivary microorganisms may offer novel diagnostic and prognostic insights into oral cancer.

METHODS: Salivary microbiota from OSCC patients and healthy individuals were analyzed using MALDI Biotyper. Saliva samples were cultured, and microbial identification was performed based on protein spectral profiles using an UltrafleXtreme MALDI-TOF mass spectrometer.

RESULTS: Thirteen OSCC patients (mean age 55 ± 11 years; 69% male) and nineteen healthy controls (mean age 55 ± 10 years; 79% male) were analyzed. Distinct microbial profiles were observed in OSCC patients, including pathogenic species previously associated with carcinogenesis, suggesting potential biomarkers for oral cancer.

CONCLUSIONS: The MALDI Biotyper is an effective, noninvasive tool for identifying salivary microbiota. Its application may support early diagnosis and prognosis of OSCC, reinforcing the significance of the oral microbiome in cancer etiology.},
}

Humans
*Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
Male
*Saliva/microbiology
*Mouth Neoplasms/microbiology
Middle Aged
Female
Pilot Projects
*Carcinoma, Squamous Cell/microbiology
Microbiota
Adult
Aged
*Bacteria, Aerobic/isolation & purification/classification

@article {pmid40320966,
year = {2025},
author = {Mkilima, T},
title = {Engineering artificial microbial consortia for personalized gut microbiome modulation and disease treatment.},
journal = {Annals of the New York Academy of Sciences},
volume = {},
number = {},
pages = {},
doi = {10.1111/nyas.15352},
pmid = {40320966},
issn = {1749-6632},
abstract = {The human gut microbiome is a complex ecosystem that plays a vital role in maintaining health and contributing to the pathogenesis of various diseases. This review proposes a transformative approach that involves engineering artificial microbial consortia-precisely designed communities of microorganisms-for personalized modulation of the gut microbiome and targeted therapeutic interventions. By integrating synthetic biology, systems biology, and advanced culturing techniques, tailored microbial consortia can be developed to perform specific functions within the gut, including the production of therapeutic molecules, modulation of immune responses, and competition against pathogenic bacteria. In vitro and in vivo studies indicate that these engineered consortia can effectively restore microbial balance and enhance host resilience. This personalized approach holds immense potential to revolutionize healthcare by addressing the root causes of diseases such as metabolic disorders, inflammatory conditions, and gastrointestinal infections through precise manipulation of the gut microbiome. Future research should focus on rigorous clinical trials to evaluate the safety, efficacy, and long-term impacts of these engineered consortia in diverse human populations, paving the way for innovative microbial therapies that promote overall health and well-being.},
}

@article {pmid40320851,
year = {2025},
author = {Kim, KS and Yang, SY and Jeong, H and Hong, M and Noh, J and Koh, H and Lee, DW},
title = {Development of a Korean Nutrition Model for In Silico Gut Microbiome Analyses Integrated With Nutrigenomics.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70090},
doi = {10.1002/mnfr.70090},
pmid = {40320851},
issn = {1613-4133},
support = {RS-2021-NR056579//Bio & Medical Technology Development Program of the National Research Foundation (NRF) of Korea/ ; //Ministry of Science and ICT (MSIT)/ ; 20018770//Bioindustrial Technology Development Program of Korea/ ; //Ministry of Trade, Industry and Energy/ ; 2025-12-0026//Yonsei University Research Fund/ ; },
abstract = {The gut microbiome plays a crucial role in human health and disease, with diet serving as a critical determinant of microbial composition and metabolic function. However, most existing nutrition databases are Western-centric, lacking comprehensive dietary information for non-Western populations, including Koreans. This limitation hinders the accuracy of in silico gut microbiome analyses and microbiome-disease associations. We developed the Korean Nutrition Model (KNM) to enhance in silico microbiome analyses by incorporating detailed macronutrient and micronutrient compositions reflective of Korean dietary patterns. KNM was constructed using a decision algorithm that integrates data from the Ministry of Food and Drug Safety and FooDB. Comparative analysis with the European Nutrition Model revealed significant differences in carbohydrate and vitamin compositions, which in turn influenced microbial growth rates and metabolic fluxes in in silico simulations. We further evaluated gut microbiota differences between Korean and European cohorts, including healthy individuals and inflammatory bowel disease patients. Our findings demonstrate that using an appropriate, population-specific nutrition model significantly improves microbiome analyses, reducing the risk of false associations. This study underscores the importance of regionally tailored dietary models and provides a framework for enhancing global dietary models to facilitate precision nutrition and microbiome-based disease interventions.},
}

@article {pmid40320531,
year = {2025},
author = {Vidaur, L and Guridi, A and Leizaola, O and Marin, J and Rello, J and Sarasqueta, C and Sorarrain, A and Marimón, JM},
title = {Respiratory dysbiosis as prognostic biomarker of disease severity for adults with community-acquired pneumonia requiring mechanical ventilation.},
journal = {Pneumonia (Nathan Qld.)},
volume = {17},
number = {1},
pages = {10},
pmid = {40320531},
issn = {2200-6133},
support = {FIS17/01463//Instituto de Salud Carlos III/ ; FIS17/01463//Instituto de Salud Carlos III/ ; },
abstract = {OBJETIVES: To ascertain the role of the lung microbiome in the development of severe pneumonia and its potential as a biomarker for disease progression.

METHODS: BAL samples from 34 adults with severe community-acquired pneumonia (CAP) (17 viral, 8 viral coinfected with bacteria and 9 bacterial) admitted to the ICU for acute respiratory failure between 2019 and 2021 were collected within the first 48 h of admission to the ICU. The microbiome was characterized via the Ion 16S Metagenomics Kit and the Ion Torrent sequencing platform. Clinical factors, including survival, mechanical ventilation duration, blood biomarkers and organ failure in terms of acute respiratory distress syndrome (ARDS), shock or acute renal failure, were correlated with microbiome characteristics.

RESULTS: The microbiome diversity in patients with viral pneumonia was significantly greater than that in patients with bacterial or coinfected pneumonia: the Shannon diversity index was 3.75 (Q1-Q3: 2.5-4.1) versus 0.4 (Q1-Q3: 0.2-1.3) and 0.48 (Q1-Q3: 0.3-1.1), respectively (p < 0.05). The microbiome diversity index was associated with severity-of-illness (APACHE II), independent of the etiology of pneumonia (B coefficient -1.845; p < 0.01). Patients with severe viral CAP who developed ARDS had a lower presence of Proteobacteria, and those who were complicated with ventilator-associated pneumonia had a higher prevalence of Acinetobacter at admission. The mortality of patients with bacterial or coinfected pneumonia was 35%. In coinfected patients, the diversity index was associated with the development of shock.

CONCLUSION: Patients with severe CAP have low respiratory microbiome diversity, indicating that respiratory microbiome diversity is a potential biomarker of disease severity.},
}

@article {pmid40320520,
year = {2025},
author = {Liu, S and Wu, J and Cheng, Z and Wang, H and Jin, Z and Zhang, X and Zhang, D and Xie, J},
title = {Microbe-mediated stress resistance in plants: the roles played by core and stress-specific microbiota.},
journal = {Microbiome},
volume = {13},
number = {1},
pages = {111},
pmid = {40320520},
issn = {2049-2618},
support = {2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2020132607//Forestry and Grassland Science and Technology Innovation Youth Top Talent Project of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 2022YFD2201600, 2022YFD2200602, 2023YFD2200203//Fundamental Research Funds for the National Key R&D Program of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; 32371906, 32022057//Project of the National Natural Science Foundation of China/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; No. B20050//The 111 Project/ ; },
mesh = {*Microbiota/physiology ; *Stress, Physiological ; *Plants/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Soil Microbiology ; Droughts ; },
abstract = {BACKGROUND: Plants in natural surroundings frequently encounter diverse forms of stress, and microbes are known to play a crucial role in assisting plants to withstand these challenges. However, the mining and utilization of plant-associated stress-resistant microbial sub-communities from the complex microbiome remains largely elusive.

RESULTS: This study was based on the microbial communities over 13 weeks under four treatments (control, drought, salt, and disease) to define the shared core microbiota and stress-specific microbiota. Through co-occurrence network analysis, the dynamic change networks of microbial communities under the four treatments were constructed, revealing distinct change trajectories corresponding to different treatments. Moreover, by simulating species extinction, the impact of the selective removal of microbes on network robustness was quantitatively assessed. It was found that under varying environmental conditions, core microbiota made significant potential contributions to the maintenance of network stability. Our assessment utilizing null and neutral models indicated that the assembly of stress-specific microbiota was predominantly driven by deterministic processes, whereas the assembly of core microbiota was governed by stochastic processes. We also identified the microbiome features from functional perspectives: the shared microbiota tended to enhance the ability of organisms to withstand multiple types of environmental stresses and stress-specific microbial communities were associated with the diverse mechanisms of mitigating specific stresses. Using a culturomic approach, 781 bacterial strains were isolated, and nine strains were selected to construct different SynComs. These experiments confirmed that communities containing stress-specific microbes effectively assist plants in coping with environmental stresses.

CONCLUSIONS: Collectively, we not only systematically revealed the dynamics variation patterns of rhizosphere microbiome under various stresses, but also sought constancy from the changes, identified the potential contributions of core microbiota and stress-specific microbiota to plant stress tolerance, and ultimately aimed at the beneficial microbial inoculation strategies for plants. Our research provides novel insights into understanding the microbe-mediated stress resistance process in plants. Video Abstract.},
}

*Microbiota/physiology
*Stress, Physiological
*Plants/microbiology
*Bacteria/classification/genetics/isolation & purification
Soil Microbiology
Droughts

@article {pmid40320452,
year = {2025},
author = {Tümmler, B and Pallenberg, ST and Dittrich, AM and Graeber, SY and Naehrlich, L and Sommerburg, O and Mall, MA},
title = {Progress of personalized medicine of cystic fibrosis in the times of efficient CFTR modulators.},
journal = {Molecular and cellular pediatrics},
volume = {12},
number = {1},
pages = {6},
pmid = {40320452},
issn = {2194-7791},
abstract = {BACKGROUND: Cystic fibrosis (CF) is a systemic disorder of exocrine glands that is caused by mutations in the CFTR gene.

MAIN BODY: The basic defect in people with CF (pwCF) leads to impaired epithelial transport of chloride and bicarbonate that can be assessed by CFTR biomarkers, i.e. the β-adrenergic sweat rate and sweat chloride concentration (SCC), chloride conductance of the nasal respiratory epithelium (NPD), urine secretion of bicarbonate, intestinal current measurements (ICM) of chloride secretory responses in rectal biopsies and in bioassays of chloride transport in organoids or cell cultures. CFTR modulators are a novel class of drugs that improve defective posttranslational processing, trafficking and function of mutant CFTR. By April 2025, triple combination therapy with the CFTR potentiator ivacaftor (IVA) and the CFTR correctors elexacaftor (ELX) and tezacaftor (TEZ) has been approved in Europe for the treatment of all pwCF who do not carry two minimal function CFTR mutations. Previous phase 3 and post-approval phase 4 studies in pwCF who harbour one or two alleles of the major mutation F508del consistently reported significant improvements of lung function and anthropometry upon initiation of ELX/TEZ/IVA compared to baseline. Normalization of SCC, NPD and ICM correlated with clinical outcomes on the population level, but the restoration of CFTR function was diverse and not predictive for clinical outcome in the individual patient. Theratyping of non-F508del CF genotypes in patient-derived organoids and cell cultures revealed for most cases clinically meaningful increases of CFTR activity upon exposure to ELX/TEZ/IVA. Likewise, every second CF patient with non-F508del genotypes improved in SCC and clinical outcome upon exposure to ELX/TEZ/IVA indicating that triple CFTR modulator therapy is potentially beneficial for all pwCF who do not carry two minimal function CFTR mutations. This group who is not eligible for CFTR modulators may opt for gene addition therapy in the future, as the first-in-human trial with a recombinant lentiviral vector is underway.

FUTURE DIRECTIONS: The upcoming generation of pwCF will probably experience a rather normal life in childhood and adolescence. To classify the upcoming personal signatures of CF disease in the times of efficient modulators, we need more sensitive CFTR biomarkers that address the long-term course of airway and gut microbiome, host defense, epithelial homeostasis and multiorgan metabolism.},
}

@article {pmid40320423,
year = {2025},
author = {Ratajczak-Zacharko, W and Skonieczna-Żydecka, K and Laszczyńska, M and Sipak, O and Lubkowska, A},
title = {Identification of an intestinal microbiota enterotypes in ageing man diagnosed with benign prostatic hyperplasia (BPH).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15603},
pmid = {40320423},
issn = {2045-2322},
support = {DEC-2021/05/X/NZ4/01805//National Science Centre, Poland/ ; FSN-318-03/22//Pomeranian Medical University , Poland/ ; },
mesh = {Humans ; Male ; *Prostatic Hyperplasia/microbiology/diagnosis ; *Gastrointestinal Microbiome/genetics ; Aged ; Feces/microbiology ; Middle Aged ; *Aging ; Case-Control Studies ; Aged, 80 and over ; },
abstract = {The intestinal microbiota, in terms of both composition and functioning, exerts a significant influence on the human body. Disturbed microbiota is a common occurrence in the context of numerous diseases. The available evidence increasingly points to a correlation between this condition and the development of prostate diseases, including benign prostatic hyperplasia and prostate cancer. 16 S sequencing of the V3-V4 region was performed and then evaluated alpha and beta diversity of the faeces microbiota of healthy (control group, N = 81) and BPH patients (study group, N = 76). The exploration of enterotypes involved the application of the Dirichlet-Multinomial model, executed for selecting community types. The study revealed no statistically significant difference in alpha diversity between the control group and the group of patients diagnosed with BPH. However, a significant difference was observed in beta diversity (Permanova test: F-value = 5.56, p-value < 0.001). The identification of enterotypes revealed significant differences between the healthy male cohort and those diagnosed with BPH (p = 0.035). In the cohort of men with BPH, the most prevalent was enterotype 3, characterized by a predominance of Blautia, Bacteroides, and Streptococcus. The occurrence of enterotype 3 was associated with an increased likelihood of BPH, exceeding threefold that of enterotype 1 (OR = 3.24). These findings suggest that alterations in the gut microbiota, particularly the presence of enterotype 3, may serve as a microbiological pattern associated with BPH.},
}

Humans
Male
*Prostatic Hyperplasia/microbiology/diagnosis
*Gastrointestinal Microbiome/genetics
Aged
Feces/microbiology
Middle Aged
*Aging
Case-Control Studies
Aged, 80 and over

@article {pmid40320144,
year = {2025},
author = {Yang, L and Lin, Z and Gao, T and Wang, P and Wang, G},
title = {The role of skin-gut-lung microbiome in allergic diseases.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2025.04.041},
pmid = {40320144},
issn = {2213-2201},
abstract = {The incidence of allergic diseases has continued to rise in recent years, affecting ∼20% of the worldwide population especially children. Allergic diseases are chronic immune diseases that greatly reduce the quality of life of patients, leading to great economic and medical burden. The epidemiological studies indicated that children who had atopic dermatitis (AD) in infancy are more likely to develop food allergy (FA) later, and then allergic asthma (AA) and allergic rhinitis (AR) in childhood, which was defined as the "atopic march" (AM). Anatomically, AM follows a spatial sequence from the skin to the gastrointestinal tract then to the respiratory tract. Although the mechanisms underlying AM remain to be elucidated, microbiome alteration was considered as a critical cause. Skin and gut are the two main habitats of microbiota, and research in recent decades also indicated the presence of bacteria in lung. We here not only summarized the roles of skin, gut, lung microbiota in AD, FA, and AA, respectively, but investigated the crosstalk effects of microbiota in each anatomic site on remote organs, including microbiota-gut-skin axis, microbiota-gut-lung axis, and microbiota-skin-lung axis. In addition, we proposed the limitations of current research and the direction of future research in this field.},
}

@article {pmid40320135,
year = {2025},
author = {Ahn, JS and Lee, YB and Han, EJ and Choi, YJ and Kim, DH and Kwok, SK and Choi, HK and Chung, HJ},
title = {Identification of specific gut microbes and their therapeutic potential in ameliorating systemic lupus erythematosus in a mouse model.},
journal = {Life sciences},
volume = {},
number = {},
pages = {123684},
doi = {10.1016/j.lfs.2025.123684},
pmid = {40320135},
issn = {1879-0631},
abstract = {AIMS: The gut microbiome significantly influences autoimmune diseases, including systemic lupus erythematosus (SLE). This study aimed to characterize the gut microbiome and metabolome in SLE and evaluate the therapeutic potential of specific microbial supplementation in MRL/lpr mice.

MATERIALS AND METHODS: MRL/lpr mice, a well-established model for SLE, were used to analyze gut microbiome changes before and after SLE symptom onset. 16S rRNA sequencing and GC-MS-based metabolic profiling were performed to identify key microbial species and associated metabolites. Selected microbes were supplemented in MRL/lpr mice for 10 weeks, and their effects on SLE symptoms and Th17/Treg balance were evaluated.

KEY FINDINGS: Eisenbergiella massiliensis, Lacrimispora saccharolytica, and Hungatella xylanolytica were significantly decreased in MRL/lpr mice following the onset of SLE symptoms. These microbes were strongly correlated with specific metabolites, including 5-cholestanol, cholesterol, p-cresol, and indole. Supplementation with these microbes alleviated SLE symptoms and modulated the Th17/Treg balance.

SIGNIFICANCE: This study highlights the critical role of gut microbiota in immune regulation and SLE symptom relief. Targeted microbial supplementation may serve as a novel therapeutic strategy for managing SLE.},
}

@article {pmid40320089,
year = {2025},
author = {Takefuji, Y},
title = {Critical Analysis of Random Forest Feature Selection: Implications for Gut Microbiome Cancer Research.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2025.03.043},
pmid = {40320089},
issn = {1528-0012},
}

@article {pmid40319889,
year = {2025},
author = {Li, Y and Zou, C and Jiang, F and Wang, F and Zhang, H and Wang, H and Wang, W},
title = {Impacts of air pollution on dynamic lung function in asthma patients: the modifying effect of phenotype susceptibility and possible relationship with airway microbiota.},
journal = {International archives of allergy and immunology},
volume = {},
number = {},
pages = {1-22},
doi = {10.1159/000546208},
pmid = {40319889},
issn = {1423-0097},
abstract = {Introduction Air pollution and meteorological factors have consistently been reported to adversely affect asthma patients. Methods We used a linear mixed-effects model to explore the relationship between air pollution and the dynamic lung function of 58 adult asthma patients with different asthma phenotypes in Beijing, China. We conducted a follow-up panel study of these patients with repeated lung function tests every day in the morning and evening by supervised spirometry from November 2020 to December 2021. Induced sputum from these subjects was collected and analyzed for the microbiome composition and associations between microbiome and lung function indices. Results We found that a 10 μg/m3 increase in PM2.5 was associated with decreases 0.79% in FEF25-75 (95% CI: 0.31 ~ 3.25), a range of decreases of 0.76%~0.83% PEF, 1.58%~1.93% for FEF25 and 1.79%~2.31% for FEF50 in the morning or evening on different lag days. Compared with the PM2.5 effect in the fall, PM2.5 in spring and winter had significant effects on FEV3, FEsV6, and FVC. O3 had significant effects on FEF25, FEF50, FEV3, FEsV6, FVC and FEV1/FEV1-predicted in summer. Significant reduction of lung function indices in range of 0.31% to 1.29% reduction for lung function indices associated with the summer Rh or spring Rh compared with fall Rh. PM2.5 had a larger adverse effect on Th2 phenotype asthmatic patients than on non-Th2 phenotype asthmatic patients. For a 10 μg/m3 increase in PM2.5, there was a 0.75% (95% CI: 0.026%, 1.52%), 0.70% (95% CI: 0.010%, 1.50%),0.75% (95% CI: 0.013%, 1.49%) and 0.37 L (95% CI: 0.062%, 0.80%) on FEF50 (evening), FEF50 (morning), FEF75 (evening) and FEV1 (morning), respectively for the Th2 phenotype compared with those for the non-Th2 phenotype. Significant differences in the sputum microbiome composition were observed between the two inflammatory phenotypes. The linear relationships between sputum microbiome and lung function indices were observed. Conclusion Our study demonstrated the possibility of phenotype-environment interactions.},
}

@article {pmid40319497,
year = {2025},
author = {Tarushi, and Gupta, GD and Kumar, M and Bihani, SC},
title = {Structure-function studies on drug-reactivating β-glucuronidase from mucin-degrading gut symbiont Akkermansia muciniphila.},
journal = {Journal of biomolecular structure & dynamics},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/07391102.2025.2496291},
pmid = {40319497},
issn = {1538-0254},
abstract = {Gut microbial β-glucuronidases (mGUS) not only regulate several hormones and neurotransmitters, they also impact the efficacy and toxicity of xenobiotics. On certain anticancer drugs, e.g. irinotecan (SN-38), mGUS activity leads to enterohepatic recirculation resulting into severe diarrhea. Here, we report the expression, purification and characterization of AmGUS, a novel β-glucuronidase from Akkermansia muciniphila. A. muciniphila is a prominent gut symbiont with beneficial effects on metabolic health and gut homeostasis. AmGUS demonstrates specificity towards glucuronide substrates with no glucosidase or galactosidase activity. Interestingly, it also shows efficient cleavage of the glucuronidated form of the anti-cancer drug, SN38, potentially leading to its enterohepatic recirculation. Furthermore, we find that AmGUS functions as a monomer, contrary to other GUS enzymes that exist as oligomers. mGUS are classified into distinct loop-types based on different active site loops around a conserved core providing substrate specificity. Computational modeling of AmGUS structure reveals that it belongs to the mL2 loop-type GUS enzymes, despite sharing significant sequence/structural similarity with the mL1 loop-type and NL-type GUSs. Interestingly, AmGUS also has a unique N-terminal loop previously not observed in any other GUS enzyme possibly aiding in the processing of drug-glucuronides. Together, these findings suggest that GUS from A. muciniphila belongs to a new class of GUS enzymes with unique active site loop structures. The presence of this unique GUS enzyme may help A. muciniphila in colonizing the human gut. Overall, this study broadens our knowledge of the structural and functional understanding of GUSome in the human gut microbiome.},
}

@article {pmid40319483,
year = {2025},
author = {Shi, FP and Zheng, ZJ and Chen, YL},
title = {Lack of bidirectional associations between gastroesophageal reflux disease and periodontitis: a systematic review and meta-analysis.},
journal = {Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus},
volume = {38},
number = {3},
pages = {},
doi = {10.1093/dote/doaf031},
pmid = {40319483},
issn = {1442-2050},
mesh = {Humans ; *Gastroesophageal Reflux/complications/epidemiology ; *Periodontitis/epidemiology/etiology/complications ; Risk Factors ; Female ; Male ; Odds Ratio ; Middle Aged ; Adult ; },
abstract = {The bidirectional relationship between gastroesophageal reflux disease (GERD) and periodontitis (PD), particularly the temporal directionality, remains unclear. A systematic review and meta-analysis were conducted to evaluate bidirectional associations between GERD and PD. Three databases (PubMed, Embase, and Cochrane Library) were systematically searched from inception to December 1, 2024. Risk estimates from individual studies were pooled using random-effects models. Five studies assessed the risk of PD in patients with GERD, while three studies evaluated the risk of GERD in patients with PD. The overall analysis suggested an increased risk of PD among patients with GERD (odds ratio [OR] = 1.27; 95% confidence interval [CI]: 1.02-1.57; p = 0.029; I2 = 96.5%). However, sensitivity analyses, limited to cohort studies (OR = 1.15; 95% CI: 0.93-1.42; P = 0.05; I2 = 96.9%) and subgroup analyses, did not support this finding. Similarly, PD patients did not exhibit a higher risk of GERD (OR = 1.19; 95% CI: 0.90-1.57; P = 0.223; I2 = 94.3%). The present study could not confirm any bidirectional associations between GERD and PD. Further high-quality longitudinal studies are required to validate these findings.},
}

Humans
*Gastroesophageal Reflux/complications/epidemiology
*Periodontitis/epidemiology/etiology/complications
Risk Factors
Female
Male
Odds Ratio
Middle Aged
Adult

@article {pmid40319450,
year = {2025},
author = {Smith, CA and Renegado, S and Ashby, B},
title = {The evolution of parasite virulence in the presence of resistance-conferring defensive symbionts.},
journal = {Journal of evolutionary biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jeb/voaf049},
pmid = {40319450},
issn = {1420-9101},
abstract = {Defensive symbionts-organisms that confer protection to their hosts against natural enemies such as parasites, predators, or herbivores-are found throughout the natural world. Theoretical and empirical studies have shown that defensive symbionts can both interfere with ecological interactions between hosts and exploiters, as well as drive exploiter evolution. Defensive symbionts are also potential candidates for biocontrol agents to help manage infectious diseases or agricultural pests. The impact of defensive symbionts on parasite ecology and evolution has therefore recently received increased empirical and theoretical attention. In this theoretical study, we investigate the impact that a defensive symbiont which protects hosts from infection (conferred resistance) has on the evolution of parasite virulence. We also explore how the extent of protection conferred by the defensive symbiont coevolves with parasite virulence, and how symbiont and parasite evolution affect the ecology of the host population in both the short- and long-term. We show that, while costly resistance-conferring defensive symbionts always select for increased parasite virulence, the overall long-term ecological effect on the host population may still be positive due to reductions in disease prevalence. This contrasts with tolerance-conferring symbionts (which protect against virulence), where the long-term ecological effects on the host population are always negative. We also show when the defensive symbiont can successfully eliminate the parasite. Resistance-conferring defensive symbionts therefore offer more promise as evolutionarily robust biocontrols than those that only confer tolerance.},
}

@article {pmid40319373,
year = {2025},
author = {Lakamp, AD and Neujahr, AC and Hille, MM and Loy, JD and Fernando, SC and Spangler, ML},
title = {Genetic influence on the composition of the ocular microbiome in preweaned beef calves.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skaf153},
pmid = {40319373},
issn = {1525-3163},
abstract = {Infectious bovine keratoconjunctivitis (IBK), commonly known as bovine pinkeye, is a disease that infects the ocular surface and surrounding tissue which is a concern to animal health and welfare as well as producer economics. Vaccinations have been shown to have variable efficacy, while limited genetics studies using either ulcer scores or binary health phenotypes have suggested that direct genetic selection for resistance would be slow. Therefore, an investigation into the host genetic component of the ocular microbiome was conducted. Animals were genotyped using either a 50K or 100K commercial genotyping array. After filtering for common markers, there were 35,374 markers available for analysis. Ocular microbiome samples were taken on approximately 600 pre-weaned beef calves at four time points. From these, amplicon sequence variants (ASV) were extracted and taxonomy assigned using the V4 region of the 16S rRNA gene. Four metrics of alpha diversity (observed richness, Chao1 index, Simpson index, and Shannon index) and the log-transformed relative abundance of each ASV at each sampling time point were used as phenotypes in a univariate animal model. The observed richness and Chao1 index had heritability estimates of approximately 0.15 at sample times 1 and 3 with estimates of 0 at sample times 2 and 4. Conversely, the Simpson and Shannon indices had heritability estimates ranging from approximately 0.12 to 0.03 at sample times 1 and 4, with estimates near zero for sample times 2 and 3. The relative abundances of 59% of ocular bacterial community were influenced by host genetics at various sampling times. Estimates of heritability ranged from 0 - 0.60, depending on time and level of taxonomic classification. A small collection of microbes previously associated with IBK (specifically Moraxella bovis, Moraxella bovoculi, and Mycoplasma bovoculi) had moderate to high heritability estimates at multiple sampling time points. This indicates selection for reduced pathogen load is possible.},
}

@article {pmid40319295,
year = {2025},
author = {Venkatasamy, L and Iannucci, J and Pereverzev, A and Hoar, J and Huber, E and Ifegbo, A and Dominy, R and El-Hakim, Y and Mani, KK and Dabney, A and Pilla, R and Sohrabji, F and Shapiro, LA},
title = {Systemic IGF-1 administration prevents traumatic brain injury induced gut permeability, dysmorphia, dysbiosis, and the increased number of immature dentate granule cells.},
journal = {Acta neuropathologica communications},
volume = {13},
number = {1},
pages = {90},
pmid = {40319295},
issn = {2051-5960},
mesh = {Animals ; *Insulin-Like Growth Factor I/administration & dosage/pharmacology ; *Brain Injuries, Traumatic/pathology/complications/drug therapy ; Male ; *Dysbiosis/prevention & control/etiology/pathology ; Rats, Sprague-Dawley ; Rats ; Permeability/drug effects ; *Dentate Gyrus/drug effects/pathology ; Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Neurons/drug effects/pathology ; },
abstract = {Traumatic brain injury (TBI) occurs in 2-3 million Americans each year and is a leading cause of death and disability. Among the many physiological consequences of TBI, the hypothalamic pituitary axis (HPA) is particularly vulnerable, including a reduction in growth hormone (GH) and insulin-like growth factor (IGF-1). Clinical and preclinical supplementation of IGF-1 after TBI has exhibited beneficial effects. IGF-1 receptors are prominently observed in many tissues, including in the brain and in the gastrointestinal (GI) system. In addition to causing damage in the brain, TBI also induces GI system damage, including inflammation and alterations to intestinal permeability and the gut microbiome. The goal of this study was to assess the effects of systemic IGF-1 treatment in a rat model of TBI on GI outcomes. Because GI dysfunction has been linked to hippocampal dysfunction, we also examined proliferation and immature granule cells in the hippocampal dentate gyrus. 10-week-old male rats were treated with an intraperitoneal (i.p.) dose of IGF-1 at 4 and 24 h after lateral fluid percussion injury (FPI). At 3- and 35-days post-injury (DPI), gut permeability, gut dysmorphia, the fecal microbiome, and the hippocampus were assessed. FPI-induced permeability of the blood-gut-barrier, as measured by elevated gut metabolites in the blood, and this was prevented by the IGF-1 treatment. Gut dysmorphia and alterations to the microbiome were also observed after FPI and these effects were ameliorated by IGF-1, as was the increase in immature granule cells in the hippocampus. These findings suggest that IGF-1 can target gut dysfunction and damage after TBI, in addition to its role in influencing adult hippocampal neurogenesis.},
}

Animals
*Insulin-Like Growth Factor I/administration & dosage/pharmacology
*Brain Injuries, Traumatic/pathology/complications/drug therapy
Male
*Dysbiosis/prevention & control/etiology/pathology
Rats, Sprague-Dawley
Rats
Permeability/drug effects
*Dentate Gyrus/drug effects/pathology
Gastrointestinal Microbiome/drug effects
Disease Models, Animal
*Neurons/drug effects/pathology

@article {pmid40319213,
year = {2025},
author = {Liu, Y and Hu, Y and Ma, B and Wang, Z and Wei, B},
title = {Gut Microbiota and Exercise: Probiotics to Modify the Composition and Roles of the Gut Microbiota in the Context of 3P Medicine.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {38},
pmid = {40319213},
issn = {1432-184X},
mesh = {*Probiotics/administration & dosage/pharmacology ; Humans ; *Gastrointestinal Microbiome/drug effects/physiology ; *Exercise/physiology ; Athletic Performance/physiology ; Precision Medicine ; Animals ; },
abstract = {Prolonged and intense physical activity can trigger stress response mechanisms across various physiological systems-including the cardiovascular, respiratory, gastrointestinal, musculoskeletal, and neuroendocrine systems-disrupting energy metabolism, immune function, redox balance, and hormonal regulation. Critically, when not accompanied by adequate recovery, such exertion may impair rather than enhance athletic performance. In parallel, there has been growing interest in probiotics as natural, safe, and accessible dietary supplements with the potential to support performance and recovery. Emerging evidence highlights the pivotal role of the gut microbiome in mediating communication along the gut-brain and gut-muscle axes, thereby influencing not only metabolic and immune functions but also neuromuscular adaptation and fatigue resistance. This review explores the mechanisms through which probiotics may enhance exercise performance, mitigate exercise-induced fatigue, and improve physiological adaptation via modulation of inflammation, oxidative stress, and metabolic signaling pathways. Framed within the context of predictive, preventive, and personalized medicine (3P medicine), this paper emphasizes the diagnostic and therapeutic potential of personalized probiotic strategies in optimizing athletic performance through the qualitative and quantitative assessment of microbiota and host responses.},
}

*Probiotics/administration & dosage/pharmacology
Humans
*Gastrointestinal Microbiome/drug effects/physiology
*Exercise/physiology
Athletic Performance/physiology
Precision Medicine
Animals

@article {pmid40319165,
year = {2025},
author = {El-Moamly, A and El-Swify, O},
title = {Raising awareness of Demodex mites: a neglected cause of skin disease.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {40319165},
issn = {1439-0973},
abstract = {BACKGROUND: Demodex mites are among the most prevalent human parasites. While commonly found on healthy individuals, an overpopulation of this arachnid resident of human skin triggers demodicosis, a neglected yet widely prevalent disease with considerable skin and eye morbidity. Despite its health impact, demodicosis remains overshadowed by other common skin diseases. This neglect has significant consequences for individual and public health, which require a paradigm shift in our understanding and management of this ubiquitous ectoparasite. We reviewed the literature to re-evaluate the pathogenicity of the Demodex mite, paying particular attention to the primary risk factors-immune dysregulation, altered microbiota, and concurrent infections-that may contribute to pathogenicity. We discuss the challenges in combating neglect of demodicosis and provide updates on various impediments in achieving this goal. We explore the issues and research gaps in various domains such as those related to parasite biology, pathogenesis, diagnosis, treatment, prevention and control. We present potential solutions and outline future prospects for tackling this important disease. Finally, we hope to catalyze greater attention and investment for this neglected public health issue.

CONCLUSION: Raising awareness of Demodex and demodicosis and its major contribution to human diseases requires a multidisciplinary approach. Efforts to prioritize its place on the global health agenda, invest in research, improve diagnostic tools, and develop new treatment strategies will lead to improved public health outcomes and a higher quality of life for those affected.},
}

@article {pmid40319164,
year = {2025},
author = {Fan, Y and Chen, J and Xu, S and Zhou, H and Shang, Y and Tian, X and Wang, B and Zhao, Y and Shan, G and Zhao, Y and Zhang, P and Chen, X},
title = {Bacillus cereus is a key microbial determinant of intractable otitis media with effusion.},
journal = {Communications medicine},
volume = {5},
number = {1},
pages = {150},
pmid = {40319164},
issn = {2730-664X},
abstract = {BACKGROUND: Currently, the mechanisms by which otitis media with effusion (OME) progresses to intractable OME is unclear. Since crosstalk between microbiome and host contributes to many diseases, we hypothesized that similar interactions could occur in the middle ear effusion (MEE) samples from patients with OME and influence intractable OME pathogenesis. This study aimed to evaluate the microbial profile of MEE samples and to determine whether there were microbial differences between the MEE microbiota of patients with intractable OME and those with rapidly cured OME.

METHODS: MEE samples were collected from 46 OME patients, including 20 from the long course group and 26 from the short course group. Metagenomic sequencing was performed on 30 of these samples, allowing the identification of microbial differences associated with varying disease durations. The difference was verified by further experimental validation, including fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR).

RESULTS: The alpha diversity indices and overall MEE microbial structure show no significant difference between the long course and short course groups, but species such as Bacillus cereus, Nocardiopsis dassonvillei, and Rothia aeria are significantly more prevalent in the MEE of long course OME patients. qPCR analyses and FISH also confirm the difference in the abundance of Bacillus cereus between the two groups.

CONCLUSIONS: Bacillus cereus plays a role in the persistence of OME infection and serves as a potential biomarker to predict OME prognosis. Further studies are warranted to explore the value of Bacillus cereus detection in informing early intervention.},
}

@article {pmid40319096,
year = {2025},
author = {Dissayabutra, T and Chuaypen, N and Somnark, P and Boonkaew, B and Udomkarnjananun, S and Kittiskulnam, P and Charoenchittang, P and Prombutara, P and Tangkijvanich, P},
title = {Characterization of gut dysbiosis and intestinal barrier dysfunction in patients with metabolic dysfunction-associated steatotic liver disease and chronic kidney disease: a comparative study.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15481},
pmid = {40319096},
issn = {2045-2322},
support = {B36G660010//This work was supported by the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation (PMU-B)/ ; HEAF67300062//This work was supported by the Thailand Science research and Innovation Fund Chulalongkorn University/ ; },
mesh = {Humans ; *Dysbiosis/microbiology ; Male ; *Gastrointestinal Microbiome ; Female ; *Renal Insufficiency, Chronic/microbiology/metabolism ; Middle Aged ; Feces/microbiology ; Fatty Acid-Binding Proteins/blood ; Aged ; Case-Control Studies ; Adult ; *Fatty Liver/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics/classification ; },
abstract = {The mechanistic role of gut microbiota in metabolic dysfunction-associated steatotic liver disease (MASLD) and chronic kidney disease (CKD) is increasingly recognized. Despite their close association, comparative data regarding gut dysbiosis in these disorders are limited. This study included 22 healthy controls and 180 patients (90 MASLD, 60 CKD, and 30 both diseases with sex- and age-matched). Fecal bacterial 16 S ribosomal RNA sequencing and butyryl-CoA: acetate CoA transferase (BCoAT) gene expression were analyzed. Plasma intestinal fatty acid binding protein (I-FABP), representing intestinal barrier dysfunction, was assessed using the ELISA method. Our data showed that alpha and beta diversities of gut microbiota differed between MASLD and healthy controls. However, only beta diversities were different between CKD and healthy individuals. The MASLD and CKD groups displayed fewer SCFA-producing genera, particularly Bifidobacterium, than healthy controls. Fecal BCoAT levels were inversely correlated with eGFR and I-FABP levels. Patients with CKD had significantly enriched pathogenic bacteria, reduced BCoAT, and increased I-FABP levels versus MASLD. Combining significant bacterial genera discriminated MASLD from CKD with high diagnostic accuracy (AUC of 0.90). Among patients with both diseases, gut microbial alterations showed mixed characteristics of MASLD and CKD. These data highlighted the shared and distinct gut dysbiosis and related biomarkers, which could provide a better understanding of MASLD and CKD pathogenesis.},
}

Humans
*Dysbiosis/microbiology
Male
*Gastrointestinal Microbiome
Female
*Renal Insufficiency, Chronic/microbiology/metabolism
Middle Aged
Feces/microbiology
Fatty Acid-Binding Proteins/blood
Aged
Case-Control Studies
Adult
*Fatty Liver/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
Bacteria/genetics/classification

@article {pmid40319018,
year = {2025},
author = {Rivera, DE and Poirier, K and Moore, S and Nicolle, O and Morgan, E and Longares, JF and Singh, A and Michaux, G and Félix, MA and Luallen, RJ},
title = {Dynamics of gut colonization by commensal and pathogenic bacteria that attach to the intestinal epithelium.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {70},
pmid = {40319018},
issn = {2055-5008},
support = {2143718//NSF IOS CAREER/ ; 2143718//NSF IOS CAREER/ ; GM146836//NIH R35/ ; },
mesh = {Animals ; *Intestinal Mucosa/microbiology ; *Bacteria/growth & development/pathogenicity/classification/genetics ; *Bacterial Adhesion ; *Gastrointestinal Microbiome ; Symbiosis ; },
abstract = {Bacterial adherence to the intestinal epithelium plays a role in niche establishment in the gut lumen. Through sampling natural populations of Caenorhabditis, we discovered several bacterial species that adhere to the intestinal epithelium via polar, intimate association, best described as attachment. These bacteria had varying effects on host fitness and physiology, with one species having negative effects, and the others exhibiting neutral effects. These bacteria can actively divide in the gut lumen, either replicating throughout the gut simultaneously or anteroposteriorly. In competition assays, animals pre-colonized with an attaching commensal bacteria reduced colonization by the pathogenic bacteria, but this effect was not seen when animals were colonized by both species simultaneously. Regardless of the colonization paradigm, populations exposed to both bacteria showed a near-identical mitigation of the pathogenic effects. Altogether, these strains illustrate the capacity of microbiome bacteria to attach, replicate, and establish a niche across the entire intestinal lumen.},
}

Animals
*Intestinal Mucosa/microbiology
*Bacteria/growth & development/pathogenicity/classification/genetics
*Bacterial Adhesion
*Gastrointestinal Microbiome
Symbiosis

@article {pmid40318838,
year = {2025},
author = {Rust, C and van den Heuvel, LL and Bardien, S and Carr, J and Pretorius, E and Seedat, S and Hemmings, SMJ},
title = {Association between the relative abundance of butyrate-producing and mucin-degrading taxa and Parkinson's disease.},
journal = {Neuroscience},
volume = {576},
number = {},
pages = {149-154},
doi = {10.1016/j.neuroscience.2025.04.050},
pmid = {40318838},
issn = {1873-7544},
abstract = {Parkinson's disease (PD) is a neurodegenerative disorder characterised by motor and non-motor symptoms. Recent evidence suggests a role for gut microbiome composition and diversity in PD aetiology. This study aimed to explore the association between the gut microbiome and PD in a South African population. Gut microbial sequencing data (cases: n = 16; controls: n = 42) was generated using a 16S rRNA gene (V4) primer pair. Alpha- and beta-diversity were calculated using QIIME2, and differential abundance of taxa was evaluated using Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC). Beta-diversity was found to differ significantly between cases and controls, with depletion in the relative abundance of Faecalibacterium, Roseburia, Dorea, and Veillonella, and enrichment of the relative abundance of Akkermansia and Victivallis. Our study found a reduction in butyrate-producing bacteria (e.g. Faecalibacterium and Roseburia) and an increase in mucin-degrading bacteria (Akkermansia) in PD cases compared to controls. These alterations might be associated with heightened gut permeability and inflammation. Longitudinal studies should address the question of whether these microbiome differences are a risk factor for, or are consequent to, the development of PD.},
}

@article {pmid40318781,
year = {2025},
author = {Wang, Z and Xie, J and Wang, G and Yang, H and Li, Z and Zhang, K and Shu, R and Xie, W and Tian, J and Li, H and Gong, W and Xia, Y},
title = {Enhanced gut damage and microbial imbalance in bullfrog tadpoles (Lithobates catesbeiana) exposed to polystyrene microplastics under high-temperature conditions.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {126339},
doi = {10.1016/j.envpol.2025.126339},
pmid = {40318781},
issn = {1873-6424},
abstract = {The potential threat posed by microplastic pollution to ecosystems has garnered widespread attention. Additionally, the combined effects of climate warming and environmental pollutants may further exacerbate the negative impacts on aquatic organisms. In this study, the effects of polystyrene microplastics (PS-MPs) on the oxidative stress status, inflammatory response, and gut microbiota composition of bullfrog tadpoles (Lithobates catesbeiana) were systematically evaluated under different temperatures. Histological analysis, various biomarkers, and microbiome methods were used. Tadpoles were exposed to 0 (control), 100, and 1000 μg/L of PS-MPs at both 25 °C and 32 °C for 28 days. The results showed that compared to low-temperature conditions, PS-MP exposure under high-temperature conditions significantly increased the total antioxidant capacity, glutathione, acid phosphatase, and lysozyme levels in the gut. Additionally, PS-MP exposure under 32 °C significantly disrupted the intestinal epithelial cell structure and increased the expression levels of pro-inflammatory factor genes. Gut microbiota analysis showed that the abundance of Cetobacterium continuously increasing with the concentration of PS-MPs. Under high-temperature conditions, PS-MP exposure further led to a decrease in microbial community diversity. These findings indicate that high-temperature environments exacerbate the negative effects of PS-MP exposure and enhance the oxidative stress and inflammatory response in the intestines of bullfrog tadpoles, which may be the primary factor leading to gut microbiota dysbiosis. This study provides scientific evidence for assessing the environmental risks of microplastics and formulating corresponding environmental protection measures, highlighting the urgency of addressing combined environmental stressors in the context of global warming.},
}

@article {pmid40318624,
year = {2025},
author = {Zeng, Y and Wu, R and He, Y and Zhang, Q and Wang, Z and Qin, P and Yang, F and Han, Y and Hao, M and Zheng, Y and Gao, L and Chen, X and Zhao, X and Zeng, Z and Lian, ZX and Xiao, W and Liu, Z and Zhao, ZB and Gong, S},
title = {Cohabitation facilitates microbiome shifts that promote isoflavone transformation to ameliorate liver injury.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.011},
pmid = {40318624},
issn = {1934-6069},
abstract = {Acetaminophen overuse is a leading cause of acute liver injury (ALI). Although ALI is linked to inter-individual differences in microbiome composition, the mechanisms remain unclear. We demonstrate that horizontal transmission of gut microbiota between male and female mice impacts ALI and identify Rikenellamicrofusus-mediated isoflavone transformation as determinants of ALI severity. R. microfusus increases upon cohabitation with bacterial β-galactosidase enhancing intestinal absorption of isoflavone biochanin-A (Bio-A). R. microfusus mono-colonization reduced ALI severity following acetaminophen overdose. Genetic or chemical-mediated inhibition of β-galactosidase blocked Bio-A release and negated the hepatoprotective effects of R. microfusus. Bio-A directly binds to pyruvate carboxylase (PC) and propionyl-CoA carboxylase subunit alpha (PCCA), augmenting the tricarboxylic acid cycle and promoting protective glutathione synthesis in hepatocytes. Additionally, immunohistochemical analysis revealed reduced hepatic PC and PCCA expression in liver failure (LF) patients. These findings highlight the impacts of microbiome composition on ALI and the ability of microbial isoflavone absorption to mitigate ALI severity.},
}

@article {pmid40318403,
year = {2025},
author = {Li, M and Ye, G and Liu, Y and Yang, T and Zhao, B and Jiang, R and Chen, G},
title = {Short-term microplastic exposure: A double whammy to lung metabolism and fecal microflora in diabetic SD rats.},
journal = {Ecotoxicology and environmental safety},
volume = {297},
number = {},
pages = {118229},
doi = {10.1016/j.ecoenv.2025.118229},
pmid = {40318403},
issn = {1090-2414},
abstract = {Diabetes has become a global health crisis, affecting over 800 million people, with serious complications such as vascular and neurological damage. While diabetes management has been extensively studied, the impact of environmental pollutants, particularly microplastics (PS), on diabetic health remains poorly understood. PS, defined as plastic particles smaller than 5 mm, are pervasive and can enter the body through inhalation or ingestion, posing potential risks. However, the effects of PS exposure, particularly in diabetes, have not been adequately explored. Most studies focus on high-concentration, long-term exposure, which does not reflect typical human exposure levels. This study investigates the effects of short-term PS exposure on diabetic SD rats, using histological, apoptotic, and omics techniques, including metabolomics, lipidomics, and 16S rDNA sequencing. Our results show that short-term PS exposure exacerbates lung and intestinal damage in diabetic rats, with significant alterations in the gut microbiome. We also observed correlations between differential metabolites and microbiota changes. These findings provide novel evidence that short-term PS exposure, at concentrations reflecting daily contact, worsens metabolic dysfunction and intestinal dysbiosis in diabetes. This study emphasizes the need to consider environmental pollutants in diabetes management and highlights potential strategies for prevention and therapy.},
}

@article {pmid40318329,
year = {2025},
author = {Hou, C and Chen, Y and Zhang, W and Yu, J and Ji, M and Cai, S and Guo, W and Ji, X and Sun, L and Liu, X and Wang, Y},
title = {An insight into the full aspects of bound polyphenols in dietary fiber: Interaction, composition, function and foundation as well as alteration in food processing.},
journal = {Food chemistry},
volume = {485},
number = {},
pages = {144553},
doi = {10.1016/j.foodchem.2025.144553},
pmid = {40318329},
issn = {1873-7072},
abstract = {Dietary fiber (DF) and polyphenols are both bioactive compounds with various health-promoting effects while close relationship between them aroused wide concern in recent years. Abundant polyphenols combine with DF and contribute greatly to its beneficial effects. Although efforts made to uncover such bound polyphenols (BPs) from different angles before, systematic overview of full aspects is deficient. Here, more details about polyphenols conjugated in DF reported recently were summarized systematically. Meanwhile, the disposition of BPs in gastrointestinal tract and their interaction with microbiome were introduced to clarify the foundation of their functions. Moreover, considering the great impacts of food processing on polyphenols, different technics used in food handling were introduced with their effects on BPs emphatically discussed to provide guideline for reasonable application of specific technics for given materials. Our work is supposed to promote the understanding of BPs in DF and facilitate their future exploitation and application as a whole.},
}

@article {pmid40318224,
year = {2025},
author = {Maritan, AJ and Clements, CS and Pratte, ZA and Hay, ME and Stewart, FJ},
title = {Sea cucumber grazing linked to enrichment of anaerobic microbial metabolisms in coral reef sediments.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf088},
pmid = {40318224},
issn = {1751-7370},
abstract = {Sea cucumbers have been overharvested world-wide, making assessments of their ecological effects challenging, but recent research demonstrated that sea cucumbers increase coral survival via disease suppression and were therefore important for facilitating reef health. The mechanisms underpinning the sea cucumber-coral interaction therefore are not well understood but are likely mediated through sea cucumber grazing of microbes from reef sediments. We explored how sea cucumber grazing alters the sediment microbiome by leveraging a healthy sea cucumber population on a reef in French Polynesia. We used quantitative PCR, 16S rRNA gene sequencing, and shotgun metagenomics to compare the sediment microbiome in cages placed in situ with or without sea cucumbers. We hypothesized that grazing would lower microbial biomass, change sediment microbiome composition, and deplete sediment metagenomes of anaerobic metabolisms, likely due to aeration of the sediments. Sea cucumber grazing resulted in a 75% reduction in 16S rRNA gene abundances and reshaped microbiome composition, causing a significant decrease of cyanobacteria and other phototrophs relative to ungrazed sediments. Grazing also resulted in a depletion of genes associated with cyanotoxin synthesis, suggesting a potential link to coral health. In contrast to expectations, grazed sediment metagenomes were enriched with marker genes of diverse anaerobic or microaerophilic metabolisms, including those encoding high oxygen affinity cytochrome oxidases. This enrichment differs from patterns linked to other bioturbating invertebrates. We hypothesize that grazing enriches anaerobic processes in sediment microbiomes through removal of oxygen-producing autotrophs, fecal deposition of sea cucumber gut-associated anaerobes, or modification of sediment diffusibility. These results suggest that sea cucumber harvesting influences biogeochemical processes in reef sediments, potentially mediating coral survival by altering the sediment microbiome and its production of coral-influencing metabolites.},
}

@article {pmid40318223,
year = {2025},
author = {Granit, L and Levi, R and Lifshitz, N and Banc-Prandi, G and Zelinger, E and Ronen, B and Kraut-Cohen, J and Naqib, A and Green, SJ and Fine, M and Yarden, O},
title = {Beneficial and detrimental fungi within the culturable mycobiome of the Red Sea coral Stylophora pistilatta.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf090},
pmid = {40318223},
issn = {1751-7370},
abstract = {The presence of fungi in the coral microbiome is increasingly recognized, yet their potential impact on the holobiont's health, particularly under stress conditions, remains underexplored. To address this gap, we isolated over 200 strains (predominantly Ascomycota) from the common scleractinian Red Sea coral, Stylophora pistillata. Using conidia from a rare (Stachybotrys chlorohalonata) and a common (Cladosporium halotolerans) fungal symbiont, we investigated their effects on coral fragments maintained at ambient (25°C) and elevated (33°C) sea temperatures. Inoculation with S. chlorohalonata resulted in significant tissue loss, across both water temperature treatments. Conversely, inoculation with C. halotolerans did not result in visible effects at ambient temperature, but mitigated tissue loss at elevated temperature. This protective effect was accompanied by reduced expression of stress-induced peroxiredoxin-6 and Rad51 host genes, yet not that of Hsp70. Additionally, potential algal symbiont photosynthetic efficiency was higher by over 25% in the elevated temperature treatment, concurrent with higher bacterial diversity, including a marked reduction (>3-fold) in the proliferation of Vibrionaceae in the C. halotolerans-treated coral nubbins. These findings reveal the contrasting impacts of fungal symbionts on coral health, highlighting the dual roles of the mycobiome in influencing holobiont resilience under environmental stress.},
}

@article {pmid40318220,
year = {2025},
author = {Putnam, EE and May, R and Freeman, N and Arrigan, D and Boylan, A and Childs, LH and Wolfe, BE},
title = {Fungi shape genome evolution of bacteria even in the absence of major growth phenotypes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf081},
pmid = {40318220},
issn = {1751-7370},
abstract = {Studies of microbial interactions often emphasize interactions with large, easily measurable growth differences and short-term ecological outcomes spanning just a few generations. However, more subtle interactions, such as those without obvious phenotypes, may play a significant role in shaping both the short-term ecological dynamics and the long-term evolutionary trajectories of microbial species. We used the cheese rind model microbiome to examine how two fungal species, Penicillium camemberti and Geotrichum candidum, impact global gene expression and genome evolution of the bacterium Pseudomonas carnis LP. Even though fungi had limited impacts on the growth of P. carnis LP, approximately 4-40% of its genome was differentially expressed, depending on the specific fungal partner. When we evolved this Pseudomonas strain alone or in co-culture with each of the fungi, we observed frequent mutations in global regulators of nitrogen regulation, secondary metabolite production, and motility, depending on the fungus. Strikingly, many strains with mutations in the nitrogen regulatory gene ntrB emerged when evolved alone or with G. candidum, but not with P. camemberti. Metabolomic and fitness experiments demonstrate that release of free amino acids by P. camemberti removes the fitness advantages conferred by ntrB mutations. Collectively, these results demonstrate that even in the absence of major short-term growth effects, fungi can have substantial impacts on the transcriptome and genomic evolution of bacterial species.},
}

@article {pmid40317954,
year = {2025},
author = {Zhou, C and Zhang, P and Ming, Y},
title = {Characteristics of Intestinal Flora in Patients With Schistosoma japonicum Infection Undergoing Splenectomy.},
journal = {Parasite immunology},
volume = {47},
number = {5},
pages = {e70008},
doi = {10.1111/pim.70008},
pmid = {40317954},
issn = {1365-3024},
support = {//National Natural Science Foundation of China/ ; },
mesh = {*Splenectomy ; *Schistosomiasis japonica/surgery/microbiology ; *Gastrointestinal Microbiome ; Humans ; Female ; Middle Aged ; Male ; Animals ; Adult ; Schistosoma japonicum ; RNA, Ribosomal, 16S/genetics ; *Dysbiosis ; Aged ; },
abstract = {Schistosomiasis japonica is a parasitic disease that seriously endangers human health. Patients with advanced Schistosoma japonicum infection often suffer from cirrhosis and portal hypertension. Splenectomy has been widely used in the treatment of these patients. Previous studies have confirmed that S. japonicum infection is closely related to the gut microbiota, but the impact of splenectomy on the gut microbiota of patients with advanced S. japonicum infection remains unclear. This study used 16sRNA sequencing technology to compare the differences in intestinal flora between patients with advanced S. japonicum infection who underwent splenectomy and non-surgical patients. We focused on the changes in the species composition, diversity and functions of the intestinal flora. Our study shows that dysbiosis of the gut microbiome occurred in patients with advanced S. japonicum infection, including changes in abundance and diversity and the disorder of biological function. The intestinal flora structure, diversity and function of patients who underwent splenectomy were significantly changed compared with those who did not undergo surgery.},
}

*Splenectomy
*Schistosomiasis japonica/surgery/microbiology
*Gastrointestinal Microbiome
Humans
Female
Middle Aged
Male
Animals
Adult
Schistosoma japonicum
RNA, Ribosomal, 16S/genetics
*Dysbiosis
Aged

@article {pmid40317839,
year = {2025},
author = {Fernandes, R and Masino, M and Flood, E and Lansdell, TA and Srikrishna, N and Mui, R and Dorrance, AM and Galligan, JJ and Xu, H},
title = {Studying the Role of Myenteric Amyloidosis in Gastrointestinal Dysmotility and Enteric Neural Dysfunction Using APP/PS1 Mice-Is It an Adequate Animal Model?.},
journal = {Neurogastroenterology and motility},
volume = {},
number = {},
pages = {e70056},
doi = {10.1111/nmo.70056},
pmid = {40317839},
issn = {1365-2982},
support = {R01 DK121272-01A1//National Institute of Diabetes and Digestive and Kidney Diseases, NIDDK, USA, which is within the National Institutes of Health./ ; R01DK121272-3S1//National Institute of Diabetes and Digestive and Kidney Diseases, NIDDK, USA, which is within the National Institutes of Health./ ; },
abstract = {BACKGROUND: The Gastrointestinal (GI) microbiome and gut-brain axis are associated with the progression and pathology of Alzheimer's disease (AD). Amyloid deposition is thought to be a driver of AD, causing synaptic dysfunction and neuronal death in the brain. Chronic constipation is a common gastrointestinal (GI) dysmotility in AD patients, which impacts patient outcomes and quality of life. It is unknown if enteric amyloidosis disrupts myenteric neuron function and causes GI dysmotility.

METHODS: Untreated male and female APP/PS1 (a transgenic murine model of brain amyloidosis) and sex-matched control mice were followed until 12 months of age. A separate cohort of mice was treated with a vehicle or the beta-secretase (BACE1) inhibitor, lanabecestat, starting at 5 months of age until 7 months. GI motility was assessed in all mice by measuring whole GI transit in vivo. Propulsive colonic motility and GI smooth muscle contractions were measured ex vivo. At 7 or 12 months old, amyloidosis in the brain and myenteric plexus was determined by immunohistochemistry or ELISA; the myenteric neural density, including the cholinergic and nitrergic neurons, was evaluated by immune staining and RT-PCR; expression of pro-inflammatory factors in the GI wall was assessed by RT-PCR.

KEY RESULTS: By 7 months of age, male and female APP/PS1 mice developed abundant amyloid plaques in the brain. Aged untreated male APP/PS1 mice also demonstrated Aβ deposition in the colonic myenteric ganglia, which was associated with increased fecal output and faster whole GI transit starting at 4-7 months old, but vehicle- and lanabecestat-treated male APP/PS1 mice had similar GI motility to their non-genetic controls until 7 months old. None of the female APP/PS1 mice showed GI dysmotility or myenteric amyloidosis. Two months of lanabecestat treatment effectively reduced amyloid plaque burden in the brains of female APP/PS1 mice but not in male APP/PS1 mice. Treatment with lanabecestat did not affect myenteric Aβ intensity or GI motility in all APP/PS1 mice. All APP/PS1 mice did not show myenteric neuronal degeneration or inflammation until 12 months old.

CONCLUSIONS: APP/PS1 mice do not recapitulate myenteric amyloidosis persistently and lack the phenotype of constipation observed in human AD patients; these mice should not be considered an adequate murine model for studying the role of myenteric amyloidosis in GI dysmotility. An adequate animal model with myenteric amyloidosis is required for further study.},
}

@article {pmid40317768,
year = {2025},
author = {Kooij, KL and Andreani, NA and Keller, L and Trinh, S and van der Gun, L and Hak, J and Garner, K and Luijendijk, M and Drost, L and Danner, U and van Elburg, A and Dempfle, A and Seitz, J and Herpertz-Dahlmann, B and Baines, JF and Adan, RAH},
title = {Antibiotic-Induced Microbial Dysbiosis Worsened Outcomes in the Activity-Based Anorexia Model.},
journal = {The International journal of eating disorders},
volume = {},
number = {},
pages = {},
doi = {10.1002/eat.24452},
pmid = {40317768},
issn = {1098-108X},
support = {MIGBAN FKZ: 01EW1906A//ERA_Net/ ; 509492174//Deutsche Forschungsgemeinschaft/ ; },
abstract = {OBJECTIVE: Anorexia nervosa (AN) is a complex psychiatric disorder characterized by persistent dieting and reduced food intake, leading to significantly low body weight. Dysbiosis in the gut microbiome of patients with AN has been suggested to contribute to the pathogenesis. Here, we used fecal microbiota transplantation (FMT) in the activity-based anorexia (ABA) rat model to investigate the impact of AN-associated gut microbiota on disease-related outcomes.

METHOD: We validated the FMT in 12 Wistar rats by depleting the gut microbiome with antibiotics and transplanting two donors' fecal samples. We then transplanted fecal samples from four patients with AN or four healthy controls in 48 rats just before the ABA model exposure and included an antibiotic-only control group. During ABA, the rats had access to a running wheel and only 1.5 h access to chow for 7 days. We monitored body weight, body temperature, food intake, wheel revolutions, and gut microbiome biodiversity and composition.

RESULTS: The antibiotic treatment significantly depleted the rats' gut microbiome and subsequent transplantation made the rats' microbiome more similar to the donors' microbiome. The antibiotic-only group showed reduced survival, as well as lower body weight and temperature during ABA. Transplanted microbiota from patients with AN and healthy controls improved outcomes in the ABA model.

DISCUSSION: We do not find evidence that the microbiome of patients with AN differentially contributes to anorexia-like phenotypes based upon partial microbiome transplantation. However, the presence of a microbiome impacts the outcome of the ABA model.},
}

@article {pmid40317421,
year = {2025},
author = {Revankar, NA and Anusha, S and Muthukumar, SP and Negi, PS},
title = {Synbiotic pineapple beverage increases life span in Caenorhabditis elegans, ameliorates cognitive impairment, and restores gut microbiome diversity in D-galactose-induced aged C57BL/6 mice.},
journal = {Biogerontology},
volume = {26},
number = {3},
pages = {99},
pmid = {40317421},
issn = {1573-6768},
support = {MLP284//Central Food Technological Research Institute, Council of Scientific and Industrial Research/ ; },
mesh = {Animals ; Galactose/toxicity ; *Gastrointestinal Microbiome/drug effects ; Caenorhabditis elegans ; *Synbiotics/administration & dosage ; *Ananas ; Mice ; *Cognitive Dysfunction/prevention & control ; Mice, Inbred C57BL ; *Longevity/drug effects ; *Aging/drug effects ; Male ; Beverages ; },
abstract = {The incidence of age-associated ailments has increased proportionately with the expansion of the aging demographic. This study aimed to evaluate the anti-aging potential of synbiotic pineapple beverage formulated with 100% pineapple juice, 1% inulin, and Lacticaseibacillus rhamnosus ATCC 53103 (10 log CFU) in Caenorhabditis elegans and D-galactose age-induced mice. The synbiotic juice-treated nematodes exhibited a 24.52% increase in their lifespan, accompanied by lower levels of reactive oxygen species and improved structural functions. In vivo studies demonstrated that synbiotic treatment positively influences age-induced mice's cerebellar function and spatial memory. Additionally, the synbiotic beverage containing 8-10 log CFU of Lacticaseibacillus rhamnosus showed a protective effect against hippocampal neuron damage. The control group displayed a higher Firmicutes/Bacteroides (F/B) ratio, whereas the significantly lower F/B ratio in the diseased groups indicated a reversal of microbial imbalance caused by D-galactose exposure. Furthermore, the consumption of synbiotic beverage mitigated telomere shortening in aged mice. The results highlight the anti-aging effects of a pineapple beverage formulated with Lacticaseibacillus rhamnosus and inulin as a synbiotic intervention. This study suggests that dietary interventions incorporating prebiotics and probiotics may serve as promising strategy for combating age-related disorders and promoting healthy aging.},
}

Animals
Galactose/toxicity
*Gastrointestinal Microbiome/drug effects
Caenorhabditis elegans
*Synbiotics/administration & dosage
*Ananas
Mice
*Cognitive Dysfunction/prevention & control
Mice, Inbred C57BL
*Longevity/drug effects
*Aging/drug effects
Male
Beverages

@article {pmid40317056,
year = {2025},
author = {Patton, S and Silva, DP and Fuques, E and Klinges, G and Muller, EM and Thurber, RLV},
title = {Antibiotic type and dose variably affect microbiomes of a disease-resistant Acropora cervicornis genotype.},
journal = {Environmental microbiome},
volume = {20},
number = {1},
pages = {46},
pmid = {40317056},
issn = {2524-6372},
support = {2025457//National Science Foundation/ ; },
abstract = {BACKGROUND: As coral diseases become more prevalent and frequent, the need for new intervention strategies also increases to counteract the rapid spread of disease. Recent advances in coral disease mitigation have resulted in increased use of antibiotics on reefs, as their application may halt disease lesion progression. Although efficacious, consequences of deliberate microbiome manipulation resulting from antibiotic administration are less well-understood- especially in non-diseased corals that appear visually healthy. Therefore, to understand how apparently healthy corals are affected by antibiotics, we investigated how three individual antibiotics, and a mixture of the three, impact the microbiome structure and diversity of a disease-resistant Caribbean staghorn coral (Acropora cervicornis) genotype. Over a 96-hour, aquarium-based antibiotic exposure experiment, we collected and processed coral tissue and water samples for 16S rRNA gene analysis.

RESULTS: We found that antibiotic type and dose distinctively impact microbiome alpha diversity, beta diversity, and community composition. In experimental controls, microbiome composition was dominated by an unclassified bacterial taxon from the order Campylobacterales, while each antibiotic treatment significantly reduced the relative abundance of this taxon. Those taxa that persisted following antibiotic treatment largely differed by antibiotic type and dose, thereby indicating that antibiotic treatment may result in varying potential for opportunist establishment.

CONCLUSION: Together, these data suggest that antibiotics induce microbiome dysbiosis- hallmarked by the loss of a dominant bacterium and the increase in taxa associated with coral stress responses. Understanding the off-target consequences of antibiotic administration is critical not only for informed, long-term coral restoration practices, but also for highlighting the importance of responsible antibiotic dissemination into natural environments.},
}

@article {pmid40317047,
year = {2025},
author = {Wang, X and Kong, X and Ding, Y and An, M and Zhu, X and Guan, Y and Niu, Y},
title = {Inverted day-night feeding during pregnancy affects the brain health of both maternal and fetal brains through increasing inflammation levels associated with dysbiosis of the gut microbiome in rats.},
journal = {Journal of neuroinflammation},
volume = {22},
number = {1},
pages = {130},
pmid = {40317047},
issn = {1742-2094},
support = {82273616//National Natural Science Foundation of China/ ; JQ2023H001//the Excellent Youth Foundation of Heilongjiang Scientific Committee/ ; },
mesh = {Animals ; Pregnancy ; Female ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/metabolism ; Rats ; *Brain/metabolism/embryology ; *Inflammation/metabolism ; Male ; Anxiety ; *Feeding Behavior/physiology ; Rats, Sprague-Dawley ; Circadian Rhythm/physiology ; Fetus ; },
abstract = {BACKGROUND: In both humans and rodents, inappropriate feeding times during pregnancy can cause maternal metabolic abnormalities, increasing the risk of neurodevelopmental disorders in both the mother and offspring. Using a rat model, this study investigates whether feeding only during the inactive phase in rats leads to anxiety-like behaviors and abnormal brain development in fetuses through gut microbiota imbalance.

METHODS: 10-week-old female rats in the inactive-phase feeding group (IF group) were first trained for daytime feeding, ensuring that energy intake was statistically insignificant and different from that of the normal diet feeding group (ND group). They were then paired with male rats, and the previous feeding regimen was continued after pregnancy. Anxiety-like behavior was evaluated using the open-field test. Maternal caecal microbiota was analyzed using 16S rRNA sequencing. Enzyme-linked immunosorbent assay (ELISA) measured serum inflammation factors. RT-PCR was employed to assess mRNA levels of integrity genes and inflammatory cytokines in the maternal hippocampi, intestines, fetal brains, and placentae.

RESULTS: There were no statistically significant differences in energy intake or body weight gain between the IF and ND groups. In the open field test, dams in the IF group exhibited anxiety-like behavior, as indicated by fewer entries into and shorter duration in the central zone. Active-phase fasting elevated maternal serum inflammatory cytokine levels and impaired antioxidant capacity. It also increased intestinal permeability and induced gut microbiota dysbiosis, characterized by a decrease in Akkermansia and an increase in Dubosiella. Changes in the expression of intestinal circadian genes and elevated intestinal inflammatory cytokines were observed. Lipopolysaccharide (LPS) translocated into the maternal circulation, activated Toll-like receptor 4 (TLR 4), and passed through the compromised placental barrier into the fetal brain, leading to increased expression of inflammatory cytokines in the fetal brain.

CONCLUSIONS: The misalignment between maternal feeding time and the biological clock during pregnancy disrupts the balance of the gut microbiota and peripheral rhythms. The impaired intestinal and placental barriers allow LPS from the gut to infiltrate the maternal hippocampus and fetal brain, increasing inflammation and impacting both maternal and fetal brain health.},
}

Animals
Pregnancy
Female
*Gastrointestinal Microbiome/physiology
*Dysbiosis/metabolism
Rats
*Brain/metabolism/embryology
*Inflammation/metabolism
Male
Anxiety
*Feeding Behavior/physiology
Rats, Sprague-Dawley
Circadian Rhythm/physiology
Fetus

@article {pmid40316878,
year = {2025},
author = {Shirzadi, P and Farokh, P and Osouli Meinagh, S and Izadi-Jorshari, G and Hajikarimloo, B and Mohammadi, G and Parvardeh, S and Nassiri-Asl, M},
title = {The Influence of the Probiotics, Ketogenic Diets, and Gut Microbiota on Epilepsy and Epileptic Models: A Comprehensive Review.},
journal = {Molecular neurobiology},
volume = {},
number = {},
pages = {},
pmid = {40316878},
issn = {1559-1182},
support = {01-33153//Shahid Beheshti University of Medical Sciences/ ; },
abstract = {About one-third of epilepsies are resistant to antiepileptic drugs; thus, uncovering new pathways in the pathophysiology of epilepsy can reduce the global disease burden. Probiotics are live, non-pathogenic microorganisms that benefit the host by regulating the gut microbiome. This review aims to study the effect of probiotics and ketogenic diets on gut microbiota and their potential as a therapy for epilepsy. We conducted a systematic search of the databases PubMed, Scopus, Embase, and the Web of Science for pertinent studies that have been published. Our search methodology was meticulously structured to be exhaustive, integrating targeted keywords and Boolean operators to guarantee the acquisition of all potentially pertinent articles. Probiotics interact with the gut microbiome, balance its composition, and influence the gut-brain axis. Moreover, they reduce neuroinflammation and oxidative stress. The ketogenic diet (KD) affects gut bacteria, influencing neurotransmitter levels and short-chain fatty acids (SCFAs), which play a role in the gut-brain axis. Studies have shown the positive effects of various probiotics in animal models of epilepsy. They demonstrate improvements in seizure activity, anxiety, and neuroinflammation. In human studies, probiotics reduced seizure frequency and enhanced quality of life in patients with drug-resistant epilepsy. We believe using probiotics or dietary interventions like KD could be a promising therapeutic strategy for managing epilepsy. This could reduce seizure frequency and make life better for patients with epilepsy.},
}

@article {pmid40316674,
year = {2025},
author = {Licinio, J and Licinio, AW and Busnello, JV and Ribeiro, L and Gold, PW and Bornstein, SR and Wong, ML},
title = {The emergence of chronic diseases of adulthood and middle age in the young: the COIDS (chronic inflammation, obesity, insulin resistance/type 2 diabetes, and depressive syndromes) noxious quartet of pro-inflammatory stress outcomes.},
journal = {Molecular psychiatry},
volume = {},
number = {},
pages = {},
pmid = {40316674},
issn = {1476-5578},
support = {R21MH126405//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; R01MH127423//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; R21MH128726//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; R21MH126405//U.S. Department of Health & Human Services | NIH | National Institute of Mental Health (NIMH)/ ; },
abstract = {Major depression, type 2 diabetes, and essential (primary) hypertension are chronic medical and psychiatric disorders that have traditionally affected primarily adults and middle-aged individuals. However, recent decades have witnessed an increasing prevalence of these conditions among children and adolescents. For diseases that typically require prolonged exposure to risk factors to emerge in childhood and adolescence, the amount of exposure to a single risk factor would have to be exceptionally high. We advance the alternative hypothesis of multiple factors acting synergistically. Biological mechanisms underlying the response to ongoing (chronic) stress are logical candidates for being a shared pathway. In the context of persistent and synergistic psychological, social, and economic pressures, unremitting stress can lead to such disease outcomes, exerting a direct influence on the emergence of chronic disorders, and it can also contribute to obesity. Depression follows the same trajectory; therefore, we should examine it as an entity whose consequences are directly reflected in behavioral outcomes, including (over-) eating. Other contributing pathways include chronic sleep deprivation, epigenetic modifications, telomere shortening, the physical environment, pathogens, and the microbiome. We introduce here the concept of the Chronic inflammation, Obesity, Insulin resistance/type 2 diabetes, and Depressive Syndromes (COIDS) noxious quartet of pro-inflammatory stress outcomes, as an increasingly common pathophysiologic state, representing a distinct presentation of type 2 allostatic overload, with direct implications for the current chronic disease epidemic. The compounded effects of a pro-inflammatory state that is fueled by four different and co-existing sources may contribute to explain the emergence of chronic diseases of adulthood and middle age in the young. PPARγ might represent a potential translational therapeutic target for those with COIDS. We propose that highly adverse environments sustain sufficient chronic stress to bring about in the young diseases that had been previously confined to adults.},
}

@article {pmid40316655,
year = {2025},
author = {Neyrinck, AM and Ahmed, H and Leyrolle, Q and Leclercq, S and Amadieu, C and Meuronen, T and Layé, S and Cani, PD and Kärkkäinen, O and Bindels, LB and Hanhineva, K and Delzenne, NM},
title = {Fecal transplantation from humans with obesity to mice drives a selective microbial signature without impacting behavioral and metabolic health.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15455},
pmid = {40316655},
issn = {2045-2322},
support = {ANR-19-NEUR-0003-03//Agence Nationale de la Recherche/ ; PDR T.0068.19 and PINT-MULTI R.8013.19//FNRS/ ; },
mesh = {Animals ; *Fecal Microbiota Transplantation/methods ; *Obesity/microbiology/therapy/metabolism ; Humans ; *Gastrointestinal Microbiome ; Mice ; Male ; *Behavior, Animal ; Feces/microbiology ; Mice, Inbred C57BL ; Female ; Metabolomics ; Metabolome ; },
abstract = {Obesity is associated with alterations in the gut microbiome that may contribute to metabolic and mental health disturbances. Fecal microbiota transplantation (FMT) from humans to mice is a model proposed to study human microbiota-associated disorders. In this study, we investigated whether gut microbiota from human donors with obesity could affect behavior and metabolomic profiles of mice. Stools from donors with obesity and from lean donors were inoculated to antibiotic-pretreated mice fed a standard low-fat diet throughout the experiment. Obese-recipient mice exhibited a lower bacterial alpha-diversity and limited changes in specific taxa (e.g., an increase in Eubacterium) but were similar to lean-recipient mice in terms of dietary intake, body weight, fat mass, anxiety/depression-like behavior and glucose homeostasis. Non-targeted LC-MS metabolomic analysis revealed no change in the portal and cava serum samples. However, 1-methylnicotinamide, indole-3-acetic acid (I3A) and methyllysine were increased in the cecal content of obese-recipient compared to lean-recipient mice. Microbial metabolites derived from amino acids were positively correlated with Eubacterium. These results indicate that FMT from donors with obesity to mice fed chow diet (low in lipids) leads to minor but persistent change in intestinal microbial-derived metabolites, without recapitulating the metabolic and behavioral alterations of obesity.},
}

Animals
*Fecal Microbiota Transplantation/methods
*Obesity/microbiology/therapy/metabolism
Humans
*Gastrointestinal Microbiome
Mice
Male
*Behavior, Animal
Feces/microbiology
Mice, Inbred C57BL
Female
Metabolomics
Metabolome

@article {pmid40316630,
year = {2025},
author = {Aya, V and Pardo-Rodriguez, D and Vega, LC and Cala, MP and Ramírez, JD},
title = {Integrating metagenomics and metabolomics to study the gut microbiome and host relationships in sports across different energy systems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15356},
pmid = {40316630},
issn = {2045-2322},
support = {Small grant//Universidad del Rosario/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Metabolomics/methods ; *Metagenomics/methods ; Male ; *Energy Metabolism ; Adult ; Athletes ; Young Adult ; *Sports ; Feces/microbiology ; Female ; Lipidomics ; },
abstract = {The gut microbiome plays a critical role in modulating host metabolism, influencing energy production, nutrient utilization, and overall physiological adaptation. In athletes, these microbial functions may be further specialized to meet the unique metabolic demands of different sports disciplines. This study explored the role of the gut microbiome in modulating host metabolism among Colombian athletes by comparing elite weightlifters (n = 16) and cyclists (n = 13) through integrative omics analysis. Fecal and plasma samples collected one month before an international event underwent metagenomic, metabolomic, and lipidomic profiling. Metagenomic analysis revealed significant microbial pathways, including L-arginine biosynthesis III and fatty acid biosynthesis initiation. Key metabolic pathways, such as phenylalanine, tyrosine, and tryptophan biosynthesis; arginine biosynthesis; and folate biosynthesis, were enriched in both athlete groups. Plasma metabolomics and lipidomics revealed distinct metabolic profiles and a separation between athlete types through multivariate models, with lipid-related pathways such as lipid droplet formation and glycolipid synthesis driving the differences. Notably, elevated carnitine, amino acid, and glycerolipid levels in weightlifters suggest energy system-specific metabolic adaptations. These findings underscore the complex relationship between the gut microbiota composition and metabolic responses tailored to athletic demands, laying the groundwork for personalized strategies to optimize performance. This research highlights the potential for targeted modulation of the gut microbiota as a basis for tailored interventions to support specific energy demands in athletic disciplines.},
}

Humans
*Gastrointestinal Microbiome
*Metabolomics/methods
*Metagenomics/methods
Male
*Energy Metabolism
Adult
Athletes
Young Adult
*Sports
Feces/microbiology
Female
Lipidomics

@article {pmid40316627,
year = {2025},
author = {Ali, A and Dolma, P and Vishnivetskaya, TA and Namgail, T and Dolma, T and Chauhan, A},
title = {Exploring prokaryotic diversity in permafrost-affected soils of Ladakh's Changthang region and its geochemical drivers.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15388},
pmid = {40316627},
issn = {2045-2322},
support = {DE-SC0020369//US Department of Energy, Office of Science, Office of Biological and Environmental Research, Genomic Science Program/ ; ECR/2016/000698//Department of Science and Technology, Science and Engineering Research Board (DST-SERB), India/ ; },
mesh = {*Permafrost/microbiology ; *Soil Microbiology ; *Soil/chemistry ; *Bacteria/genetics/classification/isolation & purification ; Biodiversity ; *Microbiota ; China ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; },
abstract = {Global warming due to climate change has substantial impact on high-altitude permafrost affected soils. This raises a serious concern that the microbial degradation of sequestered carbon can result in alteration of the biogeochemical cycles. Therefore, the characterization of permafrost affected soil microbiomes, especially of unexplored high-altitude, low oxygen arid region, is important for predicting their response to climate change. This study presents the first report of the bacterial diversity of permafrost-affected soils in the Changthang region of Ladakh. The relationship between soil pH, organic carbon, electrical conductivity, and available micronutrients with the microbial diversity was investigated. Amplicon sequencing of permafrost affected soil samples from Jukti and Tsokar showed that Proteobacteria and Actinobacteria were the dominant phyla in all samples. The genera Brevitalea, Chthoniobacter, Sphingomonas, Hydrogenispora, Clostridium, Gaiella, Gemmatimonas were relatively abundant in the Jukti samples whereas the genera Thiocapsa, Actinotalea, Syntrophotalea, Antracticibcterium, Luteolibacter, Nitrospirillum dominated the Tsokar sample. Correlation analyses highlighted the influence of soil geochemical parameters on the bacterial community structure. PCoA analyses showed that the bacterial beta diversity varied significantly between the sampling locations (PERMANOVA test (F-value: 2.3316; R[2] = 0.466, p = 0.001) and similar results were also obtained while comparing genus abundance data using the ANOSIM test (R = 0.345, p = 0.007).},
}

*Permafrost/microbiology
*Soil Microbiology
*Soil/chemistry
*Bacteria/genetics/classification/isolation & purification
Biodiversity
*Microbiota
China
RNA, Ribosomal, 16S/genetics
Phylogeny

@article {pmid40316599,
year = {2025},
author = {Vázquez-González, L and Regueira-Iglesias, A and Balsa-Castro, C and Tomás, I and Carreira, MJ},
title = {A curated bacterial and archaeal 16S rRNA Gene Oral Sequences dataset.},
journal = {Scientific data},
volume = {12},
number = {1},
pages = {729},
pmid = {40316599},
issn = {2052-4463},
support = {PI24/00222//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; ED481A-2021//Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia (Ministry of Culture, Education and University Planning, Government of Galicia)/ ; IN606B-2023/005//Consellería de Cultura, Educación e Ordenación Universitaria, Xunta de Galicia (Ministry of Culture, Education and University Planning, Government of Galicia)/ ; },
abstract = {In a given species, genomes and 16S rRNA gene sequences, along with their intragenomic copy numbers, can vary greatly across environments. The gene copy numbers are crucial for technologies which estimate microbial abundances based on gene counts, such as polymerase chain reaction and high-throughput sequencing. In these, taxa with fewer genes may be underestimated, while those with more genes might be overestimated. Therefore, it is essential to have accurate gene copy number databases specific to the niche under study. The 16S rRNA Gene Oral Sequences dataset (16SGOSeq) contains the number of 16S rRNA genes and their variants in the complete genomes of the bacterial and archaeal species present in the human oral cavity. It includes 3,192 complete genomes of oral bacteria and 191 complete genomes of oral archaea, from which the 16S rRNA gene sequences were extracted, and the sequence variants were identified. This oral-specific dataset of prokaryotic organisms and the pipeline followed for its construction can be applied by clinical microbiologists, bioinformaticians, or microbial ecologists in future microbiome research.},
}

@article {pmid40316575,
year = {2025},
author = {Uengwetwanit, T and Uawisetwathana, U and Angthong, P and Phanthura, M and Phromson, M and Tala, S and Thepsuwan, T and Chaiyapechara, S and Prathumpai, W and Rungrassamee, W},
title = {Investigating a novel β-glucan source to enhance disease resistance in Pacific white shrimp (Penaeus vannamei).},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15377},
pmid = {40316575},
issn = {2045-2322},
support = {P1652214//National Center for Genetic Engineering and Biotechnology/ ; B05F640108//NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; },
abstract = {β-glucans supplements are known for enhancing disease resistance and performance in shrimp aquaculture, but their effectiveness depends on their source and structure. This study investigated a novel β-glucan derived from the insect fungus Ophiocordyceps dipterigena BCC 2073 as a potential feed additive for Pacific white shrimp (Penaeus vannamei). To determine its feasibility, juvenile shrimps were fed diets supplemented with 0%, 0.1%, and 0.4% β-glucan oligosaccharide for 30 days prior to their performance evaluation. The groups with β-glucan supplementation showed improved immune levels and significantly higher survival rates (p-value < 0.05) when exposed to the pathogen Vibrio harveyi. Transcriptome, microbiome, and metabolome were employed to understand mechanisms of β-glucan supplement. The feed additive altered the expression of host genes linked to immunity, inflammation, and intestinal barrier function. Moreover, Vibrio spp. and Pseudoalteromonas spp. abundances were significantly modulated (p-value < 0.05) with specific Vibrio clades responding differently depending on the β-glucan concentration. Metabolomic analysis revealed immune-supporting metabolites such as hydroquinone and nicotinic acid, potentially promoting homeostasis, consistent with the observed gene expression profiles. This study highlights the potential of O. dipterigena BCC 2073 β-glucan as a novel feed additive to improve disease resistance and shrimp health.},
}

@article {pmid40316568,
year = {2025},
author = {Joshi, P and Bhattacharjee, R and Sahu, M and Gajjar, D},
title = {Insights into urinary catheter colonisation and polymicrobial biofilms of Candida- bacteria under flow condition.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {15375},
pmid = {40316568},
issn = {2045-2322},
abstract = {Most hospital-acquired urinary tract infections are the result of implanted urinary catheter, with majority of studies focused on a single species colonisation, but recently polymicrobial colonisations are being reported. In this study, indwelling urinary catheters were collected from ICU patients and the colonising microbiome was isolated and identified by the traditional; culturing method and metagenomics. It was observed that majority of catheters were colonised by polymicrobial biofilms, containing both bacterial and fungal isolates making them diverse and complex. However, the metagenomics results were quite surprising showing the presence of multiple organisms of which only 1or 2 showed growth when cultured. Later, in vitro assays were performed by selecting 6 combinations, with each combination containing one Candida spp. - C. albicans or C. tropicalis with one bacteria K. pneumoniae, P. aeruginosa or E. coli. It was observed that polymicrobial biofilms were stronger than mono-microbial biofilms, suggesting their increased surface adhesion. Furthermore, to simulate the dynamic environment in which cells are exposed to a certain level of fluid movement, a flow system was established to imitate the flow generated in colonized urinary catheter. We have observed changes in biofilm architecture, adhesion and thickness under flow conditions compared with static conditions, with a uniformly adhered biofilm with increased thickness of polymicrobial biofilms as compared to mono-species biofilms. The biofilm formed under flow was more viable than the static biofilm with higher number of live cells in flow condition.},
}

@article {pmid40316518,
year = {2025},
author = {Zhang, S and Clasen, F and Cai, H and Do, T and Shoaie, S and Carpenter, GH},
title = {Nitrate supplementation affects taste by changing the oral metabolome and microbiome.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {69},
pmid = {40316518},
issn = {2055-5008},
abstract = {Nitrate, an inorganic anion found in various foods is also present in saliva and has emerged as a potential prebiotic for the oral microbiome. Salivary glands concentrate nitrate from the bloodstream and release it into the oral cavity via the anion transporter sialin SLC17A5. In previous studies dietary nitrate supplementation altered oral bacteria composition, favouring genera like Rothia and Neisseria while reducing Streptococcus, Veillonella, Prevotella, and Actinomyces. The present study hypothesized that taste intensity might adapt to changes in the oral microbiome caused by nitrate supplementation. Participants underwent taste tests before, during, and after supplementation. All subjects showed greater levels of salivary nitrate during supplementation and had higher levels of Neisseria compared to before. Subjects were then grouped according to taste tests (before vs. during) as responders (ANOVA p < 0.05, n = 7), and non-responders (ANOVA p > 0.05, n = 6) and their salivary metabolome and oral microbiome further analysed. Responders had significantly less 5-amino pentanoate, formate, propionate and butyrate in saliva while non-responders showed no metabolite changes between before and during supplementation. In contrast, non-responders had increased Capnocytophaga gingivalis and altered lysosomal degradation pathways. Overall, nitrate supplementation shifted the oral microbiome composition in all subjects and when taste intensity was altered this correlated to bacteria-derived short-chain fatty acid production. This suggests taste perception is affected by the oral microbiome.},
}

@article {pmid40316483,
year = {2025},
author = {Zeng, S and Wang, S and Mu, D},
title = {Seeding microbes in defined early-life windows to fight diabetes.},
journal = {Trends in endocrinology and metabolism: TEM},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tem.2025.04.005},
pmid = {40316483},
issn = {1879-3061},
abstract = {Establishment of the early-life gut microbiome, coinciding with the host development, predisposes to long-term disease risk if disrupted. Recently, Hill et al. precisely delineated a critical early-life window in humans and mice during which specific fungi and bacteria play indispensable roles in β-cell development, thereby regulating lifelong metabolic homeostasis.},
}

@article {pmid40316371,
year = {2025},
author = {Werner, M and Vigani, A},
title = {The Microbiome in Critical Illness.},
journal = {The Veterinary clinics of North America. Small animal practice},
volume = {55},
number = {3},
pages = {443-458},
doi = {10.1016/j.cvsm.2025.01.008},
pmid = {40316371},
issn = {1878-1306},
abstract = {Evidence suggests that the intestinal microbiome may play an important role in the pathogenesis and progression of acute critical illness in humans and other mammals, although evidence in small animal medicine is sparse. Moreover, the intestinal microbiota plays many important metabolic roles (production of short-chain fatty acids, trimethylamine-N-oxide, and normal bile acid metabolism) and is crucial for immunity as well as defense against enteropathogens. The use of probiotics and fecal microbiota transplantation as instruments to modulate the intestinal microbiota seems to be safe and effective in studies on critically ill dogs with acute gastrointestinal diseases.},
}

@article {pmid40316177,
year = {2025},
author = {Yin, Y and Guan, M and Wu, S and Cui, C and Wang, R and Zhao, X and Yang, X and Qiao, L and Li, Y and Zhang, C},
title = {Young fecal microbiota transplantation improves working memory in aged recipient rats by increasing interleukin-4 and interleukin-17 levels.},
journal = {Neuroscience research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.neures.2025.04.005},
pmid = {40316177},
issn = {1872-8111},
abstract = {While transplanting the fecal microbiota from young to aged rodents has been extensively studied (that is, young FMT [yFMT]), its mechanism of alleviating working memory decline has not been fully elucidated. In this report, we aimed to investigate the effect of yFMT on the working memory of aged recipient rats performing delayed match-to-position (DMTP) tasks and the associated cellular and molecular mechanisms. The results revealed that yFMT mitigated the decline in DMTP task performance of aged recipients. This improvement was associated with a reshaped gut microbiota and increased levels of brain-derived neurotrophic factor, N-methyl-D-aspartate receptor subunit 1, and synaptophysin, enhancing synaptic formation and transmission. The remodeling of the gut microbiome influenced peripheral circulation and the hippocampus and medial prefrontal cortex by regulating the Th17/Treg ratio and microglial polarization. Ultimately, interleukin-4 and interleukin-17 emerged as potential key molecules driving the beneficial effects of FMT. These observations provide new insights into the gutbrain axis, emphasizing the connection between the gut and brain through the circulation system, and suggest an immunological mechanism that may help reverse age-related declines in the gut microbiota.},
}

@article {pmid40316065,
year = {2025},
author = {Hembrom, PS and Deepthi, M and Kannoth, S and Reeja, N and Antony, G and Grace, T},
title = {Amplicon Sequencing Reveals Growth-Associated Microbial Communities in Black Tiger Shrimp (Penaeus monodon).},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {107636},
doi = {10.1016/j.micpath.2025.107636},
pmid = {40316065},
issn = {1096-1208},
abstract = {Recent evidence has underscored the significance of intestinal microbes in host growth performance, shedding light on the complex relationship between gut microbiota and host physiology. Even though Penaeus monodon exhibits notable size variations attributed to rapid growth and larger body mass, the specific association of the microbial community with body size remains unexplored. In this study, we employed a 16S rRNA amplicon sequencing approach to investigate the composition, diversity, and functional potential of gut microbiota in two populations of adult P. monodon (fast-growing and slow-growing). Significant variations in microbial architecture were found between the study groups based on alpha and beta diversity analyses. Differential abundance analysis identified the enrichment of specific genera, including Desulfovibrio, Ferrimonas, and Fusibacter, in the fast-growing P. monodon. These genera have been previously implicated in female shrimp growth. Functional prediction of the observed microbiota composition highlighted the predominance of growth-associated pathways, such as iron and sulfur metabolism, in the fast-growing population. Overall, our comprehensive analysis revealed discernible differences in gut microbiota between fast-growing and slow-growing populations of P. monodon, possibly indicating dynamic changes associated with host growth and development. The variations observed in the abundance of growth-related microbial taxa between these populations may provide insights into the underlying mechanisms influencing shrimp growth and development.},
}

@article {pmid40315964,
year = {2025},
author = {Gupta, MK and Gouda, G and Moazzam-Jazi, M and Vadde, R and Nagaraju, GP and El-Rayes, BF},
title = {CRISPR/Cas9-directed epigenetic editing in colorectal cancer.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189338},
doi = {10.1016/j.bbcan.2025.189338},
pmid = {40315964},
issn = {1879-2561},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related illness and death worldwide, arising from a complex interplay of genetic predisposition, environmental influences, and epigenetic dysregulation. Among these factors, epigenetic modifications-reversible and heritable changes in gene expression-serve as crucial regulators of CRC progression. Understanding these modifications is essential for identifying potential biomarkers for early diagnosis and developing targeted therapeutic strategies. Epigenetic drugs (epidrugs) such as DNA methyltransferase inhibitors (e.g., decitabine) and bromodomain inhibitors (e.g., JQ1) have shown promise in modulating aberrant epigenetic changes in CRC. However, challenges such as drug specificity, delivery, and safety concerns limit their clinical application. Advances in CRISPR-Cas9-based epigenetic editing offer a more precise approach to modifying specific epigenetic markers, presenting a potential breakthrough in CRC treatment. Despite its promise, CRISPR-based epigenome editing may result in unintended genetic modifications, necessitating stringent regulations and safety assessments. Beyond pharmacological interventions, lifestyle factors-including diet and gut microbiome composition-play a significant role in shaping the epigenetic landscape of CRC. Nutritional and microbiome-based interventions have shown potential in preventing CRC development by maintaining intestinal homeostasis and reducing tumor-promoting epigenetic changes. This review provides a comprehensive overview of epigenetic alterations in CRC, exploring their implications for diagnosis, prevention, and treatment. By integrating multi-omics approaches, single-cell technologies, and model organism studies, future research can enhance the specificity and efficacy of epigenetic-based therapies. Shortly, a combination of advanced gene-editing technologies, targeted epidrugs, and lifestyle interventions may pave the way for more effective and personalized CRC treatment strategies.},
}

@article {pmid40315838,
year = {2025},
author = {Yu, KB and Chandra, F and Coley-O'Rourke, EJ and Paulson, ET and Novoselov, A and Zhang, D and Finnigan, D and Paramo, J and Lopez-Romero, A and Dong, TS and Schartup, AT and Hsiao, EY},
title = {An engineered gut bacterium protects against dietary methylmercury exposure in pregnant mice.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.009},
pmid = {40315838},
issn = {1934-6069},
abstract = {Despite efforts to decrease mercury emissions, chronic exposure to the neurotoxicant methylmercury (MeHg) continues to be a global problem that contributes to disparities in risk for neurological and metabolic diseases. Herein we engineer a human commensal gut bacterium, Bacteroides thetaiotaomicron (Bt), to detoxify MeHg by heterologous expression of organomercury lyase (MerB) and mercuric reductase (MerA) genes derived from a resistant bacterium isolated from Hg-polluted mines. We demonstrate that Bt[merA/B] demethylates MeHg both in vitro and within the intestines of mice orally exposed to MeHg or diets containing MeHg-rich fish. In pregnant mice exposed to dietary MeHg, Bt[merA/B] decreases MeHg accumulation in the maternal liver, brain, placenta, and fetal brain, and attenuates the expression of cellular stress genes in the fetal brain. Overall, this work provides foundational proof-of-principle supporting the ability of an engineered gut bacterium to limit MeHg bioaccumulation and reduce adverse effects of chronic MeHg exposure.},
}

@article {pmid40315837,
year = {2025},
author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD},
title = {Intraspecies dynamics underlie the apparent stability of two important skin microbiome species.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2025.04.010},
pmid = {40315837},
issn = {1934-6069},
abstract = {Adult human facial skin microbiomes are remarkably similar at the species level, dominated by Cutibacterium acnes and Staphylococcus epidermidis, yet each person harbors a unique community of strains. Understanding how person-specific communities assemble is critical for designing microbiome-based therapies. Here, using 4,055 isolate genomes and 356 metagenomes, we reconstruct on-person evolutionary history to reveal on- and between-person strain dynamics. We find that multiple cells are typically involved in transmission, indicating ample opportunity for migration. Despite this accessibility, family members share only some of their strains. S. epidermidis communities are dynamic, with each strain persisting for an average of only 2 years. C. acnes strains are more stable and have a higher colonization rate during the transition to an adult facial skin microbiome, suggesting this window could facilitate engraftment of therapeutic strains. These previously undetectable dynamics may influence the design of microbiome therapeutics and motivate the study of their effects on hosts.},
}

@article {pmid40315582,
year = {2025},
author = {Jadhav, VV and Fasina, YO and Harrison, SH},
title = {Dietary polyunsaturated fatty acids effect on cecal microbiome profile of maturing broiler chicken.},
journal = {Poultry science},
volume = {104},
number = {7},
pages = {105167},
doi = {10.1016/j.psj.2025.105167},
pmid = {40315582},
issn = {1525-3171},
abstract = {Diet has been reported to impact the diversity and function of gut microbiota. Our study investigated the effect of dietary fat types on cecal microbial composition and predicted function in broiler chickens at days 41 and 55 of age. Four dietary fat sources were evaluated and compared to a control dietary fat source of poultry fat. These were for two diets rich in omega-3 polyunsaturated fatty acids (PUFA) - fish oil and flaxseed oil, a diet rich in long-chain saturated fatty acid (SFA) - lard, and a diet rich in medium-chain saturated fatty acid - coconut oil. At day 55, broiler chickens fed a PUFA-rich diet maintained cecal microbial diversity while broiler chickens fed a SFA-rich diet exhibited a significant reduction in diversity compared to the control diet-fed chickens. More specifically, PUFA intake was associated with elevated levels of microbial carbohydrate metabolizing capability, contributing to efficient energy utilization and enhanced short-chain fatty acid production capability. In contrast, SFA-rich diets lowered abundances for key microbial families like Lachnospiraceae and Bifidobacteriaceae hampering nutrient digestibility and pathogen resistance. The microbiomes for chickens fed lard and coconut oil diets showed a significant reduction in SCFA-producing microbial taxa abundance while the microbial functional profile indicated reduced carbohydrate metabolism. Our findings underscore the contrasting effects of SFA-rich fat and PUFA-rich fat on the cecal microbiota of broiler chickens. The results suggest that incorporating PUFA-rich dietary fats into broiler feed may offer potential benefits by modulating the cecal gut microbiota toward outcomes associated with elevated carbohydrate utilization without hampering nutrient digestibility and pathogen resistance.},
}

@article {pmid40315481,
year = {2025},
author = {Ottenbrite, M and Yilmaz, G and Chan, M and Devenish, J and Kang, M and Dan, H and Lau, C and Capitani, S and Carrillo, CD and Bessonov, K and Nash, J and Topp, E and Guan, J},
title = {Food-borne Microbes Influence Conjugative Transfer of Antimicrobial Resistance Plasmids in Pre-disturbed Gut Microbiome.},
journal = {Canadian journal of microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1139/cjm-2024-0168},
pmid = {40315481},
issn = {1480-3275},
abstract = {Ingestion of antibiotic-resistant bacteria following antibiotic treatments may lead to the transfer of antimicrobial resistance genes (ARGs) within a disturbed gut microbiota. However, it remains unclear if and how microbes present in food matrices influence ARG transfer. Thus, a previously established mouse model, which demonstrated the conjugative transfer of a multi-drug resistance plasmid (pIncA/C) from Salmonella Heidelberg (donor) to S. Typhimurium (recipient), was used to assess the effects of food-borne microbes derived from fresh carrots on pIncA/C transfer. Mice were pre-treated with ampicillin, streptomycin, sulfamethazine, or left untreated as a control to facilitate bacterial colonization. Contrary to previous findings where high-density colonization of the donor and recipient bacteria occurred in the absence of food-borne microbes, the presence of these microbes resulted in a low abundance of S. Typhimurium and no detection of S. Typhimurium transconjugants in the fecal samples from any of the mice. However, in mice pre-treated with streptomycin, a significant reduction in microbial species richness allowed for the significant enrichment of Enterobacteriaceae and pIncA/C transfer to bacteria from the genera Escherichia, Enterobacter, Citrobacter, and Proteus. These findings suggest that food-borne microbes may enhance ARG dissemination by influencing the population dynamics of bacterial hosts within a pre-disturbed gut microbiome.},
}

@article {pmid40315344,
year = {2025},
author = {Zhang, B and Zhang, Y and Zhang, X and Qu, J and Ruan, C and Liao, J and Alvarez, PJJ and Yu, P},
title = {Enhanced Phytopathogen Biofilm Control in the Soybean Phyllosphere by the Phoresy of Bacteriophages Hitchhiking on Biocontrol Bacteria.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.4c09851},
pmid = {40315344},
issn = {1520-5851},
abstract = {Phage-based biocontrol has shown notable advantages in protecting plants against pathogenic bacteria in agricultural settings compared to chemical-based bactericides. However, the efficiency and scope of phage biocontrol of pathogenic bacteria are limited by the intrinsic properties of phages. Here, we investigated pathogen biofilm eradication in the phyllosphere using the phoresy system of hitchhiking phages onto carrier biocontrol bacteria. The phoresy system efficiently removed the pathogen biofilm in the soybean phyllosphere, reducing the total biomass by 58% and phytopathogens by 82% compared to the untreated control. Biofilm eradication tests demonstrated a significant combined beneficial effect (Bliss independence model, CI < 1) as phages improved carrier bacteria colonization by 1.2-fold and carrier bacteria facilitated phage infection by 1.4-fold. Transcriptomic analysis showed that phoresy significantly enhanced motility (e.g., fliC and pilD genes) and energy metabolism (e.g., pgm and pgk genes) of carrier bacteria and suppressed the defense system (e.g., MSH3 and FLS2 genes) and energy metabolism (e.g., petB and petC genes) of pathogens. Metabolomics analysis revealed that the phoresy system stimulated the secretion of beneficial metabolites (e.g., flavonoid and tropane alkaloid) that could enhance stress response and phyllosphere protection in soybeans. Overall, the phoresy of phages hitchhiking on biocontrol bacteria offers a novel and effective strategy for phyllosphere microbiome manipulation and bacterial disease control.},
}

@article {pmid40314762,
year = {2025},
author = {Wu, Q and Ning, Z and Zhang, A and Zhang, X and Sun, Z and Figeys, D},
title = {Operational Taxon-Function Framework in MetaX: Unveiling Taxonomic and Functional Associations in Metaproteomics.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.4c06645},
pmid = {40314762},
issn = {1520-6882},
abstract = {Metaproteomics analyzes the functional dynamics of microbial communities by identifying peptides and mapping them to the most likely proteins and taxa. One challenge in this field lies in seamlessly integrating taxonomic and functional annotations to accurately represent the contributions of individual microbial taxa to functional diversity. We introduce MetaX, a comprehensive tool for analyzing taxon-function relationships in metaproteomics by mapping peptides to their lowest common ancestors and assigning functions based on proportional thresholds, ensuring accurate peptide-level mappings. Importantly, MetaX introduces the Operational Taxon-Function (OTF), a new conceptual unit for exploring microbial roles and interactions within ecosystems. Additionally, MetaX includes extensive statistical and visualization tools, establishing it as a robust platform for metaproteomics analysis. We validated MetaX by reanalyzing ex vivo gut microbiome metaproteomic data exposed to various sweeteners, yielding more detailed results than traditional protein analysis. Furthermore, using the peptide-centric approach and OTF, we observed that Parabacteroides distasonis significantly responds to certain sweeteners, highlighting its role in modifying specific metabolic functions. With its intuitive, user-friendly interface, MetaX facilitates a detailed study of the complex interactions between microbial taxa and their functions in metaproteomics. It enhances our understanding of microbial roles in ecosystems and health.},
}

@article {pmid40314735,
year = {2025},
author = {Rohde, C},
title = {[Basic knowledge of phages and their therapeutic application].},
journal = {Bundesgesundheitsblatt, Gesundheitsforschung, Gesundheitsschutz},
volume = {},
number = {},
pages = {},
pmid = {40314735},
issn = {1437-1588},
abstract = {Phages (bacteriophages) are viruses that specifically infect and kill bacteria. They are very abundant in nature, playing a highly relevant role in microbial ecosystems. In medicine, they are investigated as a potential alternative or supplement to antibiotics and can be used to treat wound, urinary tract and lung infections, for example. Single phages or so-called "phage cocktails" are applied.This overview article on basic knowledge of phages sheds light on well-known keywords from classical knowledge of phage biology and on state-of-the-art research focuses. Mechanisms of phage activity are presented as a basis for therapeutic application. Particularly, the phage-host interaction, lysis mechanisms, phage morphologies and specific methods for visualisation are discussed. Being part of the human microbiome, phages contribute to immune defence, especially in the mucosa. Temperate phages that are able to reside in bacterial genomes as prophages and therefore not suitable for therapy use as well as the CrAss phages (Crassvirales) and Lak megaphages discovered in recent years are also introduced. Further topics are bacterial phage defence, phage resistance and phage-antibiotic synergies. An outlook on future research is given, emphasising the importance of a coordinated collection of scientific results.Phages should not replace antibiotics, but they can even improve their efficiency. Currently, the licensing processes for phage therapy are still challenging. However, trust in phage preparations must be based on quality, which has to be guaranteed by harmonised standards.},
}

@article {pmid40314721,
year = {2025},
author = {Tang, J and Ruan, P and Wei, Z},
title = {Untargeted Metabolomics Revealed Metabolomic Profile in Patients with Primary Systemic Sclerosis.},
journal = {Applied biochemistry and biotechnology},
volume = {},
number = {},
pages = {},
pmid = {40314721},
issn = {1559-0291},
abstract = {Systemic sclerosis (SSc) is a systemic autoimmune disease characterized by increased morbidity and mortality. The intestinal microbiome and serum metabolites had been implicated in SSc, but the connection between the gut microbiome and serum metabolites remains poorly understood. In this study, we aimed to investigate the relationship between the gut microbiome and serum metabolome in SSc patients. Untargeted metabolomics was employed to examine the metabolic profiles of SSc patients. The results revealed significant alterations in metabolic pathways, particularly beta-alanine metabolism and pyrimidine metabolism in SSc patients. Specifically, reductions in spermine and beta-alanine were observed within beta-alanine metabolism, while uridylic acid decreased in pyrimidine metabolism. Furthermore, fecal microbiome analysis showed an increased relative abundance of Firmicutes, Verrucomicrobia, and Proteobacteria in SSc patients, whereas the abundance of Bacteroidetes and Actinobacteria was reduced at the phylum level. KEGG pathway analysis, combined with transcriptomic analysis of peripheral blood from SSc patients, identified upregulation of Toll-like receptor signaling, TNF signaling, lipid and atherosclerosis pathways, IL-17 signaling, and AMPK signaling. In summary, we performed a comprehensive analysis of the metabolic profile, which may provide insights for understanding the mechanisms of SSc.},
}

@article {pmid40314699,
year = {2025},
author = {Ramzy, A and Abdelmoneim, TK and Arafat, M and Mokhtar, M and Bakkar, A and Mokhtar, A and Anwar, W and Magdeldin, S and Enany, S},
title = {Metabolomic analysis reveals key changes in amino acid metabolism in colorectal cancer patients.},
journal = {Amino acids},
volume = {57},
number = {1},
pages = {22},
pmid = {40314699},
issn = {1438-2199},
support = {(AI 42547)//The work presented here is funded by the Armed Force College of Medicine, Cairo, Egypt, and it is partially supported by Science, Technology & Innovation Funding Authority (STDF) under grant (AI 42547)./ ; (AI 42547)//The work presented here is funded by the Armed Force College of Medicine, Cairo, Egypt, and it is partially supported by Science, Technology & Innovation Funding Authority (STDF) under grant (AI 42547)./ ; },
mesh = {Humans ; *Colorectal Neoplasms/metabolism/microbiology/pathology ; *Metabolomics/methods ; Male ; Female ; Middle Aged ; Gastrointestinal Microbiome ; Aged ; *Amino Acids/metabolism ; Feces/microbiology/chemistry ; Tandem Mass Spectrometry ; Biomarkers, Tumor/metabolism ; Metabolome ; Chromatography, High Pressure Liquid ; Metabolic Networks and Pathways ; Case-Control Studies ; },
abstract = {The number of colorectal cancer (CRC) patients is steadily growing worldwide, particularly in developing nations. Nonetheless, recent advances in early detection studies and therapy alternatives have reduced CRC mortality in affluent countries, despite rising incidence. Gut microbiota and their metabolites may contribute to tumor growth and reduced therapeutic efficacy. This preliminary study sought to uncover metabolic fingerprints in colorectal cancer patients. It also emphasizes the correlation between the gut microbiome, microbial metabolism, and altered metabolites in CRC. In this study, stool samples from 20 CRC patients and matched healthy controls were enrolled. Untargeted metabolomics approach based on an ultra-high-performance liquid chromatography high-resolution mass spectrometry (UHPLC-MS/MS) were applied. Statistical approaches, pathway enrichment analysis, and network analysis were employed to unleash CRC perturbed metabolic pathways and putative biomarkers. The study identified a distinct manually curated metabolite profile that is substantially linked to CRC. The steroidogenesis, aspartate, tryptophan (Trp), and urea cycle were the most significant pathways that concurrently contributed to CRC.Prominently, among other pathways, Trp metabolism was identified as a critical pathway, indicating a possible connection between the development of CRC and gut microbiota. In a nutshell the notable resulted metabolites reveal auspicious biomarkers for the initial diagnosis as well as surveilling of CRC progression. This preliminary study highlights the potential involvement that gut bacteria may contribute in CRC patients. Further investigation into the composition of the gut microbiome associated with this metabolic profile may lead to the identification of novel biomarkers for early detection and possible targets for treatment.},
}

Humans
*Colorectal Neoplasms/metabolism/microbiology/pathology
*Metabolomics/methods
Male
Female
Middle Aged
Gastrointestinal Microbiome
Aged
*Amino Acids/metabolism
Feces/microbiology/chemistry
Tandem Mass Spectrometry
Biomarkers, Tumor/metabolism
Metabolome
Chromatography, High Pressure Liquid
Metabolic Networks and Pathways
Case-Control Studies

@article {pmid40314614,
year = {2025},
author = {Lee, WM and Ahn, SY and Lee, GS and Park, I and Kim, J and Lee, SH and Lee, S and Kim, CS},
title = {Discovery and Biosynthesis of Indole-Functionalized Metabolites from the Human Blood Bacterium, Paracoccus sanguinis, and Their Anti-Skin Aging Activity.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.4c01354},
pmid = {40314614},
issn = {1520-6025},
abstract = {The human microbiome plays a crucial role in health and disease, with microbial metabolites acting as key mediators of physiological processes. While extensive research has focused on gut-derived microbes, the metabolic contributions of blood-derived bacteria remain underexplored. Here, we investigate the facultative anaerobe Paracoccus sanguinis, a Gram-negative bacterium isolated from human blood, and its metabolome, revealing insights into its potential impacts on health and disease. Using advanced analytical methods, we characterized 12 metabolites (1-12), including six novel compounds (1-3, 9, 10, and 12). Biosynthetic studies demonstrated that these metabolites are derived through enzymatic and nonenzymatic pathways. Functional evaluations revealed significant antiaging activities for 1, 6, and 11 in TNF-α-stimulated normal human dermal fibroblasts (NHDFs), including suppression of reactive oxygen species (ROS), inhibition of matrix metalloproteinase-1 (MMP-1) secretion, and reduction of inflammatory cytokines interleukin (IL)-6 and IL-8. Among the tested compounds, 11 exhibited the highest antiaging efficacy, highlighting its potential as a candidate for therapeutic applications targeting skin aging. This study elucidates the biosynthetic pathways of P. sanguinis metabolites and their antiskin aging activity, underscoring their potential in modulating skin health and offering novel insights into the functional roles of blood-derived microbiota in human health.},
}

@article {pmid40314468,
year = {2025},
author = {Nguyen, RD and Nortey, J and Gebreegziabher, E and Hinterwirth, A and Zhong, L and Chen, C and Doan, T and Lietman, TM and Gonzales, JA},
title = {A Distinguishable Peripheral Blood and Conjunctival Transcriptome and Gut Microbiome in Sjögren's Disease: A Pilot Study.},
journal = {Eye & contact lens},
volume = {},
number = {},
pages = {},
doi = {10.1097/ICL.0000000000001186},
pmid = {40314468},
issn = {1542-233X},
support = {K23 Award EY026998//Foundation for the National Institutes of Health/ ; },
abstract = {OBJECTIVE: To create a comprehensive multi-tissue molecular atlas of Sjögren's disease by using unbiased RNA sequencing to identify differentially expressed genes (DEGs) in peripheral blood and conjunctival transcriptomes, and to characterize the ocular surface and gut microbiome profiles in participants classified as Sjögren's versus non-Sjögren's disease.

METHODS: This exploratory study used high-throughput RNA sequencing to analyze peripheral blood, conjunctival swabs, and rectal swabs from participants (11 classified as Sjögren's disease and four classified as non-Sjögren's) to identify DEGs and microbial profiles that could distinguish these groups.

RESULTS: Differential gene expression analysis revealed upregulated type I interferon (IFI44L, OASL, USP18) and complement pathways (SERPING1) in peripheral blood, alongside activation of several novel pathways in the conjunctiva including intracellular vesicle trafficking (HIP1, GOLIM4, FIG4), immunometabolism (CERS5, HPRT1, ULK2), and cytoskeletal remodeling (MARK1, IQCB1) in Sjögren's disease. In addition, distinct gut microbiome compositions were observed in Sjögren's disease participants, characterized by an increased presence of Lactobacillus reuteri species.

CONCLUSIONS: Using unbiased RNA sequencing, we confirmed the role of type I interferon and complement pathways in the peripheral blood and identified novel molecular signatures in the conjunctiva of Sjögren's disease participants. These newly identified pathways-involved in intracellular vesicle trafficking, immunometabolism, and cytoskeletal remodeling-expand our understanding of disease mechanisms beyond traditional immune pathways. In addition, we found distinct gut microbial profiles in Sjögren's disease participants, although ocular surface microbiome showed no significant differences. Such findings may suggest possible new therapeutic targets and allow for Sjögren's disease patient stratification. However, validation in larger cohorts is needed to establish clinical significance and potential applications in Sjögren's disease.},
}

@article {pmid40314439,
year = {2025},
author = {Austin, GI and Korem, T},
title = {Compositional transformations can reasonably introduce phenotype-associated values into sparse features.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0002125},
doi = {10.1128/msystems.00021-25},
pmid = {40314439},
issn = {2379-5077},
abstract = {UNLABELLED: Gihawi et al. (mBio 14:e01607-23, 2023, https://doi.org/10.1128/mbio.01607-23) argued that the analysis of tumor-associated microbiome data by Poore et al. (Nature 579:567-574, 2020, https://doi.org/10.1038/s41586-020-2095-1) is invalid because features that were originally very sparse (genera with mostly zero read counts) became associated with the phenotype following batch correction. Here, we examine whether such an observation should necessarily indicate issues with processing or machine learning pipelines. We show counterexamples using the centered log ratio (CLR) transformation, which is often used for analysis of compositional microbiome data. The CLR transformation has similarities to voom-SNM, the batch-correction method brought into question by Gihawi et al., and yet is a sample-wise operation that cannot, in itself, "leak" information or invalidate downstream analyses. We show that because the CLR transformation divides each value by the geometric mean of its sample, common imputation strategies for missing or zero values result in transformed features that are associated with the geometric mean. Through analyses of both synthetic and vaginal microbiome data sets, we demonstrate that when the geometric mean is associated with a phenotype, sparse and CLR-transformed features will also become associated with it. We re-analyze features highlighted by Gihawi et al. and demonstrate that the phenomenon of sparse features becoming phenotype-associated can also be observed after a CLR transformation, which serves as a counterexample to the claim that such an observation necessarily means information leakage. While we do not intend to address other concerns regarding tumor microbiome analyses, validate Poore et al.'s results, or evaluate batch-correction pipelines, we conclude that because phenotype-associated features that were initially sparse can be created by a sample-wise transformation that cannot artifactually inflate machine learning performance, their detection is not independently sufficient to demonstrate information leakage in machine learning pipelines. Microbiome data are multivariate, and as such, a value of 0 carries a different meaning for each sample. Many transformations, including CLR and other batch-correction methods, are likewise multivariate, and, as these issues demonstrate, each individual feature should be interpreted with caution.

IMPORTANCE: Gihawi et al. claim that finding that a transformation turned highly sparse (mostly zero) features into features that are associated with a phenotype is sufficient to conclude that there is information leakage and to invalidate an analysis. This claim has critical implications for both the debate regarding The Cancer Genome Atlas (TCGA) cancer microbiome analysis and for interpretation and evaluation of analyses in the microbiome field at large. We show by counterexamples and by reanalysis that such transformations can be valid.},
}

@article {pmid40313608,
year = {2025},
author = {Luo, J and Wang, Y},
title = {Precision Dietary Intervention: Gut Microbiome and Meta-metabolome as Functional Readouts.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {23-50},
pmid = {40313608},
issn = {2730-5848},
abstract = {Gut microbiome, the group of commensals residing within the intestinal tract, is closely associated with dietary patterns by interacting with food components. The gut microbiome is modifiable by the diet, and in turn, it utilizes the undigested food components as substrates and generates a group of small molecule-metabolites that addressed as "meta-metabolome" in this review. Profiling and mapping of meta-metabolome could yield insightful information at higher resolution and serve as functional readouts for precision nutrition and formation of personalized dietary strategies. For assessing the meta-metabolome, sample preparation is important, and it should aim for retrieval of gut microbial metabolites as intact as possible. The meta-metabolome can be investigated via untargeted and targeted meta-metabolomics with analytical platforms such as nuclear magnetic resonance spectroscopy and mass spectrometry. Employing flux analysis with meta-metabolomics using available database could further elucidate metabolic pathways that lead to biomarker discovery. In conclusion, integration of gut microbiome and meta-metabolomics is a promising supplementary approach to tailor precision dietary intervention. In this review, relationships among diet, gut microbiome, and meta-metabolome are elucidated, with an emphasis on recent advances in alternative analysis techniques proposed for nutritional research. We hope that this review will provide information for establishing pipelines complementary to traditional approaches for achieving precision dietary intervention.},
}

@article {pmid40313607,
year = {2025},
author = {Kriti, M and Ojha, R and Singh, S and Sarma, DK and Verma, V and Yadav, AK and Nagpal, R and Kumar, M},
title = {Implication of Gut Mycobiome and Virome in Type-2 Diabetes Mellitus: Uncovering the Hidden Players.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {51-64},
pmid = {40313607},
issn = {2730-5848},
abstract = {Type-2 diabetes mellitus (T2DM) is a global epidemic with significant societal costs. The gut microbiota, including its metabolites, plays a pivotal role in maintaining health, while gut dysbiosis is implicated in several metabolic disorders, including T2DM. Although data exists on the relationship between the gut bacteriome and metabolic disorders, further attention is needed for the mycobiome and virome. Recent advancements have begun to shed light on these connections, offering potential avenues for preventive measures. However, more comprehensive investigations are required to untangle the interrelations between different microbial kingdoms and their role in T2DM development or mitigation. This review presents a simplified overview of the alterations in the gut bacteriome in T2DM and delves into the current understanding of the mycobiome and virome's role in T2DM, along with their interactions with the cohabiting bacteriome. Subsequently, it explores into the age-related dynamics of the gut microbiome and the changes observed in the microbiome composition with the onset of T2DM. Further, we explore the basic workflow utilized in gut microbiome studies. Lastly, we discuss potential therapeutic interventions in gut microbiome research, which could contribute to the amelioration of the condition, serve as preventive measures, or pave the way towards personalized medicine.},
}

@article {pmid40313605,
year = {2025},
author = {Zhou, X and Chen, X and Davis, MM and Snyder, MP},
title = {Embracing Interpersonal Variability of Microbiome in Precision Medicine.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {8-13},
pmid = {40313605},
issn = {2730-5848},
}

@article {pmid40313603,
year = {2025},
author = {Pu, Y and Zhou, X and Cai, H and Lou, T and Liu, C and Kong, M and Sun, Z and Wang, Y and Zhang, R and Zhu, Y and Ye, L and Zheng, Y and Zhu, B and Quan, Z and Zhao, G and Zheng, Y},
title = {Impact of DNA Extraction Methods on Gut Microbiome Profiles: A Comparative Metagenomic Study.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {76-90},
pmid = {40313603},
issn = {2730-5848},
abstract = {UNLABELLED: In gut microbial research, DNA extraction remarkably influences study outcomes and biological interpretations. Rapid advancements in the research scale and technological upgrades necessitate evaluating new methods to ensure reliability and precision in microbial community profiling. We systematically evaluated the performance of eight recent and commonly used extraction methods using a microbial mock community (MMC) and fecal samples from two healthy volunteers, incorporating bacterial, archaeal, and fungal constituents. Performance metrics included nucleic acid assessment, microbial profile assessment, and scalability for large-scale studies, leveraging shotgun metagenomics for in-depth analysis. Despite variations in DNA quantity and quality, all methods yielded sufficient DNA for shotgun metagenomic sequencing. In the MMC microbial profile assessment, the QIAamp PowerFecal pro Kit (PF) and DNeasy PowerSoil HTP kit (PS) methods exhibited higher similarity with the theoretical composition and lower variability across technical replicates compared to other methods. For fecal samples, the extraction method accounted for 21.4% of the overall microbiome variation and significantly affected the abundances of 32% of detected microbial species. Methods using mechanical lysis with small beads, such as PF and PS, demonstrated better efficiency, indicated by increased microbial diversity in extracting DNA from Gram-positive bacteria. Furthermore, the PF and PS methods are notably simple to execute and automation-friendly, though relatively costly. Our study underscores the importance of maintaining consistency in DNA extraction methods for reliable comparative metagenomic analyses. We recommend PF and PS methods as optimal for expansive gut metagenomic research, emphasizing the critical role of mechanical lysis in DNA extraction.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-025-00232-x.},
}

@article {pmid40313601,
year = {2025},
author = {Zhao, L},
title = {Relational Stability: A New Strategy for Defining the Human Core Microbiome.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {1},
pages = {14-17},
pmid = {40313601},
issn = {2730-5848},
}

@article {pmid40313461,
year = {2025},
author = {Bessa, LJ and Egas, C and Pires, C and Proença, L and Mascarenhas, P and Pais, RJ and Barroso, H and Machado, V and Botelho, J and Alcoforado, G and Mendes, JJ and Alves, R},
title = {Linking peri-implantitis to microbiome changes in affected implants, healthy implants, and saliva: a cross-sectional pilot study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1543100},
pmid = {40313461},
issn = {2235-2988},
mesh = {Humans ; *Peri-Implantitis/microbiology ; *Saliva/microbiology ; Pilot Projects ; Cross-Sectional Studies ; *Microbiota ; *Dental Implants/microbiology ; Male ; Female ; Biofilms/growth & development ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Metagenomics ; Adult ; },
abstract = {INTRODUCTION: The rising use of dental implants is accompanied by an expected increase in peri-implant diseases, particularly peri-implantitis (PI), which poses a significant threat to implant success and necessitates a thorough understanding of its pathogenesis for effective management.

METHODS: To gain deeper insights into the role and impact of the peri-implant microbiome in the pathogenesis and progression of PI, we analyzed 100 samples of saliva and subgingival biofilm from 40 participants with healthy implants (HI group) or with co-occurrence of diagnosed PI-affected implants and healthy implants (PI group) using shotgun metagenomic sequencing. We identified the most discriminative species distinguishing healthy from diseased study groups through log ratios and differential ranking analyses.

RESULTS AND DISCUSSION: Mogibacterium timidum, Schaalia cardiffensis, Parvimonas micra, Filifactor alocis, Porphyromonas endodontalis, Porphyromonas gingivalis and Olsenella uli were associated with the subgingival peri-implant biofilm. In contrast, Neisseria sp oral taxon 014, Haemophilus parainfluenzae, Actinomyces naeslundii, Rothia mucilaginosa and Rothia aeria were more prevalent in the healthy peri-implant biofilm. Functional pathways such as arginine and polyamine biosynthesis, including putrescine and citrulline biosynthesis, showed stronger correlations with PI-affected implants. In contrast, peri-implant health was characterized by the predominance of pathways involved in purine and pyrimidine deoxyribonucleotide de novo biosynthesis, glucose and glucose-1-phosphate degradation, and tetrapyrrole biosynthesis. Our findings reveal that healthy implants in PI-free oral cavities differ significantly in microbial composition and functional pathways compared to healthy implants co-occurring with PI-affected implants, which more closely resemble PI-associated profiles. This pattern extended to salivary samples, where microbial and functional biomarkers follow similar trends.},
}

Humans
*Peri-Implantitis/microbiology
*Saliva/microbiology
Pilot Projects
Cross-Sectional Studies
*Microbiota
*Dental Implants/microbiology
Male
Female
Biofilms/growth & development
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Aged
Metagenomics
Adult

@article {pmid40313460,
year = {2025},
author = {Wang, Y and Liu, Y and Liu, X and Xu, P and Luo, M and Huang, A and Su, Z},
title = {Comprehensive analysis of transcriptome and microbiome in colorectal cancer with synchronous polyp patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1547057},
pmid = {40313460},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Feces/microbiology ; *Transcriptome ; Aged ; Gene Expression Profiling ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is a prevalent and lethal malignancy, with the role of gut microbiota in its development still unclear. This study examines differences in gut microbiota between CRC patients and healthy controls and explores their association with host gene expression to identify potential diagnostic and therapeutic targets.

METHODS: Fecal samples from 10 CRC patients and 13 healthy controls were subjected to 16S rRNA sequencing. Transcriptome sequencing of tumor tissues, normal mucosa, and colorectal polyps from same 10 CRC patients was performed to identify differentially expressed genes (DEGs). Pearson correlation analysis was employed to associate operational taxonomic units (OTUs) with host gene expression.

RESULTS: β-diversity analysis showed significant differences in microbiota between CRC patients and controls (P < 0.01). LEfSe identified 38 distinct bacterial taxa, with genera such as Bacteroides, Peptostreptococcus, and Parabacteroides being enriched in CRC patients. Transcriptome analysis uncovered 1,026 DEGs. Notably, TIMP1 and BCAT1 were positively correlated (r > 0.76, P < 0.01) with pathogenic bacteria like Fusobacterium nucleatum and Peptostreptococcus stomatis. Tumor-related genes TRPM4, MYBL2, and CDKN2A were significantly upregulated and correlated with specific bacterial taxa.

CONCLUSION: This study underscores the significant alterations in gut microbiota associated with CRC and reveals novel correlations between specific microbes and host gene expression, offering potential diagnostic markers and therapeutic targets for CRC.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Male
Female
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Feces/microbiology
*Transcriptome
Aged
Gene Expression Profiling

@article {pmid40313408,
year = {2025},
author = {Wang, M and Liu, W and Zheng, L and Ma, S and Jin, L and Zhao, D and Li, D},
title = {Broadening horizons: microbiota as a novel biomarker and potential treatment for endometriosis.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1521216},
pmid = {40313408},
issn = {1664-302X},
abstract = {As a heterogeneous disease, endometriosis is associated with diagnostic delay. Delayed diagnosis, physical discomfort, hormone therapy, and inconvenience in daily life and work all contribute to a decreased quality of life for endometriosis patients. Early clinical diagnosis is highly important for the intervention and treatment of endometriosis. Currently, reliable non-invasive diagnostic methods are lacking, and laparoscopic examination combined with pathological diagnosis is considered the "gold standard" for definitively diagnosing endometriosis. An increasing number of studies have confirmed the correlation between endometriosis and microbial ecological changes. Microbial dysbiosis is an important factor in the development and progression of endometriosis. Certain key microbial species and their metabolites can induce functional alterations in endometrial cells through various mechanisms, often preceding the emergence of clinical symptoms. Endometriosis are chronic inflammatory diseases, with an immunoinflammatory response as the pathological foundation. The microbiome may participate in the pathological mechanisms of endometriosis through multiple pathways, including mediating inflammatory responses, regulating immune responses, participating in estrogen regulation, interfering with metabolic activities, and modulating the gut-brain axis. Therefore, the microbiome holds potential as an early non-invasive diagnostic and therapeutic target for endometriosis patients. This study summarizes and analyses the correlations between microorganisms and their metabolites and the onset of endometriosis, aiming to provide novel insights into the etiology, diagnosis, and treatment of endometriosis.},
}

@article {pmid40313288,
year = {2025},
author = {Katsuhara, Y and Khan, U and Miller, ZA and Allen, IE and Oskotsky, TT and Sirota, M and Tang, AS},
title = {Decoding subphenotypes in electronic medical records within late-onset Alzheimer's disease reveals heterogeneity and sex-specific differences.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.04.24.25326306},
pmid = {40313288},
abstract = {BACKGROUND: Alzheimer's disease is a progressive neurodegenerative disorder with no curative treatment. Identifying distinct subphenotypes and understanding potential personalized modifications remain critical unmet needs.

METHODS: We applied unsupervised learning techniques to electronic medical records from UCSF to identify distinct Alzheimer's disease subphenotypes based on comorbidity profiles. We conducted enrichment analyses to determine cluster-specific comorbidities. Based on the observed sex-based differences, we subsequently conducted sex-stratified analyses to assess differences in disease manifestations between males and females. Findings were validated using an independent UC-Wide dataset.

RESULTS: Among 8,363 patients, we identified five Alzheimer's disease subphenotypes, characterized by comorbidities related to cardiovascular conditions, gastrointestinal disorders, and frailty-related conditions such as pneumonia and pressure ulcers. Sex-stratified analyses revealed significant differences in comorbidity distributions across clusters. Notably, in Cluster 2, circulatory diseases were more prevalent among males, whereas in Cluster 3, bladder stones were more common among females. Key results were consistent across the UCSF and UC-Wide datasets.

CONCLUSIONS: Our study identifies clinically meaningful Alzheimer's disease subphenotypes and highlights sex-specific variations, suggesting potential underlying biological factors such as Apolipoprotein E and gut microbiome alterations contributing to Alzheimer's disease heterogeneity. These findings underscore the need for further research into the biological mechanisms driving these differences and may inform the development of individualized therapeutic regimens.

FUNDING: This study was supported by grants from the National Institute on Aging (R01AG060393 and R01AG057683).},
}

@article {pmid40313234,
year = {2025},
author = {Leibovitzh, H and Fliss Isakov, N and Werner, L and Thurm, T and Hirsch, A and Cohen, NA and Maharshak, N},
title = {A Mushroom Based Prebiotic Supplement Pilot Study Among Patients with Crohn's Disease.},
journal = {Journal of dietary supplements},
volume = {},
number = {},
pages = {1-14},
doi = {10.1080/19390211.2025.2498127},
pmid = {40313234},
issn = {1939-022X},
abstract = {Data on a mushroom based prebiotic supplementation in patients with Crohn's disease (CD) in western population is scarce. In this pilot trial, we aimed to assess the clinical efficacy and fecal microbial compositional and functional alterations associated with 'Mycodigest,' a commercial prebiotic supplement composed of three mushroom extracts. Patients with mild to moderate CD were recruited to a single center, randomized, double-blind, placebo-controlled pilot induction trial. Clinical efficacy using the Harvey-Bradshaw index and biochemical response using C-reactive protein and fecal calprotectin were assessed at week 8 post-intervention. Fecal samples were assessed by DNA shotgun metagenomic sequencing. A multivariable linear mixed effects model was used to assess alteration in fecal microbiome composition and function pre- and post-'Mycodigest' intervention. Clinical response was higher in the 'Mycodigest' intervention (N = 10) compared to the placebo (N = 6) group (80 vs. 16.7%, respectively, p = 0.035). There were no differences in terms of biochemical response within each group pre- and post-intervention. Post-'Mycodigest' intervention, 25 species were found to be differentially abundant compared to baseline, including increase in short chain fatty acid producing bacteria, such as Parabacteroides distasonis (Beta coefficient 0.92, 95% Confidence interval [CI] 0.36-1.47) and Faecalimonas umbilicata (Beta coefficient 0.57, 95% CI 0.23-0.90). Two microbial pathways related to the metabolism of isoprenoid compounds were increased post-'Mycodigest' intervention. Mushroom based prebiotic supplementation in subjects with CD resulted in clinical improvement which may be related to post-intervention favorable compositional and functional microbial alterations.},
}

@article {pmid40313185,
year = {2025},
author = {Li, X and Huang, R and Li, P and Tang, FK and He, J and Sun, H and Wang, X and Wang, M and Lan, X and Wang, X and Wong, SSW and Jin, L and Leung, KC and Wong, HM and Wang, S and Guo, L and Ding, PH and Yu, X},
title = {Berberine-Functionalized Bismuth-Doped Carbon Dots in a Pathogen-Responsive Hydrogel System: A Multifaceted Approach to Combating Periodontal Diseases.},
journal = {ACS nano},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsnano.5c00561},
pmid = {40313185},
issn = {1936-086X},
abstract = {Periodontal disease, a global health burden linked to dysbiotic oral polymicrobial communities and disrupted immune-inflammatory responses, is critically mediated byPorphyromonas gingivalis(Pg)─the keystone pathogen that sabotages host immunity, triggers tissue inflammation and destruction, and disrupts microbiota balance. Effective therapies should combine antimicrobial action, immune modulation, virulence suppression, and microbiome restoration. Bismuth ions and berberine, which exhibit antimicrobial and epithelial barrier-protecting effects, show potential effectiveness in treating periodontal diseases but face practical limitations due to poor water solubility and bioavailability. To address this, we developed bismuth-doped carbon dots functionalized with structure-modified berberine (BiCD-Ber) as a multifunctional nanomedicine. BiCD-Ber eradicated Pg in various forms, restored Pg-perturbed immune responses in gingival fibroblasts, and preserved epithelial barrier integrity. The doped bismuth ions neutralized Pg virulence factors by blocking the catalytic sites of gingipains. To facilitate in vivo delivery, BiCD-Ber was encapsulated in a disulfide-modified hyaluronic acid hydrogel that degrades in response to Pg metabolites. This BiCD-Ber hydrogel system modulated subgingival microbiota, alleviated inflammation in gingiva, and thereby prevented alveolar bone loss. This approach to concurrently eliminating Pg, modulating inflammatory responses , suppressing virulence factors, and restoring microbiota showcases great potential in managing periodontitis effectively.},
}

@article {pmid40312907,
year = {2025},
author = {Zheng, CM and Kang, HW and Moon, S and Byun, YJ and Kim, WT and Choi, YH and Moon, SK and Piao, XM and Yun, SJ},
title = {Optimizing extraction of microbial DNA from urine: Advancing urinary microbiome research in bladder cancer.},
journal = {Investigative and clinical urology},
volume = {66},
number = {3},
pages = {272-280},
doi = {10.4111/icu.20240454},
pmid = {40312907},
issn = {2466-054X},
support = {2020R1I1A3062508/NRF/National Research Foundation of Korea/Korea ; RS-2023-00245919/NRF/National Research Foundation of Korea/Korea ; RS-2024-00342111/NRF/National Research Foundation of Korea/Korea ; 5199990614277/NRF/National Research Foundation of Korea/Korea ; /KHIDI/Korea Health Industry Development Institute/Korea ; },
mesh = {Humans ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/microbiology/urine ; *DNA, Bacterial/isolation & purification/urine ; Male ; Female ; Middle Aged ; *Urine/microbiology ; Aged ; RNA, Ribosomal, 16S ; Reproducibility of Results ; },
abstract = {PURPOSE: This study aimed to evaluate and optimize microbial DNA extraction methods from urine, a non-invasive sample source, to enhance DNA quality, purity, and reliability for urinary microbiome research and biomarker discovery in bladder cancer.

MATERIALS AND METHODS: A total of 302 individuals (258 with genitourinary cancers and 44 with benign urologic diseases) participated in this study. Urine samples were collected via sterile catheterization, resulting in 445 vials for microbial analysis. DNA extraction was performed using three protocols: the standard protocol (SP), water dilution protocol (WDP), and chelation-assisted protocol (CAP). DNA quality (concentration, purity, and contamination levels) was assessed using NanoDrop spectrophotometry. Microbial analysis was conducted on 138 samples (108 cancerous and 30 benign) using 16S rRNA sequencing. Prior to sequencing on the Illumina MiSeq platform, Victor 3 fluorometry was used for validation.

RESULTS: WDP outperformed other methods, achieving significantly higher 260/280 and 260/230 ratios, indicating superior DNA purity and reduced contamination, while maintaining reliable DNA yields. CAP was excluded due to poor performance across all metrics. Microbial abundance was significantly higher in WDP-extracted samples (p<0.0001), whereas SP demonstrated higher alpha diversity indices (p<0.01), likely due to improved detection of low-abundance taxa. Beta diversity analysis showed no significant compositional differences between SP and WDP (p=1.0), supporting the reliability of WDP for microbiome research.

CONCLUSIONS: WDP is a highly effective and reliable method for microbial DNA extraction from urine, ensuring high-quality and reproducible results. Future research should address sample variability and crystal precipitation to further refine microbiome-based diagnostics and therapeutics.},
}

Humans
*Microbiota/genetics
*Urinary Bladder Neoplasms/microbiology/urine
*DNA, Bacterial/isolation & purification/urine
Male
Female
Middle Aged
*Urine/microbiology
Aged
RNA, Ribosomal, 16S
Reproducibility of Results