@article {pmid41082307,
year = {2025},
author = {Gu, W and Wang, J and Yuan, X},
title = {The role of psychosomatic interventions on the immune system and gut microbiome diversity of pregnant women with gestational hypertension.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2025.02688},
pmid = {41082307},
issn = {1588-2640},
abstract = {This study evaluates the impact of psychosomatic interventions on the immune system and microbiome composition of pregnant women diagnosed with gestational hypertension. A case-control study on 200 pregnant women diagnosed with gestational hypertension was conducted between June 2021 and December 2024. The control group (n = 100) included pregnant women diagnosed with gestational hypertension and under only pharmacological treatment with antihypertensive drugs such as labetalol. The case group (n = 100) received standard care for hypertensive disorders in pregnancy like control group, but in addition to it, we incorporated evidence based psychosomatic medicine to this group. Psychosomatic medicine included stress management, relaxation techniques, and counseling for the study group. Primary outcomes included blood pressure levels, psychological state (SAS and SDS scores), mode of delivery, incidence of complications, neonatal outcomes, patient satisfaction, reductions in inflammatory cytokines (e.g., IL-6, TNF-alpha), and improvements in microbiome diversity. Psychosomatic intervention led to a significant increase in microbiome diversity (Shannon Index, P < 0.05). Beta-diversity analysis revealed a distinct separation in microbial community composition between the study and control groups (P = 0.02). The case group also showed a reduction in pro-inflammatory cytokines, IL-6 decreased from 40.0 to 28.0 pg mL-1 (P = 0.008) and TNF-alpha from 25.0 to 18.0 pg mL-1 (P = 0.004). The case group demonstrated significant improvements in systolic (P = 0.020) and diastolic (P = 0.003) blood pressures, psychological well-being (SAS, P = 0.006; SDS: P = 0.026), and delivery outcomes (P = 0.032). Complications were significantly lower in the case group (P = 0.013), with better neonatal outcomes, including lower rates of intrauterine distress (P = 0.011), premature birth (P = 0.003), and asphyxia (P = 0.013). Emotional resilience, coping confidence, and patient satisfaction were significantly higher in the case group (P < 0.05). These findings suggest that psychosomatic medicine may offer a novel approach for managing gestational hypertension through microbiome modulation.},
}

@article {pmid41082164,
year = {2025},
author = {Harrass, S and Quansah, M and Kumar, S and Radzieta, M and Jayawardena, B and Jones, C and David, M and Heng, B and Elbourne, LDH and Amanquah, S and Adjei, P and Capunzo, M and Aliberti, SM and Jensen, SO and Tayebi, M},
title = {Lactobacilli Probiotics Prevent Amyloid-Beta Fibril Formation In Vitro.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41082164},
issn = {1867-1314},
abstract = {Alzheimer's disease (AD) is characterized by the buildup of extracellular aggregated amyloid-β (Aβ) peptides, following sequential enzymatic cleavage of amyloid precursor protein, along with intraneuronal accumulation of hyperphosphorylated Tau proteins and subsequent neuronal loss. Despite extensive research, the precise mechanisms underlying Aβ and Tau-mediated neurodegeneration remain elusive. Inhibiting protein aggregation has been a primary focus for mitigating neuronal toxicity. Probiotics have emerged as a promising preventative measure against cognitive decline in AD, with several in vivo and clinical trials demonstrating the efficacy of select bacterial strains in slowing AD progression. However, these studies lack direct molecular evidence on the effects of probiotics on Aβ aggregation kinetic. Inhibiting protein aggregation is key to reducing neuronal toxicity. While probiotics have shown promise in preventing cognitive decline in Alzheimer's disease, supported by in vivo and clinical studies, direct molecular evidence of their impact on Aβ aggregation kinetics remains lacking. In this study, we conducted bioinformatic and physicochemical assessments, including molecular docking of proteins derived from 13 probiotic strains against Aβ and Tau, identifying four strains predicted to efficiently inhibit Aβ aggregation. Kinetic studies confirmed that both the probiotic formulation and its derived supernatant significantly inhibited the conversion of monomeric Aβ and Tau into aggregated forms. To explore bioavailability, we administered the probiotic formulation to healthy individuals and detected its presence in stool samples, demonstrating survival through the gastrointestinal tract. These findings suggest that specific probiotic strains may serve as therapeutic candidates for targeting Aβ and/or Tau aggregation, with further studies warranted to assess their potential clinical utility in AD.},
}

@article {pmid41082090,
year = {2025},
author = {Sanabani, SS},
title = {The Role of the Microbiome in Endometriosis.},
journal = {Reproductive sciences (Thousand Oaks, Calif.)},
volume = {},
number = {},
pages = {},
pmid = {41082090},
issn = {1933-7205},
support = {2022/09354-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Endometriosis is a chronic gynecological disease characterized by the presence of endometrial-like tissue outside the uterus, leading to pain and infertility. Recent research has highlighted the important role of the microbiome in various health conditions, including endometriosis. The aim of this review is to examine the central role of the microbiome in the development and treatment of endometriosis. Key findings include the influence of the gut microbiota on estrogen metabolism, whereby certain bacteria can increase estrogen levels and systemic inflammation and exacerbate endometriosis. Changes in the vaginal and endometrial microbiota are also associated with the disease, as they influence inflammatory and estrogen-dependent metabolic pathways. Dysbiosis in various microbiomes can affect inflammatory pathways, with a shift in the vaginal microbiota to the upper reproductive tract affecting endometriosis without symptoms. Probiotic interventions show promise in restoring a healthy microbiota and improving outcomes, with clinical trials demonstrating the efficacy of lactobacilli-based medications for pain relief. In addition, diet and lifestyle changes can directly impact the gastrointestinal microbiome, reducing inflammation and potentially influencing endometriosis. Future research should focus on establishing comprehensive microbiome profiles, mechanistic studies and longitudinal studies to discover new therapeutic targets and improve clinical outcomes for women with endometriosis.},
}

@article {pmid41082055,
year = {2025},
author = {Aderolu, AZ and Salam, LB and Lawal, MO and Kabiawu-Mutiu, LF and Bassey, ME and Shobande, MA},
title = {Microbial ecology and functional landscape of black soldier fly larval bioconversion of orange waste: A metataxonomic perspective.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {10},
pages = {377},
pmid = {41082055},
issn = {1573-0972},
mesh = {Animals ; Larva/microbiology/metabolism ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/metabolism/isolation & purification ; Gastrointestinal Microbiome/genetics ; *Simuliidae/microbiology ; *Citrus sinensis/metabolism ; *Diptera/microbiology ; Nigeria ; Metagenome ; Metagenomics ; Phylogeny ; },
abstract = {The accumulation of citrus waste, particularly orange waste (OW), presents significant environmental and economic challenges in Nigeria and worldwide. This study presents the first high-resolution, species-level metataxonomic analysis of OW bioconversion mediated by black soldier fly larvae (BSFL) in a West African context, addressing a critical gap in region-specific microbial ecology. Using long-read PacBio 16S rRNA sequencing and PICRUSt2-based functional prediction, microbial communities were profiled across three ecologically distinct substrates: untreated OW, BSFL gut microbiota (OW-BSFL), and post-digestion frass (OWF). Results revealed a dramatic microbial shift driven by host filtering: the OW-BSFL metagenome was overwhelmingly dominated (> 96%) by Lysinibacillus and Cytobacillus, while OWF exhibited markedly higher diversity (263 species), including Mycolatisynbacter and Sphingobacterium. Functional analysis revealed a significant enrichment of genes associated with carbohydrate (e.g., COG2814, COG0726) and amino acid metabolism (e.g., COG1173, COG0444) in the BSFL gut, indicating an elevated enzymatic processing capacity during waste digestion. In contrast, OWF displayed unique enrichment in genes associated with residual carbohydrate turnover and environmental colonization. This microbial succession highlights the selective enrichment and functional specialization that occur across the substrate-gut-frass continuum. By elucidating keystone taxa and metabolic signatures, the study not only advances understanding of insect-microbiome symbiosis but also provides a microbial blueprint for optimizing waste-to-value strategies. The findings support the deployment of BSFL bioconversion as a scalable, sustainable solution for organic waste valorization and biofertilizer production in sub-Saharan Africa's circular bioeconomy.},
}

Animals
Larva/microbiology/metabolism
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/metabolism/isolation & purification
Gastrointestinal Microbiome/genetics
*Simuliidae/microbiology
*Citrus sinensis/metabolism
*Diptera/microbiology
Nigeria
Metagenome
Metagenomics
Phylogeny

@article {pmid41081862,
year = {2025},
author = {Bandyopadhyay, A and Sarkar, D and Das, A and Das, A},
title = {Intersections of ABO blood group, secretor status, and the gut microbiome: implications for disease susceptibility and therapeutics.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {296},
pmid = {41081862},
issn = {1432-072X},
mesh = {Humans ; *ABO Blood-Group System/genetics/metabolism ; *Gastrointestinal Microbiome ; Disease Susceptibility ; Galactoside 2-alpha-L-fucosyltransferase ; Bacteria/classification/genetics/isolation & purification ; Probiotics ; },
abstract = {The human gut microbiome is a dynamic ecosystem. It is shaped by host factors, including genetic traits such as ABO blood type and associated secretor status (FUT2 gene). In secretor individuals (~ 80% of the population), ABO antigens are expressed on the gut mucosal surfaces. These antigens serve as adhesion sites and nutrient substrates for select microorganisms. Evidence links blood groups to gut microbial ecology, with taxa such as Bacteroidessp., Eubacteriumsp., and Faecalibacterium sp. exhibiting preferential colonization patterns influenced by mechanisms including mucin glycan foraging, pathogen adhesion, and competitive exclusion. ABO blood type further modulates susceptibility to infectious, metabolic, and autoimmune diseases by affecting microbiome composition. Secretor status impacts microbiota diversity and probiotic colonization Non-secretors exhibit altered Bifidobacterium sp. profiles and reduced norovirus adhesion. These insights suggest possible avenues for tailoring microbiome-based interventions; however, current evidence remains preliminary and requires validation through controlled clinical studies. We outline a conceptual model linking host genetics, microbial ecology, and health outcomes, recognizing that these associations are still being mapped. The idea of incorporating blood type and secretor status into precision microbiome approaches remains exploratory and requires rigorous validation.},
}

Humans
*ABO Blood-Group System/genetics/metabolism
*Gastrointestinal Microbiome
Disease Susceptibility
Galactoside 2-alpha-L-fucosyltransferase
Bacteria/classification/genetics/isolation & purification
Probiotics

@article {pmid41081834,
year = {2025},
author = {Olaleye, AC and Oyewusi, HA and Akinyede, KA and Oladipo, OO and Oyeyemi, BF},
title = {Bacterial community structure and secondary metabolite insights from halophiles at Oniru Beach, Lagos.},
journal = {Archives of microbiology},
volume = {207},
number = {11},
pages = {299},
pmid = {41081834},
issn = {1432-072X},
support = {TETFund 2020_2024//Institutional Based Research, TETFunD/ ; },
mesh = {Nigeria ; *Bacteria/classification/metabolism/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Secondary Metabolism ; *Microbiota ; Phylogeny ; High-Throughput Nucleotide Sequencing ; *Seawater/microbiology ; },
abstract = {This study examines the bacterial diversity and potential for secondary metabolite production of halophilic bacteria isolated from Oniru Beach, Lagos, Nigeria, a moderately saline marine environment. Using high-throughput next-generation sequencing, we profiled the bacterial community structure and complemented this with culture-dependent techniques to identify metabolite-producing strains. Physicochemical analysis revealed a slightly alkaline, oligotrophic, and low-oxygen environment enriched with bioactive metals, such as potassium, calcium, and iron, which may influence microbial adaptation and metabolic activity. Taxonomic profiling showed Proteobacteria (53.72%) as the dominant phylum, followed by Bacteroidetes (29.43%), Actinobacteria (3.88%), Deinococci (1.59%), and Firmicutes (1.37%), with Gammaproteobacteria (47.72%) being the most abundant class. Genus-level analysis highlighted Acinetobacter, Chryseobacterium, Stenotrophomonas, Enterobacter, and Pseudomonas as key constituents of this microbial community. Salt-tolerance assays and 16 S rRNA sequencing identified highly halophilic isolates, including Serratia marcescens, Staphylococcus edaphicus and Kurthia gibsonii, which displayed diverse physiological and biochemical adaptations. Gas chromatography-mass spectrometry (GC-MS) revealed a wide range of secondary metabolites, including osmolytes, fatty acids, and sugar alcohols, underscoring the metabolic versatility of these isolates. Overall, this work demonstrates that Oniru Beach hosts a complex halophilic microbiome with specialized ecological adaptations and biotechnological potential, particularly for novel bioactive compound discovery and bioremediation strategies.},
}

Nigeria
*Bacteria/classification/metabolism/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
*Secondary Metabolism
*Microbiota
Phylogeny
High-Throughput Nucleotide Sequencing
*Seawater/microbiology

@article {pmid41081763,
year = {2025},
author = {Wang, X and Feng, S and Chen, H and Zhou, B and Fan, T and Qin, Y and Zhao, L and Jiang, Y and Chen, Y},
title = {Development of an Aptamer/CRISPR-Cas12a-Based Dual-Modal Biosensor for Fusobacterium nucleatum Detection in Non-Invasive Colorectal Cancer Screening.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c04132},
pmid = {41081763},
issn = {1520-6882},
abstract = {Colorectal cancer (CRC) is the third most common cancer and leading cause of cancer-related deaths worldwide. However, current CRC screening methods are complex, invasive, and tend to exhibit low sensitivity. Recent evidence has highlighted gut microbiota dysbiosis, especially elevated Fusobacterium nucleatum levels, as a promising biomarker for CRC. In this study, a sensitive and specific detection platform was developed for F. nucleatum by combining a highly specific aptamer with rolling circle amplification (RCA) and the CRISPR/Cas12a technology. The aptamer enables specific target recognition, while RCA amplifies the target signal, and the Cas12a-mediated cleavage of a fluorescence-quenching substrate generates a quantifiable fluorescence or grayscale signal. Using a microplate reader, this assay achieved a limit of detection (LOD) of 3.68 CFU/mL; furthermore, by incorporating smartphone-assisted ImageJ grayscale analysis, it elevated the LOD to 4.30 CFU/mL, thereby enabling a dual-mode output along with on-site applicability. Additionally, the strong correlation between the two signals allowed for mutual validation. Upon application to clinical fecal samples, the developed method sensitively distinguished CRC patients from healthy controls, and its results correlated with the quantitative polymerase chain reaction results. This triple-synergistic platform, integrating aptamer specificity, RCA amplification, and CRISPR/Cas12a sensitivity, enables the noninvasive, ultrasensitive detection of F. nucleatum, supporting early CRC screening, prognosis monitoring, and microbiome-targeted therapy. Moreover, this approach overcomes the challenges of detecting low-abundance bacteria in early stage CRC and advances the precision of microbiome-based diagnostics for CRC.},
}

@article {pmid41081742,
year = {2025},
author = {Baer, JL and Kajihara, KT and Vilonen, LL and Hall, AJ and Young, CM and Yogi, DK and Medeiros, MCI and Amend, AS and Hynson, NA},
title = {Microbiome spatial scaling varies among members, hosts, and environments across model island ecosystems.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wraf228},
pmid = {41081742},
issn = {1751-7370},
abstract = {The species area relationship is a classic ecological law describing the relationship between habitat increase and the number of species. Species area relationships are resoundingly positive across macrobes such as plants and animals, and emerge through non-exclusive stochastic and deterministic processes including changes in immigration and extinction, drift, and environmental heterogeneity. Due to unique attributes of the microbial lifestyle, they may not abide by similar rules as macrobes, especially when it comes to spatial scaling. We predict that host-associated microbiomes will exhibit shallower species area relationships than free-living microbiomes due to strong host filtering, and that the species area relationships of bacteria will be shallower than fungi due primarily to differences in dispersal ability. We test these predictions in a relatively simple field system where bromeliad phytotelmata comprise aquatic ecosystems that support invertebrates and environmental substrates such as detritus. Larger phytotelmata generate larger habitat islands for microbiomes allowing us to explicitly examine their species area relationships. We find that the species area relationships of free-living and host-associated microbiomes differ, as do those of microbiome members. By assessing the relationship between environmental conditions and richness, and measuring diversity across scales, we posit that these observed differences in species area relationships are owed to differences in realized niches and dispersal abilities among microbes. These findings highlight that the classic laws of biological spatial scaling do not necessarily accurately represent microbiomes, and that the influence of area on diversity appears to be more important for some microbiomes and microbes than others.},
}

@article {pmid41081627,
year = {2025},
author = {Yuan, Q and Yang, Y and Shen, Y and Sun, B and Chen, S and Zheng, C and Lou, Y and Zheng, M},
title = {Exploring the ocular microecology and its role in pterygium based on metagenomics.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0173025},
doi = {10.1128/spectrum.01730-25},
pmid = {41081627},
issn = {2165-0497},
abstract = {Pterygium is a chronic ocular surface condition marked by fibrovascular growth extending from the conjunctiva to the cornea. Emerging evidence suggests that microbial dysbiosis may play a role in its pathogenesis. To elucidate the microbial landscape associated with pterygium, we conducted metagenomic shotgun sequencing on conjunctival sac secretions from 24 patients with pterygium and 23 healthy controls, along with 19 pterygium tissue samples. We observed significantly higher microbial richness in the disease group, with distinct taxonomic profiles compared with healthy and tissue groups. Key species enriched in the disease group included Microbacterium proteolyticum and Bacillus cereus. Functional analyses revealed elevated bacterial motility, chemotaxis, and virulence genes, alongside a notable increase in antibiotic resistance genes such as tetB and AcrAB-TolC. In contrast, pterygium tissue samples showed limited microbial diversity and no detectable virulence or resistance genes. Importantly, the predominance of Vibrio phages in tissue samples, together with the frequent detection of their bacterial host Vibrio diabolicus, suggests a potential region-specific microbial risk factor, particularly relevant in coastal populations. These findings highlight distinct microbiome and functional profiles associated with pterygium, providing new insights into its pathogenesis and possible microbiome-based therapeutic targets.IMPORTANCEUnderstanding how microbial communities contribute to ocular diseases is crucial for advancing both diagnostics and therapy. This study provides the first integrated comparison of healthy ocular surfaces, diseased ocular surfaces, and pterygium tissues, revealing distinct microbial signatures and functional disruptions. The enrichment of specific bacterial taxa, virulence factors, and antibiotic resistance genes in diseased eyes underscores their potential role in shaping local immunity and driving disease progression. Meanwhile, the discovery of distinct viral elements in pterygium tissue expands current understanding of its microecological complexity. These findings lay a theoretical foundation for the development of microbiome-informed diagnostic tools and novel therapeutic interventions for pterygium.},
}

@article {pmid41081530,
year = {2025},
author = {Ayele, H and Jo, J and Begum, K and Hu, C and Le, TM and Alam, MJ and Eubank, TA and Haidacher, SJ and Horvath, T and Hanson, BM and Garey, KW},
title = {A randomized phase 1 study investigating gut microbiome changes with moxifloxacin vs. oral vancomycin: Implications for Clostridioides difficile risk.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf512},
pmid = {41081530},
issn = {1537-6613},
abstract = {BACKGROUND: The epidemic, hypervirulent Clostridioides difficile ribotype (RT) 027 strain is associated with bacterial virulence traits, including faster germination time and resistance to moxifloxacin, a second-generation fluoroquinolone. Although linked to the RT 027 epidemic, studies to understand moxifloxacin as a high-risk antibiotic for C. difficile infection (CDI) are limited. This study assessed the microbial taxonomic profile and metabolomic changes in healthy volunteers given moxifloxacin or oral vancomycin, an antibiotic known to increase CDI risk via gut perturbation.

METHODS: This was a phase 1, nonblinded, randomized clinical trial of healthy volunteers aged 18-40 who received moxifloxacin or vancomycin for 10 days (clinicaltrials.gov NCT06030219). Stool samples were collected at baseline and 12 follow-up visits. Metataxonomics was completed by 16S V1-V3 rRNA sequencing and bile acid metabolites by LC-MS/MS.

RESULTS: Moxifloxacin therapy caused minimal microbial disruption, although changes in bacterial species from the Clostridiales order during-therapy were observed. Secondary bile acid concentrations decreased from Day 0 to Day 7 with moxifloxacin therapy. Vancomycin caused more significant changes in the microbiome, including increased Proteobacteria, decreased Clostridiales abundance, and a longer duration of decreased secondary bile acids.

CONCLUSIONS: Moxifloxacin use was associated with specific microbiome and metabolomic changes increasing CDI risk albeit for a shorter period than vancomycin. This window of vulnerability may help to explain the risk of fluoroquinolones with the faster germination time for RT 027 strains.},
}

@article {pmid41081484,
year = {2025},
author = {Grafanaki, K and Bakoli Sgourou, D and Maniatis, A and Pasmatzi, E},
title = {The exposomal imprint on rosacea: More than skin deep.},
journal = {Journal of the European Academy of Dermatology and Venereology : JEADV},
volume = {},
number = {},
pages = {},
doi = {10.1111/jdv.70112},
pmid = {41081484},
issn = {1468-3083},
abstract = {Rosacea is a chronic, inflammatory dermatosis driven by a complex interplay of genetic, environmental and lifestyle factors, collectively known as the exposome. This review explores how intrinsic contributors such as genetic susceptibility, immune dysregulation, microbiome alterations, hormonal influences and psychosocial stress intersect with extrinsic triggers like ultraviolet radiation (UVR), air pollution, dietary factors, and climate variability to shape rosacea pathogenesis. Recent advances in single-cell transcriptomics have identified fibroblasts as key components of inflammatory and vascular pathways in rosacea. Concurrently, discoveries in non-coding RNAs and RNA modifications reveal subtype-specific molecular signatures and novel biomarkers. Mendelian randomization (MR) studies further reveal causal links between rosacea and autoimmune, metabolic and gastrointestinal comorbidities-that rosacea is more than skin deep. The role of the gut-skin axis, particularly involving small intestinal bacterial overgrowth (SIBO) and Helicobacter pylori infection, reflects the importance of microbial and neuroimmune crosstalk. Disparities in diagnosis and management persist, particularly among individuals with skin of colour (SOC) and those with limited healthcare access. By integrating an exposomal framework, this review advocates for a paradigm shift in rosacea management: from reactive treatment to proactive, exposome-informed intervention. Personalized skincare, microbiome-targeted strategies, dietary modulation and psychosocial support represent emerging pillars in a holistic, precision medicine framework. Future research should prioritize exposome-informed prevention, inclusive care models, and the development of personalized interventiouns that address both cutaneous and systemic facets of rosacea.},
}

@article {pmid41081315,
year = {2025},
author = {Yang, Y and Wang, Z and Wu, R},
title = {Comparison of Three Sympatric Desert Lizards: Digestive Tract Structure, Digestive Enzyme Activities, Gut Microbiota, and Metabolites.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70007},
pmid = {41081315},
issn = {1749-4877},
support = {32260118//National Natural Science Foundation of China/ ; 2023TSYCQNTJ0034//the second group of Tianshan Talent Training Program: Youth Support Talent Project/ ; 2022D01B100//Natural Science Foundation of Xinjiang Uygur Autonomous Region/ ; },
abstract = {The flexibility of digestive tract morphology and the composition of gut microbiota play crucial roles in the environmental adaptation of reptiles. To evaluate the contributions of the dietary niches to the gut microbiota, we performed 16S rDNA sequencing and metabolite profiling for three sympatric lizard species-Teratoscincus roborowskii, Phrynocephalus axillaris, and Eremias roborowskii-and compared their goblet cell and enzyme activities of the digestive tract. The results revealed that goblet cell densities in the stomach body and pylorus were significantly higher in both T. roborowskii and E. roborowskii, which occasionally include fruit in their diets. Lipase activity was significantly higher in the insectivorous P. axillaris, while the α-amylase and cellulase activities were elevated in the omnivorous T. roborowskii and E. roborowskii. All three lizard species shared the same dominant microbiota at the phylum level. However, dietary niche differences led to P. axillaris having a higher abundance of Desulfovibrionaceae, while E. roborowskii had a significantly higher abundance of Bacteroidetes. Metabolomic profiling revealed that the metabolites involved in carbohydrate metabolism were highly upregulated in E. roborowskii, corresponding to the host's diet and metabolic pathways. Notably, a strong correlation was observed between digestive enzymes, gut microbiota, and fecal metabolites. Overall, our study suggests that the dietary niche may promote divergence or convergence of microbiota across host species, facilitating the establishment of host-specific intestinal adaptation strategies. Our findings provide insights into lizard adaptation to extreme deserts from the perspectives of the gut microbiome and digestive physiology.},
}

@article {pmid41081109,
year = {2025},
author = {Liu, Y and Wu, E and Cheng, F and Zhang, M and Rou, Q and Nuertai, Z and Xu, M and Xu, S and Li, M and Zhang, L and Nasiroula, A},
title = {Oropharyngeal microbiome dysbiosis in esophageal squamous cell carcinoma: taxonomic shifts, metabolic reprogramming, and geographic disparities in a high-incidence cohort.},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20009},
pmid = {41081109},
issn = {2167-8359},
mesh = {Humans ; *Esophageal Squamous Cell Carcinoma/microbiology/epidemiology ; Male ; China/epidemiology ; Female ; Middle Aged ; *Esophageal Neoplasms/microbiology/epidemiology ; *Microbiota ; *Dysbiosis/microbiology/epidemiology ; Incidence ; Aged ; RNA, Ribosomal, 16S/genetics ; *Oropharynx/microbiology ; Cohort Studies ; Metabolic Reprogramming ; },
abstract = {BACKGROUND: Esophageal squamous cell carcinoma (ESCC) is a leading cause of cancer mortality globally, with pronounced geographic disparities in incidence. Emerging evidence links oral microbiome dysbiosis to ESCC pathogenesis, yet comprehensive insights into microbial diversity, taxonomic shifts, and functional alterations in high-risk populations remain limited.

METHODS: Using 16S rRNA amplicon sequencing, we compared the oral microbiome of ESCC patients and healthy controls from a high-incidence region in Northwest China. Alpha and beta diversity metrics, taxonomic composition, and predicted functional pathways were analyzed to identify microbial signatures associated with ESCC.

RESULTS: ESCC patients exhibited significantly elevated microbial richness (observed amplicon sequence variants (ASVs), Chao1, ACE; p < 0.05) but comparable Shannon/Simpson diversity to controls. Unique amplicon sequence variants (ASVs) were more prevalent in ESCC samples, and principal component analysis confirmed distinct community structures (p < 0.05). Taxonomically, Streptococcus and Neisseria dominated both groups, but ESCC patients showed enrichment of Gemella (p = 0.0003) and Corynebacterium (p < 0.00001), alongside depletion of Prevotella_7 (p = 0.0002) and Moraxella (p < 0.001). Functional profiling revealed upregulated amino acid metabolism (e.g., beta-alanine and valine degradation) and downregulated carbohydrate metabolism in ESCC-associated microbiota.

CONCLUSION: This study uncovers unique oral microbial signatures in ESCC patients from a high-incidence region, characterized by increased richness, taxon-specific shifts, and metabolic reprogramming favoring amino acid catabolism. These findings highlight the potential of microbial biomarkers for ESCC detection and provide mechanistic insights into microbiome-driven carcinogenesis. The geographic specificity of the cohort underscores the urgency of tailored interventions in high-risk populations and advances our understanding of microbial contributions to esophageal cancer.},
}

Humans
*Esophageal Squamous Cell Carcinoma/microbiology/epidemiology
Male
China/epidemiology
Female
Middle Aged
*Esophageal Neoplasms/microbiology/epidemiology
*Microbiota
*Dysbiosis/microbiology/epidemiology
Incidence
Aged
RNA, Ribosomal, 16S/genetics
*Oropharynx/microbiology
Cohort Studies
Metabolic Reprogramming

@article {pmid41081102,
year = {2025},
author = {Oiler, IM and Linscott, TM and Parent, CE},
title = {Geology correlates with gut microbial community composition in the Mountainsnails (Oreohelicidae: Oreohelix).},
journal = {PeerJ},
volume = {13},
number = {},
pages = {e20080},
pmid = {41081102},
issn = {2167-8359},
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Snails/microbiology ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Idaho ; Soil/chemistry ; Geology ; Calcium Carbonate/metabolism ; },
abstract = {BACKGROUND: Species that require soil mineral macronutrients for survival may depend on specific microbiome communities to aid in nutrient processing. Land snails, which utilize environmental minerals to synthesize a shell of calcium carbonate (CaCO3), may rely on or possess distinct gut microbiome communities depending on soil mineral characteristics. Here, we investigate whether the occurrence of calcareous vs. non-calcareous soils is associated with shifts the composition of the gut microbiome of the calciphilous and highly diverse land snail genus Oreohelix from the Western United States.

METHODS: We collected snail and soil samples from nine sites in central Idaho: five near, and four away from calcium-rich geology. We sequenced the V4 region of the 16S rRNA gene of these samples to assess the gut microbiome compositions of Oreohelix land snails on and off calcium-rich substrates. After data clean-up and filtering we had 68 snail and 25 soil microbiome samples.

RESULTS: We found that snail gut microbiomes differed significantly from the surface soil microbiome, with many amplicon sequence variants being unique and ubiquitous in the snails. We also found small, but significant, differences between snails on and off calcium-rich rocks. Our findings indicate that the gut microbial community assembly process of land snails is complex and does not reflect a simple relationship with the underlying soil microbiome. While we find a pattern of differences associated with the proximity of calcium-rich geology, the snail microbiome communities are likely forming based on a variety of other factors, including diet and host filtering. Furthermore, we found multiple microbial taxa that were ubiquitous in the snails and rare in the nearby substrate microbiomes. Future work should focus on disentangling the role of habitat and the functional importance (or lack thereof) of the microbial taxa that are common to almost every sampled snail.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Snails/microbiology
RNA, Ribosomal, 16S/genetics
*Soil Microbiology
Idaho
Soil/chemistry
Geology
Calcium Carbonate/metabolism

@article {pmid41081074,
year = {2025},
author = {Kotfis, K and Szredzki, P and Maciejewska-Markiewicz, D and Sołek-Pastuszka, J and Wiśniewska, H and Lara, LF and Marlicz, M and Kaczmarczyk, M and Kukla, M and Belina, A and Koulaouzidis, G and Syczewska, M and Jakubczyk, K and Ekstedt, N and Stachowska, E and Kaniewska, M and Rydzewska, G and Łoniewski, I and Koulaouzidis, A and Marlicz, W and Skonieczna-Żydecka, K},
title = {The effect of SARS-CoV-2 infection on the liver function tests: a systematic review and meta-analysis of observational studies.},
journal = {Przeglad gastroenterologiczny},
volume = {20},
number = {3},
pages = {261-271},
pmid = {41081074},
issn = {1895-5770},
abstract = {INTRODUCTION: SARS-CoV-2 infection has been associated with respiratory distress syndrome and hepatic injury. The mechanism of liver injury is not fully understood and may be a combined effect of viral hepatitis, systemic inflammation, gut barrier disruption, microbiome alterations or drug toxicity.

AIM: We carried out a systematic review and meta-analysis to determine whether SARS-CoV-2 infection affects the level of liver-produced molecules: alanine aminotransferase (ALT), aspartate aminotransferase (AST), γ-glutamyl transferase (GGTP), bilirubin, total protein, albumin, and prothrombin (with INR).

METHODS: Ten authors independently searched PubMed and Embase from their inception until 04/03/2021 for observational studies to evaluate whether SARS CoV-2 infection influences the level of liver-produced molecules. This early search aimed to capture changes associated with the initial variants of SARS-CoV-2 before widespread vaccination efforts. Full-text studies in adult humans in which the aim was liver damage were included. Eligible studies included adult populations with more than 30 subjects, and the analysis adhered to PRISMA guidelines. Data extraction involved a thorough process to ensure accuracy, with inconsistencies resolved by senior clinicians. Statistical analysis was conducted using random effects meta-analysis of outcomes for which ≥ 2 studies contributed data, and the risk of bias was assessed using the New Ottawa Scale. The study protocol was registered in the PROSPERO database (CRD42021242958).

RESULTS: The initial search yielded 3180 hits. 2644 studies were excluded as duplicates and/or after evaluation on the title/abstract level. No additional articles were identified via hand search. There were 536 full-text articles reviewed. Overall, the search strategy yielded 252 studies that were included in the meta-analysis.

CONCLUSIONS: The overall mean liver parameter values were not altered compared to physiological values, except for GGTP, lactate dehydrogenase activity, and INR values. In the case of AST, ALT and albumin levels, mean point estimates were close to limit values of standards. SARS-CoV-2 infection triggers gut barrier defects, which results in transient elevation of liver enzymes and clotting times.},
}

@article {pmid41080808,
year = {2025},
author = {Zhang, Z and Huang, W},
title = {Exoskeleton Robot Gait Training and Its Impact on the Gut Microbiota-Brain Axis in Incomplete Spinal Cord Injury Patients: A Narrative Review of Rehabilitation Mechanisms.},
journal = {Journal of multidisciplinary healthcare},
volume = {18},
number = {},
pages = {6411-6430},
pmid = {41080808},
issn = {1178-2390},
abstract = {Exoskeleton robot-assisted gait training represents a significant advancement in neurorehabilitation for patients with incomplete spinal cord injury (iSCI). While its efficacy in improving motor function is increasingly documented, emerging evidence suggests these interventions may exert therapeutic effects through previously unrecognized physiological pathways involving the gut microbiota-brain axis. This review synthesizes current evidence regarding the bidirectional relationship between exoskeleton-based locomotor training and alterations in gut microbiome composition and function in the context of iSCI. Following spinal cord injury, significant dysbiosis occurs, characterized by reduced microbial diversity and altered taxonomic representation, which correlates with neuroinflammation, autonomic dysfunction, and impaired recovery. Exoskeleton-mediated gait rehabilitation appears to partially restore microbial homeostasis through multiple mechanisms, including autonomic nervous system regulation, altered intestinal transit time, modified intestinal barrier integrity, and immunomodulation. These microbiome modifications potentially facilitate neuroplasticity and functional recovery through microbiota-derived metabolites that traverse the blood-brain barrier or communicate via vagal afferents. The integration of metagenomic analysis with functional neuroimaging and detailed autonomic assessment in prospective studies represents a critical research direction. This emerging perspective extends beyond biomechanical rehabilitation, suggesting a comprehensive neurobiological effect that includes modulation of the microbiota-gut-brain axis, with significant implications for optimizing therapeutic strategies for individuals with incomplete spinal cord injury.},
}

@article {pmid41080582,
year = {2025},
author = {Kou, R and Guo, Y and Qin, Z and Xu, X and Liu, Y and Wei, W and Chen, Y and Jian, Z and Lan, B},
title = {Systemic dysregulation of the gut microenvironment plays a pivotal role in the onset and progression of inflammatory bowel disease.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1661386},
pmid = {41080582},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Inflammatory Bowel Diseases/microbiology/immunology/etiology/metabolism/pathology/therapy ; Dysbiosis/immunology ; Animals ; Disease Progression ; Intestinal Mucosa/immunology/microbiology/metabolism/pathology ; Disease Susceptibility ; Cellular Microenvironment ; },
abstract = {Inflammatory bowel disease (IBD) represents a multifaceted, chronic inflammatory condition affecting the gastrointestinal tract, with its underlying pathophysiological mechanisms not yet fully elucidated. Recent research has underscored the pivotal role of the gut microenvironment, a complex ecological system, in the pathogenesis of IBD. This review systematically examines the interactions between gut microenvironment components and their roles in the pathogenesis of IBD. It is now understood that gut dysbiosis results in a decrease in beneficial microbiota, such as Faecalibacterium and Roseburia, along with an increase in pathogenic bacteria, including Adherent-invasive Escherichia coli (AIEC). This microbial imbalance results in a reduction in the production of beneficial metabolites, such as short-chain fatty acids, and the accumulation of detrimental metabolites, thereby directly disrupting the gut microbiome. The resultant gut dysbiosis leads to dysfunction in intestinal stem cells (ISCs) and a reduction in the expression of tight junction (TJ) proteins, thereby further compromising the integrity of the intestinal epithelial barrier. This dysfunction allows microorganisms and harmful metabolites to penetrate the barrier, reaching the submucosal layer, where they activate both innate and adaptive immune responses, thereby initiating a complex immune cascade. Over time, this process leads to a self-sustaining inflammatory cycle that culminates in chronic IBD and potentially contributes to the development of metabolic disorders. This paper examines this cycle, elucidating the interactions among gut microbiota dysbiosis, metabolite alterations, barrier dysfunction, and immune activation that drive the pathogenesis of IBD, while also critically assessing the limitations of current therapeutic strategies. Based on our understanding of the overarching dysregulation of the gut microenvironment, we propose a paradigm shift in IBD from "controlling inflammation" to "restoring intestinal homeostasis", and from "single therapy" to "comprehensive intervention". This integrated approach encompasses microbiome remodeling, metabolite intervention, reconstruction of the immune microenvironment, and repair of barrier function. Such a multidimensional and integrated therapeutic strategy promises to effectively disrupt the pathological feedback loop, restore gut homeostasis, and offer novel theoretical and clinical insights for the precise treatment of IBD and its progression.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Inflammatory Bowel Diseases/microbiology/immunology/etiology/metabolism/pathology/therapy
Dysbiosis/immunology
Animals
Disease Progression
Intestinal Mucosa/immunology/microbiology/metabolism/pathology
Disease Susceptibility
Cellular Microenvironment

@article {pmid41080580,
year = {2025},
author = {Ding, SQ and Lyu, XY and Zhou, SY and Fang, YW and Ji, HX and Li, JY and Lü, HZ},
title = {Metformin-associated gut microbiota remodeling correlates with reinvigorated splenic immunity in aged mice: microbiome-immune crosstalk via the gut-spleen axis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1633486},
pmid = {41080580},
issn = {1664-3224},
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects/immunology ; *Metformin/pharmacology ; *Spleen/immunology/drug effects ; Mice ; Mice, Inbred C57BL ; *Aging/immunology/drug effects ; Cytokines/metabolism ; *Immunosenescence/drug effects ; Male ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND AND AIM: Immunosenescence involves age-related immune decline and chronic inflammation, with the spleen serving as a critical hub for immune dysregulation. While gut microbiota influences systemic immunity, its specific role and the potential existence of a gut-spleen axis in mediating splenic aging remains unclear. Therefore, we investigated whether metformin, a microbiota-modulating geroprotective drug, alleviates splenic immunosenescence in aged mice, specifically exploring the link between gut microbiota remodeling and splenic immune rejuvenation.

METHODS: Aged C57BL/6 mice (15-month-old) received oral metformin (300 mg/kg/day) or vehicle for 5 months. Systemic toxicity and metabolism were monitored. Splenic immune subsets were analyzed using flow cytometry and immunohistochemistry. Gut microbiota composition (16S rRNA sequencing), cytokine levels (RT-qPCR), and functional pathways were assessed.

RESULTS: Metformin caused no hepatorenal toxicity or weight changes. Treated mice exhibited increased cytotoxic T cells (Tc) and macrophages in the spleen, with reduced Th/Tc ratios and M1/M2 polarization. Pro-inflammatory cytokines (Ifng, Il17a, Il1b, Il6) decreased, while anti-inflammatory markers (Arg1, Tgfb1) rose. Gut microbiota showed enriched Akkermansia, Muribaculum, and Duncaniella, but reduced Lactobacillus. Akkermansia/Muribaculum negatively correlated with pro-inflammatory cytokines, whereas Lactobacillus and Lachnospiraceae linked to pro-inflammatory responses. Functional prediction analysis based on 16S rRNA sequencing data indicated upregulation of bile acid metabolism and oxidative phosphorylation pathways.

CONCLUSION: Metformin reshapes the gut microbiota, which is associated with mitigation of age-associated splenic immune dysregulation, favoring anti-inflammatory macrophage polarization and cytotoxic T cell expansion. Critically, our findings establish the gut-spleen axis as a key mediator of splenic immunosenescence and a novel therapeutic target, which positions metformin as a promising microbiota-directed geroprotective agent. Future research should prioritize mechanistic dissection of gut-spleen communication and clinical validation of metformin's geroprotective efficacy in human populations.},
}

Animals
*Gastrointestinal Microbiome/drug effects/immunology
*Metformin/pharmacology
*Spleen/immunology/drug effects
Mice
Mice, Inbred C57BL
*Aging/immunology/drug effects
Cytokines/metabolism
*Immunosenescence/drug effects
Male
RNA, Ribosomal, 16S/genetics

@article {pmid41080576,
year = {2025},
author = {Terrigno, K and Flamholz, ZN and Mahant Mahant, A and Agalliu, I and De Los Santos, J and Ireland, K and Keenan, J and Kazmi, JS and Correa, A and Frenette, PS and Kelly, L and Herold, BC and Manwani, D},
title = {Higher aged neutrophils and differential inflammatory profiles in sickle cell disease patients on chronic transfusion therapy versus those on hydroxyurea.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1671061},
pmid = {41080576},
issn = {1664-3224},
mesh = {Humans ; *Anemia, Sickle Cell/therapy/immunology/blood ; *Hydroxyurea/therapeutic use ; *Neutrophils/immunology/metabolism/drug effects ; Female ; Male ; Cytokines/blood ; Adolescent ; Child ; Inflammation/immunology ; *Antisickling Agents/therapeutic use ; Chemokines/blood ; Gastrointestinal Microbiome ; Child, Preschool ; *Cellular Senescence ; },
abstract = {BACKGROUND: Sickle cell disease (SCD) is characterized by a point mutation in the β globin molecule, causing the sickling of red blood cells, and leading to hemolytic anemia, pain, and end-organ damage. Hydroxyurea (HU) is a cornerstone of SCD patient treatment, while chronic transfusions (CT) are used as part of treatment for more severe SCD. Increases in aged neutrophils and inflammation have been linked to more severe SCD and contribute to vaso-occlusive crises. The current study was designed to test the hypothesis that HU reduces inflammation and aged neutrophils.

STUDY DESIGN: We compared clinical characteristics, aged neutrophils, levels of select cytokines, chemokines, and cell adhesion molecules in the blood and the Shannon diversity index (SDI) and ratio of Firmicutes/Bacteroides (F:B) in stool samples from pediatric SCD patients treated with HU (n=40) versus CT (n=14).

RESULTS: Patients in the HU group had significantly lower total and aged neutrophils (p<0.0001) compared to the CT group and also had lower levels of several chemokines including CXCL10 (IP-10), CCL2 (MCP-1) and CCL4 (MIP-1β) as well as IFN-γ and IL10. Conversely, HU was associated with higher levels of IL-1α, IL-6 and IL-8. There were no significant differences in cell adhesion markers or in markers of gut microbial dysbiosis between treatment groups. In a multivariable linear regression model, only being on CT was associated with increased number of aged neutrophils (p<0.001) whereas being on CT and having a lower SDI were associated with higher total neutrophil count.

DISCUSSION: Lower numbers of total and aged neutrophils and lower levels of several cytokines and chemokines in the HU group highlight the drug's potential to modulate leukocyte activation and recruitment. These findings suggest that adding or maintaining HU therapy in SCD patients undergoing CT could potentially enhance immunologic regulation and warrants further study.},
}

Humans
*Anemia, Sickle Cell/therapy/immunology/blood
*Hydroxyurea/therapeutic use
*Neutrophils/immunology/metabolism/drug effects
Female
Male
Cytokines/blood
Adolescent
Child
Inflammation/immunology
*Antisickling Agents/therapeutic use
Chemokines/blood
Gastrointestinal Microbiome
Child, Preschool
*Cellular Senescence

@article {pmid41080562,
year = {2025},
author = {Zhu, Z and Cheng, Y and Liu, X and Xu, X and Ding, W and Ling, Z and Liu, J and Cai, G},
title = {The microbiota-gut-brain axis in depression: unraveling the relationships and therapeutic opportunities.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1644160},
pmid = {41080562},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Depression/therapy/microbiology/metabolism/etiology ; *Brain/metabolism ; Animals ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Brain-Gut Axis ; },
abstract = {Depression, a highly prevalent and relapsing mental disorder, exacts profound personal and socioeconomic tolls globally, warranting urgent scientific and clinical attention. Emerging evidence from both preclinical models and human clinical investigations has established the microbiota-gut-brain axis (MGBA) as a critical determinant in depression pathogenesis. This intricate bidirectional network integrates gut microbiota with central nervous system function, influencing mental health through mechanisms previously underrecognized. This review systematically synthesizes gut microbiota alterations associated with depression and their impacts on neuroendocrine, neuroimmune, and metabolic pathways. Advanced therapeutic strategies targeting the MGBA are discussed, including probiotics, fecal microbiota transplantation, and artificial intelligence-enabled microbiome interventions for depression management. While challenges in standardization, mechanistic understanding, efficacy and safety remain, MGBA-centered approaches offer a promising shift toward microbiota-based diagnostics and personalized treatments for depression.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Depression/therapy/microbiology/metabolism/etiology
*Brain/metabolism
Animals
Fecal Microbiota Transplantation
Probiotics/therapeutic use
*Brain-Gut Axis

@article {pmid41080527,
year = {2025},
author = {Ghosh, S and Li, Y and Yang, X and Wu, G and Zhang, C and Zhao, L},
title = {Bacterial guilds, not genus-level taxa, mediate the protective effects of time-restricted feeding against high-fat diet-induced obesity in mice.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf127},
pmid = {41080527},
issn = {2730-6151},
abstract = {The gut microbiota functions as a complex adaptive system where microbes form structural modules known as "guilds." Each guild comprises taxonomically distinct microbes that work together as cohesive functional units, contributing to overall system function. Traditional taxon-based microbiome analyses often yield inconsistent associations with disease, limiting mechanistic insights. To address this, we compared guild-based and taxon-based approaches using datasets from a time-restricted feeding (TRF) study in mice. C57BL/6 J male mice were assigned to ad libitum feeding or TRF groups, with metabolic parameters and gut microbiota composition assessed over 12 weeks. Isocaloric TRF improved glucose tolerance and reduced weight gain in high-fat diet (HFD)-fed mice while maintaining metabolic stability in normal-fat diet-fed mice. To examine microbial contributions, 293 prevalent amplicon sequence variants (ASVs) from the 16S rRNA gene's V3-V4 regions were clustered into 34 co-abundance groups (CAGs), representing potential microbial guilds and accounting for 96% of the total sequence abundance. By contrast, the taxon-based approach classified 660 ASVs into 126 genera, capturing only 78% of the total sequence abundance while omitting 22% of sequences representing novel microbes. The 34 CAGs preserved community-level information more effectively than the 66 prevalent genera, as demonstrated by Procrustes analysis. Five CAGs correlated with improved metabolic phenotype under TRF, including unclassifiable ASVs. Notably, two key CAGs exhibited conserved diurnal rhythmicity under TRF. In contrast, ASVs within putative health-relevant genera displayed opposing TRF responses. This study underscores microbial guilds as key mediators of TRF's metabolic benefits and emphasizes the need to recalibrate taxon-based microbiome analysis biomarker discovery.},
}

@article {pmid41080526,
year = {2025},
author = {Fernández-Alonso, MJ and de Celis, M and Belda, I and Palomino, J and García, C and Gaitán, J and Wang, JT and Abdala-Roberts, L and Alfaro, FD and Angulo-Pérez, DF and Arthikala, MK and Chalasani, D and Corwin, J and Gui-Lan, D and Hernandez-Lopez, A and Nanjareddy, K and Nayaka, SC and Pasari, B and Patro, TSSK and Podile, AR and Quijano-Medina, T and Rivera, DS and Sarma, PVSRN and Shaaf, S and Trivedi, P and Yang, Q and Yin, Y and Zaady, E and Zhu, YG and Singh, BK and Delgado-Baquerizo, M and García-Palacios, P and Milla, R},
title = {Native edaphoclimatic regions shape soil communities of crop wild progenitors.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf143},
pmid = {41080526},
issn = {2730-6151},
abstract = {Unveiling the soil biological communities ecologically associated with crop wild progenitors (CWPs) in their habitats of origin is essential for advancing productive and sustainable agriculture. A field survey was conducted to investigate the edaphoclimatic conditions and soil bacterial, fungal, protist, and invertebrate communities of 125 populations of direct progenitors of major crops for world agriculture. The wild populations clustered into four ecoregions shaped by two edaphoclimatic dimensions: one summarizing variations in soil sand contents and nutrients concentrations, and the other featuring changes in aridity, soil pH, and carbon storage potential. We identified a common soil core community across CWPs that varied significantly along deserts to tropical seasonal forests and savannas. The assembly of the soil core community was driven by varying environmental preferences amongst soil biodiversity kingdoms, reflecting potential shifts in their functional profiles. The tropical ecoregion exhibited higher proportion of acidophilic bacteria, fungal, and protist parasites, whilst desert ecosystems harboured greater abundances of saprophytic fungi and heterotrophic protists. Moreover, CWPs displayed unique microhabitats that incorporate variability into the soil community assembly. Our work reveals the biogeography of soil communities associated with CWPs, the first step towards the development of microbial rewilding initiatives.},
}

@article {pmid41080487,
year = {2025},
author = {Boyle, JA and Murphy, B and Teng, F and Babaei Zadeh, P and Ensminger, I and Stinchcombe, JR and Frederickson, ME},
title = {Mutualism Mediates Legume Response to Microbial Climate Legacies.},
journal = {Ecology and evolution},
volume = {15},
number = {10},
pages = {e72271},
pmid = {41080487},
issn = {2045-7758},
abstract = {Climate change is altering both soil microbial communities and the ecological context of plant-microbe interactions. Heat, drought, and their legacies can alter soil microbiomes and potential plant symbionts, but the direct consequences of these microbial changes on plant performance and plant investment in symbiosis remain underexplored. Predicting how soil microbes modulate plant resilience to heat and drought is critical to mitigating the negative effects of climate change on ecosystems and agriculture. In this proof of concept study, we conducted growth chamber experiments to isolate the microbially mediated indirect effects of heat and drought on plant performance and symbiosis. In the first experiment, focused on drought, we found that drought and drought-treated microbes, along with their interaction, significantly decreased the biomass of Medicago lupulina plants compared to well-watered microbiomes and conditions. In a second experiment, we then tested how the addition of a well-known microbial mutualist, Sinorhizobium meliloti, affected heat- and drought-treated microbiomes' impact on M. lupulina. We found that drought-adapted microbiomes negatively impacted legume performance by increasing mortality and reducing branch number, but that adding rhizobia erased differences in plant responses to climate-treated soils. In contrast, heat-adapted microbiomes did not differ significantly from control microbiomes in their effects on a legume. Our results suggest microbial legacy effects, mutualist partners, and their interactions are important in mediating plant responses to drought, with some mutualists equalizing plant responses across microbial legacies.},
}

@article {pmid41080463,
year = {2025},
author = {Sengupta, S and , },
title = {Study research protocol for Phenome India-CSIR Health Cohort Knowledgebase: A prospective multi-modal follow-up study on a nationwide employee cohort.},
journal = {Biology methods & protocols},
volume = {10},
number = {1},
pages = {bpaf061},
pmid = {41080463},
issn = {2396-8923},
abstract = {Predicting individual health trajectories based on risk scores can help formulate effective preventive strategies for diseases and their complications. Currently, most risk prediction algorithms rely on epidemiological data from the Caucasian population, which often do not translate well to the Indian population due to ethnic diversity, differing dietary and lifestyle habits, and unique risk profiles. In this multi-center prospective longitudinal study conducted across India, we aim to address these challenges by developing clinically relevant risk prediction scores for cardio-metabolic diseases specifically tailored to the Indian population. India, which accounts for nearly 18% of the global population, also has a significant diaspora worldwide. This program targets longitudinal collection and bio-banking of samples from over 10 000 employees both working and retirees of the Council of Scientific and Industrial Research and their spouses, with baseline sample collection already completed. During the baseline collection, we gathered multi-parametric data including clinical questionnaires, lifestyle and dietary habits, anthropometric parameters, lung function assessments, liver elastography by Fibroscan, electrocardiogram readings, biochemical data, and molecular assays, including but not limited to genomics, plasma proteomics, metabolomics, and fecal microbiome analysis. In addition to exploring associations between these parameters and their cardio-metabolic outcomes, we plan to employ artificial intelligence algorithms to develop predictive models for phenotypic conditions. This study could pave the way for precision medicine tailored to the Indian population, particularly for the middle-income strata, and help refine the normative values for health and disease indicators in India.},
}

@article {pmid41080302,
year = {2025},
author = {Baloch, MB and Alphonse, C and Baldev, N and Nin-Arroyo, GM and Keezhath, R and Behara, A and Khurana, S and Nwokeji, S and Imam, B and Abarca-Pineda, YA},
title = {Cardiovascular Risk in Autoimmune Diseases: Mechanisms, Management, and Emerging Evidence.},
journal = {Cureus},
volume = {17},
number = {9},
pages = {e91897},
pmid = {41080302},
issn = {2168-8184},
abstract = {Cardiovascular disease is a leading cause of morbidity and mortality among patients with autoimmune disorders. Chronic inflammatory conditions such as rheumatoid arthritis, systemic lupus erythematosus, psoriasis, and inflammatory bowel disease are associated with accelerated atherosclerosis and other vascular complications. Persistent inflammation, dysregulated cytokine networks, and autoantibody-mediated pathways contribute to endothelial dysfunction, pro-thrombotic states, and metabolic disturbances. In addition to traditional risk factors, disease-specific elements such as chronic glucocorticoid exposure and altered lipid profiles influence overall risk. Management strategies emphasize the control of systemic inflammation alongside standard cardiovascular prevention measures. Biologic therapies targeting tumor necrosis factor, interleukin-6, and other inflammatory mediators may attenuate cardiovascular risk by slowing plaque progression. Lifestyle interventions and pharmacologic measures (e.g., statins and antihypertensives) are crucial to mitigate coexisting risks. Emerging evidence from recent cohort studies and clinical trials suggests that these targeted treatments can improve cardiovascular outcomes in autoimmune populations. Advanced vascular imaging and novel biomarkers now allow the earlier detection of subclinical atherosclerosis. Ongoing research into genetic predisposition, the gut microbiome, and new immune pathways offers deeper insight into risk mechanisms. By integrating current pathophysiologic understanding with evolving clinical data, these insights inform strategies for optimizing long-term cardiovascular health in patients with autoimmune disease.},
}

@article {pmid41080185,
year = {2025},
author = {Shahzad, M and Ahmad, HA and Ghani, M and Al Nabhani, Z},
title = {Animal models for understanding the mechanisms of malnutrition: a literature review.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1655811},
pmid = {41080185},
issn = {2296-861X},
abstract = {Malnutrition, encompassing undernutrition, micronutrient deficiencies, and overnutrition, remain a pervasive global health challenge. This underprivileged condition contributes significantly to worldwide morbidity and mortality and causes profound impairments in growth, development, immune function, and metabolic health. Understanding the underlying biological mechanisms is critical, and animal models are indispensable tools for dissecting these complex pathways and for evaluating potential nutritional interventions under controlled conditions that are infeasible in humans. This literature review comprehensively examines rodent models and explores other diverse animal models used to investigate malnutrition, ranging from invertebrates (e.g., Drosophila) and fish (zebrafish) to mammals (piglets and non-human primates). We highlight how each model has yielded mechanistic insights into malnutrition-induced pathophysiology, i.e., from altered metabolic signaling to immune dysfunction and critically evaluate their strengths and limitations in replicating the multifactorial nature of human malnutrition. Key considerations include the extent to which each model mimics human nutritional deficits or excesses, appropriate developmental stages, species-specific metabolic differences, and the influence of comorbid factors such as infection or gut microbiome alterations. We emphasize translational relevance by identifying where animal-derived findings align with clinical observations and where they diverge, underscoring the challenges in extrapolating preclinical results to human disease. Overall, this review provides a comprehensive resource to guide researchers in selecting appropriate animal models and interpreting their findings, with the ultimate goal of enhancing the translation of preclinical insights into improved strategies to address malnutrition.},
}

@article {pmid41080169,
year = {2025},
author = {Lin, X and Li, Z and Zheng, D and Du, R and Zhong, R and Lin, C and Meng, H},
title = {Effects of resistant starch consumption on anthropometric and serum parameters in adults with metabolic syndrome-related risks: a systematic review and meta-analysis.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1655664},
pmid = {41080169},
issn = {2296-861X},
abstract = {BACKGROUND: The effects of resistant starch (RS) consumption on anthropometric and serum biomarkers in adults with metabolic syndrome (MetS)-related risks, each component of which similarly increases the incidence of cardiovascular disease, have yielded inconclusive results when compared to anticipated outcomes. The heterogenous effects of RS type, delivery mode, participant characteristics, intervention conditions, and the quality of study design on the observed outcomes are considered to be insufficiently understood.

METHODS: A comprehensive search was conducted in five public databases and 30 previously published meta-analyses up to January 21, 2025, following the PRISMA guidelines. A total of 23 parallel or crossover randomized controlled trials were included for qualitative analysis via Cochrane Risk of Bias tool and the Jadad scale. Among, 19 studies were included for synthesizing effect sizes of changes in anthropometric parameters, glycemic and lipid profiles, inflammatory markers, and oxidative stress biomarkers using a random-effects model. Subgroup analysis was performed to explore contributes of heterogeneity. Sensitivity analysis and publication bias analysis were conducted.

RESULTS: RS consumption was associated with significant reductions in hip circumference (MD = -1.83 cm; 95% CI: -2.03 to -1.64), total cholesterol (MD = -0.20 mmol/L; 95% CI: -0.32 to -0.08), low-density lipoprotein cholesterol (MD = -0.11 mmol/L; 95% CI: -0.18 to -0.04), and improved superoxide dismutase levels (SMD = 0.29; 95% CI: 0.08-0.51). Waist circumference, fasting insulin, HOMA-IR, and TNF-α were reduced by RS with high heterogeneity yet. High quality of study design, participants with younger age and overweight, a supplement as delivery, a dose of up to 30 g/day, and lasting over 8 weeks partly influenced the effects.

CONCLUSION: Steady effects of RS were observed on hip circumference, total cholesterol, low-density lipoprotein cholesterol, and superoxide dismutase in adults with MetS-related risks. For the intervention with RS, it is recommended that participants be younger and overweight, with a dosage of at least 30 g/day, and over a period of 8 weeks. Future studies should be designed with high methodological quality, with considerations of delivery mode, properties, as well as gut microbiome and metabolome.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251014654 CRD420251014654.},
}

@article {pmid41080149,
year = {2025},
author = {Xu, H and Li, S and Liu, S and Zuo, YG},
title = {A Conceptual Review of Gut, Skin, and Oral Microbiota in Autoimmune Bullous Diseases: From Dysbiosis to Therapeutic Potential.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {13925-13943},
pmid = {41080149},
issn = {1178-7031},
abstract = {Autoimmune bullous diseases (AIBDs), including pemphigus and bullous pemphigoid, are chronic inflammatory skin disorders characterized by dysregulated immune responses mediated by autoantibodies that target adhesion molecules in the skin and mucous membranes. Emerging evidence highlights the pivotal role of host microbiota dysbiosis in AIBDs pathogenesis, offering novel insights into disease mechanisms and therapeutic strategies. This review systematically synthesizes the current findings on gut, skin, and oral microbiota alterations in AIBDs, emphasizing their contributions via the gut-skin axis, microbial metabolites, and pathogen-host interactions. Key innovations include uncovering how specific pathogenic and commensal microbiota influence disease progression through intriguing skin inflammation and direct barrier impairment. Notably, while some microbiota changes overlap with other dermatoses, AIBDs exhibit distinct microbial signatures associated with their unique autoimmune mechanisms targeting adhesion molecules. Furthermore, we explore microbiota-targeted therapies, such as antibiotics, probiotics, and fecal microbiota transplantation, and demonstrate their potential to restore microbial homeostasis and improve clinical outcomes. By integrating multi-omics evidence and clinical data, this review bridges mechanistic insights with translational applications, proposing microbiota modulation as a promising adjunctive therapy for AIBDs. Our analysis identifies critical research gaps, including the need for longitudinal studies and personalized microbial interventions, positioning this review at the forefront of microbiome-inflammation-autoimmunity research.},
}

@article {pmid41080146,
year = {2025},
author = {He, X and Yang, F and Qu, G and Zhang, H and Yi, M and Wang, X and Sun, S},
title = {Integrated microbial and proteomic analysis elucidates quality degradation mechanisms of fresh milk through the industrial processing stage.},
journal = {Food chemistry: X},
volume = {31},
number = {},
pages = {103062},
pmid = {41080146},
issn = {2590-1575},
abstract = {Fresh milk quality deterioration during processing is a major dairy challenge, with microbial-driven protein degradation mechanisms unclear. This study pioneers an integrated microbiome-proteome approach to systematically elucidate the dynamic interplay between microbial succession and protein quality changes during industrial processing. Microbial community analysis revealed oscillatory richness, with 2.3-fold and 1.8-fold increases during pre-treatment (PL) and refrigerated transport (RC), respectively. Pseudomonas (12.4 % → 31.7 %) and Acinetobacter (8.1 % → 19.3 %) dominated key phases, with proteomics showing significant nutrient loss (IgM: -69.8 %; IgG: -54.15 %). Integrating microbial metagenomics with proteolytic pathway analysis identified proteases from Pseudomonas and Acinetobacter as key drivers of protein degradation (68 % activity). Pasteurization cut microbial load by 82 % but paradoxically intensified nutrient loss via protein denaturation. Crucially, our data establish a time-dependent degradation model, revealing that combined microbial enzymatic action and thermal effects account for 76 % of total protein hydrolysis, providing a theoretical framework for developing targeted intervention strategies in dairy processing optimization.},
}

@article {pmid41079947,
year = {2025},
author = {Teh, Z and Garcia-Maurino Alcazar, C and Bhatia, K},
title = {Overcoming barriers to gut microbiome development through nutritional factors in the first 1,000 days of life: strategies and implications for preventing non-communicable diseases.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e18},
pmid = {41079947},
issn = {2632-2897},
abstract = {Current efforts to reduce the incidence of non-communicable disease (NCD) are slow, but increasing evidence highlights the microbiome as a potential target for prevention. The majority of microbial development occurs in the first 1,000 days of life, presenting opportunities for strategic intervention to reduce the prevalence of future NCDs. In this review, we explore the social, structural, and political barriers that may hinder physiological gut microbial development in the first 1,000 days in the context of current scientific knowledge, focusing on nutritional factors in pregnancy, and during the exclusive breastfeeding and complementary feeding periods. We summarise emerging evidence and explore obstacles to nutritional choices affecting microbial development, and unpack the rhetoric that healthy eating to develop a microbiome that supports optimum health is an individual choice. As evidence on the role of the microbiome in health and disease grows, specific attention must be applied to existing social, structural, and political barriers that may hinder optimal microbial development. Addressing the role of corporate actors and social determinants influencing dietary choices and barriers surrounding breastfeeding must be prioritised, alongside efforts to advance basic scientific research. Until a wider public health perspective is taken, the success of interventions and recommendations will be limited.},
}

@article {pmid41079946,
year = {2025},
author = {Campisi, SC and Zhang, F and Seo, M and Muha, J and Schumacher, A and De Luca, I and Bradley-Ridout, G and Merriman, K and Parkinson, J and Korczak, DJ},
title = {The gut microbiome and child and adolescent depression and anxiety: a systematic review and meta-analysis with youth consultation.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e17},
pmid = {41079946},
issn = {2632-2897},
abstract = {Decreased gut microbial diversity is associated with greater depression symptoms in adults. Findings on the relationship between the gut microbiome and depression or anxiety in children and adolescents are mixed, and evidence syntheses are needed. Seven databases were searched for peer-reviewed studies on the gut microbiome and internalizing symptoms, depression, or anxiety, in children and adolescents (<19 years). Random-effects meta-analyses of alpha diversity indices were performed. Youth advisors validated the research findings' relevance to their experiences and contributed to dissemination planning. Eight studies were included, representing 2,865 participants (mean age = 11.4 years, SD = 4.3). Study designs were cross-sectional (n = 5), longitudinal (n = 2), and interventional (n = 1). No association was found between alpha or beta diversity and internalizing problems, depression, or anxiety. Increased abundance of genera within phyla Bacillota (e.g., Fusicatenibacter) and Pseudomonadota (e.g., Escherichia), along with decreased abundance of other Bacillota genera (e.g., Faecalibacterium), were associated with depression and anxiety symptoms. This review identified preliminary associations between specific bacterial taxa and depression and anxiety in children and adolescents. Larger studies using comprehensive analytical approaches are needed to explore the role of the gut microbiome in the genesis and treatment of internalizing disorders.},
}

@article {pmid41079945,
year = {2025},
author = {Mweetwa, MN and Ahsan, K and Louis-Auguste, J and Besa, E and Posma, JM and McNulty, N and Barrat, MJ and Gordon, J and Kelly, P},
title = {Intestinal microbiome changes in response to amino acid and micronutrient supplementation: secondary analysis of the AMAZE trial.},
journal = {Gut microbiome (Cambridge, England)},
volume = {6},
number = {},
pages = {e16},
pmid = {41079945},
issn = {2632-2897},
abstract = {Microbial dysbiosis has been linked to environmental enteropathy (EE) and alterations in nutrient absorption; however, compositional modifications following exposure to supplementary nutrients are poorly understood. Here, we report the effect of amino acid and micronutrient supplementation on the gut microbiome of adults with EE. In the AMAZE trial, adults with EE were randomized to amino acids (AA) and/or micronutrients (MM) for 16 weeks in a 2 × 2 factorial design against placebo. Endoscopy was performed before and after intervention, during which duodenal aspirates were collected as well as fecal samples. 16S rRNA amplicon sequencing was performed on both these samples, and differences in bacterial community composition before and after interventions were investigated using differential abundance analysis, corrected using false discovery rate, plus alpha and beta diversity measurements. HIV seropositive participants exhibited lower alpha and beta diversity at baseline. AA and/or MM supplementation did not show significant changes in abundance or diversity of genera post-intervention compared to placebo. Micronutrient supplementation resulted in an increase in the pyruvate fermentation to acetone MetaCyc pathways compared to the placebo arm. This study provides insights into the responsiveness of the gut microbiome to micronutrient and amino acid supplementation in adults with EE.},
}

@article {pmid41079925,
year = {2025},
author = {Jin, J and Cheng, K and Chen, M and Liang, H and Zhang, W},
title = {Immunotherapy resistance in MASLD-related hepatocellular carcinoma: special immune microenvironment and gut microbiota.},
journal = {International journal of biological sciences},
volume = {21},
number = {13},
pages = {5666-5690},
pmid = {41079925},
issn = {1449-2288},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Carcinoma, Hepatocellular/therapy/immunology/microbiology/etiology ; *Liver Neoplasms/therapy/immunology/microbiology/etiology ; *Immunotherapy/methods ; *Tumor Microenvironment/immunology ; Animals ; *Non-alcoholic Fatty Liver Disease/complications/immunology ; },
abstract = {Obesity represents a major global public health challenge. Consequently, metabolic dysfunction-associated steatotic liver disease (MASLD) has become the primary driver of chronic liver disease globally and is currently the most rapidly accelerating factor contributing to hepatocellular carcinoma (HCC). However, current evidence indicates that immunotherapy, a cornerstone of HCC management, yields suboptimal results specifically in MASLD-related HCC (MASLD-HCC) cases. Various immune components constitute a special immune microenvironment in MASLD-HCC, including heterogeneous myeloid cells, lymphocytes and platelets. Furthermore, disruptions in the intestinal barrier, along with the ectopic presence of intestinal flora and metabolites, also influence the immune microenvironment in MASLD-HCC. Elucidating immune cells functions and their interplay with gut microbiota is critical to deciphering MASLD progression to carcinogenesis and immunotherapy resistance. This review synthesizes current insights into the immune microenvironment and gut microbiome in MASLD-HCC, identifies factors influencing the efficacy of immunotherapy, and summarizes potential therapeutic targets to provide detailed guidance for developing effective immunotherapy strategies for MASLD-HCC.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Carcinoma, Hepatocellular/therapy/immunology/microbiology/etiology
*Liver Neoplasms/therapy/immunology/microbiology/etiology
*Immunotherapy/methods
*Tumor Microenvironment/immunology
Animals
*Non-alcoholic Fatty Liver Disease/complications/immunology

@article {pmid41079904,
year = {2025},
author = {Gao, Y and Li, X and Luo, F and Chen, R and Zhang, X},
title = {Integrative mass spectrometry-driven multi-omics and single cell technologies in ankylosing spondylitis: insights into pathogenesis, biomarker discovery, and precision medicine.},
journal = {Journal of translational autoimmunity},
volume = {11},
number = {},
pages = {100319},
pmid = {41079904},
issn = {2589-9090},
abstract = {Ankylosing spondylitis (AS), a chronic inflammatory arthritis primarily affecting the axial skeleton, presents significant clinical challenges due to its complex pathogenesis, delayed diagnosis, and heterogeneous therapeutic responses. This review highlights the pivotal role of mass spectrometry (MS)-based multi-omics technologies in elucidating AS pathogenesis, identifying disease-specific biomarkers, and advancing precision medicine for AS. The fundamental principles of MS are outlined, encompassing ionization methods like electrospray and matrix-assisted laser desorption/ionization, mass analyzers such as orbitrap and time-of-flight, and separation systems including liquid and gas chromatography. These technologies enable highly sensitive and comprehensive profiling of proteomes, metabolomes, and lipidomes. Proteomics analyses have revealed dysregulated pathways and identified key biomarkers, including complement components, matrix metalloproteinases and the panel "C-reactive protein + serum amyloid A1", for distinguishing active AS from healthy controls and stable AS. Metabolomics studies emphasize disturbances in tryptophan-kynurenine metabolism and gut microbiome-derived metabolites, including short-chain fatty acids, thereby linking microbial imbalance to inflammatory responses. A combination of three metabolites (3-amino-2-piperidone, hypoxanthine, and octadecylamine) has shown promise as serum biomarkers for AS diagnosis. Lipidomics profiling reveals significant changes in phospholipid composition. Furthermore, emerging single cell technologies (e.g., mass cytometry) have dissected immune heterogeneity in AS, revealing chemokine signaling dysregulation in monocyte and T-cell subclusters. Persistent challenges and future advancements, such as data heterogeneity, cohort limitations, and the interpretability of artificial intelligence models for multi-omics integration were discussed. By integrating technological innovation with clinical insights, this review systematically summarizes multiple potential biomarker panels for AS, in which multi-omics-driven strategies facilitate early diagnosis, mechanistic subtyping, and personalized therapies, ultimately improving patient outcomes in AS.},
}

@article {pmid41079737,
year = {2025},
author = {Shan, N and Wang, L and Duan, C and Wu, Y and Jing, Y and Fan, H and Wang, S and Wang, Y and Wang, S and Liu, H and Cheng, K and Liu, L and Liu, S and Zhuang, R},
title = {Pretreatment with Astragalus polysaccharide alleviates heat stroke-induced intestinal injury in mice.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1612852},
pmid = {41079737},
issn = {1663-9812},
abstract = {BACKGROUND: Heat stroke (HS) is a life-threatening illness. For HS, prevention is more important than treatment. Astragalus polysaccharides (APS), a major active ingredient of Astragalus membranaceus (Fisch.) Bunge, has multiple bioactivities, including anti-inflammatory and immunoregulation. This study aimed to evaluate the protective effects of APS on intestinal injury caused by HS.

METHODS: Mice were randomized to different groups. After 1 week of APS treatment, a mouse HS model was constructed and evaluated. Intestinal injury was assessed via histopathological examination, and the inflammation level was quantified via quantitative PCR. Flow cytometry and immunofluorescence analyses were used to detect neutrophil infiltration. Gut microbiota was analyzed via 16S rRNA sequencing. Moreover, network pharmacology was employed to analyze the potential targets and functional enrichment of APS. The apoptosis levels were detected in mouse intestinal tissues and IEC-6 intestinal epithelial cells.

RESULTS: APS pretreatment (50 mg/kg BW) prolonged the survival time, delayed the increasing rate of core temperature, and markedly improved organ injuries of HS mice. APS pretreatment improved the pathological changes in the intestine, inhibited inflammation, and reduced neutrophil infiltration. APS enhances the richness of intestinal flora and may shift microbiota functions, thereby benefiting vitamin B metabolism. Network pharmacology analysis indicated the apoptosis pathway as a potential target of APS. In vivo experiments using mouse HS model and in vitro experiments using IEC-6 cells confirmed the inhibitory effect of APS on apoptosis.

CONCLUSION: The preventive effects of APS on HS-induced intestinal injury include the alteration of intestinal microbiota composition and anti-inflammatory and antiapoptotic capacity.},
}

@article {pmid41079703,
year = {2025},
author = {Akinnola, OO and Samuel, AE and Omonhinmin, CA},
title = {Dataset on characterisation of microbiome of prostate tissue and expressed prostatic secretions.},
journal = {Data in brief},
volume = {63},
number = {},
pages = {112098},
pmid = {41079703},
issn = {2352-3409},
abstract = {Prostate cancer (PCa) is the second most prevalent cancer in men, particularly affecting those of Black African descent. Nigeria currently has the fourth highest risk for PCa mortality in the world. The microbiome of the prostate has emerged as a critical factor in understanding the aetiology and progression of prostate diseases, such as prostate cancer (PCa), benign prostatic hyperplasia (BPH) , benign stromal hyperplasia (BSH) and prostatitis (PRO). This study to comparatively characterise the microbiome present in prostate tissue and expressed prostatic secretion (EPS) from 30 study subjects diagnosed with PCa, BPH, BSH and PRO and sampled from the urology clinic of Lagos State University Teaching Hospital Ikeja. Bacterial species community composition and diversity were analysed based on 16S rRNA metagenome nucleotide data to ensure the accuracy, reproducibility, and broader applicability of microbiological and genomic research. Data information allows for precise identification of organisms at the species or strain level, essential for verifying experimental results and comparisons of the isolated organism's genome with related strains, providing insights into genetic diversity, virulence factors, and metabolic pathways of the sample population microbiome.},
}

@article {pmid41079637,
year = {2025},
author = {Tóth, AG and Nagy, SÁ and Lakatos, I and Solymosi, N and Stágel, A and Paholcsek, M and Posta, K and Gömbös, P and Ferenczi, S and Szőke, Z},
title = {Impact of mycotoxins and glyphosate residue on the gut microbiome and resistome of European fallow deer.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113539},
pmid = {41079637},
issn = {2589-0042},
abstract = {Some mycotoxins and herbicide residues pose threats to animal health. These toxins might affect the gut microbiome of fallow deer. The analyzation of the intestinal content samples of this valuable game species exposed to varying levels of zearalenone (ZEA) and other toxic compounds such as aflatoxin B1, deoxynivalenol, fumonisin B1, and glyphosate residues was performed. Metagenomic analysis revealed significant alterations in the bacterial community composition. Higher ZEA levels were associated with decreased alpha diversity, whereas higher aflatoxin levels had the opposite effect. Changes in the abundance of antibiotic resistance genes (ARGs) were also observed, suggesting a potential link between mycotoxin exposure and antimicrobial resistance. Furthermore, five complete bacterial genomes were assembled from the metagenomic data. These findings highlight the complex interplay between environmental toxins, gut microbiota, and animal health. Understanding these interactions is crucial for developing strategies to mitigate the negative effects of toxin exposure on wildlife populations.},
}

@article {pmid41079634,
year = {2025},
author = {Ren, S and Zhang, D and Shi, X and Li, T and Hu, Q and Feng, Y and Hu, C and Feng, S and Zhu, Y and Gao, F},
title = {Gut virome characteristics associated with early onset of anemia and neurodevelopmental delay in preterm infants.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113578},
pmid = {41079634},
issn = {2589-0042},
abstract = {Early-onset anemia (EOA) and neurodevelopmental delay (NDD) are highly prevalent in preterm infants, causing substantial long-term health impacts. This study aimed to identify distinctive gut virome characteristics and their associations with EOA and NDD. We hypothesized that gut microbial colonization types and bacteriophage profiles may be risk factors for NDD in preterm infants with EOA. Fecal samples from 107 healthy preterm infants within the first week of life underwent virome and 16S rRNA sequencing. Consensus clustering of viral species signatures divided infants into four groups. The high EOA risk group showed significantly higher virome alpha diversity. Enriched Circoviridae sp. and uncultured Caudoviridae phage, along with reduced CRESS virus sp., were linked to elevated NDD risk. Geobacillus virus Tp84-the only bacteriophage exhibiting both temperate and virulent lifestyles-was associated with high EOA risk but low NDD risk. These findings highlight the role of gut virome in EOA and NDD pathogenesis, suggesting potential for targeted bacteriophage-based interventions to mitigate EOA-related NDD in preterm infants.},
}

@article {pmid41079626,
year = {2025},
author = {Papadopoulou, KΚ and Chatzinotas, A and Diaz-Otero, BG and Brader, G and Karpouzas, DG and Garces Ruiz, M and Alonso Prados, JL and Declerck, S and Kellari, LM and Sessitsch, A},
title = {Benefits and challenges of upcoming microbial plant protection applications sustaining planetary health.},
journal = {iScience},
volume = {28},
number = {10},
pages = {113557},
pmid = {41079626},
issn = {2589-0042},
abstract = {Plant disease outbreaks pose severe risks to global food security. Due to climate change, new diseases are expected to emerge, and the current use of chemical pesticides poses risks to environmental and human health. In the last decade, alternative plant protection agents of microbial origin have been developed, which also raise great expectations in the industry. Current products primarily represent individual microbial strains, either fungi or bacteria, which occasionally fail under field conditions due to various factors while their regulatory status differs globally. Recently, more diverse applications have started to emerge, ranging from microbial consortia, phages and protists to microbiome modulation or soil translocation. Integrated solutions, incorporating artificial intelligence are also proposed. In this review, we discuss the opportunities and challenges of these solutions, providing specific examples and discuss the regulatory needs for their market entry as well as their relevance for improving food security and planetary health.},
}

@article {pmid41078999,
year = {2025},
author = {Xu, Q and Huang, Y and Chen, X and Lin, C},
title = {A Cross-Sectional Study on the Relationship Between Urinary Enterolactone and Sleep Quality in American Obese Adults.},
journal = {Nature and science of sleep},
volume = {17},
number = {},
pages = {2529-2540},
pmid = {41078999},
issn = {1179-1608},
abstract = {OBJECTIVE: This study aimed to appraise the association between urinary enterolactone and sleep quality in American obese adults.

METHODS: Our study analyzed data from 913 obese adults (2005-2008) in the National Health and Nutrition Examination Survey (NHANES) database. Enterolactone was tested in urine specimens. The Pittsburgh Sleep Quality Index (PSQI)-like measure reconstructed for NHANES based on prior literature was used to assess sleep quality. Multivariable logistic regression models were used to calculate the associations between urinary enterolactone and sleep quality in American obese adults. We also carried out linear tests utilizing restricted cubic splines to investigate the dose-response relationship between urinary enterolactone and sleep quality. Furthermore, we conducted stratified and interaction analyses to determine whether this relationship remained consistent across various subgroups.

RESULTS: A total of 913 obese participants were included in the analyses. After adjusting for potential confounding factors, each one-unit change in log-transformed urinary enterolactone was associated with 8% lower odds of poor sleep quality (OR=0.92, 95% CI: 0.85-0.99, p=0.027). When urinary enterolactone was presented in tertiles, this inversely correlation became more significant with increasing levels of urinary enterolactone. Moreover, in stratified analyses, the relationship between urinary enterolactone and sleep quality persisted.

CONCLUSION: Urinary enterolactone, an indicator of gut microbiome health, is inversely associated with poor sleep quality in American obese adults.},
}

@article {pmid41078571,
year = {2025},
author = {Nelson, AE and Arbeeva, L and Johnson, K and Savage-Guin, S and Walker, T and Enomoto, M and Stevens, C and Koskinen, M and Cole, T and Aker, S and Thonen-Fleck, C and Azcarate-Peril, MA and Loeser, RF and Renner, JB and Golightly, YM and Lascelles, BDX},
title = {Cross-sectional associations of radiographic multiple joint osteoarthritis and symptoms, laboratory values and the gut microbiota: A multimodal study in humans and pet dogs.},
journal = {Osteoarthritis and cartilage open},
volume = {7},
number = {4},
pages = {100682},
pmid = {41078571},
issn = {2665-9131},
abstract = {OBJECTIVE: To describe the frequency of multiple joint osteoarthritis (MJOA) and symptoms, and associations with fecal microbial diversity and composition, in cohorts of humans and dogs.

DESIGN: Human participants enrolled in the community-based Johnston County Health Study (JoCoHS), and an independent cohort of pet dogs, were included. Questionnaires, functional assessments, standardized multiple joint radiographs, and pain assessments, blood and fecal samples were obtained. Microbiome analysis was done by 16S rRNA amplicon sequencing. MJOA was defined as ≥3 unique joint sites involved; symptom burden was based on self-reported/proxy measures of pain. Descriptive statistics and Spearman correlations with Benjamini-Hochberg correction were used to determine relationships among lab tests, pain, and microbiome diversity measures.

RESULTS: Human participants (n ​= ​100, 63 ​% women, mean age 56 years, mean body mass index 34 ​kg/m[2]) and 115 pet dogs (40 ​% spayed females, 57 ​% neutered males, mean age 8 years, mean weight 27 ​kg) were included; 20 ​% had radiographic MJOA (rMJOA). Microbial α-diversity did not differ between participants with or without rMJOA. However, lower levels of the Christensenellaceae R-7 group and Lachnoclostridium in humans, and the butyrate-producing bacterium, Faecalibacterium in dogs, were moderately correlated with greater pain severity, as were higher levels of Escherichia-Shigella in dogs. Faecalibacterium was more abundant in humans without rMJOA.

CONCLUSIONS: These two cohorts demonstrated remarkably similar frequencies of rMJOA (∼20 ​%), supporting the use of dogs to model naturally occurring MJOA. Taxa potentially related to rMJOA and pain were identified in this preliminary analysis, providing new insights into links between dysbiosis and MJOA.},
}

@article {pmid41078567,
year = {2025},
author = {Cavaillon, JM and Carlet, J},
title = {Reassessing sepsis research: new clues for old players and new players for an old symptom to improve patient outcomes.},
journal = {EXCLI journal},
volume = {24},
number = {},
pages = {1143-1192},
pmid = {41078567},
issn = {1611-2156},
abstract = {Sepsis remains a global health problem that causes millions of deaths each year. A rapid and accurate diagnosis is highly desired to allow a rapid use of appropriate antibiotics. A better understanding of the associated pathophysiology has been achieved these recent years. The initial appropriate immune response to infection evolves towards an overwhelmed inflammatory response involving both pro- and anti-inflammatory players that act concomitantly. It also includes cell deaths and cellular dysfunctions of leukocytes, endothelial cells and epithelial cells, associated with mitochondrial dysfunction. These dysregulations are responsible for organ impairment and alteration of immune status of circulating leukocytes. In contrast, within the tissues, an over-activation exists as illustrated by transcriptomic analyses of organs of patients deceased of sepsis, and revealed by the presence of a macrophage activation syndrome within the bone marrow. Despite progresses in understanding the mechanisms underlying sepsis and despite successful therapies in animal models, no real new therapies have emerged these recent decades. This failure may reflect the yin yang aspect of the same players of the host response such as fever, release of cytokines, or coagulation which can display both a beneficial or a detrimental role. Great hopes are now expected from precision medicine, based on patients' endotypes which should help to decipher the patient's sub-groups who could benefit from the different treatments, or to define some appropriate time windows for a given treatment. See also the graphical abstract(Fig. 1).},
}

@article {pmid41078547,
year = {2025},
author = {Hussain, A and Mojgani, N and Shah, SMA and Kousar, N and Ali, SA},
title = {The emerging role of probiotics in the management and treatment of diabetic foot ulcer: a comprehensive review.},
journal = {AIMS microbiology},
volume = {11},
number = {3},
pages = {649-678},
pmid = {41078547},
issn = {2471-1888},
abstract = {Diabetic foot ulcer (DFU) is a complex complication characterized by tissue damage and neurological problems in the lower extremities. Poor wound healing intensifies the severity of DFU, which currently has a 15%-20% prevalence and thus poses a significant healthcare challenge. DFU treatment is often considered complicated due to multifaceted problems, including high cost, low stability, and prolonged healing time. Thus, there is a need to find multidisciplinary, cost-effective, and potential treatment options. In parallel, the role of skin and gut microbiota has been highlighted, influencing the progression of DFU. Probiotics, when used in sufficient amounts, confer a health benefit to the host and are found to have a promising treatment potential for DFU. Probiotics exert beneficial effects that help to improve the management and healing of DFU, following various mechanisms like controlling hyperglycemia, enhancing immune function, modulating the microbiota, and maintaining glucose homeostasis, all of which contribute to improved management and healing of DFU. Despite the potential of probiotics in DFU treatment, their precise mechanisms, optimal strains, dosages, and experimental validation remain underexplored. To fully explore the probiotic potential for DFU, extensive animal studies and clinical trials are needed. This article provides a comprehensive overview of the current status of DFU, existing treatment options, current limitations, and the growing importance of probiotic therapy. It also emphasizes the application of advanced technologies, including artificial intelligence (AI) and machine learning (ML), in advancing DFU treatment strategies.},
}

@article {pmid41078543,
year = {2025},
author = {Vijayaram, S and Mahendran, K and Razafindralambo, H and Ringø, E and Kannan, S and Sun, YZ},
title = {Probiotics, gut microbiota, and brain health: Exploring therapeutic pathways.},
journal = {AIMS microbiology},
volume = {11},
number = {3},
pages = {501-541},
pmid = {41078543},
issn = {2471-1888},
abstract = {The gut microbiome plays a significant role in regulating gastrointestinal (GI) function and modulating the gut-brain axis, which describes the bidirectional communication between the GI tract and the central nervous system (CNS). Its involvement in digestion, immunity, and neurophysiology is well recognized. This study offers novel insights by focusing on psychobiotics, a class of probiotics with targeted neuroactive properties. These microorganisms influence brain function through defined mechanisms, including modulation of neuroinflammation, neurotransmitter production (GABA, serotonin), regulation of the hypothalamic-pituitary-adrenal (HPA) axis, and vagus nerve signaling. Our work critically examines recent advances in applications of psychobiotics for neurological disorders such as Parkinson's disease, Alzheimer's disease, multiple sclerosis, and autism spectrum disorder. By integrating evidence from microbiome research, neuroimmunology, and clinical studies, we identify promising microbial strains and mechanistic pathways with therapeutic potential. This study contributes original perspectives by highlighting underexplored microbe-host interactions and proposing targeted microbial interventions as adjuncts to conventional neurotherapies. Further research is needed to validate strain-specific effects, long-term efficacy, and safety profiles in clinical settings.},
}

@article {pmid41078532,
year = {2025},
author = {Taha, H and Issa, A and Muhanna, Z and Al-Shehab, M and Wadi, T and Awamleh, S and Ateiwi, YA and Abusido, M and Berggren, V},
title = {Microbiota-based interventions for autism spectrum disorder: a systematic review of efficacy and clinical potential.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1648118},
pmid = {41078532},
issn = {1664-302X},
abstract = {PURPOSE: Autism spectrum disorder (ASD) is increasingly linked to gut microbiota imbalances, influencing both behavioral and gastrointestinal (GI) symptoms. This systematic review assesses the efficacy of microbiota-based interventions, including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation (FMT), in improving ASD-related symptoms, aiming to provide insights into their therapeutic potential and inform future clinical applications.

METHODS: A comprehensive systematic review was conducted following PRISMA guidelines and registered in PROSPERO (CRD42024615043). A structured literature search was performed in PubMed, Cochrane Library, and Scopus to identify peer-reviewed English-language studies. Eligible studies included randomized controlled trials (RCTs), non-randomized trials (NRTs), and retrospective studies assessing the impact of microbiota-based interventions on ASD-related behavioral and GI outcomes. Two independent reviewers conducted study selection, data extraction, and quality assessment using standardized risk-of-bias tools.

RESULTS: 33 studies were included, consisting of 16 RCTs, 14 NRTs, and 3 retrospective studies. Among them, 15 assessed probiotics, 4 prebiotics, 5 synbiotics, and 9 FMT. Probiotics showed moderate behavioral improvements in ASD, with multi-strain formulations being more effective than single strains. Prebiotics and synbiotics yielded mixed results, with some studies indicating benefits in behavioral and GI symptoms. FMT demonstrated the most consistent and sustained improvements in both ASD-related behaviors and GI function. Adverse events were minimal, primarily involving transient GI symptoms.

CONCLUSION: Microbiota-targeted interventions, particularly FMT, hold promise for managing ASD symptoms, though probiotics, prebiotics, and synbiotics present variable efficacy. Standardized protocols, larger controlled trials, and personalized microbiome-based approaches are necessary to refine these therapeutic strategies and enhance clinical applicability.

https://www.crd.york.ac.uk/PROSPERO/view/CRD42024615043, identifier CRD42024615043.},
}

@article {pmid41078529,
year = {2025},
author = {Ceretto, A and Weinig, C},
title = {Rhizosphere microbiomes of field-grown B. stricta exhibit minimal diel changes in microbial membership and protein synthesis potential.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1609057},
pmid = {41078529},
issn = {1664-302X},
abstract = {The rhizosphere microbiome has a significant impact on plant health and fitness. Quantifying bacterial responses to fine-scale plant-mediated changes in the rhizosphere, such as those associated with diel cycling in host plant physiology, will increase our understanding of microbial community assembly patterns. Here, we used 16S rRNA biomarker gene (DNA) and transcript (RNA) sequencing to characterize changes in the rhizosphere community membership and PSP over short timescales in field-grown Boechera stricta (B. stricta) plants. Microbial communities characterized by 16S-rRNA-transcripts, which serve as a proxy for microbial protein synthesis potential (PSP), showed greater sensitivity to fine-scale environmental changes than did communities characterized by 16S-rRNA biomarker gene sequencing, which reflects microbial presence/absence. Significant differences were observed between communities characterized by RNA vs. DNA, with RNA-derived communities showing greater alpha and beta diversity differences between the rhizosphere vs. control soil communities within phyla and in differential abundance analysis of genera. Communities reconstructed from RNA were more sensitive to the effects of field blocks and collection timepoints. Differential abundance analysis revealed significant differences (p < 0.05) between the pre-dawn (AM) and early afternoon (PM) timepoints for five genera based on 16S rRNA transcripts. This included the plant-associated genus Curtobacterium. However, when variance was partitioned between days of collection, the amplitude of the signal between diel timepoints was non-significant. In summary, community composition and protein synthesis potential were highly sensitive to abiotic factors expressed over the small spatial scale of field blocks and short 24-h periods between collection days but showed minimal to no diel patterning.},
}

@article {pmid41078525,
year = {2025},
author = {Taggart, MG and Baah, DS and Allen, S and Khan, Z and Arnscheidt, J and Jordan, P and O'Hagan, BMG and Ibrahim, AD and Rao, JR and Ternan, NG},
title = {Fitting soil extracellular enzyme activity into the complex network of abiotic and biotic soil properties often associated with soil health.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1638267},
pmid = {41078525},
issn = {1664-302X},
abstract = {In this mini review we examine how soil extracellular enzymes play a key role in nutrient cycling, but stress that their activity alone does not fully represent ecosystem processes. We emphasize the need for more contextual environmental data-such as pH, temperature, moisture and nutrient availability-for accurate interpretation of the significance of enzyme activity in carbon and nutrient (N, P) cycling in soil ecosystems. The importance of enzymes within the soil microbiome determines its inherent capacity to support crop growth and often reflects soil quality and soil health, which are in turn governed by multiple different soil properties. Soil enzymes (e.g., phosphatase, glucosidases, glycosaminidases) activity have been used as key soil health bio indicators for monitoring soil nutrient transformations in overgeneralized statements. Although soil enzymes constitute important attributes that are closely linked to the dynamics of soil nutrient transformation and make nutrients available to plants, we suggest a multi-factor assessment for soil health measurement. We propose that this can give a pulse reading of soil nutrient health at crucial times of soil, land use, and crop management practices but that care is required to incorporate temporal soil and land use properties for correct interpretation.},
}

@article {pmid41078520,
year = {2025},
author = {Mumtaz, MZ and Castellane, TCL and Shahid, I and Tamburini, E and Bouizgarne, B},
title = {Editorial: Plant mineral microbe interactions.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1677458},
doi = {10.3389/fmicb.2025.1677458},
pmid = {41078520},
issn = {1664-302X},
}

@article {pmid41078518,
year = {2025},
author = {Liu, J and Wang, L and Su, L and Chen, J and Su, R},
title = {Exploring the gut microbiota-Parkinson's disease link: preliminary insights from metagenomics and Mendelian randomization.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1654418},
pmid = {41078518},
issn = {1664-302X},
abstract = {INTRODUCTION: The relationship between the gut microbiome and Parkinson's disease (PD) has recently attracted significant attention, with most studies focused on analyzing microbial composition. However, our understanding of the potential causal relationship between the gut microbiota and PD remains limited.

METHODS: We extracted microbiome data from the metagenome for broad taxonomic coverage and accurate functional analysis. Subsequently, Mendelian randomization was employed to elucidate the causal relationship between the gut microbiome and PD.

RESULTS: The gut microbiota in PD patients was found to be systemically imbalanced, characterized by an abnormal enrichment of potential pathogenic bacteria, a significant reduction in key beneficial bacteria, and a reorganization of intestinal metabolic functions. This state of imbalance involves significant abnormalities in multiple metabolic and regulatory pathways, including the glucose metabolism, oxidative stress response, protein homeostasis regulation, and immune signaling pathways. These findings suggest that dysbiosis may influence host neural function through multilevel metabolic interventions. Additionally, specific microbial communities are clearly associated with disease risk, with some bacterial populations promoting disease onset and others demonstrating a potentially protective effect. Although metagenomic findings require validation in larger cohorts, the results of this study indicate that changes in gut microbiota composition and function are closely related to PD onset and progression.

CONCLUSION: This study revealed that certain microorganisms traditionally considered beneficial may contribute to PD risk. This finding challenges previous assumptions and highlights the complexity of host-microbiome interactions. The identification of altered metabolic and immune pathways, particularly those involving bacteria that produce short-chain fatty acids, underscores the critical role of the gut microbiota in PD pathophysiology. However, the relatively small sample size of the current metagenomic analysis limits the generalizability of these findings. Larger, more diverse cohorts are needed to validate these results. Despite this limitation, the study provides important insights into microbiome-targeted therapeutic strategies, emphasizing the need to reconsider the roles of both beneficial and harmful microorganisms in PD.},
}

@article {pmid41078508,
year = {2025},
author = {Huang, B and Li, B and Pan, G and Huang, D and Yang, G and Ma, Y and Ya, F and Rao, M and Wei, Y},
title = {Bacillus amyloliquefaciens G02 enhances selenium uptake in lettuce (Lactuca sativa) by improving soil selenium availability and rhizosphere microbiome regulation.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1656037},
pmid = {41078508},
issn = {1664-302X},
abstract = {Selenium (Se) is an essential trace element for human, but its low availability in soils results in its inadequacy in edible crops, thereby limiting its human intake. However, the role of the plant growth-promoting bacteria in soil Se availability and the pathways involved in biofortification in edible plants remain poorly understood. In this study, a Se-tolerant, plant growth-promoting bacterium, Bacillus amyloliquefaciens strain G02, which activates Se was isolated from the soils in Se-rich fields in Guangxi, China. We employed soil microcosm and potted experiments, along with metabolomics and 16S rRNA sequencing, to investigate how strain G02 incubation promotes elemental Se (0) solubilization, soil Se activation, and Se enrichment in lettuce. The strain G02 exhibited high phosphate solubilization (87.36 mg/L), IAA production (8.35 mg/L), as well as siderophore and ACC deaminase activities. Strain G02 is capable of dissolved Se(0) and Se minerals, increased pH, and secreted metabolites enhancing Se solubility. Soil microcosm experiments showed that the incubation of strain G02 increased available Se forms [soluble selenium (SOL-Se) and exchangeable selenium (EXC-Se)] in soil. Moreover, potted experiments revealed that the incubation of strain G02 increased biomass, Se concentration in lettuce, soil enzyme activities, beneficial microbial abundance and the native bacterial taxa. The strain G02 enhances soil Se availability through metabolites secretion, Se solubilization, and rhizosphere microbial regulation, improving ability of lettuce to absorb and transport Se. This study provides novel insights into the microbially mediated Se biofortification.},
}

@article {pmid41078442,
year = {2025},
author = {Yang, J and Chen, J and Liu, Z and Qu, Y and Yue, X and Yuan, B and Li, M},
title = {The Role of the Intestinal Microbiome in the Pathogenesis and Treatment of Hyperuricemia: A Review.},
journal = {Food science & nutrition},
volume = {13},
number = {10},
pages = {e70982},
pmid = {41078442},
issn = {2048-7177},
abstract = {Hyperuricemia (HUA), characterized by elevated blood uric acid (UA) levels, is a major risk factor for gout, UA nephropathy, metabolic syndrome, and other related disorders. Traditional drug therapy for HUA includes medications (e.g., allopurinol and febuxostat) and dietary changes; however, it is limited and may be accompanied by adverse side effects such as allergies, prompting the investigation of alternative therapeutic approaches. Although the newly researched "in-situ graft polymerization" protein drug modification technology and the emerging gut microbiota transplantation technology have demonstrated innovation in regulating blood UA, they still need to overcome bottlenecks in immunogenicity, individual variability, and formulation technology. Recent research has highlighted the potential of modulating the intestinal microbiome as a promising strategy for managing HUA. Nevertheless, the mechanism by which different intestinal microbiomes affect HUA pathogenesis remains unclear. To bridge this gap, this review firstly outlines the characteristics and prevailing conditions of HUA, followed by the current status of treatment. Besides, this review integrates the findings from clinical trials and animal studies to explore in depth the pathogenic mechanisms of HUA and the potential roles and regulatory pathways of the gut microbiota in mitigating HUA. The gut microbiota act as multi-functional factors that affect HUA by reducing UA production, enhancing purine metabolism, influencing amino acid transport, and increasing UA excretion. This review addresses critical gaps in the extant literature regarding microbiota-mediated UA homeostasis and provides new perspectives for the future treatment of HUA.},
}

@article {pmid41078363,
year = {2025},
author = {Su, S and Ni, X and Lin, Y},
title = {The oral-gut microbiota axis in cardiovascular diseases: mechanisms, therapeutic targets, and translational challenges.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1658502},
pmid = {41078363},
issn = {2235-2988},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cardiovascular Diseases/microbiology/therapy/etiology ; *Dysbiosis/complications/microbiology ; *Mouth/microbiology ; Animals ; },
abstract = {The oral-gut microbiota axis, a newly recognized regulatory system, has emerged as a pivotal factor in the development of cardiovascular diseases (CVDs). This review comprehensively synthesizes the latest evidence on how the dysbiosis of oral and gut microbiota, along with their metabolic and immunological cross-talk, contributes to CVD pathogenesis, including atherosclerosis, hypertension, and heart failure. We highlight the novel "microbiota-metabolism-immunity"tri-dimensional regulatory network and explore innovative therapeutic strategies, such as precision microbiome modulation and non-invasive biomarker development. By bridging the gap between basic research and clinical translation, this review provides new insights into preventing and treating CVDs through targeting the oral-gut axis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cardiovascular Diseases/microbiology/therapy/etiology
*Dysbiosis/complications/microbiology
*Mouth/microbiology
Animals

@article {pmid41078307,
year = {2025},
author = {He, H and Xiao, M and Song, L and Tian, Y and Jia, Y},
title = {Lipidome-microbiome crosstalk as an outer niche in the skin: regulatory networks in health and disease.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf353},
pmid = {41078307},
issn = {1365-2133},
support = {//Beijing Technology and Business University/ ; //Beijing Municipal Education Commission/ ; 32100254//National Science Foundation of China/ ; },
abstract = {The skin is the outermost barrier to organisms from the external environment. This natural role, endowed by evolution, results in a nutrient-poor skin surface that enables microbial nutrition-dependent lipids to shape microbial ecology by survival pressure and nutrient preference. In turn, the skin microbiota produce microorganism-metabolized bioactive molecules (MBMs) to increase molecular diversity. This crosstalk functions as a crucial component of niche-regulating skin properties via multiple mechanisms. Furthermore, the local and remote effects of different barrier sites provide a more comprehensive explanation for the crosstalk from a global perspective. The variable function and mechanism of crosstalk may represent an evolutionary means by which the skin uses fluctuating commensal signals - the highly dynamic MBMs - to calibrate skin status and provide heterologous protection against invasive pathogens. Elucidating the reasons for the differing selectivity and catalytic efficiency of lipid-metabolizing enzymes in microorganisms and revealing the biologic processes and regulatory mechanisms of the 'co-metabolic systems' on the skin will advance diagnostic and therapeutic strategies for local cutaneous disorders and comorbid diseases of distant organs.},
}

@article {pmid41078233,
year = {2025},
author = {Ardila, CM and Vivares-Builes, AM and Pineda-Vélez, E},
title = {Molecular Biomarkers and Machine Learning in Oral Cancer: A Systematic Review and Meta-Analysis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70121},
pmid = {41078233},
issn = {1601-0825},
abstract = {OBJECTIVE: This systematic review and meta-analysis aimed to synthesize diagnostic and prognostic performance metrics of machine learning (ML)-based biomarker models in oral squamous cell carcinoma (OSCC) and to integrate biological insights through a functional metasynthesis.

METHODS: Following PRISMA 2020 guidelines, a comprehensive search was conducted up to July 2025. Eligible studies applied ML algorithms to molecular or imaging biomarkers from OSCC patients. Data synthesis incorporated meta-analysis when endpoints and designs were sufficiently comparable; otherwise, study-level results were summarized narratively.

RESULTS: Twenty-five studies encompassing 4408 patients were included. Diagnostic performance was strongest for salivary DNA methylation (AUC up to 1.00), metabolomics (AUC ≈0.92), and FTIR imaging (AUC ≈0.91), while autoantibody and microbiome models showed more variable accuracy. Prognostic models based on immune-feature signatures outperformed conventional scores, while multimodal approaches integrating imaging and metabolomics retained strong performance under external validation. Models based on pathomics and MRI radiomics also achieved clinically meaningful accuracy across independent cohorts. Functional metasynthesis revealed convergent biological processes-metabolic reprogramming, immune-inflammatory remodeling, microbiome dysbiosis, and epithelial/extracellular matrix disruption-that underpin predictive accuracy.

CONCLUSION: ML models leveraging molecular and imaging biomarkers show strong potential to improve OSCC diagnosis, risk stratification, and prognosis, particularly through multimodal integration.},
}

@article {pmid41078163,
year = {2025},
author = {Turpin, W and Kalili, H and Halfvarson, J and Croitoru, K},
title = {IBD Prediction Is Possible, but How Far Are We from Implementing It?.},
journal = {Inflammatory bowel diseases},
volume = {31},
number = {Supplement_2},
pages = {S41-S50},
doi = {10.1093/ibd/izaf197},
pmid = {41078163},
issn = {1536-4844},
support = {//Crohn's and Colitis Canada/ ; CMF108031/CAPMC/CIHR/Canada ; //Helmsley Charitable Trust/ ; //Canada Research Chair in Inflammatory Bowel Diseases/ ; 2020-02021//Swedish Research Council/ ; //Crohn's and Colitis Foundation/ ; },
mesh = {Humans ; *Biomarkers/analysis ; *Inflammatory Bowel Diseases/diagnosis ; Metabolomics ; Proteomics ; Risk Assessment ; },
abstract = {Crohn's disease and ulcerative colitis, collectively known as inflammatory bowel diseases (IBDs), are chronic gastrointestinal diseases with poorly characterized pathophysiology. Recent advancements in the identification of preclinical biomarkers of IBD have shed some insight into our ability to predict or prevent these conditions. This review discusses the growing body of research on biomarkers ranging from genetics, measures of gut permeability, and microbiome signatures to circulating proteomics and metabolomics. In addition, the review will highlight the potential application of these biomarkers for early detection and risk stratification of IBD. Notably, proteomic markers such as CXCL9 and MMP-10, along with metabolic perturbations detectable prior to clinical diagnosis, provide promising avenues for understanding IBD pathogenesis and guiding prevention strategies. Furthermore, the development of integrative risk scores, combining multiomic data with demographic and lifestyle factors, could offer a personalized approach to disease prediction and prevention. While these advances present significant opportunities, challenges remain in data complexity and variability of biomarkers. This review emphasizes the importance of continued longitudinal studies and clinical trials to validate predictive models. Ultimately, the integration of early risk prediction holds the potential to reduce IBD incidence through targeted, proactive strategies.},
}

Humans
*Biomarkers/analysis
*Inflammatory Bowel Diseases/diagnosis
Metabolomics
Proteomics
Risk Assessment

@article {pmid41078161,
year = {2025},
author = {Ribeiro-Mourão, F and Agrawal, M and Torres, J and Peter, I},
title = {Intervention(s) in the Early-Life Period to Modulate Inflammatory Bowel Disease Risk: What Could Be the Impact?.},
journal = {Inflammatory bowel diseases},
volume = {31},
number = {Supplement_2},
pages = {S27-S40},
doi = {10.1093/ibd/izaf205},
pmid = {41078161},
issn = {1536-4844},
support = {101194780//Innovative Health Initiative Joint Undertaking/ ; },
mesh = {Humans ; *Inflammatory Bowel Diseases/prevention & control/etiology ; Pregnancy ; Female ; Gastrointestinal Microbiome ; Risk Factors ; Breast Feeding ; *Prenatal Exposure Delayed Effects/prevention & control ; Infant, Newborn ; },
abstract = {The rising incidence of pediatric-onset inflammatory bowel disease (IBD) has intensified focus on the early-life period as a critical window for prevention. Accumulating observational evidence links prenatal, perinatal, and early childhood exposures to later IBD risk. Several mechanisms underpin this relationship, including gut microbiome development, immune system maturation, epigenetic modulation, and metabolic and endocrine programming. Building on this framework, this review outlines potential intervention strategies across key developmental stages-from maternal nutrition and microbiome modulation during pregnancy to delivery-related factors such as birth mode, intrapartum antibiotic use, and early breastfeeding practices. Postnatal strategies include breastfeeding promotion, timely and diverse dietary introduction, antibiotic stewardship, and minimization of detrimental environmental exposures. Such approaches may be particularly relevant for high-risk groups, notably children born to individuals with IBD. Practical guidance is provided for families affected by IBD, alongside a discussion on how universal and risk-stratified strategies may be integrated. However, it is important to note that most of these strategies remain hypothetical, with limited validation. Emerging research areas include maternal dietary interventions, microbiome-based therapies, and the utilization of digital tools for risk monitoring. This review also addresses ethical and implementation challenges inherent to early-life prevention research and intervention.},
}

Humans
*Inflammatory Bowel Diseases/prevention & control/etiology
Pregnancy
Female
Gastrointestinal Microbiome
Risk Factors
Breast Feeding
*Prenatal Exposure Delayed Effects/prevention & control
Infant, Newborn

@article {pmid41078159,
year = {2025},
author = {Torres, J and Moss, A},
title = {Introduction to the IBD Journal Supplement: "Prevention of IBD: Forecasting and Forestalling Inflammatory Bowel Disease Onset".},
journal = {Inflammatory bowel diseases},
volume = {31},
number = {Supplement_2},
pages = {S1-S2},
doi = {10.1093/ibd/izaf207},
pmid = {41078159},
issn = {1536-4844},
mesh = {Humans ; *Inflammatory Bowel Diseases/prevention & control/etiology ; Risk Factors ; Biomarkers/analysis ; Forecasting ; },
abstract = {Despite significant therapeutic advances in inflammatory bowel disease (IBD), patients still experience diagnostic delays, suboptimal outcomes, and low remission rates-highlighting the urgent need for new approaches. This IBD journal supplement gathers leading experts to examine critical aspects of disease prediction and prevention. Topics include the genetic architecture of IBD, early-life environmental risk factors and their influence on disease risk, and emerging predictive biomarkers such as microbiome signatures, gut permeability, and proteomics, among others. Insights from type 1 diabetes research inform potential strategies for disease interception in IBD. Several targets are proposed for interception and prevention of disease, and the optimal design of an IBD-prevention trial is discussed. While landmark initiatives across the globe are currently paving the way for biomarker validation and trial implementation, harmonizing terminology and defining preclinical stages are essential next steps. Ultimately, understanding disease initiation may enable transformative strategies, shifting the paradigm from treatment to true prevention and potentially altering the course of IBD.},
}

Humans
*Inflammatory Bowel Diseases/prevention & control/etiology
Risk Factors
Biomarkers/analysis
Forecasting

@article {pmid41078118,
year = {2025},
author = {Wang, Y and Yang, J and Hou, H and Song, L and Cheng, X and Liu, YX},
title = {Advancing Plant Microbiome Research Through Host DNA Depletion Techniques.},
journal = {Plant biotechnology journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/pbi.70379},
pmid = {41078118},
issn = {1467-7652},
support = {32470055//National Natural Science Foundation of China/ ; U23A20148//National Natural Science Foundation of China/ ; CAAS-BRC-CB-2025-01//Basic Research Center for Crop Biosafety Sciences/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; },
abstract = {Plants provide ecological habitats for diverse microorganisms, making accurate metagenomic sequencing essential for understanding the complex interactions that support plant growth, development and disease resistance. However, host DNA contamination poses a major challenge in plant microbiome studies, obscuring microbial genetic signatures and complicating the accurate analysis of microbial genomes. This review provides a comprehensive overview of current host DNA depletion strategies, including physical separation (e.g., filtration, gradient centrifugation), selective lysis and enzymatic treatments targeting plant cell walls. Advanced techniques such as targeted sequence capture with magnetic beads, methylation-based enrichment and nanopore selective sequencing offer additional options for host DNA removal. Despite these advances, current methods still face challenges in efficiency, specificity and applicability, emphasising the need for tailored strategies and the exploration of novel approaches for microbial enrichment. Innovations like CRISPR-Cas9 and chromatin immunoprecipitation-based host DNA depletion methods are proposed to provide novel directions for addressing current limitations. The development and refinement of host depletion techniques tailored to plant systems are crucial for enabling high-resolution, cost-effective metagenomic studies. These efforts promise to deepen our understanding of microbial diversity and functionality, ultimately accelerating microbiome-based innovations in crop improvement, sustainable agriculture and ecosystem resilience.},
}

@article {pmid41078079,
year = {2025},
author = {Shibata, R and Li, Y and Yaskolka Meir, A and Cregeen, SJ and Ross, MC and Espinola, JA and Sullivan, AF and Liang, L and Hasegawa, K and Camargo, CA and Zhu, Z},
title = {Nasopharyngeal Microbiome-Epigenome-Wide Association Analysis in Infants With Severe Bronchiolitis.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70102},
pmid = {41078079},
issn = {1398-9995},
support = {/NH/NIH HHS/United States ; //Environmental influences on Child Health Outcomes (ECHO) Program Opportunities and Innovation Fund (OIF)/ ; //Massachusetts General Hospital/ ; //the Harvard University William F. Milton Fund/ ; //American Lung Association Innovation Award/ ; },
abstract = {BACKGROUND: Bronchiolitis exposes infants to both acute burdens (e.g., hospitalization in cases of severe bronchiolitis) and increased risks for chronic respiratory sequelae (e.g., asthma). In severe bronchiolitis, recent evidence suggests distinct pathobiological roles of microbiota (e.g., viruses, bacteria) and host responses influenced by genetic and epigenetic factors. However, the relationship of airway microbiota with host DNA methylation (DNAm) in infants with severe bronchiolitis remains unknown.

METHODS: In a multi-center prospective cohort of 504 multi-ethnic infants with severe bronchiolitis (age < 1 year), using nasopharyngeal microbiome (exposure) and blood DNAm (outcome, Infinium MethylationEPIC BeadChip, Illumina) data within 24 h of the hospitalization, we conducted microbiome-epigenome-wide association studies (mbEWAS). We examined microbiota-associated differentially methylated CpGs (mbDMCs, false discovery rate [FDR] < 0.05), regions (mbDMRs, FDR < 0.05), and DNAm age acceleration. We also determined the associations of DNAm age acceleration with asthma development by age 6 years. Furthermore, we focused on asthma-related pathogenic bacteria-Haemophilus influenzae, Moraxella catarrhalis, and Streptococcus pneumoniae-for functional analyses by examining serum mbDMR-related proteins (Proseek Multiplex, Olink) and their enriched pathways (FDR < 0.10).

RESULTS: Across 23 common taxa-observed at least in 25% of the infants, we identified 1 mbDMC (S. pneumoniae, cg16594639, chr20: 39528675) and 96 mbDMRs (e.g., S. pneumoniae, chr5:27038497-27038802, CDH9; chr6:48068669-48068940, PTCHD4). A higher H. influenzae abundance was associated with DNAm age deceleration, and the deceleration was associated with a higher risk of developing asthma. In 29 mbDMRs of the asthma-related pathogenic bacteria, we identified 156 mbDMR-related proteins (e.g., MMP9, XCL1). These proteins were enriched in immune response-related pathways (e.g., regulation of ERBB signaling and eosinophil chemotaxis and migration pathways).

CONCLUSIONS: In this multi-center prospective cohort study of severe bronchiolitis, our mbEWAS suggested the microbiota-host associations that regulate immune responses.},
}

@article {pmid41077905,
year = {2025},
author = {Hernández-Terán, A and Escalante, AE and Rebolleda-Gómez, M},
title = {Plant domestication does not reduce diversity in rhizosphere bacterial communities.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70588},
pmid = {41077905},
issn = {1469-8137},
support = {LT 0047/2023-L//Human Frontier Science Program/ ; IN214124//UNAM-PAPIIT/ ; //University of California President's Postdoctoral Fellowship/ ; //School of Biological Sciences at the University of California, Irvine/ ; },
abstract = {Domestication has profoundly shaped the genetic makeup of numerous plant and animal species. While its genetic and phenotypic effects are well documented, the impact on the plant microbiome remains less understood. Two primary hypotheses have been proposed: a reduction in microbial diversity resulting from the domestication process and the diminished ability of host plants to control their microbiomes. We tested these hypotheses by comparing wild and domesticated plants across maize, wheat, barley, sunflower, tomato, cotton, bean, soybean, sorghum, rice, potato, and agave. We conducted a meta-analysis comparing the rhizosphere bacterial communities of domesticated plants and their wild relatives. Analyses focused on microbial diversity, community composition, and the degree of host influence on bacterial assemblages. Our results indicate that the effects of domestication are species-specific and context-dependent, with most domesticated plants exhibiting increased bacterial diversity and more structured communities. This study provides evidence that plant domestication does not lead to a uniform reduction in bacterial diversity or a consistent loss of host influence in bacterial assemblages. From these findings, we discuss new perspectives and the need for future studies incorporating native soils and host genetic variation, as well as analyzing diversity and microbiome function.},
}

@article {pmid41077825,
year = {2025},
author = {Yin, R and Sargsyan, D and Wu, R and Hudlikar, R and Li, S and Kuo, HC and Sarwar, MS and Zhou, Y and Gao, Z and Howell, A and Chen, C and Blaser, MJ and Tony Tong Kong, AN},
title = {Microbiome and Metabolome Alterations in Nrf2 Knockout Mice With Induced Gut Inflammation and Fed With Phenethyl Isothiocyanate and Cranberry Enriched Diets.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70283},
doi = {10.1002/mnfr.70283},
pmid = {41077825},
issn = {1613-4133},
abstract = {Cranberries contain phytochemicals with potent antioxidant properties. Phenethyl isothiocyanate (PEITC) is abundant in crucifers and possesses anti-cancer and anti-inflammatory properties. These food additives can alter gut microbiota and improve the host's health. Microbiome and microbial metabolome interactions with the host's cells help maintain gastrointestinal (GI) tract homeostasis. Cranberry and PEITC enriched diets were fed to wild-type (WT) and Nrf2 knockout (KO) mice, including those challenged with dextran sulfate sodium (DSS), and their gut microbiomes and metabolomes were examined. Relative abundances of Deferribacteres, Epsilonbacteraeota, and Proteobacteria decreased, while Firmicutes and Verrucomicrobia increased in the DSS-challenged mice samples. These trends were reversed by PEITC and cranberry enriched diets. The diets also preserved the Firmicutes-to-Bacteroidetes ratio, an endpoint associated with gut inflammation and obesity. DSS challenge altered production of several metabolites. Nrf2 KO mice samples had lower concentrations of short-chain fatty acids (SCFA) and amino acids, and higher concentrations of secondary bile acids.Nrf2 KO mice microbiomes exhibited higher richness and diversity. PEITC and cranberry enriched diets positively affected hosts' microbiomes and boosted several microbial metabolites. Phenotypic expression of Nrf2 impacted the microbiota and metabolic reprogramming induced by DSS-mediated inflammation and dietary supplements of cranberry and PEITC.},
}

@article {pmid41077748,
year = {2025},
author = {Lee, HK and Shin, CM and Chang, YH and Jo, H and Choi, J and Choi, Y and Jun, YK and Yoon, H and Park, YS and Kim, N and Lee, DH},
title = {Predictors of Treatment Response to Fecal Microbiota Transplantation in Irritable Bowel Syndrome: A Pilot Study.},
journal = {Journal of neurogastroenterology and motility},
volume = {31},
number = {4},
pages = {462-476},
doi = {10.5056/jnm24183},
pmid = {41077748},
issn = {2093-0879},
abstract = {BACKGROUND/AIMS: We aim to investigate the effectiveness, safety, and predictors of treatment response to fecal microbiota transplantation (FMT) in Korean irritable bowel syndrome (IBS) patients.

METHODS: Patients with moderate to severe diarrhea-predominant IBS (IBS-D) or mixed-type IBS (IBS-M) received FMT from one healthy donor via esophagogastroduodenoscopy. IBS-symptom severity score (IBS-SSS), Bristol stool form scale (BSFS), IBS Quality of Life (IBS-QoL) questionnaires, Hospital Anxiety and Depression Scale (HADS), and gut microbiome profiles were assessed at baseline, 4 weeks and 12 weeks post-FMT.

RESULTS: Among the 46 enrolled IBS patients, 37 patients (IBS-D:IBS-M = 28:9) completed a 12-week follow-up. Significant improvements were observed in IBS-SSS, IBS-QoL, and BSFS after 12 weeks. FMT led to increased microbial diversity and a sustained increase in beneficial bacterial genera, including Holdemanella, Ruminococcus, and Faecalibacterium. In terms of β-diversity, the distance between the patient's gut microbiome and that of the donor decreased after FMT; greater reduction in distance to donor microbiota was associated with greater symptom improvement (Unweighted UniFrac distance, P < 0.05). Responders (IBS-SSS reduction > 50 points) exhibited lower baseline relative abundances of Roseburia and Subdoligranulum, and more profound microbiome shifts toward the donor profile after FMT.

CONCLUSIONS: FMT appears to be a potentially effective treatment for moderate to severe IBS, with significant symptom relief and gut microbiota changes. Lower baseline abundances of Roseburia and Subdoligranulum and greater shifts of gut microbiome profile toward donor microbiota after FMT may predict favorable FMT response. Long-term follow-up is on the way to assessing the durability of these effects.},
}

@article {pmid41077690,
year = {2025},
author = {Peng, Y and Lee, JH and Kim, CY and Lee, J},
title = {Halophyte-Derived Kushneria Strains Enhance Salt Tolerance and Rhizosphere Dynamics in Cabbage.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70234},
pmid = {41077690},
issn = {1365-3040},
support = {//This study was supported by the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM5282533) and the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT, RS-2024-00352429)./ ; },
abstract = {Halophytic plants harbour salt-tolerant bacteria that enhance resilience to salinity. In this study, two highly halotolerant Kushneria isolates, K. konosiri (Kk) and K. marisflavi (Km), were obtained from the halophyte Suaeda maritima. Both strains tolerated up to 25% NaCl and promoted Arabidopsis thaliana growth under salt stress by producing indole-3-acetic acid, proline, and extracellular polysaccharides that mitigated osmotic stress. Inoculation with Kk or Km increased shoot and root biomass and reduced intracellular Na[+] and reactive oxygen species. Their agricultural potential was tested in cabbage (Brassica rapa), where both isolates alleviated salinity-induced growth inhibition. A combined inoculum (Kkm) showed enhanced efficacy, significantly increasing shoot biomass (1.26-fold vs. Kk; 1.23-fold vs. Km) and dry weight (1.19-fold vs. Kk; 1.13-fold vs. Km). Kkm treatment also improved the K[+]/Na[+] ratio and proline accumulation. Microbial profiling revealed that Kkm enriched Bacillus species in the rhizosphere and promoted greater biofilm formation than single strains. These findings demonstrate that Kushneria isolates function as salt-tolerant plant growth-promoting bacteria, enhancing ion homoeostasis, stress protection, and rhizosphere restructuring. This study highlights the potential of halophyte-derived microbial consortia to improve crop salt tolerance in agriculture.},
}

@article {pmid41077635,
year = {2025},
author = {Noel, S and Patel, SK and White, J and Verma, D and Menez, S and Raj, D and Parikh, C and Rabb, H and , },
title = {Metagenomic Profiling of Gut Microbiota in Kidney Precision Medicine Project Participants With CKD and AKI.},
journal = {Comprehensive Physiology},
volume = {15},
number = {5},
pages = {e70058},
doi = {10.1002/cph4.70058},
pmid = {41077635},
issn = {2040-4603},
support = {U01DK133081//KPMP/ ; U01DK133091//KPMP/ ; U01DK133092//KPMP/ ; U01DK133093//KPMP/ ; U01DK133095//KPMP/ ; U01DK133097//KPMP/ ; U01DK114866//KPMP/ ; U01DK114908//KPMP/ ; U01DK133090//KPMP/ ; U01DK133113//KPMP/ ; U01DK133766//KPMP/ ; U01DK133768//KPMP/ ; U01DK114907//KPMP/ ; U01DK114920//KPMP/ ; U01DK114923//KPMP/ ; U01DK114933//KPMP/ ; U24DK114886//KPMP/ ; UH3DK114926//KPMP/ ; UH3DK114861//KPMP/ ; UH3DK114915//KPMP/ ; UH3DK114937//KPMP/ ; R01DK104662/DK/NIDDK NIH HHS/United States ; R01DK123342/DK/NIDDK NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Renal Insufficiency, Chronic/microbiology ; *Acute Kidney Injury/microbiology ; Metagenomics/methods ; Precision Medicine/methods ; Female ; Male ; Middle Aged ; Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: The gut microbiome plays an important role in human health and disease. Kidney Precision Medicine Project (KPMP) is a well-phenotyped, kidney biopsy-proven cohort of AKI and CKD patients. Comprehensive profiling of gut microbiota can uncover novel mechanistic, diagnostic, and therapeutic strategies for CKD and AKI patients.

METHODS: We performed metagenomic whole genome sequencing (mWGS; > 25 million reads) on KPMP stool samples. mWGS data of healthy controls from 4 published studies was used. Kraken2 and MetaPhlAn3 were used for taxonomic assignment, and HUMAnN3 for functional annotation.

RESULTS: Kraken2 analysis showed significantly higher abundance of Ruminococcus bicirculans in CKD (6.47) compared to AKI (1.82) and healthy individuals (2.42; p = 0.01). Furthermore, the abundance of Gordonibacter pamelaeae increased in CKD (0.30) compared to AKI (0.07; p = 0.05) and healthy individuals (0.03). The percent mean abundance of genus Chryseobacterium was slightly higher in CKD (0.07) compared to AKI (0.05; p = 0.05) but reduced compared to healthy individuals (0.20; p < 0.001). MetaPhlAn3 identified alterations in Gordonibacter, Bacteroides, and Faecalibacterium with a significant increase in Clostridium asparagiforme in AKI (11.68) compared to CKD (0.03; p = 0.06) and healthy (0.01; p = 0.001) individuals. Roseburia hominis, Roseburia intestinalis, Dorea longicatena, and Gemmiger formicilis were significantly reduced in AKI compared to CKD and healthy individuals. LDA/HUMAnN3 analysis showed a significant correlation between several metabolites and bacterial species in this KPMP population.

CONCLUSION: Kidney biopsy-proven CKD and AKI patients show a distinct gut microbiota profile compared to healthy individuals. This high-quality dataset is a valuable resource for developing microbiome-based diagnostics and therapies for CKD and AKI.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Renal Insufficiency, Chronic/microbiology
*Acute Kidney Injury/microbiology
Metagenomics/methods
Precision Medicine/methods
Female
Male
Middle Aged
Adult
Feces/microbiology

@article {pmid41077600,
year = {2025},
author = {Xiang, X and Liu, S and Wang, H and Wang, C and Zhou, W and Chen, H and Feng, Y and He, X and Xu, G and Zhao, Q and Li, T and Liu, D and Yin, Y and He, L},
title = {Glutathione contributes to alleviating hepatic injury via host-microbiome interaction and CAR-dependent pathway.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {41077600},
issn = {1869-1889},
abstract = {Glutathione (GSH) is a potent antioxidant regulating oxidative stress, but whether exogenous GSH supplementation mitigates stress injury through host-microbiome and liver interactions remains unclear. This study aimed to determine the regulatory mechanism of GSH using in vivo (28-day-old weaned piglets) and in vitro (alpha mouse liver 12 (AML12) cells) stress injury models. Thirty-five healthy weaned piglets (mean body weight (9.52±0.20) kg) were fed diets supplemented with 0.01%, 0.03%, or 0.06% GSH for 4 weeks, followed by being injected intraperitoneally with paraquat (PQ) on days 28, 30, and 32. AML12 cells exposed to tert-butyl hydroperoxide (tBHP) were used to evaluate related mechanisms, and CINPA1was used to inhibit constitutive androstane receptor (CAR) activity. Our results showed that PQ challenge induced hepatic morphological and functional impairments, accompanied by suppression of antioxidant capacity and immune function. Notably, exogenous GSH treatment significantly increased CD4[+]/CD8[+] T lymphocyte ratio, GSH, immunoglobulin A and interleukin-10 levels in serum, reduced the secretion and gene expression of pro-inflammatory factors to alleviate liver injury. Moreover, GSH treatment significantly promoted CAR nuclear translocation and regulated the expression of detoxification genes in response to liver inflammation. Additionally, GSH treatment improved the diversity and relative abundance of colonic probiotic bacteria such as UCG_002, Christensenellaceae_R_7_group, Prevotellaceae_NK3B31_group, Prevotella, Oscillospira, and unclassified_UCG_010. Furthermore, in vitro results showed that 3 mmol L[-1] GSH administration could increase the expression of CAR pathway and antioxidant related genes, and inhibit cellular ROS production in tBHP-induced AML12 cells. However, CAR inhibition by CINPA1 prevented GSH from alleviating tBHP-induced oxidative stress injury in AML12 cells. Our results indicate that exogenous GSH treatment alleviated liver injury in piglets through host-microbiome interaction and a CAR-dependent signaling pathway.},
}

@article {pmid41077555,
year = {2025},
author = {Bazany, K and Dhar, A and Otto, K and Jing, Y and Trivedi, P},
title = {Water Deficit Stress Alters the Microbial Community Assembly, Structure, and Sources in Corn and Sugar Beet.},
journal = {Environmental microbiology},
volume = {27},
number = {10},
pages = {e70186},
doi = {10.1111/1462-2920.70186},
pmid = {41077555},
issn = {1462-2920},
support = {COL007760A//Colorado Agriculture Experimental Station/ ; 2020-67013-31801//US Department of Agriculture, National Institute of Food and Agriculture/ ; },
mesh = {*Zea mays/microbiology ; *Beta vulgaris/microbiology ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Soil Microbiology ; Fungi/genetics/classification/isolation & purification ; Stress, Physiological ; Plant Leaves/microbiology ; Rhizosphere ; Water/metabolism ; Droughts ; Osmotic Pressure ; },
abstract = {Plant-associated microbes can improve plant fitness under abiotic stress conditions like drought by providing stress-relieving benefits to the host; however, there is limited research on the complex ways in which microbial communities assemble in plants under varying environmental conditions. In a field study, we examined the bacterial, fungal, and protist communities of the rhizospheres, roots, and leaves of corn and sugar beet grown under irrigated and water deficit conditions. We hypothesised that water deficit would alter the community composition and structure of plant microbiomes by shifting the relative importance of community assembly processes and the patterns of movement from microbial sources to sinks. Using amplicon sequencing and modelling approaches, we found that the water deficit treatment led to key differences in microbial community structure and that these changes were likely driven by differences in community assembly processes and microbial source communities. Altogether, these results indicate that plant microbiome communities are shaped by available microbial sources, host selection factors, microbial interactions, and stochastic forces, and that each of these factors is influenced by osmotic stress. These findings highlight the importance of applying ecological concepts to plant microbiome research in order to elucidate the impacts of environmental factors on microbial community assembly.},
}

*Zea mays/microbiology
*Beta vulgaris/microbiology
*Microbiota
Bacteria/classification/genetics/isolation & purification
Plant Roots/microbiology
Soil Microbiology
Fungi/genetics/classification/isolation & purification
Stress, Physiological
Plant Leaves/microbiology
Rhizosphere
Water/metabolism
Droughts
Osmotic Pressure

@article {pmid41077541,
year = {2025},
author = {Mazhar, Z and Bashir, H},
title = {Microbiome-genetic interplay in intraductal papillary mucinous neoplasms: A critical appraisal of emerging evidence.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pan.2025.10.001},
pmid = {41077541},
issn = {1424-3911},
}

@article {pmid41077440,
year = {2025},
author = {Shogan, BD},
title = {The Microbiome and Surgery: A New Frontier.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {xi-xii},
doi = {10.1016/j.suc.2025.07.010},
pmid = {41077440},
issn = {1558-3171},
}

@article {pmid41077439,
year = {2025},
author = {Schenarts, PJ},
title = {Rethinking Everything: The Impact of the Microbiome.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {ix-x},
doi = {10.1016/j.suc.2025.07.002},
pmid = {41077439},
issn = {1558-3171},
}

@article {pmid41077438,
year = {2025},
author = {Alverdy, J},
title = {Preparing the Bowel for Surgery in the Era of Microbiome Sciences.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {965-974},
doi = {10.1016/j.suc.2025.06.004},
pmid = {41077438},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Preoperative Care/methods ; *Cathartics/administration & dosage ; },
abstract = {The concept that a "one-size-fits-all" approach can be universally applied to all patients undergoing colorectal surgery is waning in enthusiasm especially given the variation in risk perception among patients and surgeons. In this review, we discuss the scientific rationale in generating a microbiome readout that will inform how to selectively eliminate problematic pathogens while preserving those beneficial bacterial strains that may enhance recovery from surgery. We also provide the reader with practical decision points with which to contemplate the need for a bowel preparation with your patient.},
}

Humans
*Gastrointestinal Microbiome
*Preoperative Care/methods
*Cathartics/administration & dosage

@article {pmid41077437,
year = {2025},
author = {Barat, B and Shogan, BD},
title = {The Microbiome's Role in Driving Anastomotic Leak and Cancer Recurrence Following Colorectal Surgery.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {953-964},
doi = {10.1016/j.suc.2025.06.003},
pmid = {41077437},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Anastomotic Leak/microbiology/etiology/prevention & control ; *Neoplasm Recurrence, Local/microbiology/etiology ; *Colorectal Neoplasms/surgery/microbiology ; },
abstract = {The intestinal microbiota is composed of diverse microbial species that interact with the host, playing a vital role in immune regulation and maintaining homeostasis. Colorectal surgery has been shown to alter the gut microbiota, contributing to post-operative complications. Emerging evidence suggests that these microbial shifts influence the incidence of anastomotic leaks. In this review, we examine how the gut microbiota composition is altered in patients undergoing colon surgery, leading to anastomotic leaks, the role of collagenolytic bacteria in tissue breakdown at the anastomotic site, the connection between anastomotic leaks and cancer recurrence, and microbially based therapeutic approaches to prevent leaks.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Anastomotic Leak/microbiology/etiology/prevention & control
*Neoplasm Recurrence, Local/microbiology/etiology
*Colorectal Neoplasms/surgery/microbiology

@article {pmid40885534,
year = {2025},
author = {Gagnon, DJ and Burkholder, KM and Weissman, AJ and Riker, RR and Ryzhov, S and May, TL and DiPalazzo, J and deKay, JT and Knudsen, L and Moore, MW and Pozzessere, NA and Weatherbee, M and Kelly, M and Nigatu, AS and Sevigny, JL and Simpson, S and Thomas, WK and Callaway, CW and Geller, BJ and Sawyer, DB and Seder, DB},
title = {Ceftriaxone to Prevent Early-Onset Pneumonia in Comatose Patients Following Out-of-Hospital Cardiac Arrest: A Pilot Randomized Controlled Trial and Resistome Assessment (PROTECT).},
journal = {Chest},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chest.2025.08.007},
pmid = {40885534},
issn = {1931-3543},
support = {R01 HL173118/HL/NHLBI NIH HHS/United States ; },
abstract = {BACKGROUND: Antibiotic prophylaxis following out-of-hospital cardiac arrest (OHCA) reduces early-onset pneumonia. However, it has an uncertain impact on mortality and noninfectious outcomes, with ongoing concerns about the subsequent development of antibiotic resistance.

RESEARCH QUESTION: Does prophylactic ceftriaxone reduce the incidence of early-onset pneumonia without increasing the acquisition of antibiotic resistance genes after OHCA?

STUDY DESIGN AND METHODS: Comatose survivors of OHCA treated with targeted temperature management without a clinical diagnosis of pneumonia at admission were randomized to receive ceftriaxone 2 g or matching placebo every 12 hours for 3 days. The primary outcome was early-onset pneumonia occurring ≤ 4 days following intubation confirmed by masked adjudicators. Abundance of antibiotic resistance genes recovered from rectal swabs before-and-after study drug administration were analyzed with metagenomic sequencing.

RESULTS: A total of 411 participants were screened; 53 (13%) were randomized to treatment, and one participant withdrew, leaving 26 in each group in the final analysis. Early-onset pneumonia was diagnosed in 10 (38%) participants receiving ceftriaxone and 18 (69%) participants receiving placebo (risk ratio, 0.57; 95% CI, 0.21-1.001; P = .05). Open-label antibiotics were administered to 14 (54%) participants receiving ceftriaxone and 22 (85%) receiving placebo (risk ratio, 0.64; 95% CI, 0.43-0.94); most of the antibiotics were broad-spectrum agents (93% and 100%, respectively). After adjusting for differences in abundance of antibiotic resistance genes prior to study drug administration, participants randomized to receive ceftriaxone acquired significantly fewer antibiotic resistance genes to frequently used antibiotics in the ICU compared with those randomized to receive placebo (incidence risk ratio, 0.30; 95% CI, 0.13-0.70). Serious adverse drug effects were not reported in either treatment group.

INTERPRETATION: This trial was inconclusive regarding the impact of ceftriaxone prophylaxis on reducing the incidence of early-onset pneumonia following OHCA. However, ceftriaxone was associated with less frequent administration of open-label antibiotics and reduced acquisition of antibiotic resistance genes to frequently used antibiotics in the ICU.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov; No.: NCT04999592; URL: www.

CLINICALTRIALS: gov.},
}

@article {pmid41077436,
year = {2025},
author = {Dalal, SR},
title = {The Microbiome and Inflammatory Bowel Diseases.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {941-951},
doi = {10.1016/j.suc.2025.06.007},
pmid = {41077436},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology/therapy/immunology ; Dysbiosis/microbiology/complications ; },
abstract = {Inflammatory Bowel Diseases (IBD) are associated with a less diverse, dysbiotic intestinal microbiome that leads to alterations in immune modifying microbial metabolites. Genetic and environmental risk factors for IBD likely exert their effects through alterations of the microbiome. Transfer of synthetic microbial communities and targeted dietary interventions hold some promise in altering underlying causes of IBD.},
}

Humans
*Gastrointestinal Microbiome
*Inflammatory Bowel Diseases/microbiology/therapy/immunology
Dysbiosis/microbiology/complications

@article {pmid41077435,
year = {2025},
author = {Galbraith, NJ and White, MG},
title = {Microbiome of Young and Later-Onset Colorectal Cancer.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {925-939},
doi = {10.1016/j.suc.2025.06.002},
pmid = {41077435},
issn = {1558-3171},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/epidemiology ; *Gastrointestinal Microbiome ; Age of Onset ; },
abstract = {Young-onset colorectal cancer (YOCRC) is increasingly common in the Western world. This has been attributed to changes in diet, lifestyle, and other environmental factors which all influence the gut microbiome. This review summarizes a small number of studies that have demonstrated differences in the microbiome of YOCRC, assessed in the stool and tumoral compartment. These populations are distinct from LOCRC and are prognostically important. Further research may reveal their role in the pathogenesis of this epidemic, and microbiological interventions can alter or augment existing treatment responses.},
}

Humans
*Colorectal Neoplasms/microbiology/epidemiology
*Gastrointestinal Microbiome
Age of Onset

@article {pmid41077434,
year = {2025},
author = {Portolese, AC and Jeganathan, NA},
title = {The Microbiome and the Etiology of Diverticulitis.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {913-924},
doi = {10.1016/j.suc.2025.06.005},
pmid = {41077434},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Diverticulitis/microbiology/etiology ; Animals ; *Diverticulitis, Colonic/microbiology ; },
abstract = {This article provides a review of the existing literature on the microbiome and metabolome of diverticulosis and diverticular disease. Existing studies indicate the microbiome is less likely a cause in the development of diverticulosis. Current evidence highlighting likely etiologic microbes and metabolites in the pathogenesis of diverticular disease is presented. As most data at this time is descriptive and lacks rigorous testing in an animal model of diverticular disease, these findings are extrapolated from the existing understanding of the microbiome in inflammatory bowel disease.},
}

Humans
*Gastrointestinal Microbiome
*Diverticulitis/microbiology/etiology
Animals
*Diverticulitis, Colonic/microbiology

@article {pmid41077433,
year = {2025},
author = {Fair, L and Ward, MA},
title = {The Gut Microbiome and Bariatric Surgery.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {903-912},
doi = {10.1016/j.suc.2025.06.006},
pmid = {41077433},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Bariatric Surgery ; *Obesity, Morbid/surgery/microbiology ; },
abstract = {Obesity is a complex, multifactorial disease that is associated with significant morbidity and mortality. Recent research in bariatric surgery has shown that these surgeries can impact the composition of the gut microbiome. Postoperative alterations include increased microbial diversity and shifts in composition, such as a change in the Firmicutes/Bacteroidetes ratio. The interplay between altered gut anatomy, dietary changes, and microbiome composition creates a metabolically favorable environment that contributes to the long-term success of bariatric surgery. This review focuses on the overall impact of bariatric surgery on the gut microbiome and potential targeted therapies that can be used to improve outcomes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Bariatric Surgery
*Obesity, Morbid/surgery/microbiology

@article {pmid41077432,
year = {2025},
author = {Awad, D and Daley, D},
title = {The Role of the Microbiome in Pancreas Cancer: The Evolving Influence of the Fungal Mycobiome.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {887-902},
doi = {10.1016/j.suc.2025.06.001},
pmid = {41077432},
issn = {1558-3171},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/pathology/immunology ; *Mycobiome ; Tumor Microenvironment ; *Gastrointestinal Microbiome/physiology ; *Carcinoma, Pancreatic Ductal/microbiology ; Dysbiosis/microbiology ; Fungi ; },
abstract = {The gut microbiome has been shown to impact the progression of pancreatic ductal adenocarcinoma and the tumor's response to therapy. Microbial dysbiosis or changes in the healthy gut microbiome has been implicated in pancreatic cancer patients and influences immune cell differentiation and cancer cell behavior in the tumor microenvironment. This article summarizes the key findings from studies investigating interactions between gut microbes and components of the tumor microenvironment, with a special focus on the oncogenic effects of the fungal mycobiome.},
}

Humans
*Pancreatic Neoplasms/microbiology/pathology/immunology
*Mycobiome
Tumor Microenvironment
*Gastrointestinal Microbiome/physiology
*Carcinoma, Pancreatic Ductal/microbiology
Dysbiosis/microbiology
Fungi

@article {pmid41077431,
year = {2025},
author = {Ho, KJ and Vs, J and Abualhuda, A and Wang, B},
title = {How the Microbiome Drives Cardiovascular Disease.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {871-885},
doi = {10.1016/j.suc.2025.07.001},
pmid = {41077431},
issn = {1558-3171},
mesh = {Humans ; *Cardiovascular Diseases/microbiology/etiology ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/complications ; },
abstract = {Cardiovascular diseases (CVDs) are the leading causes of death and disability globally. Scientific and clinical evidence demonstrate that gut microbiota influence the development and natural history of CVDs through regulation of the immune/inflammatory response, intestinal barrier function, and metabolic pathways. This article provides an overview of the relationships between gut dysbiosis and coronary artery disease, heart failure, cardiovascular death, cerebrovascular disease, peripheral artery disease, and aortic aneurysms and how these relationships may lead to novel interventions for disease prevention and treatment.},
}

Humans
*Cardiovascular Diseases/microbiology/etiology
*Gastrointestinal Microbiome/physiology
*Dysbiosis/complications

@article {pmid41077430,
year = {2025},
author = {Polster, SP},
title = {The Role of the Microbiome and the Neurovascular Unit.},
journal = {The Surgical clinics of North America},
volume = {105},
number = {5},
pages = {857-869},
doi = {10.1016/j.suc.2025.06.008},
pmid = {41077430},
issn = {1558-3171},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Blood-Brain Barrier ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; },
abstract = {The gut-brain axis plays a crucial role in neurovascular diseases, linking gut microbiota to blood-brain barrier integrity, neuroinflammation, and disease progression. Conditions such as cerebral cavernous malformations, traumatic brain injury, radiation-induced damage, and stroke exhibit microbiome-driven modulation that may be relevant to explain disease variance. Microbial metabolites have been shown to influence endothelial function and secondary brain injury mechanisms. Emerging interventions of dietary modifications, probiotics, fecal microbiota transplantation, and metabolite-based therapies show promise in mitigating neurovascular damage. Future research should focus on microbiome-targeted treatments, biomarker discovery, and personalized strategies to optimize neurovascular health through gut microbiome modulation.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Blood-Brain Barrier
Probiotics/therapeutic use
Fecal Microbiota Transplantation

@article {pmid41077197,
year = {2025},
author = {Napier, EG and Doratt, BM and Cinco, IR and Stuart, EV and Geron, RD and Davies, MH and Malherbe, DC and Kohama, SG and Bermudez, L and Winthrop, KL and Fuss, C and Spindel, ER and Messaoudi, I},
title = {Age-related severity of nontuberculous mycobacterial lung disease is mediated by aberrant macrophage responses and lung microbial dysbiosis.},
journal = {The Journal of infection},
volume = {},
number = {},
pages = {106626},
doi = {10.1016/j.jinf.2025.106626},
pmid = {41077197},
issn = {1532-2742},
abstract = {OBJECTIVES: Although cases of nontuberculous mycobacteria (NTM) pulmonary disease (NTMPD) are rapidly increasing primarily in individuals over the age of 65, the host factors leading to higher occurrence in immunocompetent older patients remain elusive. This study aims to elucidate host factors leading to higher nontuberculous mycobacterial pulmonary disease occurrence in older immunocompetent patients.

METHODS: To address these challenges, we used a rhesus macaque model developed by our laboratory where macaques were infected via intrabronchial inoculation with M. avium subsp. hominissuis (MAH). Disease progression, bacterial load, microbial community compositions, and host responses were monitored longitudinally using computed tomography, culturing, 16S amplicon sequencing, histology, flow cytometry, and single cell RNA sequencing.

RESULTS: Despite comparable kinetics of bacterial clearance, computed tomography scans indicated more severe radiological outcomes in older animals which mounted predominantly an inflammatory acute phase response rather than a Th1 response. Single cell RNA sequencing indicated a persistent inflammatory signature in aged animals. Microbial community analysis revealed an age-mediated loss of an uncultured Tropheryma species that was inversely correlated with severity of radiographic changes.

CONCLUSIONS: These data reveal that nontuberculous mycobacterial pulmonary disease severity in the aged animals is driven by dysregulated inflammatory responses and dysbiosis of the lung microbiome.},
}

@article {pmid41077176,
year = {2025},
author = {Agrawal, K and Hong, ASY and Cifuentes-González, C and Kumar, VS and Rojas-Carabali, W and Zhang, S and Wang, Q and de-la-Torre, A and Gijs, M and Gill, T and Rosenbaum, JT and Rajagopala, SV and Gangaputra, S and Conforti, A and Ross, RP and Yang, P and Wong, S and Agrawal, R},
title = {Microbiome Signatures and Their Role in Uveitis: Pathogenesis, Diagnostics, and Therapeutic Perspectives.},
journal = {Progress in retinal and eye research},
volume = {},
number = {},
pages = {101409},
doi = {10.1016/j.preteyeres.2025.101409},
pmid = {41077176},
issn = {1873-1635},
abstract = {Non-infectious uveitis is a group of complex inflammatory eye diseases shaped by genetic susceptibility, immune dysregulation, and environmental cues. Among these, the mucosal microbiome-including gut, oral, and ocular surface microbial communities-has emerged as a key player in modulating systemic and ocular immune responses. Recent evidence supports a gut-eye axis wherein microbial dysbiosis alters intestinal barrier function, perturbs T cell homeostasis, and drives systemic immune activation that can breach ocular immune privilege. Specific taxa, such as Prevotella and Faecalibacterium, as well as microbial metabolites including short-chain fatty acids, have been implicated in promoting or mitigating ocular inflammation. Human leukocyte antigen (HLA) alleles, notably HLA-B27 and HLA-A29, influence both microbiome composition and disease phenotype, suggesting a gene-microbiome-immunity triad of interaction in uveitis pathogenesis. Drawing on insights from metagenomics, metabolomics, in vitro and in vivo experimental and murine models, this review delineates four key mechanisms-immune imbalance, antigenic mimicry, epithelial barrier disruption, and bacterial translocation-that underpin the key roles of microbiome in uveitis. We combine current literature and integrate findings from our research programs to highlight diagnostic and therapeutic opportunities. Microbiome-informed strategies, such as rational probiotic design, dietary modulation, and targeted microbial therapies, hold promise for complementing existing immunosuppressive regimens. Translating these insights into clinical practice requires robust multi-omic studies, longitudinal cohorts, mechanistic studies, and precision-guided intervention trials. By framing uveitis within a mucosal immunological context, this review proposes a future precision medicine roadmap for integrating microbiome science into ocular inflammatory disease management.},
}

@article {pmid41077053,
year = {2025},
author = {Wheatley, RM and Holtappels, D and Koskella, B},
title = {Evaluation of bacteriophages as a signature of microbiome health: a systematic review and meta-analysis.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101196},
doi = {10.1016/j.lanmic.2025.101196},
pmid = {41077053},
issn = {2666-5247},
abstract = {BACKGROUND: Parasites are foundational to ecosystem health both as indicator species of community productivity and as drivers of diversity. In bacterial communities, bacteriophage viruses can have such roles as they track and modulate the dynamic composition of bacterial hosts within an ecosystem. We aimed to test whether viromes can be used as broad signatures of microbiome health using previously published results across systems.

METHODS: In this systematic review and meta-analysis, we searched PubMed, Google Scholar, Scopus, and Web of Science from Jan 22, 2022, to Sept 17, 2024, for peer-reviewed, primary literature published in English, using search terms "phage diversity", "microbiome", "virome", "virus", "phageome", "disease", and "dysbiosis". Inclusion criteria were: a comparison between a dysbiosis state and a healthy state in a human or animal host; a defined host organism and microbiome site; examination of the virome; an obtained measure of virome diversity (α, β, or both); use of statistical analysis to assess whether α or β diversity are changed in dysbiosis; and sufficient methodology description on viral isolation and on virus sequence analysis pipeline. We conducted a qualitative data analysis to assess factors explaining changes to virome diversity in dysbiosis. We then calculated response ratios for each study to test for overall patterns of virome α diversity change under disturbance. Finally, we conducted a quantitative analysis on studies from which we were able to obtain paired virome and bacteriome α diversity data to examine the correlation between these data in defined health compared with defined disturbance conditions. This study was not registered.

FINDINGS: We identified a total of 74 studies for inclusion that spanned human (n=61), mouse (n=8), pig (n=3), dog (n=1), and cow (n=1) hosts and a diverse spectrum of infections and diseases. By comparing observed phage and bacterial diversity in microbiomes characterised by dysbiosis with those considered control populations, we were able to identify some key commonalities. Of the 69 studies that investigated changes to α diversity of the virome in dysbiosis, 28 (41%) reported significant changes, but with variable directional change. Of 38 datasets (from 30 studies) for which virome α diversity values were available, 22 (58%) gave a response ratio of less than 1 (α diversity decreases in dysbiosis) and 16 (42%) of more than 1 (α diversity increases in dysbiosis); however, in 27 (71%) datasets, 95% CIs overlapped with 1 (ie, no change in α diversity). We found shifting virome composition to be a more consistent signature of dysbiosis, with 47 (69%) of 68 studies reporting a significant change in viral β diversity with dysbiosis. 62 (89%) of 70 studies reported significant enrichment of system-specific viral taxa under dysbiosis. Our quantitative correlation analysis suggested that bacterial α diversity is a greater predictor of virome α diversity in healthy groups (mean r[2]=0·380; 95% CI 0·597-0·163) than in dysbiosis (mean r[2]=0·118, 0·223-0·012; sign test for asymmetric non-parametric data p=4·9 × 10[-10]).

INTERPRETATION: Overall, although specific viral signatures of dysbiosis are likely to be highly disease-specific and condition-specific, we show that existing ecological theory shows promise in predicting the relationship between bacterial and phage diversity and in providing broad signatures of dysbiosis across disease systems. Our observation that the relationship between bacterial and phage diversity breaks down under disturbance suggests that this feature could be a useful signature of dysbiosis and that future studies incorporating the virome could provide opportunity to diagnose, treat, and better understand the causes of microbiome disturbance.

FUNDING: There was no funding source for this study.},
}

@article {pmid41076929,
year = {2025},
author = {Shi, W and Xi, M and Zhang, K and Yang, J and Cheng, X and Zang, H and Fan, W},
title = {Gut microbiota as a central mediator in hydrogen gas-induced alleviation of colitis via TLR4/NF-κB and Nrf2 pathway regulation.},
journal = {International immunopharmacology},
volume = {167},
number = {},
pages = {115671},
doi = {10.1016/j.intimp.2025.115671},
pmid = {41076929},
issn = {1878-1705},
abstract = {Inflammatory bowel disease (IBD) is a chronic and relapsing autoimmune disorder of the gastrointestinal tract with incompletely elucidated pathogenesis and limited therapeutic options. Although hydrogen gas (H2) has demonstrated therapeutic efficacy in various diseases including IBD, its mechanisms of action, particularly its interaction with the gut microbiota, remain poorly characterized. This study reveals that H2 inhalation effectively reversed dextran sulfate sodium (DSS)-induced dysbiosis by suppressing the expansion of potential pathogenic bacteria (e.g., Enterobacteriaceae and Escherichia-Shigella) and promoting potential beneficial microbes (e.g., Bacteroides and Lactobacillaceae), thereby restoring microbial homeostasis. Furthermore, H2 inhalation enhanced goblet cell density and mucus production, upregulated tight junction proteins (ZO-1 and occludin), and repaired intestinal barrier integrity. It also rebalanced the Treg/Th17 cell ratio, correcting immune dysregulation. At the molecular level, H2 inhalation suppressed the TLR4/NF-κB signaling pathway and activated the Keap1/Nrf2 antioxidant axis, leading to reduced production of pro-inflammatory cytokines and oxidative stress markers, alongside elevated antioxidant enzymes, collectively ameliorating colonic injury. In brief, the ameliorative effects of H2 are likely mediated through remodeling of the gut microbiota, restoration of the epithelial barrier, suppression of inflammatory signaling, and activation of antioxidant pathways. These findings were further validated by fecal microbiota transplantation (FMT) experiments. Collectively, this study links the therapeutic effects of H2 to structural and functional reprogramming of the gut microbiome, indicating that microbial ecological restoration is a central mechanism through which H2 alleviates colitis, thereby providing a mechanistic foundation for the therapeutic application of H2 inhalation in IBD.},
}

@article {pmid41076846,
year = {2025},
author = {Al-Subhi, T and Yasir, M and Badreddine, SA and El-Kafrawy, SA and Khan, I and Hassan, AM and Othman, NA and Atrouni, AA and Kumosani, T and Azhar, EI},
title = {Alteration of bacterial community composition with respiratory infection and linkage of taxa with bacterial pathogens in Saudi Arabia from the Arabian Peninsula.},
journal = {Journal of infection and public health},
volume = {18},
number = {12},
pages = {102986},
doi = {10.1016/j.jiph.2025.102986},
pmid = {41076846},
issn = {1876-035X},
abstract = {BACKGROUND: The microbiome of the respiratory system functions as a gatekeeper of respiratory health and is influenced by respiratory diseases. The aim of this study was to identify changes in the respiratory bacterial community composition associated with respiratory infections and to explore their relationship with specific bacterial pathogens in the Saudi Arabian population.

METHODS: Nasopharyngeal samples were screened from 73 individuals, including 34 symptomatic respiratory tract infection patients, 10 asymptomatic participants, and 29 healthy controls. Respiratory pathogens were detected using real-time PCR, and the microbiota were characterized through 16S rRNA gene amplicon sequencing.

RESULTS: Alpha diversity analysis revealed a slight decrease in bacterial richness in patients and asymptomatic individuals compared to healthy controls. In beta diversity analysis, healthy controls clustered together, while most symptomatic patients clustered separately. Actinobacteria, known for maintaining microbial homeostasis and preventing pathogenic colonization, were abundant in asymptomatic and healthy controls (> 30 %) but were substantially reduced to < 20 % relative abundance in symptomatic patients. Several bacterial genera, including Abiotrophia, Capnocytophaga, Megasphaera, Campylobacter, Peptostreptococcus, Veillonella, Streptococcus, and Bulleidia, were positively correlated with respiratory infections. Corynebacterium, Dolosigranulum, and Lawsonella were more abundantly found in healthy and asymptomatic individuals. Patients harboring Streptococcus pneumoniae or methicillin-resistant Staphylococcus aureus (MRSA) exhibited distinct bacterial profiles. Genera such as Staphylococcus, Pseudomonas, and Peptoniphilus were correlated with MRSA infection, while samples positive for S. pneumoniae exhibited a relatively higher abundance of Neisseria and Prevotella. Notably, a substantial number of symptomatic patients tested negative for any of the screened pathogens by real-time PCR but still showed alterations in bacterial community composition.

CONCLUSIONS: Specific bacterial taxa showed significant differences between healthy controls and symptomatically infected patients, suggesting that bacterial community structures and groups of taxa, rather than individual bacterial taxa, may play a role in regulating respiratory infections.},
}

@article {pmid41076730,
year = {2025},
author = {Hull, MA and Sun, H},
title = {Omega-3 polyunsaturated fatty acids and gut microbiota.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
pmid = {41076730},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: Oral intake of n (omega)-3 polyunsaturated fatty acids (PUFAs) is associated with changes to gut microbiota. We review recent findings from 2024 onwards, which build the scientific case that changes to bacterial abundance, and their metabolites, contribute to the health benefits associated with n-3 PUFAs.

RECENT FINDINGS: There are now multiple studies in rodent disease models that demonstrate that n-3 PUFAs do not significantly alter bacterial diversity but, instead, alter abundance of several species that are implicated in short-chain fatty acid synthesis, in a model-specific manner. Limited intervention studies in humans, backed by larger observational studies, concur with the preclinical findings. Importantly, faecal transplantation experiments have confirmed that n-3 PUFA-induced changes to gut microbiota are causally related to reversal of the disease phenotype in two rodent models. In-vitro colonic models are now being used to understand the mechanism(s) underlying n-3 PUFA-induced changes to the gut microbiota and metabolome.

SUMMARY: Despite emerging proof that the gut microbiota contributes to n-3 PUFA activity in animal models, human data are sparse. It remains unclear how n-3 PUFAs affect changes to the gut microbiota or whether n-3 PUFA metabolism by gut microbes contributes to the host metabolome.},
}

@article {pmid41076729,
year = {2025},
author = {Burdon, IA and Psaltis, AJ},
title = {Changes in the sinus microbiome in health and chronic rhinosinusitis.},
journal = {Current opinion in otolaryngology & head and neck surgery},
volume = {},
number = {},
pages = {},
pmid = {41076729},
issn = {1531-6998},
abstract = {PURPOSE OF REVIEW: This article synthesises the recent sinus microbiome literature, identifying common themes in research findings as well as surveying the varied methodological approaches used across these studies.

RECENT FINDINGS: While there remains no clear consensus as to which microbes define dysbiosis in chronic rhinosinusitis (CRS), certain trends are emerging. Increasingly, the evidence points towards a pathogenic role in the overabundance of Moraxella, Haemophilus and Pseudomonas species, whilst the genera Cutibacterium, Anaerococcus and Dolosigranulum tend towards commensalism. However, the roles of the most common genera in the sinus microbiome, Staphylococcus and Corynebacterium, remain uncertain. Given the diversity and abundance of species within these genera, species and function-level analyses are needed to clarify their contributions to the aetiopathogenesis of CRS. Comprehensive study of the sinus microbiome in healthy individuals further shows that community composition shifts with age, suggesting that dysbiosis may manifest differently across the lifespan. Beyond bacteria, growing evidence highlights the importance of fungi and viruses, underscoring the need to incorporate these microbionts into future analyses.

SUMMARY: Progress towards a clinically meaningful consensus will require standardised approaches to sequencing, species-level resolution in these analyses, and consideration of the heterogeneous clinical and immunological subgroups of CRS.},
}

@article {pmid41076537,
year = {2025},
author = {Tseng, CH and Wu, CY},
title = {From dysbiosis to longevity: a narrative review into the gut microbiome's impact on aging.},
journal = {Journal of biomedical science},
volume = {32},
number = {1},
pages = {93},
pmid = {41076537},
issn = {1423-0127},
support = {112SBIR-10//Economic Development Bureau, Taichung City Government, Taiwan/ ; NSTC 113-2740-B-A49-003//National Science and Technology Council (NSTC), Taiwan/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Longevity ; Humans ; *Aging/physiology ; *Dysbiosis/microbiology ; Animals ; },
abstract = {Aging has become an important public health concern with the accelerated aging of the global population. The rising impetus to extend lifespan as well as healthspan has drawn attention to the gut microbiome, an indispensable yet modifiable determinant of the aging process. This narrative review addresses the complex interaction between the gut microbiome and aging, synthesizing findings in logical order. Evidence from model organisms supports the causal influence of gut microbes on host aging and longevity. Developmental evolution of the human gut microbiome throughout life stages reflects its adaptive nature affected by diet, lifestyle, hormone levels, and immune function, regulating aging through the gut-muscle and the gut-brain axes in late life. Signature characteristics of the long-lived gut microbiome, including increased diversity, elevated beneficial taxa, and enhanced gut homeostasis, lead to strategies to extend longevity. Intake of fiber, regular exercise, and pro-/pre-/postbiotic supplements are potential interventions on the gut microbiome to foster vitality in later years. Centering on these connected topics, this review identifies questions warranting investigation, with potential to improve therapeutic strategies for healthy aging.},
}

*Gastrointestinal Microbiome/physiology
*Longevity
Humans
*Aging/physiology
*Dysbiosis/microbiology
Animals

@article {pmid41076507,
year = {2025},
author = {Salah, AN and Doghish, YA and Abbass, SO and Mansour, RM and Sayed, GA and Elshami, NH and Mageed, SSA and Mohammed, OA and Abulsoud, AI and Zaki, MB and Mosalam, EM and Elrebehy, MA and Alfarsi, K and Doghish, AS},
title = {Microbiota-based therapies in oral health and disorders.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41076507},
issn = {1874-9356},
abstract = {The human oral microbiome is a complex, dynamic ecosystem critically involved in maintaining oral health and contributing to systemic well-being. Many bacteria and fungi are involved in oral cavities such as Penicillium, Rhodotorula, Saccharomycetales, Streptococcus, Veillonella, Neisseria, Actinomyces, and Schizophyllum. Disruption of microbial homeostasis, or dysbiosis, underpins a wide spectrum of oral diseases, including dental caries, periodontal disease, endodontic infections, and mucosal conditions. Recent advances in microbiome research have elucidated the mechanisms by which pathogenic microbial consortia, such as the red complex (Porphyromonas gingivalis, Tannerella. forsythia, and Treponema denticola), synergistically promote disease progression through virulence factors, metabolic interactions, and biofilm formation. Emerging microbiome-based therapies, comprising probiotics, postbiotics, predatory bacteria, and using bacteriophages, offer promising adjuncts or alternatives to traditional antimicrobial approaches by restoring microbial balance, reducing pathogenic load, and modulating host immune responses. For instance, probiotic strains like Streptococcus salivarius and Lactobacillus spp. have demonstrated efficacy in reducing plaque, gingival inflammation, and pathogenic bacteria, as well as having significant immunological modulation, while postbiotics provide similar benefits with enhanced safety and stability. Additionally, predatory bacteria such as Bdellovibrio bacteriovorus show potential for selective bacterial elimination and combating periodontal diseases that are driven by Gram-negative anaerobes. Bacteriophages offer another precision tool for targeting oral pathogens by lysing bacteria upon replication. Finally, oral microbiota transplantation aimed at treating periodontal disease by restoring a balanced microbial community in the oral cavity. These innovative strategies, combined with a nuanced understanding of biofilm dynamics and host-microbe interactions, pave the way for personalized and ecologically sustainable oral health interventions. Continued research is essential to translate these promising approaches into clinical practice, optimize delivery systems, and elucidate long-term safety and efficacy.},
}

@article {pmid41076506,
year = {2025},
author = {Ayyamuthu Rajarathinam Uma, P and Rathinasamy, PD and Thanakkan, R and Dhashnamurthi, V and Murugaiyan, S},
title = {Pink powerhouses: insights into the multifaceted role of Methylobacterium in climate-resilient farming.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41076506},
issn = {1874-9356},
abstract = {The plant microbiomes consist of a myriad of microorganisms that inhabit and interact with plant tissues and play pivotal roles in improving crop productivity and sustainability. These microbiomes constitute bacteria, fungi, archaea and viruses that have coevolved and supported plants inhabiting the Earth for millions of years. Among these, bacterial members play major functional roles in fostering plant growth and are regarded as plant growth-promoting bacteria (PGPB). One of the major bacterial genera of the plant microbiome that colonizes the entire plant system is the genus Methylobacterium. The genus Methylobacterium is categorized as a member of the class Alphaproteobacteria and is distinguished by its pink pigmentation, which is a result of the synthesis of carotenoids, mainly xanthophiles. Members of the Methylobacterium genus are commonly known as pink-pigmented facultative methylotrophs, which are ubiquitous in nature and have gained significant importance in crop production in various agricultural ecosystems because of their versatile ability to promote plant growth and enhance stress tolerance. They have the unique ability to utilize single-carbon compounds that are released during plant cell metabolism, improve plant growth, siderophore and phytohormone (auxin and cytokinin) production, and nitrogen fixation; phosphorous and zinc solubilization and induced systemic resistance against phytopathogens; protective biofilm formation; and the production of 1-aminocyclopropane-1-carboxylate deaminase to increase stress tolerance and carotenoid production for UV stress tolerance. Owing to its use as a biostimulant, biofertilizer and biocontrol agent, Methylobacterium has potential applications in agriculture for increasing soil health, crop productivity and environmental sustainability. This review provides broad perspectives on the multifaceted role and sustainable application of Methylobacterium in climate-smart agriculture.},
}

@article {pmid41076254,
year = {2025},
author = {Van De Grift, D and Kim, E and Yang, SM and Thibodeau, A and Cruickshank, J and Goddik, L and Park, SH},
title = {Investigation of seasonal microbiome changes in raw milk between conventional and organic farming practices.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-26743},
pmid = {41076254},
issn = {1525-3198},
abstract = {Raw milk microbiota is influenced by farming practices, environmental exposure, and seasonal changes. This study investigated how organic and conventional dairy farming practices influence the microbial composition of raw milk over a 1-yr period. Milk and environmental samples were collected quarterly from 7 dairy farms (4 organic and 3 conventional) in Oregon and analyzed using microbiome sequencing. Across all seasons, the microbial community of raw milk was largely similar between organic and conventional farms, with Escherichia-Shigella being the most abundant genus. Aerobic plate counts were significantly higher in conventional raw milk during winter and summer. Organic milk showed greater seasonal variation in α diversity (Shannon index 1.81 ± 0.40 in winter to 1.01 ± 0.34 in fall), whereas conventional milk remained more stable. No significant β diversity differences were observed between farming types. Shared microbial taxa between raw milk and environmental sources varied by season and farming type, reflecting the influence of confinement and grazing. For example, Romboutsia was more abundant during grazing seasons in organic farms, whereas Clostridium sensu stricto 1 appeared uniquely in conventional milk in winter. These seasonal and housing-related trends highlight how farm management shapes milk microbiota.},
}

@article {pmid41076098,
year = {2025},
author = {Karisola, P and Alenius, H},
title = {Environmental determinants of immune tolerance in asthma and allergy.},
journal = {Immunology letters},
volume = {},
number = {},
pages = {107102},
doi = {10.1016/j.imlet.2025.107102},
pmid = {41076098},
issn = {1879-0542},
abstract = {Prevalence of allergic diseases has increased globally, reflecting environmental and behavioral changes. The exposome concept encompasses cumulative chemical, microbial, nutritional, psychosocial, and physical exposures across the life course, offering a unifying framework to understand how immune tolerance is shaped or disrupted. Emerging evidence highlights that early-life exposures are particularly critical. Pollutants, endocrine disruptors, microbial deprivation, dietary shifts, and psychosocial stress contribute to barrier dysfunction, dysbiosis, and immune dysregulation, favoring Th2 dominance and allergy development. In contrast, exposures that enhance biodiversity, microbial diversity, pollution-free air, and balanced nutrition support active tolerance development, especially via regulatory T cells. Mechanistic insights point to the barrier-microbiota-immune axis as central pathways linking the environment to allergic outcomes. Translational studies, including biodiversity enrichment interventions, maternal and infant dietary strategies, and microbiome-based therapies, illustrate the potential of exposome-informed approaches to allergy prevention. However, major challenges remain in measuring complex exposure mixtures, identifying causal pathways, and integrating exposome data with systems immunology. This review synthesizes current knowledge on how the exposome modulates immune tolerance and outlines future research directions toward precision prevention. A deeper understanding of these interactions is essential to address the rising global allergy burden.},
}

@article {pmid41075923,
year = {2025},
author = {Da Silva, NDG and Santos, PSDS and Henrique-Silva, F and Magalhães, AC and Chiaratti, MR and de Jong, EJ and DenBesten, PK and Buzalaf, MAR},
title = {A novel artificial saliva enriched with CaneCPI-5 for irradiated head and neck cancer (HNC) patients: in vitro antimicrobial and anticaries effect.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106176},
doi = {10.1016/j.jdent.2025.106176},
pmid = {41075923},
issn = {1879-176X},
abstract = {OBJECTIVES: This study assessed the antimicrobial and anticaries potential of artificial saliva formulations containing CaneCPI-5, either alone or combined with fluoride and xylitol, designed for irradiated head and neck cancer (HNC) patients with hyposalivation. The impact of the combined formulation on microbial composition was also evaluated.

METHODS: Saliva from five irradiated HNC patients was mixed with McBain medium to form biofilms on irradiated bovine enamel specimens (70 Gy; n = 168). Treatments were applied for 1 minute before biofilm formation and then once daily for 5 days: artificial saliva (AS) base with 0.1% hydroxyethyl cellulose, 0.1% sodium benzoate, and 0.3% mint flavor, either alone, with 0.1 mg/mL CaneCPI-5 (AS+Cane), or with 0.1 mg/mL CaneCPI-5, 1500 ppm fluoride, and 10% xylitol (AS+Cane+F+Xyl, ASF). Controls included PBS (negative), 0.12% chlorhexidine (CHX, positive), and BioXtra® (BXT, commercial). Biofilm metabolic activity, bacterial viability, CFU counts, enamel demineralization, and microbial community composition were assessed.

RESULTS: AS+Cane+F+Xyl significantly reduced live biovolume, CFU counts, and mineral loss (ΔZ and RΔZ) compared with PBS (p < 0.001), with efficacy comparable or superior to BXT and CHX. AS+Cane also showed significant effects but with lower efficacy. ASF preserved overall microbial diversity while selectively enriching ASVs annotated as Streptococcus parasanguinis.

CONCLUSIONS: CaneCPI-5 formulations, particularly combined with fluoride and xylitol, exhibit considerable antimicrobial and enamel-protective effects while maintaining microbial diversity in this in vitro model.

CLINICAL SIGNIFICANCE: Cost-effective artificial saliva enriched with CaneCPI-5 represents a promising translational strategy for caries prevention in vulnerable populations, especially those undergoing radiotherapy for HNC.},
}

@article {pmid41075788,
year = {2025},
author = {Lane, MM and McGuinness, AJ and Mohebbi, M and Lotfaliany, M and Loughman, A and O'Hely, M and O'Neil, A and Batti, J and Kotowicz, M and Berk, M and Saunders, L and Page, R and Beattie, S and Marx, W and Jacka, FN},
title = {Food- vs. supplement-based very-low-energy diets and gut microbiome composition in women with high body mass index: A randomized controlled trial.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102417},
doi = {10.1016/j.xcrm.2025.102417},
pmid = {41075788},
issn = {2666-3791},
abstract = {In a single-blind, two-arm, randomized controlled-feeding trial (May 2021-February 2022), 47 women (30-65 years, BMI 30-45 kg/m[2]) are randomized to either a food-based or a supplement-based very-low-energy diet (VLED: 800-900 kcal/d) for 3 weeks. The food-based VLED comprises pre-packaged meals (∼93% whole-food ingredients), while the supplement-based VLED comprises shakes, soups, bars, and desserts (∼70% industrial ingredients). The primary outcome is species-level alpha diversity (Shannon index). Secondary outcomes include species richness, beta diversity, taxonomic composition, functional potential, anthropometrics, serum biomarkers, mental health, sleep, and gastrointestinal symptoms. Modified intention-to-treat (mITT) analyses (n = 45) assess diet group × time interactions as beta coefficients (β) with 95% confidence intervals (CIs). A between-group differential change is observed for the Shannon index, with a greater increase in the food-based group (mITT β: 0.37, 95% CI: 0.15-0.60). The food-based group also shows greater species richness, smaller beta diversity shifts, and compositional changes preserving fiber-degrading, health-associated taxa.},
}

@article {pmid41075532,
year = {2025},
author = {Ghafoor, D and Hayakijkosol, O and Prasetsincharoen, N and Chen, CCM and Noman, M and Chomchat, P and Kinobe, R},
title = {Characterisation of the gut microbiome and surveillance of antibiotic resistance genes in green sea turtles (Chelonia mydas).},
journal = {Marine environmental research},
volume = {212},
number = {},
pages = {107605},
doi = {10.1016/j.marenvres.2025.107605},
pmid = {41075532},
issn = {1879-0291},
abstract = {Green sea turtles (Chelonia mydas) are globally endangered marine herbivores that maintain the health of seagrass and coastal ecosystems. Their populations are declining due to human activities, including environmental pollution, which can disrupt gut microbial communities and compromise nutrition, immunity, and overall health. In this study, cloacal swabs from 139 green sea turtles categorised as captive juveniles, captive adults and wild stranded animals in the Gulf of Thailand, were analysed via shotgun metagenomic sequencing to elucidate bacterial taxonomic diversity and ARG profiles. In captive juveniles, Pseudomonadota was the most abundant phylum, followed by Ascomycota and Basidiomycota. In captive adults, Pseudomonadota exhibited an even greater predominance, with only minor contributions from unclassified bacteria and other taxa. In wild stranded green sea turtles, Pseudomonadota was dominant in their gut microbiome, but this was accompanied by notable levels of Actinomycetota, Bacteroidota, and Bacillota. Stranded turtles exhibited highest microbial diversity and variability, while captive adult turtles showed the lowest. Resistome profiling also revealed significant differences in the relative abundance of antibiotic resistance genes across all three groups. MacB (macrolide resistance) was the most abundant gene overall, with the highest abundance observed in juveniles (4.8 %). Stranded turtles exhibited elevated levels of TetA(58) (tetracycline resistance, 2.6 %) and msbA (nitroimidazole resistance, 2.2 %), while adults showed the greatest enrichment of Ecol_fabG_TRC (triclosan resistance, 3.8 %) and TxR (tetracycline resistance, 3.6 %). These data demonstrate that marked variability existed in the gut microbiome and resistome of green sea turtles across different life stages in captive or wild environments. This offers critical insights for the development of targeted conservation strategies and health management practices for both wild and captive green sea turtles. Strategies to mitigate the spread of antibiotic resistance should be developed.},
}

@article {pmid41075498,
year = {2025},
author = {Dias, MF and Nogueira, YJA and de Albuquerque, GS and Romano-Silva, MA and de Miranda, DM},
title = {A systematic review on the associations between Attention-Deficit/Hyperactivity Disorder and gut microbiome.},
journal = {Journal of psychiatric research},
volume = {191},
number = {},
pages = {597-603},
doi = {10.1016/j.jpsychires.2025.10.008},
pmid = {41075498},
issn = {1879-1379},
abstract = {Attention-Deficit/Hyperactivity Disorder (ADHD) is a prevalent neurodevelopmental condition in childhood, and growing evidence suggests a potential link between gut microbiome (GM) and ADHD symptoms via the microbiota-gut-brain axis. This systematic review aimed to evaluate current evidence on the associations between human GM and ADHD, addressing microbial composition, diversity measures, and potential pathways through which microbiota could be associated with the symptoms. A systematic search was conducted in PubMed, Embase, and Scopus databases. Fourteen studies met the eligibility criteria, which focused on original research assessing GM characteristics in individuals with ADHD. Selected articles comprised a total of 1319 participants, 67 % male, from Europe (53 %) and East Asia (47 %), mostly with children and adolescents aged 4-18 years. Alterations in microbial composition were observed among ADHD patients; including higher relative abundance of Agathobacter and Ruminococcus gnavus and decreased Faecalibacterium, identified in different studies. Results regarding alpha- and beta-diversity were inconclusive. There was also evidence of links between GM and inflammatory markers and neurotransmitter-related pathways. Despite current limitations, emerging data suggest that GM may play a role in ADHD pathophysiology, supporting its potential as a target for personalized therapeutic strategies.},
}

@article {pmid41075387,
year = {2025},
author = {Godefroy, E and Altare, F},
title = {Deciphering and harnessing gut microbiota-associated immune regulation in acute graft-versus-host disease.},
journal = {Current opinion in immunology},
volume = {97},
number = {},
pages = {102676},
doi = {10.1016/j.coi.2025.102676},
pmid = {41075387},
issn = {1879-0372},
abstract = {Allogeneic hematopoietic stem cell transplantation represents a curative treatment of choice for numerous severe hematological malignancies. While donor-derived transplanted T cells can limit disease relapse (GvT/GvL effect), they also induce, in 30-50% of the patients, acute graft-versus-host disease (aGvHD), a severe condition with elevated mortality and comorbidity rates. Gut microbiota composition has been associated with aGvHD outcome. This observation created a substantial research interest, and individual gut microbiota commensals have been acknowledged for their ability to promote immune regulation, both locally and systemically, and thus limit aGvHD-related inflammation. The mechanisms by which commensals support immune homeostasis are being decrypted at a remarkable rate. However, the trillions of micro-organisms comprising the gut microbiome interact, both directly and indirectly, with local immune cells, which is all the more critical in the context of heavy conditioning regimens these patients undergo, themselves damaging mucosal tissues and prompting inflammation. Commensals can help preserve the gut barrier integrity by actively limiting deleterious inflammation processes. Mechanistically deciphering the intricate crosstalk between gut microbes and gut immune cells, both at the species level and globally, represents a colossal challenge, but holds great promise in predicting and harnessing numerous pathological processes, including aGvHD. This review aims to examine the acquired knowledge concerning immunoregulatory responses driven by gut microbiota in the context of aGvHD. Recent preclinical and clinical studies harnessing such pathways proved to be encouraging, while substantial hurdles subsist regarding how to successfully harness this complex host/microbiota interplay to constrain aGvHD.},
}

@article {pmid41075335,
year = {2025},
author = {Ghaffar, A and Liljebjelke, K and Checkley, SL and Farooq, M and Abdul-Careem, MF},
title = {Exploring the indoor airborne microbiome and resistome in layer barns across Alberta, Canada.},
journal = {Research in veterinary science},
volume = {196},
number = {},
pages = {105930},
doi = {10.1016/j.rvsc.2025.105930},
pmid = {41075335},
issn = {1532-2661},
abstract = {The air in poultry barns carries a diverse range of microbial communities including potential opportunistic pathogens, which are important for both animal and human health. Bacteria carrying antimicrobial resistance genes (ARGs) can become airborne within poultry barns and be transmitted to animals and poultry workers, presenting a serious One Health concern. This study was aimed at characterizing the microbiome and resistome of bioaerosols sampled from layer chicken barns across Alberta. In total, 15 barns (9 cage housed and 6 floor housed) were sampled in this study using a microbial air sampler to characterize the microbiome and resistome using a shotgun metagenomic sequencing approach. The most abundant bacterial phyla found in the air of both housing systems for pullets were Bacilliota, Actinomycetota, and Bacteroidota. The respiratory pathogens such as Gallibacterium anatis, Ornithobacterium rhinotracheale, and Pasteurella multocida were relatively more abundant in the air of cage-housed barns, whereas Escherichia coli and Avibacterium paragallinarum were more prevalent in floor-housed barns. In total, 113 unique ARGs subtypes from 19 classes of antimicrobials were identified in this study. ARGs were significantly more abundant in the air of cage-housed barns compared to floor-housed barns. In particular, genes associated with resistance to tetracyclines, lincosamides, and macrolides were more frequently detected in cage-housed environments. Overall, both microbial and resistance gene levels were higher in the bioaerosols of cage-housed barns than in those from floor-housed pullet barns. The study results demonstrate the potential for air as a reservoir of ARGs and highlights microbial differences within cage and floor housing.},
}

@article {pmid41075060,
year = {2025},
author = {Fernández-Lucas, J},
title = {From tradition to innovation: the ongoing evolution of AMB express.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {147},
doi = {10.1186/s13568-025-01970-x},
pmid = {41075060},
issn = {2191-0855},
abstract = {Since its foundation in 2011, AMB Express has grown from a journal focused on classical applied microbiology and industrial biotechnology into a multidisciplinary platform covering microbiome research, antimicrobials, biocatalysis, and synthetic biology. In this Editorial, an overview of our journal's evolution is provided, along with an outline of the directions in which it should develop to maintain its status as a reference journal of applied microbiology and biotechnology.},
}

@article {pmid41075036,
year = {2025},
author = {Hatami, F and Aghelan, Z and Pouya, MR and Moulaeian, M and Rastegari, A and Abtahi, SH and Hoseini, S},
title = {Gut microbiota reconstitution and control of α-synucleinopathy with β-glucans: a promising approach for individuals with parkinson's disease.},
journal = {Metabolic brain disease},
volume = {40},
number = {7},
pages = {287},
pmid = {41075036},
issn = {1573-7365},
mesh = {*Gastrointestinal Microbiome/drug effects/physiology ; Humans ; *Parkinson Disease/drug therapy/metabolism/microbiology ; *alpha-Synuclein/metabolism ; *beta-Glucans/therapeutic use/pharmacology ; Animals ; *Synucleinopathies/drug therapy/metabolism ; Dysbiosis/drug therapy/metabolism ; },
abstract = {Parkinson's disease (PD) ranks as the second most prevalent neurodegenerative condition affecting individuals in their middle age and beyond. Its hallmark features include the abnormal accumulation of α-synuclein protein and the progressive loss of dopaminergic neurons. A substantial body of evidence supports the notion that an imbalance in the gut microbiome, known as dysbiosis, contributes to the misfolding and accumulation of α-synuclein, a key pathological feature of PD. This finding raises the possibility that restoring the gut microbiome, particularly the bacteria associated with α-synuclein, could serve as a promising therapeutic approach for PD. There is evidence that β-glucan can play an important role in the reconstitution of gut microbiome. In this regard, this study reviews the evidence showing the role of β-glucan in reducing α-synuclein accumulation and mitigating the progression of PD. This scooping review study presents promising prospects for advancing novel therapeutic approaches to benefit individuals with PD.},
}

*Gastrointestinal Microbiome/drug effects/physiology
Humans
*Parkinson Disease/drug therapy/metabolism/microbiology
*alpha-Synuclein/metabolism
*beta-Glucans/therapeutic use/pharmacology
Animals
*Synucleinopathies/drug therapy/metabolism
Dysbiosis/drug therapy/metabolism

@article {pmid41074949,
year = {2025},
author = {Malik, MZ and Nizam, R and Jacob, S and Al Alqaderi, H and Al-Mulla, F and Alqaderi, H},
title = {Microbial dysbiosis in oral cavity determines obesity status in adolescents.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {82},
number = {1},
pages = {354},
pmid = {41074949},
issn = {1420-9071},
support = {Institutional Funding//Kuwait Foundation for the Advancement of Sciences/ ; },
mesh = {Humans ; Adolescent ; *Dysbiosis/microbiology ; Female ; Male ; *Mouth/microbiology ; *Obesity/microbiology ; Microbiota/genetics ; Saliva/microbiology ; Body Mass Index ; Kuwait ; },
abstract = {The prevalence of obesity is rapidly increasing among adolescents in Kuwait. The ecological and dynamic changes within the oral microbiota during this developmental stage remain elusive. This study aimed to investigate the impact of body mass index (BMI) on salivary microbiome diversity and composition in Kuwaiti adolescents by utilizing next-generation sequencing technologies. DNA was extracted from saliva samples of 62 Kuwaiti adolescents enrolled in the nationwide Kuwait Healthy Lifestyle Study, categorized as underweight, normal weight, overweight, and obese based on their BMI percentiles. The 16 S metagenomic profiling was performed to identify the key oral lineages and genera associated with obesity through comprehensive analysis involving taxonomic composition, co-occurrence networks, and key metabolic profiles. Our study reveals an inverse relationship between oral bacterial diversity and obesity status in Kuwaiti adolescents. The obese and overweight groups showed comparatively low microbial taxa compared to those of normal weight. We identified three potential microbial biomarkers linked to obesity and overweight: Prevotella melaninogenica, Veillonella dispar, and Veillonella parvula. The abundance of Neisseria subflava and Rothia mucilaginosa in normal weight adolescents indicates their role in weight homeostasis. In- silico analysis of differentially expressed microbiota revealed increased activity of major metabolic enzymes such as glucose- 6- phosphate dehydrogenase, pyruvate oxidase, and glycogen phosphorylase, along with oxidative stress- related enzymes including superoxide reductase and glutathione peroxidase in obese and over-weight adolescents. Conversely, normal weight adolescents exhibited heightened activity of pyruvate synthase and tRNA- methyltransferase, which are linked to antioxidative pathways and balanced energy metabolism. Our study highlights taxonomic and functional shifts in the oral microbiota of Kuwaiti adolescents across varying BMI categories, signifying key microbial markers that could pave the way for future research focused on microbiome- targeted interventions in obesity management.},
}

Humans
Adolescent
*Dysbiosis/microbiology
Female
Male
*Mouth/microbiology
*Obesity/microbiology
Microbiota/genetics
Saliva/microbiology
Body Mass Index
Kuwait