@article {pmid41161812,
year = {2025},
author = {Tiwari, R and Tiwari, G and Gupta, A and Ramachandran, V},
title = {The Role of Non-Helicobacter Pylori Bacteria in the Pathogenesis of Gastric Diseases.},
journal = {Zhongguo ying yong sheng li xue za zhi = Zhongguo yingyong shenglixue zazhi = Chinese journal of applied physiology},
volume = {41},
number = {},
pages = {e20250027},
doi = {10.62958/j.cjap.2025.027},
pmid = {41161812},
issn = {1000-6834},
mesh = {Humans ; Helicobacter pylori ; Dysbiosis/microbiology ; *Stomach Diseases/microbiology ; Stomach Neoplasms/microbiology ; Helicobacter Infections/microbiology ; *Gastrointestinal Microbiome ; Fusobacterium nucleatum ; Lactobacillus ; },
abstract = {In the context of dysbiosis, chronic inflammation, and carcinogenesis, non-Helicobacter pylori bacteria are becoming more widely acknowledged as significant contributors to stomach diseases. The stomach contains a variety of bacterial communities, including Fusobacterium nucleatum, Streptococcus species, Lactobacillus species, Prevotella species, Veillonella species, and Propionibacterium acnes, according to studies employing next-generation sequencing. Because of adaptation processes like urease activity, acid-tolerant metabolism, and biofilm development, these organisms can survive in acidic environments. While some, like Lactobacillus, can create metabolites like lactic acid that may impact carcinogenic nitrosation reactions, others, including F. nucleatum and Streptococcus, cause inflammation through immune activation and cytokine production. A known stomach carcinogen, N-nitroso compound, may be formed more frequently if nitrate-reducing bacteria proliferate. Following H. pylori eradication, dysbiosis frequently involves elevated abundance of these taxa, which may impact stomach cancer risk and mucosal integrity. The need for more comprehensive microbiome-targeted therapeutic approaches is highlighted by mounting evidence that non-H. pylori bacteria interact either antagonistically or synergistically with H. pylori and host factors, causing intestinal metaplasia, gastritis, and tumour progression, even though causality is still being investigated.},
}

Humans
Helicobacter pylori
Dysbiosis/microbiology
*Stomach Diseases/microbiology
Stomach Neoplasms/microbiology
Helicobacter Infections/microbiology
*Gastrointestinal Microbiome
Fusobacterium nucleatum
Lactobacillus

@article {pmid41161643,
year = {2025},
author = {Wei, Y and Song, X and Jia, Z and Liu, X and Chen, X and Zhan, X and Mei, X and Liao, L},
title = {Gut Microbiota-Mediated Amino Acid Reprogramming in Ketamine-Induced Neurotoxicity: A Novel Microbiota-Amino Acid-Mitochondrial Axis Associated with Cognitive Deficits.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {110748},
doi = {10.1016/j.neuropharm.2025.110748},
pmid = {41161643},
issn = {1873-7064},
abstract = {Ketamine, a noncompetitive N-methyl-D-aspartate receptor antagonist, is associated with chronic abuse leading to schizophrenia-like cognitive deficits. The gut-brain axis may play a role in mediating substance-induced neurotoxicity; however, its involvement in ketamine-induced cognitive impairment remains poorly understood. Here, chronic ketamine exposure was administered intraperitoneally to C57BL/6N mice to examine its effects on gut microbiota homeostasis and associated amino acid metabolism. Cognitive deficits were evaluated using the Y-maze and novel object recognition (NOR) tests. Hippocampal ultrastructure was assessed by transmission electron microscopy (TEM). Multi-omics integration included 16S rRNA sequencing, untargeted and targeted plasma metabolomics, and Spearman correlation analysis. The results showed that ketamine-exposed mice exhibited significant cognitive impairments, including impaired spontaneous alternation in the Y-maze (P< 0.05) and a reduced discrimination index in the NOR test (P< 0.01). TEM analysis revealed hippocampal mitochondrial damage, accompanied by chromatin condensation. Gut microbiota analysis indicated dysbiosis, with a notable increase in Lachnospiraceae, Bacteroidaceae, Helicobacteraceae, and Rikenellaceae and a decrease in Verrucomicrobiaceae and Prevotellaceae at the family level. Plasma amino acid levels were also disrupted, with a significant decrease in L-glutamine, L-lysine, L-threonine and an increase in L-cysteic acid. Furthermore, strong correlations were observed between the abundance of Bacteroides, branched-chain amino acids (BCAAs), and cognitive scores (|ρ| > 0.6, P< 0.05). This study identifies the microbiota-amino acid-mitochondrial axis as the underlying mechanism driving ketamine-induced neurotoxicity. It highlights the correlation between gut microbiota-associated amino acid reprogramming and this process, offering potential targets for microbiome-based interventions to combat substance-related cognitive impairments.},
}

@article {pmid41161627,
year = {2025},
author = {Li, M and Yan, Z and Hua, W and Gong, S and Wang, Y and Chen, H and Zhang, S and Qian, J},
title = {The Chinese herbal formular Kang Shuai Lao Pian enhances health status for skin, adipose-derived stem cells, intestinal microbes and metabolites in naturally senescent mice.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {120807},
doi = {10.1016/j.jep.2025.120807},
pmid = {41161627},
issn = {1872-7573},
abstract = {Aging is a time-dependent decline in physiological function that reduces quality of life. In traditional Chinese medicine (TCM), aging is viewed as "deficiency" complicated by blood stasis and qi stagnation. "Kang Shuai Lao Pian" (KSLP) is a Ming Dynasty herbal formula widely used to repenish qi, nourish yin, calm the heart, and tranquilize the mind.

AIM OF THE STUDY: We aimed to evaluate the systemic anti-aging activity of KSLP and to decline its mode of action in naturally senescent mice.

MATERIALS AND METHODS: Male 16-18-month-old mice received daily intragastric gavage of KSLP (450 mg/kg) for 8 weeks. Skin structure, adipose distribution, neurotransmitters, adipose-derived stem cells (ADSCs) morphology and differentiation, 16S rRNA gene sequencing and untargeted metabolomics analysis of cecal feces were assessed. RNA sequencing (RNA-Seq) was performed on senescent ADSCs; metabolic-microbe correlations were analyzed by Pearson correlation.

RESULTS: KSLP restored skin structure and dermal collagen density, normalized dopamine, norepinephrine, acetylcholine, and 5-hydroxytryptamine levels, and improved ADSCs osteogenic/adipogenic capacity- changes mechanistically linked to PI3K-Akt and cytokine-cytokine receptor interaction signaling pathways. In gut, KSLP reversed age-associated shifts in Firmicutes, Epsilonbacteraeota, Ruminococcaceae, and Helicobacter and modulated 57 metabolites particularly within amino acid, fatty acid, and nucleotide metabolic pathways. Correlation analysis identified Ruminococcaceae_UCG_014, Candidatus_Saccharimonas, Helicobacter, Rikenellaceae_RC9, and Ileibacterium as keystone taxa linked to KSLP-responsive metabolites.

CONCLUSION: KSLP systemically improves skin architecture, ADSCs function, gut-microbiome balance, and metabolic profiles in naturally aged mice, supporting its clinical potential against age-related decline. Bioactivity-guided identification of active compounds and in vivo mechanistic validation are warranted.},
}

@article {pmid41161169,
year = {2025},
author = {Gao, M and Yu, W and Ren, J and Peng, H and Dong, Y and Qiu, W and An, Y and Xiao, Z and Niu, J and Song, Z},
title = {Impacts of foliar-applied polystyrene nanoplastics with different surface charges on tetracycline accumulation, phytotoxicity, and the endophytic microbiota in Chrysanthemum coronarium L.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140276},
doi = {10.1016/j.jhazmat.2025.140276},
pmid = {41161169},
issn = {1873-3336},
abstract = {Plant leaves represent a critical interface for the deposition of atmospheric nanoplastics (NPs). However, the effects of foliar-deposited NPs on antibiotic uptake and phytotoxicity are still poorly understood. This study investigated the effects of foliar application of polystyrene (PS), carboxyl-polystyrene (PSC), and amino-polystyrene (PSN) NPs on Chrysanthemum coronarium L., focusing on NPs internalization, their modulation of root-zone tetracycline (TC) uptake, and associated phytotoxic responses. Results showed that positively charged PSN significantly reduced TC accumulation in both roots (by 20.7 %-23.2 %) and leaves (by 13.6 %-15.1 %), followed by PSC and PS. Conversely, TC promoted NP retention in stomata and induced stomatal deformation. PSN exerted stronger inhibition on iron uptake and chlorophyll synthesis than PSC or PS, ultimately suppressing plant biomass more significantly. Although catalase activity increased, superoxide dismutase was significantly suppressed under NP exposure. This imbalance in antioxidant defense resulted in marked accumulation of reactive oxygen species and elevated malondialdehyde content in both leaves and roots. Under TC stress, NP spraying further exacerbated growth inhibition and oxidative damage. Microbiome analysis revealed that PSN increased bacterial richness in leaves but reduced Shannon diversity in roots. While foliar NPs exposure had limited impact on alpha diversity in TC-treated plants, it significantly enhanced microbial evenness in leaves. Notably, all three NPs induced only minor changes in the abundance of the keystone genus Pseudomonas, regardless of TC treatment. Overall, these findings demonstrate that atmospheric NPs act as key co-pollutants that alter contaminant bioavailability, intensify phytotoxicity, and reshape the composition of endophytic microbial communities.},
}

@article {pmid41161167,
year = {2025},
author = {Jawad, M and Xu, H and Nasir, S and Yin, J and Wu, C and Wang, A and Hong, N and Li, M},
title = {Microbial dysbiosis and hepatic inflammation under combined pesticide exposure: Insights into gut-liver axis disruption in Japanese medaka.},
journal = {Journal of hazardous materials},
volume = {499},
number = {},
pages = {140295},
doi = {10.1016/j.jhazmat.2025.140295},
pmid = {41161167},
issn = {1873-3336},
abstract = {Environmental pesticides such as fenvalerate (FEN) and tebuconazole (TEB) frequently co-occur in aquatic ecosystems, yet their combined impacts on gut-liver immune communication remain poorly understood. This study evaluated the chronic toxicity of FEN (0.029 mg/L), TEB (1 mg/L), and their mixture (0.01 mg/L FEN + 0.5 mg/L TEB) in adult Japanese medaka (Oryzias latipes) through an integrative approach encompassing histopathology, biochemical assays, gut microbiota profiling, and hepatic transcriptomics. Co-exposure induced significant (p < 0.05) intestinal pathology characterized by epithelial degeneration, compromised barrier integrity, and suppression of digestive and immune enzyme activities. Corresponding hepatic alterations were also significant (p < 0.05), including vacuolization, inflammatory infiltration, oxidative stress, and activation of apoptosis-related signaling pathways. Gut microbiome analysis revealed pesticide-induced dysbiosis correlated with transcriptomic changes in hepatic lipid metabolism and immune regulation, suggesting that microbial imbalance may contribute to hepatic dysfunction through gut-liver axis communication. Molecular docking further indicated that tebuconazole (TEB) exhibited a stronger binding affinity to apoptotic proteins P53 and Caspase-3 than fenvalerate (FEN), consistent with the observed upregulation of apoptosis-related genes. Collectively, this study highlights the immune-metabolic toxicity of pesticide mixtures and identifies molecular and microbial signatures relevant to environmental risk assessment.},
}

@article {pmid41161092,
year = {2025},
author = {Gu, M and Peng, X and Dai, X and Ma, X and Ge, W and Yang, S and Wei, W},
title = {Tannic acid decreased the synthesis and secretion of sIgA in the small intestine of Brandt's voles (Lasiopodomys brandtii) by modifying gut microbiota.},
journal = {Biochemical and biophysical research communications},
volume = {789},
number = {},
pages = {152846},
doi = {10.1016/j.bbrc.2025.152846},
pmid = {41161092},
issn = {1090-2104},
abstract = {Tannic acid (TA), a representative plant secondary metabolite, impairs intestinal immune function and alters intestinal microbiota abundance of Brandt's voles. Whether TA reduces intestinal immune function by modifying the gut microbiota remains unknown. In this study, Brandt's voles were divided into three groups for microbiota transplantation (FMT): normal saline (Ab), microbiota from normal saline administration (R-Con), and microbiota from TA administration (R-TA). Then, the intestinal morphology, immune indices, gut flora, and microbiota metabolites were measured after FMT. The findings showed that the sIgA content of small intestine of voles in the R-TA group were lower than in the R-con group. Additionally, the voles in the R-con group exhibited higher mRNA levels of PIgR, J-chain, BAFF, and APRIL than in the R-TA group. The ANOSIM results showed significant structural differentiation, reflecting that the β-diversity of the cecal microbiome was altered. Moreover, the voles in the R-con group had a higher concentration of butyric acid in the cecum compared to both the Ab and R-TA groups. In the experiment 2, the sIgA content in the duodenum and ileum of Brandt's voles in the TBA group (1200 mg•kg[-1]d[-1] TA + butyrate) was significantly higher than that in the TNS group (1200 mg•kg[-1]d[-1] TA + normal saline). To summarize, the "TA microbiota" decreased the slgA secretion and synthesis in the small intestine by reducing butyric acid content, thus lowering the intestinal immune capacity of Brandt's voles. The findings provide the experimental basis to prove the critical role of gut microorganisms in controlling animal physiological processes.},
}

@article {pmid41160854,
year = {2025},
author = {Kaliga, AM and Palladina, OL and Dulo, OA and Burmei, SA and Shtanagei, DV and Boyko, NV},
title = {Dynamics of gut microbiota in qualified female boxers.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {78},
number = {9},
pages = {1765-1770},
doi = {10.36740/WLek/212509},
pmid = {41160854},
issn = {0043-5147},
mesh = {Humans ; Female ; *Gastrointestinal Microbiome/physiology ; Adult ; Dysbiosis/microbiology ; *Exercise/physiology ; },
abstract = {OBJECTIVE: Aim: To analyze changes in the gut microbiota of qualified female boxers at different stages of the training cycle, influenced by physical activity of different intensity.

PATIENTS AND METHODS: Materials and Methods: The study involved nine qualified female boxers, who performed high-intensity training sessions. The study of changes in the state of the microbiota, namely its diversity, was carried out in two phases of the training cycle. A microbiological quantitative method was used, in-depth with species identification and detection of anaerobes, the unit of measurement of which was colony-forming units per gram (CFU/g). The quantitative assessment of microorganisms was performed using arithmetic mean values expressed and log-transformed values (log₁₀ CFU/g).

RESULTS: Results: High-intensity training loads were associated with microbiota changes indicative of dysbiosis. It is noticeable that the concentration of typical pathogenic genera (Candida albicans, Klebsiella pneumoniae, Streptococcus) significantly increased during the post-competition period. At the same time, classic "beneficial" bacteria (Lactobacillus and Bifidobacterium) remained within normal limits, although Bifidobacterium showed some growth. Notably, Escherichia coli (a normal representative of the microbiome) exceeded the norm during the post-competition period.

CONCLUSION: Conclusions: Increased training intensity in qualified female boxers resulted in alterations in gut microbiota composition, most notably a significant rise in Escherichia coli and other opportunistic microbes, while the levels of beneficial Lactobacillus and Bifidobacteria species remained relatively stable. These changes suggest early signs of dysbiosis, consistent with current evidence on the impact of extreme physical exertion on microbial health.},
}

Humans
Female
*Gastrointestinal Microbiome/physiology
Adult
Dysbiosis/microbiology
*Exercise/physiology

@article {pmid41160784,
year = {2025},
author = {Sims, TT and Yoshida-Court, K and El Alam, MB and Ramatlho, P and Ketlametswe, R and Ning, MS and Robertson, ES and Schmeler, KM and Colbert, LE and Klopp, AH and Grover, S},
title = {Cervical and Tumor-Associated Microbiomes in Botswana Women With and Without HIV With Carcinoma of the Cervix Before and After Definitive Chemoradiation.},
journal = {JCO global oncology},
volume = {11},
number = {},
pages = {e2500036},
doi = {10.1200/GO-25-00036},
pmid = {41160784},
issn = {2687-8941},
mesh = {Female ; Humans ; *Uterine Cervical Neoplasms/therapy/microbiology/pathology ; *Microbiota ; Botswana/epidemiology ; *HIV Infections/complications/microbiology/virology ; *Chemoradiotherapy/methods ; Middle Aged ; Adult ; *Cervix Uteri/microbiology ; },
abstract = {PURPOSE: Cervical cancer remains a significant public health concern globally and particularly in sub-Saharan Africa, where high rates of HIV infection exacerbate cervical cancer incidence. Understanding the cervical microbiome and its role in cancer progression is essential, especially in regions where both cervical cancer incidence and HIV prevalence are high. This study aimed to characterize the cervical microbiome in women living with HIV (WLWH) and HIV-negative women with squamous cell carcinoma of the cervix in Botswana, compare the microbiome between before and after chemoradiation therapy (CRT) in WLWH, and assess the prognostic value of specific microbial taxa for overall survival (OS) in WLWH.

PATIENTS AND METHODS: Cervical samples were collected from women with cervical cancer presenting to one hospital in 2018-2019. Patients' clinical data, including HIV status, were recorded. Microbial composition was analyzed using 16S rRNA gene sequencing. Microbiome diversity and composition were evaluated using alpha and beta diversity metrics. Differential microbial abundance was analyzed using linear discriminant analysis effect size. The association between microbial taxa and OS was explored using Cox proportional hazards regression.

RESULTS: WLWH (n = 42) had a significantly lower Pielou evenness index than HIV-negative women (n = 11; 0.6 v 0.7, P = .02), suggesting a more imbalanced microbiome in WLWH. WLWH had higher levels of Parvimonas and members of the Corynebacteriaceae and Micrococcaceae families, suggesting a shift toward a more pathogenic microbiome. In WLWH, CRT did not significantly alter overall microbial diversity. However, Lactobacillus and Sutterella were enriched before treatment, reflecting a less pathogenic microbiome, whereas Ruminococcus and Phascolarctobacterium and the families Caulobacterales and Flavobacteriia were enriched after treatment, reflecting microbial adaptations to the altered immune and treatment environment. Notably, higher levels of Flavobacteriia after CRT were independently associated with worse OS in WLWH.

CONCLUSION: Microbiome profiles differ between WLWH and HIV-negative women with cervical cancer in Botswana. The microbiome might have prognostic significance. Future research is needed to better understand the significance of the microbiota in cervical cancer progression and treatment outcomes and the potential role of microbiome-targeted interventions.},
}

Female
Humans
*Uterine Cervical Neoplasms/therapy/microbiology/pathology
*Microbiota
Botswana/epidemiology
*HIV Infections/complications/microbiology/virology
*Chemoradiotherapy/methods
Middle Aged
Adult
*Cervix Uteri/microbiology

@article {pmid41160438,
year = {2025},
author = {Iturbe-Espinoza, P and Sapkota, R and Ellegaard-Jensen, L and Bruun, EW and Winding, A},
title = {Effect of biochar on extracellular enzyme activity and microbiome dynamics across coarse sandy soil depths.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf105},
pmid = {41160438},
issn = {1574-6941},
abstract = {The aim was to assess the effect of straw biochar on microbiomes along the depth (30 to 80 cm) of two coarse sandy subsoils. We hypothesized that biochar modifies extracellular enzyme activities (EEA), and diversity and structure of microbiomes across the subsoil depths. Two subsoils were amended with straw biochar (0-4% w/w) and incubated for 16 months in a column experiment with two cultivations of spring barley. EEA were assessed using fluorogenic assays, while the prokaryotic and fungal communities were analyzed via 16S rRNA gene and ITS2 amplicon sequencing, respectively. Biochar significantly increased water holding capacity and pH. It also significantly decreased the phosphomonoesterase activity, suggesting enhanced soil phosphate bioavailability. In both subsoils, biochar significantly increased the prokaryotic α-diversity index. Biochar impacted prokaryotic community structures more than fungal community structures. Prokaryotic community structures were significantly different with increasing biochar content at deeper soil depths. Moreover, in both subsoils, biochar significantly increased the relative abundance of a prokaryotic consortium. We conclude that the biochar-induced improvements in physicochemical soil properties stimulate microbial diversity and functional activity across varying depths in coarse sandy subsoils. These findings are valuable for assessing the potential benefits of biochar application on agricultural subsoil health.},
}

@article {pmid41160423,
year = {2025},
author = {Medina-Rivero, AS and Ratkovich-Gonzalez, S and Ruiz-Briseño, MDR and Rosas-González, VC},
title = {The Role of Cervicovaginal Microbiota and Probiotics in Modulating HPV Persistence and Preventing Cervical Cancer.},
journal = {ACS infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsinfecdis.5c00385},
pmid = {41160423},
issn = {2373-8227},
abstract = {Cervical cancer (CC) is one of the leading causes of mortality in women worldwide, where the main risk factor is infection with the human papillomavirus (HPV). This type of cancer is a significant public health problem, especially in regions with limited access to health care and vaccination programs. In recent years, the crucial link between the cervicovaginal microbiota and immune homeostasis has been highlighted, emphasizing its protective role against infections, including HPV. The cervicovaginal microbiota is composed mostly of bacteria of the Lactobacillus genus, important for female health and pH maintenance. Many studies have documented the role of vaginal dysbiosis in patients with intraepithelial lesions and CC. This dysbiosis is characterized by an increase in anaerobic bacteria as well as an increase in the microbial diversity, which create an inflammatory microenvironment that contributes to tissue damage and HPV persistence, favoring progression to invasive cancer. Recently, the use of probiotics in oral and topical forms as well as the vaginal microbiota transplantation have been explored to restore the balance of the vaginal microbiota and enhance the immune response against HPV. However, a lack of global standardization and ethical issues have had an impact on the formal development of these interventions. We propose that modulation of the vaginal microbiota by probiotics represents a valuable complementary strategy against CC. Future research should focus on clinical trials evaluating the efficacy of probiotics in modulating the vaginal microbiome and their impact on CC incidence and progression.},
}

@article {pmid41160388,
year = {2025},
author = {Montazeri-Najafabady, N},
title = {From One-Size-Fits-All to Precision Medicine: The Promise of Personalized Probiotics.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41160388},
issn = {1867-1314},
abstract = {The paradigm of probiotic supplementation is shifting from a generic, one-size-fits-all model toward a precision-based approach tailored to the individual's unique microbiome. This review synthesizes current evidence on the development of personalized probiotic therapies, underpinned by advances in genomics and multi-omics technologies. We explore key probiotic genera-such as Lactobacillus, Bifidobacterium, and next-generation microbes-detailing their strain-specific mechanisms of action and functional roles in modulating host physiology. Our analysis of clinical applications reveals that personalized probiotic strategies can effectively reshape microbial community structure, enhance immune modulation, and ameliorate various conditions, including metabolic syndromes, gastrointestinal disorders, and neuroimmune diseases. Furthermore, we identify that the most successful interventions are those informed by pre-treatment microbial profiling, which predicts therapeutic efficacy. Despite this promise, significant challenges remain, including the lack of standardized frameworks for strain selection, limited large-scale clinical validation, and unresolved regulatory and ethical hurdles pertaining to data privacy and microbiome manipulation. This review concludes that while personalized probiotics hold immense potential to revolutionize therapeutic interventions by delivering targeted, safe, and effective microbial therapeutics, future research must prioritize the development of clinical guidelines and address these translational gaps to fully realize this potential.},
}

@article {pmid41160345,
year = {2025},
author = {Beswick, G and Major, N and Hendrickson, C and Kumar, V and Waller, M and Durrani, Z and Hotchkiss, S and Bala, A and Taylor, VH},
title = {A Scoping Review on the Role of the Microbiome as a Factor in the Bidirectional Association Between Obesity and Depression.},
journal = {Current diabetes reports},
volume = {25},
number = {1},
pages = {56},
pmid = {41160345},
issn = {1539-0829},
mesh = {Humans ; *Obesity/microbiology/complications ; *Gastrointestinal Microbiome/physiology ; *Depression/microbiology ; Inflammation/microbiology ; },
abstract = {PURPOSE OF REVIEW: Obesity is a chronic illness highly comorbid with mental health conditions, particularly depression. Among the factors involved in this association, inflammation is a consistently identified link. This review explores the emerging role of the gut microbiota as a modulator of inflammation and its potential involvement in the pathophysiological processes linking obesity and depression.

RECENT FINDINGS: Chronic low-grade inflammation is observed in both obesity and depressive disorders. Alterations in gut microbiota are increasingly implicated in inflammatory mechanisms, including increased intestinal permeability, immune activation, and short-chain fatty acid (SCFA) production, influencing leukocyte function and cytokine production. Additionally, both obesity and depression are associated with altered microbial composition. The gut microbiome contributes to chronic inflammation relevant to the pathophysiology of both obesity and depression. Accumulating evidence highlights the need for further research into how gut microbiota influences inflammatory mechanisms observed in both obesity and depression.},
}

Humans
*Obesity/microbiology/complications
*Gastrointestinal Microbiome/physiology
*Depression/microbiology
Inflammation/microbiology

@article {pmid41160321,
year = {2025},
author = {de Azevedo, CS and Schork, IG and Passos, LF and Goodhead, I and Young, RJ},
title = {The domestic cat microbiome: mapping knowledge gaps through scientometric analysis in feline microbial research.},
journal = {Veterinary research communications},
volume = {50},
number = {1},
pages = {6},
pmid = {41160321},
issn = {1573-7446},
mesh = {Animals ; Cats/microbiology ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {In this study, we present the first comprehensive scientometric analysis of research on the domestic cat microbiome, providing a transparent and data-driven overview of the field. We examined 282 publications on the microbiome of domestic cats (Felis catus) to uncover dominant research themes, methodological patterns, microbial niches, and knowledge gaps. Our results reveal a sharp rise in publications since 2012, with a peak in 2024, where most work is concentrated in high-income countries and driven by a small number of academic institutions. Current efforts are heavily focused on the bacterial gut microbiome, typically using genomic tools for taxonomic profiling in comparative designs. In contrast, research on other microbial communities (e.g., oral or skin), non-bacterial taxa, functional analyses, and behavioural outcomes remains scarce, with behavioural studies virtually absent. Although some studies report health-related effects, mainly positive or neutral, the functional roles of the microbiota and their possible influence on feline behaviour remain largely unexplored. By mapping these trends and gaps, our study provides a strategic framework for advancing microbiome research in domestic cats. These findings highlight priority areas and methodological opportunities that can guide future investigations, foster interdisciplinary collaboration, and ultimately deepen our understanding of the intricate links between microbial ecology, feline health, and behaviour. Studies connecting the microbiome with feline diseases, behaviour, and diet are strongly encouraged, given their high applicability to everyday animal care and management. Such research has the potential to improve both feline health and welfare, while also strengthening the human-cat bond.},
}

Animals
Cats/microbiology
*Microbiota
*Gastrointestinal Microbiome

@article {pmid41160250,
year = {2025},
author = {Li, Y and Zhu, M and Wang, W and Xu, Q and Cui, J and Liu, L and Liu, Y and Yang, H and Liu, Y},
title = {Comparable tongue coating microbiota profiles from a simplified single-swab versus different sampling approaches: A pilot study.},
journal = {Clinical oral investigations},
volume = {29},
number = {11},
pages = {543},
pmid = {41160250},
issn = {1436-3771},
support = {GZC20233129//the Postdoctoral Fellowship Program of CPSF/ ; 82374290//National Natural Science Foundation of China/ ; Yue Liu//Young Qihuang Scholar of the "Tens of Millions" Talent Project of China/ ; },
mesh = {Humans ; Pilot Projects ; *Tongue/microbiology ; *Microbiota ; Adult ; Male ; Female ; *Specimen Handling/methods ; Reproducibility of Results ; Biofilms ; },
abstract = {OBJECTIVE: The tongue coating microbiota has emerged as a potential biomarker for systemic diseases. However, the absence of a practical and widely applicable sampling protocol hinders cross-study comparability and limits clinical application. This pilot study aimed to evaluate the reliability of different sampling methods.

MATERIALS AND METHODS: Tongue coating samples were collected from healthy adults using four different methods, including single and multiple scrapes with sterile swabs or scraper. Metagenomic sequencing was performed to assess microbial diversity, taxonomic composition, and predicted functional profiles. DNA extraction quality, alpha- and beta-diversity metrics, taxonomic abundance at the genus and species levels, and KEGG-based functional predictions were analyzed. Spatial and structural features of the tongue biofilm were considered to interpret microbial sampling consistency.

RESULTS: The single-scrape method yielded comparable microbial profiles to multi-scrape methods, with no significant differences in alpha-diversity or beta-diversity. Taxonomic compositions at both genus and species levels were consistent across groups, with dominant taxa including Streptococcus, Prevotella, and Rothia. Functional prediction via KEGG annotation revealed minimal variation among groups, with only a few metabolic pathways showing statistically significant differences. These findings highlight the spatial stability and representative sampling potential of the tongue coating microbiota.

CONCLUSIONS: A single scrape using a sterile flocked swab provides a practical, reproducible, and cost-effective approach for tongue coating microbiota sampling. These pilot findings suggest that this simplified method yields representative microbiome data in healthy adults, although validation in larger and more diverse cohorts is required before clinical application.

CLINICAL RELEVANCE: This study demonstrates that a single-scrape sampling method yields tongue coating microbiota profiles comparable to conventional multi-scrape protocols. The findings support its potential for standardizing sampling in future large-scale studies.

TRIAL REGISTRATION: ITMCTR2024000616.},
}

Humans
Pilot Projects
*Tongue/microbiology
*Microbiota
Adult
Male
Female
*Specimen Handling/methods
Reproducibility of Results
Biofilms

@article {pmid41160190,
year = {2025},
author = {Chen, K and Ren, X and Du, R and Lei, L and Cheng, R and Hu, T},
title = {The site-specific subgingival microbiome across periodontal conditions and its relationship with clinical parameters.},
journal = {Clinical oral investigations},
volume = {29},
number = {11},
pages = {541},
pmid = {41160190},
issn = {1436-3771},
support = {Nos 81970948//the National Natural Science Foundation of China/ ; Nos 2024NSFSC0543//Sichuan Science and Technology Program/ ; },
mesh = {Humans ; *Microbiota ; Male ; Female ; Adult ; *Gingivitis/microbiology ; Middle Aged ; *Gingiva/microbiology ; *Periodontitis/microbiology ; Biofilms ; Periodontal Index ; Dysbiosis/microbiology ; },
abstract = {OBJECTIVES: To investigate site-specific subgingival microbiota by precise probing depth (PD) and their associations with clinical parameters across periodontal states.

MATERIALS AND METHODS: Participants included healthy-periodontium (n = 20), gingivitis (n = 20) and periodontitis (n = 20). 218 subgingival biofilm samples were collected from PD-based-sites, including health (n = 60), gingivitis (n = 64) and periodontitis (n = 94). Samples further categorized as unstable (PD = 1-3 mm, gingivitis) and dysbiosis (PD ≥ 4 mm, periodontitis). Full-length 16 S rRNA sequencing was performed using third-generation technology.

RESULTS: Selenomonas sputigena (S. sputigena), Filifactor alocis (F. alocis), Aggregatibacter segnis (A. segnis), Prevotella intermedia (P. intermedia), Campylobacter gracilis (C. gracilis), Porphyromonas gingivalis (P. gingivalis) positively correlated with clinical parameters-bleeding on probing, modified gingival index, plaque index and PD. Haemophilus parainfluenzae (H. parainfluenzae) negatively correlated with clinical parameters. Microbiota in gingivitis (PD = 4 mm) resembled with periodontitis deep-sites (PD ≥ 4 mm). Periodontitis (PD ≥ 4 mm) showed a dysbiotic microbial profile, where P. gingivalis, P. intermedia and F. alocis were key taxa.

CONCLUSIONS: Positive correlations with clinical parameters encompassed F. alocis, P. intermedia, C. gracilis, P. gingivalis, etc., while H. parainfluenzae showed negative relations. Gingivitis (PD = 4 mm) exhibited a microbiota resembled the PD ≥ 4 mm of periodontitis.

CLINICAL RELEVANCE: Gingivitis pseudopockets (PD = 4 mm) may exhibited periodontitis-like microbiota, suggesting that such sites should be monitored as early risk indicators for disease progression.},
}

Humans
*Microbiota
Male
Female
Adult
*Gingivitis/microbiology
Middle Aged
*Gingiva/microbiology
*Periodontitis/microbiology
Biofilms
Periodontal Index
Dysbiosis/microbiology

@article {pmid41160143,
year = {2025},
author = {Begum, M and Barsha, KF and Rahman, MM and Sarkar, MMH and Chowdhury, SF and Bhowmik, S and Shormi, AS and Bari, SM},
title = {Gut microbiome profiling of antibiotic-treated Mystus cavasius using culture-based and shotgun metagenomic approaches.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {183},
pmid = {41160143},
issn = {1572-9699},
mesh = {*Anti-Bacterial Agents/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Metagenomics/methods ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Phylogeny ; Aquaculture ; *Catfishes/microbiology ; RNA, Ribosomal, 16S/genetics ; Microbial Sensitivity Tests ; },
abstract = {Antibiotic use in aquaculture prevents disease and promotes growth but can disrupt the gut microbiome and drive resistance. The study profiled the gut microbiome of antibiotic-treated Mystus cavasius using both culture-based and shotgun metagenomic approach. Culture-dependent analysis revealed a significant 2-threefold reduction in total viable bacterial count in treated fish. Phylogenetic analysis of 12 cultured isolates revealed treatment-driven enrichment of Bacillus, Enterobacter and Aeromonas. Antibiotic susceptibility testing further revealed increased resistance profiles among isolates from treated fish. Metagenomic profiling identified over 1400 bacterial species and revealed clear taxonomic shifts. Control groups were enriched with beneficial genera such as Lactiplantibacillus and Arthrospira, while treated fish were dominated by opportunistic or resistant taxa including Plesiomonas, Staphylococcus, and Acinetobacter. These shifts were further reflected at the phylum level, with a decline in Proteobacteria and Bacteroidetes, accompanied by an increase in Firmicutes and the enrichment of antibiotic-tolerant lineages. Treated samples exhibited more uniform alpha diversity indices, suggesting a restructuring of the microbial community hierarchy following oxytetracycline exposure, whereas beta diversity analysis showed a moderate separation between control and treated groups. These findings provide critical insights into the ecological and health risks of antibiotic use in aquaculture and underscore the importance of developing sustainable alternatives for disease management in fish farming.},
}

*Anti-Bacterial Agents/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
*Metagenomics/methods
*Bacteria/classification/genetics/drug effects/isolation & purification
Phylogeny
Aquaculture
*Catfishes/microbiology
RNA, Ribosomal, 16S/genetics
Microbial Sensitivity Tests

@article {pmid41160105,
year = {2025},
author = {Singh, LS and Singha, LS and Singh, WS and Singh, YR and Marak, GK},
title = {Microbiome modulation as a therapeutic strategy for alcohol-induced gut dysbiosis and associated disorders.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {182},
pmid = {41160105},
issn = {1572-9699},
mesh = {*Dysbiosis/therapy/microbiology/chemically induced ; Humans ; *Gastrointestinal Microbiome/drug effects ; Probiotics/therapeutic use ; Animals ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; *Ethanol/adverse effects ; *Alcoholism/microbiology/therapy ; },
abstract = {Chronic alcohol consumption alters the composition of the gut microbiota, leading to dysbiosis, increased intestinal permeability, and systemic inflammation, which collectively contribute significantly to the pathogenesis of alcohol-related disorders, encompassing hepatic disease, metabolic abnormalities, immune dysfunction, and neuropsychiatric conditions. The complex interactions of alcohol with the gut ecosystem illuminate the fundamental mechanisms that result in the disruption of the gut-liver axis, the imbalance of microbial metabolites, and the emergence of leaky gut syndrome. The bidirectional gut-brain axis is similarly impaired, intensifying concerns related to addiction and cognitive deficits. Therapeutic strategies, encompassing probiotics, prebiotics, synbiotics, postbiotics, dietary alterations, and fecal microbiota transplantation, offer promising modalities for reinstating microbial balance and alleviating alcohol-induced damage. Cutting-edge treatments such as paraprobiotics and bacteriophage therapy further highlight the potential of microbiome modulation as a viable therapeutic strategy. This review underscores the urgent need for precision-targeted, microbiota-based interventions and calls for expanded clinical research to translate these insights into effective treatments for alcohol-associated disorders.},
}

*Dysbiosis/therapy/microbiology/chemically induced
Humans
*Gastrointestinal Microbiome/drug effects
Probiotics/therapeutic use
Animals
Fecal Microbiota Transplantation
Prebiotics/administration & dosage
*Ethanol/adverse effects
*Alcoholism/microbiology/therapy

@article {pmid41160089,
year = {2025},
author = {Abuzahrah, SS},
title = {The microbiome of marine sponges located on the Saudi Arabia coast of the Red sea using high-throughput 16S amplicon sequencing.},
journal = {AMB Express},
volume = {15},
number = {1},
pages = {160},
pmid = {41160089},
issn = {2191-0855},
support = {PROJECT NO.: CRP/SAU24-02//International Centre for Genetic Engineering and Biotechnology (ICGEB)/ ; },
abstract = {Marine sponges (Porifera) from the Red Sea host diverse microbial communities that are integral to sponge health, nutrient cycling, and ecological resilience. Using high-throughput 16S rRNA amplicon sequencing, we characterized the bacterial diversity and functional potential across several Red Sea sponge species. Our findings revealed that these microbiomes are dominated by Alphaproteobacteria, Gammaproteobacteria, and Roseobacteraceae, with notable contributions from bacterial taxa involved in nitrogen fixation, organic matter degradation, and antimicrobial compound production. Functional predictions indicate that these symbionts support sponge nutrition, defense, and adaptation to the extreme Red Sea environment, including high salinity and temperature. Compared to sponge microbiomes from other marine regions, the Red Sea communities display unique taxonomic compositions and enhanced metabolic and defensive capacities. This highlights the essential ecological roles and potential biotechnological applications of these symbiotic assemblages. Our study underscores the significance of exploring sponge-associated microbiomes in understudied and extreme marine ecosystems. These results provide a foundation for future bioprospecting and work on adaptive mechanisms, emphasizing the value of Red Sea sponges and their microbiota for marine biotechnology and ecosystem resilience.},
}

@article {pmid41160081,
year = {2025},
author = {Lee, HG and Kwon, S and Yeom, M and Bae, SY and Park, HJ},
title = {Changes in Gut Microbiome Following Acupuncture and Moxibustion in Patients With Parkinson Disease: Protocol for a Single-Group, Prospective, Observational Study.},
journal = {JMIR research protocols},
volume = {14},
number = {},
pages = {e76551},
doi = {10.2196/76551},
pmid = {41160081},
issn = {1929-0748},
mesh = {Humans ; *Parkinson Disease/therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; *Moxibustion/methods ; Prospective Studies ; *Acupuncture Therapy/methods ; Female ; Male ; Middle Aged ; Aged ; Adult ; Observational Studies as Topic ; },
abstract = {BACKGROUND: Parkinson disease (PD), a prevalent neurodegenerative disorder characterized by motor and nonmotor symptoms, is becoming increasingly prevalent worldwide. Conventional treatment for PD involves dopamine therapy, including levodopa; however, this treatment is ineffective for nonmotor symptoms and may cause adverse effects. The gut-brain axis has been hypothesized to promote PD, and regulation of gut microbiome, which modulates the gut-brain axis, is emerging as a treatment target. Acupuncture and moxibustion exert therapeutic effects on PD and modulate the gut microbial composition.

OBJECTIVE: We present a protocol for analyzing the effects of acupuncture and moxibustion on gut microbiome and exploring its association with symptoms in patients with PD.

METHODS: This single-group, prospective, observational study will recruit 60 patients with idiopathic PD and 20 healthy participants. Baseline gut microbiome patterns and motor and nonmotor symptoms of both groups will be compared. Patients with PD will be treated with acupuncture, moxibustion, and intradermal acupuncture twice a week for 12 weeks (24 sessions total). Motor and nonmotor symptoms and gut microbiome changes in patients with PD will be compared before starting treatment (day 0), during treatment (6 weeks), at the end of treatment (12 weeks), and 2 months after the end of treatment (20 weeks). The correlation between motor and nonmotor symptoms of PD changed by acupuncture and moxibustion treatment and changes in gut microbiome will be analyzed. Healthy participants will be assessed for motor and nonmotor symptoms of PD and gut microbiome after screening.

RESULTS: This study was supported by the National Research Foundation of Korea, funded by the Ministry of Science and ICT (Information and Communication Technology), Republic of Korea, and recruitment for the study started on October 21, 2021. As of February 19, 2025, recruitment and observation ended, and data analysis is being conducted.

CONCLUSIONS: This is the first clinical study to assess the effects of acupuncture and moxibustion on gut microbiome and explore its association with symptoms in patients with PD. The results will provide clinical evidence to explain the microbiome-gut-brain axis mechanism of acupuncture and moxibustion for PD and suggest the possibility of acupuncture as an alternative therapy for PD.

TRIAL REGISTRATION: Clinical Research Information Service KCT0006669; https://tinyurl.com/42jsxs5a.

DERR1-10.2196/76551.},
}

Humans
*Parkinson Disease/therapy/microbiology
*Gastrointestinal Microbiome/physiology
*Moxibustion/methods
Prospective Studies
*Acupuncture Therapy/methods
Female
Male
Middle Aged
Aged
Adult
Observational Studies as Topic

@article {pmid41159707,
year = {2025},
author = {Scantlebury, MH and Choudhary, A and Ng, AC and Gavrilovici, C},
title = {Ketogenic diet for infantile epileptic spasms.},
journal = {Epilepsia open},
volume = {},
number = {},
pages = {},
doi = {10.1002/epi4.70168},
pmid = {41159707},
issn = {2470-9239},
support = {//Hotchkiss Brain Institute/ ; //Alberta Children's Hospital Research Institute/ ; PJT 461929/CAPMC/CIHR/Canada ; },
abstract = {Approximately half of all cases of Infantile Epileptic Spasms Syndrome (IESS) do not respond to vigabatrin and hormonal therapies. There is no clear consensus as to the second-line therapy for IESS. Ketogenic diet (KD) has emerged as an effective treatment for certain drug-resistant epilepsies and in many cases of IESS. Understanding the mechanism of action of the KD in IESS will allow for harnessing the power of the KD and discovering novel therapeutics for IESS. In this review, we will summarize the current state of knowledge of the action of the KD in IESS derived from animal models. We emphasize the importance of the KD in altering respiration to cause brain acidosis. In addition, we review recent data implicating altered gut microbiome and the tryptophan-serotonin-kynurenine pathway in KD animals with infantile epileptic spasms syndrome. PLAIN LANGUAGE SUMMARY: Infantile Epileptic Spasms Syndrome is a serious seizure condition in babies, often resistant to standard drugs, failing in half of cases. Animal studies helped unravel multiple mechanisms through which a high-fat, low-carb ketogenic diet can control seizures, including altering gut bacteria, reducing inflammation, balancing brain chemicals, boosting mitochondrial function, or adjusting breathing to slightly acidify the brain. These findings could lead to new, targeted therapies that are simpler to use and more accessible for families facing this challenging condition.},
}

@article {pmid41159664,
year = {2025},
author = {Schwab, C and Lang, H and Stegmüller, S and Hosek, J and Marietou, A and Huertas-Díaz, L and Li, Q and Krings, APS and Zander, A and Kræmer Sundekilde, U and Richling, E},
title = {Microbial Transformation of Dietary Glycerol Contributes to Intestinal Acrolein Formation and Urinary Excretion.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70289},
doi = {10.1002/mnfr.70289},
pmid = {41159664},
issn = {1613-4133},
support = {RI 1176/12-1//Deutsche Forschungsgemeinschaft DFG/ ; RI 1176/13-1//Deutsche Forschungsgemeinschaft DFG/ ; },
abstract = {The aldehyde acrolein has been associated with diabetes, cardiovascular, respiratory, and neurodegenerative diseases, and gut microbiota possesses the potential for acrolein release via the key enzyme glycerol/diol dehydratase (PduCDE). This study aimed at estimating the contribution of gut microbiota to endogenous acrolein production. To minimize confounding sources, we investigated the intestinal acrolein-producing potential of 20 volunteers housed under defined conditions. Glycerol was present in every meal and was detected in feces, suggesting availability to intestinal microbiota. Based on fecal metagenomics and pduC analysis, all volunteers showed potential for intestinal glycerol transformation to acrolein; the genus Anaerobutyricum was the major contributor across donors and time. Levels of urine biomarkers N-acetyl-S-(3-hydroxypropyl)-L-cysteine (3-HPMA) and N-acetyl-S-(carboxyethyl)-L-cysteine (CEMA) were higher after the consumption of meals with high glycerol levels, suggesting immediate microbial transformation to acrolein. Only a small proportion of acrolein metabolites was recovered in urine, possibly due to high compound reactivity. Donors could be separated into 3-HPMA or CEMA phenotypes based on the predominance of urine biomarkers, and phenotypes related to overall fecal microbiota and fermentation metabolite profiles. Our data show that oral fat/glycerol intake together with intestinal microbiota activity might temporarily increase endogenous acrolein formation and that urinary biomarkers link to the intestinal microbiome.},
}

@article {pmid41159302,
year = {2025},
author = {Petrullo, L and Santangeli, A and Wistbacka, R and Husby, A and Raulo, A},
title = {Indirect Environmental Effects on the Gut-Brain Axis in a Wild Mammal.},
journal = {Molecular ecology},
volume = {},
number = {},
pages = {e70149},
doi = {10.1111/mec.70149},
pmid = {41159302},
issn = {1365-294X},
support = {//Svensk-Österbottniska samfundet/ ; //Societas pro Fauna et Flora Fennica/ ; DEB-2010726//Directorate for Biological Sciences/ ; },
abstract = {Inconspicuous interactions between host physiological systems and resident microbial communities may underlie how animals respond to environmental change. For example, immunity and metabolism are regulated in part by the gut microbiota, which can be shaped indirectly by host neuroendocrine function via a 'gut-brain axis'. Yet the sensitivity of this axis in wild vertebrates remains ambiguous. Here, we investigate covariation among environmental quality, glucocorticoids and gut microbiota in a vulnerable population of Siberian flying squirrels (Pteromys volans) inhabiting a region impacted by variable rates of human disturbance. We test competing hypotheses related to direct versus indirect environmental effects (via the gut-brain axis) on adult and juvenile gut microbial communities. Adults housed a richer gut microbiota and had higher hair glucocorticoids that covaried with microbial composition, while juveniles lacked any hormone-microbiome covariation. Environmental quality (patch size and habitat diversity) predicted variation in glucocorticoids but not variation in microbial diversity, suggesting no direct effects on gut microbiota. Instead, structural equation models revealed indirect environmental effects of habitat quality on microbiota via elevations in glucocorticoids in adults. Among juveniles, habitat-induced hormonal responses had no downstream effects on microbial diversity. Together, this provides evidence for age-dependent indirect effects of the environment quality on gut microbial composition in a wild mammal by way of the host neuroendocrine system.},
}

@article {pmid41159234,
year = {2025},
author = {Blanes Hernández, R and de Cossio Tejido, S and Puchades Gimeno, F and García-Bustos, V and Salavert Lletí, M},
title = {Legends, dogmas, presumptions, and demystifications in antibiotic therapy.},
journal = {Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia},
volume = {38 Suppl 1},
number = {},
pages = {70-79},
doi = {10.37201/req/s01.11.2025},
pmid = {41159234},
issn = {1988-9518},
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/administration & dosage ; Antimicrobial Stewardship ; Inappropriate Prescribing ; },
abstract = {Suboptimal antimicrobial use is a global challenge driven by entrenched misconceptions and dogmas. This article aims to critically evaluate and debunk several widespread myths in infectious disease management that lead to overdiagnosis and overtreatment. Through a nonsystematic literature review, this manuscript examines key misconceptions across various aspects of antimicrobial therapy, including administration routes, drug mechanisms, treatment duration, and the interplay with infection source control. It also explores the influence of evolving concepts like long-acting antimicrobials and the human microbiome. We challenge the dogmas that intravenous antibiotics are superior to oral agents, that longer courses are always better, and that bactericidal drugs are more effective than bacteriostatic ones. The review highlights the paramount importance of source control and surgical intervention in treating severe infections and cautions against misinformation surrounding the human microbiome. The medical community must critically re-evaluate long-standing clinical practices to improve antibiotic stewardship. By debunking these myths, we can promote a more precise, safe, and effective approach to antimicrobial use, ultimately reducing unnecessary prescribing and combating antimicrobial resistance.},
}

Humans
*Anti-Bacterial Agents/therapeutic use/administration & dosage
Antimicrobial Stewardship
Inappropriate Prescribing

@article {pmid41159233,
year = {2025},
author = {Soriano-Cuesta, MC and López-Olivencia, M and Candel, FJ and García-Plaza, S},
title = {Therapeutic approach in the critically ill patient with suspected multidrug resistance.},
journal = {Revista espanola de quimioterapia : publicacion oficial de la Sociedad Espanola de Quimioterapia},
volume = {38 Suppl 1},
number = {},
pages = {63-69},
doi = {10.37201/req/s01.10.2025},
pmid = {41159233},
issn = {1988-9518},
mesh = {Humans ; *Critical Illness ; *Drug Resistance, Multiple, Bacterial ; *Anti-Bacterial Agents/therapeutic use ; *Bacterial Infections/drug therapy/microbiology ; Sepsis/drug therapy/microbiology ; Drug Therapy, Combination ; },
abstract = {The treatment of infections caused by multidrug-resistant microorganisms (MDROs) in critically ill patients remains a major clinical challenge due to the high mortality associated with therapeutic failure. Delays in administering effective antibiotics is a determining factor, especially in patients with sepsis. The presence of MDROs is one of the main causes of failure of empirical treatment. Identifying patients at risk of MDRO infection is essential, although complex. Factors such as prior use of antibiotics disrupt the intestinal microbiome balance and promote colonization by MDROs. Immunosuppression, disruption of physical barrier, systemic or organ-specific frailty, and the length of hospital stay increase the risk of colonization and infection by MDROs. In patients with sepsis and a high risk of MDRO infection, empirical therapy should be broad-spectrum and administered early. Traditionally, combination therapy has been recommended, preferably including a classical β-lactam together with aminoglycosides or colistin-drugs that may be suboptimal in certain infection sites and are associated with significant toxicity risks. The new broad-spectrum β-lactams, already validated as first-line targeted treatment, are emerging as a promising empirical option in selected patients. Their early use, guided by colonization status, can optimize initial coverage in terms of spectrum and pharmacokinetic/pharmacodynamic, and reduces delays in the initiation of effective treatment. This strategy should be integrated into antimicrobial stewardship programs and be followed by deescalation once microbiological results are available.},
}

Humans
*Critical Illness
*Drug Resistance, Multiple, Bacterial
*Anti-Bacterial Agents/therapeutic use
*Bacterial Infections/drug therapy/microbiology
Sepsis/drug therapy/microbiology
Drug Therapy, Combination

@article {pmid41159037,
year = {2025},
author = {Somani, VK and Aggarwal, S and Garg, R and Takeuchi, Y and Singh, S},
title = {Editorial: Understanding the impact of microbes on tumor progression and prevention: unveiling new avenues for cancer therapy.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1705365},
doi = {10.3389/fimmu.2025.1705365},
pmid = {41159037},
issn = {1664-3224},
}

@article {pmid41159034,
year = {2025},
author = {Peipert, D and Montgomery, TL and Toppen, LC and Lee, MFJ and Scarborough, MJ and Krementsov, DN},
title = {Colonization by Akkermansia muciniphila modulates central nervous system autoimmunity in an ecological context-dependent manner.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1655428},
pmid = {41159034},
issn = {1664-3224},
mesh = {Animals ; *Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Autoimmunity ; Mice ; Mice, Inbred C57BL ; *Central Nervous System/immunology/microbiology ; *Multiple Sclerosis/immunology/microbiology ; Female ; Akkermansia ; *Verrucomicrobia/immunology ; Disease Models, Animal ; },
abstract = {INTRODUCTION: Multiple sclerosis is autoimmune disease of the central nervous system (CNS) in which myelin-reactive immune attack drives demyelination and subsequent disability. Various studies have documented elevated abundance of the commensal gut bacterium Akkermansia muciniphila (A. muciniphila) in people with multiple sclerosis compared to healthy control subjects, suggesting that its elevated abundance may be a risk factor for the development of CNS autoimmunity. However, A. muciniphila is considered beneficial in various other pathological contexts, and recent studies suggest that A. muciniphila may be paradoxically associated with reduced disability and progression in multiple sclerosis. Moreover, experimental modulation of A. muciniphila levels in experimental autoimmune encephalomyelitis (EAE), an autoimmune model of multiple sclerosis, has generated conflicting results, suggesting that the effects of this microbe on CNS autoimmunity could be context-dependent.

METHODS: To address this possibility, we generated two distinct microbiome models in C57BL/6J mice, each stably colonized by A. muciniphila or A. muciniphila-free, providing divergent ecological contexts in which A. muciniphila may exert a differential impact. We used EAE, flow cytometry, full-length 16S DNA sequencing, and mass spectrometry to assess the impact of A. muciniphila colonization on neurological outcomes, immune responses, gut microbiome composition, and short-chain fatty acid (SCFA) production, respectively. Dietary intervention was used to assess the functional consequences of differences in gut microbiota metabolic capacity.

RESULTS: We found that A. muciniphila colonization increased EAE severity only in a specific microbiome context, in conjunction with increased Th17 responses and CNS-infiltrating immune cells. Profiling of gut microbiome composition revealed that A. muciniphila colonization drove a reduction of Clostridia, key producers of SCFAs, specifically in the microbiome model in which A. muciniphila exacerbates EAE. Inferred metagenomic analyses suggested reduced SCFA production in the presence of A. muciniphila, which was confirmed by mass spectrometry. Consistently, provision of high dietary fiber as a substrate for SCFA production suppressed EAE only in the context of the Clostridia-rich microbiome sensitive to A. muciniphila colonization.

DISCUSSION: Taken together, our data suggest that the effect of A. muciniphila on CNS autoimmunity is highly dependent on the overall composition of the gut microbiome and suggest that this microbe may contribute to decreased gut SCFA metabolism in multiple sclerosis.},
}

Animals
*Encephalomyelitis, Autoimmune, Experimental/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Autoimmunity
Mice
Mice, Inbred C57BL
*Central Nervous System/immunology/microbiology
*Multiple Sclerosis/immunology/microbiology
Female
Akkermansia
*Verrucomicrobia/immunology
Disease Models, Animal

@article {pmid41158776,
year = {2025},
author = {Casagrande Pierantoni, D and Conti, A and Corte, L and Tosti, G and Benincasa, P and Cardinali, G and Guiducci, M},
title = {Microbial community dynamics in rotational cropping: seasonality vs. crop-specific effects.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1675394},
pmid = {41158776},
issn = {1664-302X},
abstract = {INTRODUCTION: Soil microbial communities are central to soil health and plant productivity, yet their responses to crop rotation and seasonal changes remain incompletely understood. Understanding how crop identity and phenology shape these communities is essential for optimizing agricultural sustainability.

METHODS: This study examined how different crop species and their growth stages influence the diversity, composition, and functional characteristics of soil microbiota in a long-term crop rotation system. We integrated high-throughput DNA sequencing with soil chemical and spectroscopic analyses to assess microbial community dynamics across three key seasonal time points.

RESULTS: Our results indicate that while crop species and their growth stages can influence microbial community structure, these effects were generally modest and variable. In contrast, seasonal factors and soil physicochemical properties-particularly electrical conductivity-exerted stronger and more consistent effects on microbial beta diversity. Despite shifts in taxonomic composition, a core microbiome dominated by Acidobacteriota and Bacillus persisted across crops and seasons. Functional predictions revealed a seasonal peak in nitrification potential during warmer months, suggesting environmental rather than crop-driven control of this process.

DISCUSSION: These findings highlight the resilience of soil microbiomes under rotational systems and underscore the dominant role of seasonal and abiotic factors in shaping microbial community dynamics. A better understanding of these interactions can inform agricultural practices aimed at sustaining microbial functionality and promoting long-term soil health.},
}

@article {pmid41158521,
year = {2025},
author = {Kalla Veedu, A and Vijayakumar, S and Joseph, HA and Thomas, J},
title = {Impact of gut probiotic metabolites on phenylketonuria.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1682110},
pmid = {41158521},
issn = {2235-2988},
mesh = {*Phenylketonurias/therapy/microbiology/metabolism ; *Probiotics/therapeutic use/metabolism/administration & dosage ; Humans ; *Gastrointestinal Microbiome/physiology ; Phenylalanine/metabolism ; Phenylalanine Hydroxylase/genetics ; Animals ; },
abstract = {Phenylketonuria is an unusual inherited metabolic disease induced by mutations of the phenylalanine hydroxylase gene, resulting in phenylalanine accumulation. The current treatments only focus on restricting lifelong dietary intake of phenylalanine, posing a significant challenge to concordance and living standards. Emerging evidence on phenylketonuria disorders underscores the gut microbiome involving probiotics as a key mediator of host metabolic processes. This review encompasses the insights into the pathophysiology of phenylketonuria, gut probiotics, the amino acid metabolism of phenylalanine, the mechanism of action of probiotics, and the therapeutic potential of the treatments available.},
}

*Phenylketonurias/therapy/microbiology/metabolism
*Probiotics/therapeutic use/metabolism/administration & dosage
Humans
*Gastrointestinal Microbiome/physiology
Phenylalanine/metabolism
Phenylalanine Hydroxylase/genetics
Animals

@article {pmid41158520,
year = {2025},
author = {Bao, Z and Niu, L and Ma, Y and Deng, X and Wang, L and Tao, M and Yu, R},
title = {Characterization of the airway microbiome in preterm infants with bronchopulmonary dysplasia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1654502},
pmid = {41158520},
issn = {2235-2988},
mesh = {Humans ; *Bronchopulmonary Dysplasia/microbiology ; Infant, Premature ; *Microbiota ; Male ; Female ; Infant, Newborn ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Gestational Age ; Cohort Studies ; *Bacteria/classification/genetics/isolation & purification ; Trachea/microbiology ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics/chemistry ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND AND AIMS: Bronchopulmonary dysplasia (BPD) represents a persistent respiratory condition that primarily affects preterm infants, distinguished by abnormal lung development and function. Previous studies have indicated a significant association between the pulmonary microbiome and various respiratory diseases. This study aimed to compare the airway microbiome composition and its temporal changes in preterm infants with and without BPD.

METHODS: We conducted a cohort study involving 14 infants diagnosed with BPD and 10 preterm infants without BPD, all born at a gestational age (GA) < 32 weeks. Tracheal aspirates were collected on day 1 during intubation, as well as on days 7 and 14 following the intubation procedure. Subsequently, bacterial DNA was extracted, and the 16S rRNA genes were amplified and sequenced to characterize the airway microbiome.

RESULTS: The demographic and clinical features, such as gestational age, birth weight, and sex ratio, were similar across the groups. However, BPD infants required prolonged duration for Continuous Positive Airway Pressure (25.0 d vs 8.5 d, P = 0.001), oxygen therapy (38.0 d vs 20.5 d, P = 0.001), antibiotic treatment (9.5 d vs 4.5 d, P = 0.004), and prolonged hospital admissions (44.0 d vs 25.5 d, P = 0.002). Microbiome analysis revealed that the BPD infants exhibited reduced bacterial diversity at birth and a consistent pattern of diminished bacterial diversity over time compared to the non-BPD group, as indicated by a lower Shannon index. The BPD group also showed a distinct microbial community composition, with significant differences in β-diversity observed at day 14 post-incubation. At the phylum level, both groups exhibited an increase in Firmicutes in the first two weeks, while the BPD group showed a progressive decline in the relative abundance of Bacteroidetes. At the genus level, the BPD infants exhibited an increased proportion of Streptococcus and Acinetobacter, and a decreased abundance of Prevotella over time.

CONCLUSIONS: These findings indicate that the airway microbiome in infants with BPD is characterized by reduced diversity and distinct microbial profiles, which may contribute to the pathogenesis of the disease. Understanding these microbiome dynamics may help develop targeted therapeutic strategies aimed at modulating the microbiome to prevent or mitigate BPD in preterm infants.},
}

Humans
*Bronchopulmonary Dysplasia/microbiology
Infant, Premature
*Microbiota
Male
Female
Infant, Newborn
RNA, Ribosomal, 16S/genetics
DNA, Bacterial/genetics
Gestational Age
Cohort Studies
*Bacteria/classification/genetics/isolation & purification
Trachea/microbiology
Sequence Analysis, DNA
DNA, Ribosomal/genetics/chemistry
*Respiratory System/microbiology

@article {pmid41158463,
year = {2025},
author = {Huang, X and Lu, S and Li, X and Wu, J and Zu, Q and Duan, Z and Luo, M and Jia, Y},
title = {Multi-omics profiling reveals the role of 4-ethylbenzoic acid in promoting proliferation and invasion of cervical cancer.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1591531},
pmid = {41158463},
issn = {2296-858X},
abstract = {BACKGROUND: Cervical cancer (CC) is a global health challenge, ranking fourth among cancers in women. Microbiome-metabolome interactions influence human papillomavirus (HPV) associated carcinogenesis, but specific microbial metabolites driving malignant progression remain undefined. This study aimed to identify potential biomarkers for distinguishing CC, and further explore their role in the progression of CC.

METHODS: Non-targeted metabolomics was employed to profile alterations in the vaginal microenvironment across clinical cohorts, including individuals with CC, individuals with cervical intraepithelial neoplasia (CIN), HPV-positive individuals, and HPV-negative individuals. Targeted metabolomics was then used to confirm the expression of 4-ethylbenzoic acid (4-EA) levels and its role in CC was explored using cell counting kit-8, 5-ethynyl-2'-deoxyuridine, colony formation, transwell, and wound healing assays. Proteomics was used to investigate the effects of 4-EA on CC cells.

RESULTS: The metabolic profiles of vaginal secretions in the CC group differed significantly from those in the other three groups. Untargeted metabolomics identified 27 CC-specific metabolites (VIP > 2, p < 0.05), revealing a marked elevation of 4-EA and its close relationship with vaginal microorganisms. Clinico-pathological correlations revealed progressive 4-EA accumulation across the cervical carcinogenesis stages. Additionally, 4-EA promoted the proliferation, migration, and invasion of CC cells in vitro. Proteomic reprogramming of CC cells following 4-EA treatment identified 14 highly expressed proteins associated with poor prognosis.

CONCLUSION: This multi-omics investigation identified 4-EA as a novel candidate metabolite and a potential biomarker of CC. Identification of key proteins may provide new insights for interventions targeting the development of CC.},
}

@article {pmid41158440,
year = {2025},
author = {Leo, F and Nilsson, J and Arike, L and Kumar, S and Hilton, E and Lood, R and Thornton, DJ and Duncan, GA and Svensäter, G and Wickström, C},
title = {Functional divergence of MdpS and MdpS2 reveals mucin-targeting strategies in Streptococcus oralis.},
journal = {Journal of oral microbiology},
volume = {17},
number = {1},
pages = {2571186},
pmid = {41158440},
issn = {2000-2297},
abstract = {BACKGROUND: Mucin degradation is essential for understanding oral microbial adaptation, yet the enzymes involved remain incompletely understood. Herein, we have characterised two mucin-degrading proteases, MdpS and MdpS2, from the oral commensal Streptococcus oralis.

MATERIALS AND METHODS: MdpS2 was characterised using physicochemical assays and substrate profiling and was compared to MdpS. Further Mdp characterisation included structural modelling, and functional assays analysing the gene expression during biofilm growth on salivary MUC5B, enzyme-induced biofilm dispersal, and mucus degradation analysed through nanoLC-MS/MS, sedimentation profiling, and microrheology.

RESULTS: MdpS2 shared conformational homology with MdpS despite low sequence identity and showed greater tolerance to pH and sodium chloride. Both genes were significantly upregulated during late stationary biofilm phase. MdpS and MdpS2 hydrolysed MUC5B extensively, with overlapping but distinct hydrolysis patterns. MdpS2 promoted biofilm dispersal and caused a pronounced reduction in MUC5B size and compactness. Microrheology showed selective modulation of MUC5B-rich mucus by MdpS2, while MdpS affected both MUC5B and MUC5AC networks.

CONCLUSIONS: MdpS and MdpS2 exhibit complementary biochemical and functional profiles, supporting their roles in mucin degradation and biofilm remodelling. These findings advance our understanding of how early colonizing streptococci may interact with mucosal surfaces, influence biofilm dynamics and oral ecology, and suggest potential applications in targeting mucus-related disorders.},
}

@article {pmid41158324,
year = {2025},
author = {Fatemi, S and Kriefall, NG and Yogi, D and Weber, D and Hynson, NA and Medeiros, MCI and Sadowski, P and Amend, AS},
title = {Microbial composition and function are nested and shaped by food web topologies.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf175},
pmid = {41158324},
issn = {2730-6151},
abstract = {Food webs govern interactions among organisms and drive energy fluxes within ecosystems. With an increasing appreciation for the role of symbiotic microbes in host metabolism and development, it is imperative to understand the extent to which microbes conform to, and potentially influence, canonical food web efficiencies and structures. Here, we investigate whether bacteria and their taxa and functional genes are compositionally nested within a simple model food web hierarchy, and the extent to which this is predicted by the trophic position of the host. Using shotgun and amplicon sequencing of discrete food web compartments within replicate tank bromeliads, we find that both taxonomy and function are compositionally nested and largely mirror the pyramid-shaped distribution of food webs. Further, nearly the entirety of bacterial taxa and functional genes associated with hosts are contained within host-independent environmental samples. Community composition of bacterial taxa did not significantly correlate with that of functional genes, indicating a high likelihood of functional redundancy. Whereas bacterial taxa were shaped by both location and trophic position of their host, functional genes were not spatially structured. Our work illustrates the advantages of applying food web ecology to predict patterns of overlapping microbiome composition among unrelated hosts and distinct habitats. Because bacterial symbionts are critical components of host metabolic potential, this result raises important questions about whether bacterial consortia are shaped by the same energetic constraints as hosts, and whether they play an active role in food web efficiency.},
}

@article {pmid41158094,
year = {2025},
author = {Han, H and Li, Y and Wang, L and Jin, Z and Zhou, W and Zhang, B and Jia, C and Zhang, W and Wang, Y and Qiu, L and Bing, S and Wang, S and Ren, Z},
title = {Liver-Microbiome Crosstalk Mediates the Protective Effects of Artemisinin in Clostridium perfringens Models.},
journal = {Microbial biotechnology},
volume = {18},
number = {11},
pages = {e70235},
doi = {10.1111/1751-7915.70235},
pmid = {41158094},
issn = {1751-7915},
support = {K3031225021//Shaanxi Provincial Financial Agricultural Special Funds/ ; K4050723310//People's Government of Shaanxi Province under the Yijun County Meat Rabbit Industry Technology Development Cooperation Program/ ; },
mesh = {Animals ; *Clostridium perfringens/drug effects ; Rabbits ; *Clostridium Infections/drug therapy/microbiology/pathology ; *Liver/microbiology/drug effects/metabolism ; Mice ; *Artemisinins/pharmacology/administration & dosage ; Disease Models, Animal ; Cytokines/metabolism ; Gastrointestinal Microbiome/drug effects ; },
abstract = {Clostridium perfringens is a multi-host opportunistic pathogen whose plasmid-encoded toxins cause gas gangrene, necrotic enteritis and enterotoxemia, resulting in substantial economic losses in animal husbandry. In light of antibiotic bans and the need for alternatives, we employed reverse network pharmacology to screen and in vitro validate artemisinin (ART), then assessed its efficacy in murine and rabbit infection models challenged with C. perfringens type F. ART treatment did not significantly affect body weight change or intestinal histopathological damage. However, it significantly modulated inflammatory cytokines and antioxidant parameters in a tissue- and species-dependent manner. Specifically, ART increased serum TNF-α in mice, decreased IL-1β in rabbits and elevated IL-10 in multiple tissues. In addition, ART enhanced hepatic SOD and T-AOC in mice and reduced hepatic MDA in rabbits. Microbiota analysis revealed limited and subtle shifts in community structure following ART intervention. Transcriptomic analysis further indicated that ART treatment induced marked changes in hepatic gene expression, particularly involving detoxification, lipid metabolism and stress response pathways, with notable species-specific differences in enrichment profiles. While correlation analysis suggested associations of Anaerotruncus with hepatic detoxification genes and Bacteroides with inflammation-regulatory genes, these genus-level findings are based on correlation only and should be interpreted with caution given the lack of significant changes in overall microbial community structure. Collectively, these results indicate that ART can modulate host inflammatory and antioxidant responses, but its impact on gut microbiota composition in C. perfringens infection models appears limited, and the biological significance of observed genus-level associations remains to be elucidated.},
}

Animals
*Clostridium perfringens/drug effects
Rabbits
*Clostridium Infections/drug therapy/microbiology/pathology
*Liver/microbiology/drug effects/metabolism
Mice
*Artemisinins/pharmacology/administration & dosage
Disease Models, Animal
Cytokines/metabolism
Gastrointestinal Microbiome/drug effects

@article {pmid41157986,
year = {2025},
author = {Zurawski, E and Hey, M},
title = {Gut Healthism: The Penetrating Gaze and Depoliticising Forces of Direct-to-Consumer Microbiome Testing Kits.},
journal = {Sociology of health & illness},
volume = {47},
number = {8},
pages = {e70111},
doi = {10.1111/1467-9566.70111},
pmid = {41157986},
issn = {1467-9566},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Direct-To-Consumer Screening and Testing ; },
abstract = {In recent years, scientific attention towards the gut has interpellated everyday consumers to test and intervene on their gut microbiome in the hopes of improving their overall health. Based on a discursive analysis of direct-to-consumer testing kits, we detail how their rhetoric individualises health interventions in the name of procuring a 'healthy' gut microbiome while obscuring the social, communal and environmentally predicated relations that inhere to a kind of health reliant on microbes. Drawing on Robert Crawford's original conceptualisation, we identify an emergent 'gut healthism' amid the tangle of the contemporary microbiome revolution, technopolitical outgrowths of the Human Genome Project, collapsing healthcare infrastructures, and the ills of the modern industrialised food system. Through gut healthism, we argue that the kits enable a hyperfixation on the gut, which becomes mediated by scientific expertise to view and quantify microbes as health markers, whose gaze disembodies guts and depoliticises diet. By examining current moves in gut microbiome products, we also detail the divergences and complications that gut healthism brings to Crawford's framework, highlighting the problem with solutions such as DTC kits and how they do little to address the grand health challenges of our time.},
}

Humans
*Gastrointestinal Microbiome
*Direct-To-Consumer Screening and Testing

@article {pmid41157756,
year = {2025},
author = {Petkova, M and Chavdarov, P and Shilev, S},
title = {Linking Soil Microbial Functional Profiles to Fungal Disease Resistance in Winter Barley Under Different Fertilisation Regimes.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/plants14203199},
pmid = {41157756},
issn = {2223-7747},
support = {KP-06-DO 02/5//Bulgarian National "Science Fund"/ ; 771134//ERA-Nets SusCrop/ ; 696356//FACCE ERA-GAS/ ; },
abstract = {Barley (Hordeum vulgare L.) is a major fodder crop whose productivity is often reduced by phytopathogens, especially during early growth. Understanding how soil fertility management and microbial communities influence disease outcomes is critical for developing sustainable strategies that reduce fungicide dependence and enhance crop resilience. This study evaluated the resistance of the winter barley cultivar "Zemela" to powdery mildew (Blumeria graminis f. sp. hordei), brown rust (Puccinia hordei), and net blotch (Pyrenophora teres f. maculata). The crop was cultivated under two soil management systems-green manure and conventional-and five fertilisation regimes: mineral, vermicompost, combined, biochar, and control. Phytopathological assessment was integrated with functional predictions of soil microbial communities. Field trials showed high resistance to powdery mildew (RI = 95%) and brown rust (RI = 82.5%), and moderate resistance to net blotch (RI = 60%). While ANOVA indicated no significant treatment effects (p > 0.05), PCA explained 82.3% of the variance, revealing clear clustering of microbial community functions by soil management system and highlighting the strong influence of fertilisation practices on disease-related microbial dynamics. FAPROTAX analysis suggested that organic amendments enhanced antifungal functions, whereas conventional systems were dominated by nitrogen cycling. FUNGuild identified higher saprotrophic and mycorrhizal activity under organic and combined treatments, contrasting with greater pathogen abundance in conventional plots. Overall, results demonstrate that soil fertilisation practices, together with microbial functional diversity, play a central role in disease suppression and crop resilience, supporting sustainable barley production with reduced reliance on chemical inputs.},
}

@article {pmid41157735,
year = {2025},
author = {Lepres, LA and Molnár, A and Geiger, A and Váczy, KZ and Geml, J},
title = {Landscape-Level Drivers of Fungal Communities in Grapevine, Fruit Trees, and Semi-Natural Shrublands in a Habitat Matrix.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/plants14203178},
pmid = {41157735},
issn = {2223-7747},
support = {TKP-2021- NKTA-16//Ministry of Culture and Innovation of Hungary/ ; },
abstract = {The grapevine microbiome is shaped by a complex interplay of biotic and abiotic factors, affecting microbial community structure and plant health. This study investigates the diversity, composition, and dynamics of fungal communities associated with grapevine (Vitis vinifera) and neighboring cultivated plants, as well as plants from semi-natural vegetation, including pear (Pyrus communis), apricot (Prunus armeniaca), dogrose (Rosa canina), and blackthorn (Prunus spinosa), in a landscape-level habitat matrix. Using metabarcoding techniques, fungal communities from leaves and woody tissues of grapevine and neighboring plants were analyzed over a growing season. Fungal richness and abundance differed significantly among host plants, with woody tissues exhibiting higher diversity. Host plant identity was the primary factor shaping wood-associated fungal communities (15.7% of explained variance), whereas sampling time dominated in leaves (16.3%), with sampling site having a weaker effect in both cases. Pathogenic fungi associated with grapevine trunk diseases, such as Diaporthe, Eutypa, and Phaeomoniella, were identified across grapevine and neighboring plants, suggesting that multiple hosts may act as reservoirs for fungal inoculum. These findings highlight the complex interactions between fungal communities, host plants, and environmental factors, underscoring the need for landscape-level approaches to plant protection that account for both cultivated and surrounding ecosystems.},
}

@article {pmid41157277,
year = {2025},
author = {Nam, S and Hong, S and Park, IY and Shin, S},
title = {Vaginal Microbiome and Functional Pathway Alterations in Preterm Premature Rupture of Membranes Revealed by 16S rRNA Sequencing.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/life15101604},
pmid = {41157277},
issn = {2075-1729},
support = {2021R1A2C1013541//National Research Foundation of Korea/ ; RS-2025-25423587//National Research Foundation of Korea/ ; 2024-ER1801-00//Korea National Institute of Health/ ; },
abstract = {Preterm prelabor rupture of membranes (PPROM) is a leading cause of preterm birth and significant neonatal morbidity. The vaginal microbiome is implicated in its pathogenesis, but its detailed characteristics and functional consequences remain to be fully elucidated. This study aimed to provide a comprehensive, multi-faceted analysis of the vaginal microbiome and its functional potential in pregnant women with PPROM compared to healthy term controls. We collected vaginal fluid samples from eight PPROM and seven healthy control (HC) pregnant women. The vaginal microbiome was analyzed using 16S rRNA gene sequencing. We assessed community composition and state types (CSTs), alpha and beta diversity, co-occurrence networks, and predicted functional pathways using PICRUSt2. A molecular bacterial vaginosis (molBV) score was also calculated to determine the clinical relevance of the dysbiosis. The PPROM microbiome was characterized by a significant depletion of Lactobacillus crispatus-dominated communities (CST I) and a shift towards L. iners-dominated (CST III) or polymicrobial (CST IV) communities, which was consistent with a BV-positive molBV score. Alpha diversity was significantly higher in the PPROM group, and beta diversity analysis confirmed a distinct microbial structure between the two groups. Co-occurrence network analysis revealed a collapse of the protective, Lactobacillus-centered network in the PPROM group, which was replaced by a densely interconnected network of anaerobic bacteria with Gardnerella vaginalis as a key hub. Functionally, the PPROM microbiome was enriched for amino acid biosynthesis pathways, in contrast to the HC group, which was enriched for nucleotide and peptidoglycan biosynthesis. PPROM appears to be linked with a complex vaginal dysbiosis that encompasses significant alterations in microbial composition, diversity, interactions, and functional potential. These findings highlight the vaginal microbiome as a critical factor in the pathogenesis of PPROM and suggest its potential for risk stratification and as a therapeutic target to improve pregnancy outcomes.},
}

@article {pmid41157172,
year = {2025},
author = {Carata, E and Destino, M and Tenuzzo, BA and Panzarini, E},
title = {Inter-Organ Crosstalk in Neurodegenerative Disease.},
journal = {Life (Basel, Switzerland)},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/life15101499},
pmid = {41157172},
issn = {2075-1729},
abstract = {Inter-organ communication plays a vital role in the pathogenesis of neurodegenerative diseases (ND), including Alzheimer's disease (AD), Parkinson's disease (PD), and Amyotrophic Lateral Sclerosis (ALS). Emerging research highlights the involvement of the gut-brain axis, immune system, and peripheral metabolic systems in modulating neuroinflammation, protein misfolding, and neuronal dysfunction by releasing cytokines, adipokines, growth factors, and other soluble factors, which in turn affect neuronal health and systemic inflammation. This review explores the complex bidirectional interactions between the brain and peripheral organs, including the gut, adipose tissue, liver, muscle, bone and immune system. Notably, the gut microbiome's role in neurodegenerative diseases through the gut-brain axis, the impact of adipose tissue in inflammation and metabolic regulation, and the muscle-brain axis with its neuroprotective myokines are also discussed. Additionally, we examine the neuro-immune axis, which mediates inflammatory responses and exacerbates neurodegeneration, and liver-brain axis that is implicated in regulating neuroinflammation and promoting disease progression. Dysregulation of inter-organ pathways contributes to the systemic manifestations of neurodegenerative diseases, offering insights into both potential biomarkers and therapeutic targets, and, in turn, promising strategies for preventing, diagnosing, and treating neurodegenerative diseases.},
}

@article {pmid41156868,
year = {2025},
author = {Lamont, RF and Ali, A and Jørgensen, JS},
title = {Recent Advances in the Role of Bacteriophages in the Aetiology and Therapy of Vaginal Dysbiosis in the Form of Bacterial Vaginosis and the Prevention of Preterm Birth.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102410},
pmid = {41156868},
issn = {2076-2607},
abstract = {Bacterial vaginosis is more than a mild inconvenience for women and has been shown to be an important cause of morbidity and mortality in women through sexually transmitted infections, and in babies due to late miscarriage and preterm birth. The aetiology of bacterial vaginosis remains unclear but there is increasing evidence to support sexual transmission as a cause. Preterm birth is a major cause of neonatal and perinatal mortality and morbidity worldwide and a huge cost on healthcare. The earlier bacterial vaginosis is detected in pregnancy, the greater the risk of an adverse outcome like preterm birth. Bacteriophages influence the vaginal microbiome, resulting in a eubiotic or dysbiotic state that may have implications on the prediction and prevention of preterm birth. We have provided the evidence to link vaginal dysbiosis in the form of bacterial vaginosis with the prediction and prevention of preterm birth. We have also explored the role of bacteriophages in bacterial vaginosis and the possibility of therapeutic interventions. Bacteriophages play an important role in the aetiology of vaginal dysbiosis and novel therapeutic interventions may help in the prediction and prevention of preterm birth through achieving vaginal eubiosis.},
}

@article {pmid41156864,
year = {2025},
author = {Mora-Vargas, CD and Grobeisen-Duque, O and Villavicencio-Carrisoza, O and Aguilar-Ayala, DA and Castellanos-Diaz, O and Martinez-Salazar, MG and Rosas-Balan, A and Flores-Rueda, V and Leon-Juarez, M and Guzman-Huerta, M and Camargo-Marin, L and Villegas-Mota, MI and Zaga-Clavellina, V and Aguilera-Arreola, MG and Helguera-Repetto, AC},
title = {Urobiome Signatures of Recurrent Urinary Tract Infections in Adolescent Pregnancy: A Longitudinal Study.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102406},
pmid = {41156864},
issn = {2076-2607},
support = {FOSISS FONDO SECTORIAL DE INVESTIGACIÓN EN SALUD Y SEGURIDAD SOCIAL 290038//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; },
abstract = {Adolescent pregnancy is a significant public health concern, with maternal and fetal risks compounded by pregnancy-related anatomical, hormonal, and urinary changes that predispose to urinary tract infections (UTIs). Alterations in the urinary microbiome may further influence infection susceptibility, yet little is known about its role during adolescent pregnancy. This study analyzed the urinary microbiome of adolescent pregnant patients and its association with UTI and recurrent UTI (rUTI) across gestation. Healthy adolescents were enrolled in the first trimester and followed through subsequent trimesters, with urine samples collected at each visit for microbiological diagnosis. Patients were classified as healthy (34 samples), single UTI (22 samples), or rUTI (31 samples), and oxford-nanopore 16S rRNA sequencing was used to assess taxonomic composition, microbial diversity, and operational taxonomic units. Distinct trimester-specific patterns were observed, with Lactobacillus iners progressively increasing and L. kitasatonis emerging as a dominant taxon during adolescent pregnancy. Interestingly, rUTI cases showed persistent E. coli, reduced L. kitasatonis and L. ultunensis in the second trimester, and the appearance of Fannyhessea vaginae (Atopobium vaginae) in the third. These findings suggest a potential microbial signature of rUTI in adolescent pregnancy, underscoring the need for personalized preventive strategies and the establishment of microbiome-based clinical cutoffs.},
}

@article {pmid41156863,
year = {2025},
author = {Rajput, AP and Sun, D and Zhou, S and Meegaskumbura, M},
title = {Distinct Gut and Skin Microbiomes of a Carnivorous Caecilian Larva (Ichthyophis bannanicus) Show Ecological and Phylogenetic Divergence from Anuran Tadpoles.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102405},
pmid = {41156863},
issn = {2076-2607},
support = {Guangxi University's startup-funding to Madhava Meegaskumbura;Postdoctoral Project funding to Amrapali Prithvisingh Rajput//Guangxi University/ ; },
abstract = {The amphibian microbiome plays a vital role in host health, yet the bacterial communities of caecilians (Order: Gymnophiona) remain largely uncharacterised. We investigated this by providing the first characterisation of the gut and skin microbiome of larval Ichthyophis bannanicus, a carnivorous caecilian, using 16S rRNA gene metabarcoding. Our analyses show distinct communities between the faecal samples and skin, with significant enrichment of Laribacter in faeces and Flavobacterium on skin. Despite significant variation in their community structures, the core genera Escherichia-Shigella were shared between both regions, suggesting similar microbial exchange in the aquatic environments. Skin bacterial diversity exhibited relatively higher richness, but lower evenness than that of faeces. Further, the skin bacterial community exhibited more complex interactions, suggesting stronger resilience to changes. The relationships and interactions of skin and faecal bacterial communities suggest their interactive effects on the host's overall health. Compared with anuran tadpoles, the I. bannanicus larval microbiome showed taxonomic overlap, but possessed certain unique core bacteria. This work on an understudied amphibian lineage is foundational, highlighting how diet, phylogeny, and aquatic environment shape microbial communities and informing future research into amphibian health and disease.},
}

@article {pmid41156854,
year = {2025},
author = {Elkayal, N and Zakeer, S and Azab, M and Abdellah, A and Shabayek, S},
title = {Microbial Communities and Physicochemical Properties of the Nile River Water in the Suez Canal Area.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102395},
pmid = {41156854},
issn = {2076-2607},
abstract = {Monitoring freshwater resources is crucial to drinking water quality. The Ismailia Canal supplies most freshwater to the Suez Canal area in Egypt. However, information on the freshwater microbiome is limited in this region. A total of 59 freshwater samples were collected. Along with determining the physicochemical properties of the samples, we used conventional methods to identify indicator bacteria. To overcome limitations of conventional culture, we employed high-throughput 16S rRNA gene sequencing, taxonomy profiling, and functional prediction to study uncultivated microbial communities. Total and fecal coliforms prevailed in 100% and 80% of samples, respectively. Predominant contaminants included E. coli, fecal streptococci, Pseudomonas aeruginosa, and Staphylococcus aureus. Taxonomic profiling revealed dominance of Proteobacteria and Actinobacteriota. Proteobacteria showed a positive correlation with Bacteroidetes and a negative correlation with Actinobacteria. Most samples had similar bacterial community structures, despite location-driven variability. Elevated bacterial loads were notable at the Qassasin district, which exhibited the highest relative abundance of genes associated with bacterial infections. This study provides key insights into the impact of freshwater microbiome on public health.},
}

@article {pmid41156846,
year = {2025},
author = {Liu, Y and Shang, Y and Wang, X and Li, X and Yu, Z and Zeng, Z and Chen, Z and Wang, L and Xiang, T and Huang, X},
title = {Metagenomics and In Vitro Growth-Promoting Experiments Revealed the Potential Roles of Mycorrhizal Fungus Humicolopsis cephalosporioides and Helper Bacteria in Cheilotheca humilis Growth.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102387},
pmid = {41156846},
issn = {2076-2607},
support = {31872181//National Natural Science Foundation of China/ ; 2021QDL062//Research Start-up Funds from the Hangzhou Normal University/ ; 2025JCXK01//Interdisciplinary Research Project of Hangzhou Normal University/ ; },
abstract = {In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the promotion of plant growth and nutrient uptake. However, the microbial community and key microbial species that function during the growth of the myco-heterotrophic plant Cheilotheca humilis remain unclear. In this study, we evaluated the microbial community associated with Cheilotheca humilis, which was confirmed via morphological characteristics typical of this plant species. Metagenomic analysis showed that the Afipia carboxidovorans was dominant at species level. Based on the LDA score, Bradyrhizobium ottawaense exhibited the higher abundance in the CH-B group (related to bud) while Afipia carboxidovorans was identified from the CH-F group (related to flower). Microbial co-occurrence networks showed that the Rhizobium genus, Herbaspirillum genus, and Cyanobacteriota were defined as core functional microbial species. To explore the potential microorganisms, metagenome-assembled genomes (MAGs) of the rhizosphere microbiome identified 14 medium- and high-quality MAGs, mainly involved in carbon fixation, nitrogen transformation, and phosphorus metabolism, possibly providing nutrients for the plant. Furthermore, a total of 67 rhizospheric and 66 endophytic microorganisms were isolated and obtained. In vitro experiments showed that the mycorrhizal helper bacteria (MHBs) Rhizobium genus and Pseudomonas genus possessed the ability of nitrogen fixation, phosphate solubilization, and siderophores production. Most importantly, the mycorrhizal fungus Humicolopsis cephalosporioides was obtained, which could potentially produce cellulase to supply carbohydrates for host. The findings suggest the mycorrhizal fungus Humicolopsis cephalosporioides and helper bacteria have great potential in the growth of the myco-heterotrophic plant Cheilotheca humilis.},
}

@article {pmid41156834,
year = {2025},
author = {Kakumyan, P and Yang, L and Liu, S and Saninjuk, K and Dong, Q and Pan, X and Yu, C and Zhao, Y},
title = {Sustainable Recycling of Mushroom Residue as an Effective Substitute for Cotton Hull Waste in Volvariella volvacea Cultivation: Evidence from Physicochemical and Microbiome Analyses.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102372},
pmid = {41156834},
issn = {2076-2607},
support = {2024YFD1200204//National Key R&D Program of China/ ; 19390743000//Shanghai Committee of Science and Technology/ ; 2020-02-08-00-12-F01479//Shanghai Agricultural Commission Program/ ; },
abstract = {Mushroom residue (MR) is extensively produced during the industrialized cultivation of mushrooms, and its utilization is environmentally sustainable. Cotton hull waste (CW) serves as a common raw material for the cultivation of Volvariella volvacea in China. This study compared MR- and CW-based cultivation formulas with respect to their physicochemical characteristics, bacterial communities, and functional dynamics during substrate fermentation (composting). Xylanase production was greater in the MR formula than in the CW formula. Conversely, cellulase (CMCase) was generated at higher levels in the CW formula compared to the MR formula. Interestingly, the biological efficiency of MR was found to be comparable to that of CW, but the cost of MR was much lower. The dynamics of bacterial communities and their associated metabolic functions during substrate fermentation were monitored using 16S rRNA metagenomics techniques. Significant alterations in bacterial community structure were observed within both formulas throughout the preparation phase. Indicator species analysis revealed distinct patterns of bacterial diversity development between MR- and CW-based composts during fermentation. Metabolic function analysis indicated that carbohydrate and amino acid metabolism remained relatively active throughout this process. These results suggest that the MR formula is equally effective as conventional CW compost for supporting V. volvacea cultivation, while also offering a lower raw material cost.},
}

@article {pmid41156832,
year = {2025},
author = {Tokamani, M and Liakopoulos, P and Tegopoulos, K and Zigkou, AM and Triantaphyllidis, G and Kamidis, N and Grigoriou, ME and Sandaltzopoulos, R and Kolovos, P},
title = {Spatiotemporal Dynamics of Microbial and Fish Communities in the Thracian Sea Revealed by eDNA Metabarcoding.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102373},
pmid = {41156832},
issn = {2076-2607},
support = {1671/22-03-2023//Green Fund/ ; },
abstract = {The Thracian Sea, a semi-enclosed coastal basin in the northeastern Aegean Sea, represents a dynamic marine environment influenced by freshwater inputs, stratification, and seasonal variability. Here, we investigated the spatiotemporal dynamics of microbial and ichthyofaunal communities using environmental DNA (eDNA) and high-throughput sequencing across various stations in the vicinity of the Thracian Sea, in consecutive months (through spring and summer). Seawater samples were collected from the surface and thermocline layers, and environmental parameters were recorded to examine their influence on biodiversity patterns. Microbial communities exhibited strong seasonal and depth-related structuring. Alpha diversity was highest in spring and declined during summer, while beta diversity analyses revealed clear clustering by month and depth. Dominant taxa included Alphaproteobacteria (SAR11), Cyanobacteria (Synechococcus, Prochlorococcus), with distinct core microbiomes. Fish communities, identified via CytB metabarcoding, displayed marked temporal turnover but limited spatial segregation. While alpha diversity metrics did not differ significantly, beta diversity analyses showed seasonal shifts with dominant taxa such as Raja spp., Engraulis spp., and Diplodus sargus. Multivariate and co-structure analyses (Mantel, Procrustes) revealed moderate but significant concordance between microbial and fish communities and support the existence of similar biodiversity responses to environmental parameters across temporal and spatial variability. Co-occurrence networks further present depth-specific associations, with surface communities being more cooperative and phototrophic, while thermocline networks showed modularity and potential ecological specialization. This study highlights the value of integrated eDNA-based monitoring in revealing seasonal biodiversity dynamics and ecological interactions in coastal marine ecosystems, supporting future spatial planning and conservation strategies in the Thracian Sea.},
}

@article {pmid41156831,
year = {2025},
author = {Ramji, N and Hu, P and Muñoz Bodnar, A and Braga, CP and Snowball, J and Swift, D and Ye, H and Xie, S and Trenner, R and Klukowska, M and Schneiderman, E and Biesbrock, AR},
title = {Multi-Omics Insights into Gingivitis from a Clinical Trial: Understanding the Role of Bacterial and Host Factors.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102371},
pmid = {41156831},
issn = {2076-2607},
support = {n/a//Procter & Gamble (United States)/ ; },
abstract = {Poor oral health is a neglected epidemic, potentially contributing to systemic health issues. We employed a multi-omics approach to investigate the biological changes associated with gingivitis and the effects of stannous fluoride (SnF2) dentifrice on microbial composition and salivary proteomics in an eight-week clinical trial involving 39 participants categorized as high (n = 20) and low bleeders (n = 19). Baseline assessments revealed significant microbial dysbiosis in high bleeders, characterized by a higher abundance of Porphyromonas and Fusobacterium, alongside compromised epithelial barriers and increased inflammation. Following SnF2 treatment, a substantial reduction in these bacteria, and an increase in Rothia and Haemophulis, were observed, correlating with improved clinical measures, including reduced bleeding and inflammation indices. In total, 80 proteins (including pro-inflammatory cytokines, alarmin keratins, and matrix metalloproteinases) showed a significant reduction in high bleeders after treatment, with 29 overlapping the disease biomarkers in the plasma atlas, supporting the role of SnF2 in mitigating oxidative stress and enhancing epithelial integrity. Furthermore, SnF2 treatment significantly reduced collagen degradation, suggesting the preservation of tissue integrity. These findings highlight that SnF2 not only improves local oral health but may also benefit systemic health, showcasing the value of a multi-omics approach in understanding the interconnections among oral microbiota, inflammatory responses, and systemic health outcomes.},
}

@article {pmid41156828,
year = {2025},
author = {Stock, EK and Rota, K and Dunn, B and Vasquez, M and Hernandez-Velazquez, D and Lespes, A and Bosmans, S and Smith, JC and Kyndt, JA},
title = {Seasonal Variations of the Nebraska Salt Marsh Microbiome: Environmental Impact, Antibiotic Resistance, and Unique Species.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102369},
pmid = {41156828},
issn = {2076-2607},
support = {NSF OIA-2044049//EPSCoR NE/ ; },
abstract = {The Nebraska Salt Marshes are unique inland saltwater ecosystems, and this exploratory study is aimed at understanding the microbial composition and diversity that is providing the underlying support for these ecosystems. The microbiome shows both temporal and spatial variations that are concurrent with seasonal variations in salinity, temperature, and vegetation growth. Whole genome metagenomics analysis showed the predominance of purple non-sulfur bacteria in each season, indicating their importance in the marsh ecosystem. The fall season showed the highest microbial diversity and coincided with the highest levels of antimicrobial resistance markers to a variety of natural and synthetic antibiotics. In addition to the metagenomics approach, we also isolated and sequenced several unique species, most of them belonging to what appear to be new species of purple non-sulfur or purple sulfur bacteria. Both the metagenomics analysis and isolated species indicate that the nitrogen and sulfur cycling is well balanced in these marshes by a high relative abundance of purple bacteria. Noteworthy is the isolation of a new strain of Vibrio cholerae, which is a known human intestinal pathogen, that was predominantly present in the fall samples carrying several antibiotic resistance markers. Overall, the Nebraska salt marsh microbiome showcases both seasonal variations in microbial composition, a concerning prevalence of multiple antibiotic resistance, and the presence of unique bacterial species well-adapted to its distinctive alkaline and saline environment.},
}

@article {pmid41156813,
year = {2025},
author = {Mollova, D and Baev, V and Iliev, I},
title = {In Vitro Probiotic Modulation of Specific Dietary Complex Sugar Consumption in Fecal Cultures in Infants.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102352},
pmid = {41156813},
issn = {2076-2607},
support = {KP-06-M81/6//Bulgarian Science Fund/ ; },
abstract = {Establishing the relative stability of the gastrointestinal microbiome after birth is a long and complex process, and it occurs under various influences. The human gut microbiome plays a crucial role in influencing an individual's health and well-being across all stages of life. Breastfeeding, the introduction of solid food at a certain stage after birth, and the type of food largely determine the composition of the developing microbiome. The influence of probiotics on the early development of the microbiome is gaining increasing interest. The method of in vitro co-cultivation with probiotic strains provides a clearer picture of the influence of these microorganisms on the community and the functional changes that the infant's microbiome undergoes. We used fecal samples to study this influence by conducting metagenomic sequencing to determine the composition of the microbiome and a series of cultivations to determine the absorption of various fibers and prebiotic sugars from breast milk. We found statistically significant differences in the absorption of prebiotic sugars isolated from breast milk, as well as better absorption of several substrates in the presence of a probiotic strain.},
}

@article {pmid41156809,
year = {2025},
author = {Wadop, YN and Vasquez, EL and Mathews, JJ and Muhammad, JAS and Pirela Mavarez, R and Satizabal, CL and Gonzales, MM and Tanner, J and Maestre, G and Fonteh, AN and Seshadri, S and Kautz, TF and Fongang, B},
title = {Differential Patterns of Gut and Oral Microbiomes in Hispanic Individuals with Cognitive Impairment.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102350},
pmid = {41156809},
issn = {2076-2607},
support = {P30 AG066546/AG/NIA NIH HHS/United States ; 5P30AG059305-03/AG/NIA NIH HHS/United States ; RF1AG061729A1/AG/NIA NIH HHS/United States ; 5U01AG052409-04/AG/NIA NIH HHS/United States ; NS017950, UF1NS125513, K01NS126489/NS/NINDS NIH HHS/United States ; },
abstract = {Alterations in both oral and gut microbiomes have been associated with Alzheimer's disease and related dementia (ADRD). While extensive research has focused on the role of gut dysbiosis in ADRD, the contribution of the oral microbiome remains relatively understudied. This study aims to evaluate distinct patterns and potential synergistic effects of oral and gut microbiomes in a cohort of predominantly Hispanic individuals with cognitive impairment (CI) and without cognitive impairment (NC). We conducted 16S rRNA gene sequencing on stool and saliva samples from 32 participants (17 CI, 15 NC; 62.5% female, mean age = 70.4 ± 6.2 years) recruited in San Antonio, Texas, USA. Differential abundance analysis evaluated taxa with significant differences between both groups. While diversity metrics showed no significant differences between CI and NC groups, differential abundance analysis revealed an increased presence of oral genera such as Dialister, Fretibacterium, and Mycoplasma in CI participants. Conversely, CI individuals exhibited a decreased abundance of gut genera, including Shuttleworthia, Holdemania, and Subdoligranulum, which are known for their anti-inflammatory properties. No evidence was found for synergistic contributions between oral and gut microbiomes in the context of CI. Our findings suggest that like the gut microbiome, the oral microbiome of CI participants undergoes significant modifications. Notably, the identified oral microbes have been previously associated with periodontal diseases and gingivitis. These results underscore the necessity for further investigations with larger sample sizes to validate our findings and elucidate the complex interplay between oral and gut microbiomes in ADRD pathogenesis.},
}

@article {pmid41156806,
year = {2025},
author = {Sindi, AS},
title = {The Association Between Maternal Diet and the Human Milk Microbiome: A Review of Evidence and Methodological Challenges.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102347},
pmid = {41156806},
issn = {2076-2607},
abstract = {The human milk (HM) microbiome plays an important role in shaping the infant gut microbiota, with potential implications for immune development and both short- and long-term health. Among the maternal and infant factors influencing HM microbial composition, maternal diet represents a modifiable determinant. However, evidence regarding the impact of diet on the HM microbiota remains limited, and the methodological quality of available studies is variable. This review synthesises findings from 15 observational and interventional studies, critically evaluating dietary assessment approaches, milk collection protocols, microbiome analysis methods, and control of confounding factors. Current evidence suggests that maternal intake of macronutrients, micronutrients, and bioactive compounds may influence HM bacterial composition and functional potential, though results are inconsistent. Key limitations across studies include small sample sizes, short intervention periods, lack of appropriate control groups, variable aseptic sampling methods, inadequate contamination controls, and insufficient adjustment for confounders. To advance the field, we recommend larger, multicentre randomised controlled trials with longer intervention durations, incorporation of dietary biomarkers, standardised HM collection and processing protocols, and advanced multi-omics approaches. Strengthening methodological rigour is essential to generate robust evidence that can guide dietary interventions aimed at optimising the HM microbiota and improving infant health outcomes.},
}

@article {pmid41156805,
year = {2025},
author = {Ampe, T and Decroix, L and De Pauw, K and Meeusen, R and Demuyser, T and Roelands, B},
title = {Nutritional and Physiological Demands Shape the Gut Microbiome of Female World Tour Cyclists.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102345},
pmid = {41156805},
issn = {2076-2607},
abstract = {This cross-sectional study investigated whether elite female World Tour cyclists have a specific gut microbiome compared to non-athlete female controls, potentially resulting from the unique physiological and dietary demands of high-level endurance cycling. Fourteen female cyclists and thirteen matched controls provided fecal samples during a period of reduced training (off-season cycling). The samples were analyzed using 16S rRNA gene sequencing and short-chain fatty acid (SCFA) quantification. The results revealed significant differences in microbiome composition. The cyclists showed a higher abundance of Bacteroidota (72.7% vs. 15.3%) and a lower abundance of Firmicutes (22.1% vs. 62.5%) compared to the controls, along with reduced alpha-diversity (Shannon index, p < 0.05). Fiber-fermenting families such as Lachnospiraceae and Ruminococcaceae were depleted, consistent with a carbohydrate-focused and relatively low-fiber diet. Interestingly, fecal SCFA levels did not differ, suggesting functional adaptation of the microbiome. These findings indicate that the elite female cyclists may have developed a "performance-adapted" gut microbiome. However, due to the cross-sectional design, causality cannot be established, and the long-term health implications remain uncertain.},
}

@article {pmid41156799,
year = {2025},
author = {Cai, Z and Shi, J and Fu, S and Lv, L and Li, F and Liu, Q and Zhang, H and Bao, S},
title = {Ecological Effects and Microbial Regulatory Mechanisms of Functional Grass Species Assembly in the Restoration of "Heitutan" Degraded Alpine Grasslands.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102341},
pmid = {41156799},
issn = {2076-2607},
support = {2025-NK-P25//Qinghai Provincial Science and Technology Commissioner Program: Demonstration and Promotion of Organic Forage Cultivation Technologies in Dari County/ ; 2023-ZJ-923M//the Qinghai Provincial Natural Science Foundation/ ; },
abstract = {The restoration of "Heitutan" degraded grasslands on the Qinghai-Tibetan Plateau was hindered by suboptimal grass species mixtures, leading to low vegetation productivity, impaired soil nutrient cycling, and microbial functional degradation. Based on a 22-year controlled field experiment, this study systematically elucidated the regulatory mechanisms of different artificial grass mixtures on vegetation community characteristics, soil physicochemical properties, and bacterial community structure and function. The results demonstrated that mixed-sowing treatments significantly improved soil conditions and enhanced aboveground biomass. The HC treatment (Elymus nutans Griseb. + Poa crymophila Keng ex L. Liu cv. 'Qinghai' + Festuca sinensis Keng ex S. L. Lu cv. 'Qinghai') achieved aboveground biomass of 1580.0 and 1645.0 g·m[-2], representing 66.14% and 60.91% increases, respectively, compared to the HA monoculture (E. nutans). Concurrently, this treatment increased soil organic matter content by 52.3% and 48.4%, total nitrogen by 59.4% and 69.2%, while reducing electrical conductivity by 48.99% and 51.72%, with optimal pH stabilization (7.34-7.38). These findings confirmed that optimized grass mixtures effectively enhance soil physicochemical properties and carbon-nitrogen retention. Microbiome analysis revealed that the HE treatment (E. nutans + P. crymophila + F. sinensis + Poa poophagorum Bor. + Festuca kryloviana Reverd. cv. 'Huanhu') exhibited superior α-diversity indices (OTU, Shannon, Ace, Chao1, Pielou) with increases of 9.36%, 4.20%, 15.0%, 1.76%, and 13.4%, respectively, over HA, accompanied by optimal community evenness (lowest Simpson index). Core bacterial phyla included Pseudomonadota (22.7-29.9%), Acidobacteriota (21.5-23.6%), and Actinomycetota (13.6-16.0%), with significant suppression of pathogenic bacteria. Co-occurrence network analysis identified specialized functional modules, with HC and HD treatments (E. nutans + P. crymophila + F. sinensis + P. poophagorum) forming a "nitrogen transformation-antibiotic secretion" network (57.3% positive connections). Structural equation modeling (SEM) revealed that mixed sowing had the strongest direct effect on bacterial diversity (β = 0.76), surpassing indirect effects via soil (β = 0.37) and vegetation (β = 0.11). Redundancy analysis (RDA) identified vegetation cover (24.7% explained variance) and soil pH (20.0%) as key drivers of bacterial community assembly. Principal component analysis (PCA) confirmed HC and HD treatments as the most effective restoration strategies. This study elucidated a tripartite "vegetation-soil-microorganism" restoration mechanism, demonstrating that intermediate-diversity mixtures (3-4 species) optimize ecosystem recovery through niche complementarity, pathogen suppression, and enhanced nutrient cycling. These findings provided a scientific basis for species selection in alpine grassland restoration.},
}

@article {pmid41156784,
year = {2025},
author = {Pagán-Rivera, LH and Godoy-Vitorino, F and Meléndez-Vázquez, NM and Ocasio-Rivera, SE and Santiago-Gascot, ME and Santiago, JM and Salgado, I and González, V and Martínez-Guzmán, O and Cáceres-Chacón, M and Torrado-Tapias, A and Miranda, JD},
title = {The Effect of Cefazolin on the Gut Microbiome of Female Rats After Spinal Cord Injury.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102324},
pmid = {41156784},
issn = {2076-2607},
support = {SC1GM144032/GM/NIGMS NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; 1P20GM156713-01/GM/NIGMS NIH HHS/United States ; P30-GM149367/GM/NIGMS NIH HHS/United States ; 2U54MD007600/MD/NIMHD NIH HHS/United States ; #2022-00125//Puerto Rico Science & Technology Trust/ ; },
abstract = {Spinal cord injury (SCI) is a devastating neurological state that could lead to motor, sensory, and autonomic dysfunction. In addition to its direct impact on the central nervous system, SCI exerts systemic effects, including disruption of gut homeostasis and alterations in the gut microbiota, which can contribute to sustained inflammation and hinder functional recovery. While antibiotic administration during the acute phase of SCI is clinically indicated, it may exacerbate microbial dysbiosis. In this study, we investigate the combined effects of SCI and cefazolin treatment on the gut microbiome of female rats. Animals were assigned to three groups: NAÏVE (no intervention), SHAM (cefazolin only), and INJURY (T10 spinal cord contusion plus cefazolin). Cefazolin was administered for seven days after the injury, fecal samples were collected at baseline (day 0), and on days 7, 14, 21, and 28 post-SCI. DNA was extracted and subjected to 16S rRNA gene amplicon sequencing, followed by bioinformatic analysis. Our findings revealed significant microbial dysbiosis in the INJURY group, including reduced alpha diversity and distinct shifts in microbial composition. These changes were most prominent during the acute phase post-SCI. Our findings highlight the compounding effects of spinal trauma and antibiotic exposure on the gut microbiome and suggest that maintaining microbial stability may represent a promising avenue to support recovery after SCI.},
}

@article {pmid41156777,
year = {2025},
author = {Kianpour Rad, S and Li, R and Yeo, KKL and Wu, F and Tomita, Y and Price, TJ and Ingman, WV and Townsend, AR and Smith, E},
title = {Bacterial Infections and Their Cell Wall Ligands Differentially Modulate Doxorubicin Sensitivity in Triple-Negative Breast Cancer Cells.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102317},
pmid = {41156777},
issn = {2076-2607},
abstract = {BACKGROUND: Triple-negative breast cancer (TNBC) is an aggressive subtype with limited treatment options and poor clinical outcomes. Emerging evidence suggests that the tumor-associated microbiome may influence disease progression and therapy response.

METHODS: We investigated how the Gram-negative bacterium Pseudomonas aeruginosa and Gram-positive bacterium Staphylococcus aureus, together with their cell wall components lipopolysaccharide (LPS) and lipoteichoic acid (LTA), modulate doxorubicin (DOX) efficacy in TNBC cells. Using gentamicin protection combined with flow cytometry of eFluor 450-labeled bacteria and CFU quantification, we assessed bacterial uptake, persistence, and effects on drug response in MDA-MB-468, MDA-MB-231, and MDA-MB-453 cells.

RESULTS: Both bacteria entered TNBC cells and survived for several days in a cell line-dependent manner. Notably, bacterial infection and purified cell wall ligands (LPS and LTA) significantly increased DOX accumulation and enhanced cytotoxicity in MDA-MB-468 and MDA-MB-231, but not in MDA-MB-453. The similar effects of LPS and LTA implicate Toll-like receptor signaling (TLR2 and TLR4) in modulating drug uptake.

CONCLUSIONS: These findings demonstrate that bacterial infection and associated ligands can enhance doxorubicin uptake and cytotoxicity in TNBC cells, implicating TLR signaling as a potential contributor. Our results highlight the importance of host-microbe interactions in shaping chemotherapy response and warrant further investigation into their therapeutic relevance.},
}

@article {pmid41156764,
year = {2025},
author = {Wang, J and Gu, H and Gao, H and Zhang, T and Jiang, F and Song, P and Liu, Y and Fan, Q and Xu, Y and Zhang, R},
title = {Insights into Cold-Season Adaptation of Mongolian Wild Asses Revealed by Gut Microbiome Metagenomics.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102304},
pmid = {41156764},
issn = {2076-2607},
support = {32360139//National Natural Science Foundation of China/ ; 2023LHMS03067//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; LHZX-2023-02//Joint Grant from Chinese Academy of Sciences -People's Government of Qinghai Province on San-jiangyuan National Park/ ; },
abstract = {The Mongolian wild ass (Equus hemionus hemionus) is a flagship species of the desert-steppe ecosystem in Asia, and understanding its strategies for coping with cold environments is vital for both revealing its survival mechanisms and informing conservation efforts. In this study, we employed metagenomic sequencing to characterize the composition and functional potential of the gut microbiota, and applied DNA metabarcoding of the chloroplast trnL (UAA) g-h fragment to analyze dietary composition, aiming to reveal seasonal variations and the interplay between dietary plant composition and gut microbial communities. In the cold season, Bacteroidota and Euryarchaeota were significantly enriched, suggesting enhanced fiber degradation and energy extraction from low-quality forage. Moreover, genera such as Bacteroides and Alistipes were also significantly enriched and associated with short-chain fatty acid (SCFA) metabolism, bile acid tolerance, and immune modulation. In the cold season, higher Simpson index values and tighter principal coordinates analysis (PCoA) clustering indicated a more diverse and stable microbiota under harsh environmental conditions, which may represent an important microecological strategy for the host to cope with extreme environments. Functional predictions based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) further indicated upregulation of metabolic and signaling pathways, including ABC transporters, two-component systems, and quorum sensing, suggesting multi-level microbial responses to low temperatures and nutritional stress. trnL-based plant composition analysis indicated seasonal shifts, with Tamaricaceae detected more in the warm season and Poaceae, Chenopodiaceae, and Amaryllidaceae detected more in the cold season. Correlation analyses revealed that dominant microbial phyla were associated with the degradation of fiber, polysaccharides, and plant secondary metabolites, which may help maintain host energy and metabolic homeostasis. Despite the limited sample size and cross-sectional design, our findings highlight that gut microbial composition and structure may be important for host adaptation to cold environments and may also serve as a useful reference for future studies on the adaptive mechanisms and conservation strategies of endangered herbivores, including the Mongolian wild ass.},
}

@article {pmid41156762,
year = {2025},
author = {Pitts, E and Grainger, B and McKenzie, D and Fiorenza, S},
title = {Associations Between the Gut Microbiome and Outcomes in Autologous Stem Cell Transplantation: A Systematic Review.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102302},
pmid = {41156762},
issn = {2076-2607},
abstract = {Autologous stem cell transplantation (ASCT) is the standard frontline consolidation strategy in fit, eligible patients with chemosensitive multiple myeloma, and it also serves as salvage option in other haematological malignancies, such as diffuse large B cell lymphoma. Moreover, ASCT is known to disrupt the gut microbiome (GM), and the impact on clinical outcomes has been understudied. The aim of this review is to examine the associations between the GM and outcomes in patients undergoing ASCT. Using the PRISMA 2020 guidelines for systematic reviews and meta-analyses, a total of 11 articles were included in this review, comprising both observational studies (cohort studies, case-control studies) and interventional trials (randomised controlled trials). Consistent findings included a notable decrease in beneficial bacteria, including Bacteriodetes, Firmicutes and Faecalibacterium prausnitzii, which maintain gut homeostasis and modulate immune responses. Conversely, an increase in pathogenic bacteria, including Escherichia coli, Enterococcus spp. and Klebsiella spp., was observed post-transplantation. This review includes an overview of the GM following ASCT and the techniques commonly used to assess it, and highlights gaps, thereby identifying key areas for future research, although conclusions are limited by variation in sample size and reporting inconsistencies. Understanding the GM's role in ASCT may lead to interventions that optimise patient outcomes through therapeutic manipulation of the GM.},
}

@article {pmid41156756,
year = {2025},
author = {Doulberis, M},
title = {Editorial for the Special Issue "Gut Microbiome in Homeostasis and Disease, 2nd Edition".},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102297},
pmid = {41156756},
issn = {2076-2607},
abstract = {The gut microbiome has emerged lately as a cornerstone of human (patho)physiology, intricately involved in the complex regulation of the immune system, metabolic pathways, and neurobehavioral patterns [...].},
}

@article {pmid41156743,
year = {2025},
author = {Bang, WY and Moon, JS and Kim, H and Lee, HB and Kim, D and Shin, M and Jung, YH and Shin, J and Yang, J},
title = {Therapeutic Modulation of the Gut Microbiome by Supplementation with Probiotics (SCI Microbiome Mix) in Adults with Functional Bowel Disorders: A Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102283},
pmid = {41156743},
issn = {2076-2607},
support = {RS-2025-02216704//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, Forestry, and Fisheries/ ; },
abstract = {Functional bowel disorders (FBDs) are chronic gastrointestinal conditions characterized by recurrent symptoms associated with gut microbiota dysbiosis. Although accumulating evidence suggests that probiotics can improve symptoms in patients with FBD, the underlying mechanisms remain to be fully elucidated. In this randomized, double-blind, placebo-controlled clinical trial, 38 adults meeting the Rome IV diagnostic criteria of functional constipation (FC) and functional diarrhea (FD) received either a multi-strain probiotic complex or placebo for 8 weeks. Clinical outcomes were evaluated using the Irritable Bowel Syndrome Severity Scoring System (IBS-SSS), bowel habits questionnaire, and IBS Quality of Life (IBS-QoL) instrument. Fecal samples were collected at baseline and at week 8 for gut microbiota profiling via 16S rRNA gene sequencing and metabolomic analysis using gas chromatography-mass spectrometry. Probiotic supplementation significantly reduced the severity of abdominal bloating and its interference with quality of life, and improved the body image domain of the IBS-QoL. Beta diversity analysis showed significant temporal shifts in the probiotic group, while 16S rRNA sequencing revealed an increased relative abundance of Faecalibacterium prausnitzii and Blautia stercoris. Fecal metabolomic analysis further indicated elevated levels of metabolites implicated in the gut-brain axis. Multi-strain probiotic supplementation alleviated gastrointestinal symptoms and improved aspects of psychosocial well-being in adults with FBDs, potentially through modulation of the human gut microbiome.},
}

@article {pmid41156742,
year = {2025},
author = {Xian, K and Sang, J and Su, J and Huang, N and Wu, W and He, J and Liu, B and Fu, C},
title = {Microbial Diversity in the Rhizosphere Soils of Three Different Populations of Paphiopedilum helenae, a Critically Endangered Wild Orchid.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102282},
pmid = {41156742},
issn = {2076-2607},
support = {32160096//National Natural Science Foundation of China/ ; GKAB24010014//Key Development Program of Guangxi Province/ ; 22-035-26//Guangxi Key Laboratory of Plant Conservation and Restoration Ecology in Karst Terrain/ ; },
abstract = {In the Red List of Threatened Species, released by International Union for Conservation of Nature (IUCN), Paphiopedilum helenae has been classified as an endangered species. It exhibits exceptional decorative value and germplasm resource potential. To elucidate the ecological adaptation of this species and the characteristics of its rhizosphere microbiome, bacterial 16S rRNA and fungal ITS sequences of three wild populations of P. helenae were investigated using Illumina high-throughput sequencing technology and the microbial community structures and diversities were systematically compared. These three populations were spanned across distinct geographical locations in Longzhou County, Guangxi. The results showed that the bacterial community in the rhizosphere soil of P. helenae comprised 31 phyla, primarily including Actinobacteriota, Proteobacteria, Chloroflexi and Acidobacteriota. On the other hand, the fungal community consisted of 10 phyla, dominated by Ascomycota and Basidiomycota. There were significant differences in the diversity of rhizosphere microbes across different populations of P. helenae. The LG population had the highest bacterial richness (Chao index: 2912.71 ± 131.73; p < 0.05) and diversity (Shannon index: 6.40 ± 0.06; p < 0.01), while the MQ population had the lowest diversity (Shannon index: 3.47 ± 0.24; p < 0.01) of fungi. The degree of variation in fungal β-diversity was significantly higher than that of bacteria. Soil organic matter (SOM) and available nitrogen (AN) contents were the core factors shaping the microbial communities in the rhizosphere soil of P. helenae, which jointly explained 49.87% and 16.39% of variations in the bacterial and fungal communities. Furthermore, population-specific enrichment of functionally significant microorganisms was evident. Population MQ was enriched with plant growth-promoting and stress-resistant fungi, such as Geminibasidium, Trichoderma, etc. Population LG was enriched with oligotrophic bacteria (e.g., Patescibacteria), while population SL exhibited an overwhelming dominance of Ascomycota (93.25%) and enrichment of pathogenic fungal genus Nigrospora. This research revealed the variations in the functional adaptation strategy of P. helenae and the microbial communities in the rhizosphere soils across different geographical locations. This suggests that microbial community imbalance in rhizosphere soil may be one of the factors leading to the endangerment of this plant species. The study proposed a differentiated protection strategy for endangered plant species based on microbial resources. The results provide a theoretical basis for development of a "microorganism-assisted protection" strategy for ecological restoration and sustainable utilization of endangered orchid plants.},
}

@article {pmid41156737,
year = {2025},
author = {Munoz-Price, LS and Atkinson, SN and Lam, V and Buchan, B and Ledeboer, N and Salzman, NH and Pan, AY},
title = {Longitudinal Gut Microbiome Changes Associated with Transitions from C. difficile Negative to C. difficile Positive on Surveillance Tests.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102277},
pmid = {41156737},
issn = {2076-2607},
abstract = {Clostridioides difficile is an obligate anaerobe and is primarily transmitted via the fecal-oral route. Data characterizing the microbiome changes accompanying transitions from non-colonized to C. difficile colonized subjects are currently lacking. In this retrospective cohort study, we examined 16S rRNA gene sequencing data in a total of 481 fecal samples belonging to 107 patients. Based on C. difficile status over time, patients were categorized as Negative-to-Positive, Negative Control, and Positive Control. A linear mixed effects model was fitted to investigate the changes in the Shannon α-diversity index over time. Zero-inflated negative binomial/Poisson mixed effects models or generalized linear mixed models with negative binomial/Poisson distribution were used to investigate the changes in taxon counts over time among different groups. A total of 107 patients were eligible for the study. The median number of stool samples per patient was 3 (IQR 2-4). A total of 42 patients transitioned from C. difficile negative to positive (Negative-to-Positive), 47 patients remained negative throughout their tests (Negative Control) and 18 were always C. difficile positive (Positive Control). A significant difference in microbiome composition between the last negative samples and the first positive samples were shown in Negative-to-Positive patients, ANOSIM p = 0.022. In Negative-to-Positive patients, the phylum Pseudomonadota and family Enterobacteriaceae increased significantly in the first positive samples compared to the last negative samples, p = 0.0075 and p = 0.0094, respectively. Within the first 21 days, Actinomycetota decreased significantly over time in the Positive Control group compared to the other two groups (p < 0.001) while Bacillota decreased in both the Negative-to-Positive group and Positive Control. These results demonstrate that the transition from C. difficile negative to C. difficile positive is associated with alterations in gut microbial communities and their compositional patterns over time. Moreover, these changes play an important role in both the emergence and intensification of the gut microbiome dysbiosis in patients who transitioned from C. difficile negative to positive and those who always tested positive.},
}

@article {pmid41156729,
year = {2025},
author = {Carnaggio, AA and Barthet, MM},
title = {It's a Question at the 'Root' of the Problem: Fungal Associations of Dionaea muscipula (Venus' Flytrap) Roots in Its Native Habitat.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102269},
pmid = {41156729},
issn = {2076-2607},
support = {//US Fish & Wildlife Services; Coastal Carolina University Coastal Marine and Wetlands Science Master's program; the Coastal Carolina University Graduate Student Research Incentive Grant; Savannah Presbytery's M.K. Pentecost Ecology Fund Grant/ ; },
abstract = {Carnivorous plants survive in harsh habitats with limited nutrients and a low pH. Much focus has been placed on carnivorous trap evolution as the primary mechanism to increase nutrient acquisition through insect digestion. Soil microbiome, however, may also play a pertinent role in nutrient acquisition influencing plant vigor and overall success. Dionaea muscipula, commonly known as the Venus' flytrap, is endemic to rims of the Carolina Bays located in southeast North Carolina and northeast South Carolina, where D. muscipula survives in nutrient poor soils with a vestigial root system. We utilized a combination of microscopy, plating, and metagenomics, to investigate the presence/absence of fungal partners that may contribute to success and vigor of D. muscipula in its native habitat in order to further conservation of this carnivorous plant. Results support that D. muscipula forms both mycorrhizal and fungal endophytic associations, most likely to aid nutrient uptake from otherwise nutrient-poor soils, as well as aid in stress defense. Several ectomycorrhizal, endophytic, and saprophytic fungal species were identified from the surrounding rhizosphere of D. muscipula roots presenting a first glimpse into fungal communities that may influence D. muscipula physiology and compose the microbiome of the Carolina Bays ecosystem.},
}

@article {pmid41156716,
year = {2025},
author = {Coe, CL and Lubach, GR and Amaral, WZ and Phillips, GJ and Lyte, M and Georgieff, MK and Rao, RB and Connor, JR},
title = {Infantile Anemia and Iron Treatments Affect the Gut Microbiome of Young Rhesus Monkeys.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102256},
pmid = {41156716},
issn = {2076-2607},
support = {MH104198, HD089989/NH/NIH HHS/United States ; 10000/GATES/Gates Foundation/United States ; },
abstract = {The influence of iron deficiency anemia and iron treatments on the gut microbiome was evaluated in young rhesus monkeys. First, the hindgut bacterial profiles of 12 iron-deficient anemic infants were compared to those of 9 iron-sufficient infants at 6 months of age, a time when the risk of anemia is high due to rapid growth. After this screening, the anemic monkeys were treated with either parenteral or enteral iron. Seven monkeys were injected intramuscularly with iron dextran, the typical weekly treatment used in veterinary practice. Four other anemic infants were treated with a novel oral supplement daily: yeast genetically modified to express ferritin. Fecal specimens were analyzed using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Bacterial species richness in anemic infants was not different from that of iron-sufficient infants, but beta diversity and LEfSe analyses of bacterial composition indicated that the microbiota profiles were associated with iron status. Both systemic and oral iron increased alpha and beta diversity metrics. The relative abundance of Ruminococcaceae and other Firmicutes shifted in the direction of an iron-sufficient host, but many different bacteria, including Mollicutes, Tenericutes, and Archaea, were also enriched. Collectively, the findings affirm the important influence of the host's iron status on commensal bacteria in the gut and concur with clinical concerns about the possibility of adverse consequences after iron supplementation in low-resource settings where children may be carriers of iron-responsive bacterial pathogens.},
}

@article {pmid41156706,
year = {2025},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {The Gut Microbiome in Enteric Viral Infections: Underlying Mechanisms and Therapeutic Approaches.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102247},
pmid = {41156706},
issn = {2076-2607},
abstract = {Despite growing recognition of the role of the gut microbiome in host health and in modulating pathogen activity, the dynamic and reciprocal relationship between enteric viruses and the gut microbial ecosystem remains insufficiently defined and requires further exploration. This comprehensive review examines the bidirectional interplay between the gut microbiome and enteric viral infections by addressing (i) viruses associated with gastrointestinal alterations, (ii) how enteric viral infections alter the composition and function of the gut microbiome, (iii) how the gut microbiome modulates viral infectivity and host susceptibility, and (iv) current microbial-based approaches for preventing or treating enteric viral infections. Gastrointestinal viral infections induce gut microbiome dysbiosis, marked by reductions in beneficial bacteria and increases in potentially pathogenic populations. Specific gut microorganisms can modulate host susceptibility, with certain bacterial genera increasing or decreasing infection risk and disease severity. Pattern recognition receptors in the intestinal epithelium detect microbial signals and trigger antimicrobial peptides, mucus, and interferon responses to control viral replication while maintaining tolerance to commensal bacteria. The gut microbiome can indirectly facilitate viral infections by creating a tolerogenic environment, suppressing antiviral antibody responses, and modulating interferon signaling, or directly enhance viral replication by stabilizing virions, promoting host cell attachment, and facilitating coinfection and viral recombination. In turn, commensal gut bacteria can inhibit viral entry, enhance host antiviral responses, and strengthen mucosal barrier function, contributing to protection against gastrointestinal viral infections. Probiotics and fecal microbiota transplantation constitute potential microbial-based therapeutics that support antiviral defenses, preserve epithelial integrity, and restore microbial balance. In conclusion, the role of the gut microbiome in modulating enteric viral infections represents a promising area of future investigation. Therefore, integrating microbiome insights with virology and immunology could enable predictive and personalized strategies for prevention and treatment.},
}

@article {pmid41156698,
year = {2025},
author = {Zhao, M and Zeng, S and Shao, L and Wang, L and Zhang, T and Lu, H and Zeng, W},
title = {Antibiotic Residues in Muscle Tissues of Lueyang Black-Bone Chickens Under Free-Range Mountainous Conditions and Their Association with Gut Microbiota.},
journal = {Microorganisms},
volume = {13},
number = {10},
pages = {},
doi = {10.3390/microorganisms13102239},
pmid = {41156698},
issn = {2076-2607},
support = {2024NC-YBXM-161//Research Project of the Shaanxi Science and Technology Department/ ; 24JR046//Key Scientific Research Program of the Shaanxi Provincial Department of Education/ ; },
abstract = {The absorption, transport, and distribution of antibiotics in animals are influenced by the composition and function of the intestinal microbial community. However, most existing studies have focused on intensive farming systems involving the artificial addition of antibiotics. For free-range local chicken breeds in mountainous areas without antibiotic additives, systematic research on the presence of antibiotic residues in their muscle tissues and their association with the gut microbiota is lacking. Therefore, in this study, mountainous free-range Lueyang black-bone chickens were selected as the research subjects, employing non-targeted metabolomics and microbiomics to analyze the distribution of antibiotics in intestinal tissues (duodenum and caecum) and muscle tissues (breast and leg muscles), and their correlations with the intestinal microbiota. Metabolomics detected 47 antibiotics in intestinal tissues and 22 in muscle tissues, with 9 common to both tissues, including clinically and veterinary relevant antibiotics such as oxacillin, kanamycin, and tobramycin. Microbiomics analysis indicated significant differences in microbial communities between the duodenum and caecum at the genus level. LEfSe analysis identified seven characteristic genera in the duodenum (e.g., Bacteroides, Alistipes) and five in the caecum (e.g., Lactobacillus, Ureaplasma). Pearson correlation analysis further revealed that these shared antibiotics were significantly associated with the differential genera in the intestine. For instance, oxacillin exhibited a positive correlation with both Bacteroides and Alistipes. Kanamycin was positively correlated with Alistipes, whereas tobramycin showed a negative correlation with Bacteroides. These results indicate that antibiotic residues were present in both intestinal and muscle tissues of Lueyang black-bone chickens raised under free-range mountainous conditions. The nine antibiotics common to both tissues are likely absorbed in the intestines and transported to muscles via the bloodstream. It is hypothesized that the gut microbiota may play a potential regulatory role in this process, providing a theoretical basis for understanding microecological mechanisms under environmental antibiotic exposure.},
}

@article {pmid41156654,
year = {2025},
author = {West, N and Boz, V and Zanotta, N and Cason, C and Campisciano, G and Casuccio, A and Gianfrilli, D and Fasciana, TMA and Capra, G and Salfa, MC and Sesti, F and Suligoi, B and Valent, F and Brunelli, L and Comar, M},
title = {Human Papillomavirus: An Old New History.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/pathogens14101043},
pmid = {41156654},
issn = {2076-0817},
support = {SD 13/18//Ministero della Salute/ ; },
mesh = {Humans ; *Papillomavirus Infections/epidemiology/prevention & control/virology ; *Papillomaviridae/genetics/classification ; Papillomavirus Vaccines/immunology/administration & dosage ; Female ; Adolescent ; Male ; Human Papillomavirus Viruses ; },
abstract = {Human papillomavirus (HPV) represents the most common sexually transmitted infection worldwide and a major public health challenge. Nearly all sexually active individuals will acquire HPV during their lifetime, with the highest prevalence observed in adolescents and young adults shortly after sexual debut. More than 200 genotypes have been described, ranging from low-risk types, mainly responsible for benign lesions, to high-risk types, which are associated with cervical, anogenital, and head and neck cancers. While most infections are transient and spontaneously cleared by the immune system, persistent high-risk HPV can lead to precancerous lesions and malignant transformation, often in synergy with other sexually transmitted pathogens or in the context of microbiome imbalance. The introduction of vaccines and advanced screening technologies has substantially modified prevention strategies. Vaccination coverage remains heterogeneous, with persistent gaps particularly among males due to cultural, social, and educational barriers. Schools are increasingly recognized as strategic environments to promote awareness, sex education, and gender-neutral vaccination. Innovative approaches such as microbiome modulation, therapeutic vaccines, and liquid biopsy biomarkers are emerging as promising perspectives. This review aims to provide an updated overview of HPV epidemiology, clinical impact, prevention strategies, and future frontiers, with special attention to adolescents as a priority target group.},
}

Humans
*Papillomavirus Infections/epidemiology/prevention & control/virology
*Papillomaviridae/genetics/classification
Papillomavirus Vaccines/immunology/administration & dosage
Female
Adolescent
Male
Human Papillomavirus Viruses

@article {pmid41156619,
year = {2025},
author = {Sultankulova, KT and Kozhabergenov, NS and Shynybekova, GO and Almezhanova, MD and Zhaksylyk, SB and Abayeva, MR and Chervyakova, OV and Argimbayeva, TO and Orynbayev, MB},
title = {Metagenomic Profile of Bacterial Communities of Hyalomma scupense and Hyalomma asiaticum Ticks in Kazakhstan.},
journal = {Pathogens (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/pathogens14101008},
pmid = {41156619},
issn = {2076-0817},
mesh = {Animals ; Kazakhstan ; *Metagenomics/methods ; *Ixodidae/microbiology ; Male ; Female ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Cattle ; *Microbiota ; *Metagenome ; DNA, Bacterial/genetics ; },
abstract = {Ticks are important vectors of pathogens affecting humans and animals, posing a serious threat to health. For the first time, we studied the metagenomic profile of the microbial composition of Hyalomma scupense and Hyalomma asiaticum ticks in Kazakhstan. A total of 94 adult H. asiaticum and H. scupense ticks collected from randomly selected cattle in Kazakhstan in 2023 were analyzed. 16S rRNA gene sequencing was performed using the Ion Torrent NGS platform. Taxonomic classification was carried out in the BV-BRC platform with the Kraken2 database. Metagenomic analysis revealed 26 bacterial genera, including both pathogenic and symbiotic taxa. In H. scupense, the dominant groups were Francisella (89.0%), Staphylococcus (76.0%) and Candidatus Midichloria (61.0%), while in H. asiaticum, they were Francisella (99.0% and 95.0%) and Helcococcus (65.0%). In male H. scupense, the proportion of Francisella reached 89%, whereas in females, it varied from 2% to 28%. In H. asiaticum, Helcococcus accounted for 65% in males compared to 11% in females. This is the first report on the metagenomic profile of the microbiota of H. scupense and H. asiaticum in Kazakhstan. The detection of pathogens indicates a risk of their transmission to humans and animals and highlights the need to develop new tick control strategies.},
}

Animals
Kazakhstan
*Metagenomics/methods
*Ixodidae/microbiology
Male
Female
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Cattle
*Microbiota
*Metagenome
DNA, Bacterial/genetics

@article {pmid41156563,
year = {2025},
author = {Modrego, J and Pantoja-Arévalo, L and Gómez-Garre, D and Gesteiro, E and González-Gross, M},
title = {Dairy-Gut Microbiome Interactions: Implications for Immunity, Adverse Reactions to Food, Physical Performance and Cardiometabolic Health-A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {20},
pages = {},
doi = {10.3390/nu17203312},
pmid = {41156563},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/immunology ; *Dairy Products/adverse effects ; Animals ; Milk ; Probiotics ; *Immunity ; Cardiometabolic Risk Factors ; },
abstract = {Background/Objective: Milk and fermented dairy products are widely consumed functional foods and beverages, offering not only essential nutrients but also bioactive compounds with potential to modulate host immunity, metabolism, and the gut microbiome. This narrative review aims to synthesize current knowledge on the relationship between dairy consumption, gut microbiome, immune modulation, adverse reactions to food, physical performance and cardiometabolic health. Methods: An extensive literature analysis was conducted to explore how milk and fermented dairy products modulate the gut microbiome and influence the immune and cardiometabolic health. This study synthesis focused on key dairy bioactive compounds, such as probiotics, miRNAs, milk-derived peptides and exosomes and on evaluating their proposed mechanisms of action in inflammation and metabolic regulation, and their possible influence on physical performance through gut-microbiome interactions. Additionally, advances in metagenomic and metabolomic technologies were reviewed for their potential to uncover host-microbiota interactions relevant to precision nutrition strategies. Results: Fermented dairy products have shown potential in promoting beneficial bacteria growth such as Lactobacillus and Bifidobacterium, short-chain fatty acid synthesis and reduction in proinflammatory biomarkers. Specific dairy-derived peptides and exosomal components may further support gut barrier integrity, immune regulation and improve physical performance and reduce cardiometabolic risk factors. Additionally, emerging evidence links individual gut microbiota profiles to specific metabolic responses, including tolerance to lactose and bovine milk proteins. Conclusions: Integrating microbiome science with traditional nutritional paradigms enhances our understanding of how dairy influences immune and cardiometabolic health. Overall, current evidence suggests that investigating dairy-microbiome interactions, alongside lifestyle factors such as physical activity, may inform future personalized nutrition strategies aimed at supporting metabolic and immune health.},
}

Humans
*Gastrointestinal Microbiome/physiology/immunology
*Dairy Products/adverse effects
Animals
Milk
Probiotics
*Immunity
Cardiometabolic Risk Factors

@article {pmid41156558,
year = {2025},
author = {Cares, K and Lima Oliveira, M and Bryner, A and Man, B and Chen, Z and Bernabé, BP and Schmidt, ML and Fitzgibbon, M and Gabel, K},
title = {Time-Restricted Eating and Prebiotic Supplementation Demonstrate Feasibility and Acceptability in Young Adult Pediatric Cancer Survivors: A Randomized Controlled Pilot Trial.},
journal = {Nutrients},
volume = {17},
number = {20},
pages = {},
doi = {10.3390/nu17203306},
pmid = {41156558},
issn = {2072-6643},
support = {T32CA057699/CA/NCI NIH HHS/United States ; L30CA295383/CA/NCI NIH HHS/United States ; },
mesh = {Humans ; *Prebiotics/administration & dosage ; *Cancer Survivors ; Female ; Male ; Pilot Projects ; Adolescent ; Young Adult ; *Dietary Supplements ; Feasibility Studies ; Child ; Body Composition ; *Neoplasms ; Adult ; Gastrointestinal Microbiome ; Body Weight ; },
abstract = {BACKGROUND: The optimization of treatment for pediatric cancer has increased 5-year survivor rates to over 80%. Currently, there are almost half a million survivors of a pediatric cancer alive in the United States, with numbers increasing worldwide. Despite increased survivorship, pediatric cancer survivors (PCSs) are at high risk for long-term chronic disease, including cardiometabolic dysregulation at an early age due to cancer-related treatments. PCSs often have increased adiposity, perturbation in the gut microbiome, and chronic systemic inflammation compared to age-matched controls. Time-restricted eating (TRE) has emerged as an effective dietary intervention to promote weight loss in individuals with increased adiposity and cardiometabolic disease. Prebiotic supplements may enhance the efficacy of TRE by promoting satiety via the gut microbiome. Given the accessibility of both TRE and prebiotic supplements, this type of dietary intervention may be ideal for young adult PCSs. The purpose of this study was to determine the feasibility and acceptability of 12 weeks of TRE with and without a prebiotic supplement among young adult PCSs. Changes in body weight, body composition, and cardiometabolic disease risk markers were explored.

METHODS: Feasibility was measured based on recruitment (n = 20), retention (>80%), and adherence to the TRE eating window and prebiotic (>80%), and acceptability was measured based on a validated survey. Body weight, body composition, blood pressure, and additional blood-based cardiometabolic disease risk markers were also measured before and following the intervention.

RESULTS: Feasibility was not met based on recruitment (n = 13), but retention and adherence exceeded the a priori hypothesis. Acceptability also met the a priori hypothesis. Improvements were observed in some cardiometabolic disease risk markers, including a significant decrease in fat mass and visceral fat mass in both groups following the intervention.

CONCLUSIONS: Given the positive outcomes related to retention, adherence, and acceptability, as well as some cardiometabolic disease risk markers, a larger and longer study of TRE and prebiotic supplementation in PCSs is warranted. However, innovative recruitment strategies should be implemented, such as leveraging social media and targeting larger geographical areas, given recruitment challenges.},
}

Humans
*Prebiotics/administration & dosage
*Cancer Survivors
Female
Male
Pilot Projects
Adolescent
Young Adult
*Dietary Supplements
Feasibility Studies
Child
Body Composition
*Neoplasms
Adult
Gastrointestinal Microbiome
Body Weight

@article {pmid41156512,
year = {2025},
author = {Li, Z and Li, Y and Wang, Y and Chen, J and Liu, Y},
title = {The Athlete Gut Microbiome: A Narrative Review of Multi-Omics Insights and Next-Generation Probiotic Strategies.},
journal = {Nutrients},
volume = {17},
number = {20},
pages = {},
doi = {10.3390/nu17203260},
pmid = {41156512},
issn = {2072-6643},
support = {RGPIN-2025-04127//Natural Sciences and Engineering Research Council of Canada/ ; },
mesh = {*Probiotics ; Humans ; *Gastrointestinal Microbiome/physiology ; *Athletes ; *Athletic Performance/physiology ; Multiomics ; },
abstract = {The gut microbiome plays a pivotal role in athletic health and performance by influencing metabolism, immunity, gastrointestinal integrity, and recovery. Advances in high-throughput sequencing and integrative multi-omics approaches have provided unprecedented insights into how microbial communities adapt to the physiological demands of training and competition. Key microbial taxa, including short-chain fatty acid producers, lactate utilizers, and carbohydrate fermenters, have been linked to enhanced endurance, reduced inflammation, and improved recovery, opening exciting opportunities for targeted probiotic interventions. While conventional probiotics remain valuable, next-generation engineered strains hold particular promise, supported by recent regulatory milestones such as FDA approvals of engineered probiotics and gene-edited livestock. In this narrative review, we synthesize recent multi-omics research to examine mechanistic links between the athlete gut microbiome and performance, evaluate current and emerging probiotic strategies, and highlight challenges related to personalization, standardization, and regulation. With longitudinal, performance-oriented trials and harmonized frameworks, microbiome-targeted interventions are poised to move beyond exploratory research toward evidence-based, precision tools that optimize athletic performance and recovery.},
}

*Probiotics
Humans
*Gastrointestinal Microbiome/physiology
*Athletes
*Athletic Performance/physiology
Multiomics

@article {pmid41156468,
year = {2025},
author = {Caicedo, N and Liscano, Y and Oñate-Garzón, J},
title = {Bioactive Peptides from Quinoa (Chenopodium quinoa Willd.) as Modulators of the Gut Microbiome: A Scoping Review of Preclinical Evidence.},
journal = {Nutrients},
volume = {17},
number = {20},
pages = {},
doi = {10.3390/nu17203215},
pmid = {41156468},
issn = {2072-6643},
support = {call No. DGI-01-2025//Universidad Santiago de Cali/ ; },
mesh = {*Chenopodium quinoa/chemistry ; *Gastrointestinal Microbiome/drug effects ; *Peptides/pharmacology ; Humans ; Animals ; Prebiotics ; Dysbiosis/microbiology ; },
abstract = {Background: Gut microbiome dysbiosis is implicated in numerous chronic diseases. While quinoa possesses a rich nutritional profile with prebiotic potential, the specific capacity of its bioactive peptides to modulate gut microbial communities is not well understood. This scoping review systematically maps the preclinical evidence on the gut microbiome modulatory effects of quinoa-derived bioactive peptides to identify mechanisms, characterize their therapeutic potential, and guide future clinical translation. Methods: Following PRISMA-ScR guidelines, we searched six databases for preclinical studies investigating quinoa-derived peptides or hydrolysates and their effects on gut microbiota. Results: From 834 records, 19 studies met the inclusion criteria. Quinoa interventions demonstrated consistent effects, with 83% of studies reporting enhancement of beneficial genera and 67% an increase in alpha diversity. Disease-specific microbial signatures were observed; for instance, obesity models showed a reduced Firmicutes/Bacteroidetes ratio, while colitis models exhibited decreased Proteobacteria. Butyrate production was consistently enhanced. Methodologically, peptide generation has evolved from traditional fermentation toward more efficient enzymatic hydrolysis. Conclusions: Preclinical evidence strongly suggests that quinoa-derived bioactive peptides act as robust, context-dependent modulators of the gut microbiome. These findings position quinoa as a promising functional ingredient for precision gut health interventions, though clinical translation requires standardized preparations and validation in human trials.},
}

*Chenopodium quinoa/chemistry
*Gastrointestinal Microbiome/drug effects
*Peptides/pharmacology
Humans
Animals
Prebiotics
Dysbiosis/microbiology

@article {pmid41156372,
year = {2025},
author = {Pan, M and Chen, H and Deng, K and Xiao, K},
title = {Organ-on-a-Chip Models of the Female Reproductive System: Current Progress and Future Perspectives.},
journal = {Micromachines},
volume = {16},
number = {10},
pages = {},
doi = {10.3390/mi16101125},
pmid = {41156372},
issn = {2072-666X},
support = {2024-Y01//the Open Research Fund of Southeast University and Jiangsu Province Hospital/ ; },
abstract = {The female reproductive system represents a highly complex regulatory network governing critical physiological functions, encompassing reproductive capacity and endocrine regulation that maintains female physiological homeostasis. The in vitro simulation system provides a novel tool for biomedical research and can be used as physiological and pathological models to study the female reproductive system. Recent advances in this technology have evolved from 2D and 3D printing to organ-on-a-chip (OOC) and microfluidic systems, which has emerged as a transformative platform for modeling the female reproductive system. These microphysiological systems integrate microfluidics, 3D cell culture, and biomimetic scaffolds to replicate key functional aspects of reproductive organs and tissues. They have enabled precise simulation of hormonal regulation, embryo-endometrium interactions, and disease mechanisms such as endometriosis and gynecologic cancers. This review highlights the current state of female reproductive OOCs, including ovary-, uterus-, and fallopian tube-on-a-chip system, their applications in assisted reproduction and disease modeling, and the technological hurdles to their widespread application. Though significant barriers remain in scaling OOCs for high-throughput drug screening, standardizing protocols for clinical applications, and validating their predictive value against human patient outcomes, OOCs have emerged as a transformative platform to model complex pathologies, offering unprecedented insights into disease mechanisms and personalized therapeutic interventions. Future directions, including multi-organ integration for systemic reproductive modeling, incorporation of microbiome interactions, and clinical translation for mechanisms of drug action, will facilitate unprecedented insights into reproductive physiology and pathology.},
}

@article {pmid41156060,
year = {2025},
author = {Park, HM and Lee, J and Lee, SY and Kim, CH and Kim, HR},
title = {Changes in Gut Microbiome According to Probiotic Intake in Rectal Cancer Patients Undergoing Diverting Stoma Repair: Study Protocol.},
journal = {Journal of clinical medicine},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/jcm14207190},
pmid = {41156060},
issn = {2077-0383},
support = {HCRI23015//Chonnam National University Hwasun Hospital Institute of Biomedical Science/ ; },
abstract = {Background: The gut microbiome is crucial in sustaining intestinal balance and general health. Following rectal cancer surgery, the creation of a diverting stoma to protect the anastomosis results in a defunctioned colon, leading to dysbiosis. The effect of probiotic intake on gut dysbiosis following ileostomy repair remains uncertain. Thus, this study aims to determine the changes in gut microbiota based on the intake of probiotics after diverting stoma repair. Methods: This single-center, parallel, prospective pilot study will include patients with primary rectal cancer planning to undergo a diverting stoma during rectal cancer surgery. The study will comprise 20 patients, with 10 patients receiving synbiotics after stoma repair and 10 patients not receiving probiotics. The primary endpoint is the change in the gut microbiota of the resting colon based on the intake of probiotics, assessed through fecal testing at the following time points: before bowel resection, immediately after diverting stoma repair, and 3 weeks after diverting stoma repair. Changes in gut microbiota will be evaluated using alpha- and beta-diversity analyses based on 16S rRNA sequencing of fecal samples. Discussion: This study is the first prospective cohort trial investigating changes in the gut microbiota of the resting colon based on oral probiotic administration in patients undergoing diverting stoma repair. This trial is anticipated to clarify the impact of probiotic intake in these patients. Trial registration: Clinical Research Information Service (CRIS) of the Republic of Korea, KCT0008392, Registered on 27 April 2023.},
}

@article {pmid41155883,
year = {2025},
author = {Pîrvulescu, LE and Popescu, SC and Popescu, R and Voiculescu, VM and Negrei, C},
title = {Skin Microbiome, Nanotoxicology, and Regulatory Gaps: Chronic Cosmetic Exposure and Skin Barrier Dysfunction-A Systematic Review.},
journal = {Pharmaceutics},
volume = {17},
number = {10},
pages = {},
doi = {10.3390/pharmaceutics17101246},
pmid = {41155883},
issn = {1999-4923},
abstract = {Background: Engineered nanoparticles (NPs)-titanium dioxide, silver, zinc oxide and silica-are widely used in cosmetics for UV protection, antimicrobial activity and texturising effects. Chronic consumer-level exposure may impair skin-barrier integrity, disturb microbiome composition and dysregulate immune signalling via the gut-skin axis. Current regulatory frameworks typically omit chronic- or microbiome-focused safety assessments, leaving potential gaps. Objectives: This study aimed to evaluate the long-term effects of cosmetic-relevant NPs (titanium dioxide, silver, zinc oxide, silica) on skin and gut microbiota, epithelial-barrier integrity and immune signalling-including telocyte- and exosome-mediated pathways-and to identify regulatory shortcomings, particularly the absence of microbiome endpoints, validated chronic models and consideration of vulnerable populations. Methods: Following PRISMA 2020, PubMed, Scopus and Web of Science were searched for English-language in vivo animal or human studies (December 2014-April 2025) meeting chronic-exposure criteria (≥90 days in rodents or >10% of lifespan in other species; for humans, prolonged, repetitive application over months to years consistent with cosmetic use). Although not registered in PROSPERO, the review adhered to a pre-specified protocol. Two independent reviewers screened studies; risk of bias was assessed using a modified SYRCLE tool (animal) or adapted NIH guidance (zebrafish). Owing to heterogeneity, findings were synthesised narratively. Results: Of 600 records, 450 unique articles were screened, 50 full texts were assessed and 12 studies were included. Oral exposure predominated and was associated with dysbiosis, barrier impairment, immune modulation and metabolic effects. Dermal models showed outcomes from minimal change to pronounced immune activation, contingent on host susceptibility. Comparative human-animal findings are summarised; telocyte and exosome pathways were largely unexplored. Regulatory reviews (EU SCCS, US FDA and selected Asian frameworks) revealed no requirements for chronic microbiome endpoints. Limitations: Evidence is limited by the small number of eligible studies, heterogeneity in NP characteristics and exposure routes, predominance of animal models and a scarcity of longitudinal human data. Conclusions: Cosmetic nanoparticles may disrupt the microbiome, compromise barrier integrity and trigger immune dysregulation-risks amplified in vulnerable users. Existing regulations lack requirements for chronic exposure, microbiome endpoints and testing in vulnerable groups, and neglect mechanistic pathways involving telocytes and exosomes. Long-term, real-world exposure studies integrating gut-skin microbiome and immune outcomes, and harmonised global nanomaterial-safety standards, are needed to ensure safer cosmetic innovation.},
}

@article {pmid41155805,
year = {2025},
author = {Radu, CM and Radu, CC and Zaha, DC},
title = {Salivary and Microbiome Biomarkers in Periodontitis: Advances in Diagnosis and Therapy-A Narrative Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {10},
pages = {},
doi = {10.3390/medicina61101818},
pmid = {41155805},
issn = {1648-9144},
mesh = {Humans ; *Biomarkers/analysis ; *Saliva/chemistry/microbiology ; *Periodontitis/diagnosis/therapy/microbiology/physiopathology ; *Microbiota/physiology ; Dysbiosis ; },
abstract = {Background and Objectives: Periodontitis is a common chronic inflammatory disease and a leading cause of tooth loss worldwide. Traditional diagnostic methods, such as probing and radiographic assessment, are retrospective and fail to detect ongoing disease activity. In recent years, salivary biomarkers and oral microbiome profiling have emerged as promising tools for earlier detection and precision-based management. The aim of this review is to synthesize current evidence on salivary and microbiome-derived biomarkers in periodontitis and to evaluate their translational potential in diagnostics and therapy. Materials and Methods: A narrative review was performed using PubMed, Scopus, and Web of Science to identify studies published between 2020 and 2025. Search terms included periodontitis, salivary biomarkers, oral microbiome, dysbiosis, and precision therapy. Priority was given to systematic reviews, meta-analyses, and translational studies that addressed diagnostic or therapeutic applications. Eligible publications included English-language original studies and reviews reporting on the diagnostic or therapeutic relevance of salivary or microbiome biomarkers in periodontitis. Results: Salivary biomarkers such as cytokines, matrix metalloproteinases (MMPs), oxidative stress markers, microRNAs, and extracellular vesicles (EVs) show consistent associations with disease activity and treatment outcomes. Oral microbiome studies reveal that both classical pathogens and community-level dysbiosis contribute to disease risk. Translational advances include chairside immunoassays, biosensors, lab-on-a-chip devices, and artificial intelligence (AI)-driven analyses. Biomarker-guided therapies-such as microbiome modulation, natural bioactive compounds, host-response modulation, and smart biomaterials-are being evaluated with increasing frequency in translational studies. Conclusions: By integrating salivary and microbiome biomarkers with novel diagnostic technologies and emerging therapies, this review complements existing systematic evidence and offers a translational roadmap toward precision periodontology.},
}

Humans
*Biomarkers/analysis
*Saliva/chemistry/microbiology
*Periodontitis/diagnosis/therapy/microbiology/physiopathology
*Microbiota/physiology
Dysbiosis

@article {pmid41155754,
year = {2025},
author = {Amaritei, O and Mierlan, OL and Dinu, CA and Chiscop, I and Matei, MN and Gutu, C and Gurau, G},
title = {TMAO and Cardiovascular Disease: Exploring Its Potential as a Biomarker.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {10},
pages = {},
doi = {10.3390/medicina61101767},
pmid = {41155754},
issn = {1648-9144},
mesh = {Humans ; *Methylamines/analysis/blood/metabolism/adverse effects ; *Cardiovascular Diseases/physiopathology/etiology/blood ; *Biomarkers/analysis/blood ; Gastrointestinal Microbiome/physiology ; Animals ; },
abstract = {Gut microbiota has increasingly been shown to exert effects beyond the gastrointestinal tract, some of which are mediated through its metabolites, such as trimethylamine N-oxide (TMAO)-a compound converted by gut bacteria from dietary choline found predominantly in animal products that is associated with cardiovascular disease (CVD). However, a significant gap persists in human clinical trials assessing its potential causal role. This narrative review aims to present the current understanding of the gut microbiome, TMAO, and their relationship with CVD, while proposing future directions that may support the use of TMAO as a biomarker and guide potential interventions to reduce its harmful impact. Both animal and human studies have demonstrated a link between TMAO and CVD, with animal studies also indicating a causal effect-showing increased cardiovascular risk following TMAO administration and reduced risk when TMAO is eliminated. While direct extrapolation from animal models to humans is limited due to biological differences, these findings offer a foundation for the development of well-designed clinical trials in human populations. Although direct approaches to target TMAO-such as trimethylamine (TMA) lyase inhibitors and antisense oligonucleotide (ASO) therapy-have shown promising results in animal studies, they have yet to be investigated in human trials, leaving indirect strategies such as dietary changes and probiotics as the only currently available options.},
}

Humans
*Methylamines/analysis/blood/metabolism/adverse effects
*Cardiovascular Diseases/physiopathology/etiology/blood
*Biomarkers/analysis/blood
Gastrointestinal Microbiome/physiology
Animals

@article {pmid41155724,
year = {2025},
author = {Lis, A and Maj, P and Świętek, A and Romuk, E},
title = {The Role of Various Types of Diets in the Treatments of Depressive Disorders.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {61},
number = {10},
pages = {},
doi = {10.3390/medicina61101737},
pmid = {41155724},
issn = {1648-9144},
support = {BNW-1-149/K/3/O//Silesian Medical University/ ; },
mesh = {Humans ; *Depressive Disorder/diet therapy/physiopathology ; *Diet/methods ; Oxidative Stress/physiology ; Diet, Ketogenic/methods ; Diet, Mediterranean ; },
abstract = {Depression is a prevalent and disabling psychiatric disorder, characterized by persistent disturbances in mood, cognition, and physiological processes, which collectively lead to substantial impairments in daily functioning and quality of life. This review provides a comprehensive overview of the biological mechanisms implicated in the pathophysiology of depression, including neurotransmitter dysregulation, oxidative stress, inflammatory processes, hypothalamic-pituitary-adrenal (HPA) axis dysfunction, mitochondrial impairment, and alterations in the gut-brain axis. Furthermore, it explores the role of diet in both the prevention and management of depression, with particular emphasis on Mediterranean, anti-inflammatory, and ketogenic dietary patterns, while contrasting these with the detrimental impact of a Western dietary pattern. Specific nutrients-such as n-3 polyunsaturated fatty acids (PUFAs), B-complex vitamins, vitamins D and E, zinc, selenium, and polyphenols-are highlighted for their potential roles in modulating neurotransmission, attenuating inflammation, and supporting gut microbiota homeostasis. Despite growing scientific interest in nutrition-based interventions, current evidence on the comparative efficacy of different dietary approaches remains limited. Future research is warranted to elucidate the therapeutic potential of dietary strategies as adjuncts to conventional treatments for depression and to facilitate the development of evidence-based nutritional recommendations for clinical practice.},
}

Humans
*Depressive Disorder/diet therapy/physiopathology
*Diet/methods
Oxidative Stress/physiology
Diet, Ketogenic/methods
Diet, Mediterranean

@article {pmid41155510,
year = {2025},
author = {Coccurello, R},
title = {Disrupting the Gut-Brain Axis: How Artificial Sweeteners Rewire Microbiota and Reward Pathways.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010220},
pmid = {41155510},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Reward ; Animals ; *Sweetening Agents/pharmacology/adverse effects ; *Brain/drug effects/metabolism ; *Brain-Gut Axis/drug effects ; Dysbiosis/chemically induced ; },
abstract = {Artificial sweeteners, or non-caloric sweeteners (NCSs), are widely consumed as sugar substitutes to reduce energy intake and manage obesity. Once considered inert, accumulating evidence now shows that NCSs interact with host physiology, altering gut microbiota composition and neural circuits that regulate feeding. This review synthesizes current knowledge on how NCSs disrupt the gut-brain axis (GBA), with particular focus on microbiota-mediated effects and neural reward processing. In homeostatic regulation, NCS-induced dysbiosis reduces beneficial taxa such as Akkermansia muciniphila and Faecalibacterium prausnitzii, diminishes short-chain fatty acid production, impairs gut barrier integrity, and promotes systemic inflammation. These changes blunt satiety signaling and favor appetite-promoting pathways. Beyond homeostasis, NCSs also rewire hedonic circuits: unlike caloric sugars, which couple sweet taste with caloric reinforcement to robustly activate dopaminergic and hypothalamic pathways, NCSs provide sensory sweetness without energy, weakening reward prediction error signaling and altering neuropeptidergic modulation by orexin, neurotensin, and oxytocin. Microbial disruption further exacerbates dopaminergic instability by reducing precursors and metabolites critical for reward regulation. Together, these top-down (neural) and bottom-up (microbial) mechanisms converge to foster maladaptive food seeking, metabolic dysregulation, and increased vulnerability to overeating. Identifying whether microbiome-targeted interventions can counteract these effects is a key research priority for mitigating the impact of NCSs on human health.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Reward
Animals
*Sweetening Agents/pharmacology/adverse effects
*Brain/drug effects/metabolism
*Brain-Gut Axis/drug effects
Dysbiosis/chemically induced

@article {pmid41155504,
year = {2025},
author = {Urzică, RN and Crețu, B and Căruntu, A and Bucurica, S and Farcasiu, AT and Ciupescu, LM and Scheau, C and Căruntu, C},
title = {The Molecular Interplay Between Oral Microbiome and Oral Cancer Pathogenesis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010212},
pmid = {41155504},
issn = {1422-0067},
mesh = {Humans ; *Mouth Neoplasms/microbiology/pathology/etiology/therapy/metabolism ; *Microbiota ; *Mouth/microbiology ; Animals ; Fusobacterium nucleatum ; Dysbiosis/microbiology ; *Carcinoma, Squamous Cell/microbiology/pathology ; Signal Transduction ; },
abstract = {The oral microbiome plays a key role in oral cancer pathogenesis through mechanisms such as chronic inflammation, dysregulated proliferation, and increased tumor invasiveness. Dysbiosis, frequently present in premalignant and malignant lesions, may initiate or accelerate malignant transformation. Oral squamous cell carcinoma (OSCC), representing over 90% of oral cancers and affecting more than 350,000 people worldwide each year, is strongly linked to microbial shifts. Common periodontal pathogens such as Fusobacterium nucleatum and Porphyromonas gingivalis are often enriched in OSCC. These bacteria may promote tumorigenesis by activating NF-κB and STAT3 pathways, suppressing apoptosis, and modulating host immune responses. Additional potential mechanisms include the production of reactive oxygen species (ROS) and genotoxins, inhibition of tumor suppressors such as p53, disruption of cell-cycle regulation via cyclin-dependent kinase pathway, and upregulation of β-catenin and toll-like receptor signaling. These molecular alterations cause DNA damage, immune surveillance evasion, angiogenesis, promoting tumor progression. Microbiota-modulating therapies, such as Lactobacillus probiotics, may complement standard treatments by restoring balance, boosting immunity, and limiting tumor growth. Engineered bacteriotherapy, microbiome-targeted immunomodulators, and microbiota-based diagnostics expand therapeutic options in oral cancer and, combined with advances in precision medicine, may support more personalized treatments and improved outcomes.},
}

Humans
*Mouth Neoplasms/microbiology/pathology/etiology/therapy/metabolism
*Microbiota
*Mouth/microbiology
Animals
Fusobacterium nucleatum
Dysbiosis/microbiology
*Carcinoma, Squamous Cell/microbiology/pathology
Signal Transduction

@article {pmid41155486,
year = {2025},
author = {Nowicka, D and Kucharczyk, E and Pawłuszkiewicz, K and Korgiel, M and Busłowicz, T and Ponikowska, M},
title = {Topical Probiotics as a Novel Approach in the Treatment of Chronic Dermatoses Associated with Skin Dysbiosis: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010195},
pmid = {41155486},
issn = {1422-0067},
mesh = {Humans ; *Probiotics/administration & dosage/therapeutic use ; *Dysbiosis/microbiology/complications ; *Skin/microbiology/drug effects/pathology ; *Skin Diseases/microbiology/therapy/drug therapy/etiology ; Chronic Disease ; Microbiota ; Administration, Topical ; },
abstract = {The skin microbiome plays a pivotal role in maintaining skin homeostasis, immune regulation, and barrier integrity. Dysbiosis, characterized by altered diversity and function of the microflora, contributes to the pathogenesis of chronic inflammatory dermatoses such as atopic dermatitis, psoriasis, acne vulgaris, hidradenitis suppurativa, rosacea, and photoaging. This narrative review, based on searches in PubMed, Scopus, and Google Scholar, summarizes current evidence on the role of topical probiotics in the prevention and management of inflammatory dermatoses, drawing mainly on studies from the past decade and, where relevant, earlier works published between 1975 and 2025. Evidence indicates that topical probiotics modulate local immune responses, enhance antimicrobial peptide synthesis, inhibit pathogenic microorganism colonization, and support skin barrier regeneration. Additional benefits include accelerated wound healing and reduced environmental damage. However, study results are heterogeneous, and designs vary, with limited data on long-term effects, particularly in paediatric and immunosuppressed populations. Topical probiotics are a promising therapeutic approach for chronic inflammatory dermatoses linked to microbiota dysbiosis. They can restore microbial balance, support barrier function, suppress pathogenic microorganisms, and promote skin regeneration. Despite consistent reports of clinical improvement and improved cutaneous defence mechanisms, small sample sizes, methodological heterogeneity, and the absence of standardized dosing regimens limit current evidence. Long-term safety data are limited, especially for vulnerable patient groups. Rigorous randomized controlled trials with standardized protocols and larger, diverse populations are needed to confirm efficacy, ensure safety, and guide clinical implementation.},
}

Humans
*Probiotics/administration & dosage/therapeutic use
*Dysbiosis/microbiology/complications
*Skin/microbiology/drug effects/pathology
*Skin Diseases/microbiology/therapy/drug therapy/etiology
Chronic Disease
Microbiota
Administration, Topical

@article {pmid41155435,
year = {2025},
author = {Kuprin, A and Baklanova, V},
title = {The Microbiome as a Protagonist of Xylophagous Insects in Adaptation to Environmental Conditions and Climate Change.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010143},
pmid = {41155435},
issn = {1422-0067},
mesh = {Animals ; *Climate Change ; *Insecta/microbiology/physiology ; *Microbiota ; *Adaptation, Physiological ; Ecosystem ; Symbiosis ; Forests ; *Gastrointestinal Microbiome ; },
abstract = {Xylophagous insects represent a diverse group of species whose life cycles are trophically associated with wood at various stages of decomposition. In forest ecosystems, they play a pivotal role in wood degradation and biogeochemical nutrient cycling. Their remarkable adaptation to feeding on structurally complex and nutrient-poor woody substrates has been largely mediated by long-term symbiotic interactions with gut microbiota. This review synthesizes current knowledge on the molecular and ecological mechanisms underlying insect-microbiota interactions, with particular attention paid to the impact of environmental stressors-including elevated temperature, shifts in moisture regimes, and pollution-on microbial community structure and host adaptive responses. We critically evaluate the strength of evidence linking climate-driven microbiome shifts to functional consequences for the host and the ecosystem. The ecological implications of microbiota restructuring, such as impaired wood decomposition, decreased disease resistance, facilitation of xylophagous species spread, and alterations in key biotic interactions within forest biocenoses, are discussed. Particular emphasis is placed on the integration of multi-omics technologies and functional assays for a deeper, mechanistic understanding of microbiota roles. We also assess the potential and limitations of microbiome-based approaches for insect population management, with the overall goal of maintaining and enhancing the resilience of forest ecosystems under ongoing climate change.},
}

Animals
*Climate Change
*Insecta/microbiology/physiology
*Microbiota
*Adaptation, Physiological
Ecosystem
Symbiosis
Forests
*Gastrointestinal Microbiome

@article {pmid41155411,
year = {2025},
author = {Caliman-Sturdza, OA and Hamamah, S and Iatcu, OC and Lobiuc, A and Bosancu, A and Covasa, M},
title = {Microbiome and Long COVID-19: Current Evidence and Insights.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010120},
pmid = {41155411},
issn = {1422-0067},
support = {760073/23.05.2023, code 285/30.11.2022, within Pillar III, Component C9, Investment 8.//Romania's National Recovery and Resilience Plan/ ; 760073/23.05.2023, code 285/30.11.2022, within Pillar III, Component C9, Investment 8.//Romania's National Recovery and Resilience Plan/ ; },
mesh = {Humans ; *COVID-19/microbiology/complications ; *Gastrointestinal Microbiome ; SARS-CoV-2 ; Dysbiosis/microbiology ; Post-Acute COVID-19 Syndrome ; Probiotics/therapeutic use ; *Microbiota ; },
abstract = {Long COVID, also referred to as post-acute sequelae of SARS-CoV-2 infection (PASC), is characterized by persistent multi-systemic symptoms such as fatigue, cognitive impairment, and respiratory dysfunction. Accumulating evidence indicates that gut and oral microbiota play an important role in its pathogenesis. Patients with long COVID consistently exhibit reduced microbial diversity, depletion of beneficial short-chain fatty acid (SCFA)-producing species such as Faecalibacterium prausnitzii and Bifidobacterium spp. and enrichment of proinflammatory taxa including Ruminococcus gnavus, Bacteroides vulgatus, and Veillonella. These alterations may disrupt intestinal barrier integrity, sustain low-grade systemic inflammation, and influence host immune and neuroendocrine pathways through the gut-brain and gut-lung axes. Distinct microbial signatures have also been associated with symptom clusters, including neuropsychiatric, respiratory, and gastrointestinal manifestations. Proposed mechanisms linking dysbiosis to long COVID include impaired SCFA metabolism, tryptophan depletion, microbial translocation, and interactions with host immune and inflammatory responses, including autoantibody formation and viral antigen persistence. Preliminary interventional studies using probiotics, synbiotics, and fecal microbiota transplantation suggest that microbiome-targeted therapies may alleviate symptoms, although evidence remains limited and heterogeneous. This review synthesizes current literature on the role of gut and oral microbiota in long COVID, highlights emerging microbial biomarkers, and discusses therapeutic implications. While causality remains to be firmly established, restoring microbial balance represents a promising avenue for diagnosis, prevention, and management of long COVID.},
}

Humans
*COVID-19/microbiology/complications
*Gastrointestinal Microbiome
SARS-CoV-2
Dysbiosis/microbiology
Post-Acute COVID-19 Syndrome
Probiotics/therapeutic use
*Microbiota

@article {pmid41155313,
year = {2025},
author = {Challa, V and Prajapati, SK and Gangani, S and Yadav, D and Lekkala, L and Jain, S and Yadav, H},
title = {Microbiome-Aging-Wrinkles Axis of Skin: Molecular Insights and Microbial Interventions.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms262010022},
pmid = {41155313},
issn = {1422-0067},
mesh = {Humans ; *Skin Aging/physiology ; *Microbiota ; *Skin/microbiology/metabolism ; Probiotics/therapeutic use ; Animals ; Extracellular Matrix/metabolism ; },
abstract = {Skin aging is a complex biological process influenced by both intrinsic factors such as hormonal changes, genetic programming, and immunosenescence and extrinsic stressors including ultraviolet (UV) radiation (particularly UV-A and UV-B), pollution, and lifestyle habits. One of the most prominent manifestations of skin aging is wrinkle formation, which arises from the progressive degradation of key extracellular matrix (ECM) components like collagen and elastin. Emerging evidence highlights the skin microbiome as a critical, yet underappreciated, modulator of these structural changes. This review summarizes current understanding of how aging alters skin structure and microbial composition, and how these changes contribute to wrinkle development. Age-associated skin is characterized by reduced hydration, sebum production, and barrier integrity, accompanied by a shift in microbial communities. These microbial shifts promote local inflammation, matrix metalloproteinase (MMP) activation, and oxidative stress, all of which accelerate ECM degradation. We further discuss how commensal microbes and their bioactive products such as probiotics and postbiotics can counteract wrinkle formation. Clinical studies support the efficacy of strains such as Lactobacillus plantarum HY7714 and Bifidobacterium breve in improving skin elasticity and reducing wrinkle depth. Additionally, this review highlights the emerging role of microbiome-based interventions in skincare, including oral supplements, topical formulations, and postbiotic-enriched products. Overall, we emphasized the therapeutic potential of microbiome modulation as a novel strategy for maintaining skin health and preventing wrinkle formation during aging.},
}

Humans
*Skin Aging/physiology
*Microbiota
*Skin/microbiology/metabolism
Probiotics/therapeutic use
Animals
Extracellular Matrix/metabolism

@article {pmid41155291,
year = {2025},
author = {Watai, K and Taniguchi, M and Azuma, K},
title = {The Gut-Brain-Immune Axis in Environmental Sensitivity Illnesses: Microbiome-Centered Narrative Review of Fibromyalgia Syndrome, Myalgic Encephalomyelitis/Chronic Fatigue Syndrome, and Multiple Chemical Sensitivity.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms26209997},
pmid = {41155291},
issn = {1422-0067},
mesh = {Humans ; *Fibromyalgia/microbiology/immunology/therapy ; *Fatigue Syndrome, Chronic/microbiology/immunology/therapy ; *Gastrointestinal Microbiome/immunology ; *Multiple Chemical Sensitivity/microbiology/immunology/therapy ; *Brain/immunology/metabolism ; Animals ; *Brain-Gut Axis/immunology ; },
abstract = {Environmental sensitivity illnesses-including fibromyalgia syndrome (FMS), myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), and multiple chemical sensitivity (MCS)-are chronic, disabling disorders characterized by hypersensitivity to environmental stimuli, persistent fatigue, widespread pain, and neurocognitive and autonomic dysfunction. Although their diagnostic criteria differ, increasing evidence suggests overlapping clinical features and shared biological mechanisms. A unifying hypothesis highlights the gut-brain-immune axis, where alterations in the intestinal microbiome, epithelial barrier dysfunction, and aberrant immune signaling interact with central sensitization and systemic metabolic dysregulation. Recent studies demonstrate reduced microbial diversity, depletion of anti-inflammatory taxa (e.g., Faecalibacterium prausnitzii, Bifidobacterium), and enrichment of pro-inflammatory Clostridium species across these conditions. These shifts likely alter production of short-chain fatty acids, amino acid metabolites, and complex lipids, with downstream effects on mitochondrial function, neuroinflammation, and host energy metabolism. Moreover, emerging clinical interventions-including probiotics, prebiotics, synbiotics, and fecal microbiota transplantation-suggest a potential role for microbiome-targeted therapies, though controlled evidence remains limited. This review synthesizes current knowledge on microbiome alterations in FMS, ME/CFS, and MCS, emphasizing their convergence on metabolic and immune pathways. By integrating microbial, immunological, and neurophysiological perspectives, we propose a microbiome-centered framework for understanding environmental sensitivity illnesses and highlight avenues for translational research and therapeutic innovation.},
}

Humans
*Fibromyalgia/microbiology/immunology/therapy
*Fatigue Syndrome, Chronic/microbiology/immunology/therapy
*Gastrointestinal Microbiome/immunology
*Multiple Chemical Sensitivity/microbiology/immunology/therapy
*Brain/immunology/metabolism
Animals
*Brain-Gut Axis/immunology

@article {pmid41155245,
year = {2025},
author = {Ukraincev, NI and Kashutina, MI and Kasatkina, LI and Abduraimov, AB and Zhernov, YV},
title = {Mammary Gland Microbiota in Benign Breast Diseases.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms26209951},
pmid = {41155245},
issn = {1422-0067},
support = {25-18-00901//Russian Science Foundation/ ; },
mesh = {Humans ; Female ; *Microbiota ; *Mammary Glands, Human/microbiology ; *Breast Diseases/microbiology ; Dysbiosis/microbiology ; Mastitis/microbiology ; Breast Neoplasms/microbiology ; },
abstract = {The human microbiome is a critical factor in health and disease. While its association with breast cancer (BC) has been increasingly studied, this review provides a dedicated synthesis of the microbiota's role in benign breast diseases (BBDs)-a common yet microbiologically overlooked spectrum of conditions. The primary aim of this work is to consolidate the current understanding of the composition, origins, and functional mechanisms of the mammary gland (MG) microbiota specifically in the context of BBD and to evaluate its potential for novel diagnostic and therapeutic targets. We detail the distinct MG microbiota, formed via exogenous (e.g., cutaneous, translocation) and endogenous (e.g., enteromammary, lymphohematogenous) pathways, and its interaction with the host through estrogen metabolism, immunomodulation, and epigenetic modifications. This narrative review reveals unique dysbiotic patterns in BBD, characterized by distinct microbial signatures, such as the enrichment of Corynebacterium kroppenstedtii in granulomatous mastitis and the presence of Staphylococcus aureus in fibroadenomas and lactational mastitis. Furthermore, specific gut microbial profiles are identified in BBD patients, including an increased abundance of genera such as Clostridium and Faecalibacterium, alongside a decrease in Collinsella and Alistipes compared to healthy controls. These specific taxa represent compelling candidates for diagnostic biomarkers. We conclude that microbial dysbiosis is a significant component of BBD pathogenesis. A paradigm shift toward multi-omics approaches and mechanistic studies is now essential to translate these associations into clinical applications. Understanding the BBD-specific microbiome holds the promise of revolutionizing patient care through microbiota-based diagnostics for differentiating benign subtypes and novel, personalized therapeutic strategies aimed at restoring microbial homeostasis.},
}

Humans
Female
*Microbiota
*Mammary Glands, Human/microbiology
*Breast Diseases/microbiology
Dysbiosis/microbiology
Mastitis/microbiology
Breast Neoplasms/microbiology

@article {pmid41155242,
year = {2025},
author = {Ruiz-Pozo, VA and Cadena-Ullauri, S and Guevara-Ramírez, P and Tamayo-Trujillo, R and Paz-Cruz, E and Cabrera-Andrade, A and Zambrano, AK},
title = {Molecular Mechanisms and Therapeutic Perspectives of Gut Microbiota, Autophagy, and Apoptosis in Cholangiocarcinoma Pathophysiology.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms26209949},
pmid = {41155242},
issn = {1422-0067},
mesh = {Humans ; *Cholangiocarcinoma/microbiology/therapy/physiopathology/pathology ; *Gastrointestinal Microbiome ; *Autophagy ; *Apoptosis ; Animals ; *Bile Duct Neoplasms/microbiology/therapy/pathology/physiopathology ; Probiotics/therapeutic use ; Dysbiosis/microbiology ; },
abstract = {Cholangiocarcinoma (CCA) is an aggressive malignancy of the biliary tract with rising global incidence and limited treatment options. Its pathogenesis involves a complex interplay of genetic mutations, epigenetic dysregulation, inflammatory signaling, and environmental influences. Emerging evidence highlights the pivotal role of the gut-liver axis and microbiota dysbiosis in shaping biliary homeostasis and disease progression. Alterations in microbial composition disrupt apoptosis and autophagy, two key processes regulating cell survival and death, thereby contributing to tumorigenesis, metastasis, and therapy resistance. Specific taxa, including Enterococcus, Escherichia coli, Pseudomonas, Bifidobacterium, and Bacillus, demonstrate strain-dependent effects, acting either as tumor promoters through genotoxic metabolites and immune evasion or as potential tumor suppressors by inducing apoptosis and immune activation. These findings underscore the context-dependent roles of microbiota in CCA biology. Importantly, microbiota modulation offers novel therapeutic opportunities. Dietary interventions such as probiotics, prebiotics, and nutritional strategies, alongside innovative microbiome-targeted therapies, hold promise for restoring microbial balance, enhancing antitumor immunity, and improving patient outcomes. This review integrates current molecular and microbiological evidence to propose the gut microbiota as both a biomarker and a therapeutic target in CCA, opening avenues for precision medicine approaches in hepatobiliary oncology.},
}

Humans
*Cholangiocarcinoma/microbiology/therapy/physiopathology/pathology
*Gastrointestinal Microbiome
*Autophagy
*Apoptosis
Animals
*Bile Duct Neoplasms/microbiology/therapy/pathology/physiopathology
Probiotics/therapeutic use
Dysbiosis/microbiology

@article {pmid41155136,
year = {2025},
author = {Bitter, M and Weigel, M and Mengel, JP and Ott, B and Windhorst, AC and Tello, K and Imirzalioglu, C and Hain, T},
title = {Assessment of Microbiome-Based Pathogen Detection Using Illumina Short-Read and Nanopore Long-Read Sequencing in 144 Patients Undergoing Bronchoalveolar Lavage in a University Hospital in Germany.},
journal = {International journal of molecular sciences},
volume = {26},
number = {20},
pages = {},
doi = {10.3390/ijms26209841},
pmid = {41155136},
issn = {1422-0067},
support = {TRR 84/3 Innate Immunity of the Lung, B08//Deutsche Forschungsgemeinschaft/ ; 519/03/06.001-(0002) LOEWE-Diffusible Signals B03//Hessian Ministry of Science and Research, Arts and Culture (HMWK)/ ; MB2021 JLU TRAINEE//Faculty of Medicine at Justus Liebig University Giessen/ ; },
mesh = {Humans ; *Microbiota/genetics ; *High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Female ; *Bronchoalveolar Lavage Fluid/microbiology ; Aged ; Germany ; *Bacteria/genetics/isolation & purification/classification ; Hospitals, University ; Bronchoalveolar Lavage ; Nanopore Sequencing/methods ; Adult ; *Respiratory Tract Infections/microbiology/diagnosis ; Aged, 80 and over ; },
abstract = {Lower respiratory tract infections (LRTIs) represent a significant global health concern, and the accurate identification of pathogens is crucial for patient care. Culture-based methods are the gold standard, but their detection abilities are limited. Next-generation sequencing (NGS) offers a promising method for comprehensive microbial detection, providing valuable information for clinical practice. In this study, 144 bronchoalveolar lavage fluid samples were collected, culture-based diagnostics were performed, and bacterial microbiome profiles were generated by short-read sequencing of the V4 region of the 16S rRNA gene using Illumina technologies and long-read sequencing with Oxford Nanopore Technologies (ONT) to determine the full-length 16S rRNA gene. The most common genera detected by NGS included Streptococcus, Staphylococcus, Veillonella, Prevotella, Rothia, Enterococcus, and Haemophilus. Short-read sequencing detected cultured bacteria at the genus level in ~85% of cases, while long-read sequencing demonstrated agreement with cultured species in ~62% of cases. In three cases, long-read sequencing identified the uncommon potential lung pathogen Tropheryma whipplei not detected with traditional culturing techniques. The NGS results showed a partial overlap with culture as the current diagnostic gold standard in LRTI. Additionally, NGS detected a broader spectrum of bacteria, revealed fastidious potential pathogens, and offered deeper insights into the complex microbial ecosystem of the lungs.},
}

Humans
*Microbiota/genetics
*High-Throughput Nucleotide Sequencing/methods
RNA, Ribosomal, 16S/genetics
Middle Aged
Male
Female
*Bronchoalveolar Lavage Fluid/microbiology
Aged
Germany
*Bacteria/genetics/isolation & purification/classification
Hospitals, University
Bronchoalveolar Lavage
Nanopore Sequencing/methods
Adult
*Respiratory Tract Infections/microbiology/diagnosis
Aged, 80 and over

@article {pmid41155052,
year = {2025},
author = {Bubulac, L and Gheorghe, IR and Ungureanu, E and Bogdan-Andreescu, CF and Albu, CC and Gheorghe, CM and Mușat, O and Eremia, IA and Panea, CA and Burcea, A},
title = {Promoting Re-Epithelialization in Diabetic Foot Wounds Using Integrative Therapeutic Approaches.},
journal = {Bioengineering (Basel, Switzerland)},
volume = {12},
number = {10},
pages = {},
doi = {10.3390/bioengineering12101053},
pmid = {41155052},
issn = {2306-5354},
abstract = {Background: Diabetes mellitus is a heterogeneous chronic disease with an increasing global prevalence. In Romania, 11.6% of the population is affected, yet only 6.46% receive treatment. Among diabetic patients, 15-25% develop skin lesions that may progress to ulceration and necrosis, significantly impairing quality of life and increasing the risk of complications. Methods: We conducted a prospective study including 28 patients (14 in the control group and 14 in the intervention group) with type I or II diabetes and chronic ulcers of the calf or foot (>4 cm[2]). The control group received standard therapy with debridement, dressings, antibiotics when indicated, and local and systemic ozone therapy. The intervention group was treated with an Integrative Therapeutic Protocol combining ozone therapy, pulsed electromagnetic field therapy (PEMF), colon hydrotherapy with probiotic supplementation, and an anti-inflammatory alkaline diet. Wound healing (reduction in ulcer surface area) was the primary endpoint; secondary endpoints included changes in glycemia and inflammatory biomarkers. Results: After 8 weeks, the intervention group achieved 86.2% re-epithelialization versus 58.2% in controls (p < 0.01). Significant improvements were also observed in blood glucose level (-38%), HbA1c (-25%), CRP (-26%), and fibrinogen (-28%) relative to baseline, with differences versus controls reaching statistical significance. Conclusions: The Integrative Therapeutic Protocol accelerated wound healing and improved glycemic and inflammatory profiles compared with ozone therapy alone. Although an alkaline diet was recommended, adherence and its specific contribution were not objectively monitored; therefore, this component should be interpreted with caution.},
}

@article {pmid41154995,
year = {2025},
author = {Kc, A and Paudel, R},
title = {Meta-Analysis of the Gut Microbiome: An African American Representation.},
journal = {International journal of environmental research and public health},
volume = {22},
number = {10},
pages = {},
doi = {10.3390/ijerph22101591},
pmid = {41154995},
issn = {1660-4601},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Black or African American/statistics & numerical data ; Feces/microbiology ; Male ; Female ; Adult ; White ; },
abstract = {The human gut hosts approximately 100 trillion microbes, forming a complex ecosystem critical to the body's metabolism, nutrition, and immune function. Despite growing research, African Americans remain underrepresented in clinical studies. This study addresses the gap through a comprehensive meta-analysis of gut microbiome datasets. Fecal sample data from amplicon sequencing were analyzed using a bioinformatics pipeline that incorporated DADA2 for sequence processing and Phyloseq for diversity analysis within RStudio (v2024.09.0+375). Statistical approaches, including Wilcoxon tests, Kruskal-Wallis tests, PERMANOVA, and ANCOM-BC, identified significant microbial differences. Results revealed that African Americans exhibited lower microbial diversity. Beta diversity metrics demonstrated a stronger effect of ethnicity compared to diet, age, sex, and BMI, highlighting its significance in microbiome variation. Similarly, ANCOM-BC identified Clostridium sensu stricto 1 significantly enriched in healthy African Americans, while Dialister was depleted, a finding with potential clinical relevance given previous research linking reduced Dialister abundance with depression. Additionally, machine learning approaches were found to potentially complement traditional statistical methods by handling class imbalance and identifying complex microbial associations. By addressing critical gaps in microbiome research, this study underscores the importance of inclusive datasets in enhancing disease risk prediction and ensuring that microbiome-based health interventions are equitable and broadly applicable.},
}

*Gastrointestinal Microbiome
Humans
*Black or African American/statistics & numerical data
Feces/microbiology
Male
Female
Adult
White

@article {pmid41154837,
year = {2025},
author = {Shah, J and Lee, R and Pathuri, S and Zheng, J and Ong, J and Suh, A and Rezaei, K and Mudhar, G and Parsons, AD and Park, J and Lee, AG},
title = {The Brown Bear and Hibernating Mammals as a Translational Model for Human Resilience: Insights for Space Medicine, Critical Care, and Austere Environments.},
journal = {Biology},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/biology14101434},
pmid = {41154837},
issn = {2079-7737},
abstract = {Long-term spaceflight induces multisystem stress, including cardiovascular deconditioning, skeletal muscle atrophy, immune suppression, and neuro-ocular syndromes. Current countermeasures reduce symptoms but cannot replicate the synergistic resilience needed for extended missions or critical illness. Hibernating animals, specifically brown bears (Ursus arctos), survive prolonged immobility, starvation, and bradycardia without resultant pathology. This review incorporates adaptations observed in bears and certain torpid species, including reversible insulin resistance, suppression of muscle atrophy genes MuRF1 and Atrogin-1, and maintenance of the heart despite seasonal production decline. The thirteen-lined ground squirrels (Ictidomys tridecemlineatus) maintain retinal structure and synaptic stability throughout torpor, avoiding neuro-ocular complications despite prolonged inactivity. Mechanisms span from RBM3-dependent synaptic maintenance, titin isoform remodeling under the control of RBM20, mTOR and FOXO pathway regulation, remodeled hydrogen sulfide metabolism, and microbiome-mediated nitrogen salvage. These adaptations are different from human adaptation to microgravity and disuse and offer translational candidates for synthetic torpor, probiotic engineering, neuroprotection, and protein-sparing therapy. Hibernators are not passive stress subjects; they perform coordinated anticipatory responses in multiple organs. Comparing these systems in large and small hibernators, we aim to uncover a biologically realistic path to human resilience. These findings guide a shift from reactive, pharmacological measures for preserving human health during space flight, intensive care, and extreme environments towards proactive, biologically initiated measures.},
}

@article {pmid41154794,
year = {2025},
author = {Ji, R and Zhao, X and Chen, Z and Ge, Y and Wu, Z and Wang, X},
title = {Hepatocyte Growth Factor Differentially Modulates Oral Microbiota in Early vs. Late Experimental Periodontitis.},
journal = {Biology},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/biology14101393},
pmid = {41154794},
issn = {2079-7737},
support = {81700985//National Natural Science Foundation of China/ ; 2024A03J0138//Guangzhou Municipal Science and Technology Bureau/ ; 202201020203//Guangzhou Science and Technology Program/ ; },
abstract = {BACKGROUND: Periodontitis is a chronic disease triggered by disturbed oral microbiota. We have previously reported that hepatocyte growth factor (HGF) could mitigate early-stage experimental periodontitis but exacerbate the condition in its late stage. Here, we investigated the impact of HGF on the periodontal microbiome during periodontitis progression.

METHODS: We established ligation-induced periodontitis in wild-type (WT) mice and HGF high-expression transgenic (HGF-Tg) mice. We quantified the levels of IL-6 and TNF-α in periodontal tissues, as well as the serum concentrations of CTXI and PINP. Ligatures were collected on days 0, 7, and 28 after ligation for 16S rRNA sequencing and microbial analysis.

RESULTS: HGF significantly altered the diversity of ligatures during periodontitis. Interestingly, specific microbial genera, such as Lactobacillus, exhibited opposing trends between the two disease stages of HGF-Tg mice, aligning with the different effects of HGF on periodontitis progression. We also identified some taxa, such as Sphingomonas, associated with IL-6, TNF-α, CTXI, and PINP. The predicted inflammatory pathways (e.g., IL-17 signaling pathways) were enriched in HGF-Tg mice on day 28 but decreased on day 7.

CONCLUSIONS: HGF exerted different influences on the microbiota of ligatures during early and late stages of periodontitis, which may account for the divergent effects of HGF on periodontitis progression.},
}

@article {pmid41154691,
year = {2025},
author = {Kiełbowski, K and Plewa, P and Zadworny, J and Stodolak, P and Jędrasiak, A and Bakinowska, E and Pawlik, A},
title = {What Is the Involvement of Gut Microbiome in the Pathophysiology of Diabetes?.},
journal = {Biomolecules},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biom15101463},
pmid = {41154691},
issn = {2218-273X},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Diabetes Mellitus/microbiology/physiopathology/metabolism ; Animals ; Inflammation/microbiology ; Hypoglycemic Agents/therapeutic use ; },
abstract = {Diabetes mellitus (DM) encompasses a group of metabolic diseases characterised by abnormal glucose levels. The pathophysiology of DM involves intricate disruptions in glucose metabolism and immune regulation. The gut microbiome is known to play a crucial role in human health and disease, and changes in its composition have been reported in numerous conditions, including DM. In this review, we discuss recent findings on the intricate relationship between the gut microbiome and DM, including its complications. We highlight the involvement of gut microorganisms in inflammation and metabolic processes, and we summarise current evidence on how antidiabetic therapies influence microbiome composition and activity. Finally, we explore the potential role of microbiome monitoring in predicting treatment response.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Diabetes Mellitus/microbiology/physiopathology/metabolism
Animals
Inflammation/microbiology
Hypoglycemic Agents/therapeutic use

@article {pmid41154689,
year = {2025},
author = {Parisi, GF and Papale, M and Pecora, G and Presti, S and Tosto, M and Mulé, E and Ornato, V and Aloisio, D and Leonardi, S},
title = {Evolving Cystic Fibrosis Care: Lung Immunology and Emerging Health Challenges in the Era of CFTR Modulators.},
journal = {Biomolecules},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biom15101460},
pmid = {41154689},
issn = {2218-273X},
mesh = {Humans ; *Cystic Fibrosis/immunology/drug therapy ; *Cystic Fibrosis Transmembrane Conductance Regulator/metabolism/genetics ; *Lung/immunology/drug effects/pathology ; Quality of Life ; },
abstract = {The introduction of CFTR modulators has dramatically shifted the clinical management of cystic fibrosis (CF) from a life-limiting pediatric condition to a chronic disease with broader health implications. This review explores the impact of these advancements on lung immunology and the emerging spectrum of health challenges. While these modulators have reduced traditional pulmonary complications by mitigating inflammation and infection, they also introduce new considerations for long-term health management. As patients experience longer lives, issues such as the increased risk of certain cancers and other systemic complications like CF-related diabetes and liver disease are gaining attention. Understanding the interplay between CFTR modulators, immune response, and the development of these conditions is essential for optimizing patient outcomes. This review highlights the importance of integrated care strategies that address both the respiratory improvements and emerging health risks associated with longer life expectancy in CF patients. By fostering a comprehensive approach, we aim to enhance the overall quality of life and address the complex needs of individuals navigating CF in the modern therapeutic landscape.},
}

Humans
*Cystic Fibrosis/immunology/drug therapy
*Cystic Fibrosis Transmembrane Conductance Regulator/metabolism/genetics
*Lung/immunology/drug effects/pathology
Quality of Life

@article {pmid41154627,
year = {2025},
author = {Benameur, T and Hasan, A and Toufig, H and Panaro, MA and Filannino, FM and Porro, C},
title = {Microbiota-Derived Extracellular Vesicles as Potential Mediators of Gut-Brain Communication in Traumatic Brain Injury: Mechanisms, Biomarkers, and Therapeutic Implications.},
journal = {Biomolecules},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biom15101398},
pmid = {41154627},
issn = {2218-273X},
mesh = {Humans ; *Brain Injuries, Traumatic/metabolism/therapy/microbiology ; *Extracellular Vesicles/metabolism ; Biomarkers/metabolism ; *Gastrointestinal Microbiome ; Animals ; *Brain/metabolism ; Blood-Brain Barrier/metabolism ; },
abstract = {Traumatic brain injury (TBI) remains a major global health problem, contributing significantly to morbidity and mortality worldwide. Despite advances in understanding its complex pathophysiology, current therapeutic strategies are insufficient in addressing the long-term cognitive, emotional, and neurological impairments. While the primary mechanical injury is immediate and unavoidable, the secondary phase involves a cascade of biological processes leading to neuroinflammation, blood-brain barrier (BBB) disruption, and systemic immune activation. The heterogeneity of patient responses underscores the urgent need for reliable biomarkers and targeted interventions. Emerging evidence highlights the gut-brain axis as a critical modulator of the secondary phase, with microbiota-derived extracellular vesicles (MEVs) representing a promising avenue for both diagnosis and therapy. MEVs can cross the intestinal barrier and BBB, carrying biomolecules that influence neuronal survival, synaptic plasticity, and inflammatory signaling. These properties make MEVs promising biomarkers for early detection, severity classification, and prognosis in TBI, while also offering therapeutic potential through modulation of neuroinflammation and promotion of neural repair. MEV-based strategies could enable tailored interventions based on the individual's microbiome profile, immune status, and injury characteristics. The integration of multi-omics with artificial intelligence is expected to fully unlock the diagnostic and therapeutic potential of MEVs. These approaches can identify molecular subtypes, predict outcomes, and facilitate real-time clinical decision-making. By bridging microbiology, neuroscience, and precision medicine, MEVs hold transformative potential to advance TBI diagnosis, monitoring, and treatment. This review also identifies key research gaps and proposes future directions for MEVs in precision diagnostics and gut microbiota-based therapeutics in neurotrauma care.},
}

Humans
*Brain Injuries, Traumatic/metabolism/therapy/microbiology
*Extracellular Vesicles/metabolism
Biomarkers/metabolism
*Gastrointestinal Microbiome
Animals
*Brain/metabolism
Blood-Brain Barrier/metabolism

@article {pmid41154595,
year = {2025},
author = {Zhao, Y and Xiong, N and Ji, X and Zhang, D and Jia, Q and Qin, L and Wu, X and Tan, D and Xie, J and He, Y},
title = {A Dual Regulatory Mechanism of Hormone Signaling and Fungal Community Structure Underpin Dendrobine Accumulation in Dendrobium nobile.},
journal = {Biomolecules},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biom15101366},
pmid = {41154595},
issn = {2218-273X},
support = {82460705, U24A20793, 82460748//National Natural Science Foundation of China/ ; QKJ [2022] 048//Guizhou Engineering Research Center of Industrial Key-technology for Dendrobium Nobile/ ; QKHPTRC-CXTD[2023]024, QKHPTRC-GCC[2023]075//Department of Science and Technology of Guizhou Province/ ; ZYDC202302146//Guizhou Province University Student Innovation Fund of Zunyi Medical University/ ; },
mesh = {*Dendrobium/microbiology/metabolism/genetics ; Signal Transduction ; *Plant Growth Regulators/metabolism/genetics ; *Fungi/metabolism/genetics ; Alkaloids/metabolism ; Transcriptome ; Gene Expression Profiling ; *Mycobiome ; Gene Expression Regulation, Plant ; },
abstract = {(1) Objective: The biosynthesis of medicinal secondary metabolites in Dendrobium nobile Lindl. is regulated by complex environmental, hormonal, and microbial interactions. However, the mechanisms by which subtle variations in plant elevation shape metabolite accumulation through plant-microbe-hormone networks remain largely unexplored. (2) Methods: We conducted a multi-omics investigation of D. nobile cultivated under simulated wild conditions at four elevation gradients (347-730 m) in Chishui, China. High-throughput transcriptome sequencing and ITS-based fungal community profiling were combined with hormone quantification and functional prediction (FUNGuild), enabling integrated analysis of hormone pathway activation, microbial structure-function dynamics, and dendrobine levels. (3) Reults: This study systematically investigated D. nobile cultivated under simulated wild conditions across four elevation gradients (347-730 m) in the Danxia region of Chishui, China. We identified a dual regulatory mechanism underlying the elevation-dependent accumulation of dendrobine alkaloids, involving both plant hormone signaling and endophytic fungal communities. Transcriptomic analyses revealed coordinated upregulation of key hormone pathway genes, including DELLA, PYR/PYL, SnRK2, COI1-JAZ-MYC2, and NPR1-TGA, particularly in CY01Y samples at 670 m elevation from ChiYan base in Chishui city, which corresponded to the highest dendrobine content. Concurrently, functional prediction of the ITS-based fungal sequencing data revealed that CY01Y harbored a stable, functionally enriched fungal community dominated by saprotrophs, fungal parasites, and plant pathogens. (4) Conclusions: Through integrative hormone profiling, gene expression, and microbial function analysis, we propose that elevation-induced environmental cues reshape hormone pathways both directly and indirectly via microbial feedback. Specific microbial taxa were identified as potential modulators of hormone signaling and secondary metabolism. The coordinated interaction between plant hormones and endophytic fungi supports a hormone-microbiome-metabolite network that dynamically regulates dendrobine biosynthesis in response to micro-elevation variation.},
}

*Dendrobium/microbiology/metabolism/genetics
Signal Transduction
*Plant Growth Regulators/metabolism/genetics
*Fungi/metabolism/genetics
Alkaloids/metabolism
Transcriptome
Gene Expression Profiling
*Mycobiome
Gene Expression Regulation, Plant

@article {pmid41154584,
year = {2025},
author = {Primavera, D and Carta, MG and Tusconi, M and Kalcev, G and Atzori, L and Ferreli, C and Romero Ramirez, R and Peddio, L and Casu, C and Fais, S and Orrù, G and Scano, A},
title = {Oral Microbiota Taxa and Pri-miRNA Expression in Bipolar Disorder: A Case-Control Study.},
journal = {Biomolecules},
volume = {15},
number = {10},
pages = {},
doi = {10.3390/biom15101355},
pmid = {41154584},
issn = {2218-273X},
support = {Project: "Genetic biomarkers useful for the prevention of bipolar disorder", Prot. U1726.2025/AI.1719.CN, Prat. 2025.1758. Italy, 22 May, 2025//Fondazione di Sardegna/ ; },
mesh = {Humans ; *Bipolar Disorder/microbiology/genetics/metabolism ; *MicroRNAs/genetics/metabolism ; Male ; Female ; Case-Control Studies ; Adult ; Middle Aged ; *Microbiota ; *Mouth/microbiology ; Saliva/microbiology ; },
abstract = {Background/Objectives: Emerging evidence suggests a role for oral microbiota in mood disorders, particularly bipolar disorder (BD), complementing established links between gut dysbiosis and psychiatric symptoms. This study investigates the composition of oral microbial taxa and the expression of inflammation-related pri-miRNAs (146a and 155) in individuals with BD, aiming to explore their potential as biomarkers in the oral-gut-brain axis. Methods: A matched case-control design was implemented, recruiting 25 BD patients and 46 controls matched by age and sex. Salivary samples were collected, and microbial profiling was conducted via real-time qPCR targeting major bacterial phyla and genera. Pri-miRNA 146a and 155 expression was evaluated through RT-qPCR using validated primers. Statistical comparisons between groups were performed using Fisher's exact test and non-parametric tests for continuous variables. Results: Microbial analysis revealed significant reductions (p < 0.01) in α-Proteobacteria, γ-Proteobacteria, and Actinobacteria in BD patients versus controls. A shift toward a higher Firmicutes/Bacteroidetes ratio was observed in the BD cohort, suggesting differences in the oral biotic status between the two groups. However, pri-miRNA 146a and 155 expression levels did not differ significantly between the groups and exhibited high inter-individual variability. Conclusions: The findings indicate that oral microbiota composition differs in BD patients, potentially influencing systemic homeostasis through interactions with gut microbial communities and SCFA pathways. These findings should be interpreted as preliminary and hypothesis-generating given the modest sample size. While pri-miRNAs 146a and 155 did not distinguish BD status, the observed microbial taxa alterations should be regarded as exploratory and hypothesis-generating. Larger, longitudinal studies are required to clarify their potential role in BD pathogenesis and risk assessment.},
}

Humans
*Bipolar Disorder/microbiology/genetics/metabolism
*MicroRNAs/genetics/metabolism
Male
Female
Case-Control Studies
Adult
Middle Aged
*Microbiota
*Mouth/microbiology
Saliva/microbiology

@article {pmid41154562,
year = {2025},
author = {Hui, F and Zhao, Y and Akonyani, ZP and Guo, Y and Guo, X and Zhang, Q and Meng, F and Li, L and Shi, B and Yan, S},
title = {Rectal Microbiomes and Serum Metabolomics Reveal Changes in Serum Antioxidant Status and Immune Responses of Dezhou Donkeys in Late Gestation to Parturition.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antiox14101253},
pmid = {41154562},
issn = {2076-3921},
support = {BR220120//Yanli Zhao/ ; zdzx2018001//Sumei Yan/ ; BR22-13-13//Sumei Yan/ ; },
abstract = {Parturition is a critical event in the reproductive cycle of dairy animals, accompanied by multiple physiological changes in sex hormones, metabolism, antioxidant capacity, and immune function. However, the changes in the rectal microbiota and metabolic products of Jennies from late gestation to parturition affect serum antioxidant capacity and anti-inflammatory responses, but it is still unclear. The present study aimed to investigate the serum antioxidant capacity and anti-inflammatory responses of Dezhou donkeys from late gestation to parturition by analyzing rectal microbiomes and serum metabolomics. Nine pregnant multiparous Dezhou Jennies, aged 6.0 ± 0.1 years, with a body weight of 292 ± 33 kg, an average parity number of 2.7 ± 0.1, and similar expected dates of confinement (35 ± 4 days), were selected for this study. The study investigates the changes in antioxidant capacity and inflammatory responses, as well as the alterations in rectal microbiota structure and serum metabolites, in Jennies at 35 days prepartum (B1), 7 days prepartum (B2), and at 0 h postpartum (B3). The results showed that from groups B1 to B2, serum activity of GSH-Px, IL-10, and GLU concentrations were decreased significantly. In contrast, the concentrations of MDA, IgG, LF, IL-1β, IL-2, IL-6, TNF-α, and ROS increased significantly. From groups B2 to B3, serum activities of GSH-Px, CAT, SOD, and T-AOC, as well as the concentrations of MDA, IgG, IL-2, AST, ALP, and BHBA, were significantly increased, whereas the concentrations of IL-4, IL-10, and CRE decreased considerably. Therefore, from 35 days prepartum to parturition, Jennies experienced a gradually intensifying oxidative stress and inflammatory states, with the inflammatory response being the most severe at parturition, and with enhanced antioxidant capacity corresponding to increased oxidative damage. Microbiome analysis revealed that the group B1 significantly increased the relative abundance of Prevotella and Fibrobacteres. Group B2 significantly increased the relative abundance of Prevotellaceae_UCG-001, Streptococcus, and Acetitomaculum. Group B3 showed a significant upregulation of the relative abundance of Norank_f__F082, Lachnospiraceae_UCG-009, and Prevotellaceae_UCG-004. At the same time, metabolomics analysis revealed that, compared with group B1, group B3 may alleviate inflammation and enhance the body's antioxidant function by upregulating the tryptophan and arginine metabolic pathways and enriching the differential metabolites (L-tryptophan, L-kynurenine, 3-Indoleacetonitrile, N-acetylglutamic acid). Concurrently, the elevation of these differential metabolites may be associated with the relative abundance of the beneficial bacterium Lachnospiraceae_UCG-009. However, the increase in LysoPC, a fatty acid oxidation product in glycerophospholipid metabolism, as well as the correlation between the sucrose content in the galactose metabolic pathway and the abundance of Paracoccus, indicates the reason why the Jennies are in a state of oxidative stress. Furthermore, group B1 may enhance the serum anti-inflammatory response in Jennies during late gestation by increasing the levels of estrogen in the steroid hormone biosynthesis metabolic pathway. These results could provide useful information for improving the health levels at the specific physiological stages and processes in Dezhou donkeys.},
}

@article {pmid41154457,
year = {2025},
author = {Iaccarino, J and Mignini, I and Maresca, R and Giansanti, G and Esposto, G and Borriello, R and Galasso, L and Ainora, ME and Gasbarrini, A and Zocco, MA},
title = {The Impact of Air Pollution on the Lung-Gut-Liver Axis: Oxidative Stress and Its Role in Liver Disease.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {14},
number = {10},
pages = {},
doi = {10.3390/antiox14101148},
pmid = {41154457},
issn = {2076-3921},
abstract = {The expression "lung-gut-liver axis" refers to the interconnected processes occurring in the lungs, gastrointestinal tract, and liver, particularly in relation to immune function, microbial regulation, and metabolic responses. Over the past decade, growing concern has emerged regarding the detrimental impact of air pollution on liver disease. Air pollutants, including particulate matter (PM) and chemical gases such as nitrogen oxides (NOx), can influence the microbiome in the lungs and gut by generating reactive oxygen species (ROS), which induce oxidative stress and local inflammation. This redox imbalance leads to the production of altered secondary microbial metabolites, potentially disrupting both the alveolar-capillary and gut barriers. Under these conditions, microbes and their metabolites can translocate to the liver, triggering inflammation and contributing to liver diseases, particularly metabolic dysfunction-associated steatotic liver disease (MASLD), cirrhosis, and hepatocellular carcinoma (HCC). This manuscript aims to review recent findings on the impact of air pollution on liver disease pathogenesis, exploring the molecular, genetic, and microbiome-related mechanisms underlying lung-gut-liver interactions, providing insights into potential strategies to prevent or mitigate liver disease progression.},
}

@article {pmid41154402,
year = {2025},
author = {Quagliariello, V and Forte, P and Ciappina, G and Colarusso, L and Giorgi, C and Fiorica, F and Bottari, A and Di Mauro, G and Maurea, N and Berretta, M},
title = {Fusobacteriumnucleatum: Pathophysiological and Clinical Involvement in Inflammatory Bowel Diseases, Colorectal Cancer and Cardiovascular Diseases.},
journal = {Cancers},
volume = {17},
number = {20},
pages = {},
doi = {10.3390/cancers17203348},
pmid = {41154402},
issn = {2072-6694},
support = {PNRR-MCNT1-2023-12378355//UNIONE EUROPEA/ ; },
abstract = {Fusobacterium nucleatum is a Gram-negative anaerobe that occupies a central ecological niche in oral biofilms but has emerged as a trans-compartmental pathogen implicated in gastrointestinal and cardiovascular diseases. In inflammatory bowel diseases, Fusobacterium nucleatum adheres to the intestinal epithelium via adhesins such as FadA, disrupts tight junctions, and induces Toll-like receptor-mediated inflammatory cascades, amplifying epithelial permeability and sustaining mucosal inflammation. In colorectal cancer, Fusobacterium nucleatum promotes carcinogenesis through multiple mechanisms, including β-catenin activation, modulation of oncogenic microRNAs, and immune evasion via Fap2-TIGIT signaling, while also fostering a pro-inflammatory and immunosuppressive tumor microenvironment. Its enrichment correlates with advanced tumor stage, chemoresistance, and poor prognosis, underscoring its potential as a biomarker and therapeutic target. Beyond the gut, Fusobacterium nucleatum has been detected in atherosclerotic plaques and endocardial tissues, where it contributes to endothelial dysfunction, foam cell formation, oxidative stress, and plaque instability, thereby linking chronic oral infection with cardiovascular risk. Collectively, evidence suggests that Fusobacterium nucleatum acts as a pathophysiological connector across IBD, CRC, and CVD through conserved mechanisms of adhesion, immune modulation, and inflammation. Understanding these processes provides opportunities for innovative interventions, ranging from targeted antimicrobials and host-directed therapies to dietary and microbiome-based strategies, aimed at mitigating the systemic burden of this organism and improving clinical outcomes across multiple diseases.},
}

@article {pmid41154099,
year = {2025},
author = {Thibodeau, A and Kim, E and Yang, SM and Goddik, L and Kim, HY and Park, SH},
title = {The Effects of Milking and Cleaning Procedures on the Quality and Microbiome of Raw Goat Milk.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/foods14203563},
pmid = {41154099},
issn = {2304-8158},
support = {Not applicable//ER Jackman Friends and Alumni and the Park lab/ ; },
abstract = {The rising popularity of raw goat milk has heightened concerns about its safety. This study examined how differences in milking and cleaning practices influence the quality and microbiota of goat milk from small-scale Oregon farms during July and August. Milk quality was assessed through somatic cell counts (SCCs) and components, while microbiota was evaluated using viable counts and 16S rRNA sequencing. Sequencing revealed a diverse microbial community, dominated by genera such as Staphylococcus, Escherichia-Shigella, and Pseudomonas, with pathogenic taxa like Salmonella and Campylobacter largely absent or detected at negligible levels. Alpha diversity varied significantly among sample types but not across farms, and beta diversity indicated considerable dissimilarity in microbial composition. Importantly, regression models identified significant associations between hygiene practices and bacterial abundance: the absence of glove use and hand sanitation was linked to increased levels of Escherichia-Shigella, Kocuria, Enterococcus, and Corynebacterium, while the use of bleach-chlorhexidine sanitizer was associated with higher Deinococcus. These findings highlight the role of rigorous hygiene protocols in shaping the microbiota of raw goat milk and emphasize the need for targeted practices to minimize contamination risks.},
}

@article {pmid41154025,
year = {2025},
author = {Zheng, H and Su, ZC and Huang, ST and Li, DL and Yuan, ZD and Xu, JC and Wu, RH and Lin, LG and Gan, LS},
title = {4-Vinylguaiacol in Citri Reticulatae 'Chachiensis' Pericarpium Volatile Oil: A Microbial-Mediated Aging Marker Enhances Glucose Metabolism.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {20},
pages = {},
doi = {10.3390/foods14203489},
pmid = {41154025},
issn = {2304-8158},
support = {2022A0505020026//the Guangdong and Macao cooperation project from Department of Science and Technology of Guangdong Province and Jiangmen Science and Technology Bureau/ ; 22077111, 82073715//National Natural Science Foundation of China/ ; FDCT 0064/2021/AJG//the Science Technology Development Fund, Macao SAR/ ; 2021WGALH11, 2022WGALH15//the Hong Kong / Macao Joint Research and Development Fund Project of Wuyi University/ ; },
abstract = {Influenced by various physical, chemical, and microbial factors, the aging process of Citri Reticulatae 'Chachiensis' Pericarpium (CRCP) poses a complex scientific challenge. Drawing inspiration from the perspective of traditional Chinese medicine, volatile oils were extracted from CRCP aged 1, 3, 5, and 7 years by steam distillation and subsequently analyzed by GC-MS. The results revealed that the relative percentage of 4-vinylguaiacol (4-VG) increased progressively with aging. Nineteen volatile oil components were further assessed for their glucose metabolism-enhancing activities, with 4-VG emerging as a key active compound. Notably, 4-VG remarkably enhanced insulin-stimulated glucose uptake in C2C12 myotubes. Moreover, 4-VG demonstrated potent antihyperglycemic effects by upregulating IRS-1/Akt/GSK-3β phosphorylation in the insulin signaling pathway on a high-fat diet and STZ-induced diabetic mouse model. In addition, the metabolic pathway of 4-VG, from ferulic acid and then to vanillin and guaiacol, was verified via HPLC-UV, metabolomics, and microbiome analyses, which confirmed the microbial conversion of 4-VG within CRCP. The metabolic pathway was ultimately validated by isolating and identifying Priestia aryabhattai, Bacillus velezensis, and Aspergillus fumigatus from CRCP, with further in vitro culture and biotransformation experiments confirming its functionality and efficiency. These findings provide new insights and experimental evidence that deepen our understanding of the aging process of CRCP.},
}