@article {pmid40744840,
year = {2025},
author = {Zhan, J and Cheng, B and Guo, K and Tao, X and Cai, X and Li, Z and Tang, Z and Zhan, J and Wu, C},
title = {Absolute quantitative metagenomic analysis reveals unique gut bacteria underlying berberine and metformin's anti-metabolic disorders effects.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0008425},
doi = {10.1128/spectrum.00084-25},
pmid = {40744840},
issn = {2165-0497},
abstract = {This study aimed to evaluate the potential functional bacteria in the efficacy of two drugs in ameliorating diet-induced metabolic disorder model using absolute and relative quantification methods and to evaluate the benefit of absolute quantification compared with relative quantification. The gut microbiota is implicated in the pathogenesis of various chronic diseases, including diet-induced metabolic disorder model. Berberine (BBR) and metformin (MET) are commonly used in the clinical management of metabolic disorder, yet their effects on gut microbiota regulation differ. This study employs both relative and absolute quantitative methods to assess the differential impacts of these drugs on the modulation of gut microbiota in metabolic disorder mice. Both BBR and MET effectively ameliorate the condition of metabolic disorder. While some relative quantitative sequencing results contradicted the absolute sequencing data, the latter was more consistent with the actual microbial community composition. Absolute quantitative sequencing provides a more accurate reflection of the drug's effects. Notably, both absolute and relative quantitative sequencing demonstrated an upregulation of Akkermansia.IMPORTANCEOur study underscores the importance of absolute quantitative analysis in accurately representing the true microbial counts in a sample and evaluating the modulatory effects of drugs on the microbiome, which plays a vital role in the study of the microbiome.},
}

@article {pmid40744839,
year = {2025},
author = {Hardman, M and Higgi, S and Hanson, L and Schutz, K and Wargo, MJ and Teneback, CC and Daniels, TWV and van der Gast, C and Rivett, DW},
title = {Nontuberculous mycobacteria remodel lung microbiota in cystic fibrosis-associated respiratory infections.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0038225},
doi = {10.1128/spectrum.00382-25},
pmid = {40744839},
issn = {2165-0497},
abstract = {Nontuberculous mycobacterial (NTM) infections in people with cystic fibrosis (pwCF) can have detrimental effects on prognosis and pose significant challenges to treatment. However, there are still questions regarding the contribution and influence of NTMs on the respiratory microbiome and the mechanisms by which NTMs cause infections. Here, we investigate the impact of NTM infection on microbiome composition and lung function (percent predicted forced expiratory volume in 1 second). Primary comparisons were between culture-positive cohorts for Mycobacterium avium complex and Mycobacterium abscessus complex and those who were culture-negative for NTMs and attending outpatient clinics. Additionally, the consequence of cystic fibrosis transmembrane conductance regulator (CFTR) modulator therapy status and positive NTM culture was assessed in terms of microbiome change. Our data suggest that the presence of NTM significantly alters the diversity and the composition of the lung microbiota in pwCF, including those receiving CFTR modulator therapies. Importantly, significant associations were detected between NTM presence and changes in abundance of Pseudomonas aeruginosa and Burkholderia cepacia complex members, inferring modulatory effects of NTMs on respiratory microbiomes. This study contributes to the understanding of NTM infection and these organisms' interaction with the respiratory microbiome and CFTR modulator therapy, highlighting the need for further research in this area.IMPORTANCEThe influence of NTM infection in pwCF is still debated, and the extent of their contribution to mortality and morbidity is still questioned. Findings in this study highlight a link between the presence of NTMs and significant alterations in the composition of the respiratory microbiome, particularly with respect to some of the canonical CF pathogens, especially Pseudomonas aeruginosa and members of the Burkholderia cepacia complex. This indicates that complex relationships are occurring within the microbiome. This study further contributes to the understanding of NTM infection in pwCF, with and without CFTR modulator therapy, and highlights the need for further research in this area. The knowledge gained from this study has implications for treatment strategies and management, ultimately aiming to improve and prolong the lives of pwCF.},
}

@article {pmid40744696,
year = {2025},
author = {Lee, HJ},
title = {Effects of Particulate Matter on Obstructive Sleep Apnea and Obesity.},
journal = {Journal of rhinology : official journal of the Korean Rhinologic Society},
volume = {32},
number = {2},
pages = {67-75},
doi = {10.18787/jr.2025.00016},
pmid = {40744696},
issn = {2384-4361},
support = {//Chung-Ang University/ ; },
abstract = {With accelerated global urbanization, understanding the impact of pollutant emissions and air pollution on obstructive sleep apnea (OSA) and obesity has become increasingly important. Particulate matter (PM) is a major component of air pollution. Recent studies have reported that PM influences OSA, obesity, and obesity-related metabolic disorders. The primary mechanisms proposed to underlie the effects of PM on OSA involve chronic inflammation and oxidative stress in the nasal epithelia. Regarding obesity, PM induces chronic inflammation in the hypothalamus, adipose tissue, skeletal muscle, and mitochondria; oxidative stress in white adipose tissue, the lungs, and the thyroid; activation of lipogenesis genes; changes in adipose tissue distribution; dysbiosis of the intestinal microbiome; and disruption of circadian rhythms. Therefore, reducing air pollution, including PM concentrations, represents a potential strategy for treating OSA and obesity and preventing related complications. Further prospective longitudinal studies in human participants are needed to clarify the effects of PM on the risk of OSA and obesity and to elucidate the underlying mechanisms.},
}

@article {pmid40744347,
year = {2025},
author = {Jacobs, JP and Labus, JS and Dong, TS and Shin, AS and , and Mayer, EA and Chang, L},
title = {Extraintestinal symptoms in irritable bowel syndrome are associated with stress reactivity and the gut microbiome in a sex-dependent manner.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2025.07.026},
pmid = {40744347},
issn = {1542-7714},
}

@article {pmid40744021,
year = {2025},
author = {Komaroff, AL and Dantzer, R},
title = {Causes of symptoms and symptom persistence in long COVID and myalgic encephalomyelitis/chronic fatigue syndrome.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102259},
doi = {10.1016/j.xcrm.2025.102259},
pmid = {40744021},
issn = {2666-3791},
abstract = {Debilitating symptoms for many years can follow acute COVID-19 ("long COVID"), myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), and various post-acute infection syndromes (PAISs). Together, long COVID and ME/CFS affect 60-400 million individuals, globally. Many similar underlying biological abnormalities have been identified in both conditions including autoantibodies against neural targets, endothelial dysfunction, acquired mitochondrial dysfunction, and a pro-inflammatory gut microbiome. Each of these abnormalities may directly cause some of the symptoms. In addition, the symptoms also may be caused by ancient, evolutionarily conserved symptomatic and metabolic responses to vital threats-sickness behavior and torpor-responses mediated by specific, recently discovered neural circuits. These neural circuits constitute a symptom-generating pathway, activated by neuroinflammation, which may be targeted by therapeutics to quell neuroinflammation. Many factors cause the symptoms to become chronic, including persistent infectious agents (and/or their nucleic acids and antigens) and the fact that many of the underlying biological abnormalities reinforce each other, creating ongoing physiological vicious cycles.},
}

@article {pmid40744013,
year = {2025},
author = {Arnoldini, M and Sharma, R and Moresi, C and Chure, G and Chabbey, J and Slack, E and Cremer, J},
title = {Quantifying the varying harvest of fermentation products from the human gut microbiota.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2025.07.005},
pmid = {40744013},
issn = {1097-4172},
abstract = {Fermentation products released by the gut microbiota provide energy and regulatory functions to the host. Yet, little is known about the magnitude of this metabolic flux and its quantitative dependence on diet and microbiome composition. Here, we establish orthogonal approaches to consistently quantify this flux, integrating data on bacterial metabolism, digestive physiology, and metagenomics. From the nutrients fueling microbiota growth, most carbon ends up in fermentation products and is absorbed by the host. This harvest varies strongly with the amount of complex dietary carbohydrates and is largely independent of bacterial mucin and protein utilization. It covers 2%-5% of human energy demand for Western diets and up to 10% for non-Western diets. Microbiota composition has little impact on the total harvest but determines the amount of specific fermentation products. This consistent quantification of metabolic fluxes by our analysis framework is crucial to elucidate the gut microbiota's mechanistic functions in health and disease.},
}

@article {pmid40743743,
year = {2025},
author = {Liu, S and Dong, H and Lu, H and Li, Y and Zhang, G and Mi, Y and Wang, X},
title = {Dynamic changes in composition during processing of Lonicerae japonicae flos black tea.},
journal = {Food chemistry},
volume = {493},
number = {Pt 1},
pages = {145684},
doi = {10.1016/j.foodchem.2025.145684},
pmid = {40743743},
issn = {1873-7072},
abstract = {Lonicerae japonicae flos (LJF) black tea is a fermented tea and it is hypothesized that microbial communities have an important role in shaping the functional and aroma components during processing. This study investigated dynamic compositional changes during LJF black tea processing using GC-IMS, LC MS, and microbiome analysis. Chemical analysis showed that processing was associated with increased content of functional components such as quinic acid, kaempferol, and luteolin, as well as aroma components such as acetic acid ethyl ester, 1-hexanol, and nonanal. These changes collectively contributed to the distinct functional chemical profiles and aroma characteristic of LJF black tea. Also, microbial sequencing analysis revealed that bacterial communities, including Bacillus, Staphylococcus and Chryseobacterium spp., were associated with the formation of these chemical profiles, probably via hydrolysis of glycosidic bonds and formation of amino acids or their derivatives, thereby accelerating synthesis of featured volatile components.},
}

@article {pmid40743285,
year = {2025},
author = {Herman, C and Bolyen, E and Simard, A and Gehret, L and Caporaso, JG},
title = {Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt.},
journal = {PLoS computational biology},
volume = {21},
number = {7},
pages = {e1013299},
doi = {10.1371/journal.pcbi.1013299},
pmid = {40743285},
issn = {1553-7358},
abstract = {We present q2-fmt, a QIIME 2 plugin that provides diverse methods for assessing the extent of microbiome engraftment following fecal microbiota transplant. The methods implemented here were informed by a recent literature review on approaches for assessing FMT engraftment, and cover aspects of engraftment including Community Coalescence, Indicator Features, and Resilience. q2-fmt is free for all use, and detailed documentation illustrating worked examples on a real-world data set are provided in the project's documentation.},
}

@article {pmid40742986,
year = {2025},
author = {Manica-Cattani, MF and Mânica da Cruz, IB and Sato-Miyata, Y and Trindade, LS and Rogalski, F and Ribeiro, EE and Tsuda, M and Aigaki, T},
title = {Characterization of a Drosophila model to study functions of guarana seeds.},
journal = {PloS one},
volume = {20},
number = {7},
pages = {e0328985},
doi = {10.1371/journal.pone.0328985},
pmid = {40742986},
issn = {1932-6203},
mesh = {Animals ; *Drosophila melanogaster/physiology/genetics/drug effects/metabolism ; Longevity/drug effects ; Oxidative Stress/drug effects ; *Seeds/chemistry ; *Paullinia/chemistry ; Transcriptome ; Female ; Fertility/drug effects ; Feces/microbiology ; Male ; Metabolomics ; },
abstract = {The seeds of the Amazonian fruit, guarana (Paullinia cupana), have been used as traditional medicine and, in recent years, as an ingredient in commercial energy beverages. However, mechanisms underlying the beneficial effects of guarana are not well understood. To establish a model system to study molecular mechanisms underlying the beneficial effects of guarana, we investigated how its ingestion affects physiology in the fruit fly, Drosophila melanogaster. We found that guarana enhanced oxidative stress resistance, longevity, physical activity, and fecundity of flies. To deepen our understanding of guarana function, we performed transcriptomic, metabolomic, and fecal microbiome analyses. Transcriptomic analysis identified 58 upregulated and eight downregulated genes in guarana-fed flies. Highly upregulated genes included those encoding detoxification enzymes, such as cytochromes P450 (CYPs), glutathione S-transferases (GSTs), and Juvenile hormone epoxide hydrolase 1 (Jheh1). Metabolomic analysis identified glutathione metabolism, an antioxidant system, as being promoted by guarana ingestion. These findings likely represent the molecular basis for enhanced oxidative stress resistance and longevity in guarana-fed flies. We also analyzed fecal microbiota composition and found significant changes: guarana increased the proportion of probiotic Lactobacillus species, some species known to extend longevity. At the same time, it decreased the proportion of Enterococcus faecalis, a species known to reduce longevity. These changes might have contributed to the beneficial effects of dietary guarana. Thus, we demonstrate that guarana exerts beneficial effects in flies and provide fundamental data for further investigation of its biological mechanisms in Drosophila.},
}

Animals
*Drosophila melanogaster/physiology/genetics/drug effects/metabolism
Longevity/drug effects
Oxidative Stress/drug effects
*Seeds/chemistry
*Paullinia/chemistry
Transcriptome
Female
Fertility/drug effects
Feces/microbiology
Male
Metabolomics

@article {pmid40742978,
year = {2025},
author = {Reig, A},
title = {Chronic endometritis, chronic questions: a narrative review of current practices.},
journal = {Current opinion in obstetrics & gynecology},
volume = {},
number = {},
pages = {},
doi = {10.1097/GCO.0000000000001053},
pmid = {40742978},
issn = {1473-656X},
abstract = {PURPOSE OF REVIEW: Chronic endometritis is a condition that may affect reproductive outcomes, particularly in patients with unexplained infertility, recurrent implantation failure, or recurrent pregnancy loss. This review concisely summarizes the available literature, highlighting some of the controversies on this topic.

RECENT FINDINGS: Although embryo selection through preimplantation genetic testing for aneuploidy has improved, many euploid embryo transfers still fail, prompting interest in endometrial factors such as chronic endometritis. Chronic endometritis is typically asymptomatic and diagnosed by identifying plasma cells in endometrial biopsy specimens; however, diagnostic criteria vary widely regarding biopsy timing, staining techniques, and threshold definitions, contributing to inconsistent prevalence and outcomes across studies. It is often attributed to chronic infection and is treated with empirical or culture-guided antibiotics, though reported cure rates vary significantly. While some studies suggest that treating chronic endometritis improves reproductive outcomes, evidence is limited by methodological heterogeneity. Meta-analyses support treatment, yet diagnostic inconsistencies and potential effects of antibiotics on the microbiome remain concerns.

SUMMARY: While frequently diagnosed in the infertility setting, the true prevalence and impact of chronic endometritis remain unclear. The heterogeneity of the existing literature and the lack of large prospective cohort studies remain challenges to fully understanding the condition, particularly regarding the general infertile population.},
}

@article {pmid40742751,
year = {2025},
author = {Fischer, MT and Xue, KS and Costello, EK and Dvorak, M and Raboisson, G and Robaczewska, A and Caty, SN and Relman, DA and O'Connell, LA},
title = {Effects of parental care on skin microbial community composition in poison frogs.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
doi = {10.7554/eLife.103331},
pmid = {40742751},
issn = {2050-084X},
support = {DP2HD102042/NH/NIH HHS/United States ; Erwin Schroedinger Stipend J-4526B//Austrian Science Fund/ ; },
mesh = {Animals ; *Skin/microbiology ; *Microbiota ; *Anura/microbiology/physiology ; Larva/microbiology ; Female ; Male ; *Bacteria/classification/isolation & purification/genetics ; Poison Frogs ; },
abstract = {Parent-offspring interactions constitute the first contact of many newborns with their environment, priming community assembly of microbes through priority effects and shaping host health and disease. Microbe acquisition during parental care is well studied in humans and agriculturally relevant species but remains poorly understood in other vertebrate groups, such as amphibians. Here, we investigate vertical transmission of skin microbiota in poison frogs (Dendrobatidae), where fathers transport tadpoles piggyback-style from terrestrial clutches to aquatic nurseries. We found that substantial bacterial colonization of embryos begins after hatching, suggesting that the vitelline envelope acts as a microbial barrier. A cross-foster experiment demonstrated that poison frogs performing tadpole transport serve as a source of skin microbes for tadpoles on their back. To study how transport impacts skin communities of tadpoles in an ecologically relevant setting, we sampled sympatric species that do or do not exhibit tadpole transport in their natural habitat. We did not find a higher degree of similarity between microbial communities of tadpoles and adults in species that transport their offspring compared to those that do not. Similarly, communities of tadpoles were no more similar to their caregiver than to unrelated adults, indicating that most caregiver-associated microbes do not remain in tadpole communities long-term. Nonetheless, some taxa persisted on tadpoles over development. This study is the first to demonstrate that offspring transport facilitates transmission of parental skin microbes in anurans.},
}

Animals
*Skin/microbiology
*Microbiota
*Anura/microbiology/physiology
Larva/microbiology
Female
Male
*Bacteria/classification/isolation & purification/genetics
Poison Frogs

@article {pmid40742547,
year = {2025},
author = {Shedaliya, U and Adwani, G and Anju, TR and Krishnakumar, A and Kumar, A},
title = {Role of the microbiome in diabetic wound healing: implications for new therapeutic approaches.},
journal = {Archives of microbiology},
volume = {207},
number = {9},
pages = {208},
pmid = {40742547},
issn = {1432-072X},
mesh = {Humans ; *Wound Healing ; *Microbiota ; *Skin/microbiology ; Animals ; Probiotics/therapeutic use ; *Diabetes Complications/microbiology/therapy ; Dysbiosis/microbiology ; *Diabetes Mellitus/microbiology ; },
abstract = {Diabetic wounds present a persistent clinical challenge due to delayed healing and an increased risk of infection and complications. The rising global prevalence of diabetes and the associated burden of chronic, non-healing wounds highlight the urgent need for innovative and effective therapeutic strategies. Recent research has underscored the critical yet often overlooked role of the skin microbiome in modulating wound healing outcomes. This review explores the complex interactions between the skin microbiome and diabetic wound healing, aiming to inform the development of microbiome-based interventions. The review begins by outlining the composition and physiological functions of the skin microbiome, emphasizing its roles in maintaining cutaneous homeostasis, immune regulation, and barrier integrity. It then examines how diabetes-induced hyperglycemia disrupts microbial balance, leading to dysbiosis, impaired immune responses, and increased colonization by opportunistic pathogens. These alterations contribute to the formation of persistent biofilms, chronic inflammation, impaired angiogenesis, and ultimately, delayed wound repair. Mechanisms by which the microbiome exacerbates wound pathology are discussed, alongside emerging therapeutic strategies targeting the wound microbiota. These include probiotics, prebiotics, bacteriophage therapy, antimicrobial peptides, and microbiome-responsive dressings. Innovative approaches such as photoimmuno-antimicrobial therapies and advanced drug delivery systems are also considered for their potential to enhance treatment efficacy. Despite these promising developments, significant challenges remain in deciphering the full complexity of microbiome-host interactions and translating this knowledge into clinical practice. The review emphasizes the future potential of personalized, microbiome-based therapies tailored to individual microbial profiles and advocates for a precision medicine approach to diabetic wound care. Additionally, it highlights the need for further research into non-bacterial components of the microbiome and the integration of multi-omics technologies with advanced wound management strategies.},
}

Humans
*Wound Healing
*Microbiota
*Skin/microbiology
Animals
Probiotics/therapeutic use
*Diabetes Complications/microbiology/therapy
Dysbiosis/microbiology
*Diabetes Mellitus/microbiology

@article {pmid40742521,
year = {2025},
author = {Shen, Y and Meng, L and Li, Y and Yang, J},
title = {Bacteroides ovatus Has the Potential to Be a Next-Generation Probiotic Strain.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {40742521},
issn = {1867-1314},
support = {(CX (24) 1020)//the Jiangsu Provincial Agricultural Science and Technology Independent Innovation Fund Project/ ; No. BK20233003//the Jiangsu Basic Research Center for Synthetic Biology Grant/ ; No. 32200154//National Natural Science Foundation of China/ ; },
abstract = {Bacteroides ovatus (B. ovatus), a key member of the gut microbiota, is strongly associated with host health, thereby emerging as a promising candidate for the development of next-generation probiotics. This bacterium is linked to various pathophysiological conditions and shows potential probiotic biological activity, particularly in modulating metabolism and treating certain diseases. In the present review, we aim to provide a comprehensive synthesis of the established biological attributes of B. ovatus, while also elucidating the patterns and characteristics of its abundance fluctuations across diverse clinical indications. We also investigate the influence of probiotics, prebiotics, natural products, dietary patterns, and other extrinsic factors on the dynamic changes in B. ovatus abundance. Additionally, an evaluative and prospective analysis of the potential applications of B. ovatus in the realms of functional nutrition and specialized medical foods is presented. Finally, we highlight the transformative potential of B. ovatus in functional nutrition and specialized medical foods, providing a basis for the development of novel microbiome preparations.},
}

@article {pmid40742509,
year = {2025},
author = {Aziz, T and Shabbir, MA and Sarwar, A and Yang, Z and Lin, L and Al-Megrin, WAI and Shami, A and Alwethaynani, MS and Alhhazmi, AA and Al-Asmari, F and Al-Joufi, FA and Fallatah, D},
title = {Revealing Lactiplantibacillus Plantarum K25 Derived (Z)-18-Octadec-9-Enolide in Modulating Aquaporin-8 in Colorectal Cancer by Bridging the Gut Microbiome and Membrane Biology.},
journal = {Cell biochemistry and biophysics},
volume = {},
number = {},
pages = {},
pmid = {40742509},
issn = {1559-0283},
}

@article {pmid40742382,
year = {2025},
author = {Hutchings, B and López-Legentil, S and Stefaniak, LM and Nydam, ML and Erwin, PM},
title = {Depuration of a solitary ascidian depletes transient bacteria without altering microbiome alpha-diversity.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiaf078},
pmid = {40742382},
issn = {1574-6941},
abstract = {Depuration, or the process of clearing impurities from the gut, is commonly applied to marine food products due to its efficacy at removing human pathogens from shellfish and edible ascidians. Recent studies also reported applications to gut microbiome studies, where depuration of filter-feeding animals helped reduce transient bacteria and identify resident symbionts. Here, we examined the impact of depuration on bacteria in the branchial sac, gut, and hepatic gland of the solitary ascidian Pyura vittata. Replicates were kept in filtered seawater for four days prior to dissection ("aquaria-depuration") and compared to samples that were immediately processed following collection ("wild-no depuration") and replicates kept in unfiltered seawater for four days ("aquaria-control"). 16S rRNA gene sequence analysis revealed no significant differences among ascidian sources for microbial alpha-diversity but significant shifts in beta-diversity. Depuration reduced the number of core bacteria markedly (66-84%) across all body regions, and bacteria that remained post-depuration consisted of genera associated with enhanced host health and resilience within other marine symbioses. Our results suggest that microbial profiles obtained following depuration do not substantially differ from those of non-depurated animals, but depuration can help differentiate transient from core and resident taxa in complex host-microbiome symbioses.},
}

@article {pmid40742353,
year = {2025},
author = {Yang, Y and Duan, Y and Su, C and Sheng, J and Zhu, L and Xie, Y and Liu, H and Tang, N and Qiu, Y and Lu, C and Chen, C and Mao, L and Fu, X},
title = {The impact of preoperative biliary drainage on bile colonization of patients undergoing pancreaticoduodenectomy.},
journal = {Annals of medicine},
volume = {57},
number = {1},
pages = {2540024},
doi = {10.1080/07853890.2025.2540024},
pmid = {40742353},
issn = {1365-2060},
mesh = {Humans ; *Pancreaticoduodenectomy/adverse effects/methods ; Female ; Male ; *Drainage/methods/adverse effects ; Retrospective Studies ; Middle Aged ; *Bile/microbiology ; Aged ; *Surgical Wound Infection/epidemiology/microbiology/etiology/prevention & control ; *Preoperative Care/methods/adverse effects ; Risk Factors ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {BACKGROUND: Preoperative biliary drainage (PBD) may be performed for jaundiced patients with periampullary tumors. This study aimed to evaluate the impact of PBD on biliary microbiome and perioperative complications in patients undergoing pancreaticoduodenectomy (PD).

METHODS: This retrospective study enrolled 323 patients who underwent PD between March 2018 and March 2024. Intraoperative bile specimens were obtained for microbiological analysis of species identification and antimicrobial resistance patterns..

RESULTS: PBD was performed in 191 (59.1%) of the 323 patients. Organ/space surgical site infection (SSI) (51.8% vs 37.9%, p < 0.001) and bacterial colonization of bile (90.6% vs 28.0%, p < 0.001) were significantly more frequent in patients with PBD. PBD was identified as an independent risk factor of organ/space SSI (OR = 1.837, 95% CI: 1.158-2.916, p = 0.010) and associated with increased contamination with polymicrobial mixed flora (47.1% vs 4.5%, p < 0.001), K. pneumoniae (23.6% vs 0.8%, p < 0.001), E. faecalis (14.1% vs 1.5%, p < 0.001), E. faecium (6.8% vs 0.8%, p = 0.009). This shift corresponded to higher resistance to piperacillin-tazobactam (23.1% vs 0.0%, p = 0.038), cefoperazone-sulbactam (25.3% vs 0.0%, p = 0.021), ciprofloxacin (36.1% vs 6.3%, p = 0.006), and levofloxacin (47.4% vs 4.8%, p < 0.001). Patients with positive bile culture had a significantly higher occurrence of organ/space SSI than the negative group (53.3% vs 32.7%, p < 0.001). K. pneumoniae was identified as an independent risk factor for organ/space SSI (OR = 2.636, 95% CI: 1.353-5.137, p = 0.004).

CONCLUSIONS: There were fundamental differences in the bile microbiome profile and antibiotic resistance of patients with/without PBD. These findings suggest that adjusting perioperative antibiotic regimens based on biliary culture may be warranted.},
}

Humans
*Pancreaticoduodenectomy/adverse effects/methods
Female
Male
*Drainage/methods/adverse effects
Retrospective Studies
Middle Aged
*Bile/microbiology
Aged
*Surgical Wound Infection/epidemiology/microbiology/etiology/prevention & control
*Preoperative Care/methods/adverse effects
Risk Factors
Anti-Bacterial Agents/therapeutic use

@article {pmid40742298,
year = {2025},
author = {Morder, KM and Nguyen, M and Wilfahrt, DN and Dahmani, ZL and Burr, AB and Xie, B and Morikone, M and Nieves-Rosado, H and Gunn, WG and Hurd, DE and Wang, H and Mullett, SJ and Bossong, K and Gelhaus, SL and Rajasundaram, D and Kane, LP and Delgoffe, GM and Das, J and Davar, D and Overacre-Delgoffe, AE},
title = {Sucralose consumption ablates cancer immunotherapy response through microbiome disruption.},
journal = {Cancer discovery},
volume = {},
number = {},
pages = {},
doi = {10.1158/2159-8290.CD-25-0247},
pmid = {40742298},
issn = {2159-8290},
abstract = {Gut microbiota composition is directly associated with response to immunotherapies in cancer. How the diet impacts the gut microbiota and downstream immune responses to cancer remains unclear. Here, we show that consumption of a common non-nutritive sweetener, sucralose, modifies microbiome composition, restricts T cell metabolism and function, and limits immunotherapy response in preclinical models of cancer and advanced cancer patients treated with anti-PD-1 based immune checkpoint inhibitors (ICIs). Sucralose consumption is associated with a reduction in microbiota-accessible arginine, and amino acid supplementation or fecal microbiome transfer (FMT) from anti-PD-1 responder mice completely restores T cell function and immunotherapy response. Overall, sucralose consumption destabilizes the gut microbiota, resulting in compromised T cell function and ablated ICI response in cancer.},
}

@article {pmid40742180,
year = {2025},
author = {Tang, G and Carr, AV and Perez, C and Ramos Sarmiento, K and Levy, L and Lampe, JW and Diener, C and Gibbons, SM},
title = {Metagenomic estimation of absolute bacterial biomass in the mammalian gut through host-derived read normalization.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0098425},
doi = {10.1128/msystems.00984-25},
pmid = {40742180},
issn = {2379-5077},
abstract = {Absolute bacterial biomass estimation in the human gut is crucial for understanding microbiome dynamics and host-microbe interactions. Current methods for quantifying bacterial biomass in stool, such as flow cytometry, quantitative polymerase chain reaction (qPCR), or spike-ins, can be labor-intensive, costly, and confounded by factors like water content, DNA extraction efficiency, PCR inhibitors, and other technical challenges that add bias and noise. We propose a simple, cost-effective approach that circumvents some of these technical challenges: directly estimating bacterial biomass from metagenomes using bacterial-to-host (B:H) read count ratios. We compared B:H ratios to the standard methods outlined above, demonstrating that B:H ratios are useful proxies for bacterial biomass in stool and possibly in other host-associated substrates. B:H ratios in stool were correlated with bacterial-to-diet (B:D) read count ratios, but B:D ratios exhibited a substantial number of outlier points. Host read depletion methods reduced the total number of human reads in a given sample, but B:H ratios were strongly correlated before and after host read depletion, indicating that host read depletion did not reduce the utility of B:H ratios. B:H ratios showed expected variation between health and disease states and were generally stable in healthy individuals over time. Finally, we showed how B:H and B:D ratios can be used to track antibiotic treatment response and recovery. B:H ratios offer a convenient alternative to other absolute biomass quantification methods, without the need for additional measurements, experimental design considerations, or machine learning, enabling robust absolute biomass estimates directly from stool metagenomic data.IMPORTANCEIn this study, we asked whether normalization by host reads alone was sufficient to estimate absolute bacterial biomass directly from stool metagenomic data, without the need for synthetic spike-ins, additional experimental biomass measurements, or training data. The approach assumes that the contribution of host DNA to stool is more constant or stable than biologically relevant fluctuations in bacterial biomass. We find that host read normalization is an effective method for detecting variation in gut bacterial biomass. Absolute bacterial biomass is a key metric that often gets left out of gut microbiome studies, and empowering researchers to include this measure more broadly in their metagenomic analyses should serve to improve our understanding of host-microbiota interactions.},
}

@article {pmid40742109,
year = {2025},
author = {Jones, KR and Song, Y and Rinaldi, SS and Moran, NA},
title = {Effects of priority on strain-level composition of the honey bee gut community.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0082825},
doi = {10.1128/aem.00828-25},
pmid = {40742109},
issn = {1098-5336},
abstract = {Host-associated microbiomes are complex communities shaped by interactions between members. The type VI secretion system (T6SS), among other bacterial weapons, allows gram-negative bacteria to deliver toxic effectors into competitors. In this study, we investigated the impact of differential colonization timing on the competitive advantage associated with T6SS possession using Snodgrassella alvi, a core symbiont of the honey bee gut microbiome. Following a timeline based on the natural establishment window of the gut microbiome, we sequentially inoculated newly emerged bees with fluorescently labeled strains that differed in presence of the T6SS-1. When inoculated simultaneously, the T6SS-1-possessing strain (wkB2) consistently excluded the T6SS-1-lacking strain (wkB332); however, when given a 5-day advantage, the second strain was consistently excluded regardless of strain identities. With a 1-day advantage, the effect of priority was weakened, but wkB332 was able to persist following introduction of wkB2. Utilizing a wkB2 T6SS-1 knockout strain, we repeated our 24 hour priority experiments and found that the T6SS-1 contributes to invasion outcomes along with other mechanisms of competition. Through fluorescent microscopy, we explored how coexisting strains in these experimental scenarios organize spatially within the bee ileum. Our results demonstrate that colonization timing can have lasting consequences for strain composition of the established microbiome. These findings illustrate the influence of stochastic processes in microbial community assembly and emphasize that differences in colonization timing may alter competitive outcomes between taxa, impacting taxon coexistence.IMPORTANCEThe bacterial gut communities of honey bees possess considerable strain-level diversity between hives, between individual bees, and within individual bees. However, the factors underlying strain coexistence are unclear. Here, we provide support for timing of colonization, or priority effects, as one factor driving this strain-level diversity. Our results show that priority inoculation can prevent colonization by subsequent competing bacterial strains and mitigate advantages conferred through bacterial weaponry. Further, a brief window of priority can facilitate the coexistence of strongly and weakly competitive strains within single bees. These results add to our understanding of the impacts of priority effects in host-associated microbial communities. Such an understanding can aid the development of future probiotic strategies aimed at improving honey bee health.},
}

@article {pmid40742104,
year = {2025},
author = {Vieira, FC and Mandadi, KK and Ramasamy, M and de Souza, A and Callahan, K and Fyle, C and Kamemoto, A and Koontz, AG and Yang, C and Crowley, R and Kou, KGM and Maloney, KN and Roper, MC},
title = {Amicoumacins produced by the native citrus microbiome isolate Bacillus safensis inhibit the Huanglongbing-associated bacterial pathogen "Candidatus Liberibacter asiaticus".},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0086925},
doi = {10.1128/aem.00869-25},
pmid = {40742104},
issn = {1098-5336},
abstract = {Huanglongbing (HLB) is a devastating citrus disease associated with the gram-negative, phloem-limited, and unculturable bacterium "Candidatus Liberibacter asiaticus (CLas)," which is transmitted by the Asian citrus psyllid Diaphorina citri. Despite extensive research, effective, long-term, and sustainable solutions for managing HLB remain elusive. Oxytetracycline (OTC) is currently used as an emergency measure, but there is an urgent need for alternative compounds to complement or replace OTC. In this study, we identified amicoumacins, a class of antimicrobial compounds produced by the bacterium Bacillus safensis CB729 isolated from the citrus microbiome, and demonstrated their ability to suppress CLas. Genome mining of B. safensis CB729, combined with metabolomic analysis and bioassay-guided fractionation, revealed the presence of amicoumacins and related derivatives in fractions inhibitory to Liberibacter crescens, a culturable surrogate for CLas. We tested commercially available synthetic amicoumacins A and B, along with a B. safensis-derived amicoumacin mixture, against L. crescens and CLas. We determined the MICs of amicoumacin A (1.25 µg/mL) and amicoumacin B (10 µg/mL) against L. crescens. Furthermore, amicoumacin B and the amicoumacin mixture significantly reduced CLas populations in ex vivo citrus hairy root assays. This study highlights the potential of amicoumacins as a promising group of natural products for the management of HLB, offering valuable insights for the development of novel and sustainable disease control strategies.IMPORTANCEFor two decades, the citrus industry has been severely impacted by Huanglongbing (HLB), a devastating disease caused by "Candidatus Liberibacter asiaticus (CLas)" and transmitted by the Asian citrus psyllid (Diaphorina citri). Despite extensive research, effective, long-term, and sustainable solutions remain unavailable for growers. Currently, medically relevant antibiotics, such as oxytetracycline (OTC), are used as an emergency response to combat HLB in Florida, the most affected citrus-producing state in the U.S. This underscores the urgent need for alternative treatments that can be used in rotation or as replacements for OTC. Here, we present amicoumacins, a group of bioactive secondary metabolites with antibiotic properties. We identified amicoumacin B and its derivatives from the culture broth of a Bacillus safensis isolate, native to citrus, and demonstrated their ability to inhibit Liberibacter spp. and reduce CLas populations in citrus tissue. This study highlights how microbial discovery can lead to the identification of antimicrobial compounds with potential applications in plant disease management.},
}

@article {pmid40742099,
year = {2025},
author = {Skupa, SA and Cooper, KM and Smith, AL and Drengler, EM and Eiken, AP and Schmitz, E and Waldron, GM and Mathew, G and Primeaux, M and Dhawan, P and Talmon, GA and D'Angelo, CR and El-Gamal, D},
title = {Gut microbiome profiling in Eµ-TCL1 mice reveals intestinal changes and a dysbiotic signature specific to chronic lymphocytic leukemia.},
journal = {Cancer research communications},
volume = {},
number = {},
pages = {},
doi = {10.1158/2767-9764.CRC-25-0022},
pmid = {40742099},
issn = {2767-9764},
abstract = {The gut microbiome's role in the pathogenesis of hematological malignancies is actively being explored; yet studies in chronic lymphocytic leukemia (CLL) are limited. Using the Eµ-TCL1 murine model of CLL, we identify a unique and dysbiotic disease-associated gut microbiome that develops in mice over time. Leukemic mice show an increase in abundance of pathogenic bacteria, specifically members of the Proteobacteria phylum. We found that this dysbiotic microenvironment is associated with CLL involvement within the intestinal tract and high levels of markers indicative of altered tight junction permeability (e.g., CLDN2, sCD14, zonulin). Moreover, utilizing the syngeneic model of CLL in tandem with a microflora antibiotic-ablation approach, we found that leukemic mice receiving microflora-ablating antibiotics show marked changes to the gut microbiome and a delayed disease onset compared to mice receiving antibiotics-free water. Immunophenotyping of murine spleens showed that this delay in disease was accompanied by more tumor-reactive CD8+ T cells that co-expressed fewer inhibitory receptors (e.g., PD-1, LAG3, TIM3). These findings confirm a dysbiotic gut microbiome develops during CLL disease and demonstrate unique intestinal involvement and potential immune dysregulation occurring during CLL progression that may be influencing the overall microbial signature.},
}

@article {pmid40742095,
year = {2025},
author = {Romanenko, M and Bartsch, M and Piven, L and Hahn, A and Müller, M},
title = {Gut microbiota and circadian disruption in humans: Is there a rationale for metabolic disorders?.},
journal = {Chronobiology international},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/07420528.2025.2536521},
pmid = {40742095},
issn = {1525-6073},
abstract = {Circadian disruption, arising from behaviors such as shift work and sleep deprivation, is increasingly prevalent and associated with metabolic disorders, including obesity, type 2 diabetes, and cardiovascular disease. The gut microbiome plays a crucial role in metabolic homeostasis by producing metabolites - such as short-chain fatty acids, secondary bile acids, and microbial-associated molecular patterns - that influence nutrient absorption, immune responses, and host metabolism in alignment with circadian rhythms. This review explores how circadian disruptors influence the human gut microbiome, focusing on changes in microbial composition, diversity, and functionality, and their implications for metabolic health. Preclinical studies demonstrate that circadian disruptions alter microbial composition, reduce rhythmicity, and impair functionality, contributing to metabolic disorders. However, human studies often report inconsistent findings, with microbial functionality appearing more sensitive to disruptions than composition. Eating patterns affect both the gut microbiome and circadian alignment; their optimization could realign microbial and host rhythms to promote metabolic homeostasis. Future research should focus on longitudinal and interventional studies using advanced methodologies, such as real-time intestinal gas measurements, to capture dynamic microbial activity in humans. Understanding microbial responses to circadian disruptors could inform therapeutic strategies targeting host-microbe interactions to improve metabolic health.},
}

@article {pmid40741852,
year = {2025},
author = {Saccaram, C and Simonin, M and Boutet, S and Brosse, C and Peng, S and François, T and Collet, B and Perreau, F and Sourdeval, D and Marais, C and Barret, M and Rajjou, L and Corso, M},
title = {Elucidating the interplay between metabolites and microorganisms in the spermosphere of common bean (Phaseolus vulgaris L.) seeds.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0070725},
doi = {10.1128/msystems.00707-25},
pmid = {40741852},
issn = {2379-5077},
abstract = {UNLABELLED: The spermosphere, the dynamic interface surrounding germinating seeds, is shaped by the intricate interplay between seed-exuded natural compounds and seed-associated microbial communities. In this work, we provide the first comprehensive metabolomic and microbiome characterization of common bean (Phaseolus vulgaris) spermosphere of eight genotypes produced in two contrasted production regions. Through an integrated approach, we explored the metabolomic and microbiota composition in the spermosphere of germinating common bean seeds and elucidated their environmental and genotype regulation. We detected and analyzed 2,467 metabolite features (Mf) through untargeted metabolomics categorized into fourteen metabolic categories, highlighting the prevalence of amino acids, flavonoids, and terpenoids. Genotype was the key factor influencing the chemical composition of the spermosphere. Furthermore, we identified 19 bacterial families and 23 fungal families inhabiting the spermosphere, with both genotype and seed production location exerting varying degrees of influence on microbial community composition. Through a multiscale integrated approach, we revealed specific associations between metabolites and microorganisms, such as negative correlation between flavonoids and Bacillus spp., emphasizing the genotype-dependent nature of these interactions. This comprehensive investigation sheds light on the mechanisms underlying seed germination and the complex interactions between plant genotypes, seed exudates, environmental conditions, and microbial communities in the spermosphere. These findings provide a framework for developing innovative strategies to promote seed health and sustainable crop production.

IMPORTANCE: The spermosphere, the dynamic interface around germinating seeds, is shaped by the intricate interplay between seed-exuded compounds and microbial communities. Despite the importance of these interactions for eventual seedling emergence and health, little knowledge is available on the subject. We are the first to comprehensively analyze the chemical and microbial diversity of the spermosphere of Phaseolus vulgaris (common bean). We identified thousands of primary and specialized metabolites, highlighting their diversity but largely unknown roles in germinating seed-environment interactions. We revealed significant genotype-driven differences in the chemical composition as well as the influence of both genotype and seed production location on microbial community structure in the spermosphere. Our metabolome-microbiome integrative analysis suggests that common bean shapes the spermosphere microbiome through specific seed exudates. This research advances our understanding of the metabolic capabilities and ecological roles of seed microbiota within the spermosphere, contributing to our understanding of seed health and vigor.},
}

@article {pmid40741779,
year = {2025},
author = {Zhou, F and Zhang, H and Zhong, W and Yang, H and Zhou, L and Yang, Z-J and Hu, Y and Zheng, Y},
title = {Regional-scale biogeographical patterns of soil- and root-associated microbial communities across nine planted Chinese fir forests.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0045025},
doi = {10.1128/msphere.00450-25},
pmid = {40741779},
issn = {2379-5042},
abstract = {Chinese fir (Cunninghamia lanceolata) is an economically important plantation tree species. Gaining insights into the belowground microbiome of Chinese fir is critical for optimizing plantation management and enhancing timber production. In this study, we investigated microbial community structures in both rhizospheric soil and root samples from nine Chinese fir plantations (sites) at a regional scale. Moreover, we analyzed relationships between tree growth and microbial community structures and soil properties. Our results revealed that significantly higher bacterial and fungal richness was observed in rhizospheric soils than in tree roots. Differing distribution patterns of soil- and root-associated bacterial and fungal community compositions were observed across different sites. Soil nitrate was the key factor shaping root-associated bacterial diversity, and both soil total nitrogen and nitrate were the critical drivers influencing root-associated fungal community composition. There were apparent geographical variations in the biomass and growth increment of Chinese fir trees, with soil moisture emerging as the strongest predictor for these two parameters. Moreover, soil-associated bacterial community composition, root-associated bacterial diversity, and root-associated fungal community composition were identified as the primary determinants of tree biomass. Our findings highlight the critical but different contributions of soil- and root-associated bacterial and fungal communities to the productivity of trees in subtropical plantations.IMPORTANCEChinese fir plantations are widely distributed in Southeast China and characterized by their considerable economic significance. Belowground microbial communities play pivotal roles in shaping forest ecosystem functions. Nevertheless, knowledge of the relationship between microbial communities and tree growth is scarce. Here, we investigated soil- and root-associated bacterial and fungal communities and their relationships with the tree growth of nine Chinese fir plantations in subtropical regions. We found that both compartment and site factors influenced bacterial and fungal diversity and community composition. Apparent geographical variations in the biomass and growth increment of Chinese fir trees were observed. Moreover, soil-associated bacterial community composition, root-associated bacterial diversity, and fungal community composition were identified as the primary determinants of tree biomass. Altogether, this study provides a comprehensive analysis of microbial communities in mature Chinese fir planted forests, offering new insights into their roles in supporting forest productivity.},
}

@article {pmid40741759,
year = {2025},
author = {Tubassam, M and Younus, Z and Habib, R and Imran, M},
title = {Draft genome sequences of multidrug-resistant Escherichia coli strains from the human gut.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0047925},
doi = {10.1128/mra.00479-25},
pmid = {40741759},
issn = {2576-098X},
abstract = {Draft genome sequences of multidrug-resistant Escherichia coli strains isolated from human gut are reported here. The size of the draft genome ranged from 4,985,384 to 5,220,996 bp. Genome annotation predicted 3,731-3,909 protein-coding genes while 47-60 antimicrobial resistance genes.},
}

@article {pmid40741744,
year = {2025},
author = {Young, M and Natarajan, O and Lim, SJ and Dishaw, LJ},
title = {Pseudovibrio ascidiaceicola 5337, a marine bacterial symbiont of the ascidian gut with unusual genome features.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0059425},
doi = {10.1128/mra.00594-25},
pmid = {40741744},
issn = {2576-098X},
abstract = {We isolated Pseudovibrio ascidiaceicola strain 5337, a gut bacterium of the ascidian Ciona robusta, from Mission Bay, San Diego. The genomic assembly is 6.94 Mb and 99.99% complete, comprising 22 contigs and 6,613 protein-coding genes. Unicycler identified seven circular contigs, and PHASTEST identified 11 prophage regions, including two gene transfer agents.},
}

@article {pmid40741424,
year = {2025},
author = {Abbasi, E and Khodadadi, I},
title = {High-fat diet may increase the risk of insulin resistance by inducing dysbiosis.},
journal = {Metabolism open},
volume = {27},
number = {},
pages = {100381},
pmid = {40741424},
issn = {2589-9368},
abstract = {High-fat diet (HFD) poses various health risks, such as obesity, insulin resistance (IR), fatty liver, gut microbiota dysbiosis, cognitive impairment, inflammation, and oxidative stress. HFD can alter gastrointestinal function and structure, resulting in changes of the intestinal mucosa, gastric secretions, intestinal connective tissue, intestinal motility, intestinal metabolomics profiles, and intestinal microbiota. The intestine and its microbiota process nutrients and produce molecules that can regulate insulin action and secretion. Changes in the gut microbiome (dysbiosis) and their products may have long-term effects that are not fully understood. Gut microbiota have long been documented to induce metabolic endotoxemia by releasing lipopolysaccharide, which causes systemic inflammation and insulin resistance (IR). HFD may has direct roles in the development of insulin resistance (IR). HFD can induce dysbiosis by reducing SCFAs and decreasing the activation of free fatty acid receptors (FFARs). Furthermore, HFD can increase the activation of the toll-like receptor (TLR) pathway. Hence, HFD by inducing inflammation, oxidative stress, endotoxemia, and hyperglycemia can increase the risk of IR. Therefore, this review aims to delineate the role of gut microbiota directly or indirectly involved in HFD-induced IR. These findings may clarify valuable preventive and therapeutic targets for countermeasures to IR in people who use the Western diet.},
}

@article {pmid40741391,
year = {2025},
author = {Díaz, GY and Perry, MA and Cárdenas, LS and Da Silva, VA and Scheck, K and Tschofen, SA and Tuffs, SW and Willerth, SM},
title = {Protocol for 3D Bioprinting a Co-culture Skin Model Using a Natural Fibrin-Based Bioink as an Infection Model.},
journal = {Bio-protocol},
volume = {15},
number = {14},
pages = {e5380},
pmid = {40741391},
issn = {2331-8325},
abstract = {The skin microbiome, a diverse community of microorganisms, plays a crucial role in maintaining skin health and homeostasis. Traditional studies have relied on two-dimensional (2D) models, which fail to recreate the complex three-dimensional (3D) architecture and cellular interactions of in vivo human skin, and animal models, which have species-specific physiology and accompanying ethical concerns. Consequently, both types of models fall short in accurately replicating skin physiology and understanding its complex microbial interactions. Three-dimensional bioprinting, an advanced tissue engineering technology, addresses these limitations by creating custom-designed tissue scaffolds using biomaterial-based bioinks containing living cells. This approach provides a more physiologically relevant 3D structure and microenvironment, allowing the incorporation of microbial communities to better reflect in vivo conditions. Here, we present a protocol for 3D bioprinting an in vitro skin infection model by co-culturing human keratinocytes and dermal fibroblasts in a high-viscosity, fibrin-based bioink to mimic the dermis and epidermis. The bioprinted skin tissue was co-infected with Staphylococcus aureus and Staphylococcus epidermidis to mimic bacterial skin disease. Bacterial survival was assessed through colony-forming unit enumeration. By incorporating bacteria, this protocol offers the potential to serve as a more representative in vivo 3D bioprinted skin infection model, providing a platform to study host-microbe interactions, immune responses, and the development of antimicrobial therapeutics. Key features • This protocol provides a detailed description of the cell culture process for both keratinocyte and fibroblast cells. • This protocol outlines step-by-step preparation of the high-viscosity fibrin bioink and chemical crosslinker. • The protocol uses an extrusion-based bioprinter, with an easy-to-follow methodology that clarifies the printing details, including the incorporation of skin cells into the bioink. • This protocol details how the bacteria are inoculated into the construct to achieve the co-infection 3D skin model.},
}

@article {pmid40741383,
year = {2025},
author = {Hoffelner, DK and Hendrikx, T},
title = {Emerging therapy targets to modulate microbiome-mediated effects evident in cardiovascular disease.},
journal = {Frontiers in cardiovascular medicine},
volume = {12},
number = {},
pages = {1631841},
pmid = {40741383},
issn = {2297-055X},
abstract = {The human gut microbiota influences host metabolism, immune responses, and inflammation, with microbial dysbiosis linked to metabolic disorders and increased cardiovascular disease risk. Notably, metabolites such as short-chain fatty acids, trimethylamine N-oxide, and bile acids, which are influenced by the microbiome and its functional composition, have been implicated in vascular health, immune modulation, and atherosclerosis. This review summarizes recent findings on the gut-heart axis, demonstrating the intricate interplay between microbial communities, dietary influences and cardiovascular health. Recognizing the microbiome's impact on CVD could yield novel therapeutic targets, including prebiotics, probiotics, and precision medicine approaches that modulate microbial diversity and activities to reduce residual CVD risk.},
}

@article {pmid40741187,
year = {2025},
author = {Zhao, H and Zhang, XW and Li, X},
title = {Lifestyle factors in hepatocellular carcinoma: From pathogenesis to prognosis.},
journal = {World journal of clinical oncology},
volume = {16},
number = {7},
pages = {107723},
pmid = {40741187},
issn = {2218-4333},
abstract = {Hepatocellular carcinoma (HCC) represents a major global health burden, ranking third as the leading cause of cancer-related mortality worldwide. This comprehensive review examines the substantial body of evidence linking modifiable lifestyle factors to HCC pathogenesis and clinical outcomes. We systematically evaluate dietary components, alcohol consumption patterns, tobacco use, physical activity levels, and emerging factors including metabolic disorders, psychological stress, and sleep disturbances. These factors collectively influence hepatocarcinogenesis through diverse biological mechanisms, including genotoxic damage, metabolic dysregulation, chronic inflammatory responses, and gut microbiome-mediated pathways. The accumulated data underscore the urgent need to integrate lifestyle interventions into multidisciplinary HCC management.},
}

@article {pmid40741099,
year = {2025},
author = {Khurana, A and Hartmann, P},
title = {Gut microbiome-specific nanoparticle-based therapeutics for liver diseases.},
journal = {World journal of gastroenterology},
volume = {31},
number = {27},
pages = {109105},
pmid = {40741099},
issn = {2219-2840},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Liver Diseases/microbiology/therapy/drug therapy ; *Nanoparticles/chemistry ; *Nanoparticle Drug Delivery System ; Drug Delivery Systems/methods ; Animals ; Precision Medicine/methods ; Artificial Intelligence ; Dysbiosis/microbiology ; Liver/pathology/drug effects ; },
abstract = {Alcohol-associated liver disease, metabolic dysfunction-associated steatotic liver disease, and metabolic dysfunction-associated steatohepatitis are chronic liver diseases (CLDs) driven by metabolic dysregulation, immune dysfunction, and gut microbiome alterations. Current treatments are inadequate and provide only symptomatic relief in most cases, underscoring the urgent need for forward-looking approaches. The disturbances in gut and liver communication contribute towards disease progression, making microbiome-based therapeutic strategies an area of growing interest. Nanoparticles have emerged as a powerful tool for drug delivery with high targetability, stability, and targeted release. Further, artificial intelligence offers a transformative approach by accelerating nanoparticle design, optimizing microbial therapy formulations, predicting treatment responses, and personalizing interventions based on patient-specific microbiota compositions. Herein, we give an overview of important liver diseases, key nanocarrier types, and the approaches wherein nanocarriers have been integrated to modulate gut microbiota for the therapy of CLDs. We also describe future directions and the challenges, which need to be overcome for wide scale application and tailored use of gut microbiome-focused nano-drug delivery carriers for the therapy of CLDs. Despite current hurdles, the integration of nanotechnology, microbiome therapeutics, and artificial intelligence-driven precision medicine holds immense promise for reshaping the treatment landscape of CLDs.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Liver Diseases/microbiology/therapy/drug therapy
*Nanoparticles/chemistry
*Nanoparticle Drug Delivery System
Drug Delivery Systems/methods
Animals
Precision Medicine/methods
Artificial Intelligence
Dysbiosis/microbiology
Liver/pathology/drug effects

@article {pmid40741037,
year = {2025},
author = {Mentado-Sosa, E and Guerra-Solano, JM and Raffa, RB and Pagán, OR and Pisciotta, J},
title = {Microbiome Alteration Prevents Abstinence-Induced Nicotine Withdrawal in a Well-Established Planarian Model.},
journal = {Cureus},
volume = {17},
number = {7},
pages = {e89075},
pmid = {40741037},
issn = {2168-8184},
abstract = {The prevalence of substance use disorders (SUDs) is unequally distributed across socioeconomic strata. Although several genetic predispositions and psychosocial influences play integral roles, environmental factors are undoubtedly additional contributors. We propose that a potential common factor could be diet. More specifically, circumstances such as economic challenges could lead to limited food choices and poor-quality diets, and this could result in differences in microbiome composition compared to less SUD-susceptible populations having otherwise similar risk factors. The current study investigated the effect of altering the microbiome on drug withdrawal from nicotine using a standard planarian model. Planarians (Girardia dorotocephala) were treated with the broad-spectrum antibiotics ampicillin (a ß-lactam) and kanamycin (a non-ß-lactam), alone and in combination, and microbiomes were analyzed using culture techniques, microscopy, and metagenomic methods. Alphaproteobacteria such as Sphingomonadaceae were detected in the microbiome. Ampicillin or kanamycin reduced the microbiome diversity, notably reducing Sphingomonas and Pedobacter bacteria. One-week treatment with ampicillin and kanamycin did not affect planarian spontaneous locomotor activity. However, pretreatment with ampicillin, but not kanamycin or the combination, significantly attenuated abstinence-induced nicotine withdrawal-like behavior. These results suggest that alteration of the microbiome decreases nicotine withdrawal in this planarian species, and, more broadly, supports the idea that the microbiome might influence the susceptibility and/or maintenance of SUDs.},
}

@article {pmid40740992,
year = {2025},
author = {Guo, S and Zhao, J and Zhu, R and Fan, Z and Liu, S and Wu, W},
title = {Epigenetic modifications of gut microbiota and their potential role in atherosclerosis.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1638240},
pmid = {40740992},
issn = {1663-9812},
abstract = {Emerging evidence positions the gut microbiota as a pivotal regulator of host metabolism and immunity, particularly in atherosclerosis pathogenesis, with epigenetic mechanisms serving as fundamental mediators of gene expression control. This review systematically summarizes gut microbiome-driven epigenetic pathways, encompassing DNA methylation, histone modifications, non-coding RNA networks and their interplay with atherosclerosis-related pathological processes. We synthesize current evidence on microbiota-epigenome crosstalk, highlighting its potential mechanistic contributions to atherosclerotic plaque development.},
}

@article {pmid40740973,
year = {2025},
author = {Ma, Q and Wang, N and Zheng, X and Liu, J and Che, Y and Wang, J},
title = {Altered Nasal Microbiota-Metabolome Interactions in Allergic Rhinitis: Implications for Inflammatory Dysregulation.},
journal = {Journal of inflammation research},
volume = {18},
number = {},
pages = {9919-9934},
pmid = {40740973},
issn = {1178-7031},
abstract = {OBJECTIVE: The aim of this study was to investigate the correlation between nasal microbiome, metabolites, and their potential contribution to the pathogenesis of allergic rhinitis (AR), a widespread chronic inflammatory disorder that poses a considerable healthcare burden worldwide. Immune dysregulation and environmental factors are key in the development of allergic responses, but the importance of host-microbiota interactions in influencing these responses is gaining recognition.

METHODS: 32 AR patients and 20 healthy controls underwent 16S rDNA sequencing and untargeted metabolomics analysis. Microbial diversity, composition, and functional pathways were compared between groups. Metabolomic alterations were evaluated using LC-MS/MS, and correlations between microbiota and metabolites were analyzed.

RESULTS: While α-diversity did not differ significantly between groups, β-diversity analysis revealed distinct microbial community shifts in AR patients. Specifically, Actinobacteria and Bacteroidetes abundances were increased, and genera Vibrio and Aeromonas were significantly enriched. Metabolomic profiling identified 528 differential metabolites, including altered levels of LPC, and pathway analysis highlighted disrupted linoleic acid metabolism, arachidonic acid metabolism, and tryptophan metabolism. Correlation analysis revealed significant associations between specific microbial taxa (eg, Aeromonas, Vibrio) and metabolites (eg, LPC, arachidonic acid), suggesting a potential link between microbiota-derived metabolic shifts and inflammatory responses in AR.

CONCLUSION: The perturbation of nasal microbiota-metabolite interactions may play a role in the pathogenesis of AR, emphasizing the need for future investigations into potential pathophysiological mechanisms.},
}

@article {pmid40740937,
year = {2025},
author = {Zhang, L and Hu, L and Tan, L and Zhang, Z and Chen, M and Gan, W and Chen, L and Zou, Y and Wang, S and Pang, Y and Fan, Z and Liu, J},
title = {The dysbiosis of gut microbiota and dysregulation of metabolites in IgA nephropathy and membranous nephropathy.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1618947},
pmid = {40740937},
issn = {2296-858X},
abstract = {INTRODUCTION: Immunoglobulin A nephropathy (IgAN) and membranous nephropathy (MN) are among the most common forms of primary glomerular diseases, with a rising global incidence. Despite their clinical importance, the underlying pathogenesis of these diseases and the development of reliable non-invasive diagnostic tools remain inadequately understood. Accumulating evidence suggests that gut microbiota and its associated metabolites may play a crucial role in the development of kidney diseases via the gut-kidney axis. However, comprehensive studies integrating both microbiome and metabolomic data in IgAN and MN are still limited.

METHODS: In this study, we performed integrated metagenomic sequencing and untargeted metabolomic profiling to investigate alterations in gut microbial composition and systemic metabolic changes associated with IgAN and MN. Fecal samples were collected from 24 patients with IgAN, 20 patients with MN, and 17 healthy controls. Microbial diversity and composition were assessed using metagenomic analysis, while metabolic profiles were evaluated through untargeted LC -MS-based metabolomics. Multivariate statistical analyses and biomarker modeling were employed to identify discriminative features and evaluate diagnostic performance. Microbiota-metabolite correlation networks were constructed to explore potential mechanistic links.

RESULTS: Metagenomic analysis showed that both the IgAN and MN groups had significantly reduced α-diversity. Although β-diversity analysis did not reveal significant differences between the three groups, the IgAN and MN groups exhibited higher sample dispersion than the control group. Notably, both IgAN and MN patients showed a decrease in the abundance of certain specific microbial taxa. A total of 34 and 28 differentially abundant microbial species were identified in IgAN and MN, respectively, compared to healthy controls, with 16 taxa consistently downregulated in both disease groups. Notably, Streptococcus oralis was significantly enriched in the MN group, while [Clostridium] innocuum was markedly depleted. Metabolomic profiling identified 307 and 209 differentially abundant metabolites in IgAN and MN, respectively. Dipeptides (e.g., prolylleucine) were consistently upregulated, while the levels of certain short-chain fatty acids (SCFA) were reduced. Multivariate biomarker models demonstrated excellent diagnostic performance, achieving area under the curve (AUC) of 0.919 (IgAN vs. control), 0.897 (MN vs. control) and 0.912 (IgAN vs. MN), surpassing individual metabolite markers.

DISCUSSION: Our findings highlight significant alterations in gut microbial composition and systemic metabolite profiles in both IgAN and MN patients compared to healthy individuals. The consistent reduction in microbial diversity and SCFA-producing taxa, along with characteristic changes in metabolic signatures, supports the involvement of the gut-kidney axis in disease pathogenesis. The diagnostic models developed in this study provide promising non-invasive biomarkers for distinguishing IgAN and MN with high accuracy. These results contribute novel insights into the microbe-metabolite interplay in glomerular diseases and offer potential targets for future diagnostic and therapeutic strategies.},
}

@article {pmid40740914,
year = {2025},
author = {Koo, TH and Lee, YL and Leong, XB and Hayati, F and Zakaria, MH and Zakaria, AD},
title = {Multi-omics perspectives for gastrointestinal malignancy: A systematic review.},
journal = {World journal of gastrointestinal surgery},
volume = {17},
number = {7},
pages = {107110},
pmid = {40740914},
issn = {1948-9366},
abstract = {BACKGROUND: Gastrointestinal (GI) malignancies, including gastric and colorectal cancers, remain one of the primary contributors to cancer-related illness and death globally. Despite the availability of conventional diagnostic tools, early detection and personalized treatment remain significant clinical challenges. Integrated multi-omics methods encompassing genomic, transcriptomic, proteomic, metabolomic, and microbiome profiles have emerged as powerful tools for advancing precision oncology, improving diagnostic accuracy, and informing therapeutic strategies.

AIM: To investigate the application of multi-omics approaches in the early detection, risk stratification, treatment optimization, and biomarker discovery of GI malignancies.

METHODS: The systematic review process was conducted in accordance with the PRISMA 2020 guidelines. Five databases, PubMed, ScienceDirect, Scopus, ProQuest, and Web of Science, were searched for studies published in English from 2015 onwards. Eligible studies involved human subjects and focused on multi-omics integration in GI cancers, including biomarker identification, tumor microenvironment analysis, tumor heterogeneity, organoid modeling, and artificial intelligence (AI)-driven analytics. Data extraction included study characteristics, omics modalities, clinical applications, and evaluation of study quality conducted with the Cochrane risk of bias 2.0 instrument.

RESULTS: A total of 17196 initially identified articles, 20 met the inclusion criteria. The findings highlight the superiority of multi-omics platforms over traditional biomarkers (e.g., carcinoembryonic antigen and carbohydrate antigen 19-9 in detecting early stage GI cancers. Key applications include the identification of circulating tumor DNA, extracellular vesicles, lipidomic and proteomic signatures, and the adoption of AI algorithms to enhance diagnostic precision. Multi-omics analysis has also revealed the mechanisms of immune modulation, tumor microenvironment regulation, metastatic behavior, and drug resistance. Organoid models and microbiota profiling have contributed to personalized therapeutic strategies and immunotherapy optimization.

CONCLUSION: Multi-omics approaches offer significant advancements in the early diagnosis, prognostic evaluation, and personalized treatment of GI malignancies. Their integration with AI analytics, organoid biobanking, and microbiota modulation provides a pathway for precision oncology research.},
}

@article {pmid40740867,
year = {2025},
author = {Li, H and Meza, LA and Shahi, SK and Zhang, Z and Wen, W and Hu, D and Lin, H and Mangalam, AK and Luo, J},
title = {Effects of alcohol on gut microbiome in adolescent and adult MMTV-Wnt1 mice.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1557040},
pmid = {40740867},
issn = {2234-943X},
abstract = {INTRODUCTION: Breast cancer is the most frequently diagnosed cancer in women worldwide. Alcohol consumption is a significant and modifiable risk factor, yet the mechanisms linking alcohol to breast cancer progression remain unclear. Recent evidence suggests that the gut microbiome-a complex ecosystem that modulates metabolism, immunity, and inflammation-may act as a mediator of alcohol-induced tumor promotion. We hypothesized that binge-like alcohol exposure induces gut dysbiosis, which in turn drives systemic inflammation and carcinogenic processes.

METHODS: We utilized MMTV-Wnt1 transgenic mice, a well-established model for mammary tumor development, along with wild-type FVB mice. Adolescent and adult female mice were administered binge-like doses of ethanol via intraperitoneal injection. Fecal samples were collected and analyzed by 16S rRNA gene sequencing to assess microbial diversity, composition, and taxonomic changes in response to alcohol exposure.

RESULTS: Binge-like alcohol exposure significantly reduced gut microbial richness in adult Wnt1 and FVB mice. In both adolescent and adult mice, alcohol markedly altered the composition of the gut microbiota across both strains. Differential abundance analysis identified specific microbial taxa significantly impacted by ethanol treatment, suggesting targeted perturbations of the gut microbial community.

CONCLUSION: Our findings demonstrate that intraperitoneal binge-like alcohol exposure induces gut dysbiosis in both tumor-prone and wild-type mice. These alterations in the gut microbiome may contribute to the pro-inflammatory and tumor-promoting effects of alcohol in breast tissue. This study provides insights into the potential role of gut dysbiosis in alcohol-induced mammary tumor promotion and offers avenues for future research.},
}

@article {pmid40740764,
year = {2025},
author = {Liu, B and Jin, J and Zhou, Y and Shang, Z and Meng, P and Du, M and Geng, F and Gao, X and Zhao, F and Su, Z and Pan, X},
title = {Oligosaccharides from the seeds of Dolichos lablab L. promote gut microbial metabolite L-arginine production to alleviate cyclophosphamide-induced immunosuppression.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1587426},
pmid = {40740764},
issn = {1664-3224},
mesh = {Animals ; *Cyclophosphamide/adverse effects ; *Arginine/metabolism/biosynthesis ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Oligosaccharides/pharmacology/isolation & purification ; *Seeds/chemistry ; *Fabaceae/chemistry ; *Immune Tolerance/drug effects ; Male ; Immunosuppression Therapy ; Immunosuppressive Agents ; },
abstract = {INTRODUCTION: Dolichos lablab L. is a nutritionally and medicinally significant legume, yet research on its bioactive oligosaccharides remains limited. This study investigates the potential of Dolichos lablab L. oligosaccharides to ameliorate cyclophosphamide (CTX)-induced immunosuppression and intestinal damage.

METHODS: Crude oligosaccharides were purified to yield mixture SRSV (86% sugar content), comprising sucrose, raffinose, stachyose, and verbascose (mass ratio 19:16.8:50:14.2). Immunosuppressed mice (CTX-induced) were treated with SRSV (150 mg/kg). Gut microbiota (GM) diversity was analyzed via 16S rRNA sequencing, and serum metabolites were profiled using metabolomics. GM-depleted mice (antibiotic-treated) and L-arginine supplementation experiments were used for mechanistic validation.

RESULTS: SRSV preserved intestinal villi integrity, reversed CTX-induced immune organ atrophy, and restored the CD4+T/CD8+T ratio. It enhanced bone marrow hematopoiesis, elevated peripheral white blood cell and lymphocyte counts, and modulated serum TNF-α levels. SRSV increased GM diversity, enriching beneficial taxa (e.g., Ruminococcus, UBA1819, Anaerofustis) while reducing pathogenic Atopobiaceae. Antibiotic-induced GM depletion abrogated SRSV's protective effects. Metabolomics identified L-arginine as a key upregulated metabolite, linked to arginine biosynthesis. L-arginine supplementation alone replicated SRSV's immunoprotective outcomes.

DISCUSSION: SRSV attenuates CTX-induced immunosuppression through GM-dependent mechanisms and L-arginine-mediated immunomodulation. GM integrity is essential for SRSV efficacy, as its depletion abolishes protection. The restitution of L-arginine levels underpins SRSV's capacity to restore immune homeostasis.

CONCLUSION: SRSV from Dolichos lablab L. is a promising natural adjuvant for mitigating chemotherapy-induced immunosuppression and intestinal injury, acting via GM modulation and arginine biosynthesis pathways.},
}

Animals
*Cyclophosphamide/adverse effects
*Arginine/metabolism/biosynthesis
*Gastrointestinal Microbiome/drug effects
Mice
*Oligosaccharides/pharmacology/isolation & purification
*Seeds/chemistry
*Fabaceae/chemistry
*Immune Tolerance/drug effects
Male
Immunosuppression Therapy
Immunosuppressive Agents

@article {pmid40740643,
year = {2025},
author = {Ahmadi-Khorram, M and Hatami, A and Asghari, P and Jafarzadeh Esfehani, A and Afshari, A and Javdan, F and Nematy, M},
title = {Probiotics mitigate stress and inflammation in malnourished adults via gut microbiota modulation: a randomized controlled trial.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1615607},
pmid = {40740643},
issn = {2296-861X},
abstract = {OBJECTIVE: Malnutrition negatively affects mental health by altering neurotransmitter function and increasing stress responses. The gut-brain axis is pivotal in this process, and probiotics may mitigate stress. The current study examined the effects of multi-strain probiotic supplementation on stress levels in underweight individuals using the Perceived Stress Scale (PSS).

METHODS: A double-blind, randomized, placebo-controlled trial involved 100 underweight participants were randomized to receive either a probiotic supplement (Lactobacillus acidophilus, L. casei, L. rhamnosus; 3 × 10[9] CFU) or placebo for 8 weeks. Stress levels, anthropometric measures, and inflammatory markers (ESR, CRP) evaluated at baseline and post-intervention.

RESULTS: Ninety participants (mean age: 26.22 ± 7.42 years) completed the study (probiotic: n = 47; placebo: n = 43). Baseline age (p = 0.051) and gender (p = 0.101) showed no significant differences. Post-intervention, the probiotic group exhibited significant weight increases (p = 0.005), waist circumference (p = 0.038), and hip circumference (p = 0.008), and a significant reduction in Perceived Stress Scale (PSS) scores (p < 0.001) in comparison to the placebo. Inflammatory markers (ESR, CRP) also decreased significantly in the probiotic group (p < 0.001). Within-group analysis revealed improvements in anthropometric measures and inflammatory markers in both groups (p < 0.05), but stress reduction was more pronounced in the probiotic group (34% vs. 9.3%, p = 0.017). A significant time-group interaction was observed for stress scores (p < 0.001).

DISCUSSION: The findings suggest that probiotic supplementation reduces stress levels in underweight individuals, possibly through gut microbiota modulation and inflammation reduction. Further research with larger samples and microbiome analysis is warranted.

CONCLUSION: In conclusion, administering probiotics to underweight patients positively impacts their mental health and exhibits anti-inflammatory effects.

CLINICAL TRIAL REGISTRATION: https://irct.behdasht.gov.ir/trial/69130, identifier IRCT20230310057667N1.},
}

@article {pmid40740347,
year = {2025},
author = {Kawasaki, R and Kukimoto, I and Nishio, E and Otani, S and Nishizawa, H and Maeda, Y and Iwata, A and Fujii, T},
title = {Distinct cervical microbiome and metabolite profiles before and after menopause: implications for cervical cancer progression.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1589277},
pmid = {40740347},
issn = {2235-2988},
mesh = {Humans ; Female ; Middle Aged ; *Microbiota ; *Uterine Cervical Neoplasms/microbiology/pathology/metabolism/virology ; RNA, Ribosomal, 16S/genetics ; *Menopause ; Disease Progression ; MicroRNAs/genetics ; *Cervix Uteri/microbiology ; Adult ; Papillomavirus Infections/complications/virology ; Uterine Cervical Dysplasia/microbiology/pathology ; Cytokines ; Bacteria/classification/genetics/isolation & purification ; *Metabolome ; Chemokine CCL5 ; Carcinoma, Squamous Cell/microbiology/pathology ; Aged ; },
abstract = {INTRODUCTION: Cervical cancer is the fourth most common malignancy in women and is primarily caused by persistent infection with high-risk human papillomavirus (HPV). In addition, host immune responses, genetic factors, and lifestyle habits also have etiological roles. The cervicovaginal microbiome undergoes dynamic changes during menopause, which may be involved in the progression of cervical neoplasia. We aimed to elucidate the association between cervical microenvironmental changes and the progression of cervical neoplasia before and after menopause by integrating analyses of the cervical microbiome, related metabolites, cytokines, and microRNAs.

METHODS: A total of 248 HPV-positive women with cervical neoplasia, including 17 with cervical intraepithelial neoplasia (CIN1), 80 with CIN2, 82 with CIN3, and 69 with squamous cell carcinoma (SCC), were enrolled. As normal controls, 48 HPV-negative healthy women were included. Each group was stratified based on the mean menopausal age of 50 years. Cervical mucus was analyzed according to the methods outlined below. The microbiota was profiled by 16S rRNA gene sequencing, metabolites were analyzed by ultra-HPLC-tandem mass spectrometry, RT-qPCR was used for miRNA expression analysis, and RANTES levels were quantified by multiplex bead array. Data analysis was performed using MicrobiomeAnalyst and MetaboAnalyst.

RESULTS: In the SCC group, Prevotella and Atopobium were the key bacterial genera among the younger group, while Peptoniphilus, Fusobacterium, and Porphyromonas were more prevalent in elderly group (LDA score > 4.5). We observed a consistent positive correlation between Atopobium and xanthine in younger groups with CIN2 or worse (p < 0.0001). However, no such correlations were detected in elderly women. In addition, Atopobium, Adlercreutzia, and Gardnerella showed significant positive correlation with nicotinic acid in younger women with SCC compared to the elderly women (p < 0.0001). In the younger SCC women, several metabolites were significantly elevated in groups with high expression levels of RANTES, miR-20b-5p, and miR-155-5p.

CONCLUSION: The cervical microbiome undergoes changes during menopause, and may influence disease progression by interacting with metabolites, cytokines, and miRNAs. These results highlight the potential for personalized medicine for cervical cancer that is tailored to different age groups.},
}

Humans
Female
Middle Aged
*Microbiota
*Uterine Cervical Neoplasms/microbiology/pathology/metabolism/virology
RNA, Ribosomal, 16S/genetics
*Menopause
Disease Progression
MicroRNAs/genetics
*Cervix Uteri/microbiology
Adult
Papillomavirus Infections/complications/virology
Uterine Cervical Dysplasia/microbiology/pathology
Cytokines
Bacteria/classification/genetics/isolation & purification
*Metabolome
Chemokine CCL5
Carcinoma, Squamous Cell/microbiology/pathology
Aged

@article {pmid40740338,
year = {2025},
author = {Mancabelli, L and Tarracchini, C and Longhi, G and Alessandri, G and Ventura, M and Turroni, F},
title = {Dissecting the molecular interactions between botanical extracts and the human gut microbiota.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1610170},
pmid = {40740338},
issn = {1664-302X},
abstract = {Over millions of years, humans and their gut microbes have developed a symbiotic relationship that benefits both organisms. Many plants and herbs consumed as food by humans, such as aloe vera gel and dandelion root extracts, contain bioactive compounds with recognized therapeutic or preventive effects. However, the impact of these botanicals on the composition and functionality of the human gut microbiota is not yet understood. In this study, the molecular impact of these botanicals on reconstructed human gut microbiota was assessed by in-vitro bioreactor experiments followed by metagenomics and transcriptomic approaches, highlighting both taxonomic and functional changes in the human gut microbiome. Furthermore, cross-feeding activities established by common human gut microbial taxa like Bacteroides spp. when cultivated on these extracts were assessed. In conclusion, the results show that botanicals affect intestinal populations that are highly dependent on the microbial taxa present and that trophic interactions are established in few key gut members.},
}

@article {pmid40740318,
year = {2025},
author = {Lin, T and Xu, Z and Chen, J and Wang, X and Li, Q and Ye, B and Hu, C},
title = {Bibliometric and visualized analysis of the relationship between rheumatoid arthritis and periodontitis-related bacteria using CiteSpace software.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1589331},
pmid = {40740318},
issn = {1664-302X},
abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a chronic systemic autoimmune disease of unknown etiology. Recent studies have indicated a potential relationship between the oral microbiome and the onset and progression of RA. However, research trends in this area have not been comprehensively examined. The aim of this study was to conduct a bibliometric analysis of the relationship between RA and the oral microbiome from January 1, 1995, to January 10, 2024, to elucidate the research landscape, including hot topics and emerging trends.

METHODS: We extracted literature related to RA and the oral microbiome from the Web of Science database. Utilizing CiteSpace software, we analyzed publications, countries, institutions, authors, and keywords through a visual knowledge graph to assess research hotspots and trends.

RESULTS: In total, 833 articles were identified, revealing a consistent increase in the number of annual publications in this field over the study period. The United States has emerged as the leading country in terms of publication volume, with Harvard University being the most prolific institution. Among the authors, Jan Potempa has the highest number of publications. Keyword analysis indicated that current research hotspots concerning the relationship between RA and the oral microbiome primarily focus on Porphyromonas gingivalis, periodontitis, inflammation, expression, and peptidylarginine deiminase. Investigating the mechanisms by which oral and intestinal microorganisms influence RA, as well as developing intervention strategies targeting these microbiotas, is anticipated to be a significant future research direction.

CONCLUSION: This study characterized the trends in the literature regarding the relationship between RA and the oral microbiome, providing valuable insights for scholars pursuing further research.},
}

@article {pmid40740256,
year = {2025},
author = {Wen, S and Liu, M and Pan, C and Zhang, L and Yan, R and Xu, Z},
title = {Research progress on immunometabolism and gut microbiota in cryptococcal meningitis: mechanisms and therapeutic implications.},
journal = {Frontiers in neuroscience},
volume = {19},
number = {},
pages = {1622349},
pmid = {40740256},
issn = {1662-4548},
abstract = {Cryptococcal meningitis (CM) is a fatal central nervous system infection caused by Cryptococcus neoformans breaching the blood-brain barrier (BBB), carrying a mortality rate approaching 100% in untreated individuals, while even survivors following treatment often experience neurological complications including optic nerve atrophy, memory impairment, hydrocephalus, and motor dysfunction. Current research has yet to fully elucidate the complex pathological mechanisms of CM, particularly leaving a significant gap in the systemic analysis within the dynamic interaction network of immunity, metabolism, and the gut microbiota. This article systematically integrates the interplay of immune responses, metabolic reprogramming, and the gut microbiome to reveal the pathogenesis of CM across multiple dimensions: in immune regulation, the phagocytic-inflammatory equilibrium in macrophages and CD4 + T cells defends against pathogen invasion, but hyperactivated immune responses may damage the BBB and exacerbate neural injury; metabolically, host iron overload induces ferroptosis, disrupting the BBB via lipid peroxidation, while inositol metabolism provides substrates for cryptococcal capsular synthesis, enhancing its virulence and promoting CNS invasion; the gut microbiota, meanwhile, modulates immune homeostasis via the "gut-brain axis," with its metabolites (e.g., short-chain fatty acids) enhancing BBB integrity and suppressing neuroinflammation through immunomodulation. We propose a combined therapeutic strategy of "immunomodulators + metabolic inhibitors + microbiota intervention," moving beyond traditional single-factor research paradigms to establish a multi-omics integrated framework for the precise treatment of CM-spanning molecular mechanisms to clinical translation-and propelling the field of neuroinfectious diseases towards a host-pathogen-microenvironment systemic regulation paradigm.},
}

@article {pmid40740002,
year = {2025},
author = {Pozas-Schacre, C and Bischoff, H and Vizon, C and Raviglione, D and Clerissi, C and Bonnard, I and Nugues, MM},
title = {Contact- and Water-Mediated Interactions With an Allelopathic Macroalga Drive Distinct Coral Microbiome and Metabolome.},
journal = {Environmental microbiology},
volume = {27},
number = {8},
pages = {e70160},
doi = {10.1111/1462-2920.70160},
pmid = {40740002},
issn = {1462-2920},
support = {ANR-18-CE02-0009-01//Agence Nationale de la Recherche/ ; //Ecole Pratique des Hautes Etudes (EPHE - PSL)/ ; },
mesh = {*Anthozoa/microbiology/metabolism ; Animals ; *Metabolome ; *Microbiota ; Seawater/microbiology ; Coral Reefs ; *Seaweed/physiology ; *Allelopathy ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {Macroalgal proliferation constitutes a major threat to coral reef resilience. Macroalgae can affect corals by altering their microbiome and metabolome. However, our understanding of the spatial scale of these effects and the influence of environmental factors is limited. We conducted a manipulative field experiment to investigate how interaction types (direct contact and close proximity) with the allelopathic macroalga Dictyota bartayresiana and prevailing water current influence the microbiome and metabolome of the coral Pocillopora acuta and its near-surface seawater. Coral tissue damage was spatially constrained to the algal contact zone. Direct contact caused significant increases in harmful bacteria at the expense of beneficial ones in side coral fragments. Non-significant changes were observed within the microbiome of apex fragments, suggesting a resistance of the coral holobiont to colony-wide microbial colonisation. The coral metabolome responded to both algal contact and proximity. We detected several compounds potentially relevant for oxidative stress mitigation and coral defence. This metabolomic response was similar between apex and side fragments, supportive of a colony-wide metabolomic response. In the near-surface coral seawater, only a microbial response to algal contact was detected. We conclude that coral holobionts are capable of colony-wide metabolomic responses to maintain homeostasis against macroalgal competitors.},
}

*Anthozoa/microbiology/metabolism
Animals
*Metabolome
*Microbiota
Seawater/microbiology
Coral Reefs
*Seaweed/physiology
*Allelopathy
Bacteria/classification/isolation & purification/genetics

@article {pmid40739703,
year = {2025},
author = {Song, M and Zhou, W and Fan, J and Jia, C and Xiong, W and Wei, H and Tao, S},
title = {Diarrheal microbiota-derived extracellular vesicles drive intestinal homeostasis dysfunction via miR-125b/NF-κB-mediated macrophage polarization.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2541036},
doi = {10.1080/19490976.2025.2541036},
pmid = {40739703},
issn = {1949-0984},
mesh = {*MicroRNAs/genetics/metabolism ; Animals ; *Extracellular Vesicles/metabolism/genetics ; *Gastrointestinal Microbiome ; *Macrophages/immunology/metabolism ; Mice ; *NF-kappa B/metabolism/genetics ; Humans ; Homeostasis ; *Diarrhea/microbiology ; Intestinal Mucosa/microbiology/metabolism ; Mice, Inbred C57BL ; Signal Transduction ; Male ; Female ; },
abstract = {Gut microbiota-derived extracellular vesicles (EVs) are emerging mediators of microbiota-host crosstalk, but their roles in diarrheal diseases remain poorly understood. Here, we revealed that EVs isolated from diarrheal donors' intestinal microbiota trigger pro-inflammatory macrophage polarization and compromise intestinal epithelial barrier integrity in both conventional and pseudo-germ-free mice, demonstrating their intrinsic pathogenicity independent of viable microbes. miRNAs sequencing analysis identified miR-125b as a highly enriched miRNA in diarrheal microbiota-derived EVs, which directly targets the 3' untranslated region of NF-κBIA, leading to its degradation and subsequent activation of the NF-κB signaling pathway. This molecular cascade drives macrophages toward a pro-inflammatory phenotype characterized by elevated TNF-α and IL-1β secretion, ultimately disrupting tight junction proteins (ZO-1, Occludin) and increasing intestinal permeability. Strikingly, adoptive transfer of primary macrophages pre-exposed to miR-125b recapitulated barrier dysfunction in recipient mice. Our study uncovers a tripartite axis linking diarrheal microbiota-derived EVs, pro-inflammatory macrophage polarization via EVs-miR-125b, and intestinal homeostasis breakdown, highlighting the underappreciated role of EVs-borne miRNAs in reshaping host immunity. These findings position EVs as both biomarkers and potential targets for further exploration for diarrhea-related inflammatory gut disorders, offering a nanotechnology-inspired strategy to modulate EVs-mediated interkingdom communication in microbiome-associated diseases.},
}

*MicroRNAs/genetics/metabolism
Animals
*Extracellular Vesicles/metabolism/genetics
*Gastrointestinal Microbiome
*Macrophages/immunology/metabolism
Mice
*NF-kappa B/metabolism/genetics
Humans
Homeostasis
*Diarrhea/microbiology
Intestinal Mucosa/microbiology/metabolism
Mice, Inbred C57BL
Signal Transduction
Male
Female

@article {pmid40739603,
year = {2025},
author = {Tao, R and Wang, X and Zhen, X and Xia, R and Chen, K and Zhang, H and Deng, Y and Zhang, S},
title = {Skin Microbiome alterations in heroin users revealed by full-length 16S rRNA sequencing.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {461},
pmid = {40739603},
issn = {1471-2180},
support = {2022YFC3302004//National Key Research and Development Program of China/ ; 2022YFC3302004//National Key Research and Development Program of China/ ; 82202080//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Skin/microbiology ; *Microbiota/genetics ; Adult ; *Bacteria/genetics/classification/isolation & purification ; Male ; *Heroin Dependence/microbiology ; DNA, Bacterial/genetics ; Phylogeny ; Female ; Sequence Analysis, DNA ; Middle Aged ; Heroin ; Young Adult ; Skin Microbiome ; },
abstract = {BACKGROUND: Identifying key characteristics of unknown suspects, such as age, height, and drug use, is essential for advancing forensic investigations.

METHODS: In this study, we employed full-length 16S rRNA gene sequencing to analyze the bacterial communities of nasal skin (NaS), oral epithelial skin (OrE), and palm skin (PaS) in heroin users and healthy controls.

RESULTS: Our results revealed a significant reduction in bacterial community diversity among heroin users compared to the control group. Notably, bacterial composition differences were more pronounced in OrE and PaS than in NaS, with genus-level variations being more significant than those at the phylum level. Differential bacterial taxa were identified across all three distinct skin sites, with the most remarkable differences observed in OrE samples. In both NaS and OrE, the differential bacterial genera between the two groups were predominantly aerobic. In addition, the Random Forest model constructed based on the RFE feature selection strategy demonstrated strong potential of OrE bacteria for distinguishing heroin users from non-users, achieving an optimal classification accuracy of over 94% and AUC values exceeding 0.988.

CONCLUSION: In conclusion, this study highlights the differences in bacterial diversity between heroin users and healthy controls across different skin sites, supporting the potential use of skin bacterial features as forensic identifiers for heroin use. Future research should explore the mechanisms underlying these microbiome alterations and incorporate larger sample sizes to enhance the robustness of findings.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Skin/microbiology
*Microbiota/genetics
Adult
*Bacteria/genetics/classification/isolation & purification
Male
*Heroin Dependence/microbiology
DNA, Bacterial/genetics
Phylogeny
Female
Sequence Analysis, DNA
Middle Aged
Heroin
Young Adult
Skin Microbiome

@article {pmid40739580,
year = {2025},
author = {Song, J and Zhang, W and Wang, D},
title = {Gut microbiome in gastrointestinal neoplasms: from mechanisms to precision therapeutic strategies.},
journal = {Gut pathogens},
volume = {17},
number = {1},
pages = {57},
pmid = {40739580},
issn = {1757-4749},
abstract = {BACKGROUND: The incidence of Gastrointestinal Neoplasms (GI neoplasms) continues to increase globally. Colorectal cancer (CRC), in particular, has emerged as the second leading cause of cancer-related mortality worldwide. Now, Specific pathogenic bacteria, such as Fusobacterium nucleatum (F. nucleatum) and Helicobacter pylori (H. pylori), critically promote tumorigenesis through multiple mechanisms, including the induction of genotoxic damage, host metabolic reprogramming, and remodeling of the tumor immune microenvironment. Notably, a dysbiotic Gut Microbiome (GM) state significantly compromises patient response rates to cancer therapeutics. This review aims to systematically analyze the core molecular mechanism of GM affecting tumor development and explore the precise intervention strategies guided by clinical translation.

METHODS: This systematic review adhered to the PRISMA-2020 guidelines. We conducted a comprehensive literature search in PubMed (2008-2025) using key terms including "Gut Microbiome", "Gastrointestinal Neoplasms", "Fecal Microbiota Transplantation (FMT)", "immunotherapy resistance", "precision-based interventions", and "emerging research frontiers". Preclinical and clinical studies investigating the mechanisms, diagnostic applications, and therapeutic interventions of the GM in GI neoplasms were included.

RESULTS: This review systematically elucidates the tripartite mechanisms by which the GM influences the initiation and progression of GI neoplasms. And we innovatively proposed the "Proinflammation-metabolism-Immune framework (Dysbiosis of the GM jointly leads to the occurrence, development and metastasis of GI neoplasms by driving three interrelated processes: chronic inflammation (Proinflammation), reshaping the Metabolism of the host and TME(Metabolism), and inhibiting or altering the host Immune surveillance (Immune))" To deepen the understanding of host-microbe interactions. Based on this framework, we focused on discussing the therapeutic strategy targeting GM and confirmed its significant impact on the efficacy of anti-cancer treatment. Although these strategies have demonstrated clinical potential, current research is still mainly confined to preclinical models and the early clinical trial stage. To address this, we outline future directions: Integrating emerging technologies like multi-omics and artificial intelligence will enable dynamic monitoring and real-time modulation of microbial activity. This integration aims to establish a novel paradigm for microbiome-based personalized precision medicine.

DISCUSSION: This review systematically clarifies that GM is a key target for optimizing the treatment of GI neoplasms. Future research should integrate multi-omics and AI technologies for dynamic microbial monitoring and modulation, paving the way for microbiome-based precision medicine. Overcoming challenges in standardization and clinical translation is essential.},
}

@article {pmid40739406,
year = {2025},
author = {Alsabri, M and Rath, S and Abo-Elnour, DE and Shaban, NS and Aziz, MM and Aboali, AA and Dafallah, MA and Gamboa, LL},
title = {Efficacy of probiotics in reducing the duration and severity of acute gastroenteritis in children: A meta-analysis of randomized controlled trials.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70172},
pmid = {40739406},
issn = {1536-4801},
support = {//None/ ; },
abstract = {OBJECTIVES: Acute gastroenteritis is a leading global health concern among children, causing significant morbidity and mortality. Despite advances in treatment, effective management remains a challenge. Probiotics aim to restore gut homeostasis by correcting intestinal dysbiosis. This systematic review and meta-analysis aims to assess the efficacy of probiotics in reducing the severity and duration of diarrhea in children with acute gastroenteritis.

METHODS: A comprehensive literature search was conducted across four major databases using the keywords "acute diarrhea," "pediatric," and "probiotics," among others. Only double-arm randomized clinical trials (RCTs) were included, focusing on the efficacy of probiotics in treating pediatric acute diarrhea. Data analysis was performed using Stata 16.0, with a random-effects model applied to account for study variability.

RESULTS: Out of 1470 studies screened, 25 RCTs involving 5170 patients (2552 in the probiotic group and 2618 in the placebo group) met the inclusion criteria. Probiotics significantly reduced the overall duration of diarrhea (mean difference [MD]: -7.76; 95% confidence interval [CI]: -14.60 to -0.91; p = 0.03). Diarrhea frequency was notably reduced on Day 2 (MD: -1.03; 95% CI: -2.06 to 0.00; p = 0.05) and Day 5 (MD: -0.51; 95% CI: -0.83 to -0.18; p = 0.002). Probiotics also significantly reduced the duration of vomiting (MD: -0.19; 95% CI: -0.28 to -0.09; p < 0.01), with a nonsignificant trend in fever reduction.

CONCLUSION: This meta-analysis demonstrates the clinical efficacy of probiotics in reducing the duration of diarrhea and vomiting in children with acute gastroenteritis. Future trials are recommended to further explore the role of specific probiotic strains and combinations to enhance treatment outcomes.},
}

@article {pmid40739286,
year = {2025},
author = {Darriaut, R and Lailheugue, V and Wastin, J and Tran, J and Martins, G and Ballestra, P and Masneuf-Pomarède, I and Ollat, N and Lauvergeat, V},
title = {Rhizobacteria from vineyard and commercial arbuscular mycorrhizal fungi induce synergistic microbiome shifts within grapevine root systems.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27884},
doi = {10.1038/s41598-025-12673-5},
pmid = {40739286},
issn = {2045-2322},
mesh = {*Vitis/microbiology/growth & development ; *Mycorrhizae/physiology ; *Plant Roots/microbiology/growth & development ; Soil Microbiology ; *Microbiota ; Rhizosphere ; Bacteria/isolation & purification/classification ; },
abstract = {The addition of bacteria and arbuscular mycorrhizal fungi (AMF) is a strategy used to protect plants against disease and improve their growth and yield, known as biocontrol and biostimulation, respectively. In viticulture, the plant growth promotion (PGP) potential of bacteria endogenous to vineyard soil has been underexplored. Furthermore, most research about microbial biostimulants focuses on the effect on the plant, but little is known on how their application modify the soil and root microbial ecosystem, which may have an impact on plant growth and resistance. The objectives of this work were (1) to identify bacteria present in vineyard soils with functional PGP traits, (2) to test their PGP activity on young grapevines, in combination with AMF, (3) to assess the impact on the microbial communities and their inferred functions in the rhizosphere and plant roots. Two hundred bacteria were isolated from vineyards and characterized for their biochemical PGP activities. The most efficient were tested in vitro, both singly and in combination, on Lepidium sativum and grapevine plantlets. Two Pseudomonas species particularly increased in vitro growth and were selected for further testing, with and without two Glomus species, on grapevines planted in soil experiencing microbial dysbiosis in a greenhouse setting. After five months of growth, the co-application of PGP rhizobacteria and AMF significantly enhanced root biomass and increased the abundance of potentially beneficial bacterial genera in the roots, compared to untreated conditions and single inoculum treatments. Additionally, the prevalence of Botrytis cinerea, associated with grapevine diseases, decreased in the root endosphere. The combined inoculation of bacteria and AMF resulted in a more complex bacterial network with higher metabolic functionality than single inoculation treatments. This study investigates the effects of adding indigenous rhizobacteria and commercial fungi on the root system microbiota and vine growth in a soil affected by microbial dysbiosis. The results show a remodeling of microbial communities and their functions associated with a beneficial effect on the plant in terms of growth and presence of pathogens. The observed synergistic effect of bacteria and AMF indicates that it is important to consider the combined effects of individuals from synthetic communities applied in the field.},
}

*Vitis/microbiology/growth & development
*Mycorrhizae/physiology
*Plant Roots/microbiology/growth & development
Soil Microbiology
*Microbiota
Rhizosphere
Bacteria/isolation & purification/classification

@article {pmid40739184,
year = {2025},
author = {Tang, HB and Si, YX and Li, HD and Dang, W and Lu, HL},
title = {Intestinal microbial dysbiosis under nitrite stress in juvenile three-keeled pond turtles, Mauremys reevesii.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {466},
doi = {10.1186/s12866-025-04198-8},
pmid = {40739184},
issn = {1471-2180},
support = {32471577//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Turtles/microbiology ; *Nitrites/toxicity ; *Gastrointestinal Microbiome/drug effects ; *Dysbiosis/microbiology/veterinary/chemically induced ; *Bacteria/classification/genetics/drug effects/isolation & purification ; Stress, Physiological ; Intestines/microbiology ; *Water Pollutants, Chemical/toxicity ; Aquaculture ; },
abstract = {BACKGROUND: Nitrite is one of the primary pollutants in high-density aquaculture systems, and may cause various toxic effects (e.g., oxidative damage, metabolic and immune dysregulation, histological inflammation, etc.) on economically important aquaculture species, such as echinoderms, crustaceans and fish. Nitrite can also disrupt the intestinal function and microbiota in some fish and amphibians. However, intestinal physiological and microbial responses of cultured turtles under nitrite stress were rarely explored.

METHOD: Twenty Mauremys reevesii juveniles were exposed to different nitrite levels and fed with a commercial diet. Their intestinal content samples were analyzed for microbial diversity and composition.

RESULTS: Nitrite exposure reduced intestinal microbial diversity, with lower α-diversity values in higher-concentration exposed turtles. It also changed the microbial composition. After exposure, the abundances of Bacteroidetes and Firmicutes decreased, but that of Proteobacteria increased at the phylum level. Similarly, abundances of some potentially beneficial bacterial genera, e.g., Prevotella_1, Christensenellaceae_R-7, Muribaculaceae_ge, were shown to decrease, but those of putatively pathogenic genera, e.g., Halomonas, Nesterenkonia, increased at the genus level. Furtherly, potentially altered metabolic pathways (e.g., biosynthesis of ansamycins and vancomycin group antibiotics) were revealed by functional predictions of intestinal microbiota.

CONCLUSION: This study highlighted intestinal microbial dysbiosis and prevalence of putatively pathogenic bacteria in cultured turtles under nitrite stress. Excessive levels of nitrite would alter the health status of aquatic animals by disrupting their intestinal microbiome.},
}

Animals
*Turtles/microbiology
*Nitrites/toxicity
*Gastrointestinal Microbiome/drug effects
*Dysbiosis/microbiology/veterinary/chemically induced
*Bacteria/classification/genetics/drug effects/isolation & purification
Stress, Physiological
Intestines/microbiology
*Water Pollutants, Chemical/toxicity
Aquaculture

@article {pmid40739108,
year = {2025},
author = {Jana, SK and Bhattacharya, R and Mukherjee, S and Gupta, S and Hui, SP and Chattopadhyay, A and Biswas, SR and Mandal, S},
title = {Phytobacter sp. RSE02 is a rice seed endophytic plant probiotic bacterium with human probiotic features and cholesterol-lowering ability.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {27865},
doi = {10.1038/s41598-025-11212-6},
pmid = {40739108},
issn = {2045-2322},
mesh = {Animals ; *Probiotics/pharmacology ; Humans ; Mice ; *Oryza/microbiology ; *Seeds/microbiology ; *Hypercholesterolemia ; *Cholesterol/metabolism/blood ; Caco-2 Cells ; Zebrafish ; Diet, High-Fat/adverse effects ; *Anticholesteremic Agents/pharmacology ; *Endophytes ; Male ; },
abstract = {Research on seed microbiota has gained significant attention due to its role as a primary inoculum that enhances seedling growth, fitness, and productivity. This study explores the characteristics of the plant-probiotic seed-endophyte Phytobacter sp. RSE02, which demonstrates distinctive beneficial probiotic features in animal models. We examine the safety and probiotic potential of RSE02 in human cell lines, zebrafish, and mice. Notably, RSE02 can utilize cholesterol as its sole carbon source; however, it does not adhere to the Caco-2 cell line or the zebrafish gut. Importantly, RSE02 is non-toxic across all tested models. We further explore its cholesterol-utilizing ability to determine its efficacy in mitigating hypercholesterolemia and body fat deposits in mice when administered orally. In a high-fat diet mouse model, RSE02 significantly lowered blood cholesterol levels and reduced body weight, peritoneal fat deposits, and liver weight. Additionally, the treatment with RSE02 led to decreased levels of total blood protein, MDA, and GSH in high-fat diet mice. Genomic analysis of RSE02 revealed the absence of virulence or toxin-producing genes while identifying gene clusters responsible for synthesizing key vitamins such as folate, biotin, and vitamin B12. The findings highlight the dual functionality of Phytobacter sp. RSE02 in enhancing plant and animal health, challenging traditional notions of probiotics, and offering prospects for innovative solutions in sustainable agriculture and cardiovascular health interventions.},
}

Animals
*Probiotics/pharmacology
Humans
Mice
*Oryza/microbiology
*Seeds/microbiology
*Hypercholesterolemia
*Cholesterol/metabolism/blood
Caco-2 Cells
Zebrafish
Diet, High-Fat/adverse effects
*Anticholesteremic Agents/pharmacology
*Endophytes
Male

@article {pmid40738965,
year = {2025},
author = {Böhm, D and Russ, E and Guchelaar, HJ and Ziemons, J and Penders, J and Smidt, ML and van Best, N and Deenen, MJ},
title = {The role of the gut microbiota in chemotherapy response, efficacy and toxicity: a systematic review.},
journal = {NPJ precision oncology},
volume = {9},
number = {1},
pages = {265},
doi = {10.1038/s41698-025-01034-0},
pmid = {40738965},
issn = {2397-768X},
support = {NWA.1389.20.165//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.165//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.165//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; NWA.1389.20.165//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
abstract = {There is growing evidence for the relationship between the gut microbiota and the effect of chemotherapy. Therefore, this systematic review provides an overview of the current evidence on the effects of the gut microbiota on chemotherapy response, efficacy and toxicity in patients with cancer. PubMed, Web of Science, and EMBASE were searched to collect studies on cancer patients treated with chemotherapy that evaluated tumor response, efficacy, or toxicity, and included microbiome analysis through fecal samples. A total of 22 studies were included. Bacteria associated with better response in lung tumors were, amongst others, a relatively higher abundance of Streptococcus mutans, Enterococcus casseliflavus, and Bacteroides, while bacteria linked to response in gastrointestinal tumors included, among others, higher relative abundances of Lactobacillaceae, Bacteroides fragilis, and Roseburia faecis. Distinctive bacterial taxa were associated with clinical therapy, although causality was not proven. Targeting the gut microbiota during chemotherapy is considered to be a promising approach to enhance the response and to prevent toxicity of chemotherapy.},
}

@article {pmid40738767,
year = {2025},
author = {Cauwenberghs, E and De Boeck, I and Delanghe, L and Van Rillaer, T and Demuyser, T and Spacova, I and Verhulst, S and Van Hoorenbeeck, K and Lebeer, S},
title = {Shallow metagenomic shotgun sequencing improves detection of pathogenic species in cystic fibrosis respiratory samples.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2025.07.011},
pmid = {40738767},
issn = {1873-5010},
abstract = {BACKGROUND: Chronic infection and inflammation of the lungs contribute significantly to disease progression in persons with cystic fibrosis (pwCF). Treatment regimens are largely based on isolating the putative causative pathogen(s) from respiratory samples using basic culturing methods. While this strategy has shown to be highly valuable in the management of CF, the approach is time-consuming and often misses detection of pathogenic microbes that are more difficult to culture, including Mycobacterium spp.

METHODS: In our proof-of-concept study, we evaluated shallow metagenomic shotgun sequencing to detect potential infection-causing pathogens at species level in sputum, oropharyngeal and salivary samples of pwCF (n = 13), and compared it to culture results from the clinic and standard 16S rRNA V4 amplicon sequencing.

RESULTS: Shallow shotgun sequencing improved the detection of pathogenic species in respiratory samples compared to culture methods. In particular, shallow shotgun sequencing could detect pathogenic species associated with CF, specifically Staphylococcus aureus, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Achromobacter xylosoxidans, Haemophilus influenzae and Mycobacterium spp. in sputum, oropharyngeal and/or salivary samples. Notably, Mycobacterium spp. was not detected based on 16S rRNA amplicon sequencing. Moreover, our approach was able to distinguish S. aureus from S. epidermidis and H. influenzae from H. parainfluenzae. This is not possible with 16S amplicon sequencing, but highly valuable in a clinical setting.

CONCLUSIONS: The improved detection of CF pathogens and other critical microbiome members as well as insights into their relative abundance within the community, could provide more knowledge on patient's disease status leading to more personalized medicine and ultimately benefit patient care.},
}

@article {pmid40738263,
year = {2025},
author = {Bostick, JW and Connerly, TJ and Thron, T and Needham, BD and de Castro Fonseca, M and Kaddurah-Daouk, R and Knight, R and Mazmanian, SK},
title = {Genotype and microbiome shape immunity in a sex-specific manner in mouse models of Alzheimer's disease.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.bbi.2025.07.028},
pmid = {40738263},
issn = {1090-2139},
abstract = {Preclinical studies have revealed that the microbiome broadly affects immune responses and deposition and/or clearance of amyloid-beta (Aβ) in mouse models of Alzheimer's disease (AD), but whether, and how, the microbiome shapes central and peripheral immune profiles in AD models remains unknown. We examined adaptive immune responses in two mouse models containing AD-related genetic predispositions (3xTg and 5xFAD) in the presence or absence of the microbiome to determine if it promotes dysregulated immune responses and cognition in AD. T and B cells were altered in central nervous system (CNS)-associated lymph nodes and systemic immune tissues between genetic models and wildtype mice, with earlier signs of heightened immune activity in females. Systemic immune responses were modulated by the microbiome and differed by sex. Further, the absence of a microbiome in germ-free mice resulted in increased cognitive deficits, primarily in males. These data reveal sexual dimorphism in early signs of immune activity and microbiome effects, and highlight how sex and the microbiome shape responses in mouse models of AD.},
}

@article {pmid40731263,
year = {2025},
author = {Wu, J and Jibril, SM and Liu, R and Yang, B and Xu, Y and Wang, L and Wang, Y and Li, C},
title = {Micronutrient deficiency reshapes plant-microbe interaction networks: unraveling microbial community dynamics and functional adaptability in a sterile system.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {979},
pmid = {40731263},
issn = {1471-2229},
abstract = {UNLABELLED: Micronutrient deficiencies critically influence plant development and plant–microbe interactions, yet their role in reshaping microbial community dynamics remains poorly resolved. Here, we hypothesized that micronutrient deprivation alters plant-associated microbiomes through physiological and microbiota-mediated pathways, with cascading effects on plant growth and stress adaptation. Using axenic conditions, we subjected Gypsophila paniculata tissue culture seedlings to copper (Cu), manganese (Mn), molybdenum (Mo), and boron (B) deficiencies. We integrated 16S rRNA/ITS sequencing, functional prediction, and co-occurrence network analysis to unravel microbial responses. Our results demonstrate that Cu deficiency reduced bacterial alpha diversity (25% decline in Shannon index, p < 0.05), while Mn, Mo, and B deficiencies enhanced microbial richness (Chao1 increase: 15–30%). Taxonomic profiling revealed stress-adapted genera (Luteibacter, Lactobacillus, Akkermansia) as key responders, with Pseudomonas abundance decreasing under Cu/B deficiency but increases under Mn/Mo deprivation. Functional shifts included suppressed photosynthesis-associated bacteria under Cu limitation and enriched nitrogen-cycling taxa (e.g., denitrifiers) in Mo-deficient seedlings. Network analysis revealed intensified microbial interactions under Mn/Mo deficiency, with lower microbial interactions under Cu/B deficient treatments. Crucially, we propose a bidirectional "plant–microbe" regulatory axis: Cu deficiency directly impairs plant growth by disrupting photosynthetic symbionts and enriching potential pathogens, while Mn/Mo deprivation enriched endophytic taxa linked to potential nutrient metabolism and stress resilience. This study pioneers a sterile-system approach to decouple micronutrient effects from soil confounders, offering mechanistic insights into microbiome-driven plant adaptation.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12870-025-06966-0.},
}

@article {pmid40741483,
year = {2024},
author = {Hunter, C and Dia, K and Boykins, J and Perry, K and Banerjee, N and Cuffee, J and Armstrong, E and Morgan, G and Banerjee, HN and Banerjee, A and Bhattacharya, S},
title = {An investigation for phylogenetic characterization of human pancreatic cancer microbiome by 16S rDNA sequencing and bioinformatics techniques.},
journal = {Journal of solid tumors},
volume = {14},
number = {1},
pages = {1-9},
pmid = {40741483},
issn = {1925-4067},
abstract = {Pancreatic cancer is a significant public health concern, with increasing incidence rates and limited treatment options. Recent studies have highlighted the role of the human microbiome, particularly the gut microbiota, in the development and progression of this disease. Microbial dysbiosis, characterized by alterations in the composition and function of the gut microbiota, has been implicated in pancreatic carcinogenesis through mechanisms involving chronic inflammation, immune dysregulation, and metabolic disturbances. Researchers have identified specific microbial signatures associated with pancreatic cancer, offering potential biomarkers for early detection and prognostication. By leveraging advanced sequencing and bioinformatics tools, scientists have delineated differences in the gut microbiota between pancreatic cancer patients and healthy individuals, providing insights into disease pathogenesis and potential diagnostic strategies. Moreover, the microbiome holds promise as a therapeutic target in pancreatic cancer treatment. Interventions aimed at modulating the microbiome, such as probiotics, prebiotics, and fecal microbiota transplantation, have demonstrated potential in enhancing the efficacy of existing cancer therapies, including chemotherapy and immunotherapy. These approaches can influence immune responses, alter tumor microenvironments, and sensitize tumors to treatment, offering new avenues for improving patient outcomes and overcoming therapeutic resistance. Overall, understanding the complex interplay between the microbiome and pancreatic cancer is crucial for advancing our knowledge of disease mechanisms and identifying innovative therapeutic strategies. Here we report phylogenetic analysis of the 16S rDNA microbial sequences of the pancreatic cancer mice microbiome and corresponding age matched healthy mice microbiome. We successfully identified differentially abundant microbiota in pancreatic cancer.},
}

@article {pmid40738245,
year = {2025},
author = {Thomova, T and Jedlickova, H and Bohm, J and Holochova, P and Ruzicka, F and Linhartova, PB},
title = {EFFECT OF SYSTEMIC THERAPIES ON SKIN BACTERIOME IN PATIENTS WITH ATOPIC DERMATITIS: A PILOT PROSPECTIVE STUDY.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2025.07.006},
pmid = {40738245},
issn = {1523-1747},
abstract = {Atopic dermatitis is a complex disease that requires treatments addressing skin barrier disruption, inflammation, and microbial imbalance. Here, we aimed to investigate the effects of four different therapies on clinical outcomes and skin bacteriome in patients with atopic dermatitis, namely: Janus kinase inhibitors, dupilumab, cyclosporine A, and topical corticosteroids (intermittently used methylprednisolone aceponate). Samples from 60 patients were collected before treatment and after three and six months and their bacteriome diversity and composition were analyzed. All treatment groups showed significant improvement in disease severity after three months; however, only dupilumab resulted in a marked reduction in serum immunoglobulin E levels and an almost complete depletion of Staphylococcus aureus. The relative abundance of this bacterium correlated with disease severity and remained significantly lower in patients receiving dupilumab compared to those treated with cyclosporine A or topical corticosteroids. While overall bacteriome alpha diversity remained unchanged, the ratio of Staphylococcus to Corynebacterium and Cutibacterium decreased significantly after Janus kinase inhibitors as well as dupilumab treatment but remained stable with cyclosporine A and topical corticosteroids. These results indicate that addressing type 2 inflammation by targeted drugs alters the skin bacteriome towards a healthy balance, while traditional anti-inflammatory treatments have minimal impact on microbial composition.},
}

@article {pmid40738110,
year = {2025},
author = {Fang, H and Anhê, FF and Zada, DK and Barra, NG and E-Lacerda, RR and McAlpin, BT and Wylie, R and Berthiaume, L and Audet-Walsh, É and O'Dwyer, C and Ghorbani, P and Fullerton, MD and Gagnon, C and Tchernof, A and Marette, A and Schertzer, JD},
title = {Gut substrate trap of D-lactate from microbiota improves blood glucose and fatty liver disease in obese mice.},
journal = {Cell metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmet.2025.07.001},
pmid = {40738110},
issn = {1932-7420},
abstract = {L-lactate participates in metabolism, including the Cori cycle, but less is known about D-lactate. We found that circulating D-lactate was higher in humans and mice with obesity. D-lactate increased hepatic glycogen, triglycerides, and blood glucose more than equimolar L-lactate in mice. Stable isotope analyses showed that D-lactate is metabolized in mice and in hepatocytes to pyruvate, TCA intermediates, lipids, and glucose. The gut microbiota is the main source of blood D-lactate. Colonization of mice with a bacterial strain that produced D-lactate elevated blood glucose more than an L-lactate producer. Oral delivery of a biocompatible polymer that traps gut D-lactate, forcing fecal excretion, lowered blood glucose and insulin resistance in obese mice in a polymer length- and dose-dependent manner. This D-lactate trap lowered hepatic inflammation and fibrosis in mice with metabolic dysfunction-associated fatty liver disease (MAFLD)/metabolic dysfunction-associated steatohepatitis (MASH). Therefore, microbial-derived D-lactate contributes to host glucose and lipid metabolism and can be trapped to improve metabolic disease during obesity.},
}

@article {pmid40738103,
year = {2025},
author = {Carter, MM and Demis, D and Perelman, D and St Onge, M and Petlura, C and Cunanan, K and Mathi, K and Maecker, HT and Chow, JM and Robinson, JL and Sabag-Daigle, A and Sonnenburg, ED and Buck, RH and Gardner, CD and Sonnenburg, JL},
title = {A human milk oligosaccharide alters the microbiome, circulating hormones, and metabolites in a randomized controlled trial of older adults.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102256},
doi = {10.1016/j.xcrm.2025.102256},
pmid = {40738103},
issn = {2666-3791},
abstract = {Aging-related immune dysfunction is linked to cancer, atherosclerosis, and neurodegenerative diseases. This 6-week randomized controlled trial evaluated whether 2'-fucosyllactose (2'-FL), a human breast milk oligosaccharide with established benefits in infants and animal models, could improve gut microbiota and immune function in 89 healthy older adults (mean age 67.3 years). While the primary endpoint of cytokine response change was not met, 2'-FL supplementation increased gut Bifidobacterium levels and elevated serum insulin, high-density lipoprotein (HDL) cholesterol, and FGF21 hormone. Bifidobacterium "responders" experienced additional metabolic and proteomic changes and also performed better on a cognitive test of visual memory. Nonresponders were more likely to lack Bifidobacterium in their gut microbiota at the start of the intervention. Multi-omics analysis indicated a systemic response to 2'-FL, which could be detected in blood and urine, showcasing the potential of this prebiotic to provide diverse benefits for healthy aging. This trial was registered at ClinicalTrials.gov (NCT03690999).},
}

@article {pmid40738085,
year = {2025},
author = {Li, J and Wang, D and Zhang, Q and He, X and Liu, P and Ye, L and Ren, H and Zhang, XX},
title = {Prevalence and functional impact of the interactions between lysogenic phages and hosts in activated sludge systems: Insights from large-scale metagenomics and experimental evidence.},
journal = {Water research},
volume = {286},
number = {},
pages = {124270},
doi = {10.1016/j.watres.2025.124270},
pmid = {40738085},
issn = {1879-2448},
abstract = {Bacteriophages are the most common biological entities in the activated sludge (AS) of wastewater treatment plants (WWTPs), playing an important role in maintaining or regulating the microbial community. However, the interactions between bacteria and lysogenic phages in AS systems remain poorly understood. In this study, we reconstructed metagenome-assembled genomes (MAGs) from 43 full-scale WWTPs across five countries and found that over 55 % of MAGs in AS were lysogenic, highlighting the widespread interactions between lysogenic phages and their hosts. Additionally, diverse novel prophages embedded in the lysogenic MAGs formed complex phage-host interactions, as revealed by the phage-host network, underscoring the intricate relationships between prophages and their microbial hosts. Through in-silico approaches and experimental validation, we confirmed the inducibility and activity of the prophages, showing that prophage induction significantly contributes to the lysis of microorganisms involved in the aerobic oxidation of organic matter, as well as nitrogen and phosphorus removal. This work represents a pioneering large-scale genome-centric metagenomic study, coupled with experimental validation, that uncovers the predominance of lysogenic phage-host interactions in AS systems. It advances our understanding of the pivotal role of prophages in shaping the AS microbiome, particularly in influencing the microbial processes responsible for pollutant degradation and nitrogen and phosphorus removal.},
}

@article {pmid40737867,
year = {2025},
author = {Carvalho, LM and da Mota, JCNL and Ribeiro, AA and Carvalho, BG and Martinez, JA and Nicoletti, CF},
title = {Precision nutrition for obesity management: a gut microbiota-centered weight-loss approach.},
journal = {Nutrition (Burbank, Los Angeles County, Calif.)},
volume = {140},
number = {},
pages = {112892},
doi = {10.1016/j.nut.2025.112892},
pmid = {40737867},
issn = {1873-1244},
abstract = {Obesity is a complex and multifactorial condition strongly associated with metabolic burdens and cardiovascular diseases. This review focuses on precision nutrition as a strategy for obesity management, exploring how personalized interventions can modulate the composition and functionality of the gut microbiome to promote weight loss and improve metabolic health. A growing body of evidence suggests that imbalances in gut microbiota composition directly impact lipid metabolism, immune and inflammatory pathways, and appetite regulation mechanisms. Furthermore, the review discusses the relationship between gut microbiota and dietary factors, highlighting how certain types of diets (such as the Mediterranean diet and fiber-rich diets) can promote the production of short-chain fatty acids (SCFAs) and the growth of beneficial bacteria associated with weight regulation and reduced inflammation. While diet is the primary factor modulating the gut microbiota, factors such as genetics and epigenetic characteristics, body composition, maternal nutritional, type of birth delivery, physical activity and even drug use also play significant roles in this modulation. Although the use of precision nutrition approaches still faces challenges, such as cost and variability in individual response, the integration of omics technologies, artificial intelligence, and machine learning appear to offer great potential as tools to identify specific microbial and genetic profiles that allow for the personalization of nutritional interventions. These technologies enable large-scale analysis of dietary, genomic, and microbial factors to create dietary strategies to prevent or treat obesity that meet the specific metabolic needs of each individual. Thus, the application of these tools in clinical settings could transform obesity management, creating data-driven interventions that enhance treatment effectiveness.},
}

@article {pmid40737346,
year = {2025},
author = {Winner, KM and Chanderraj, R and Nuppnau, M and He, Y and Petouhoff, AM and Falkowski, NR and Woods, RJ and Schaub, JA and Heung, M and Ranjan, P and Luth, JE and Bongers, KS and Sjoding, MW and Dickson, RP},
title = {Anti-Anaerobic Antibiotics, Gut Microbiota, and Sepsis-associated Acute Kidney Injury.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1164/rccm.202411-2281OC},
pmid = {40737346},
issn = {1535-4970},
abstract = {RATIONALE: Acute kidney injury (AKI) is a common complication of sepsis. Anti-anaerobic antibiotics, which deplete gut commensal bacteria, are common in the initial management of sepsis. Recent studies have reported an association between anti-anaerobic antibiotics and mortality, but the mechanisms underlying this relationship remain unknown.

OBJECTIVE: To determine whether anti-anaerobic antibiotics and gut microbiome disruption increase patient susceptibility to sepsis-associated AKI.

METHODS: We identified a cohort of patients with sepsis and performed four complementary analyses: 1) comparing AKI incidence among patients who did and did not receive early anti-anaerobic antibiotics, 2-3) two instrumental variable analyses using the 2015-16 piperacillin-tazobactam shortage to determine the effect of anti-anaerobic antibiotics on the onset and resolution of AKI, and 4) a matched case-control study comparing gut microbiota in septic patients who did and did not develop AKI. We then modeled sepsis in genetically-identical but microbially-heterogenous mice and compared creatinine elevation with gut microbiota.

MEASUREMENTS AND MAIN RESULTS: In a retrospective cohort study (N=12,776), early exposure to anti-anaerobic antibiotics was independently associated with a 61% increased risk of sepsis-associated AKI (95% CI-37%-92%). In instrumental variable analyses of AKI onset (N=3,036) and resolution (N=2,177), treatment with anti-anaerobic antibiotics (piperacillin-tazobactam) was associated with an increased hazard of AKI onset (HR-1.65, 95% CI-1.18-2.30) and decreased AKI resolution (HR-0.74, 95% CI-0.61-0.88). In a matched case-control study of gut microbiota in 372 patients with sepsis, increased gut bacterial density and enrichment with Enterobacteriaceae and Lachnospiraceae spp. predicted subsequent AKI onset. In a murine model of sepsis (N=53), creatinine elevation was strongly associated with vendor and gut community composition (P<0.001 for all), with relative abundance of Lachnospiraceae spp. explaining 18% of variation in serum creatinine.

CONCLUSIONS: Anti-anaerobic antibiotics are associated with increased risk of AKI in sepsis, potentially via modulation of the gut microbiome.},
}

@article {pmid40737178,
year = {2025},
author = {Yan, R and Zheng, R and Han, Y and Song, G and Huo, B and Sun, H},
title = {Meta-analysis of gut microbiome reveals patterns of dysbiosis in colorectal cancer patients.},
journal = {Journal of medical microbiology},
volume = {74},
number = {7},
pages = {},
doi = {10.1099/jmm.0.002042},
pmid = {40737178},
issn = {1473-5644},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/complications ; *Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Introduction. Colorectal cancer (CRC) is a malignant tumour in which dysbiosis of the gut microbiome is a contributing factor in the development of cancer. However, the species composition and species-specific changes in the gut microbiome related to CRC still require comprehensive investigation.Hypothesis. There is a significant difference in gut microbiome between CRC patients and healthy individuals.Aim. The microbiome-based association test methods are used for the association between the microbiome and host phenotypes, and linear discriminant analysis effect size (LEfSe) analysis is employed to search for microbial biomarkers associated with CRC.Methodology. We conducted a meta-analysis of microbiome data from multiple cohorts, totalling 1,462 samples and 320 genus-level features. Considering the data obtained under different experimental conditions, we removed the batch effect using conditional quantile regression. Then, we employed the common analysis processes and methods of microbiome data, including microbial diversity analysis, microbiome-based association test analysis and microbial differential abundance analysis.Results. The experimental results showed that there were significant differences in α-diversity between the CRC group and the healthy group, as well as in the overall microbial community (PERMANOVA P-value less than 0.05). LEfSe analysis also demonstrated the genus-level features enriched in the gut of CRC patients and the genus-level features enriched in the gut of healthy individuals. Notably, the batch effect-corrected data exhibit more significant performance than the raw data.Conclusion. Gut microbiome composition is a significant factor associated with the development of CRC. Enterobacter and Fusobacterium enriched in the gut of CRC patients may be CRC-related microbial biomarkers, while Bacteroides and Faecalibacterium enriched in the gut of healthy individuals are core genera of the healthy gut. In addition, batch effects in microbiome data caused by differences in sample handling may lead to false discoveries, especially large-scale microbiome data. These findings could deepen the understanding of the role played by gut microbes in CRC and are expected to provide recommendations for the diagnosis of cancer and the development of new microbial therapies.},
}

Humans
*Colorectal Neoplasms/microbiology/complications
*Dysbiosis/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification

@article {pmid40737134,
year = {2025},
author = {Beck, LC and Sproat, T and Lamb, CA and Filby, A and McDonald, D and Masi, AC and Young, GR and Hambleton, S and Embleton, ND and Stewart, CJ and Berrington, JE},
title = {Temporal characterization of the gut microbiome and metabolome in preterm infants.},
journal = {Microbial genomics},
volume = {11},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001440},
pmid = {40737134},
issn = {2057-5858},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Metabolome ; Infant, Newborn ; *Infant, Premature/metabolism ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Female ; Male ; *Bacteria/genetics/classification/metabolism/isolation & purification ; Metabolomics ; },
abstract = {Preterm infants experience abnormal microbial colonization, which coupled with their vulnerable physiology can increase the risk of disease. Understanding the factors influencing the complex relationship between the temporal development of the gut microbiome and functional metabolites derived from microbe-microbe and microbe-host interaction is therefore critical. In this study, 266 longitudinal stool samples from 66 very preterm infants underwent 16S rRNA gene sequencing to analyse gut microbial structure. To further explore the functional status of these gut members, a subset of these samples underwent stool metabolomics (n=101). Statistically significant associations were found with age for both the gut microbiota (P<0.001) and metabolite profiles (P<0.001). Relationships between the gut microbiome and metabolome showed concordance, with 691 significant correlations after adjustment between the top 10 most abundant bacterial taxa and all 977 identified metabolites. Lactobacillus had the highest number of significant correlations (31%), amongst which was a strong positive correlation with equol sulphate, an oestrogen produced by intestinal bacteria. This study reveals consistent relationships between the diet, gut microbiota composition and metabolic function. The findings provide valuable insights into the microbial and metabolic dynamics of the preterm gut and the relationships underlying gut microbiome structure and function in vulnerable preterm infants. Further research is needed to confirm these findings and explore their implications for infant health and development.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Metabolome
Infant, Newborn
*Infant, Premature/metabolism
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Female
Male
*Bacteria/genetics/classification/metabolism/isolation & purification
Metabolomics

@article {pmid40736894,
year = {2025},
author = {Child, HT and Barber, DG and Maneein, S and Clayton, J and Love, J and Tennant, RK},
title = {Laboratory and In-Field Metagenomics for Environmental Monitoring.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {2955},
number = {},
pages = {71-88},
doi = {10.1007/978-1-0716-4702-8_5},
pmid = {40736894},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Environmental Monitoring/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; Computational Biology/methods ; Gene Library ; },
abstract = {Direct sequencing of DNA from environmental samples (eDNA) is increasingly utilized to provide a census of natural and industrial habitats. The methodology required to perform metagenomics can be divided into three distinct stages: DNA Purification, Library Preparation and Sequencing, and Bioinformatic Analysis. Here we demonstrate an end-to-end protocol that can be utilized either in the field or laboratory for metagenomic analysis of environmental samples utilizing the Oxford Nanopore Technologies MinION sequencing platform.},
}

*Metagenomics/methods
*Environmental Monitoring/methods
High-Throughput Nucleotide Sequencing/methods
Sequence Analysis, DNA/methods
Computational Biology/methods
Gene Library

@article {pmid40736775,
year = {2025},
author = {Yoon, W and Park, Y and Kwon, S and Han, C and Kim, S and Choe, YJ and Lee, JS and Yoo, Y},
title = {Fungal Microbiome Diversity in Urban Forest Decreases Asthma and Allergic Inflammation.},
journal = {Allergy, asthma & immunology research},
volume = {17},
number = {4},
pages = {460-472},
doi = {10.4168/aair.2025.17.4.460},
pmid = {40736775},
issn = {2092-7355},
support = {NRF-2022R1F1A1074688/NRF/National Research Foundation of Korea/Korea ; RQ202101495/KEITI/Korea Environmental Industry and Technology Institute/Korea ; },
abstract = {PURPOSE: Recent attention has been directed toward understanding how exposure to green areas in residential urban environments can impact asthma morbidity. Limited and inconsistent results have explored the link between exposure to greenness and asthma, highlighting the need for further research in this area. We analyzed airborne fungal microbiomes from urban forests and urban centers to better understand how airborne microorganisms affect asthma and allergic inflammatory responses.

METHODS: Fungi were isolated from air samples collected from 25 urban forests and 4 urban centers in Seoul Metropolitan City, and the diversity of fungal microbiomes was analyzed. The number of asthma episodes in each district in Seoul Metropolitan City was examined using data from the National Health Insurance. Allergic inflammatory responses of fungi from the urban forests and urban centers were measured using human mast cells (HMC-1) and an experimental asthma animal model.

RESULTS: Fungal microbiome diversity in urban forests was significantly higher than in urban centers. A significant inverse correlation was observed between the number of urban forests per each district and asthma episodes among residents. Allergic inflammation in the activated HMC-1 cells and lungs of the asthma animal model was significantly suppressed by the fungal strains isolated from the urban forest samples compared to those from the urban centers.

CONCLUSIONS: Fungal microbiome diversity, particularly from the urban forests, plays a role in reducing asthma morbidity and can modulate allergic inflammation. Residential proximity to urban forests was positively associated with current asthma, potentially indicating a role in reducing allergic inflammation through the diversity of the fungal microbial flora. These findings support the increasing public recognition of urban forest as an essential component of health-supportive environments.},
}

@article {pmid40736683,
year = {2025},
author = {Cuerva, MJ and Bartha, I and Escribano, E and Chueca, G and de Aguado, MP and Espinosa-Martos, I and Esteban, S and De La Calle, M and Jimenez, E and Bartha, JL},
title = {Gut microbiome differences after vaginal birth in relation to rupture of membranes at term: a prospective longitudinal cohort study of twins.},
journal = {European journal of pediatrics},
volume = {184},
number = {8},
pages = {511},
pmid = {40736683},
issn = {1432-1076},
support = {PI19/00915//Instituto de Salud Carlos III/ ; },
mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; Pregnancy ; Prospective Studies ; Longitudinal Studies ; Infant, Newborn ; *Pregnancy, Twin ; *Twins ; *Delivery, Obstetric ; *Fetal Membranes, Premature Rupture/microbiology ; Adult ; Feces/microbiology ; Gestational Age ; Male ; Term Birth ; },
abstract = {UNLABELLED: The purpose of this study is to investigate the impact of intrapartum events, such as rupture of membranes and vaginal examinations, on the infant gut microbiome in twins born vaginally. This prospective longitudinal cohort study included pregnant women with twin pregnancies beyond 36 weeks of gestation undergoing vaginal births. Stool samples were collected from newborns on days 4 and 28 for gut microbiome analysis using 16S rDNA sequencing. The infants were followed for at least 1 year. Forty babies were followed in this study. Gestational age at birth was 37.07 (36.75-37.57) weeks. Significant differences were observed between the first and second twins in the number of vaginal examinations (5.50 (4.00-7.25) vs. 1.00 (1.00-1.00), P < 0.001) and the rupture of membranes to birth time (524 (324-734.5) vs. 7.5 (4.5-9.0) minutes, P < 0.001). Bifidobacterium spp. were present in all samples, with differing relative abundance profiles on day 4 and day 28. On day 4, the first twins had over 50% Bifidobacterium spp., while second twins had less than 25%. By day 28, 75% of samples showed similar Bifidobacterium spp. profiles. Microbiome changes over time were more significant in second twins. At the species level, 20-40% of samples exhibited significant Bifidobacterium longum on day 4, higher in first twins compared to second twins.

CONCLUSION:  Differences in the microbiome and its evolution between first and second twins were noted within the first 4 and 28 days of life, influenced by membrane rupture duration and the number of vaginal examinations for the first twin.

WHAT IS KNOWN: •Differences in the gut microbiome have been shown between infants born via cesarean and vaginal birth. •Colonization by maternal microbiota at birth is influenced by multiple perinatal factors.

WHAT IS NEW: •Between twins born vaginally, the gut microbiome differs based on the duration of membrane rupture and the number of vaginal examinations. •This difference is noticeable on day 4 of life but ceases to be noticeable by day 28.},
}

Humans
Female
*Gastrointestinal Microbiome
Pregnancy
Prospective Studies
Longitudinal Studies
Infant, Newborn
*Pregnancy, Twin
*Twins
*Delivery, Obstetric
*Fetal Membranes, Premature Rupture/microbiology
Adult
Feces/microbiology
Gestational Age
Male
Term Birth

@article {pmid40736560,
year = {2025},
author = {Braglia, C and Cutajar, S and Magagnoli, S and Asciano, D and Burgio, G and Di Gioia, D and Baffoni, L and Alberoni, D},
title = {The Ground Beetle Poecilus (Carabidae) Gut Microbiome and Its Functionality.},
journal = {Microbial ecology},
volume = {88},
number = {1},
pages = {83},
doi = {10.1007/s00248-025-02579-0},
pmid = {40736560},
issn = {1432-184X},
support = {ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; ALMAIDEA-2018//University of Bologna/ ; },
mesh = {Animals ; *Coleoptera/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Nosema/isolation & purification/genetics ; High-Throughput Nucleotide Sequencing ; DNA, Bacterial/genetics ; Solanum lycopersicum ; },
abstract = {Ground beetles of the genus Poecilus (Carabidae) play key ecological roles in pest control and soil health. However, their gut microbiome remains largely unexplored despite increasing interest in insect-associated microbiota and its environmental implications. This study used next-generation sequencing and qPCR to characterise the gut microbiome of Poecilus beetles collected from organic and conventional tomato fields. Core microbiota were identified through prevalence-abundance filtering, revealing dominant genera including Gilliamella, Weissella, Enterobacter, and Enterococcus, alongside several low-abundance but consistently present taxa. Notably, Carnobacterium was detected for the first time in an insect host, and Nosema ceranae was identified for the first time in Carabidae, expanding the known host range of this microsporidian pathogen. Functional predictions based on 16S rRNA data and comparative genomic analysis showed enrichment in pathways related to amino acid synthesis, protein degradation, and monosaccharide metabolism. Significant inter-individual variation in microbial diversity and predicted functionality was observed, with lowest diversity and metabolic potential in beetles from conventionally managed fields, potentially indicating dysbiosis and environmental stress. The detection of Nosema and Serratia pathogens in some individuals adds new insights into pathogen dynamics within carabid beetles. Our findings reveal that the gut microbiome of Poecilus may be shaped by environmental factors and agricultural practices, influencing host health and ecological performance. These insights support the use of Poecilus as a bioindicator for soil ecosystem health and highlight the potential of microbiome-based metrics in agroecological monitoring.},
}

Animals
*Coleoptera/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Nosema/isolation & purification/genetics
High-Throughput Nucleotide Sequencing
DNA, Bacterial/genetics
Solanum lycopersicum

@article {pmid40736539,
year = {2025},
author = {Ebadpour, N and Faraji, N and Abavisani, M and Karav, S and Sahebkar, A},
title = {Mechanistic insights into postbiotics as therapeutic agents in type 2 diabetes management.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00210-025-04456-6},
pmid = {40736539},
issn = {1432-1912},
abstract = {The rising prevalence of type 2 diabetes mellitus (T2DM) alongside its associated morbidity and complications underscores the need for adjunctive therapies beyond glycemic control and lifestyle modification. Emerging evidence implicates gut microbiota-derived metabolites in the modulation of host energy homeostasis. One of these metabolites, postbiotics-the bioactive substances created during the fermentation of probiotics-have now become a promising therapeutic. Postbiotics, which contain short-chain fatty acids (SCFAs), exopolysaccharides (EPS), peptidoglycans, bacteriocins, vitamins, and neurotransmitters, have numerous mechanisms that regulate glucometabolism, improve insulin sensitivity, and are able to attenuate systemic inflammation. These compounds are able to regulate insulin receptor signaling and hepatic glucose production by modulating such key metabolic pathways as glycolysis and gluconeogenesis. Based on the previous preclinical and clinical evidence, postbiotic compounds exhibit mechanistic plausibility as adjunct therapies for T2DM. However, due to heterogeneity in patient microbiomes and a lack of standardized formulations that limit current applicability, further investigations are required. Future investigations should focus on dose-finding, long-term safety, and stratification of responders based on microbial and metabolic phenotypes. This review explores the role of postbiotics in T2DM from a mechanistic point of view, highlights their clinical significance in T2DM management, and discusses the next avenue to improve the therapeutic approaches.},
}

@article {pmid40736524,
year = {2025},
author = {Lee, GJ and Kim, SY and Tran, TQT and Lee, J and Nam, KH and Yun, SK and Park, J},
title = {Scalp Bacterial Profile and Antibiotics Susceptibility Pattern in Patients With Primary Cicatricial Alopecia.},
journal = {Annals of dermatology},
volume = {37},
number = {4},
pages = {241-249},
doi = {10.5021/ad.25.022},
pmid = {40736524},
issn = {2005-3894},
support = {2022R1A2C4001257/NRF/National Research Foundation of Korea/Korea ; H12300860//Korea Health Industry Development Institute/Republic of Korea ; },
abstract = {BACKGROUND: Primary cicatricial alopecia (PCA) is a group of disorders causing irreversible hair loss because of hair follicle destruction. Although bacterial colonization is suspected to contribute to PCA pathogenesis, its role remains unclear.

OBJECTIVE: To investigate bacterial colonization patterns and antibiotic susceptibility profiles in patients with PCA compared to those with non-inflammatory scalp conditions.

METHODS: This retrospective study analyzed bacterial cultures from scalp swabs of 161 subjects (68 patients with PCA and 93 controls) at a tertiary hospital between June 2011 and December 2023. Bacterial species and antibiotic resistance rates were evaluated using subgroup analyses of neutrophilic PCA (NCA).

RESULTS: PCA cultures showed a higher prevalence of Staphylococcus aureus (24.3%) and S. lugdunensis (8.1%) than controls, where S. capitis (54.5%) was predominant. Gram-negative bacteria were more frequent in the PCA group (13.5%) than in the control group (9.9%), with Klebsiella spp. (10.9%) being the most prevalent. Resistance rates were significantly higher in PCA for benzylpenicillin, fusidic acid, erythromycin, clindamycin, oxacillin, and telithromycin (p<0.05). Methicillin-resistant S. aureus was identified in 15% of S. aureus isolates from NCA cases. Gram-negative bacteria in PCA also exhibited increased resistance to ampicillin and ampicillin/sulbactam.

CONCLUSION: PCA exhibits distinct bacterial colonization and elevated antibiotic resistance, particularly in the neutrophilic subtypes. Bacterial culture and susceptibility testing are essential for targeted therapies in clinical practice. Further multicenter microbiome analyses with mechanistic studies are needed to elucidate bacterial contributions to PCA pathogenesis.},
}

@article {pmid40736264,
year = {2025},
author = {Mauk, KE and Miramón, P and Lorenz, MC and Lortal, L and Naglik, JR and Hube, B and Bimler, L and Kheradmand, F and Corry, DB},
title = {Commensal colonization of Candida albicans in the mouse gastrointestinal tract is mediated via expression of candidalysin and adhesins.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0056725},
doi = {10.1128/spectrum.00567-25},
pmid = {40736264},
issn = {2165-0497},
abstract = {The ubiquitous fungal pathogen Candida albicans has the potential to either asymptomatically colonize the gastrointestinal (GI) tract or become an invasive pathogen through mechanisms that remain incompletely understood. Here we explored the fungal, host, and environmental factors that influence the ability of C. albicans to colonize the mouse GI tract using a representative clinical strain, CLCA10. After a single gavage challenge (5 × 10[6] CFU C. albicans), specific pathogen-free (SPF) mice remained colonized with C. albicans strain CLCA10, but not other Candida species, for at least 58 days with the fungus confined largely to the gut luminal contents. Colonized mice exhibited no weight loss or other signs of active infection, and CLCA10 did not disrupt the gut microbiome. Moreover, C. albicans colonization with CLCA10 was not substantially affected by the mouse commercial source or the method used to cultivate the fungus prior to gavage. Although some genetically manipulated C. albicans strains were unable to robustly colonize, strain SC5314 also colonized the mouse gut despite having enhanced pathogenicity. C. albicans CLCA10 gut colonization in part depended on the hypha-associated adhesins Als3 and Hwp1 and the peptide toxin candidalysin and could not be eradicated by potent antifungal therapy. Thus, this study concludes that C. albicans gut colonization in the mouse is critically dependent on fungal hyphal factors, the targeting of which could enhance strategies to reduce C. albicans gut colonization and the intractable threat to human health it represents.IMPORTANCECandida albicans is an important human fungal pathogen and a ubiquitous colonizer of the gastrointestinal (GI) tract. However, it is not understood how C. albicans persists within the GI tract and from which it may disperse to cause disease. Here, we demonstrated that multiple strains of C. albicans, including the widely used SC5314 strain, robustly colonize the mouse GI tract for at least 2 months. This colonization caused no disruption to the host tissue or bacterial microbiome and was resistant to clearance by antifungal drugs. Importantly, colonization was mediated by proteins expressed by C. albicans that are known to be involved in fungal virulence and unrelated to experimental conditions. Overall, this work identifies mechanisms by which C. albicans persists in the GI tract, enhancing our knowledge of host-fungal interactions during commensal colonization and potentially how to reduce such colonization.},
}

@article {pmid40736248,
year = {2025},
author = {Huang, X and Wu, R and Liang, X and Yu, Z and Qin, P and Wang, Z and Guo, P and Zeng, Y and Yan, Z and Xiao, W and Ma, Y},
title = {Streptococcus salivarius-derived ilexgenin A alleviates pneumonia through the gut-lung axis.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0073125},
doi = {10.1128/msystems.00731-25},
pmid = {40736248},
issn = {2379-5077},
abstract = {The alteration of gut microbiota during critical illness is associated with adverse clinical outcomes. This connection between intestinal dysbiosis and poor outcomes has prompted the idea that restoring healthy microbial communities could offer a novel approach to life-support treatment for patients with severe pneumonia. In this study, using 16S rRNA sequencing and fecal microbiota transplantation (FMT), we demonstrated that alterations in intestinal microbiota structure during pneumonia exacerbate disease outcomes. A notable feature of these alterations is the reduction in the relative levels of Streptococcus salivarius (S. salivarius). In combination with metabolomics analysis, we found that the administration of S. salivarius increased the level of ilexgenin A (IA) in mice, which enhances the resistance of mice to Pseudomonas aeruginosa (P. aeruginosa)-induced pneumonia. Mechanistically, IA regulates lipopolysaccharide-induced overexpression of macrophage inflammation through Toll-like receptor 4 (TLR4)-mediated NF-κB and MAPK signaling pathways. Our findings reveal the role of the microbial-immune axis in pneumonia, highlighting the potential of S. salivarius and IA in providing promising treatment strategies for pneumonia.IMPORTANCEOne of the major challenges faced by the clinical microbiome research community is to convert the connections between dysbiosis and negative clinical outcomes into rationalized and targeted therapeutic interventions. In the present work, 30 fecal samples from pneumonia and non-pneumonia patients were subjected to FMT and 16S rRNA analysis. The results revealed that a characteristic feature of gut microbiota dysbiosis in pneumonia hosts is the reduction of S. salivarius. Supplementation with S. salivarius can effectively enhance the resistance of mice to P. aeruginosa pneumonia. Moreover, we confirmed the anti-inflammatory effects of IA derived from S. salivarius both in vivo and in vitro. Thus, these findings enhance our understanding of how gut microbiota influences the outcomes of pneumonia and underscore the potential of S. salivarius as a precision microbial therapeutic for combating pneumonia.},
}

@article {pmid40736175,
year = {2025},
author = {Shi, Q and Wei, Z and Pang, J and Qudsi, AI and Wei, M and Zhang, Z and Zhang, Y and Wang, Z and Chen, K and Xu, X and Lu, X and Liang, Q},
title = {Achromobacter in the Conjunctival Sac Microbiota: Potential Association With Acanthamoeba Keratitis Related to Orthokeratology Lenses.},
journal = {Investigative ophthalmology & visual science},
volume = {66},
number = {9},
pages = {71},
doi = {10.1167/iovs.66.9.71},
pmid = {40736175},
issn = {1552-5783},
mesh = {Humans ; Male ; Female ; *Microbiota ; *Acanthamoeba Keratitis/microbiology/etiology ; *Conjunctiva/microbiology ; Adult ; *Achromobacter/isolation & purification/genetics/physiology ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; *Orthokeratologic Procedures/adverse effects/instrumentation ; Acanthamoeba ; *Contact Lenses/adverse effects ; Young Adult ; DNA, Bacterial/genetics/analysis ; Dysbiosis/microbiology ; Middle Aged ; },
abstract = {PURPOSE: Acanthamoeba keratitis (AK) is a severe infection linked to orthokeratology lens use, whereas the involvement of conjunctival microbiota in AK remains poorly understood. This study investigates microbiota dysbiosis in AK pathogenesis to inform microbiota-based interventions.

METHODS: Conjunctival swabs from 14 patients with AK and 10 healthy controls underwent 16S rRNA sequencing. Microbiome analysis compared diversity, taxa, and metabolic pathways. Functional assays quantified Achromobacter-enhanced Acanthamoeba adhesion and migration. Metagenomics and fluorescence in situ hybridization (FISH) with species-specific probes confirmed endosymbiosis.

RESULTS: Patients with AK showed reduced bacterial diversity compared with the healthy controls (P < 0.001) but similar richness. Relative abundance of Achromobacter in the AK group was higher compared to the healthy control group (P < 0.001). Achromobacter dominated microbiota among the AK group, being identified as a key biomarker via the linear discriminant analysis effect size (LEfSe). In vitro, Achromobacter increased Acanthamoeba adhesion (P = 0.007) and the migration area (P < 0.05). Metagenomic analysis and FISH further showed Achromobacter spp. as potential endosymbionts of Acanthamoeba. Kyoto Encyclopedia of Genes and Genomes (KEGG) revealed upregulated phenylalanine, fatty acid, and propanoate metabolism in the AK group (all P < 0.001). MetaCyc highlighted enriched pyruvate fermentation to isobutanol, aerobic respiration I, and L-isoleucine biosynthesis II in the AK group (P < 0.001).

CONCLUSIONS: AK-associated conjunctival dysbiosis features Achromobacter dominance, reduced diversity, and altered metabolism. Achromobacter is associated with enhanced adhesion and migration of Acanthamoeba, indicating a possible symbiotic interaction and its potential as a biomarker and therapeutic target.},
}

Humans
Male
Female
*Microbiota
*Acanthamoeba Keratitis/microbiology/etiology
*Conjunctiva/microbiology
Adult
*Achromobacter/isolation & purification/genetics/physiology
In Situ Hybridization, Fluorescence
RNA, Ribosomal, 16S/genetics
*Orthokeratologic Procedures/adverse effects/instrumentation
Acanthamoeba
*Contact Lenses/adverse effects
Young Adult
DNA, Bacterial/genetics/analysis
Dysbiosis/microbiology
Middle Aged

@article {pmid40736085,
year = {2025},
author = {Hogue, T and Das, P and Reczek, S and Hampton-Marcell, J and Ford, Y and Raval, D and Carroll, I and Cook, MD},
title = {Effect of Acute Gut Butyrate Delivery on Blood Pressure in Black Individuals With Hypertension: A Proof-of-Concept Randomized Controlled Study.},
journal = {Journal of the American Heart Association},
volume = {},
number = {},
pages = {e039759},
doi = {10.1161/JAHA.124.039759},
pmid = {40736085},
issn = {2047-9980},
abstract = {BACKGROUND: Hypertension is a global health crisis linked to increased heart disease and stroke. Black individuals have the greatest burden of hypertension and related diseases. Recent research suggests that the gut microbial production of short-chain fatty acids, such as butyrate, is associated with blood pressure (BP) regulation. We hypothesize that acutely increasing gut butyrate would lead to a significant reduction in BP within a 24-hour period.

METHODS: Ten Black adults with normal BP and 10 with stage 1 hypertension (age and sex-matched) participated in this study. In a crossover experiment, participants with hypertension randomly self-administered a low dose (5 mmol/L) and a high dose (80 mmol/L) butyrate enema 7 days apart. Blood butyrate levels were measured before and 30 minutes post enema, with BP monitored via 24-hour ambulatory devices. Preintervention fecal samples were sequenced via the V4 region of the 16S rRNA gene and microbiome characteristics assessed.

RESULTS: We observed that daytime systolic BP was significantly lower after the 80 mmol/L butyrate enema. There was no significant difference in blood butyrate between controls and the group with hypertension before or after either enema. Microbial diversity did not significantly differ between groups; however, pathways for carbohydrate fermentation were significantly lower with differentially abundance butyrate-producing microbes in participants with hypertension compared with those with normal BP.

CONCLUSIONS: This study suggests that increasing gut butyrate availability can improve BP. The findings bolster the evidence that gut butyrate regulates BP and supports studies needed to test strategies to boost gut butyrate availability for BP control.

REGISTRATION: URL: https://www.clinicaltrials.gov; Unique identifier NCT04415333.},
}

@article {pmid40735951,
year = {2025},
author = {Liang, C and Zhou, Z and Li, P and Xiao, H},
title = {The role of Gram-positive cocci in cancer initiation, progression, and its application in therapy.},
journal = {International journal of cancer},
volume = {},
number = {},
pages = {},
doi = {10.1002/ijc.70063},
pmid = {40735951},
issn = {1097-0215},
support = {81903199//National Natural Science Foundation of China/ ; 81802871//National Natural Science Foundation of China/ ; 2021JJ40373//Natural Science Foundation of Hunan Province/ ; 2023JJ30901//Natural Science Foundation of Hunan Province/ ; S202212652011//Hunan Province College Students' Research Learning and Innovative Experiment Project/ ; },
abstract = {Tumors are one of the most critical health issues and a leading cause of human mortality. Over the past two decades, research on the human microbiome and its functions has revealed microbiota-focused strategies for health and disease. Several studies have demonstrated the presence of intratumoral bacteria in many solid tumors, with distinct microbial compositions across different cancer types. Notably, recent studies have shown that the distribution of Gram-positive cocci differs between tumor patients and healthy individuals. Mechanistic investigations indicate that Gram-positive cocci and their metabolites play roles in inducing genomic instability and mutations, influencing epigenetic modifications, promoting inflammatory responses, regulating host immunity, and activating invasion and metastasis. With the deepening understanding of the mechanisms underlying Gram-positive cocci in tumors, novel anti-tumor therapies have been investigated. In this review, we summarize the distribution of Gram-positive cocci within the human body, explore their complex roles in the initiation, progression, and metastasis of tumors, and overview their potential in early cancer diagnosis, prognostic assessment, and therapeutic strategies. Finally, we discuss the prospects and limitations of targeting or harnessing Gram-positive cocci in cancer.},
}

@article {pmid40735808,
year = {2025},
author = {Maffei, VJ and Bertoni, AG and Wood, AC and Rotter, JI and Crago, O and Chen, YI and Petrosino, JF and Hoffman, KL and Goodarzi, MO and Jensen, ET},
title = {Menopause factors and alterations in gut microbiota and insulin homeostasis: A cross-sectional analysis of the microbiome and insulin longitudinal evaluation study (MILES).},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.16578},
pmid = {40735808},
issn = {1463-1326},
support = {P30-DK063491/DK/NIDDK NIH HHS/United States ; R01-DK109588/DK/NIDDK NIH HHS/United States ; UL1-TR001420/TR/NCATS NIH HHS/United States ; UL1-TR001881/TR/NCATS NIH HHS/United States ; 58-3092-5-001//Agricultural Research Service/ ; },
abstract = {AIM: To assess the risk for impaired insulin homeostasis as a function of menopause-related factors and gut microbiota dysbiosis in non-diabetic, post-menopausal women.

MATERIALS AND METHODS: Baseline data (n = 175 women) from the Microbiome and Insulin Longitudinal Evaluation Study (MILES) were used, including insulin and dysglycaemia indices calculated from a 2-h oral glucose tolerance test, untargeted peripheral metabolomics, targeted peripheral short chain fatty-acid levels and faecal bacterial microbiota surveyed by whole-metagenomic sequencing.

RESULTS: After adjustment for covariates, menopause age <50 years and use of hormone replacement therapy (HRT) were associated with lower Matsuda et al. insulin sensitivity index levels (β = -0.232, confidence interval (CI) = [-0.450, -0.014] and β = -0.275, CI = [-0.444, -0.107], respectively) but not pre-menopausal gynaecologic surgery. Pre-menopausal gynaecologic surgery was significantly associated with faecal microbiota beta diversity driven by a relative increase in diabetogenic Ruminococcus gnavus and Clostridium species and a decrease in protective Alistipes species and Akkermansia muciniphila relative abundances. A reduction in two glycerophospholipids in the plasmalogen class significantly statistically mediated an inverse association between gynaecologic surgery before menopause and insulin sensitivity.

CONCLUSIONS: Menopause age and history of HRT are more strongly associated with insulin resistance than gynaecologic surgery before menopause. However, gynaecologic surgery is associated with shifts in gut microbial composition and plasma metabolite levels with a potential to contribute to future diabetes risk.},
}

@article {pmid40735623,
year = {2025},
author = {Cao, H and Ye, H and Tian, Y and Zhang, J and Xie, Y and Chen, Y and Mo, Q and Huang, S and Tao, Y and Liu, T},
title = {Functional areas shape indoor microbial structure and potential risks in university dormitories.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1604064},
pmid = {40735623},
issn = {1664-302X},
abstract = {Exposure to indoor microbes, particularly potential pathogens, poses significant health risks to occupants. While the indoor microbiome has been extensively studied in various settings, its spatial distribution in university dormitories within hot and humid climates remains poorly understood. In this study, 56 samples were collected from four functional areas (air conditioning, sink, toilet, and floor) in student dormitories in Shenzhen, China. 16S rRNA gene sequencing revealed that the indoor microbial communities were predominantly composed of human-associated genera such as Kocuria, Corynebacterium, and Staphylococcus, with marked compositional differences among functional zones. FAPROTAX predictions further identified 74 potential human pathogens, mainly linked in literature to the risks of nosocomial infections and pneumonia. Notably, a significant portion of these pathogens belongs to the genus Acinetobacter, with elevated concentrations found in air conditioning systems, suggesting their potential as reservoirs of clinically relevant microbes. Environmental variations across room functional areas significantly influenced the composition profile of the microbiome, while the impact of occupant characteristics appeared negligible. Key environmental factors, particularly temperature, played a major role in shaping both microbial and pathogen dynamics. Floor surfaces were identified as key microbial hotspots, exhibiting complex microbial networks that interacted strongly with communities from other functional areas. This underscores the floor's vital role in maintaining connectivity within the indoor environment. The assembly processes of indoor microbial and predicted pathogen communities were both dominated by stochastic processes, with the former primarily governed by dispersal limitations and the latter by ecological drift. Overall, this study provides critical insights into the spatial distribution, environmental drivers, and assembly mechanisms of microbial and pathogen communities in university dormitories, contributing to future assessments of indoor microbial exposure and hygiene management.},
}

@article {pmid40735614,
year = {2025},
author = {Liu, Z and Wang, M and Lei, Y and Xu, K and Fan, L},
title = {Gut microbiota: emerging biomarkers and potential therapeutics for premature ovarian failure.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1606001},
pmid = {40735614},
issn = {1664-302X},
abstract = {Premature ovarian failure is a prevalent gynecological endocrine disorder with an increasing incidence rate each year, impacting women's physical and mental health. The causes of POF are poorly understood, but genetic, immune, iatrogenic, environmental, and psychological factors are key contributors. Clinically, POF manifests as oligomenorrhea, amenorrhea, elevated follicle-stimulating hormone (FSH) levels, and decreased estrogen levels, leading to infertility in women. POF not only impacts reproductive function but also elevates the risk of cardiovascular diseases, osteoporosis, depression, anxiety, cognitive decline, and neurological disorders, thereby adversely affecting women's mental health and quality of life over the long term. The gut microbiota (GM) comprises a vast and complex microbial community within the human gastrointestinal tract. GM dysregulation is closely associated with numerous human diseases, including autoimmune diseases, allergic disorders, cardiovascular diseases, cancers, and metabolic disorders. Studies have shown that GMs play a pivotal role in female reproductive health, participating in the pathogenesis of reproductive endocrine disorders through direct or indirect involvement in sex hormone regulation, stimulation of inflammatory cytokine production, modulation of immune function, metabolic homeostasis, and regulation of neurotransmitter synthesis. Recently, advancements in human microbiology have highlighted the significant interest in the connection between POF and the gut microbiome. Researching the molecular mechanisms by which GMs and their metabolites regulate the occurrence of POF opens up a new direction for studying the pathogenesis of POF. This research aims to identify an efficient, non-invasive, and accurate diagnostic method for clinical diagnosis and treatment of POF, providing novel theoretical insights and precise intervention strategies for the clinical prevention and treatment of POF.},
}

@article {pmid40735439,
year = {2025},
author = {Wang, Q and Han, Y and Pang, L and Zhou, Z and Dai, L},
title = {Gut microbiome remodeling in chronic kidney disease: implications of kidney replacement therapies and therapeutic interventions.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1620247},
pmid = {40735439},
issn = {2296-858X},
abstract = {The escalating global burden of end-stage renal disease (ESRD), driven by aging populations and rising metabolic comorbidities, underscores the urgent need for innovative therapeutic strategies. Emerging evidence highlights the gut microbiome as a pivotal modulator of renal pathophysiology through the gut-kidney axis, with microbial dysbiosis exacerbating gut microbial metabolites (e.g., uremic toxins), systemic inflammation, and multi-organ damage. This narrative review explores the divergent impacts of kidney replacement therapies (KRT)-hemodialysis (HD) and peritoneal dialysis (PD)-on gut microbiota dynamics: HD is associated with Firmicutes and Proteobacteria enrichment, reduced butyrate-producing taxa (e.g., Faecalibacterium, Roseburia), and systemic microbial translocation; whereas PD-driven glucose absorption and iron supplementation foster pathogenic proliferation (e.g., Enterobacteriaceae) and impair short-chain fatty acid (SCFA) metabolism. Current interventions, including probiotics, prebiotics, plant-based diets (PBDs), and fecal microbiota transplantation (FMT), demonstrate potential in mitigating dysbiosis and uremic toxin accumulation. PBDs reduce inflammatory markers (IL-6, CRP) and lower all-cause mortality risk by 24% in PD patients; synbiotics (e.g., Lactobacillus casei + galactooligosaccharides) reduce serum p-cresyl sulfate by 20% in HD patients; and FMT increases levels of short-chain fatty acids (propionate, butyrate) and lowers trimethylamine N-oxide (TMAO) concentrations in streptozotocin-induced diabetic nephropathy mouse models. However, clinical translation remains challenged by small sample sizes, heterogeneous outcomes, and a lack of hard endpoints. Future research must prioritize standardized protocols, personalized microbial profiling, and synergistic integration of dietary and microbiome-targeted therapies. Bridging mechanistic insights with clinical validation will advance precision medicine in ESRD management, offering transformative potential for patients burdened by this therapeutic impasse.},
}

@article {pmid40735239,
year = {2025},
author = {Teglas, T and Radak, Z},
title = {Probiotic supplementation for optimizing athletic performance: current evidence and future perspectives for microbiome-based strategies.},
journal = {Frontiers in nutrition},
volume = {12},
number = {},
pages = {1572687},
pmid = {40735239},
issn = {2296-861X},
abstract = {The association between microbiota and physical activity is currently a key focus in sports performance research, and the effects of probiotics administration on athletes represent a relatively new area of research. While existing research highlights the promising potential of probiotics, our understanding of how they benefit highly active individuals remains incomplete. Nonetheless, it appears that probiotics have a beneficial effect on mental health, cognitive functions, sleep, gastrointestinal, and upper respiratory symptoms in adult humans. Additionally, the probiotic supplementation and their performance effects of different types of exercise are crucial when building a training program. In most cases, probiotic supplementation is effective in two major types of exercise: probiotics show strain and duration-specific effects both on endurance-based and intermittent-exercise associated sport. The supplementation can reduce inflammatory process activity and stress-related factors, e.g., anxiety, depression, in intermittent exercise-associated sports. In endurance-based sports, probiotics enhanced lipid metabolites, including short-chain and polyunsaturated fatty acids, modulated the maximal oxygen capacity, and reduced gastrointestinal symptoms. Exploring the relationship between probiotics, microbiome, and exercise performance could offer valuable insights for optimizing training techniques and strategies for professional athletes.},
}

@article {pmid40734949,
year = {2025},
author = {Miyata, S and Iwamoto, K and Ito, M and Okada, I and Matsuyama, N and Fujimoto, A and Kogo, Y and Nishiwaki, H and Ueyama, J and Ohno, K and Ozaki, N},
title = {Gut Microbiome Composition Changes During Insomnia Treatment with Lemborexant.},
journal = {Nature and science of sleep},
volume = {17},
number = {},
pages = {1709-1726},
pmid = {40734949},
issn = {1179-1608},
abstract = {PURPOSE: Insomnia is a common disorder worldwide. Growing evidence has revealed that the microbiota-gut-brain axis contributes to the regulation of sleep continuity and duration, both directly and indirectly. Although lemborexant is effective in treating insomnia, its effect on the gut microbiota remains unclear. Here, we investigated the relationship between the gut microbiota and hypnotic use in insomnia.

PARTICIPANTS AND METHODS: We enrolled 29 adults with insomnia and performed sleep electroencephalography and stool analyses at baseline and after 4 and 12 weeks of open-label lemborexant treatment. Changes in gut microbiota were analyzed using 16S rRNA sequencing and metabolite analysis was performed to assess short-chain fatty acids (SCFAs).

RESULTS: Beta diversity (Jaccard dissimilarity) and Firmicutes/Bacteroidetes ratio significantly increased after administration of lemborexant for 12 weeks (p < 0.05). Seven genera were significantly different (p < 0.05). Among these, Tannerellaceae Parabacteroides decreased significantly after 12 weeks of lemborexant treatment (p = 0.013), even after correcting for false discovery rates. Akkermansia was strongly negatively correlated with sleep efficiency (r = -0.754, p = 0.0003). Allisonella showed opposite correlations with latency to persistent sleep and sleep efficiency after 12 weeks of lemborexant treatment (r = 0.523, p = 0.018, r = -0.516, p = 0.020, respectively). There were no significant differences in SCFAs during the treatment period.

CONCLUSION: Our findings suggest that prolonged lemborexant treatment in individuals with insomnia may induce notable shifts in gut microbiota composition, including a significant reduction in Parabacteroides underscoring the potential interaction between hypnotic use and gut microbial balance.},
}

@article {pmid40734927,
year = {2025},
author = {Brock, ML and Larkin, AA and Martiny, AC},
title = {Roles of physical disturbance and biome properties in shaping microbial communities within Indian Ocean eddies.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf110},
pmid = {40734927},
issn = {2730-6151},
abstract = {Oceanic eddies create localized upwelling and downwelling systems and are thought to alter microbial communities through environmental selection and dispersal. Though how these eddy-driven mechanisms contribute to microbial outcomes within a broader environmental context is unknown. We proposed that (1) eddies are a large disturbance that exert a significant influence on bacterial community and functional diversity as well as taxonomic and functional composition and (2) that the combined processes of environmental selection and dispersal determine bacterial outcomes within eddies. To address these hypotheses, we integrated bacterial genomics and environmental conditions from 26 eddies across the Indian Ocean. We observed that the biome had a strong, primary influence in shaping all aspects of bacterial communities with eddies playing a weak, secondary role. Additionally, there was minimal evidence of an effect of environmental selection or dispersal in shaping bacterial community diversity. Our observations highlight the variability in bacterial responses within and between eddy types and emphasize the importance of understanding eddy characteristics and broader biome attributes in interpreting bacterial responses.},
}

@article {pmid40734913,
year = {2025},
author = {Huang, B and An, H and Gui, M and Qiu, Y and Xu, W and Chen, L and Li, Q and Yao, S and Lin, S and Khrustaleva, TA and Wang, R and Lin, J},
title = {Qingjie Fuzheng Granule prevents colitis-associated colorectal cancer by inhibiting abnormal activation of NOD2/NF-κB signaling pathway mediated by gut microbiota disorder.},
journal = {Chinese herbal medicines},
volume = {17},
number = {3},
pages = {500-512},
pmid = {40734913},
issn = {2589-3610},
abstract = {OBJECTIVE: This study investigates the efficacy and mechanisms of Qingjie Fuzheng Granules (QFG) in inhibiting colitis-associated colorectal cancer (CAC) development via RNA sequencing (RNA-seq) and 16S ribosomal RNA (rRNA) correlation analysis.

METHODS: CAC was induced in BALB/c mice using azoxymethane (AOM) and dextran sulfate sodium (DSS), and QFG was administered orally to the treatment group. The effects of QFG on CAC were evaluated using disease index, histology, and serum T-cell ratios. RNA-seq and 16S rRNA analysis assessed the transcriptome and microbiome change. Key pharmacodynamic pathways were identified by integrating these data and confirmed via Western blotting and immunofluorescence. The link between microbiota and CAC-related markers was explored using linear discriminant analysis effect size and Spearman correlation analysis.

RESULTS: Long-term treatment with QFG prevented AOM/DSS-induced CAC formation, reduced levels of interleukin (IL)-1β, tumor necrosis factor-alpha (TNF-α), IL-6, and interferon γ (IFN-γ), and increased CD3[+] and CD4[+]/CD8[+] T cells ratio, without causing hepatic or renal toxicity. A 16S rRNA analysis revealed that QFG rebalanced the Firmicutes/Bacteroidetes ratio and mitigated AOM/DSS-induced microbiota disturbances. Transcriptomics and Western blotting analysis identified the nucleotide-binding oligomerization domain-containing protein 2 (NOD2)/nuclear factor kappa-B (NF-κB) pathway as key for QFG's treatment against CAC. Furthermore, QFG decreased the abundance of Bacilli, Bacillales, Staphylococcaceae, Staphylococcus, Lactobacillales, Aerococcus, Alloprevotella, and Akkermansia, while increasing Clostridiales, Lachnospiraceae, Lachnospiraceae_NK4A136_group, Ruminococcaceae, and Muribaculaceae, which were highly correlated with CAC-related markers or NOD2/NF-κB pathway.

CONCLUSION: By mapping the relationships between CAC, immune responses, microbiota, and key pathways, this study clarifies the mechanism of QFG in inhibiting CAC, highlighting its potential for clinical use as preventive therapy.},
}

@article {pmid40734872,
year = {2025},
author = {Espinoza Urzua, I and Vidal Vidal, MI and Vega Solano, M and Bedoya Jaramillo, JE and de la Cruz Donis, GG and Valverde, AR},
title = {Skin Barrier Dysfunction in Chronic Dermatoses: From Pathophysiology to Emerging Therapeutic Strategies.},
journal = {Cureus},
volume = {17},
number = {6},
pages = {e86937},
pmid = {40734872},
issn = {2168-8184},
abstract = {Multidisciplinary investigations have confirmed the critical role of skin barrier dysfunction in the pathogenesis of various chronic dermatoses. However, the heterogeneity in disease presentation, inconsistent assessment criteria, and the lack of therapeutic standardization across clinical settings limit the universal applicability of current findings. The aim of this review is to evaluate the pathophysiological basis of skin barrier impairment in chronic skin conditions, assess the clinical efficacy of emerging therapeutic strategies, and address ongoing challenges and future directions. Skin barrier dysfunction underlies the initiation and perpetuation of inflammatory dermatoses such as atopic dermatitis, psoriasis, and ichthyoses, where disruptions in lipid composition, filaggrin deficiency, and impaired tight junction integrity contribute to disease chronicity. Innovative treatment approaches, including targeted biologics, barrier-repair emollients, and microbiome-modulating therapies, have demonstrated encouraging results in restoring barrier function and controlling inflammation. Emerging nanotechnological and gene-editing therapies offer promising frontiers for precision skin repair. Evidence supports that restoration of the barrier not only alleviates clinical symptoms but also reduces flare frequency and improves patient quality of life. Despite progress, therapeutic implementation faces obstacles such as patient adherence variability, lack of long-term outcome data, and inter-study inconsistencies in outcome measures. This review emphasizes the necessity of standardized protocols and unified barrier assessment tools to enhance clinical translation. The growing body of evidence advocates for integrating barrier-targeted strategies as a central element in the management of chronic dermatoses, thereby improving disease control and overall dermatological care.},
}

@article {pmid40734533,
year = {2025},
author = {Lin, X and Liu, J and Yang, W and Zhang, H and Zhang, L},
title = {Autoinducer-2 Mediated Quorum Sensing Stabilizes Cooperation between Pantoea alhagi and Synthetic Bacterial Communities, Synergistically Improving Drought Tolerance in Wheat.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c04543},
pmid = {40734533},
issn = {1520-5118},
abstract = {Quorum sensing (QS), a mechanism of intercellular communication, plays a crucial role in regulating the microbial community behavior and function. However, the role of the LuxS/AI-2 system in shaping wheat rhizosphere microbiota remains unclear. In this study, the luxS gene, encoding autoinducer-2 (AI-2) synthase, was deleted from Pantoea alhagi LTYR-11Z, resulting in significantly impaired biofilm formation, AI-2 production, and root colonization. A 4-week pot experiment revealed that the wild-type (WT) strain markedly altered the composition, diversity, and structure of rhizosphere bacterial communities compared to the control and ΔluxS mutant groups. Notably, AI-2-mediated microbial recruitment enhanced hybrid biofilm formation. Potting drought experiments showed that AI-2 signaling induced SynCom collaboration, allowing WT+SynCom to activate antioxidant enzymes more efficiently and increase the total N/P concentration in wheat, alleviating drought stress damage. These findings demonstrate that QS acts as a selective force in the rhizosphere microbiome assembly, enriching plant-beneficial species and improving stress resilience.},
}

@article {pmid40733607,
year = {2025},
author = {Shrivastav, K and Nasser, H and Ikeda, T and Nema, V},
title = {Possible Crosstalk and Alterations in Gut Bacteriome and Virome in HIV-1 Infection and the Associated Comorbidities Related to Metabolic Disorder.},
journal = {Viruses},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/v17070990},
pmid = {40733607},
issn = {1999-4915},
mesh = {Humans ; *Gastrointestinal Microbiome ; *HIV Infections/virology/complications/microbiology ; *Virome ; *Metabolic Diseases/virology/microbiology ; Dysbiosis ; HIV-1 ; Comorbidity ; },
abstract = {Improved antiretroviral therapy (ART) has significantly increased the life expectancy of people living with HIV (PLWH). At the same time, other complications like metabolic syndrome (MetS) are coming up as new challenges to handle. This review aims to explore the emerging evidence of gut microbiome and virome alterations in human immunodeficiency virus-1 (HIV-1) infection and associated metabolic disorders, such as type-2 diabetes (T2DM) and cardiovascular disease (CVD), with a focus on their interplay, contribution to immune dysfunction, and potential as therapeutic targets. We conducted a comprehensive review of the current literature on gut bacteriome and virome changes in HIV-1-infected individuals and those with metabolic comorbidities emphasizing their complex interplay and potential as biomarkers or therapeutic targets. HIV-1 infection disrupts gut microbial homeostasis, promoting bacterial translocation, systemic inflammation, and metabolic dysregulation. Similarly, metabolic disorders are marked by reduced beneficial short-chain fatty acid-producing bacteria and an increase in pro-inflammatory taxa. Alterations in the gut virome, particularly involving bacteriophages, may exacerbate bacterial dysbiosis and immune dysfunction. Conversely, some viral populations have been associated with immune restoration post-ART. These findings point toward a dynamic and bidirectional relationship between the gut virome, bacteriome, and host immunity. Targeted interventions such as microbiome modulation and fecal virome transplantation (FVT) offer promising avenues for restoring gut homeostasis and improving long-term outcomes in PLWH.},
}

Humans
*Gastrointestinal Microbiome
*HIV Infections/virology/complications/microbiology
*Virome
*Metabolic Diseases/virology/microbiology
Dysbiosis
HIV-1
Comorbidity

@article {pmid40733597,
year = {2025},
author = {Mohamed, E and Van Cleemput, J and Şahin, B and Van den Broeck, W and Boyen, F and Nauwynck, H},
title = {Streptococcus equi subsp. zooepidemicus Supernatant Containing Streptolysin S Alters the Equine Nasal and Vaginal Mucosa, Modulating Equine Herpesvirus 1, 3 and 4 Infections.},
journal = {Viruses},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/v17070980},
pmid = {40733597},
issn = {1999-4915},
support = {2021060310//Egyptian Ministry of Higher Education and Scientific Research/ ; GOA013-17//Ghent University/ ; G035920N//Research Foundation - Flanders/ ; },
mesh = {Animals ; Horses ; Female ; *Vagina/virology/microbiology ; *Herpesviridae Infections/veterinary/virology ; Herpesvirus 1, Equid/physiology/drug effects ; *Streptolysins/pharmacology/metabolism ; *Horse Diseases/virology/microbiology ; Virus Replication/drug effects ; *Nasal Mucosa/virology/drug effects/microbiology ; Mucous Membrane/virology/drug effects ; *Bacterial Proteins/pharmacology/metabolism ; Herpesvirus 4, Equid/physiology/drug effects ; *Streptococcus ; *Streptococcus equi ; Varicellovirus/physiology/drug effects ; },
abstract = {The equine respiratory and reproductive tract microbiomes are complex and subject to constant fluctuations. Among the microbial inhabitants, Streptococcus equi subsp. zooepidemicus (SEZ) is recognized as the dominant bacterium. It is an opportunistic pathogen that may occasionally lead to various types of infections. A key virulence factor of SEZ is the streptolysin S (SLS) toxin, which is responsible for the characteristic β-hemolysis on blood agar and tissue damage. Viruses and bacteria may interact and aggravate lesions and disease. This study aimed to evaluate the impact of an SLS-containing supernatant from SEZ on the nasal and vaginal mucosa and the subsequent replication of equine herpesviruses. The SLS-containing supernatant was prepared, and three 10-fold dilutions (optical density "OD" 10[-2], 10[-3], 10[-4]) were applied to equine nasal and vaginal explants. Untreated and EGTA-treated explants served as controls. Epithelial integrity was assessed by measuring the thickness and intercellular spaces. Nasal explants were inoculated with EHV-1 and EHV-4, while vaginal explants received EHV-1 and EHV-3. Viral replication was estimated via immunofluorescence staining and confocal microscopy. SLS-containing supernatants 10[-2] and 10[-3] compromised epithelial integrity. Viral replication increased in explants treated with SLS 10[-3], demonstrating SLS's damaging effects on the epithelium, facilitating equine herpesvirus replication.},
}

Animals
Horses
Female
*Vagina/virology/microbiology
*Herpesviridae Infections/veterinary/virology
Herpesvirus 1, Equid/physiology/drug effects
*Streptolysins/pharmacology/metabolism
*Horse Diseases/virology/microbiology
Virus Replication/drug effects
*Nasal Mucosa/virology/drug effects/microbiology
Mucous Membrane/virology/drug effects
*Bacterial Proteins/pharmacology/metabolism
Herpesvirus 4, Equid/physiology/drug effects
*Streptococcus
*Streptococcus equi
Varicellovirus/physiology/drug effects

@article {pmid40733588,
year = {2025},
author = {Banicod, RJS and Javaid, A and Tabassum, N and Jo, DM and Hassan, MI and Kim, YM and Khan, F},
title = {Marine Bacteriophages as Next-Generation Therapeutics: Insights into Antimicrobial Potential and Application.},
journal = {Viruses},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/v17070971},
pmid = {40733588},
issn = {1999-4915},
support = {RS-2023-00241461//Basic Science Research Program through the National Research Foundation of Korea (NRF), funded by the Ministry of Education/ ; RS-2025-02373103//the Korea Institute of Marine Science & Technology Promotion (KIMST), funded by the Ministry of Oceans and Fisheries/ ; },
mesh = {*Bacteriophages/physiology/classification/genetics ; *Phage Therapy/methods ; Humans ; *Seawater/virology/microbiology ; Bacteria/virology/drug effects ; *Bacterial Infections/therapy ; *Aquatic Organisms/virology ; Animals ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Microbial infections are an escalating global health threat, driven by the alarming rise of antimicrobial resistance (AMR), which has made many conventional antibiotics increasingly ineffective and threatens to reverse decades of medical progress. The rapid emergence and spread of multidrug-resistant bacteria have severely limited treatment options, resulting in increased morbidity, mortality, and healthcare burden worldwide. In response to these challenges, phage therapy is regaining interest as a promising alternative. Bacteriophages, the most abundant biological entities, have remarkable specificity toward their bacterial hosts, enabling them to selectively eliminate pathogenic strains. Phage therapy presents several advantages over conventional antibiotics, which include minimal disruption to the microbiome and a slower rate of resistance development. Among the various sources of phages, the marine environment remains one of the least explored. Given their adaptation to saline conditions, high pressure, and variable nutrient levels, marine bacteriophages mostly exhibit enhanced environmental stability, broader host ranges, and distinct infection mechanisms, thus making them highly promising for therapeutic purposes. This review explores the growing therapeutic potential of marine bacteriophages by examining their ecological diversity, biological characteristics, infection dynamics, and practical applications in microbial disease control. It also deals with emerging strategies such as phage-antibiotic synergy, genetic engineering, and the use of phage-derived enzymes, alongside several challenges that must be addressed to enable clinical translation and regulatory approval. Advancing our understanding and application of marine phages presents a promising path in the global fight against AMR and the development of next-generation antimicrobial therapies.},
}

*Bacteriophages/physiology/classification/genetics
*Phage Therapy/methods
Humans
*Seawater/virology/microbiology
Bacteria/virology/drug effects
*Bacterial Infections/therapy
*Aquatic Organisms/virology
Animals
Anti-Bacterial Agents/pharmacology

@article {pmid40733475,
year = {2025},
author = {Cho, DY and Jang, MY and Lee, HY and Jeong, JB and Kim, DH and Bang, DY and Kim, HR and Jeong, YR and Haque, MA and Lee, JH and Cho, KM},
title = {Rhizospheric Bacterial Distribution Influencing the Accumulation of Isoflavones, Phenolics, Flavonoids, and Antioxidant Activity in Soybean Roots Within Hydroponic System.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
doi = {10.3390/plants14142238},
pmid = {40733475},
issn = {2223-7747},
support = {Glocal University 30 Project//Gyeongsang National University/ ; },
abstract = {This study investigates how root color in soybeans affects isoflavone composition, rhizosphere bacterial diversity, total phenolics, total flavonoids, and antioxidant activity under a hydroponic cultivation system. Notably, soybean-brown roots (SBRs) accumulated significantly higher contents of isoflavones, exhibiting approximately a 14.9-fold increase in total glycosides (141.75 to 2121.59 µg/g), 7.3-fold increase in total malonyl-β-glycosides (127.52 to 930.45 µg/g), 2.8-fold increase in total aglycones (1825.90 to 5145.21 µg/g), and 3.9-fold increase in total isoflavones (2095.16 to 8197.26 µg/g) than soybean-white roots (SWRs). Isolated rhizosphere bacteria profiling revealed γ-Proteobacteria as the predominant class in both root types, constituting 77.6% and 73.9% of the bacterial community in SWRs and SBRs, respectively. However, SBRs supported a more diverse bacterial ecosystem, harboring thirteen genera compared to only eight genera in SWRs. Enhanced total phenolics, total flavonoids, and radical scavenging activity were also associated with the SBRs. These findings shed light on the dynamic interplay between root traits, bacterial interactions, and secondary metabolite biosynthesis in hydroponically grown soybeans. This work not only advances our understanding of plant root-microbiome-metabolite relationships but also offers a novel approach to exploring the potential of enhancing secondary metabolites in soybean plants through precision cultivation.},
}

@article {pmid40733440,
year = {2025},
author = {Tuxun, A and Xiang, Y and Shao, Y and Son, JE and Yamada, M and Yamada, S and Tagawa, K and Baiyin, B and Yang, Q},
title = {Soilless Cultivation: Precise Nutrient Provision and Growth Environment Regulation Under Different Substrates.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
doi = {10.3390/plants14142203},
pmid = {40733440},
issn = {2223-7747},
support = {2025YFHZ0183//Science and Technology Department of Sichuan Province/ ; ASTIP-CAAS//Chinese Academy of Agricultural Sciences/ ; 2023YFF1001500//Ministry of Science and Technology of the People's Republic of China/ ; No. S2024001//Ministry of Agriculture and Rural Affairs/ ; },
abstract = {Soilless cultivation technology is a key means of overcoming traditional agricultural resource limits, providing an important path to efficient and sustainable modern agriculture by precisely regulating crop rhizospheric environments. This paper systematically reviews the technical system of soilless cultivation, nutrient solution management strategies, the interaction mechanism of rhizosphere microorganisms, and future development directions, aiming to reveal its technical advantages and innovation potential. This review shows that solid and non-solid substrate cultivation improves resource utilization efficiency and yield, but substrate sustainability and technical cost need urgent attention. The dynamic regulation of nutrient solution and intelligent management can significantly enhance nutrient absorption efficiency. Rhizosphere microorganisms directly regulate crop health through nitrogen fixation, phosphorus solubilization, and pathogen antagonism. However, the community structure and functional stability of rhizosphere microorganisms in organic systems are prone to imbalance, requiring targeted optimization via synthetic biology methods. Future research should focus on the development of environmentally friendly substrates, the construction of intelligent environmental control systems, and microbiome engineering to promote the expansion of soilless cultivation towards low-carbon, precise, and spatial directions. This paper systematically references the theoretical improvements and practical innovations in soilless cultivation technology, facilitating its large-scale application in food security, ecological protection, and resource recycling.},
}

@article {pmid40733434,
year = {2025},
author = {Ma, S and Tang, T and Du, C and Yang, Z and Gan, B},
title = {Engineering Oilseed Microbiome Synergy for Saline Alkaline Soil Restoration.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
doi = {10.3390/plants14142197},
pmid = {40733434},
issn = {2223-7747},
support = {2024ZW005//Open Project of Key Laboratory of Crop Quality improvement of Anhui Province/ ; },
abstract = {Soil salinization poses a critical threat to global agriculture, necessitating innovative strategies for sustainable remediation. This review synthesizes advances in leveraging plant-microbe interactions to remediate saline-alkali soils, focusing on oilseed crops-Brassica napus, Glycine max, Arachis hypogaea, Helianthus annuus, and Sesamum indicum-as keystone species for ecosystem restoration. These crops exhibit unique adaptive strategies, including root architectural plasticity and exudate-mediated recruitment of stress-resilient microbiomes (Proteobacteria, Actinobacteria, and Ascomycota), which collectively stabilize soil structure and enhance nutrient cycling, ion homeostasis, and soil aggregation to mitigate soil salinity and alkalinity. Emerging technologies further amplify these natural synergies: nanomaterials optimize nutrient delivery and microbial colonization, while artificial intelligence (AI) models predict optimal plant growth-promoting rhizobacteria (PGPR) combinations and simulate remediation outcomes. This integration establishes a roadmap for precision microbiome engineering, offering scalable strategies to restore soil health and ensure food security in saline-alkali ecosystems.},
}

@article {pmid40733380,
year = {2025},
author = {Appenroth, KJ and Oláh, V and Ishizawa, H and Sree, KS},
title = {7th International Conference on Duckweed Research and Applications: Depicting an Era of Advancing Research Translation Toward Practical Applications.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {14},
pages = {},
doi = {10.3390/plants14142143},
pmid = {40733380},
issn = {2223-7747},
abstract = {Duckweeds are aquatic monocotyledonous plants known to be the smallest and the fastest growing angiosperms. The 7th International Conference on Duckweed Research and Applications (7th ICDRA) was held in Bangkok, Thailand, from 12th to 16th November 2024. The conference drew young and experienced scientists from across the world who presented their research in varied fields. This conference report presents the highlights of the advancements in the field of duckweed research and application in the sections: Genomics and Cell Biology; Diversity, Ecology, Evolution; Physiology, Reproduction, Metabolomics; Microbiome and Interactions; Applications; and Future Outlook. The next conference, 8th ICDRA, will be held in Naples, Italy, in 2026.},
}

@article {pmid40733023,
year = {2025},
author = {Ramisetty, BS and Singh, R and Hu, M and Wang, MZ},
title = {A Parent-Metabolite Middle-Out PBPK Model for Genistein and Its Glucuronide Metabolite in Rats: Integrating Liver and Enteric Metabolism with Hepatobiliary and Enteroluminal Transport to Assess Glucuronide Recycling.},
journal = {Pharmaceutics},
volume = {17},
number = {7},
pages = {},
doi = {10.3390/pharmaceutics17070814},
pmid = {40733023},
issn = {1999-4923},
support = {2504120//University of Kansas General Research Fund/ ; P30GM145499/GM/NIGMS NIH HHS/United States ; R01AI139198//National Institute of Allergy and Infectious Diseases (NIAID)/ ; K12TR004522/TR/NCATS NIH HHS/United States ; },
abstract = {Background: Glucuronide recycling in the gut and liver profoundly affects the systemic and/or local exposure of drugs and their glucuronide metabolites, impacting both clinical efficacy and toxicity. This recycling also alters drug exposure in the colon, making it critical to establish local concentration for drugs targeting colon (e.g., drugs for colon cancer and inflammatory bowel disease). Methods: In this study, a parent-metabolite middle-out physiologically based pharmacokinetic (PBPK) model was built for genistein and its glucuronide metabolite to estimate the systemic and local exposure of the glucuronide and its corresponding aglycone in rats by incorporating UDP-glucuronosyltransferase (UGT)-mediated metabolism and transporter-dependent glucuronide disposition in the liver and intestine, as well as gut microbial-mediated deglucuronidation that enables the recycling of the parent compound. Results: This parent-metabolite middle-out rat PBPK model utilized in vitro-to-in vivo extrapolated (IVIVE) metabolic and transporter clearance values based on in vitro kinetic parameters from surrogate species, the rat tissue abundance of relevant proteins, and saturable Michaelis-Menten mechanisms. Inter-system extrapolation factors (ISEFs) were used to account for transporter protein abundance differences between in vitro systems and tissues and between rats and surrogate species. Model performance was evaluated at multiple dose levels for genistein and its glucuronide. Model sensitivity analyses demonstrated the impact of key parameters on the plasma concentrations and local exposure of genistein and its glucuronide. Our model was applied to simulate the quantitative impact of glucuronide recycling on the pharmacokinetic profiles in both plasma and colonocytes. Conclusions: Our study underlines the importance of glucuronide recycling in determining local drug concentrations in the intestine and provides a preliminary modeling tool to assess the influence of transporter-mediated drug-drug interactions on glucuronide recycling and local drug exposure, which are often misrepresented by systemic plasma concentrations.},
}

@article {pmid40732998,
year = {2025},
author = {Herrera, M and Byerley, LO},
title = {Dietary Nitrogen and Its Role in the Gut Microbiome and Inflammatory Bowel Disease: A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
doi = {10.3390/nu17142373},
pmid = {40732998},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/microbiology/metabolism ; *Nitrogen/metabolism ; *Diet ; Dysbiosis ; Animals ; },
abstract = {In recent years, gut microbiota has emerged as a critical regulator of gastrointestinal health and disease, with its role in inflammatory bowel disease (IBD)-including Crohn's disease and ulcerative colitis-being particularly significant. Among the many factors influencing the gut microbiota, dietary components such as fibers, fats, and polyphenols have received substantial attention. However, nitrogen-containing compounds, such as amino acids, nitrates, urea, and even nucleic acids, such as purines, remain underexplored despite their integral role in shaping microbial ecology, host metabolism, and immune responses. Some of these compounds are metabolized by gut bacteria into bioactive molecules such as short-chain fatty acids, ammonia, and nitric oxide, which exert diverse effects on mucosal integrity and inflammation. IBD pathophysiology is characterized by chronic inflammation, microbial dysbiosis, and compromised epithelial barriers. Nitrogen metabolism contributes significantly to these processes by influencing microbial composition, metabolite production, and host immune pathways. The breakdown of various nitrogen-containing compounds in the body leads to the production of byproducts, such as ammonia and hydrogen sulfide, which have been implicated in mucosal damage and immune dysregulation. At the same time, nitrogen-derived molecules, such as short-chain fatty acids and nitric oxide, exhibit protective effects, underscoring the dual role of dietary nitrogen in health and disease. This narrative review highlights the complex interactions between dietary nitrogen sources, gut microbiota, and IBD pathogenesis. We summarize the mechanisms by which nitrogen compounds influence microbial dynamics, identify their contributions to inflammation and barrier dysfunction, and explore their therapeutic potential. Multidisciplinary approaches integrating clinical, metabolomic, and microbiome research are essential to unravel the full scope of nitrogen's role in gut health and identify novel therapeutic targets.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Inflammatory Bowel Diseases/microbiology/metabolism
*Nitrogen/metabolism
*Diet
Dysbiosis
Animals

@article {pmid40732988,
year = {2025},
author = {Gong, H and Zuo, H and Wu, K and Gao, X and Lan, Y and Zhao, L},
title = {Systemic and Retinal Protective Effects of Butyrate in Early Type 2 Diabetes via Gut Microbiota-Lipid Metabolism Interaction.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
doi = {10.3390/nu17142363},
pmid = {40732988},
issn = {2072-6643},
support = {20241050//Project of Administration of Traditional Chinese Medicine of Guangdong Province of China/ ; 32270621 and 81721003//National Natural Science Foundation of China/ ; 2021A1515110235 and 2024A1515010651//Guangdong Basic and Applied Basic Research Foundation/ ; 2020YFA0112701//National Key Research and Development Program of China/ ; 2023A03J0186//Guangzhou City-University Joint Foundation/ ; 2023B1212060018//The Science and Technology Planning Project of Guangdong Province/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Lipid Metabolism/drug effects ; Mice, Inbred C57BL ; *Diabetes Mellitus, Type 2/drug therapy/complications/microbiology/metabolism ; *Diabetic Retinopathy/prevention & control/etiology ; Mice ; Male ; *Retina/drug effects ; Diabetes Mellitus, Experimental/drug therapy ; Diet, High-Fat/adverse effects ; *Butyric Acid/pharmacology ; *Butyrates/pharmacology ; Blood Glucose/metabolism ; Dysbiosis ; },
abstract = {Background: Early neurovascular unit (NVU) impairment plays a critical role in the pathogenesis of diabetic retinopathy (DR), often preceding clinically detectable changes. Butyrate, a short-chain fatty acid (SCFA) derived from gut microbiota, has shown promising metabolic and anti-inflammatory effects. Methods: This study investigated the protective potential of oral butyrate supplementation in a mouse model of early type 2 diabetes mellitus (T2DM) induced by a high-fat diet and streptozotocin. Mice (C57BL/6J) received sodium butyrate (5 g/L in drinking water) for 12 weeks. Retinal NVU integrity was assessed using widefield swept-source optical coherence tomography angiography (WF SS-OCTA), alongside evaluations of systemic glucose and lipid metabolism, hepatic steatosis, visual function, and gut microbiota composition via 16S rRNA sequencing. Results: Butyrate supplementation significantly reduced body weight, fasting glucose, serum cholesterol, and hepatic lipid accumulation. Microbiome analysis demonstrated a partial reversal of gut dysbiosis, characterized by increased SCFA-producing taxa (Ruminococcaceae, Oscillibacter, Lachnospiraceae) and decreased pro-inflammatory, lipid-metabolism-related genera (Rikenella, Ileibacterium). KEGG pathway analysis further revealed enrichment in microbial lipid metabolism functions (fabG, ABC.CD.A, and transketolase). Retinal vascular and neurodegenerative alterations-including reduced vessel density and retinal thinning-were markedly attenuated by butyrate, as revealed by WF SS-OCTA. OKN testing indicated partial improvement in visual function, despite unchanged ERG amplitudes. Conclusions: Butyrate supplementation mitigates early NVU damage in the diabetic retina by improving glucose and lipid metabolism and partially restoring gut microbial balance. This study also underscores the utility of WF SS-OCTA as a powerful noninvasive tool for detecting early neurovascular changes in DR.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Lipid Metabolism/drug effects
Mice, Inbred C57BL
*Diabetes Mellitus, Type 2/drug therapy/complications/microbiology/metabolism
*Diabetic Retinopathy/prevention & control/etiology
Mice
Male
*Retina/drug effects
Diabetes Mellitus, Experimental/drug therapy
Diet, High-Fat/adverse effects
*Butyric Acid/pharmacology
*Butyrates/pharmacology
Blood Glucose/metabolism
Dysbiosis

@article {pmid40732952,
year = {2025},
author = {Li, H and Gu, L},
title = {Effect of Dealcoholized Muscadine Wine on the Development of Spontaneous Colitis and Gut Microbiome in IL-10[-/-] Mice.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
doi = {10.3390/nu17142327},
pmid = {40732952},
issn = {2072-6643},
support = {2019-67017-29366//National Institute of Food and Agriculture/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Interleukin-10/genetics/deficiency ; *Colitis/prevention & control/microbiology ; Male ; Mice, Inbred C57BL ; *Wine/analysis ; Mice ; Mice, Knockout ; Colon/metabolism/microbiology ; Cytokines/metabolism/blood ; Disease Models, Animal ; Anthocyanins/pharmacology/analysis ; Polyphenols/pharmacology ; Ellagic Acid/analysis ; },
abstract = {Background/Objectives: Colitis is a chronic condition affecting millions worldwide. Purple muscadine wine polyphenols have a unique composition and possible disease-preventive properties. This study aims to determine how dealcoholized muscadine wine (DMW) affects the development of colitis and gut microbiome in IL-10[-/-] mice, compared to wild types (WT). Methods: Six-week-old male IL-10[-/-] and WT C57BL/6 mice were fed either a DMW-supplemented diet (4.8% v/w) or a control diet based on AIN-93M for 154 days. Colitis severity was evaluated by disease activity, intestinal permeability, gene expression of cytokines and tight junction proteins in the colon, and inflammatory cytokines in the serum. Fecal samples were collected for gut microbiome profiling via 16S rRNA gene sequencing. Results: DMW contained predominantly anthocyanins and a significant amount of ellagic acid. IL-10[-/-] mice developed mild colitis as indicated by the disease activity index. DMW × gene interactions decreased intestinal permeability, colonic mRNA levels of IL-1β, and serum TNF-α in the IL-10[-/-] mice. DMW suppressed the colonic mRNA levels of IL-6, enhanced the gene expression of ZO-1, but did not influence the mRNA level of TNF-α or occludin. While DMW did not alter α-diversity of the gut microbiome, it significantly influenced β-diversity in the WT mice. DMW significantly reduced the relative abundances of Akkermansia in the IL-10[-/-] and WT mice. DMW and DMW×gene interaction decreased the relative abundance of Parasutterella only in IL-10[-/-] mice. Conclusions: These results suggested that polyphenols from DMW interacted with genes to moderately alleviate the development of colitis in IL-10[-/-] mice and could be a useful dietary strategy for IBD prevention.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Interleukin-10/genetics/deficiency
*Colitis/prevention & control/microbiology
Male
Mice, Inbred C57BL
*Wine/analysis
Mice
Mice, Knockout
Colon/metabolism/microbiology
Cytokines/metabolism/blood
Disease Models, Animal
Anthocyanins/pharmacology/analysis
Polyphenols/pharmacology
Ellagic Acid/analysis

@article {pmid40732945,
year = {2025},
author = {Kulecka, M and Jaworski, P and Zeber-Lubecka, N and Bałabas, A and Piątkowska, M and Czarnowski, P and Frączek, B and Tarnowski, W and Mikula, M and Ostrowski, J},
title = {The Gut Microbiome Obesity Index: A New Analytical Tool in the Metagenomics Workflow for the Evaluation of Gut Dysbiosis in Obese Humans.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
doi = {10.3390/nu17142320},
pmid = {40732945},
issn = {2072-6643},
support = {2018/29/B/NZ7/00809//National Science Center/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Obesity/microbiology ; Male ; Female ; *Metagenomics/methods ; Adult ; Feces/microbiology ; *Dysbiosis/microbiology/diagnosis ; Body Mass Index ; Middle Aged ; Bacteria/classification/genetics ; Workflow ; Case-Control Studies ; Young Adult ; },
abstract = {Background/Objectives: Our aim was to create a new method for analyzing metagenomics data, named the gut microbiome obesity index, using a set of taxa/biological functions that correlated with BMI. Methods: A total of 109 obese patients (73 women and 36 men, median BMI 43.0 kg/m[2]), 87 healthy control (HC) individuals (39 females and 48 males, median BMI 22.7 kg/m[2]), and 109 esports players (five females and 104 males, median BMI 23.0 kg/m[2]) were included in the study. To conduct metagenomic and metabolomic analyses, DNA and selected metabolites were isolated from fecal samples and used for whole-genome shotgun sequencing and gas chromatography/mass spectrometry, respectively. Results: Compared with HCs and esports players, obese patients with a BMI > 40 kg/m[2] had a significantly higher alpha diversity, as analyzed by the Shannon index, and significant dissimilarities in beta diversity. Both richness and diversity measures were correlated with BMI. Compared with HCs and esports players, 12 differential bacteria were found in the overall obesity group and 42 were found in those with a BMI > 40 kg/m[2]. Most of the altered species belonged to the Lachnospiraceae family. When the logarithmic relationship of the sums of the bacteria correlated with BMI was calculated to establish a taxonomic health index, it better differentiated between the obesity groups than a standard analytical pipeline; however, it did not differentiate between the HC and the BMI < 35 kg/m[2] obesity group. Therefore, we created a functional index based on BMI-associated biological pathways, which differentiated between all obesity groups. Conclusions: Of the obesity indices used to distinguish between healthy and obese microbiota analyzed in this study, a function-based index was more useful than a taxonomy-based index. We believe that gut microbiome indexes could be useful as part of routine metagenomics evaluations. However, an index developed in one geographical area might not be applicable to individuals in a different region and, therefore, further studies should develop separate indices for different populations or geographical regions rather than relying on a single index.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Obesity/microbiology
Male
Female
*Metagenomics/methods
Adult
Feces/microbiology
*Dysbiosis/microbiology/diagnosis
Body Mass Index
Middle Aged
Bacteria/classification/genetics
Workflow
Case-Control Studies
Young Adult

@article {pmid40732941,
year = {2025},
author = {Marano, G and Rossi, S and Sfratta, G and Acanfora, M and Anesini, MB and Traversi, G and Lisci, FM and Rinaldi, L and Pola, R and Gasbarrini, A and Sani, G and Gaetani, E and Mazza, M},
title = {Gut Microbiota in Women with Eating Disorders: A New Frontier in Pathophysiology and Treatment.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
doi = {10.3390/nu17142316},
pmid = {40732941},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; *Feeding and Eating Disorders/microbiology/physiopathology/therapy ; Dysbiosis/microbiology/physiopathology/therapy ; Probiotics/therapeutic use ; Prebiotics/administration & dosage ; Fecal Microbiota Transplantation ; },
abstract = {Emerging evidence highlights the critical role of the gut microbiota in the development and progression of eating disorders (EDs), particularly in women, who are more frequently affected by these conditions. Women with anorexia nervosa, bulimia nervosa, and binge eating disorder exhibit distinct alterations in gut microbiota composition compared to healthy controls. These alterations, collectively termed dysbiosis, involve reduced microbial diversity and shifts in key bacterial populations responsible for regulating metabolism, inflammation, and gut-brain signaling. The gut microbiota is known to influence appetite regulation, mood, and stress responses-factors closely implicated in the pathogenesis of EDs. In women, hormonal fluctuations related to menstruation, pregnancy, and menopause may further modulate gut microbial profiles, potentially compounding vulnerabilities to disordered eating. Moreover, the restrictive eating patterns, purging behaviors, and altered dietary intake often observed in women with EDs exacerbate microbial imbalances, contributing to intestinal permeability, low-grade inflammation, and disturbances in neurotransmitter production. This evolving understanding suggests that microbiota-targeted therapies, such as probiotics, prebiotics, dietary modulation, and fecal microbiota transplantation (FMT), could complement conventional psychological and pharmacological treatments in women with EDs. Furthermore, precision nutrition and personalized microbiome-based interventions tailored to an individual's microbial and metabolic profile offer promising avenues for improving treatment efficacy, even though these approaches remain exploratory and their clinical applicability has yet to be fully validated. Future research should focus on sex-specific microbial signatures, causal mechanisms, and microbiota-based interventions to enhance personalized treatment for women struggling with eating disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
*Feeding and Eating Disorders/microbiology/physiopathology/therapy
Dysbiosis/microbiology/physiopathology/therapy
Probiotics/therapeutic use
Prebiotics/administration & dosage
Fecal Microbiota Transplantation

@article {pmid40732915,
year = {2025},
author = {Deshmukh, H and Mendóza, R and Santos, JM and Sivaprakasam, S and Elmassry, MM and Miranda, JM and Pham, PQ and Driver, Z and Bender, M and Dufour, JM and Shen, CL},
title = {Effect of Peanut Shell Extract and Luteolin on Gut Microbiota and High-Fat Diet-Induced Sequelae of the Inflammatory Continuum in a Metabolic Syndrome-like Murine Model.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
doi = {10.3390/nu17142290},
pmid = {40732915},
issn = {2072-6643},
support = {Internal fund//Texas Tech University Health Sciences Center/ ; Foundation//The CH Foundation/ ; B1-0028//Robert A. Welch Foundation/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; Male ; *Metabolic Syndrome/drug therapy/microbiology ; *Plant Extracts/pharmacology ; Mice ; Disease Models, Animal ; *Luteolin/pharmacology ; *Inflammation/drug therapy/etiology ; *Arachis/chemistry ; Oxidative Stress/drug effects ; Kidney/drug effects/metabolism ; Mice, Inbred C57BL ; Insulin Resistance ; Dysbiosis ; },
abstract = {Background: Metabolic syndrome (MetS) is characterized by chronic inflammation, oxidative stress, and mitochondrial dysfunction. MetS is associated with increased intestinal permeability and dysbiosis. The objective of this study was to investigate the effects of peanut shell extract (PSE) and luteolin (LUT) on the kidneys, colon, and ileum in a MetS-like murine model. Methods: Thirty-six male Slc6a14[y/-] mice were divided into four groups: low-fat diet (LFD), high-fat diet (HFD), HFD + 200 mg PSE/kg BW (PSE, p.o.), and HFD + 100 mg LUT/kg BW (LUT, p.o.) for 4 months. Outcome measures included glucose homeostasis, intestinal permeability, gut microbiome composition, and mRNA gene expression of mitochondrial homeostasis and inflammation/oxidative stress in the kidneys, colon, and ileum. Results: HFD resulted in glucose dysregulation with hyperglycemia and insulin resistance. PSE and LUT improved insulin tolerance and beta-cell function. PSE and LUT mitigated HFD-increased serum lipopolysaccharide-binding protein concentration. Perturbations in the gut microbiome were associated with HFD, and PSE or LUT reversed some of these changes. Specifically, Phocaeicola vulgatus was depleted by HFD and reverted by PSE or LUT. Relative to the LFD group, the HFD group (1) upregulated mitochondrial fusion (MFN1, MFN2, OPA1), mitophagy (TLR4, PINK1, LC3B), and inflammation (NFκB, TNFα, IL6), and (2) downregulated mitochondrial fission (FIS1, DRP1), biosynthesis (PGC1α, NRF1, NRF2, TFAM), electron transport chain (complex I), and antioxidant enzyme (SOD1) in the kidneys, colon, and ileum. Conclusions: PSE and LUT reversed such HFD-induced changes in the aforementioned gene expression levels.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Diet, High-Fat/adverse effects
Male
*Metabolic Syndrome/drug therapy/microbiology
*Plant Extracts/pharmacology
Mice
Disease Models, Animal
*Luteolin/pharmacology
*Inflammation/drug therapy/etiology
*Arachis/chemistry
Oxidative Stress/drug effects
Kidney/drug effects/metabolism
Mice, Inbred C57BL
Insulin Resistance
Dysbiosis

@article {pmid40732911,
year = {2025},
author = {Senarath, RMUS and Oikari, LE and Bharadwaj, P and Jayasena, V and Martins, RN and Fernando, WMADB},
title = {The Therapeutic Potential of Butyrate and Lauric Acid in Modulating Glial and Neuronal Activity in Alzheimer's Disease.},
journal = {Nutrients},
volume = {17},
number = {14},
pages = {},
doi = {10.3390/nu17142286},
pmid = {40732911},
issn = {2072-6643},
mesh = {*Alzheimer Disease/drug therapy/metabolism ; Humans ; *Neuroglia/drug effects/metabolism ; *Neurons/drug effects/metabolism ; Animals ; *Lauric Acids/pharmacology/therapeutic use ; *Butyrates/pharmacology/therapeutic use ; Neuroprotective Agents/pharmacology ; Oxidative Stress/drug effects ; Amyloid beta-Peptides/metabolism ; },
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder marked by amyloid-β plaque accumulation, tau tangles, and extensive neuroinflammation. Neuroinflammation, driven by glial cells like microglia and astrocytes, plays a critical role in AD progression. Initially, these cells provide protective functions, such as debris clearance and neurotrophic support. However, as AD progresses, chronic activation of these cells exacerbates inflammation, contributing to synaptic dysfunction, neuronal loss, and cognitive decline. Microglia release pro-inflammatory cytokines and reactive oxygen species (ROS), while astrocytes undergo reactive astrogliosis, further impairing neuronal health. This maladaptive response from glial cells significantly accelerates disease pathology. Current AD treatments primarily aim at symptomatic relief, with limited success in disease modification. While amyloid-targeting therapies like Aducanumab and Lecanemab show some promise, their efficacy remains limited. In this context, natural compounds have gained attention for their potential to modulate neuroinflammation and promote neuroprotection. Among these, butyrate and lauric acid are particularly notable. Butyrate, produced by a healthy gut microbiome, acts as a histone deacetylase (HDAC) inhibitor, reducing pro-inflammatory cytokines and supporting neuronal health. Lauric acid, on the other hand, enhances mitochondrial function, reduces oxidative stress, and modulates inflammatory pathways, thereby supporting glial and neuronal health. Both compounds have been shown to decrease amyloid-β deposition, reduce neuroinflammation, and promote neuroprotection in AD models. This review explores the mechanisms through which butyrate and lauric acid modulate glial and neuronal activity, highlighting their potential as therapeutic agents for mitigating neuroinflammation and slowing AD progression.},
}

*Alzheimer Disease/drug therapy/metabolism
Humans
*Neuroglia/drug effects/metabolism
*Neurons/drug effects/metabolism
Animals
*Lauric Acids/pharmacology/therapeutic use
*Butyrates/pharmacology/therapeutic use
Neuroprotective Agents/pharmacology
Oxidative Stress/drug effects
Amyloid beta-Peptides/metabolism