@article {pmid41166910,
year = {2025},
author = {Mao, YQ and Song, SY and Xu, Q and Zang, TT and Wang, LS and Shen, L and Ge, JB},
title = {Dietary fiber pectin supplement attenuates atherosclerosis through promoting Akkermansia-related acetic acid metabolism.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {148},
number = {},
pages = {157373},
doi = {10.1016/j.phymed.2025.157373},
pmid = {41166910},
issn = {1618-095X},
abstract = {BACKGROUND: Atherosclerosis (AS) is a vascular disease caused by chronic inflammation, and its incidence and mortality rates are still on the rise. Recent studies have revealed that the structure and function of gut microbiota are significantly correlated with the occurrence and development of AS, providing novel insights into the mechanisms of cardiovascular diseases. Multiple studies have clarified that dietary fiber pectin alter the structure and function of the gut microbiota. At the same time, it has also been found that dietary fiber pectin can alleviate atherosclerosis.

PURPOSE: The aim is to explore whether the gut microbiota mediates the anti-atherosclerotic effects of pectin, and to elucidate the underlying molecular mechanisms.

METHODS: We established an atherosclerosis model in ApoE[-/-] mice by feeding a high-fat and high-cholesterol diet. We combined antibiotic depleted gut microbiota and transplanted the fecal microbiota to demonstrate that the effect of dietary fiber pectin in alleviating atherosclerosis depends on the gut microbiota. Subsequently, we explored the material basis of the anti-atherosclerotic effect mediated by the gut microbiota through 16 s rRNA sequencing, targeted metabolomics detection, and bacterial culture methods.

RESULTS: We conducted experiments on ApoE[-/-] mice to deplete gut microbiota with antibiotics and then perform fecal microbiota transplantation, and the results showed that supplementation with dietary fiber pectin attenuates atherosclerosis in a gut microbiome dependent manner. Through 16S rRNA sequencing, we found that supplementation of dietary fiber pectin could enrich the abundance of Akkermansia (Akk). In addition, administration with Akk was sufficient to prevent the progression of atherosclerosis in a diet-induced model. Mechanistically, Akk produced acetic acid through fermentation of pectin, and then inhibited the proliferation of Lactococcus lactis (l.lactis) in arterial plaque to exert anti-atherosclerosis effect.

CONCLUSIONS: Our results suggest that dietary fiber pectin enriches the abundance of Akk, which inhibits the proliferation of the atherosclerotic-related bacterium, l.lactis, by producing acetic acid in ApoE[-/-] mice. Our findings first reveal that pectin prevents the development of atherosclerosis through gut microbiota. Additionally, based on the theory of the "gut-vessel" axis, we demonstrate that dietary fiber pectin enriched the abundance of Akk in the gut, which elevated the level of acetic acid and further inhibit the abundance of l. within atherosclerotic plaques. These data provide new clues and strategies for the clinical treatment of atherosclerosis.},
}

@article {pmid41166850,
year = {2025},
author = {Qiu, X and Wang, Y and Yu, T and Li, D and Tan, Y and Huo, Z and Yan, X},
title = {Vibrio parahaemolyticus infection in Manila clams (Ruditapes philippinarum): A case study of microbiome perturbation.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {57},
number = {},
pages = {101655},
doi = {10.1016/j.cbd.2025.101655},
pmid = {41166850},
issn = {1878-0407},
abstract = {The homeostasis of gill microbiota is essential for marine organisms' health, yet pathogen invasion disrupt this balance, impacting host physiology. As the farming density rises in the shellfish aquaculture industry, the Manila clam (Ruditapes philippinarum) has shown increased susceptibility to pathogens, with Vibrio parahaemolyticus representing a major economic threat. This study delves into the effects of V. parahaemolyticus on the gill microbiota of R. philippinarum (Ruditapes philippinarum) through histopathological analysis and 16S rRNA gene sequencing. At 72 hour post-infection (hpi), severe inflammatory reactions and gill damage were observed, accompanied by significant changes in microbial community structure. At 72 hpi, microbial diversity significantly shifted, with a decrease in Bacteroidota and Vibrionimonas, while Bradyrhizobium became dominant. By 96 hpi, Acidobacteriota and Chloroflexi increased, suggesting organic matter accumulation and redox alterations. LEfSe analysis identified Enterobacteriaceae, Streptomycetaceae, and Streptomycetales as biomarker taxa at 72 hpi. Metabolic pathways with increased abundance relative to 0 hpi included nucleoside metabolism, replication, and purine metabolism, while glycine, serine, and threonine metabolism showed a decreased abundance. Our findings illustrate that V. parahaemolyticus infection disrupts microbial and metabolic homeostasis in the gill of R. philippinarum, eliciting substantial inflammatory damage and offering insights into molecular mechanisms underlying clam susceptibility and potential mortality.},
}

@article {pmid41166814,
year = {2025},
author = {Li, H and Song, K and Zhang, X and Wang, S and Yang, L},
title = {Integrated untargeted and targeted metabolomics and microbiome profiling reveal the effects of storage duration on the flavor quality of Rizhao Jinhua white tea.},
journal = {Food chemistry},
volume = {496},
number = {Pt 2},
pages = {146811},
doi = {10.1016/j.foodchem.2025.146811},
pmid = {41166814},
issn = {1873-7072},
abstract = {The post-fermented tea develops enhanced quality attributes with prolonged storage. In this study, we explored the dynamic changes in sensory characteristics, untargeted and targeted metabolomics, and microbial communities of Rizhao Jinhua white tea (WFB) across different storage years. Storage process reduced bitterness and astringency, while improving overall mellowness. Levels of total polyphenols, amino acids, theaflavins, and thearubigins declined significantly, whereas theabrownin reached its peak at year 5. Among 118 identified differential metabolites, flavonoids exhibited the most pronounced variations. Further targeted quantification of flavonoids revealed catechin, epicatechin, epigallocatechin, quercitrin, and isorhamnetin as key flavor determinants. This was related to glycosylation, hydrogenation, hydroxylation, and hydrolysis reactions occurring during storage. Dominant microbial genera such as Aspergillus and Pseudomonas continuously promoted flavonoids transformations during storage. The outcomes of this research support better approaches to flavor quality optimization in stored Jinhua white tea.},
}

@article {pmid41166334,
year = {2025},
author = {Yang, S and Wang, K and Hu, Y and Zhang, L and Zhang, C and Liu, Y and Li, Z and Jiang, L and Han, Y and Naowarojna, N and Wei, Y and Zhang, Y},
title = {Studies on Two Convergently Evolved Cysteate Synthases in Sulfonolipid Biosynthesis.},
journal = {ACS chemical biology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acschembio.5c00142},
pmid = {41166334},
issn = {1554-8937},
abstract = {Capnine-like sulfonolipids are sulfonate-containing analogs of sphingolipids found in many Bacteroidetes bacteria, where they govern essential functions such as gliding motility, outer membrane polysaccharide assembly, and antibiotic susceptibility. In gut-associated anaerobic Bacteroidetes, these sulfonolipids also modulate host-microbe interactions. In aerobic bacteria, the capnine precursor cysteate is produced by a pyridoxal phosphate (PLP)-dependent cysteate synthase (CapA1), a close homologue of cystathionine β-synthase (CBS). By contrast, the mechanism of cysteate production in anaerobic Bacteroidetes bacteria has not been biochemically studied. Herein, we report the characterizations of archaeal cysteate synthase homologue from the anaerobic bacteria Alistipes finegoldii (AfCapA2). Biochemical assays confirm its ability to catalyze the conversion of O-phosphoserine (OPS) to cysteate. Crystal structures of AfCapA2 in complex with PLP and OPS-PLP identify essential catalytic residues and reveal a structural similarity to threonine synthase, unlike CapA1, which is more similar to CBS. Comparative analysis of CapA1 and this nonorthologous CapA2, including structural differences, catalytic versatility, and phylogenetic distribution across Bacteroidetes, suggests convergent evolution of cysteate synthase activity. Our work clarifies the details of sulfonolipid synthesis in anaerobic bacteria and the biochemical origins of this structurally distinctive lipid in the gut microbiome.},
}

@article {pmid41166319,
year = {2025},
author = {Sanam, M and Hossain, CFTZ and Hyder, TB and Tarannum, R and Oishi, JF and Rahman, KMM and Islam, SBU and Bulbul, N and Sultana Jime, J and Shishir, MA and Safa, A and Fakruddin, M},
title = {Bridging two worlds: Host Microbiota crosstalk in health and dysregulation.},
journal = {Innate immunity},
volume = {31},
number = {},
pages = {17534259251392993},
doi = {10.1177/17534259251392993},
pmid = {41166319},
issn = {1753-4267},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; *Dysbiosis/immunology ; Signal Transduction ; Immunity, Innate ; Homeostasis ; *Host Microbial Interactions/immunology ; Adaptive Immunity ; Bile Acids and Salts/metabolism ; Fatty Acids, Volatile/metabolism ; },
abstract = {The gut microbiota plays a crucial role in various physiological functions, such as the production of microbial compounds and maintaining homeostatic equilibrium by complex host-microbial interactions. However, any shift in the constitution and diversity of the microbiota or abnormal interaction with the host can prompt the development of dysbiosis. This review thus illustrates that microbial metabolites, notably short-chain fatty acids, tryptophan metabolites, bile acids, and polyamines, exert significant regulatory effects on innate and adaptive immunological processes, immune response and intestinal barrier integrity through specific receptor activation, involving TLRs, NODs, GPCRs, nuclear receptors, and Wnt/β-catenin. It further explores the disruption of host signalling pathways, caused by dysbiosis, promoting the transcription of specific genes and activating pro-inflammatory pathways. Consequently, this suggests that microbiota acts beyond general health, eventually contributing to gastrointestinal, metabolic, and neurological disorders. Lastly, this review highlights therapeutic approaches required to restore balance and uphold physiological balance.},
}

Humans
*Gastrointestinal Microbiome/immunology
Animals
*Dysbiosis/immunology
Signal Transduction
Immunity, Innate
Homeostasis
*Host Microbial Interactions/immunology
Adaptive Immunity
Bile Acids and Salts/metabolism
Fatty Acids, Volatile/metabolism

@article {pmid41166306,
year = {2025},
author = {Zhang, ZF and Huang, JE and Phurbu, D and Qu, ZS and Liu, F and Cai, L},
title = {A deep metagenomic atlas of Qinghai-Xizang Plateau lakes reveals their microbial diversity and salinity adaptation mechanisms.},
journal = {Cell reports},
volume = {44},
number = {11},
pages = {116483},
doi = {10.1016/j.celrep.2025.116483},
pmid = {41166306},
issn = {2211-1247},
abstract = {The Qinghai-Xizang Plateau (QXP), harboring the planet's highest density of plateau lakes, offers an exceptional biogeographic environment for studying extremophilic microbial communities and their adaptation to salinity. Through deep metagenomic sequencing, we construct the Qinghai-Xizang Lake Sediment Genome (QXLSG) catalog, a high-resolution genomic catalog comprising 5,866 metagenome-assembled genomes (MAGs), 58.16 million non-redundant protein encoding genes, and 19,008 biosynthetic gene clusters. Notably, 80.78% of the 2,742 species-level MAGs represent undescribed taxa, significantly expanding the known microbial diversity. Salinity emerges as the primary environmental factor influencing microbial community. Functional annotation highlights that the "salt-out" strategy, particularly the uptake of glycine betaine, is the main mechanism for salinity tolerance. This strategy is prevalent in both hypersaline lake communities and the dominant microbial phyla. Overall, this study provides a crucial genetic resource for future bioprospecting and deepens our understanding of the fundamental mechanisms of microbial adaptation to extreme saline environments.},
}

@article {pmid41166299,
year = {2025},
author = {Scully, S and Earley, B and Smith, PE and Finnie, MSJ and McAloon, C and Buckley, F and Kenny, DA and Waters, SM},
title = {Characterisation of the bacterial and archaeal microbiota in fresh colostrum collected from a single, spring-calving dairy herd.},
journal = {PloS one},
volume = {20},
number = {10},
pages = {e0335718},
doi = {10.1371/journal.pone.0335718},
pmid = {41166299},
issn = {1932-6203},
mesh = {*Colostrum/microbiology ; Animals ; Cattle ; *Archaea/genetics/classification/isolation & purification ; Female ; *Bacteria/genetics/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Dairying ; Pregnancy ; },
abstract = {There is increasing evidence to support the existence of a naturally occurring colostral microbiome, which may influence the development of the gastrointestinal microbiota and immune function of the calf. The objective of this study was to characterize the prokaryotic community of colostrum collected fresh (within 2h parturition) from primi- and multiparous Holstein-Friesian (n = 17) and Jersey (n = 10) cows. Extracted microbial DNA underwent qPCR and Illumina amplicon sequencing of the V4 region of the 16S rRNA gene. High throughput amplicon sequencing data was analysed using a variety of R packages. Taxonomy was assigned using the SILVA database (v. 138.1). No effect of breed or parity was observed on alpha (α; Shannon) diversity and community composition. The mean Shannon score was 3.33 (SE 0.14), indicating a diverse community within sample. A total of 681 genus-level amplicon sequence variant (ASV) groups were identified prior to filtering for relative abundance (RA) of >0.05%. Nineteen bacterial genera were identified as core. The predominant bacterial phyla observed were Bacillota, Pseudomonadota, and Actinomycetota. Community membership consisted of common gut commensals, with many members exhibiting diverse metabolic functions. Within the archaeal community, Methanobrevibacter had the highest RA, accounting for 85.99%. No observed differences between breeds suggests that farm origin may be more influential than breed on microbiota composition. The presence of archaea and strict anaerobes highlights the need to investigate the existence of an entero-mammary pathway in cattle. This is the first study jointly characterising bacteria and archaea in colostrum from different breeds from the same dairy herd under pasture-based conditions. The diverse bacterial community observed warrants further investigation into its role in calf health in early life. Specific microbes, like Lachnospiraceae, should be investigated for their potential in the development of probiotics and preventative practices for better calf health.},
}

*Colostrum/microbiology
Animals
Cattle
*Archaea/genetics/classification/isolation & purification
Female
*Bacteria/genetics/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Dairying
Pregnancy

@article {pmid41166275,
year = {2025},
author = {Kašperová, B and Mego, M and Čierniková, S and Ševčíková, A and Kašperová, S and Vranovský, A and Drgoňa, L},
title = {Nutrition of patients undergoing haematopoietic stem cell transplantation.},
journal = {Klinicka onkologie : casopis Ceske a Slovenske onkologicke spolecnosti},
volume = {38},
number = {5},
pages = {345-357},
doi = {10.48095/ccko2025345},
pmid = {41166275},
issn = {1802-5307},
mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Nutritional Status ; *Malnutrition/etiology ; },
abstract = {BACKGROUND: Haematopoietic stem cell transplantation is associated with increased demands for adequate caloric intake and heightened risk of macronutrient and micronutrient depletion. Carbohydrates, proteins, and fats represent a key source of energy and structural components for transplanted patients, who often have limited oral intake because of mucositis and loss of appetite and increased nutritional requirements due to catabolism, inflammation, and tissue regeneration. Deficiencies in vitamins and trace elements occurring in some patients play a crucial role in enzymatic reactions, antioxidant defense, immune function, and tissue repair. Preparative regimen also causes damage of the intestinal mucosa and, in combination with antibiotic therapy, reduces the diversity of the microbiome. According to the latest evidence, patient nutrition has an impact on the short- and long-term outcomes of transplantation. Recognition of malnutrition and catabolism in these patients is difficult in routine practice; closer analysis of body composition and early intervention by a clinical nutritionist may be helpful. Adequate nutrient replacement is an important aspect of maintaining nutritional balance and good recovery.

AIM: The aim of this article is to provide an overview of nutrition, its specific components and nutritional disorders in oncology patients, as well as to summarize specific complications of aggressive treatment in patients undergoing hematopoietic stem cell transplantation and underline the need for early nutritional intervention in this group of patients.},
}

Humans
*Hematopoietic Stem Cell Transplantation/adverse effects
*Nutritional Status
*Malnutrition/etiology

@article {pmid41166162,
year = {2025},
author = {McMahan, RH and Najarro, KM and Giesy, LE and Evans, MR and Schnabl, B and Orlicky, DJ and Frank, DN and Kovacs, EJ},
title = {Intestinal REG3G Protects Against Gastrointestinal Dysfunction in a Murine Model of Ethanol Intoxication and Burn Injury.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002737},
pmid = {41166162},
issn = {1540-0514},
abstract = {Nearly half of the burn patients in the United States are under the influence of alcohol at the time of injury and alcohol intoxication is associated with poor clinical outcomes. Ethanol has been shown to worsen burn-induced intestinal dysfunction and inflammation, facilitating bacterial translocation from the intestine to the mesenteric lymph nodes and systemic circulation. Regenerating islet-derived protein 3-gamma (REG3G), an antimicrobial peptide crucial for maintaining intestinal homeostasis, protects mice from ethanol-induced bacterial translocation. In this study, we utilized a murine model to determine whether REG3G protects against the combined effects of acute ethanol exposure and burn injury. Mice with intestinal epithelial cell-specific overexpression of REG3G (Reg3g-Tg) were evaluated for gut barrier function, intestinal and hepatic inflammatory cytokines, and antimicrobial peptide expression after ethanol and burn injury. Additionally, we performed 16S rRNA gene sequencing of fecal microbiota. Our results demonstrate that ethanol exposure before burn injury downregulates the antimicrobial peptide REG3G in the ileum, when compared to burn alone. Intestine-specific overexpression of REG3G reversed several gastrointestinal effects of the combined injury, reducing intestinal inflammation and preventing bacterial translocation to the lymph nodes. Moreover, Reg3g-Tg mice exhibited reduced liver inflammation after combined injury, suggesting that improving intestinal function can also influence extra-intestinal organs. These findings highlight the therapeutic potential of REG3G in mitigating the effects of burn injury and alcohol intoxication.},
}

@article {pmid41166145,
year = {2025},
author = {Ding, W and Zhang, H and Wen, J and Xiong, G and Cheng, M and Liu, J and Zhao, Y and Miao, Q and Deng, H and Xu, Z and Mi, L and Tan, Z and Su, L and Long, Y and Ning, K},
title = {A multi-omics analysis reveals a gut microbiome-LPC metabolic axis driving postoperative inflammation in cardiopulmonary bypass patients.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002722},
pmid = {41166145},
issn = {1540-0514},
abstract = {BACKGROUND: Patients undergoing cardiac surgery with cardiopulmonary bypass (CSCPB) are at substantial postoperative risk, which may be influenced by alterations in gut microbiota and metabolites. The roles of these biological changes in postoperative outcomes remain inadequately explored.

METHODS: We collected 54 preoperative samples and 33 postoperative samples from 60 CSCPB patients. Metagenomic and metabolomic sequencing were performed to identify the gut microbiota and serum and fecal metabolites. We examined the dynamics pattern of these microbiota and metabolites, as well as their associations with the postoperative risk. Additionally, we developed a predictive model for postoperative risk based on preoperative microbiome and metabolome data.

RESULTS: We revealed significant alterations of gut microbiota (P = 0.012), serum metabolites (P = 3.50e-10) and fecal metabolites (P = 0.0081) in patients following CSCPB, among which lysophosphatidylcholines (LPCs) exhibited notable changes. Particularly, we identified a potential regulatory function of the microbiota on LPC metabolism, which further influence the postoperative risk. The predictive model for ICU stay duration achieved a mean absolute error (MAE) of 1.27 days and an R² of 0.63, suggesting its utility in assessing postoperative risk. Also, our study provides a valuable resource (catalogue GM3C) for further investigation into potential medical targets in CSCPB patients, comprising more than 2,000 metagenome-assembled genomes and 3 million unigenes.

CONCLUSIONS: Our study reveals that the gut microbiome and LPC-centered metabolism form a functional network influencing postoperative risk in CSCPB patients. These findings underscore the role of gut-derived signals in modulating non-infectious inflammatory responses and host imbalance, offering a multi-omics framework for decoding systemic complications beyond classical sepsis paradigms.

TRIAL REGISTRATION: ClinicalTrials.gov (NCT04032938). Registered 25 July 2019, https://clinicaltrials.gov/study/NCT04032938#study-record-dates.},
}

@article {pmid41165913,
year = {2025},
author = {de Farias, BO and Dos Santos Lopes, E and Pereira, BC and Pimenta, RL and Parente, CET and Seldin, L and Saggioro, EM},
title = {Poultry slaughterhouse wastewater as a driver of bacterial community shifts and the spread of antibiotic resistance genes in aquatic ecosystems.},
journal = {Environmental monitoring and assessment},
volume = {197},
number = {11},
pages = {1268},
pmid = {41165913},
issn = {1573-2959},
mesh = {*Wastewater/microbiology ; Animals ; *Abattoirs ; *Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Poultry ; Genes, Bacterial ; Waste Disposal, Fluid ; RNA, Ribosomal, 16S ; Environmental Monitoring ; Anti-Bacterial Agents ; *Water Microbiology ; Microbiota ; },
abstract = {Poultry slaughterhouse wastewater (PSW) is a source of environmental pollutants, harboring pathogens and antibiotic resistance genes (ARGs). This study aimed to assess the effects of conventional biological treatment of PSW on the bacterial community and its efficiency in removing ARGs, as well as to evaluate the impact of its discharge on the receiving river. Samples were collected from raw sewage, treated effluent, and upstream and downstream river sites. Total metagenomic DNA was extracted for real-time PCR quantification of 16S rRNA, yccT gene (Escherichia coli), and ARGs, which were selected based on their ability to confer resistance to clinically relevant antibiotics and their prevalence in poultry-associated environments, including resistance to tetracyclines (tetM), beta-lactams (blaTEM), sulfonamides (sul1), and quinolones (qnrS). Amplicon sequencing of 16S rRNA V3-V4 region was used to assess bacterial community structure. Treated effluent significantly altered the downstream microbiome, reducing bacterial richness by up to 72.3% and diversity by 25.4%. Effluent-associated phyla such as Pseudomonadota (37%), Bacillota (28%), and Bacteroidota (26%) became dominant in the downstream river samples. Enterobacterales increased after treatment, and E. coli increased by 2.93 logs downstream. All ARGs increased after treatment and remained elevated downstream, with qnrS and sul1 rising by 3.77 and 3.87 logs, respectively. These findings highlight PSW treatment plants as a potential point of selection and dissemination of antimicrobial resistance (AMR)-related bacteria and genes. Inefficient treatment contributes to shifts in river bacterial communities and the spread of AMR.},
}

*Wastewater/microbiology
Animals
*Abattoirs
*Drug Resistance, Microbial/genetics
Bacteria/genetics
Poultry
Genes, Bacterial
Waste Disposal, Fluid
RNA, Ribosomal, 16S
Environmental Monitoring
Anti-Bacterial Agents
*Water Microbiology
Microbiota

@article {pmid41165889,
year = {2025},
author = {Sternau, M and Czajkowski, M and Błaczkowska, A and Żawrocki, A and Dolny, M and Matuszewski, M},
title = {Penile microbiome in histopathologically confirmed lichen sclerosus: a comparative study of urethral and preputial swabs.},
journal = {World journal of urology},
volume = {43},
number = {1},
pages = {653},
pmid = {41165889},
issn = {1433-8726},
mesh = {Humans ; Male ; *Lichen Sclerosus et Atrophicus/microbiology/pathology ; *Microbiota ; Prospective Studies ; *Urethra/microbiology ; Adult ; Middle Aged ; *Foreskin/microbiology ; *Penile Diseases/microbiology/pathology ; Young Adult ; },
abstract = {PURPOSE: The study examines the microbial compositions of patients with lichen sclerosus (LS) compared to control group, and individuals with other penile conditions. The aim is to address the critical question regarding the etiology of penile LS and to explore the potential involvement of the microbiome in its pathogenesis.

METHODS: In this prospective single-centre study, 73 uncircumcised male patients undergoing circumcision for phimosis were enrolled between January 2023 and April 2024. Foreskin and urethral swabs were obtained prior to surgery to isolate Candida, aerobic, and anaerobic microorganisms and sexually transmitted pathogens. Patients were categorised into LS (n = 44) and non-LS (n = 29) groups based on histopathological findings. Additionally, a control group, which consisted of patients with healthy foreskin, has been specified to conduct further analysis.

RESULTS: No statistically significant differences were observed in the prevalence of specific bacterial or viral pathogens between the LS and non-LS groups and between the LS/non-LS and control group. The most common commensal organisms were Staphylococcus coagulase-negative (48% and 34% respectively) and Corynebacterium spp. (27% and 17% respectively), whereas Enterococcus faecalis (14%) and Escherichia coli (16%) were the most frequent pathogens in LS group, and Streptococcus agalactiae (21%) was the most abundant pathogen in non-LS group. HPV was detected in 5% of patients with LS and in 14% of patients without LS. There were no statistically significant differences in CRP levels and BMI. In exploratory multivariable models adjusting for age and BMI, the presence of Streptococcus agalactiae was associated with lower odds of LS (OR 0.19; 95% CI 0.04-0.92; p = 0.04; FDR = 0.07); however, given limited power, these results should be interpreted cautiously.

CONCLUSIONS: Our study demonstrated no significant association between specific microbial or viral profiles and penile lichen sclerosus. However, due the fact that the culture-based approach employed in this study may underestimate the diversity of the penile microbiome, further research is warranted.},
}

Humans
Male
*Lichen Sclerosus et Atrophicus/microbiology/pathology
*Microbiota
Prospective Studies
*Urethra/microbiology
Adult
Middle Aged
*Foreskin/microbiology
*Penile Diseases/microbiology/pathology
Young Adult

@article {pmid41165775,
year = {2025},
author = {Dohadwala, S and Shah, P and Farrell, MK and Politch, JA and Marathe, J and Costello, CE and Anderson, DJ},
title = {Sialidases derived from Gardnerella vaginalis and Prevotella timonensis remodel the sperm glycocalyx and impair sperm function.},
journal = {Glycobiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/glycob/cwaf067},
pmid = {41165775},
issn = {1460-2423},
abstract = {Bacterial vaginosis (BV), a dysbiosis of the vaginal microbiome, affects approximately 30% of women worldwide (up to 50% in some regions) and is associated with several adverse health outcomes including preterm birth and increased incidence of sexually transmitted infections (STIs). BV-associated bacteria such as Gardnerella vaginalis and Prevotella timonensis damage the vaginal mucosa through the activity of sialidase enzymes that remodel the epithelial glycocalyx and degrade mucin glycoproteins. This damage may contribute to adverse health outcomes. However, whether BV-associated glycolytic enzymes also damage sperm has not yet been determined. Here, we show that sialidase-mediated glycocalyx remodeling of human sperm increases sperm susceptibility to damage and adversely affects their function in vitro. Specifically, we report that sperm motility was not adversely affected by sialidase treatment, but desialylated human sperm demonstrate increased susceptibility to agglutination and complement-mediated cytotoxicity as well as impaired transit through cervical mucus. Our results demonstrate mechanisms by which BV-associated sialidases affect sperm survival and function and potentially contribute to adverse reproductive outcomes such as infertility.},
}

@article {pmid41165608,
year = {2025},
author = {Velten Mendes, M and Lima, TC and Amormino, MS and de Oliveira, JS and Barroso, FLA and Boudry, G and Moreira-Júnior, RE and Brunialti-Godard, AL},
title = {Predicted functional alterations in colonic microbiota metabolism underlie ethanol consumption and preference behavior in mice.},
journal = {Alcohol, clinical & experimental research},
volume = {},
number = {},
pages = {},
doi = {10.1111/acer.70165},
pmid = {41165608},
issn = {2993-7175},
support = {406958/2022//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Pró-Reitoria de Pesquisa, Universidade Federal de Minas Gerais/ ; //Instituto Nacional de Ciências e Tecnologia sobre Substâncias Psicoativas/ ; //Pós-Graduação em Genética (ICB/UFMG)/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; APQ-03984-24//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; APQ-045517-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; },
abstract = {BACKGROUND: Alcohol use disorder (AUD) is a complex condition affecting several body systems. Gut microbiota alterations, intestinal-barrier disruption, and the consequent translocation of metabolites foster chronic inflammation, lower short-chain fatty acid (SCFA) output, and depleted beneficial bacteria may contribute to transcriptional, epigenetic, and metabolic changes that influence ethanol preference.

METHODS: Two experimental phases were used. T1 (8 weeks): mice received either the American Institute of Nutrition standard diet (AING) or a high-sugar-butter (HSB) diet. T2 (4 weeks): HSB animals switched to AING (SWITCH), while AING mice maintained the same diet. Each diet arm was split into ethanol (EtOH; free access to 10% ethanol) or H2O, generating four groups (AING + H2O, AING + EtOH, SWITCH + H2O, and SWITCH + EtOH). Sample processing involved colonic-content collection, 16S rRNA sequencing, microbiome profiling, functional inference, metabolic-network analysis, and SCFA/amino acid quantification.

RESULTS: SWITCH + EtOH mice displayed high ethanol consumption and preference, whereas AING + EtOH mice showed ethanol aversion. Their colonic microbiota differed markedly; amino acid metabolism fell, secondary bile acid synthesis rose, and SCFA production dropped in SWITCH + EtOH animals. Direct measurements confirmed significant reductions in butyrate, acetate, propionate, and selected amino acids. Network analysis revealed enrichment of bacterial metabolism, oxidative stress, and dopamine pathway genes.

CONCLUSIONS: Diet-induced dysbiosis, reflected in shifts in microbiota-derived metabolites, was associated with excessive alcohol intake; the metabolites identified can represent potential therapeutic targets for AUD.},
}

@article {pmid41165420,
year = {2025},
author = {Gonçalves, IC and Pontes, A and Gonçalves, C and Sá-Nogueira, Id},
title = {FrlP, an ABC type I importer component of Bacillus subtilis: regulation and impact in bacterial fitness.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0032025},
doi = {10.1128/jb.00320-25},
pmid = {41165420},
issn = {1098-5530},
abstract = {Bacillus subtilis is able to catabolize fructosamines, also known as Amadori rearrangement products. The frlBONMD-frlP operon mediates this process and is subjected to specific and global regulation. Although the degradation pathway favoring α-glycated amino acids is known, the mechanisms of substrate uptake have remained unclear. In this study, mutagenic and functional analyses revealed that FrlONM, a type I ABC importer, along with the nucleotide-binding domain (NBD) FrlP, is required for the uptake of fructosevaline. Transcriptional and translation frlP-lacZ fusions indicated that frlP is induced by fructosevaline and negatively regulated by the FrlR repressor. In addition, we show that MsmX, a multitask NBD of B. subtilis, is also able to serve as an energy motor of this type I ABC importer and that its presence alongside FrlP is vital for optimal growth on fructosevaline. To address the physiological significance of this functional redundancy, we assessed the distribution of ABC type I NBDs FrlP and MsmX across the Bacillaceae family. MsmX is homogeneously distributed in the Bacillaceae family tree, while FrlP is restricted to the Bacillus subtilis group, suggesting that the presence of FrlP together with other components of the fructosamines operon is important for bacterial fitness in plant-associated ecological niches.IMPORTANCEBacillus subtilis is widely applied in the industry as a microbial cell factory, as a biofertilizer for sustainable agriculture, in the animal feed industry and as human probiotic. In its natural environment, B. subtilis helps to shape the gut microbiome and the phytomicrobiome. Fructosamines, or Amadori rearrangement products, are ubiquitously found in nature and serve as precursors of toxic cell end-products implicated in the pathology of human diseases. This study provides a solid contribution to a deep knowledge of transport mechanisms, genetic regulation, and physiological relevance of fructosamines utilization in B. subtilis. Moreover, it highlights an unusual strategy to adapt to alterations in nutrient availability by swapping the energy providing domain of ABC transporters.},
}

@article {pmid41165402,
year = {2025},
author = {Nakatani, H and Suetake, N and Hori, K},
title = {Antimicrobial-producing bacteria from fish epidermal mucus alter the fish epidermal bacterial flora and host resistance to infection.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0145025},
doi = {10.1128/aem.01450-25},
pmid = {41165402},
issn = {1098-5336},
abstract = {The emergence of antimicrobial-resistant bacteria in aquaculture has raised the need for alternative strategies to control fish infections. Antimicrobial-producing bacteria have been explored as probiotics or biocontrol agents, but their mechanisms of action and impact on host-associated microbiota remain poorly understood. Here, we identified Pseudomonas mosselii KH-ZF1, a bacterium isolated from fish epidermal mucus, as a producer of antimicrobial substances. When applied to zebrafish, strain KH-ZF1 transiently adhered to the epidermal mucus and altered the composition of the skin microbiota. Under an appropriate administration condition, strain KH-ZF1 treatment significantly improved survival in zebrafish infected with Yersinia ruckeri and suppressed pathogen growth on the skin surface. However, in the absence of strain KH-ZF1 or inappropriate conditions, Y. ruckeri dominated the epidermal bacterial community. The antimicrobial compound produced by strain KH-ZF1 was identified as Fluviol C, a pigmented metabolite previously reported from Pseudomonas fluorescens. Fluviol C inhibited the growth of multiple fish pathogens at experimentally determined concentrations (0.5-32 µg/mL) but exhibited toxicity to zebrafish even below its minimum inhibitory concentration. Intriguingly, fluviol C, at sub-inhibitory levels, induced bacterial substitution in the epidermal microbiota, mimicking the effects of strain KH-ZF1. These findings demonstrate that strain KH-ZF1 alters host resistance to infection by promoting bacterial substitution on the fish skin by producing fluviol C. Our study highlights a microbiota-mediated mechanism by which antimicrobial-producing bacteria can control infection through the fish epidermis, suggesting a potential microbiota-mediated approach for disease control in aquaculture.IMPORTANCEWe show that bacteria producing antibacterial substances, isolated from fish skin mucus, can inhibit percutaneous infections in aquatic environments. These bacteria effectively altered the skin mucus bacterial flora and suppressed pathogen growth. Fish skin acts as a barrier against infections, with its microorganisms being considered to play a crucial role in prevention. Our study highlighted the potential use of these specific microorganisms in the fish skin mucus as a novel fish disease control strategy. By targeting fish skin mucus bacteria that produce antimicrobial substances, we could develop a new approach to managing diseases in aquaculture, such as probiotics for fish skin. This research underscores the importance of studying fish epidermal microorganisms for innovative disease management.},
}

@article {pmid41165394,
year = {2025},
author = {Rozo-Lopez, P and Torres, V and Torres, J and Drolet, BS and Käfer, S and Parker, BJ},
title = {Heritable viral symbionts in the family Iflaviridae are widespread among aphids.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0160625},
doi = {10.1128/aem.01606-25},
pmid = {41165394},
issn = {1098-5336},
abstract = {UNLABELLED: Heritable microbes shape host phenotypes and serve as important drivers of evolution. While interactions between insects and bacterial symbionts have been extensively studied, the prevalence and evolution of insect-viral symbioses remain poorly understood. We discovered multiple new species of iflaviruses in aphids, an important model for research on symbiosis, and found these microbes to be widespread across aphid species. We show that iflaviruses are persistently maintained in asexual host lines without apparent fitness costs while being transmitted vertically from mothers to offspring. Using field data and phylogenetic evidence, we found that aphid iflaviruses move horizontally among host species, but laboratory experiments showed that horizontal transmission does not result in persistent infections. Using quantitative PCR and immunohistochemistry, we discovered that viral infections localize in the host fat bodies and developing embryos. Surprisingly, we also found viral infections inside bacteria-housing cells called bacteriocytes, along with a positive correlation between viral and bacterial symbiont density. Together, our work suggests that iflaviruses are widespread heritable symbionts in aphids.

IMPORTANCE: In recent years, the rise of metatranscriptome sequencing has led to the rapid discovery of novel viral sequences in insects. However, few studies have carefully investigated the dynamics of insect-virus interactions to produce a general understanding of viral symbiosis. Aphids are an important model for understanding the evolution and molecular basis of symbiosis, but whether viruses are forming persistent symbiotic relationships with aphids remains unclear. Here, we show that heritable iflaviruses are a widespread but previously unrecognized part of the aphid heritable microbiome. Aphid iflaviruses are transmitted alongside bacteria from mothers to offspring, potentially via specialized bacteriocytes that house symbiotic microbes. Our findings suggest that aphids establish persistent relationships with iflaviruses and are likely coevolving with these viral symbionts.},
}

@article {pmid41165341,
year = {2025},
author = {Gallardo-Cartagena, JA and German-Quiñones, DLG and Rosas-Benancio, FG and Tafur, KT and Velásquez-Velásquez, DR and Cabello, R and Konda, KA and Celum, C and Sanchez, JL},
title = {High Willingness to Use and Recommend Doxycycline Postexposure Prophylaxis for Bacterial STI Prevention in Peru.},
journal = {Sexually transmitted diseases},
volume = {},
number = {},
pages = {},
doi = {10.1097/OLQ.0000000000002268},
pmid = {41165341},
issn = {1537-4521},
abstract = {BACKGROUND: Bacterial sexually transmitted infections (STIs) remain prevalent among men who have sex with men (MSM) and transgender women (TGW) in Peru. Doxycycline postexposure prophylaxis (doxy-PEP) is a promising prevention strategy, but data from Latin America remain limited.

METHODS: We conducted two online surveys in Lima, Peru (September-October 2024). One assessed willingness to use doxy-PEP among MSM and TGW; the other assessed willingness to recommend doxy-PEP among healthcare providers (HCPs). Logistic regression evaluated correlates of high willingness.

RESULTS: Of 730 eligible MSM and TGW, 447 completed outcome measures. Overall, 82.1% expressed willingness to use doxy-PEP, 34.2% with high willingness. High willingness was associated with ≥5 anal sex partners in past three months (aOR 1.86; 95% CI 1.06-3.24), prior HIV preexposure prophylaxis (HIV-PrEP) use (aOR 2.56; 95% CI 1.40-4.71), living with HIV (aOR 2.74; 95% CI 1.44-5.24), and concern about needing a prescription (aOR 3.33; 95% CI 1.99-5.66). Concerns about side effects (aOR 0.55; 95% CI 0.31-0.98) and microbiome disruption (aOR 0.51; 95% CI 0.29-0.87) were negatively associated. Most participants preferred doxy-PEP over daily doxycycline (64.0% vs 28.6%). Among 132 HCPs, 54.5% were involved in HIV/STI care; 87.1% expressed willingness to recommend doxy-PEP, and 89.4% would do so if included in national guidelines. Limited diagnostic capacity and risk of unofficial use were most frequently endorsed concerns.

CONCLUSIONS: High willingness to use or recommend doxy-PEP was observed among clients and HCPs in Peru, providing evidence to guide integration into sexual health services in Latin America.},
}

@article {pmid41165334,
year = {2025},
author = {Horvath, M and Kang, HG and Wu, T-C and Aiken, E and Castaneda, DC and Akkurt, S and Marches, F and Anczuków, O and Palucka, K and Oh, J},
title = {Host-specific bacterial modulation of airway gene expression and alternative splicing.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0057725},
doi = {10.1128/msphere.00577-25},
pmid = {41165334},
issn = {2379-5042},
abstract = {The human microbiome varies extensively between individuals. While there are numerous studies investigating the effects of inter-individual differences on microbiome composition, there are few studies investigating inter-individual effects on microbial modulation of the host or host-specific effects. To address this knowledge gap, we colonized human bronchial epithelial air-liquid interface tissue cultures generated from six different adults with one of three phylogenetically diverse bacteria and compared how each microbe differentially modulated host gene expression in each of the six donors. Microbial treatment had the strongest effect on transcription, followed by donor-specific effects. Gene pathways differed markedly in their donor and microbe specificity; interferon expression was highly donor-dependent, while transcription of epithelial barrier and antibacterial innate immunity genes was predominantly microbially driven. Moreover, we evaluated whether microbial regulation of alternative splicing was modulated by the donor. Strikingly, we found significant nonredundant, donor-specific regulation of alternative splicing exclusively in the gram-positive commensal microbes. These findings highlight that microbial effects on the human airway epithelium are not only species-specific but also deeply individualized, underscoring the importance of the host context in shaping microbe-induced transcriptional and splicing responses.IMPORTANCEMicrobiota are integral regulators of host gene expression, utilizing diverse mechanisms that are shaped by the interplay between microbiome composition and inter-individual differences, i.e., host-specific factors. While previous studies have characterized inter-individual variation in microbiome composition and the effects of variable microbiome composition on the host, the extent to which host-specificity itself regulates host-microbe interactions remains poorly understood. In this study, we address this gap by characterizing changes in epithelial gene expression from six different human donors following colonization with one of three phylogenetically diverse bacteria. By systematically comparing donor-specific responses, we demonstrate that host specificity is a key determinant of the host transcriptional response to microbial colonization. Importantly, we demonstrate that the effects of host specificity are not uniform, but instead are dependent on the colonizing microbe. Our findings underscore the complexity of host-microbe relationships and establish host specificity as a significant factor shaping host-microbe interactions.},
}

@article {pmid41165314,
year = {2025},
author = {Nauwynck, W and Sakarika, M and Faust, K and Boon, N},
title = {Differential recovery of chain-elongating bacteria: comparing droplet, plating, and dilution-to-extinction methods.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0135625},
doi = {10.1128/msystems.01356-25},
pmid = {41165314},
issn = {2379-5077},
abstract = {Microbial chain elongation via reverse β-oxidation offers a more sustainable route to produce medium-chain fatty acids like caproate, commodity chemicals typically produced via (petro)chemical processes. Thermophilic anaerobic microbiomes allow production at a high rate and selectivity but remain poorly understood due to the limited cultivability of their members. To better access functional taxa from a thermophilic chain-elongating reactor community, we applied multiple isolation strategies: conventional anaerobic plating, dilution-to-extinction (DTE), droplet-based microfluidics, and fluorescence-activated cell sorting (FACS). We evaluated the taxonomic range and cultivation success of each method using 16S rRNA gene sequencing. Each method yielded a distinct subset of microbial taxa. While Clostridium acetireducens-related strains were consistently isolated across all strategies, key thermophilic chain elongators (e.g., Thermocaproicibacter melissae-like organisms) only appeared in DTE. Droplet microfluidics enriched the most unique taxa in total, mostly rare taxa, including Caproicibacter and Thermoanaerobacterium spp. Plating yielded the lowest diversity, recovering only dominant taxa. FACS-based approaches failed to yield isolates, likely due to stress during processing. Comparing droplet-based isolation to DTE revealed critical insights: although droplets offer higher throughput, which intrinsically increases the chance of capturing rare taxa, not all DTE-cultivated organisms grew in droplets. This suggests additional contributing factors (apart from an increased throughput), such as encapsulation stress and droplet-specific microenvironments. These findings clarify the advantages and limitations of droplet cultivation strategies, allowing a more informed application of these techniques to access the so-called "microbial dark matter."IMPORTANCEMany environmentally and industrially relevant microbes remain uncultured, limiting our ability to understand and use them. This is especially true in thermophilic anaerobic microbiomes, which are promising systems for producing sustainable chemicals from organic waste streams. In this study, we explored how different cultivation strategies influence which microbes can be isolated from a thermophilic chain-elongating reactor. By comparing traditional and novel methods, including droplet microfluidics, we showed that each method recovers a unique set of microbes. While droplet-based methods enable high sampling depth with minimal effort and excel at isolating rare microbes, we found that they also introduce clear biases, as certain organisms recovered by other methods did not grow in droplets. Our work highlights the importance of the cultivation method in isolation success and helps shine a light on the selective forces at play in droplet-based microbial isolation.},
}

@article {pmid41165307,
year = {2025},
author = {Wang, Y and Malmuthuge, N and Yao, J and Guan, LL},
title = {Revisiting cattle respiratory health: key roles of the gut-lung axis in the dynamics of respiratory tract pathobiome.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0018025},
doi = {10.1128/mmbr.00180-25},
pmid = {41165307},
issn = {1098-5557},
abstract = {SUMMARYDespite the increasing preventative efforts (vaccines, hygiene, pre-conditioning), respiratory tract (RT) infections pose a significant challenge across mammalian species. Recently, there has been a greater emphasis on promoting healthy microbiome colonization to mitigate respiratory infection in humans and livestock species. In livestock animals, especially in cattle, RT microbiome research has mainly focused on characterizing the respiratory tract microbial community in healthy and sick animals, aiming to identify microbiota linked to disease or health status. However, this approach overlooked the dynamics of RT microbiome that comprises commensal opportunistic pathogens (an element of the pathobiome) contributing to the infection and disease pathogenesis. Moreover, there is a lack of attempts to evaluate the interactions among host immunity-microbiome-pathobiome during pathogenesis for the development of successful microbiome-based interventions to improve cattle respiratory health. Recent research has revealed new insights into the gut-lung axis (GLA) and the regulatory role of the gut microbiota in determining host susceptibility or resilience to respiratory infections. Therefore, this review aims to critically discuss the roles of RT microbiome (including pathobiome) and GLA in respiratory health, while elucidating the mechanisms driving the dynamic transition from a commensal state to pathogenic state during microbiome dysbiosis and immune dysregulation, and identifying microbiome targets for RT health improvement.},
}

@article {pmid41165062,
year = {2025},
author = {Senar, N and Zwinderman, AH and Hof, MH},
title = {Sparse Canonical Correlation Analysis for Multiple Measurements With Latent Trajectories.},
journal = {Biometrical journal. Biometrische Zeitschrift},
volume = {67},
number = {6},
pages = {e70090},
doi = {10.1002/bimj.70090},
pmid = {41165062},
issn = {1521-4036},
mesh = {*Biometry/methods ; Humans ; Correlation of Data ; Models, Statistical ; },
abstract = {Canonical correlation analysis (CCA) is a widely used multivariate method in omics research for integrating high-dimensional datasets. CCA identifies hidden links by deriving linear projections of observed features that maximally correlate datasets. An important requirement of standard CCA is that observations are independent of each other. As a result, it cannot properly deal with repeated measurements. Current CCA extensions dealing with these challenges either perform CCA on summarized data or estimate correlations for each measurement. While these techniques factor in the correlation between measurements, they are suboptimal for high-dimensional analysis and exploiting this data's longitudinal qualities. We propose a novel extension of sparse CCA that incorporates time dynamics at the latent variable level through longitudinal models. This approach addresses the correlation of repeated measurements while drawing latent paths, focusing on dynamics in the correlation structures. To aid interpretability and computational efficiency, we implement an ℓ 0 $\ell _0$ penalty to enforce fixed sparsity levels. We estimate these trajectories fitting longitudinal models to the low-dimensional latent variables, leveraging the clustered structure of high-dimensional datasets, thus exploring shared longitudinal latent mechanisms. Furthermore, modeling time in the latent space significantly reduces computational burden. We validate our model's performance using simulated data and show its real-world applicability with data from the Human Microbiome Project. This application highlights the model's ability to handle high-dimensional, sparsely, and irregularly observed data. Our CCA method for repeated measurements enables efficient estimation of canonical correlations across measurements for clustered data. Compared to existing methods, ours substantially reduces computational time in high-dimensional analyses as well as provides longitudinal trajectories that yield interpretable and insightful results.},
}

*Biometry/methods
Humans
Correlation of Data
Models, Statistical

@article {pmid41164979,
year = {2025},
author = {Zhang, M and Wang, R and Khan, RAA and Zhan, X and Ren, S and Jiang, H and Zheng, C and Wu, Y and Yang, F and Yu, X and Liu, T},
title = {Trichoderma asperellum FJ035 Restructure the Rhizosphere Microbiome to Control the Cucumber Fusarium Wilt.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70250},
pmid = {41164979},
issn = {1365-3040},
support = {//This study was supported by the PhD Scientific Research and Innovation Foundation of the Education Department of Hainan Province, the Joint Project of Sanya Yazhou Bay Science and Technology City, the Innovation Research Project of Graduate Students in Hainan Province, the Key Research and Development Program Project of Hainan Province, the Collaborative Innovation Center of Nanfan and High-Efficiency Tropical Agriculture of Hainan University, and the National Natural Science Foundation of China./ ; },
abstract = {The rhizosphere microbial community serves as a protective barrier against soil-borne diseases. However, it is unclear how Trichoderma influences the rhizosphere microbial community to control cucumber Fusarium wilt (CFW). This study demonstrated that Trichoderma asperellum FJ035 effectively suppresses CFW under continuous cropping by altering the rhizosphere microbiome, as confirmed through microbiome transfer experiments. Amplicon sequencing combined with cultivation-based methods showed that T. asperellum FJ035 modifies the composition and abundance of cucumber rhizosphere microbial communities. Based on these findings, a synthetic consortium, TB11, was constructed containing T. asperellum FJ035 and 30 bacterial strains that effectively controlled CFW and promoted cucumber growth. We simplified this consortium to TB5, comprising six strains closely related to T. asperellum FJ035, with a 71.43% reduction in CFW and 54.69% increase in plant weight. Further investigation revealed that T. asperellum FJ035 promotes the colonisation of B5 in cucumber roots and forms a protective microbiota to resist Fusarium oxysporum infection. This study reported a novel mechanism by which T. asperellum FJ035 prevents and controls CFW by regulating native bacterial communities in the rhizosphere. Moreover, the construction of synthetic consortia is described as a sustainable strategy for healthy cucumber cultivation.},
}

@article {pmid41164885,
year = {2025},
author = {Hosseinkhani, F and Chevalier, C and Marizzoni, M and Park, R and Bos, S and Dunjko, AK and van Duijn, CM and Harms, AC and Frisoni, GB and Hankemeier, T},
title = {Plasma and feces multiomics unveil cognition-associated perturbations of chronic inflammatory pathways of the gut-microbiota-brain axis.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {21},
number = {10},
pages = {e70844},
doi = {10.1002/alz.70844},
pmid = {41164885},
issn = {1552-5279},
support = {184.034.019//Dutch Research Council (NWO)/ ; 175.2019.032//Dutch Research Council (NWO)/ ; //Private Foundation of Geneva University Hospitals: A.P.R.A.-Association Suisse pour la Recherche sur la Maladie d'Alzheimer, Genève/ ; //Fondation Segré, Genève/ ; //Race Against Dementia Foundation, London, UK/ ; //Fondation Child Care, Genève/ ; //Fondation Edmond J. Safra, Genève/ ; //Fondation Minkoff, Genève/ ; //Fondazione Agusta, Lugano/ ; //McCall Macbain Foundation, Canada/ ; //Nicole et René Keller, Genève/ ; //Fondation AETAS, Genève/ ; //Clinical Research Center, University Hospital and Faculty of Medicine/ ; //Italian Ministry of Health (Ricerca Corrente)/ ; //Hôpitaux Universitaires de Genève/ ; 175.2019.032//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Feces/microbiology/chemistry ; Male ; Female ; *Dysbiosis/metabolism ; *Cognitive Dysfunction/metabolism/microbiology ; Aged ; *Inflammation/metabolism ; *Brain/metabolism ; Cytokines/blood ; Multiomics ; },
abstract = {INTRODUCTION: Gut-microbiota dysbiosis has been linked to cognitive decline. Given its role in metabolism, immunity, and environmental interactions, broader molecular signaling alterations are likely.

METHODS: We analyzed gut microbiota composition, plasma and fecal metabolites, and inflammatory cytokines across cognitive stages, from healthy controls to dementia.

RESULTS: Alpha diversity declined with increasing cognitive impairment severity. Short-chain fatty acid-producing Firmicutes and Bacteroidota decreased from 76% and 17% in controls to 59% and 11% in dementia, respectively. Proteobacteria (e.g., Escherichia-Shigella) rose from < 2% to 4%, and Verrucomicrobiota from 3% to 11%. Despite overall Firmicutes decline, Ruminococcus gnavus, a mucus-degrading species, increased in dementia. These shifts correlated with elevated plasma cytokines, suggesting a link between gut dysbiosis and systemic inflammation. Bacteria-associated metabolites, including bile acids, trimethylamine N-oxide, oxylipins, sugars, and fatty acids were significantly altered. Changes were seen as early as subjective cognitive decline.

DISCUSSION: Larger studies are needed to validate these findings and explore microbiome-based interventions.

HIGHLIGHTS: Examined gut microbiota, inflammation, and metabolic changes in cognitive impairment stages Early metabolic changes in feces detected before plasma alterations Observed shifts in gut microbiota and inflammation associated with cognitive decline Suggests potential for early biomarkers based on gut metabolites Calls for larger, longitudinal studies to validate findings.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Feces/microbiology/chemistry
Male
Female
*Dysbiosis/metabolism
*Cognitive Dysfunction/metabolism/microbiology
Aged
*Inflammation/metabolism
*Brain/metabolism
Cytokines/blood
Multiomics

@article {pmid41164876,
year = {2025},
author = {Chen, H and Lu, Z and Xiao, C and Wang, X and Xi, Y and Yan, Y and Zheng, JS and Chen, YM and Deng, K},
title = {Association Between Alternative Complement Pathway and Carotid Plaque and the Underlying Gut Microbial and Inflammatory Biomarkers: A Cohort Study.},
journal = {Arteriosclerosis, thrombosis, and vascular biology},
volume = {},
number = {},
pages = {},
doi = {10.1161/ATVBAHA.125.322968},
pmid = {41164876},
issn = {1524-4636},
abstract = {BACKGROUND: The alternative pathway (AP) plays a crucial role in triggering complement activation and promoting chronic inflammation. This study aims to investigate the longitudinal association between AP and atherosclerosis, and explore the potential role of gut microbiota and inflammatory factors in their association.

METHOD: This study was based on a 9-year prospective cohort of 3382 participants from Guangzhou, China (mean age±SD, 57.75±5.85 years; 68.8% female), with data on serum APACPs (AP-associated complement proteins) and carotid plaque (measured by ultrasound) repeatedly measured up to 3×. Baseline inflammatory markers were evaluated in 923 participants, and gut shotgun metagenome data were obtained from 1567 participants. Mendelian randomization analysis was performed using genome-wide significant genetic variants as instrumental variables to suggest potential causal associations.

RESULTS: Both longitudinal and prospective analyses consistently demonstrated positive associations between carotid plaque and 3 complement components: C3 (odds ratios [95% Cl] for the highest versus lowest quartiles, 1.36 [1.07-1.74] in longitudinal analysis and 1.29 [1.06-1.56] in prospective analysis), CFB (complement factor B; 1.36 [1.07-1.72] in longitudinal analysis and 1.39 [1.15-1.69] in prospective analysis), and CFH (complement factor H; 1.39 [1.10-1.76] in longitudinal analysis and 1.31 [1.07-1.61] in prospective analysis). Mendelian randomization analysis suggested a potential causal association between CFB and carotid plaque. Inflammatory factors (CRP [C-reactive protein] and IL-6 [interleukin-6]) and microbial species (Ruminococcus bromii, Roseburia hominis, Rothia mucilaginosa, Collinsella stercoris, Olsenella scatoligenes, and Bacteroides massiliensis) were significantly associated with both APACPs and carotid plaque (P<0.05). For example, butyrate-producing bacterium R bromii was inversely associated with CFB and carotid plaque (odds ratios [95% CI], 0.83 [0.79-0.88]) and may mediate the CFB-carotid plaque association (proportion mediated, 13.5%; P=0.005). Microbial risk score (weighted sum of selected microbial species; proportion mediated, 42.6%; P<0.001) and total immune factors (the sum of all inflammatory factors; proportion mediated, 19.0%; P=0.002) mediated the association between Total-APACPs (sum of standardized carotid plaque-related APACPs [C3, CFB, and CFH]) and carotid plaque.

CONCLUSIONS: Our study showed a negative association between the AP and carotid plaque in a longitudinal cohort. Gut microbiota and inflammatory biomarkers may provide mechanistic insights into the association between the AP and atherosclerosis. Our findings pave the way for the development of new therapeutic targets for atherosclerosis.},
}

@article {pmid41164761,
year = {2025},
author = {Su, D and Li, Q and Lai, X and Song, Y and Li, H and Ai, Z and Zhang, Q and Shao, W and Yang, M and Zhu, G},
title = {Correction: Sargassum pallidum reduces inflammation to exert antidepressant effect by regulating intestinal microbiome and ERK1/2/P38 signaling pathway.},
journal = {Frontiers in pharmacology},
volume = {16},
number = {},
pages = {1653830},
doi = {10.3389/fphar.2025.1653830},
pmid = {41164761},
issn = {1663-9812},
abstract = {[This corrects the article DOI: 10.3389/fphar.2024.1424834.].},
}

@article {pmid41164513,
year = {2025},
author = {Alsakr, A},
title = {Periodontal Diseases and Host Modulation Therapies.},
journal = {Journal of pharmacy & bioallied sciences},
volume = {17},
number = {Suppl 3},
pages = {S2052-S2054},
pmid = {41164513},
issn = {0976-4879},
abstract = {In periodontal diseases, bacteria and microbes serve as the primary pathogens that initiate the condition, while the host refers to the body that hosts these microorganisms. Host modulation therapy is a drug-based treatment that can be used along with systematic periodontal therapy to help the disease get better and stop tissue damage. There is a new way to treat periodontitis called "Host-Modulation Therapy" (HMT). It involves reducing the bacteria biofilm through daily good oral hygiene and regular scaling and root planing (SRP). Using host modulation therapies to lower inflammation, restore microbiome balance, and change the immune response of the host holds a lot of promise for better periodontal disease treatment. This review examines host modulation in treating and preventing periodontal diseases. The review encompasses a variety of studies that evaluate pharmaceutical agents, probiotics, and immunomodulatory methods.},
}

@article {pmid41164408,
year = {2025},
author = {Staab, S and Mayer, KI and Cárdenas, A and Peixoto, RS and Schreiber, F and Voolstra, CR},
title = {UniCor and UniCorP: a novel metric and hierarchical feature selection algorithm for microbial community analysis.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf174},
pmid = {41164408},
issn = {2730-6151},
abstract = {The rapid advancement of technologies and methods in the life sciences has significantly increased the availability of big data, presenting new challenges for its analysis. Microbiome datasets, in particular, are characterized by extensive feature sets with defined but complex hierarchical structures that are often overlooked or underutilized. Here we introduce a novel metric, UniCor, to identify UNIquely CORrelated eNtities (UNICORNs) in quantitative datasets associated with continuous target variables. These datasets may include microbiome community structures in relation to environmental factors (e.g., temperature, pH, salinity) or biotic variables (e.g., thermal tolerance, oxidative stress). The UniCor metric combines the uniqueness of a given feature within a dataset with its correlation to a target variable of interest. To further enhance its utility, we developed a propagation algorithm (UniCorP), which exploits inherent dataset hierarchies, such as taxonomic levels in microbiome datasets, by selecting and propagating features based on their UniCor metric. Using bacterial community datasets with hierarchical taxonomic annotations and various continuous environmental variables, we demonstrate the ability of the novel metric to reduce features and increase predictive performance in cross-validated Random Forest Regressions. After propagating features with UniCorP and enriching the hierarchical levels with UNICORNs, the predictive performance consistently outperformed control trials for taxonomic aggregation, even at the least granular hierarchical level, allowing a substantial reduction of the feature space. We also compared the metric to existing methods for feature aggregation, showing that it offers stable, competitive predictive performance and feature reduction, within a simple and adaptable framework.},
}

@article {pmid41164407,
year = {2025},
author = {Ma, P and Mu, W and Wang, Y and Liu, Y and Zou, Y and Lu, Z and Pang, S and Pan, H and Zhang, L and Chen, L and Yang, Y and Lin, X and Kuang, Z and Luo, W and Liu, G and Wang, S},
title = {Blastocystis load mediates the gut microbiome associations with within-host diversity of Blastocystis in non-human primates.},
journal = {ISME communications},
volume = {5},
number = {1},
pages = {ycaf170},
pmid = {41164407},
issn = {2730-6151},
abstract = {Blastocystis is a prevalent gut eukaryote intricately associated with the gut microbiota. This genetically diverse protozoan exhibits significant intra-host subtype heterogeneity, yet the implications of this diversity for the host gut microbiome remain poorly understood. Here, we investigated the interactions between Blastocystis and gut microbiota in non-human primates at the level of subtypes, using a comprehensive investigation of gut microbiota for Blastocystis carriers of captive Macaca fascicularis (discovery cohort, n = 100) and Macaca mulatta (validation cohort, n = 26). We identified highly prevalent intra-host co-occurrence patterns of Blastocystis SSU rRNA-based subtypes, primarily dominated by Subtype 1 (ST1) or ST3. These patterns were associated with compositional and structural variations in the gut microbiome but were not significantly influenced by host covariates such as sex, age, or BMI. Specifically, Ruminococcaceae-enterotype was enriched in the patterns dominated by ST1, whereas Limosilactobacillus-enterotype was predominantly identified in the patterns dominated by ST3. Variance partitioning and mediation analyses revealed that the absolute abundance of Blastocystis was a critical determinant in elucidating this microbiota association across subtype concurrent patterns. In vivo experiments in a new cohort (n = 11) demonstrated that lactic acid bacteria, enriched in the Limosilactobacillus-enterotype, were sufficient to reduce Blastocystis load. We validated the strong association between gut microbiome composition and Blastocystis load in M. mulatta, confirming that specific microbial features could quantitatively predict Blastocystis status in both species. These findings highlight the close links of the gut microbiome with within-host subtype diversity patterns and absolute abundance of Blastocystis.},
}

@article {pmid41164342,
year = {2025},
author = {Harris, NC and Hallam, J},
title = {Individual variation within parasite communities of endangered African lions.},
journal = {Royal Society open science},
volume = {12},
number = {10},
pages = {250501},
pmid = {41164342},
issn = {2054-5703},
abstract = {Prey depletion and human-wildlife conflict threaten the critically endangered West African populations of lion (Panthera leo leo), which occupy less than 1.1% of their historic range in West Africa. These threats may alter behaviour through prey selection and affect exposure to parasites to compromise their health. We extracted DNA from faecal samples collected in four national parks in Benin, Burkina Faso and Senegal to characterize haemoparasites, nemabiome and microbiome. We used microsatellite markers to differentiate individuals and five primer sets to complete molecular analyses. From 20 individuals (12 males and 8 females), we found significant differences in the species richness and composition for all parasite groups across host populations and individual lions. We detected haemoparasites, including Babesia and Sarcocystis species, along with Blechomonas, a kinetoplastid, all of which raise potential health concerns. The nemabiome was dominated by Ancylostoma species (hookworms) with additional detections of lungworms from the genera Oslerus and Troglostrongylus. Significant interactions were found between population-level microbiome richness and both nemabiome and haemoparasite diversity. Our study provides the first effort to determine the parasite diversity among West African lion populations using non-invasive metabarcoding. Our findings highlight metabarcoding as a powerful tool to assess spatial variation in health and parasite diversity metrics for an endangered apex predator.},
}

@article {pmid41164289,
year = {2025},
author = {Mishra, P and Logan, AC and Prescott, SL},
title = {Reimagining criminal accountability: microbial and omics perspectives in the evolution of legal responsibility.},
journal = {Journal of law and the biosciences},
volume = {12},
number = {2},
pages = {lsaf022},
doi = {10.1093/jlb/lsaf022},
pmid = {41164289},
issn = {2053-9711},
abstract = {Recent advances in microbiome science and omics technologies are reshaping our understanding of human behavior, suggesting that microbial communities significantly influence cognition, impulse control, and aggression. Emerging studies in neuromicrobiology, including fecal transplant studies, are pointing toward a causal role for gut microbes and their metabolites in human cognition and behavior. This essay introduces the legalome-a framework integrating microbial perspectives, including microbiome and omics sciences, into the courts and larger criminal justice system. We argue that the legalome is on a trajectory that will move the field of neurolaw forward, and challenge traditional doctrines of mens rea and culpability. Drawing on recent court decisions related to auto-brewery syndrome, and neuro-microbiological research, we examine how subtle biological processes influence behavior in ways overlooked by current legal standards. Recent findings raise questions about criminal intent, biological determinism, and equitable access to scientific defenses. At the same time, emergent research also suggests potential for microbiome-based rehabilitative interventions. Despite methodological challenges, we advocate for interdisciplinary collaboration to harmonize biological research with legal principles, creating a more nuanced framework for justice in the twenty-first century. The legalome provides concrete implementation protocols and assessment tools that demonstrate practical utility for courts, practitioners, and policymakers.},
}

@article {pmid41164228,
year = {2025},
author = {Wei, S and Yin, H and Hu, X and Chi, Y and Zhang, L and Zhang, B and Qian, K and Xu, W},
title = {Detection of antimicrobial peptides from fecal samples of FMT donors using deep learning.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1689589},
pmid = {41164228},
issn = {2297-1769},
abstract = {INTRODUCTION: Antimicrobial peptides (AMPs) represent a class of short peptides that are widely distributed in organisms and are regarded as an effective means to tackle bacterial resistance, potentially functioning as substitutes for onventional antibiotics.

METHODS: We employed metagenomics in combination with deep learning to mine AMPs from the 120 fecal microbiota transplantation (FMT) donor metagenome. Subsequently, a comprehensive analysis of the candidate AMPs was conducted through metaproteomic cross-validation, solubility analysis, cross-validation with other prediction tools, correlation analysis, and molecular dynamics simulations. Finally, four candidate AMPs were selected for chemical synthesis, and experimental validation identified two with broad-spectrum antimicrobial activity. Furthermore, molecular docking was utilized to further analyze the antimicrobial mechanisms of the candidate AMPs.

RESULTS: Our approach successfully predicted 2,820,488 potential AMPs. After a comprehensive analysis, four candidate AMPs were selected for synthesis, two of which exhibited broad-spectrum antimicrobial activity. Molecular docking provided further insight into the binding mechanisms of these peptides.

DISCUSSION: This study demonstrates the feasibility of discovering functional AMPs from the human fecal microbiome using computational and experimental approaches, highlights the potential of mining novel AMPs from the fecal microbiome, and provides new insights into the therapeutic mechanisms of FMT.},
}

@article {pmid41163934,
year = {2025},
author = {Jafari, M and Alipour, M and Zamani, S and Mohtasham Amiri, A and Pourabbas, P and Hasannejad-Bibalan, M},
title = {Probiotics as a Complementary Medicine in Neurologic Disorders.},
journal = {Health science reports},
volume = {8},
number = {11},
pages = {e71422},
pmid = {41163934},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Today, neurological and neuropsychiatric disorders, including depression, anxiety, Parkinson's disease (PD), Alzheimer's disease (AS), autism spectrum disorder (ASD), and multiple sclerosis (MS), contribute significantly to global disability and healthcare burden. Most current treatment options only provide symptomatic relief and are limited by challenges such as drug resistance, systemic side effects, and poor blood-brain barrier permeability. The growing interest in the gut-brain axis has encouraged exploration of the gut microbiota as a potential therapeutic target. Probiotics-live microorganisms that may confer health benefits to the host-have been proposed to modulate the gut-brain axis through immune, metabolic, and neurochemical pathways.

METHODS: In this narrative review, a targeted search was performed across multiple databases to identify relevant articles, from which the key relationships and strategies were extracted. Then, we represented the findings to provide a comprehensive overview of the topic and highlight emerging trends and gaps in the literature.

RESULTS: Emerging preclinical and clinical studies suggest that specific probiotic strains can improve neurological symptoms by reducing neuroinflammation, supporting gut barrier integrity, and influencing neurotransmitter production. However, findings remain heterogeneous due to strain specificity, individual microbiome diversity, and methodological differences across studies. Preclinical and clinical studies suggest that specific probiotic strains can improve neurological symptoms by reducing neuroinflammation, enhancing gut barrier integrity, and influencing neurotransmitter production. Evidence supports their potential as adjunctive treatments for major neurological and neuropsychiatric disorders, including depression, anxiety, ASD, PD, AD, and MS, particularly in patients with gut dysbiosis or gastrointestinal comorbidities. However, findings remain heterogeneous due to strain specificity, individual microbiome variability, and methodological differences across studies.

CONCLUSION: This brief review summarizes the current evidence on the use of probiotics in neurological disorders, discusses potential mechanisms of action, and highlights safety considerations and limitations. Future directions include personalized probiotic therapies, large-scale randomized controlled trials, and integration with conventional neurological therapies. Overall, probiotics could be a low-risk, complementary option in the evolving field of neurotherapy, but more rigorous evidence is needed before definitive clinical recommendations can be made.},
}

@article {pmid41163826,
year = {2025},
author = {Alrahimi, JS and Ahmed, FA and Haneef, AA and Atar, D},
title = {Integrative Perspectives on Atherosclerosis: From Molecular Mechanisms to Therapeutic Approaches.},
journal = {Saudi journal of medicine & medical sciences},
volume = {13},
number = {4},
pages = {239-252},
pmid = {41163826},
issn = {2321-4856},
abstract = {Atherosclerosis, a leading cause of cardiovascular disease, is a complex, multifactorial disorder involving lipid accumulation, chronic inflammation, immune dysregulation, and metabolic disturbances. Recent advances highlight critical roles for the Stimulator of Interferon Genes (STING) pathway, macrophage immunometabolism (the metabolic reprogramming of immune cells), oxidative DNA damage, neutrophil heterogeneity, sex disparities, and interactions with the gut microbiome and non-coding RNAs (molecules that regulate gene expression without coding for proteins). This integrative review synthesizes current knowledge from molecular, immunological, and epidemiological perspectives to illuminate key mechanisms in atherogenesis. We critically examine emerging mechanistic insights, including STING-mediated inflammation and macrophage metabolic reprogramming, and their roles in plaque initiation and progression. The review further evaluates novel therapeutic approaches, ranging from established lipid-lowering agents (e.g., statins, PCSK9 inhibitors, inclisiran, and bempedoic acid) to anti-inflammatory strategies (e.g., IL-1β and IL-6 inhibitors) and potential STING-targeted interventions. By integrating recent discoveries across basic and clinical science, this review emphasizes the need for personalized, multi-targeted therapies addressing inflammation, metabolism, and immune signaling. We propose a research roadmap prioritizing translational studies that link molecular mechanisms to clinical outcomes, ultimately aiming to improve prevention and management of atherosclerotic cardiovascular disease.},
}

@article {pmid41163804,
year = {2025},
author = {Zhang, S and Zhang, K and Zheng, CX and Gao, YF and Deng, GR and Zhang, X and Yuan, Y and Jia, T and Tang, SY and He, GX and Gong, Z and Zhao, N and Ma, B and Tian, H and Zhang, H and Li, Z and Di-Wu, YC and Liu, YH and Kong, L and Ma, J and Jin, Y and Sui, BD},
title = {D-Mannose Alleviates Type 2 Diabetes and Rescues Multi-Organ Deteriorations by Controlling Release of Pathological Extracellular Vesicles.},
journal = {Exploration (Beijing, China)},
volume = {5},
number = {5},
pages = {20240133},
pmid = {41163804},
issn = {2766-2098},
abstract = {Type 2 diabetes (T2D) is a prevalent metabolic disease inducing alterations of multiple organ systems with currently no cure. Extracellular vesicles (EVs) have been increasingly noticed as one critical paracrine communicator inducing insulin resistance and metabolic disorders in T2D, but clinically available pharmaceuticals for controlling pathological EV release is lacking. Here, we discover that the natural monosaccharide D-mannose exists with an altered level in the db/db mouse T2D model. Intriguingly, oral administration of D-mannose with the drinking water safely ameliorates diabetic symptoms in db/db mice. D-mannose administration does not critically regulate the gut microbiome and circulatory T lymphocytes in treating T2D, while administrated D-mannose rapidly accumulates in the liver, alleviates hepatic steatosis and rescues insulin resistance. Regarding the mechanism, the T2D pathological EVs released by macrophages are targeted and reduced by D-mannose, which metabolically inhibits CD36 expression and restores function of hepatocytes. Importantly, by regulating macrophage EV release, D-mannose administration reveals extra-hepatic benefits and retards diabetic bone loss. Taken together, our findings unveil D-mannose as a candidate T2D therapeutic and highlight sugars governing intercellular EV crosstalk, paving an avenue for pharmaceutical T2D approaches with amelioration of multi-organ deteriorations.},
}

@article {pmid41163404,
year = {2025},
author = {Ricks, KD and Raglin, SS and Kent, AD},
title = {Signatures of local nitrogen adaptation in the Brachypodium distachyon root microbiome.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.70684},
pmid = {41163404},
issn = {1469-8137},
support = {NREC 2021-2-360190-334//Illinois Nutrient Research and Education Council/ ; ILLU-875-637//National Institute of Food and Agriculture/ ; DE-SC0018420//Biological and Environmental Research/ ; },
abstract = {Plants associate with diverse microbiomes that impact their fitness, yet the contribution of the microbiome to plant adaptation is uncertain. As plant recruitment of its microbiome can be both highly variable and genetically determined, we hypothesized this recruitment process may be the result of adaptive evolution, and contributing to plant local adaptation. We investigated the evolution and adaptive benefit of plant-microbiome recruitment by characterizing the rhizosphere communities across a genotypic panel of Brachypodium distachyon in a common garden experiment. By linking microbial communities to their host genotype's historic environment, we identified signatures of selection on plant-microbiome recruitment. Plant-microbiome composition was significantly correlated with the host genotype's historic environment, with enrichment of microbial traits aligned to local resource conditions. For example, genotypes from low-nitrogen environments recruited communities enriched in nitrogen acquisition traits. In a complementary experiment evaluating plant nitrogen response, these same genotypes were well-adapted to low-nitrogen environments, contingent on the presence of key nitrogen-cycling microbes. These results suggest that local adaptation in plants may partially be mediated by recruitment of beneficial microbiomes. This perspective suggests that plant adaptation may be an emergent property of host-microbe interactions, where evolutionary responses favor traits that promote recruitment of locally beneficial microbiomes.},
}

@article {pmid41163402,
year = {2025},
author = {Szóstak, N and Kozłowski, P and Zuo, T and Philips, A},
title = {The role of gut mycobiome in responses to cancer immunotherapy.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2571433},
doi = {10.1080/19490976.2025.2571433},
pmid = {41163402},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Mycobiome ; *Neoplasms/therapy/immunology/microbiology ; *Immunotherapy ; Animals ; Tumor Microenvironment/immunology ; *Fungi/classification/immunology ; Dysbiosis/microbiology/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; },
abstract = {The gut microbiome has emerged as an important modulator of cancer progression and therapy response, yet the role of its fungal component, the gut mycobiome, remains poorly understood. In this review, we summarize current knowledge on the relationship between intestinal fungi and cancer, with a particular focus on the potential influence of the gut mycobiome on the efficacy of immune checkpoint inhibitors (ICIs). Drawing from both human studies and preclinical models, we discuss evidence linking fungal dysbiosis to altered immune responses and therapy outcomes in cancer patients. Specific fungal taxa, such as Candida and Malassezia, have been associated with changes in the tumor microenvironment and modulation of host immunity. We also review the proposed mechanisms through which fungi may impact antitumor immunity, including interactions with immune receptors and production of bioactive metabolites. Although research in this field is still in its early stages, emerging data suggest that the gut mycobiome may serve as a biomarker for immunotherapy response and a potential target for therapeutic intervention. A better understanding of host-fungus interactions in the gut could contribute to the development of personalized strategies to improve the effectiveness and safety of cancer immunotherapy.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Mycobiome
*Neoplasms/therapy/immunology/microbiology
*Immunotherapy
Animals
Tumor Microenvironment/immunology
*Fungi/classification/immunology
Dysbiosis/microbiology/immunology
Immune Checkpoint Inhibitors/therapeutic use

@article {pmid41163367,
year = {2025},
author = {Seyoum, Y and de Lucia, C and Khalifa, K and Bergland, AK and Aarsland, D and van der Giezen, M},
title = {Gut enterotype- and body mass index (BMI)-dependent effects of anthocyanin supplementation on gut microbiota composition in individuals at risk for cognitive decline: a randomized placebo-controlled trial.},
journal = {Gut microbes},
volume = {17},
number = {1},
pages = {2570862},
doi = {10.1080/19490976.2025.2570862},
pmid = {41163367},
issn = {1949-0984},
mesh = {Humans ; *Anthocyanins/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; Aged ; Middle Aged ; Male ; Female ; Body Mass Index ; *Cognitive Dysfunction/microbiology ; Aged, 80 and over ; Double-Blind Method ; Dietary Supplements ; *Bacteria/classification/genetics/isolation & purification/drug effects ; RNA, Ribosomal, 16S/genetics ; Cognition/drug effects ; },
abstract = {Anthocyanins, bioactive flavonoids found in berries, modulate gut microbiota composition and influence health outcomes. This study investigated the effects of anthocyanin supplementation on gut microbiota and cognition in older adults (60-80 y) at risk of cognitive decline due to mild cognitive impairment (MCI) or cardiometabolic disorders (CMD). In a 24-week, randomised, double-blind, placebo-controlled trial (n = 99), participants received anthocyanin capsules or placebo. Gut microbiota composition was profiled using 16S rRNA sequencing, considering factors such as baseline enterotype, body mass index (BMI), and age. Overall, alpha diversity remained unchanged, while beta diversity indicated modest but significant intervention effects at the amplicon sequence variants level. Baseline enterotype strongly influenced responsiveness: enterotype one (higher diversity, eubiotic taxa) showed modest but consistent shifts, whereas enterotype two (dysbiotic, Bact2-like) exhibited broader but less coherent changes. BMI-specific responses included enrichment of Oscillibacter and Ezakiella in healthy-weight individuals and Bacteroidota taxa in obese participants, alongside consistent reductions in Firmicutes. Age stratification revealed heterogeneous, quartile-specific taxa modulations. Cognitive performance, measured by episodic memory, was unaffected, and microbial shifts did not mediate intervention effects. These findings demonstrate that anthocyanins selectively modulate the gut microbiome in an age-, BMI-, and enterotype-dependent manner, underscoring the importance of personalized microbiome-informed nutritional interventions.},
}

Humans
*Anthocyanins/administration & dosage
*Gastrointestinal Microbiome/drug effects
Aged
Middle Aged
Male
Female
Body Mass Index
*Cognitive Dysfunction/microbiology
Aged, 80 and over
Double-Blind Method
Dietary Supplements
*Bacteria/classification/genetics/isolation & purification/drug effects
RNA, Ribosomal, 16S/genetics
Cognition/drug effects

@article {pmid41163310,
year = {2025},
author = {Mundt, C and Yusufoğlu, B and Kudenko, D and Mertoğlu, K and Esatbeyoglu, T},
title = {AI-Driven Personalized Nutrition: Integrating Omics, Ethics, and Digital Health.},
journal = {Molecular nutrition & food research},
volume = {},
number = {},
pages = {e70293},
doi = {10.1002/mnfr.70293},
pmid = {41163310},
issn = {1613-4133},
abstract = {Personalized nutrition (PN) aims to prevent and manage chronic diseases by providing individualized dietary guidance based on genetic, metabolic, and lifestyle data. Artificial intelligence (AI) has become a key enabler in PN by analyzing large-scale, multiomics datasets in obesity, diabetes, cardiovascular, and gastrointestinal disorders, where digital twins and health knowledge graphs support personalized interventions. Current findings demonstrate that AI models can guide microbiome-based dietary interventions, and support obesity management, thereby extending the scope of conventional nutritional strategies as supported by deepened bibliometric analyses. This study highlights the global increase in AI-based PN studies, accelerated by digital health demands and the COVID-19 pandemic, and the expansion of traditional nutrition strategies through machine learning approaches with the integration of microbiome-based models and omics. However, challenges such as algorithmic bias, limited generalizability, and data privacy remain. To overcome these issues, diverse datasets, explainable AI approaches, and standardized multicenter validation protocols are proposed. These steps are critical for transforming AI-supported PN from a conceptual potential into a fair, reliable, and clinically applicable structure. The growing consensus in the literature highlights that AI can support individual and societal health goals by transforming nutrition science through predictive, adaptive, and ethically based approaches.},
}

@article {pmid41163286,
year = {2025},
author = {Shankar, A and Sharma, Y and Rastogi, M and Tulsawani, R and Kumar, P},
title = {Ganoderma lucidum: A Medicinal Mushroom with Prebiotic and Anticancer Potential in Gastrointestinal Cancers.},
journal = {Current pharmaceutical biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113892010377275250930170651},
pmid = {41163286},
issn = {1873-4316},
abstract = {INTRODUCTION: Ganoderma lucidum is considered a medicinal mushroom, as it primarily improves gut health by modulating the gut microbiota. As an abundant source of bioactive metabolites, antioxidants, and industrial enzymes, mushrooms make significant contributions to functional foods, nutrition, and pharmaceuticals. Polysaccharides derived from G. lucidum exhibit prebiotic potential, promoting the growth and activity of beneficial gut microorganisms.

METHODS: This review examines the impact of white rot basidiomycetes metabolites on colorectal cancer treatment. We have compiled and analyzed data from PubMed, Google Scholar, and ResearchGate, presenting a comprehensive report with a table for clear understanding.

RESULTS: Evidence from in vivo and in vitro studies demonstrates that G. lucidum has potential as a gastrointestinal cancer inhibitor by inducing pro-apoptosis, autophagy, G0/G1 cell cycle arrest, and immunomodulation.

DISCUSSION: Bioactive metabolites and polysaccharides have prebiotic potential, enhancing the growth and activity of beneficial gut microorganisms that may lower the risk of gastrointestinal cancers by modifying gut bacteria. The prebiotic properties may boost immunity, reduce inflammation, and strengthen intestinal barrier integrity.

CONCLUSION: The current review explores the therapeutic potential of G. lucidum and other medicinal mushrooms as dietary supplements, focusing on their impact on the gut microbiome and gastrointestinal cancer.},
}

@article {pmid41163279,
year = {2025},
author = {Singh, V and Shirbhate, E and Kore, R and Veerasamy, R and Sharma, PC and Tiwari, AK and Rajak, H},
title = {Targeting Microbiome-Derived Exosomes to Overcome Cancer Therapy Resistance: Mechanisms, Implications, and Opportunities.},
journal = {Mini reviews in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113895575416455251014053321},
pmid = {41163279},
issn = {1875-5607},
abstract = {Despite recent advances in both preclinical and cancer therapies, the growing problem of treatment resistance remains one of the most critical challenges in oncology. To overcome the drawbacks of current oncologic treatments, there is a pressing need for new approaches and potential therapeutic strategies. The interaction between the host microbiome and cancer has recently attracted significant research. Among the various routes of microbiome-cancer interaction, microbiome- derived exosomes also offer an intriguing avenue. Exosomes, which are small extracellular vesicles, originate from several distinct types of cells, including microbiome-associated cells. These vesicles participate in intra- and intercellular communication as well as alteration of the tumour microenvironment. Emphas In light of their possible functions as treatment response modifiers and mediators, this review seeks to explain an intricate link between cancer therapy resistance and exosomes produced from the microbiome. Preclinical studies reveal that microbiome-derived exosomes operate through horizontal transfer of resistance-conferring enzymes and TLR4/MYD88-dependent signalling, demonstrating 2-5 fold upregulation of resistance-associated miRNAs in drug-resistant models. Clinical evidence shows Akkermansia muciniphila improves anti-PD-1 immunotherapy outcomes. Fusobacterium nucleatum- derived vesicles promote oxaliplatin resistance through autophagy activation. We investigate how microbiota-derived exosomes might leverage resistance to conventional cancer treatments and their consequences for these treatments. However, limitations include inter-individual microbiome variability, challenging isolation protocols, and regulatory hurdles under FDA guidelines. We examine the possible applications of microbiome-derived exosomes as therapeutic and diagnostic tools, thereby reflecting the applicability of these findings in clinical practice. This offers an interesting path for new therapeutic approaches meant to solve treatment resistance and raise patient survival.},
}

@article {pmid41163185,
year = {2025},
author = {Debnath, SC and Bell, AG and McMurtrie, J and Temperton, B and Tyler, CR},
title = {Skin and gill microbiome profiles and network structures in farmed tilapia (Oreochromis niloticus) and their relationships with health conditions.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {113},
pmid = {41163185},
issn = {2524-4671},
abstract = {BACKGROUND: Tilapia is one of the most popular finfish in aquaculture, but various emerging infectious diseases are limiting the growth of the tilapia aquaculture industry globally. The external mucosal microbiomes of fish act as a first line of defence for maintaining host health. However, how skin and gill microbiomes differ between healthy and naturally infected tilapia remains poorly understood. Here, we employed 16S rRNA and 18S rRNA high-throughput metabarcoding to characterise the microbiome of tilapia skin, gills, and water from ponds reported with diseased and non-diseased conditions, and to investigate signatures of microbial dysbiosis related to health conditions.

RESULTS: Microbial diversity varied significantly across different sample types (gill, skin and pond water) and geographical locations. Skin and gill microbiomes from reported non-diseased conditions differed in the presence of the commensal genus Cetobacterium, while diseased gill-skin were enriched with pathogenic genera including Flavobacterium, Aeromonas, Vibrio, Vogesella, and Klebsiella. Additionally, the relative abundance of diatom Cyclotella in pond water under diseased conditions appeared to be almost double that of non-diseased pond water, albeit this was statistically non-significant. Cetobacterium formed a core component of the bacterial genera in the non-diseased gill and skin microbiome. In contrast, Aeromonas formed a core component of the core microbiome in the diseased gill and skin microbiomes. Analysis of the microbial co-occurrence network in the diseased skin and gill found it to be relatively less complex compared with these tissues in the non-diseased state.

CONCLUSIONS: The findings show that the tilapia microbiome differs across the skin and gill tissue surfaces, and from the pond waters in which they are cultured. In reported diseased cases, these microbiomes show enrichment of potential pathogenic genera and less complex microbial co-occurrence networks, which may be used as an indicator of microbial dysbiosis in aquaculture systems. Understanding how these alterations may be used to predict potential disease outbreaks requires an understanding of the functional impacts of the changes in the microbial assemblages, allowing for timely interventions to mitigate the impacts of disease in the aquaculture system.},
}

@article {pmid41163155,
year = {2025},
author = {Young, CE and Samuel, MA},
title = {Microglia sensing of peripheral signals that bridge the brain and body.},
journal = {Molecular neurodegeneration},
volume = {20},
number = {1},
pages = {114},
pmid = {41163155},
issn = {1750-1326},
mesh = {Humans ; *Microglia/metabolism ; Animals ; *Brain/metabolism/immunology ; *Signal Transduction/physiology ; *Neurodegenerative Diseases/metabolism ; Blood-Brain Barrier/metabolism ; },
abstract = {Microglia are the resident immune cell of the brain, and alterations in microglia signaling have been implicated in many neurodegenerative disorders. While microglia responses to central cues and other brain cell types are well documented, studies are increasingly investigating the impact of peripherally derived signals on microglia function. A diverse array of peripheral cues, including dietary components, hormones, and bacteria metabolites and components from the microbiome cross the blood brain barrier and directly influence microglia state through ligand-receptor interactions. This review highlights the complexity of brain-body interactions from the perspective of microglia function and proposes the idea that microglia could serve as a central hub of detection and regulation of body state changes. In addition, improving understanding of how microglia respond to peripheral cues will allow for improved preclinical experimental design. As peripheral cues have the potential to be more readily manipulated than central cues, these interactions also have implications for the treatment of many diseases and neurodegenerative disorders.},
}

Humans
*Microglia/metabolism
Animals
*Brain/metabolism/immunology
*Signal Transduction/physiology
*Neurodegenerative Diseases/metabolism
Blood-Brain Barrier/metabolism

@article {pmid41163128,
year = {2025},
author = {Xiao, LF and Li, Y and Lian, H and Liu, X and Wen, Y and Chen, X and Huang, W and Li, B and Luo, L and Wang, X and Tutt, C and Zheng, J and Wang, VY and Shao, NY},
title = {Comprehensive metagenomic analysis of the giant panda's oral microbiome reveals distinct taxonomic and functional characteristics.},
journal = {Animal microbiome},
volume = {7},
number = {1},
pages = {114},
pmid = {41163128},
issn = {2524-4671},
}

@article {pmid41163086,
year = {2025},
author = {Mooney, R and Corbett, E and Giammarini, E and Rodgers, K and Donet, C and Mui, E and Ansari, ATA and Ransingh, A and Vernekar, PS and Walia, HK and Sharma, J and Connolly, J and Hursthouse, A and Mukherji, S and Mukherji, S and Henriquez, FL},
title = {The Microbial Trojan Horse and Antimicrobial Resistance: Acanthamoeba as an Environmental Reservoir for Multidrug Resistant Bacteria.},
journal = {Environmental microbiology},
volume = {27},
number = {11},
pages = {e70193},
doi = {10.1111/1462-2920.70193},
pmid = {41163086},
issn = {1462-2920},
support = {NE/T012986/1//Natural Environment Research Council/ ; BT/IN/Indo-UK/AMR-Env/01/SM/2020-21//Department of Biotechnology, Ministry of Science and Technology, India/ ; },
mesh = {*Acanthamoeba/microbiology ; *Bacteria/drug effects/genetics/isolation & purification ; *Drug Resistance, Multiple, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Geologic Sediments/microbiology ; Microbial Sensitivity Tests ; },
abstract = {Antimicrobial resistance (AMR) is shaped by environmental pressures, yet the role of microbial predators such as Acanthamoeba in resistance dynamics remains poorly characterized. In this study, Acanthamoeba-associated bacterial communities (AAB) exhibited significantly higher multidrug resistance than sediment-associated bacterial communities (SAB) in a polluted estuarine system. All isolated amoebae belonged to the T4 genotype, suggesting selection for resilient host organisms. AAB displayed elevated multiple antibiotic resistance (MAR) indices and increased resistance to multiple antibiotic classes, particularly aminoglycosides, macrolides, fluoroquinolones and β-lactams. Correlation analysis revealed that resistance in AAB, but not SAB, was associated with potentially toxic elements (PTEs) known to influence phagocyte survival, including arsenic, vanadium, and calcium. These elements may select for traits that confer metal and antibiotic resistance. The findings support a model where protists act as selective environments for AMR, favoring bacteria that possess enhanced tolerance mechanisms. This work provides the first direct evidence linking PTE exposure to the intracellular resistome of Acanthamoeba-associated bacteria. It underscores the need for AMR monitoring frameworks that include protist-bacteria interactions, with implications for One Health and environmental risk assessment strategies. Moreover, this approach is scalable for application in low/middle-income countries, where AMR burden is greatest and surveillance capacity remains limited.},
}

*Acanthamoeba/microbiology
*Bacteria/drug effects/genetics/isolation & purification
*Drug Resistance, Multiple, Bacterial
*Anti-Bacterial Agents/pharmacology
Geologic Sediments/microbiology
Microbial Sensitivity Tests

@article {pmid41162880,
year = {2025},
author = {Jeon, HB and Won, H and Kim, HJ and Kim, SH and Chen, Y and Long, J and Tang, SL and Bathige, SDNK and Park, KI},
title = {Microbiome of wild oysters: assessing diversity and detecting potential pathogens using a metabarcoding approach.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {700},
pmid = {41162880},
issn = {1471-2180},
support = {RS-2022-KS221679//Korea Institute of Marine Science & Technology Promotion (KIMST)/ ; RS-2022-NR069484//National Research Foundation of Korea/ ; },
mesh = {Animals ; *DNA Barcoding, Taxonomic/methods ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Crassostrea/microbiology ; Biodiversity ; Republic of Korea ; *Ostreidae/microbiology ; Taiwan ; Philippines ; Eukaryota/genetics/classification/isolation & purification ; },
abstract = {BACKGROUND: The Pacific oyster (Crassostrea gigas) and the hooded oyster (Saccostrea cucullate) are ecologically and economically important species in the northwestern Pacific Ocean. However, sustainable oyster farming faces challenges from pathogenic diseases and environmental changes. Understanding microbial diversity in oysters is essential for managing pathogens, maintaining healthy microbial communities, and addressing microbial imbalances. This study aimed to investigate the diversity and composition of bacterial and protist communities in wild oysters from South Korea (C. gigas), Taiwan, and the Philippines (S. cucullata) using a metabarcoding approach.

RESULTS: Gill tissue and environmental DNA (eDNA) samples were analyzed to assess microbial community structure across species and regions. Bacterial richness significantly exceeded protist richness in all samples. Bacterial diversity was negatively correlated with sea surface temperature and positively correlated with latitude, indicating that temperature is a key driver of regional variation in bacterial community composition. Several potentially pathogenic protist and bacterial taxa were detected, including Perkinsus marinus, Bonamia ostreae, Haplosporidium costale, and Vibrio bathopelagicus. Notably, P. marinus and B. ostreae were identified in S. cucullata from Taiwan, while H. costale was detected in C. gigas from South Korea. Most pathogens occurred at low infection intensities and without clinical signs of disease. Challenges in detecting protist diversity due to sequencing depth and host-derived nontarget amplification were also noted, highlighting the importance of using protist-specific primers.

CONCLUSIONS: This study demonstrates the utility of metabarcoding for characterizing microbial communities and detecting pathogens in two oyster species, C. gigas and S. cucullate, across geographically distinct regions. Bacterial richness was influenced by environmental gradients such as sea surface temperature and latitude, while several key protist pathogens (P. marinus, B. ostreae, H. costale) were detected at low infection intensities in asymptomatic oysters. Limitations in protist detection due to sequencing depth and host amplification highlight the need for optimized primers and complementary approaches such as multiomics and microscopy. These findings provide a foundation for understanding host-microbe-environment interactions. Specifically, our results can inform targeted monitoring programs for the early detection of pathogens and guide selective breeding initiatives for disease-resistant oyster strains, thereby enhancing the long-term resilience of oyster aquaculture under changing environmental conditions.},
}

Animals
*DNA Barcoding, Taxonomic/methods
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
*Crassostrea/microbiology
Biodiversity
Republic of Korea
*Ostreidae/microbiology
Taiwan
Philippines
Eukaryota/genetics/classification/isolation & purification

@article {pmid41162873,
year = {2025},
author = {Zhou, X and Huang, J and Zhu, Y and Wei, Y and Liao, L and Li, J and He, Y and Yang, S},
title = {The distinct characteristics of the endophytic microbiome and metabolome within the root system result in varying abilities of watermelon resistance against Fusarium wilt.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1475},
pmid = {41162873},
issn = {1471-2229},
support = {Guike2023AB17011//Key R&D Planning Project of Guangxi/ ; Guike2023AB17011//Key R&D Planning Project of Guangxi/ ; Guinongke 2021YT045//Basic research project of Guangxi Academy of Agricultural Science/ ; Guinongke 2021ZX19//Science and technology development project of Guangxi Academy of Agricultural Science/ ; nycytxgxcxtd-17-04; nycytxgxcxtd-17-01//National modern Agricultural Technology System/ ; },
mesh = {*Citrullus/microbiology/metabolism/immunology ; *Plant Roots/microbiology/metabolism ; *Metabolome ; *Plant Diseases/microbiology/immunology ; *Endophytes/physiology ; *Disease Resistance ; *Fusarium/physiology ; *Microbiota ; },
abstract = {BACKGROUND: The structure of endophytic microbial communities and metabolic functions differ significantly among plant varieties with different resistance levels. Currently, there is a lack of research articles that combine microbiomics and metabolomics to explore the mechanism of resistance to wilt disease in watermelon. To seek out the antagonistic microorganisms and metabolites against watermelon wilt from different watermelon varieties, we investigated the characteristics of endophytic microbial communities, metabolic features and functions in the roots of wilt-resistant (RW) and susceptible (SW) watermelon varieties.

RESULTS: The results suggested that significant differences of endophytic microbial communities and metabolites could be found in the roots between RW and SW. Meanwhile, the endophytic bacterial genera such as Chryseobacterium, Pseudomonas, Delftia, Lechevalieria, unclassified_f__Methylophilaceae, Tahibacter, and the endophytic fungal genera, unclassified_p__Basidiomycota, Neocosmospora, unclassified_f__Lasiosphaeriaceae, Edenia were the unique dominant bacterial and fungal genera in the roots of RW, respectively. Additionally, the differential metabolites, including Galactinol, Sucrose, Stachyose, Coniferyl Aldehyde, Coniferin, 5-Hydroxyconiferyl alcohol, 4-Coumaryl alcohol, 3-Hydroxybenzoic Acid, and the metabolic pathways including Galactose metabolism, Phenylpropanoid biosynthesis, Phenylalanine, tyrosine and tryptophan biosynthesis significantly upregulated in wilt resistant watermelon varieties.

CONCLUSION: This study systematically reveals, for the first time, the synergistic defense mechanisms between root endophytic microbiome and metabolome during Fusarium wilt resistance formation in watermelon. Significantly, we have identified potential functional microorganisms, key metabolites, and critical pathways that actively contribute to these defense mechanisms. However, the specific functions of these potential antagonistic microorganisms and metabolites still need further validation. These findings provide a novel perspective for crop disease resistance research, transcending the limitations of traditional single-factor analytical paradigms, while establishing a methodological foundation for developing multi-omics integrated approaches in crop disease resistance regulation strategies.},
}

*Citrullus/microbiology/metabolism/immunology
*Plant Roots/microbiology/metabolism
*Metabolome
*Plant Diseases/microbiology/immunology
*Endophytes/physiology
*Disease Resistance
*Fusarium/physiology
*Microbiota

@article {pmid41162857,
year = {2025},
author = {Liu, Y and Xu, C and Chen, S and Chu, G and Yu, K and Wang, D},
title = {Beyond genotype: the influence of developmental stage on rice rhizospheric microbiome-metabolome networks.},
journal = {BMC plant biology},
volume = {25},
number = {1},
pages = {1471},
pmid = {41162857},
issn = {1471-2229},
support = {32201899//the Young Scientists Fund of the National Natural Science Foundation of China/ ; CPSIBRF-CNRRI-202410//the Central Public-interest Scientific Institution Basal Research Fund/ ; 2023C02005-4//the "Pioneer" and ''Leading Goose" Key R&D Program of Zhejiang/ ; CARS-01//the National Rice Industry Technology System/ ; },
}

@article {pmid41162659,
year = {2025},
author = {Campbell, IW and Basta, DW and Zingl, FG and Sullivan, EJ and Doranga, S and Waldor, MK},
title = {Anoxia activates CRISPR-Cas immunity in the mouse intestine.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {41162659},
issn = {2058-5276},
support = {P30 DK034854/DK/NIDDK NIH HHS/United States ; R01 AI042347/AI/NIAID NIH HHS/United States ; Investigator program//Howard Hughes Medical Institute (HHMI)/ ; },
abstract = {The natural context in which CRISPR-Cas systems are active in Enterobacteriaceae has remained enigmatic. Here we find that the Citrobacter rodentium type I-E CRISPR-Cas system is activated by the oxygen-responsive transcriptional regulator Fnr in the anoxic environment of the mouse intestine. Since Fnr-dependent regulation is predicted in ~41% of Enterobacteriaceae cas3 orthologues, we propose that anoxic regulation of CRISPR-Cas immunity is an adaptation that protects Enterobacteriaceae against threats from foreign DNA within the intestinal microbiome.},
}

@article {pmid41162426,
year = {2025},
author = {Zhao, Y and Yao, S and Umar, A and Huang, J and Chen, S and Yu, Z},
title = {Comprehensive multi omics explore the microbial function in metabolic pathway flow during altered diet.},
journal = {NPJ science of food},
volume = {9},
number = {1},
pages = {212},
pmid = {41162426},
issn = {2396-8370},
support = {82270564//National Natural Science Foundation of China/ ; 32170071//National Natural Science Foundation of China/ ; 2022JJ30916//Natural Science Foundation of Hunan Province/ ; 2022M713521//China Postdoctoral Science Foundation/ ; 2023CXQD059//Central South University Innovation-Driven Research Programme/ ; },
abstract = {High-protein diet (HPD) and high-fiber diet (HFiD) are two common types of diet, and the transition from HPD to HFiD frequently happens in people who perform diet control. Gut microbiota provide a bridge between diet and health. However, most of the research left out the metabolic landscape change and gut microbial influence under this kind of altered diet. Here, we examined gut microbiome and metabolites change using multi-omics (16S rRNA gene sequencing, shotgun metagenomics, LC-MS/MS metabolomics), and machine-learning methods were introduced to capture the response of gut microbiota to altered diet and associate the variable metabolites and microbial factors. The results suggest that the conversion from HPD to HFiD improves the gut microbial diversity and promotes the pathways of tryptophan, galactose, fructose, and mannose metabolism, which are associated with different gut microbiota and special metabolites. Among them, Faecalibacterium rodentium and Akkermansia muciniphila indicate potential roles in the multi-metabolism. Although these findings are exploratory and hypothesis-generating, they provide a foundation for future mechanistic investigations and emphasize the importance of diverse diets.},
}

@article {pmid41162403,
year = {2025},
author = {Kowal, M and Sorokowski, P and David, O and Iuga, IA and Renwick, S and Sorokowska, A},
title = {Microbiome and well-being: a meta-analysis.},
journal = {NPJ biofilms and microbiomes},
volume = {11},
number = {1},
pages = {201},
pmid = {41162403},
issn = {2055-5008},
support = {PNRR-III-C9-2023-I8-CF 32/28.07.2023//European Union/ ; PNRR-III-C9-2023-I8-CF 32/28.07.2023//European Union/ ; PNRR-III-C9-2023-I8-CF 32/28.07.2023//European Union/ ; PNRR-III-C9-2023-I8-CF 32/28.07.2023//European Union/ ; PNRR-III-C9-2023-I8-CF 32/28.07.2023//European Union/ ; },
mesh = {Humans ; *Microbiota ; Male ; Female ; *Bacteria/classification/genetics/isolation & purification ; *Mental Health ; },
abstract = {The human microbiome may play a significant role in both health and disease. However, most studies to date have focused on the microbiome's role in pathogenesis, while its potential role in promoting well-being remains underexplored. We conducted the first meta-analysis synthesizing empirical evidence on associations between the human microbiome and psychological well-being. Based on eight analyzed studies (N = 2526 participants), we found that both microbial diversity and taxonomic abundance were positively associated with psychological well-being, with diversity emerging as the stronger predictor. Notably, these associations appeared consistent across sex and age. This study provides preliminary evidence that microbiome composition may support salutogenic processes and offers a foundation for future integration of microbiome science into psychological and clinical interventions. However, given the small number of empirical studies included in the meta-analysis, the generalizability of these findings remains limited. Further research is required to strengthen and refine our understanding of the microbiome-well-being relationship.},
}

Humans
*Microbiota
Male
Female
*Bacteria/classification/genetics/isolation & purification
*Mental Health

@article {pmid41162327,
year = {2025},
author = {Trunfio, M and Smith, D and Gaitan, N and Awad, M and Porrachia, M and Wells, A and Rivera-Nieves, J and Hastie, E and Riggs, P and Gianella, S and Chaillon, A},
title = {HIV Reservoir Dynamics and Bacteriome Composition Along the Gut Axis.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiaf546},
pmid = {41162327},
issn = {1537-6613},
abstract = {BACKGROUND: The gastrointestinal (GI) tract is a major reservoir of HIV and home to the body's most diverse microbiome. However, the role of gut bacteriome in modulating local HIV persistence remains uninvestigated.

METHODS: Leveraging rapid autopsy samples (n=113) from 24 people with HIV (PWH) in the Last Gift cohort, we performed 16S rRNA sequencing and quantified total HIV DNA and msTat/Rev RNA (ddPCR) across five GI segments (duodenum, jejunum, ileum, colon, rectum). Associations between relative abundance of bacterial taxa and reservoir characteristics were analyzed using multivariable models.

RESULTS: HIV DNA levels were highest in the jejunum, intermediate in duodenum and ileum, and lowest in the colon and rectum (p<0.05 for all). HIV transcriptional activity was higher-than-expected relatively to the reservoir size in duodenum and ileum. Bacterial communities significantly differed in richness and composition across the segments (PERMANOVA p=0.002). Higher richness was associated with increased HIV transcriptional activity in the small bowel (ρ=0.32, p=0.015), and decreased activity in the large bowel (ρ=-0.41, p=0.013). Segment-specific associations between taxa and HIV reservoir were observed; among these, short-chain fatty acid-producers, mucin-degraders, and bile acid-metabolizers were consistently associated with reduced reservoir size and activity in the large bowel, but with enhanced transcription in proximal segments. Sensitivity analyses by antibiotic exposure, cancer, and viral load confirmed robustness of findings.

CONCLUSIONS: The gut bacteriome modulates HIV reservoir size and activity, and these effects vary along the GI tract. This regional specificity must be considered when designing bacteriome-based strategies to reduce HIV persistence and improve cure efforts.},
}

@article {pmid41162230,
year = {2025},
author = {Neo, VK and Fong, SW and Ng, LFP},
title = {From structure to immunity: how skin shapes age-related vulnerability to Chikungunya virus infections.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.10.001},
pmid = {41162230},
issn = {1878-4380},
abstract = {Arboviral diseases are resurging globally, with Chikungunya virus (CHIKV) demonstrating a troubling capacity for large-scale outbreaks. In 2024, CHIKV re-emerged in Réunion Island with 47 500 cases and 12 deaths reported by May 2025. Notably, infants and the elderly were disproportionately affected, two age groups with distinct and underexplored vulnerabilities in immune defense, particularly at the skin. As the skin is the primary site of CHIKV inoculation and a key immunological barrier, age-dependent changes in the skin likely influence infection outcomes. Yet, it remains an overlooked target for intervention. This review explores how developmental and aging-associated alterations in the skin's structure, immune composition, and the microbiome shape arboviral pathogenesis, with a particular emphasis on CHIKV, and guides research toward age-tailored interventions for vulnerable populations.},
}

@article {pmid41162178,
year = {2025},
author = {Zhang, Q and Zhang, Y and Zhu, J and Gao, Y and Zeng, W and Qi, H},
title = {Microbiome Profiling of Pretreated Human Breast Milk Using Shotgun Metagenomic Sequencing.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2506012},
doi = {10.4014/jmb.2506.06012},
pmid = {41162178},
issn = {1738-8872},
mesh = {*Milk, Human/microbiology ; Humans ; Female ; *Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Metagenome ; Sequence Analysis, DNA ; Archaea/genetics/classification/isolation & purification ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {This study explored the metagenomic sequencing methodology for analyzing the breast milk microbiome and elucidated its composition. Twenty-two breast milk samples were collected from 11 healthy lactating women. By optimizing microbial cell wall disruption parameters and developing a nucleic acid extraction method, microbial DNA/RNA libraries were constructed and subjected to metagenomic next-generation sequencing (mNGS), microbial standards spiked into breast milk at serial dilutions served to validate the method's reliability. The sequencing data underwent rigorous quality control and classification using the Kraken2 software and a self-generated database. The breast milk microbiome was found to comprise 21 phyla, 234 genera, and 487 species, with Firmicutes and Proteobacteria being the dominant phyla. At the genus level, Staphylococcus and Streptococcus were the most abundant, while at the species level, Staphylococcus aureus, Streptococcus bradystis, and Staphylococcus epidermidis were the most prevalent. The microbial profiles of the left and right breast milk samples were consistent at the phylum, genus, and species levels. Besides common bacteria, diverse viral, eukaryotic, and archaeal sequences were also detected. Functional profiling revealed that the "lactose and galactose degradation I" pathway accumulated the highest read count, whereas the L-valine biosynthesis pathway was detected most frequently. This study provides a comprehensive understanding of the healthy breast milk microbiome, highlighting the presence of specific flora colonization and the distinct yet correlated microbial environments in bilateral breast milk, laying the groundwork for future research into the interactions between breast milk microbiota and maternal and infant health outcomes.},
}

*Milk, Human/microbiology
Humans
Female
*Microbiota/genetics
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
*Bacteria/classification/genetics/isolation & purification
Adult
Metagenome
Sequence Analysis, DNA
Archaea/genetics/classification/isolation & purification
Phylogeny
DNA, Bacterial/genetics

@article {pmid41162177,
year = {2025},
author = {Nam, Y and Seo, G and Kim, Y and Kim, SR and Kim, JN},
title = {Comparative Analysis of Microbial Communities and Biopolymer Production in Kombucha.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2508004},
doi = {10.4014/jmb.2508.08004},
pmid = {41162177},
issn = {1738-8872},
mesh = {Cellulose/biosynthesis/metabolism ; Fermentation ; Biopolymers/biosynthesis/metabolism ; *Bacteria/metabolism/classification/genetics/isolation & purification ; *Microbiota ; *Kombucha Tea/microbiology ; Yeasts/metabolism/classification/genetics/isolation & purification ; Ethanol/metabolism ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Acetobacteraceae/metabolism/isolation & purification ; },
abstract = {While the microbial diversity of kombucha has been previously investigated, only a limited number of studies have explicitly distinguished between the symbiotic culture of bacteria and yeast (SCOBY) and the liquid broth, and even fewer have directly associated microbial diversity with bacterial cellulose production. This study investigated the microbial communities present in commercially available kombucha products by using both culture-based and molecular analysis methods, along with metabolite profiling by chemical analyses. Culture-based methods identified key cellulose-producing strains, including Komagataeibacter intermedius, K. rhaeticus, and Novacetimonas hansenii, while next-generation sequencing revealed Komagataeibacter as the dominant bacterial genus in kombucha. Yeast communities in kombucha were predominated by Zygosaccharomyces bisporus and Z. parabailii. As fermentation progressed, all kombucha samples exhibited typical fermentation dynamics, characterized by progressive sucrose depletion and an increase in ethanol and acetate production. Given the promising industrial applications of bacterial cellulose, the biopolymer content of kombucha was evaluated. Among the kombucha samples, K2 showed the highest cellulose yield (4.50 ± 2.28 g), and N. hansenii was identified as the most efficient cellulose producer among the isolates. This integrative approach provides critical insights into the role of microbial communities in regulating kombucha fermentation. Specifically, this study delineated the core microbiota required for stable fermentation and identified strains with enhanced cellulose-producing capacity. Beyond defining the key microbial taxa associated with kombucha production, these findings underscore the industrial potential of kombucha-derived cellulose producers and present a strategy for optimizing bacterial cellulose yield in large-scale applications.},
}

Cellulose/biosynthesis/metabolism
Fermentation
Biopolymers/biosynthesis/metabolism
*Bacteria/metabolism/classification/genetics/isolation & purification
*Microbiota
*Kombucha Tea/microbiology
Yeasts/metabolism/classification/genetics/isolation & purification
Ethanol/metabolism
High-Throughput Nucleotide Sequencing
Phylogeny
Acetobacteraceae/metabolism/isolation & purification

@article {pmid41162173,
year = {2025},
author = {Peng, G and Sun, B and Gao, S and Cheng, J and Chen, S and Shi, G and Zhang, L},
title = {Protective and Reparative Effects of Tremella aurantialba Extract against Skin Photoaging and Its Underlying Mechanisms.},
journal = {Journal of microbiology and biotechnology},
volume = {35},
number = {},
pages = {e2507053},
doi = {10.4014/jmb.2507.07053},
pmid = {41162173},
issn = {1738-8872},
mesh = {*Skin Aging/drug effects/radiation effects ; Animals ; Humans ; Mice ; Ultraviolet Rays/adverse effects ; Skin/drug effects/radiation effects/metabolism ; *Plant Extracts/pharmacology/chemistry ; HaCaT Cells ; Reactive Oxygen Species/metabolism ; Antioxidants/pharmacology ; Cell Movement/drug effects ; Cell Survival/drug effects ; Metabolomics ; },
abstract = {While Tremella aurantialba (T. aurantialba) is known for its significant antioxidant and anti-inflammatory activities, its role in skin photoaging remains unclear. In this study, we elucidated the protective mechanisms of T. aurantialba extract (TAE) against ultraviolet A and ultraviolet B (UVA/UVB)-induced skin photoaging. Using UHPLC-Q-Orbitrap-MS analysis, a total of 24 compounds were identified from TAE, including trigonelline (22.83%), isonicotinic acid (18.16%), acetylcholine (16.66%), choline (15.02%), and 2-hydroxyphenylalanine (6.85%). In vitro investigations revealed that TAE significantly enhanced the survival rate of UVB-induced HaCaT cells, promoted cell migration, and increased the migration rates to above 50%, while concurrently reducing reactive oxygen species (ROS) levels. In vivo, TAE suppressed abnormal epidermal thickening and mast cell infiltration induced by UVA/UVB in the dorsal skin of mice, and facilitated the restoration of collagen fibers. Metabolomics analysis indicated that TAE mitigated photoaging mainly by modulating the sphingolipid and glycerophospholipid metabolic pathways. Skin microbiome analysis showed that TAE boosts Bacillota and Bacteroidota while suppressing Exiguobacterium and Lachnospiraceae, consequently restoring skin microbiota balance and facilitating skin repair. Transcriptome analysis demonstrated that genes modulated by TAE were primarily concentrated in lipid metabolism, circadian rhythm, and response to oxygen-containing compounds. This suggests TAE facilitated skin barrier repair and mitigated UVA/UVB-induced photoaging by modulating cellular physiological rhythms and lipid metabolism, while controlling oxidative stress. In conclusion, TAE mitigates UVA/UVB-induced damage via multi-targeted antioxidant, anti-inflammatory, and skin barrier repair-promoting effects, thereby establishing a scientific basis for its application in developing functional foods and cosmetics to target photoaging.},
}

*Skin Aging/drug effects/radiation effects
Animals
Humans
Mice
Ultraviolet Rays/adverse effects
Skin/drug effects/radiation effects/metabolism
*Plant Extracts/pharmacology/chemistry
HaCaT Cells
Reactive Oxygen Species/metabolism
Antioxidants/pharmacology
Cell Movement/drug effects
Cell Survival/drug effects
Metabolomics

@article {pmid41162084,
year = {2025},
author = {Subhagan, SR and Pathrose, B and Chellappan, M and Dharaneedharan, D},
title = {Beyond gut and neural mechanisms: A multi-organ system perspective on insecticide resistance.},
journal = {Pesticide biochemistry and physiology},
volume = {215},
number = {},
pages = {106701},
doi = {10.1016/j.pestbp.2025.106701},
pmid = {41162084},
issn = {1095-9939},
mesh = {*Insecticide Resistance ; Animals ; *Insecticides/pharmacology ; *Insecta/drug effects/physiology ; Fat Body/metabolism/drug effects ; Malpighian Tubules/metabolism/drug effects ; },
abstract = {Insecticide resistance has usually been studied through isolated mechanisms, primarily focusing on target-site insensitivity, metabolism and cuticular modifications. However, substantial gaps remain in understanding how various organs and systems interact and work together to contribute to resistance. Emerging research, highlights resistance as a multi-organ phenomenon, where multiple physiological systems contribute to detoxification, toxin transport, immune modulation, trade-offs, stress adaptation and survival under insecticidal pressure. This review explores the role of fat body metabolism, circulatory transport, transgenerational effects, respiratory adjustments, Malpighian tubule excretion and endocrine regulation in shaping insecticide resistance. These organ systems engage in complex inter-organ signaling and compensatory mechanisms, allowing resistant insects to mitigate the toxic effects of insecticides while maintaining fitness. Advancements in research such as multi-omics technologies, single-cell RNA sequencing and advanced imaging techniques can provide deeper insights into these systemic adaptations and help develop more precise and targeted management strategies. However, challenges remain in deciphering inter-organ communication, identifying tissue-specific resistance markers, and developing field-ready diagnostic methods. Addressing these gaps through functional genomics, systems biology, and microbiome-targeted strategies will be crucial for sustainable pest control. By integrating multi-organ system perspectives, future research can develop more effective and targeted resistance management approaches, ensuring the long-term efficacy of insecticides used.},
}

*Insecticide Resistance
Animals
*Insecticides/pharmacology
*Insecta/drug effects/physiology
Fat Body/metabolism/drug effects
Malpighian Tubules/metabolism/drug effects

@article {pmid41162056,
year = {2025},
author = {Peng, Y and Zhang, X and Wang, G and Liu, Q and Zhan, T and Xu, S and Xiao, G and Du, G and Wang, W and Chen, B},
title = {BbCFEM7 contributes to the virulence of entomopathogenic fungi by competing for iron with Enterococcus mundtii.},
journal = {Pesticide biochemistry and physiology},
volume = {215},
number = {},
pages = {106666},
doi = {10.1016/j.pestbp.2025.106666},
pmid = {41162056},
issn = {1095-9939},
mesh = {Animals ; *Beauveria/pathogenicity/genetics/metabolism ; Virulence ; *Enterococcus/metabolism/pathogenicity ; *Iron/metabolism ; Hemolymph/microbiology/metabolism ; *Fungal Proteins/genetics/metabolism ; Gastrointestinal Microbiome ; },
abstract = {Common in fungal extracellular membrane (CFEM) domain proteins are a unique family of extracellular membrane proteins in fungi. Beauveria bassiana, as a entomopathogenic fungus, plays a critical role in the biological control of agricultural and forestry pests. However, the mechanism of interaction between entomopathogenic fungi and host gut microbes is rarely reported. The contribution of the BbCFEM7 gene to fungal growth virulence and immune defense was evaluated. According to the gut microbial diversity results, the absence of BbCFEM7 had a considerable influence on the insect gut bacterial communities, especially enterococcus. The infection with ΔBbCFEM7 strains significantly affected the contents of fatty acids (including short-chain fatty acids), organic acids, and indole metabolites in insect gut and hemolymph when compared to wild type strain (WT). Enterococcus mundtii was isolated in a fungus-infected insect hemolymph. According to in vitro and in vivo experiments, fungi and bacteria exerted an inhibitory effect on the growth of each other through rapid iron acquisition. Our study demonstrated that when B. bassiana infected insects, BbCFEM7 competed for iron ions with the E. mundtii escaping from the gut to the hemolymph, inducing metabolic dysregulation in the gut and hemolymph, thereby evading host immunity and augmenting fungal virulence. Enriching the host infection mechanism of fungal CFEM domain proteins, the results of this study provide a new reference for supplementing the Anna Karenina Principle (AKP) and further revealing the interaction between insect gut bacteria and pathogenic fungi.},
}

Animals
*Beauveria/pathogenicity/genetics/metabolism
Virulence
*Enterococcus/metabolism/pathogenicity
*Iron/metabolism
Hemolymph/microbiology/metabolism
*Fungal Proteins/genetics/metabolism
Gastrointestinal Microbiome

@article {pmid41162031,
year = {2025},
author = {Zhang, Z and Zhou, T and Pan, C and Li, M and Wang, J and Wang, X and Wang, S and Hu, Z and Sun, R and Li, D},
title = {Nanoselenium-driven reduction in chemical fungicide usage: Eco-safety enhancement in pepper Phytophthora capsici control.},
journal = {Pesticide biochemistry and physiology},
volume = {215},
number = {},
pages = {106639},
doi = {10.1016/j.pestbp.2025.106639},
pmid = {41162031},
issn = {1095-9939},
mesh = {*Phytophthora/drug effects ; *Fungicides, Industrial/pharmacology ; Plant Diseases/prevention & control/microbiology ; *Capsicum/microbiology/drug effects ; *Selenium/pharmacology/chemistry ; Strobilurins/pharmacology ; Pyrimidines ; },
abstract = {Phytophthora blight, caused by Phytophthora capsici, poses a devastating threat to pepper production, driving heavy reliance on chemical pesticides like azoxystrobin. However, the rapid evolution of fungicide resistance in P. capsici and the environmental risks of conventional agrochemicals demand sustainable alternatives. While nano‑selenium (nano-Se) is known to enhance plant antioxidant capacity and modulate secondary metabolism, its role in regulating plant secondary metabolite-microbe interactions for oomycete resistance remains underexplored. Here, we engineered a nano-Se formulation as a green nanofungicide, demonstrating superior anti-oomycete efficacy (EC50 = 8 mg/L) compared to azoxystrobin and berberine. Nano-Se directly triggered peroxidative damage in P. capsici hyphae, inducing intracellular leakage, respiratory suppression, and irreversible cell death. Bidirectional translocation of nano-Se within pepper plants enhanced systemic antioxidant defenses and growth, while reprogramming coumarin and phenylpropanoid biosynthesis pathways. This metabolic rewiring elevated antifungal coumarins (6-nitrocoumarin, 6-hydroxycoumarin), phytohormones (JA, SA), and phenolic acids (ferulic acid, sinapic acid), with 6-nitrocoumarin (10 mg/L) exhibiting potent P. capsici suppression via dual modulation of redox homeostasis and secondary metabolism. Critically, nano-Se remodeled the rhizosphere microbiome, enriching plant-beneficial taxa and fostering pathogen-suppressive microbial consortia. By synergizing coumarin-mediated antifungal activity with microbiome engineering, nano-Se reduced chemical dependency while enhancing pepper resistance to P. capsici. Our findings provide a mechanistic roadmap for deploying nano-Se as an eco-safe agrochemical, addressing fungicide resistance and environmental hazards in soilborne disease management.},
}

*Phytophthora/drug effects
*Fungicides, Industrial/pharmacology
Plant Diseases/prevention & control/microbiology
*Capsicum/microbiology/drug effects
*Selenium/pharmacology/chemistry
Strobilurins/pharmacology
Pyrimidines

@article {pmid41161821,
year = {2025},
author = {Zhou, Z and Lin, JR and Li, J and Huang, X and Yuan, L and Huang, J and Xie, W and Lu, J and Huang, W and He, S and Yu, D and Zhang, H and Ge, X and Li, M and Mao, Y and Yang, F and Cui, ZK and Su, X and Zhan, Y and Liu, L},
title = {Metagenomic next-generation sequencing unraveled the characteristic of lung microbiota in patients with checkpoint inhibitor pneumonitis: results from a prospective cohort study.},
journal = {Journal for immunotherapy of cancer},
volume = {13},
number = {10},
pages = {},
doi = {10.1136/jitc-2025-012444},
pmid = {41161821},
issn = {2051-1426},
mesh = {Humans ; Male ; Female ; Prospective Studies ; *High-Throughput Nucleotide Sequencing/methods ; *Immune Checkpoint Inhibitors/adverse effects/pharmacology ; Middle Aged ; *Metagenomics/methods ; *Microbiota ; *Pneumonia/chemically induced/microbiology/diagnosis ; Aged ; *Lung/microbiology ; Bronchoalveolar Lavage Fluid/microbiology ; },
abstract = {BACKGROUND: Checkpoint inhibitor pneumonitis (CIP) is among the most lethal immune-related adverse events in patients with cancer receiving immunotherapy. This study aims to characterize the lung microbiome in patients with CIP and evaluate its diagnostic potential.

METHODS: In a prospective clinical trial (NCT06192303), bronchoalveolar lavage fluid samples (BALF) were obtained from 38 patients presenting clinical symptoms and radiographic evidence of pneumonitis following immunotherapy. The cohort included 14 cases of pure-type CIP (PT-CIP), 14 cases of mixed-type CIP, and 10 cases of pulmonary infection (PI). Metagenomic next-generation sequencing (mNGS) of BALF was employed to delineate the lung microbiota profiles. Using linear discriminant analysis effect size, we discerned characteristic microbiota among the three groups and further explored the associations of signature microbiota with host immune-inflammatory markers. Functional enrichment analysis revealed potential metabolic reprogramming and differences in biological functions between patients with CIP and PI. Finally, leveraging four machine-learning models, we ascertained the clinical value of BALF microbiota profiles in diagnosing CIP.

RESULTS: The composition of lung microbiota differed significantly between patients with CIP and PI. Microbial taxa, such as Porphyromonas, Candida, Peptostreptococcus, Treponema, and Talaromyces, exhibited distinct abundance patterns across the three groups. Correlation analysis revealed a significant positive relationship between Candida abundance and host immune-inflammatory markers, such as neutrophil-lymphocyte ratio, platelet-lymphocyte ratio, monocyte-lymphocyte ratio, and systemic immune inflammation index. In contrast, Porphyromonas demonstrated a significant negative correlation. Compared with the patients with PT-CIP, the lung microbiota of patients with PI exhibited a more diverse biological and metabolic profile. Additionally, machine learning models based on BALF microbiota profiles could accurately diagnose CIP, with the decision tree model showing the best diagnostic performance (area under the curve: 0.88).

CONCLUSIONS: Our study represents the unique characterization of the lung microbiota profiles across distinct CIP subtypes and establishes a diagnostic model for CIP based on the decision tree. These findings emphasize the value of BALF mNGS in improving the diagnosis of CIP.},
}

Humans
Male
Female
Prospective Studies
*High-Throughput Nucleotide Sequencing/methods
*Immune Checkpoint Inhibitors/adverse effects/pharmacology
Middle Aged
*Metagenomics/methods
*Microbiota
*Pneumonia/chemically induced/microbiology/diagnosis
Aged
*Lung/microbiology
Bronchoalveolar Lavage Fluid/microbiology

@article {pmid41152791,
year = {2025},
author = {Liu, H and Li, F and Zhang, J and Li, M and Zhu, W and Lin, Y and Hong, G and Liu, Z},
title = {Airway Candida diversity in COPD patients and its differential stimulatory effects on lung inflammation in mice.},
journal = {BMC pulmonary medicine},
volume = {25},
number = {1},
pages = {495},
pmid = {41152791},
issn = {1471-2466},
support = {82202629//National Natural Science Foundation of China/ ; 82371200//National Natural Science Foundation of China/ ; 82100385//National Natural Science Foundation of China/ ; 3502Z20234010//Xiamen Medical and Health Key Project/ ; },
abstract = {BACKGROUND: The airway microbiome is altered in chronic obstructive pulmonary disease (COPD) individuals with high fungal diversity, which manifests mainly as an increase in the diversity of Candida genera. Acute exacerbation of COPD (AECOPD) is a crucial process in disease progression. The airway Candida species diversity in AECOPD patients and their differential stimulatory effects on airway inflammation in mice remain unclear.

AIMS AND METHODS: To investigate the diversity of airway Candida species involved in AECOPD and assess their differential effects on airway inflammation in mice. We conducted airway bacterial and fungal microbiota surveys using 16S rRNA (V4 region) sequencing, ITS1 sequencing, and fungal cultures from sputum samples of 63 AECOPD patients. Subsequently, five Candida species isolated from airways were nasally colonized into mice. He staining, qPCR and 16S rRNA V4 region sequencing of mouse lung tissues were performed to explore the host inflammatory responses to different Candida species.

RESULTS: Candida species were detected in the sputum of 50 (80.95%) of the 63 volunteers with AECOPD. Candida albicans, Candida glabrata, Candida parapsilosis, Candida orthopsilosis, and Candida dubliniensis were the five most prevalent species. Nasal Candida colonization in mice caused varying degrees of inflammation, with H&E staining scores of 2–7. Mouse body weight decreases significantly on days 11 and 13 after exposure to Candida albicans, Candida krusei, Candida parapsilosis, or Candida tropicalis. After a Candida albicans infection, significant increases in IL-8 and IL-1β in the mouse airways were observed. The mouse lung microbiota shifted after the addition of Candida species, with Prevotella, Streptococcus, Sutterella, Ralstonia, Sphingomonas, and Bradyrhizobiaceae being the genera identified among the six groups.

CONCLUSION: The airways of AECOPD patients exhibit a high diversity of Candida species, each triggering distinct inflammatory patterns in mouse lungs. These findings warrant investigation into species-specific mechanisms in Candida-related COPD.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12890-025-03795-7.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Animals
Cats/microbiology
*Microbiota
*Gastrointestinal Microbiome

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

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

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

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

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

TRIAL REGISTRATION: ITMCTR2024000616.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

DERR1-10.2196/76551.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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