@article {pmid41559789,
year = {2026},
author = {Bartsch, M and Hemmelrath, L and Kerlikowsky, F and Bruns, A and Burhop, M and Nebl, J and Greupner, T and Strowig, T and Lesker, TR and Amend, L and Vital, M and Berkemeyer, S and Hahn, A and Müller, M},
title = {Gut microbiome mediates the association between dietary quality and metabolic risk in a heterogeneous adult population.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-026-01077-5},
pmid = {41559789},
issn = {1743-7075},
abstract = {BACKGROUND: Diet is a determinant of metabolic health, partly through its effects on the gut microbiome, which influences nutrient metabolism, inflammation, and energy balance. We investigated the mediating role of gut microbiome features in the association between dietary quality and metabolic risk.

METHODS: In this cross-sectional study, we included 269 adults aged 25-76 years with heterogeneous metabolic profiles, BMI ranging from 17.5 to 47.6 kg/m², and fasting glucose levels between 5.6 and 6.9 mmol/L. Dietary quality was assessed using the Healthy Eating Index (HEI-MON), the Planetary Health Diet Index (PHEI-MON), and the alternate Mediterranean Diet Score (aMED), derived from food-frequency questionnaires and three-day food records. Metabolic risk was quantified using a continuous metabolic syndrome score (cMetS) incorporating waist circumference, mean arterial pressure, HDL cholesterol, triglycerides, and fasting glucose. Microbiome composition (16 S rRNA gene sequencing) and predicted SCFA pathways were analyzed using adjusted multiple linear regression, PERMANOVA, and differential abundance analysis. Mediation analyses examined microbial features as potential mediators of the association between diet and metabolic risk.

RESULTS: Higher HEI-MON, PHEI-MON, and aMED were associated with lower cMetS (q < 0.01). Christensenellaceae R7 group and Ruminococcaceae NK4A214 group were enriched with higher dietary quality and lower cMetS (q < 0.1), whereas Lachnoclostridium were associated with lower diet quality and higher cMetS (q < 0.1). The Enterotype Dysbiosis Score (EDS) correlated inversely with dietary quality (PHEI-MON q = 0.04) and positively with cMetS (q = 0.04). Butyrate-synthesis pathways were more abundant in individuals with higher dietary quality (q < 0.05) and inversely associated with cMetS (q < 0.05). Mediation analysis indicated that the Ruminococcaceae NK4A214 group, the Christensenellaceae R7 group, and Lachnoclostridium accounted for up to 16% of the association between diet and metabolic risk.

CONCLUSION: Better dietary quality is associated with lower metabolic risk and positive gut microbiome signatures across taxonomic, functional, and stability-related aspects. Certain taxa statistically mediated these associations, highlighting gut microbiome features that may contribute to observed links between dietary patterns and metabolic health.},
}

@article {pmid41559776,
year = {2026},
author = {Hu, LZ and Wang, ZJ and Yao, K and Yang, KF and Xu, R and Zhan, XY and Zhou, MS and Jia, H},
title = {Microbial metabolic profiling reshapes NF-κB-mediated immune metabolic network: a new mechanism for CRC development.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07672-z},
pmid = {41559776},
issn = {1479-5876},
support = {No. 82204685//National Natural Science Foundation of China/ ; No. LJKMZ20221795//Department of Education of Liaoning Province/ ; },
}

@article {pmid41559696,
year = {2026},
author = {Silva, JMM and Azevedo, JLLC and Bezerra, KG and Guilarde, AO and Souza, LCS and Guimarães, RF and Leite, P and Júnior, HM and Gardinassi, LG and Romão, PRT and Fonseca, SG},
title = {Resilient gut microbiome is linked to immune control in HIV-1 infection.},
journal = {Biology direct},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13062-025-00720-0},
pmid = {41559696},
issn = {1745-6150},
support = {2014-50890/5//Institute of Investigation in Immunology- iii-INCT-CNPq/ ; },
}

@article {pmid41559539,
year = {2026},
author = {Jiang, H and Zeng, W and Huang, J and Pei, Y and Wang, Y and Zhu, P and Yang, F and Zhang, X and Fang, H and Qiu, T and Peng, A and Wang, J},
title = {Gut microbiota composition and functionality are associated with prolactin-secreting pituitary adenoma and serum lipid levels.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04592-2},
pmid = {41559539},
issn = {1471-2180},
support = {82172603//National Natural Science Foundation of China/ ; },
}

@article {pmid41559043,
year = {2026},
author = {Lin, Y and Li, S and Xu, X and Hu, X and Li, Y and Liang, S and Meng, J and Li, H and Li, Z and Xiong, D and Chen, H and Lai, J and Bao, Y and Liu, Z and Chu, J and Chen, X and Zhang, X and Liu, X and Lee, SY and An, S},
title = {Intermittent fasting inhibits Tp53-driven glioma through gut microbiota-mediated methionine-m[6]A regulation.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-68512-2},
pmid = {41559043},
issn = {2041-1723},
abstract = {Intermittent fasting (IF) has emerged as a potential cancer treatment modality, although its tumor-suppressive effects are limited. Glioblastoma (GBM) can be classified into CDKN2A subtype and TP53 subtype. Here, we discover that the efficacy of IF is correlated with tumor subtypes of GBM. IF significantly inhibite GBM progression in mice with the Tp53 GBM model, whereas its inhibitory effect is not significant in the Cdkn2a GBM model. Multi-omics sequencing is performed in the IF-responsive Tp53 GBM mouse model, delineating a comprehensive molecular profiling of IF that including the spatial transcriptome, spatial metabolome, single-cell transcriptome, single-cell RNA methylation, metabolome, and microbiome. Through systematic biological analysis and rescue experiments conducted in IF-responsive Tp53 GBM mice model, we demonstrate that the efficacy of IF is primarily mediated by alterations in the gut microbiota, which subsequently modulate the production of the microbial metabolite methionine sulfoxide. Methionine sulfoxide, by regulating m[6]A modification, inhibits the TGF-β signaling pathway, resulting in suppressing GBM progression. This study proposes a genotype-based hypothesis for the therapeutic effects of IF on tumors, and elucidates the potential RNA modification-related molecular mechanisms underlying the effective suppression of GBM by IF.},
}

@article {pmid41559005,
year = {2026},
author = {Li, F and Jiao, X and Sun, A and Zheng, Y and Shen, JP and He, JZ and Hu, HW},
title = {Phyllosphere Keystone Beneficial Specialists Enhance Yield in Nutrient Deficiency-Resistant Sorghum Cultivars.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70402},
pmid = {41559005},
issn = {1365-3040},
support = {FT230100158//Australian Research Council/ ; DP240101821//Australian Research Council/ ; 202204041101001//International Cooperation and Exchanges of Shanxi province/ ; 42307168//National Natural Science Foundation of China/ ; },
abstract = {The phyllosphere, the aboveground interface between plant leaves and their microbial residents, plays a vital yet underappreciated role in crop productivity. While root- and soil-associated microbiomes are well-studied, the ecological assembly and yield-related effects of host-mediated phyllosphere microbial communities remain largely understudied, particularly under field conditions. This study investigates the phyllosphere microbiomes of sorghum cultivars resistant and susceptible to nutrient deficiency, focusing on how host genotype mediates microbial community assembly, keystone enrichment, and yield outcomes. The β-diversity of phyllosphere microbiomes differs significantly between resistant and susceptible cultivars, with resistant lines also showing more modular co-occurrence networks enriched in keystone taxa. These cultivars supported a higher abundance of keystone beneficial specialists (KBS), predominantly affiliated with Bacteroidia and Bacilli, and their abundance was positively correlated with yield. In contrast, susceptible cultivars exhibited lower and more taxonomically dispersed KBS, with a negative correlation between KBS and yield. Structural equation modeling suggested that while soil properties consistently promoted yield across cultivars, the impact of KBS on yield was genotype-dependent. These findings reveal a host-driven microbial mechanism linking phyllosphere composition to yield performance and highlight KBS as potential targets for microbiome-informed breeding or foliar microbial applications to improve crop productivity in sustainable systems.},
}

@article {pmid41558879,
year = {2026},
author = {Chen, Q and Liu, X and Jiang, ZH},
title = {Bile acids as gatekeepers: Orchestrating gut-liver axis for metabolic and immune balance.},
journal = {Hepatobiliary & pancreatic diseases international : HBPD INT},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.hbpd.2026.01.001},
pmid = {41558879},
issn = {1499-3872},
abstract = {Bile acids (BAs) represent the terminal products of cholesterol catabolism and are integral to a wide range of physiological processes. The maintenance of BAs homeostasis is essential for human health, with disruptions being implicated in various liver and intestinal disorders. The gut-liver axis, a bidirectional communication network connecting multiple organ systems, plays a crucial role in preserving both metabolic and immune homeostasis. Recent evidence suggests that BAs are key modulators within this axis, influencing intestinal barrier function, immune responses, and the composition of the gut microbiome. This review synthesizes recent advances in our understanding of BAs, including their origins, circulation within the gut-liver axis, and diverse roles in physiology, thereby highlighting the critical functional significance of this BAs-mediated network.},
}

@article {pmid41558673,
year = {2026},
author = {Al-Andoli, M and Schoch, S and Markovic, A and Mühlematter, C and Beaugrand, M and Jenni, OG and Liamlahi, R and Walser, JC and Nielsen, D and Kurth, S},
title = {Stool Dynamics and the Developing Gut Microbiome During Infancy.},
journal = {Journal of biological rhythms},
volume = {},
number = {},
pages = {7487304251407313},
doi = {10.1177/07487304251407313},
pmid = {41558673},
issn = {1552-4531},
abstract = {The infant gut microbiome is a dynamic ecosystem, and it is key to early development, immune maturation, and overall health. Recent insights reveal that the gut microbiota undergoes changes across the 24-h day, raising the possibility that it may act as a "zeitgeber," supporting the host's sleep-wake organization. Despite its importance, timing factors influencing microbiome composition are poorly understood, limiting its use as a health indicator. This study investigates the relationship between stool dynamics (defecation interval, time of sampling), sleep pressure (interval since last sleep), meal timing, and gut microbial composition. Stool samples from 198 healthy infants, aged 3 to 31 months, were analyzed to assess microbial diversity, richness evenness, and abundance. Our findings reveal that longer intervals between bowel movements are associated with increased microbial diversity, evenness, and richness. Stool timing is associated with shifts in microbial composition, especially in younger infants, indicating diurnal microbial fluctuations to become more stable as infants mature. Longer periods of wakefulness were associated with increased microbial diversity in early infancy, although this effect appeared to diminish with age. Feeding schedules had limited effects on the gut microbiome. Longer fasting before sampling showed no significant associations with most microbial parameters, except for a positive association with microbial richness. At the phylum level, results indicate that infant gut microbial composition is influenced by behavior and physiology. Longer intervals between bowel movements were associated with shifts in bacterial abundance, with Proteobacteria decreasing and Actinobacteria increasing. In addition, later stool sampling times revealed higher Actinobacteria levels, and longer fasting was associated with reduced Bacteroidetes. Sleep pressure showed a trend effect with Firmicutes displaying a slight decrease in infants who had been awake longer. Our findings underscore the importance of time-based factors on infant gut microbiome composition.},
}

@article {pmid41558536,
year = {2026},
author = {Kasuma, N and Fitri, H and Wulandari, RW and Ernesto, G and Juwita, DR and Effendi, MDS and Wirza, TR},
title = {Salivary Microbiome Differences in Stunted and Healthy Children: A Metagenomic Analysis.},
journal = {European journal of dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0045-1814094},
pmid = {41558536},
issn = {1305-7456},
abstract = {This study aimed to compare the composition and diversity of the salivary microbiome in stunted and nonstunted children using 16S rRNA gene sequencing to explore the relationship between nutritional status and oral microbiota.A total of 20 saliva samples were collected from children aged 6 to 10 years, comprising two groups: stunted (n = 10) and healthy controls (n = 10). Deoxyribonucleic acid was extracted, and the V3-V4 region of the 16S rRNA gene was amplified and sequenced. Bioinformatics analysis included taxonomic assignment, calculation of relative abundance, α diversity (using Shannon and Simpson indices), β diversity (UniFrac-based principal coordinate analysis and permutational multivariate analysis of variance [PERMANOVA]), and differential abundance testing using the Mann-Whitney U test.The dominant phyla in both groups were Proteobacteria, Firmicutes, and Bacteroidota, with Proteobacteria being more prevalent in the stunted group. At the genus level, Neisseria and Veillonella were more abundant in stunted children. Notably, Veillonella was significantly elevated in the stunted group (28.6%) compared with controls (14.9%, p = 0.0376). Alpha diversity indices revealed a higher diversity trend in the stunted group, although this difference was not statistically significant (Shannon, p = 0.130; Simpson, p = 0.762). Beta diversity analysis revealed no considerable clustering between groups (PERMANOVA p > 0.05), indicating moderate interindividual variability but no clear group separation.Children with stunted growth demonstrated distinct microbial signatures in their salivary microbiota, particularly in the increased abundance of Proteobacteria and Veillonella, suggesting a potential link between chronic undernutrition and oral microbial dysbiosis. These findings underscore the need for additional studies to investigate the impact of nutritional status on oral and systemic health through the microbiome axis.},
}

@article {pmid41558386,
year = {2026},
author = {Yinhang, W and Jing, Z and Zhanbo, Q and Jiang, L and Qing, Z and Qi, Z and Yin, J and Jianwen, S and Wei, W and Shuwen, H},
title = {Establishment of threshold of human gut microbes and risk assessment system for colorectal cancer.},
journal = {Computers in biology and medicine},
volume = {203},
number = {},
pages = {111484},
doi = {10.1016/j.compbiomed.2026.111484},
pmid = {41558386},
issn = {1879-0534},
abstract = {BACKGROUND: Being involved in the occurrence of colorectal cancer (CRC), gut microbes are potential targets for early diagnosis of CRC. Defining the threshold of these characteristic bacteria could provide a basis for the clinical application of microorganisms as novel tumor markers for CRC.

OBJECTIVE: To sort out and define the threshold of related bacteria and the ecological characteristics of gut bacteria.

METHODS: A total of 8021 fecal samples from healthy people and 497 from CRC patients in the public database were collected to analyse the reference range. CRC-related bacteria and gut microbial characteristics were screened by literature review and analysed. CRC related bacteria and 5-95 % medians of gut microbial characteristics in healthy populations were used as reference value. 16S rRNA Miseq sequencing (175 CRC patients and 175 healthy people) and PacBio sequencing (200 CRC patients and 200 healthy people) were used to detect stool DNA sequence. The community composition of gut microbiota between CRC and healthy subjects was plotted; the species differences were analysed by Lefse analysis. R studio software was used to analyse CRC-related bacteria and gut microbial characteristics.

RESULTS: A total of 218 CRC-associated bacteria and 15 gut microbial characteristics, such as enterotypes and Firmicutes/Bacteroidetes ratio, were reviewed and analysed. A 5-95 % threshold for these 218 CRC-associated bacteria and 15 gut microbiome signatures was developed to provide criteria for the normal range of gut bacteria. The CRC evaluation intelligent system software was developed and it could quickly calculate the value of 218 CRC related bacteria and 15 gut microbial characteristics using sequencing data, and assess whether they are within the threshold. And this software has the function of predicting CRC risk. The accuracy of CRC risk assessment ranged from 89.14 % to 91.50 %.

CONCLUSION: We established, for the first time, quantitative thresholds for CRC-associated bacteria and have driven advances in microbial risk prediction for CRC.},
}

@article {pmid41558353,
year = {2026},
author = {Wang, L and Liang, Z and Liang, J and Ge, L and Zou, L and Fan, Y and Xu, Q and Zhang, Y and Lv, B and Zhao, K and Wu, Y and Li, P},
title = {Multi-omics reveals taxonomic and functional adaptations of soil microbiota to Bt toxin exposure.},
journal = {Journal of hazardous materials},
volume = {503},
number = {},
pages = {141175},
doi = {10.1016/j.jhazmat.2026.141175},
pmid = {41558353},
issn = {1873-3336},
abstract = {Bt toxins released from transgenic Bt plants exhibit biocidal activity and are considered exogenous environmental hazards in soil ecosystems. Here, we employed an integrated multi-omics approach to systematically characterize the taxonomic and functional regulatory mechanisms and adaptive strategies of soil microorganisms in response to Bt toxin exposure across a gradient of concentrations. Our findings demonstrate that different application amounts of Bt toxins significantly influenced both toxin persistence in soil and the soil nutrition multifunctionality (SNM) index. Notably, none of the tested Bt toxin concentrations exerted adverse effects on the diversity or complexity of soil microbial communities. Correlation analysis revealed that SNM was significantly positively associated with bacterial α-diversity (Sobs and Shannon indices) and microbial network edge numbers, but showed no such association with fungal communities, indicating distinct response patterns between soil bacteria and fungi to Bt toxin exposure. Divergent responses were also observed in the taxonomic and functional diversity of microbial communities under Bt toxin addition. Comparative transcriptomic analysis between Bt500_100 and Bt0_100 samples revealed that microorganisms downregulated energy metabolism pathways while upregulating genes associated with cell motility and environmental adaptation. These results collectively indicate that soil microorganisms employ adaptive metabolic strategies to mitigate nutrient limitation induced by the declining bioavailability of Bt toxin in soil environments.},
}

@article {pmid41558335,
year = {2026},
author = {Duell, EB and Loecke, TD and Hansen, PM and Koziol, L and Ramos, RJ and Sikes, BA and Bever, JD and McKenna, TP},
title = {Functional consequences of land-use history: Plant community and soil microbiome mediation of nutrient loss, soil aggregate stability, and soil erosion.},
journal = {The Science of the total environment},
volume = {1014},
number = {},
pages = {181311},
doi = {10.1016/j.scitotenv.2025.181311},
pmid = {41558335},
issn = {1879-1026},
abstract = {Alterations in land-use practices pose serious threats to biodiversity and ecosystem functioning, affecting ecosystem services such as soil stability and nutrient cycling. Conversely, the collective interactions between plants, soils, and associated soil microbiomes play a critical role in the maintenance of various ecosystem services. We found evidence of the degradation of soil microbiomes with land-use, as microbial composition, measured by amplicon sequencing targeting bacteria (16S), fungi (ITS), and AM fungi (LSU), differed between unplowed prairies, post-agricultural grasslands, and annual agricultural fields across Kansas (p = 0.003, 0.001, and 0.01, respectively). We then tested functional impacts on soil ecosystem services of the soil microbiome differences by conducting a greenhouse experiment that manipulated full-factorial combinations of soil microbiome composition of land-use history and plant assemblage. Specifically, we examined soil detachment, water-stable macroaggregates, and nitrate leaching through the soil profile, as well as plant and AM fungal biomass. Soil microbiomes, plant composition, and their interactions had strong influences on every metric of ecosystem function. Notably, native plant communities were more sensitive to degradation of the microbiome. Furthermore, living soil microbiomes, regardless of land-use history, reduced soil detachment, promoted formation of water-stable macroaggregates, and facilitated greater nitrate retention, highlighting the importance of soil microbiomes for many physical and biogeochemical processes. Moreover, the realized functional benefits of microbiome composition depended on the plant community. These results highlight the complexities of plant-soil-microbial interactions in the context of land-use histories, displaying the importance of intact microbiomes, especially AM fungi, in mitigating environmental consequences of agricultural intensification.},
}

@article {pmid41558287,
year = {2026},
author = {Yan, S and Chen, S and Shen, T and Zeng, S and Wang, J and Zhang, Z and Li, B and Zhou, H and Long, Y and Zhang, D},
title = {Association between environmental exposure, gut microbiome and risk of gestational diabetes mellitus in Guangzhou, China.},
journal = {Ecotoxicology and environmental safety},
volume = {310},
number = {},
pages = {119747},
doi = {10.1016/j.ecoenv.2026.119747},
pmid = {41558287},
issn = {1090-2414},
abstract = {Gestational diabetes mellitus (GDM) is a prevalent pregnancy complication. Both environmental changes and gut dysbiosis have been associated with increased risk of GDM. While environmental exposures may influence gut microbiome, the exact mechanisms linking these factors to GDM risk remain poorly understood. The study aimed to investigate the relationships between environmental exposures, gut microbiome and GDM risk. A population-based cohort study was conducted in Guangzhou, China from January 2017 to September 2017, enrolling 260 women with GDM and 508 normal pregnancies. Ambient pollution and meteorological exposures during different pregnancy windows were estimated for each participant. We identified the changes in gut microbiome characteristics related to environmental exposures. Temperature exposure during the preconception period was most strongly associated with alterations in the gut microbiome observed during the second trimester, particularly in women who developed GDM. Multivariate logistic regression and interaction analyses showed potential relationships between temperature exposure, gut microbiome and GDM risk. These findings contribute to the understanding of the relationship between environmental exposures, gut microbiome and GDM, providing insights into public health strategies to shield pregnant women from the detrimental effects of environmental exposures.},
}

@article {pmid41558030,
year = {2026},
author = {Fan, C and Hayase, T and Chang, CC and Glover, IK and Flores, II and McDaniel, LK and Ortega, MR and Sanchez, CA and El-Himri, RK and Brown, AN and Karmouch, JL and Jamal, MA and Ahmed, SS and Halsey, TM and Jin, Y and Tsai, WB and Prasad, R and Enkhbayar, A and Mohammed, A and Schmiester, M and Damania, AV and Ajami, NJ and Wargo, JA and Peterson, CB and Rondon, G and Al-Juhaishi, T and Alousi, AM and Molldrem, JJ and Champlin, RE and Shpall, EJ and Martens, E and Arias, CA and Jenq, RR and Hayase, E},
title = {Fecal carbohydrate-degrading bacteria are associated with reduced incidence of lower gastrointestinal GVHD.},
journal = {Blood advances},
volume = {},
number = {},
pages = {},
doi = {10.1182/bloodadvances.2025016780},
pmid = {41558030},
issn = {2473-9537},
abstract = {Lower gastrointestinal graft-versus-host disease (LGI-GVHD) carries morbidity and mortality for patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT), with critical contributions from the intestinal microbiome. In a retrospective cohort of metagenomic sequencing of allo-HSCT patient stool (n = 90), we found that a reduction in specific Parabacteroides and Bacteroides species around the time of engraftment contributes to LGI-GVHD risk. Given the known diverse carbohydrate degrading functionality of these bacteria, we investigated gene abundances for Carbohydrate-Active enZyme (CAZyme) and found that Parabacteroides merdae, Parabacteroides distasonis and Bacteroides ovatus abundances were significantly correlated with CAZymes in patients who did not develop LGI-GVHD compared to those who did. The specific gene abundances of xylosidase, which contribute to the degradation of xylose-containing polysaccharides, were significantly associated with reduced risk of LGI-GVHD. Together, these findings show the importance of carbohydrate degrading functionality of putative beneficial bacteria in mediating risk of LGI-GVHD.},
}

@article {pmid41557647,
year = {2026},
author = {Alvendal, C and Hasselrot, T and Balduck, M and Edfeldt, G and Schuppe-Koistinen, I and Brauner, A and Altman, D and Broliden, K and Bohm-Starke, N},
title = {Vaginal chlorhexidine gluconate versus fluconazole for recurrent vulvovaginal candidiasis: A randomized noninferiority trial.},
journal = {PloS one},
volume = {21},
number = {1},
pages = {e0340862},
pmid = {41557647},
issn = {1932-6203},
mesh = {Female ; Humans ; *Candidiasis, Vulvovaginal/drug therapy/microbiology ; *Chlorhexidine/analogs & derivatives/administration & dosage/therapeutic use/adverse effects ; *Fluconazole/administration & dosage/therapeutic use/adverse effects ; Adult ; *Antifungal Agents/therapeutic use/administration & dosage ; Candida albicans/drug effects ; Vagina/microbiology/drug effects ; Recurrence ; Young Adult ; Administration, Intravaginal ; Microbiota/drug effects ; Treatment Outcome ; Biofilms/drug effects ; },
abstract = {BACKGROUND: Recurrent vulvovaginal candidiasis (RVVC) is a common condition characterized by frequent relapses, often without a clearly identifiable cause. Fluconazole (FLZ) is the standard treatment but concerns about emerging resistance and drug interaction highlight the need for alternative therapies. Chlorhexidine gluconate (CHG), known for its antifungal and biofilm-disrupting properties, has been proposed as a potential alternative.

OBJECTIVE: To evaluate the efficacy, tolerability, and microbiome impact of a vaginal CHG formulation compared to oral FLZ in the treatment of RVVC caused by Candida albicans.

METHODS: An open label randomized non-inferiority trial was conducted to compare vaginal CHG and FLZ treatments. Primary outcome was negative cultures for C. albicans. Resistance profiles and changes in the vaginal microbiome composition were also assessed.

RESULTS: The study was terminated early due to local irritation associated with CHG and the study design was transitioned into a pilot study. CHG treatment showed comparable efficacy to FLZ in clearing C. albicans infections and preventing recurrences, although the sample size was limited. All 11 participants in the FLZ group cleared the infection after one week treatment, compared to 9 out 11 in the CHG group. No harmful changes to the vaginal microbiome were observed in the CGH or FLZ group. FLZ promoted a shift toward Lactobacillus crispatus dominance, unlike CHG. Notably, 16% of C. albicans isolates exhibited reduced susceptibility or resistance to FLZ.

CONCLUSION: Due to the limited number of participants, we cannot conclusively determine whether CHG is non-inferior to FLZ in terms of efficacy for clearing acute C. albicans infections or preventing recurrences. While the current CHG formulation caused local irritation and is not suitable for clinical use, its antifungal and biofilm-inhibiting properties remain promising. Further development of less irritative CHG formulations may offer a valuable alternative for RVVC treatment, particularly in the context of rising FLZ resistance.},
}

Female
Humans
*Candidiasis, Vulvovaginal/drug therapy/microbiology
*Chlorhexidine/analogs & derivatives/administration & dosage/therapeutic use/adverse effects
*Fluconazole/administration & dosage/therapeutic use/adverse effects
Adult
*Antifungal Agents/therapeutic use/administration & dosage
Candida albicans/drug effects
Vagina/microbiology/drug effects
Recurrence
Young Adult
Administration, Intravaginal
Microbiota/drug effects
Treatment Outcome
Biofilms/drug effects

@article {pmid41556698,
year = {2026},
author = {Cao, F and Liu, A and Tong, J and Guo, C and Zhang, H and Pang, Y and Tang, K and Yu, Q and Guo, J},
title = {Integrative multi-omics analysis reveals gut-skin axis mechanisms and novel therapeutic target GALE in atopic dermatitis.},
journal = {mSystems},
volume = {11},
number = {1},
pages = {e0140325},
pmid = {41556698},
issn = {2379-5077},
support = {82074443//National Natural Science Foundation of China/ ; WXLH202403001//Sichuan Provincial central of Traditional Chinese Medicine/ ; 24ZYZYTS0310//Central and Local Goverments Lead the Project/ ; },
mesh = {Humans ; *Dermatitis, Atopic/genetics/drug therapy/metabolism/microbiology ; *Gastrointestinal Microbiome ; Molecular Docking Simulation ; *Skin/metabolism/pathology ; Molecular Dynamics Simulation ; Female ; Male ; Methotrexate/pharmacology ; Adult ; Multiomics ; },
abstract = {UNLABELLED: The gut-skin axis represents a critical but poorly understood pathway in atopic dermatitis (AD) pathogenesis. This study aimed to establish causal relationships between gut microbiota and AD risk while identifying key molecular bridges and therapeutic targets. We integrated multiple analytical approaches, including single-cell RNA sequencing analysis of skin biopsies from five AD patients and four healthy controls, intercellular communication network analysis, pseudotime trajectory inference, reverse drug prediction, molecular docking, and molecular dynamics simulations. Analysis revealed increased keratinocyte heterogeneity and enhanced immune cell communication in atopic dermatitis (AD) samples. Intersection analysis between gut microbial metabolite-associated genes and skin pathology-related genes identified seven key bridging genes (AKR1C2, GALE, GGH, NR4A1, PLA2G4B, TYMS). Functional annotation indicated that these genes are primarily involved in vitamin precursor metabolism, suggesting that the Eubacterium eligens group influences AD pathogenesis mainly through vitamin precursor-mediated pathways that regulate systemic immune responses. Pseudotime trajectory analysis demonstrated dynamic temporal gene expression patterns during disease progression. Molecular docking revealed an unexpectedly high-affinity binding between methotrexate and GALE (binding energy = -10.4 kcal/mol), which exceeded its binding affinity for the classical target TYMS (-7.5 kcal/mol). Molecular dynamics simulations further confirmed the stable binding conformation of the protein-ligand complexes. This study provides mechanistic insights into how the Eubacterium eligens group influences atopic dermatitis through vitamin precursor-mediated systemic immune modulation and identifies GALE as a novel therapeutic target. The findings provide mechanistic insights into the gut-skin axis and support developing precision medicine approaches integrating microbiome interventions with targeted pharmacotherapy for AD management.

IMPORTANCE: Genetic-level evidence of gut microbiota causality in atopic dermatitis: this study established a causal relationship between specific gut microbiota and the risk of atopic dermatitis at the genetic level, providing strong genetic evidence for the "gut-skin axis" theory. GALE is identified as a novel therapeutic target with redefined methotrexate mechanism: molecular docking study unexpectedly found that GALE binding affinity of MTX was significantly higher than that of its classical target TYMS, suggesting that GALE may be an important but previously unrecognized target of MTX in the treatment of AD. Multi-omics integration framework reveals increased keratinocyte heterogeneity: integrating single-cell RNA sequencing and computational pharmacology provided a cellular and molecular basis for understanding the characteristics of chronicity and recurrence of the disease.},
}

Humans
*Dermatitis, Atopic/genetics/drug therapy/metabolism/microbiology
*Gastrointestinal Microbiome
Molecular Docking Simulation
*Skin/metabolism/pathology
Molecular Dynamics Simulation
Female
Male
Methotrexate/pharmacology
Adult
Multiomics

@article {pmid41556662,
year = {2026},
author = {Zhang, N and Atoni, E and Nyaruaba, R and Kibaba, P and Shadrack, K and Wang, F and Agwanda, B and Zheng, Z and Dai, J and Yuan, Z and Xia, H},
title = {Host and geography shape microbial communities in Kenyan mosquitoes: insights from metatranscriptomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0142725},
doi = {10.1128/msystems.01427-25},
pmid = {41556662},
issn = {2379-5077},
abstract = {Mosquitoes harbor diverse microbial communities that influence their potential to transmit pathogens. However, the ecological drivers shaping these microbiomes, particularly in under-sampled regions like Africa, remain poorly resolved. We conducted a large-scale metatranscriptomic survey of 3,940 Aedes and Culex mosquitoes from diverse ecological zones across Kenya. Our analyses revealed that viruses dominated the overall transcriptome, while bacteria exhibited the greatest taxonomic richness. Geographic location emerged as the primary driver of microbial community structure, whereas host genus identity shaped virome diversity at local or city-level scales. Culex mosquitoes harbored higher viral richness, particularly in coastal regions, while Aedes supported more diverse bacterial assemblages. Microbial co-occurrence networks exhibited distinct topologies across hosts: Culex networks featured cross-domain interactions and viral keystone taxa, whereas Aedes networks were more cohesive and robust, centered on bacterial hubs. We identified 102 distinct viruses from 24 families, including 31 putative novel RNA viruses. Segment-resolved phylogenies revealed cryptic clades within Bunyavirales, Picornavirales, and other lineages. Collectively, our findings highlight the scale-dependent influences of geography and host identity on mosquito microbiomes in East Africa and demonstrate the utility of metatranscriptomics in uncovering hidden microbial diversity and ecological interactions. These insights provide a foundation for ecologically informed arthropod vector surveillance and microbiome-based intervention strategies.IMPORTANCEMosquitoes are more than just flying syringes; they are complex ecosystems hosting a variety of microbes. Understanding what shapes this microbial world inside mosquitoes is key to developing new control strategies. Our study of nearly 4,000 mosquitoes from Kenya reveals that where a mosquito lives matters most for its overall microbial makeup, but its genus dictates which viruses it carries. We discovered that different mosquito types have distinct microbial social networks: one type has a fragile network centered on viruses, while the other has a resilient network built around bacteria. This means that strategies to disrupt disease transmission by targeting mosquito microbes may need to be tailored to a specific mosquito genus. Our work provides a map of these microbial ecosystems, highlighting potential new viruses and offering insights for future public health surveillance and interventions.},
}

@article {pmid41556651,
year = {2026},
author = {Nguyen, VTT and König, S and Formes, H and Al Taleb, Z and Steinert, F and Bufe, B and Eggert, S and Stegmüller, S and Schermer, Y and Richling, E and Kins, S and Reinhardt, C and Endres, K},
title = {Monocolonization with Bacteroides thetaiotaomicron exerts region-specific effects on Alzheimer's disease-related traits in the murine brain.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0074425},
doi = {10.1128/spectrum.00744-25},
pmid = {41556651},
issn = {2165-0497},
abstract = {UNLABELLED: Bacteroides thetaiotaomicron (B. theta) dominates the gut microbiome of most mammals. This strictly anaerobic gut symbiont colonizes the mucus layer of host intestinal epithelial cells in both healthy and diseased conditions. Reduced neuronal and vagal afferent innervation observed in germ-free mice was found to be normalized by colonization with B. theta. In addition to deficits in gut innervation, germ-free mice have been reported to have reduced neuronal number and neurotransmitter levels in the brain. Here, we investigated the hallmarks of Alzheimer's disease (AD) in the brain of germ-free mice compared to mice mono-colonized with B. theta. We analyzed the number of mature neurons, neurotransmitter transporters, amyloid precursor protein processing, and inflammatory status in three brain regions: the hippocampus, prefrontal cortex (PFC), and cerebellum. The hippocampus and the PFC are regions thought to be highly susceptible to pathogenesis, whereas the cerebellum is thought to be only mildly affected. Interestingly, secretion of neuroprotective sAPPα decreased in hippocampus and remained unchanged in PFC, while levels were increased in the cerebellum in response to bacterial colonization. In addition, the number of presynaptic boutons increased in the hippocampus but remained unaffected in the cerebellum.

IMPORTANCE: The gut microbiome has been reported to not only contribute to diseases of the gastrointestinal tract but also to interfere with and potentially even initiate diseases of other organ systems, such as the brain. Interference with the gut microbiome has been shown to elicit cognitive changes, for example, in rodent models of AD. Colonization with the common gut microbe B. theta not only affected the brain per se in our study but also showed specific brain region-dependent effects related to AD. This implies that evaluating the impact the microbiome might have on brain disorders needs a much more detailed investigation in the future with spatial and also potentially time resolution.},
}

@article {pmid41556507,
year = {2026},
author = {Cheng, S and Tang, X and Huang, X and Li, Y and Huang, S and He, D and Moreno-Jiménez, E and Xu, J and Rillig, MC and Dai, Z and Delgado-Baquerizo, M},
title = {Stressor Combinations Shift Soil Microbial Communities From Rare to Unknown Taxa and Alter Genomic Strategies.},
journal = {Global change biology},
volume = {32},
number = {1},
pages = {e70704},
doi = {10.1111/gcb.70704},
pmid = {41556507},
issn = {1365-2486},
support = {41721001//National Natural Science Foundation of China/ ; 2019YFC1803704//National Key Research and Development Program of China/ ; +226-2024-00029//The Fundamental Research Funds for the Central Universities/ ; },
mesh = {*Soil Microbiology ; *Microbiota ; Metagenomics ; *Metagenome ; *Stress, Physiological ; Biodiversity ; *Climate Change ; Ecosystem ; Bacteria/genetics/classification ; },
abstract = {Soil microorganisms constitute the largest portion of Earth's biodiversity. However, soil microorganisms are also highly sensitive to on-going global change, and the influence of an increasing number of stressors on common, rare, and unknown taxa across large environmental gradients remains virtually unknown. Here, we combined a large-scale spatial field survey across multiple different ecosystems and found that the diversity and abundance of soil rare taxa were significantly reduced under high environmental stressor number (i.e., a high number of stressors passing a 75% stressor threshold). Strikingly, the abundance of unknown soil taxa and unknown genes increased with increasing environmental stress number. We further identified the metagenome-assembled genomes (MAGs) that were considered as relatively common taxa using metagenomics. Compared to 9% of negative responders, 32% of common MAGs were resistant or positively responsive to multiple stress, displaying a reduced potential for cellular processes and an enhanced potential for environmental, genetic, and metabolic processes. Our study suggests that as stress increases, we would have less rare, but more unknown microorganisms and unique genomes of resistant common taxa, suggesting major changes in the soil microbiome in a world subjected to multiple global change stressors.},
}

*Soil Microbiology
*Microbiota
Metagenomics
*Metagenome
*Stress, Physiological
Biodiversity
*Climate Change
Ecosystem
Bacteria/genetics/classification

@article {pmid41556455,
year = {2026},
author = {Zhang, H and Yan, X and Hou, Y and Ou, C and Luo, S and Liu, C and Li, Z and Zhang, G and Chen, T},
title = {Polyphenols Nonmonotonically Modulate the Inulin-Driven Gut Microbial Network In Vivo.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13003},
pmid = {41556455},
issn = {1520-5118},
abstract = {The interaction between dietary fiber and polyphenols in modulating gut microbiota is complex and not fully understood. This study investigated how the polyphenol structure (complex tannic acid vs simple ferulic acid) and dosage (20-320 mg/kg) modulated the gut microbiota and metabolic profile shaped by a high-dose inulin diet. Our results showed that all treatments were well-tolerated with no observed adverse health outcomes. While polyphenol addition did not cause large-scale shifts in overall microbiota composition, it fundamentally restructured the underlying microbial network. Each polyphenol established a distinct hub species, with Oscillospira for tannic acid and Allobaculum for ferulic acid. This restructuring was accompanied by nonmonotonic dose-response changes in short-chain fatty acid production, an effect attributed to a shifting balance between the polyphenols' trophic and antimicrobial activities. Our findings demonstrate that in a high-fiber context, polyphenols act as subtle modulators, rather than primary drivers, whose structure and dose critically shape the microbiome function.},
}

@article {pmid41556347,
year = {2026},
author = {},
title = {Correction to: HLRMDB: a comprehensive database of the human microbiome with metagenomic assembly, taxonomic classification, and functional annotation by analysis of long-read and hybrid sequencing data.},
journal = {Nucleic acids research},
volume = {54},
number = {2},
pages = {},
doi = {10.1093/nar/gkag014},
pmid = {41556347},
issn = {1362-4962},
}

@article {pmid41556141,
year = {2026},
author = {Dellisanti, W and Zhang, Q and Bollati, E and Seveso, D and Ferrier-Pagès, C and Younis, C and Camp, EF and Kühl, M},
title = {Interactive effects of warming and iron supplementation on O2 dynamics, trace metal content, and microbial diversity within different compartments of two Mediterranean corals.},
journal = {Biology open},
volume = {15},
number = {1},
pages = {},
doi = {10.1242/bio.062357},
pmid = {41556141},
issn = {2046-6390},
support = {101062810//European Union/ ; GBMF9206//Gordon and Betty Moore Foundation/ ; 202207940005//China Scholarship Council/ ; //European Union, Gordon and Betty Moore Foundation/ ; },
mesh = {*Anthozoa/metabolism/microbiology/physiology ; Animals ; *Iron/metabolism ; *Oxygen/metabolism ; *Microbiota ; *Trace Elements/metabolism/analysis ; *Global Warming ; Mediterranean Sea ; Symbiosis ; Temperature ; Biodiversity ; },
abstract = {Mediterranean corals living in coastal habitats are subjected to natural fluctuations in temperature and nutrient availability, including substantial iron (Fe) inputs via terrestrial runoff (up to 14.5 nM). While Fe is essential for coral and symbiont metabolism, the assimilation rate, physiological thresholds, and spatial allocation of Fe within coral compartments, and its interactive effects with warming, remain poorly understood. Here, we provide the first characterization of oxygen (O2) dynamics, trace metal content, and microbial community composition in two Mediterranean corals, Cladocora caespitosa and Eunicella singularis, exposed to chronic warming (18-24°C) and Fe(III) supplementation (20 nM day-1). We show that although these corals are not Fe-limited, increased temperature enhanced the Fe uptake in the algal symbionts of C. caespitosa. In C. caespitosa, Fe supplementation reduced the O2 availability within the gastrovascular cavity (GVC) and altered the composition and diversity of GVC microbial communities. In E. singularis, interactive effects of Fe and warming reduced GVC O2 availability within the GVC, and warming increased metal content, while the microbiome resembled the surrounding seawater. These intraspecific differences in the sensitivity of the coral holobiont to warming and Fe supplementation could have important implications for the resilience of Mediterranean corals to ongoing climate stress, underscoring the importance of considering coral compartments in ecophysiological research.},
}

*Anthozoa/metabolism/microbiology/physiology
Animals
*Iron/metabolism
*Oxygen/metabolism
*Microbiota
*Trace Elements/metabolism/analysis
*Global Warming
Mediterranean Sea
Symbiosis
Temperature
Biodiversity

@article {pmid41556096,
year = {2026},
author = {Aguirre Morgado, NP and Pereira Suárez, AL and Chabay, P and Peña Rodríguez, M and Amarillo, ME and Mangiaterra, T and Bueno Urquiza, L and Rubio Sánchez, AX and Vega Magaña, N},
title = {Tonsillar Microbial Signature of Fusobacterium nucleatum Associated With Epstein-Barr Virus Latency.},
journal = {Journal of medical virology},
volume = {98},
number = {1},
pages = {e70808},
doi = {10.1002/jmv.70808},
pmid = {41556096},
issn = {1096-9071},
support = {//PROINPEP/ ; //PROSNII/ ; //PROAC/ ; },
mesh = {Humans ; *Fusobacterium nucleatum/genetics/isolation & purification/classification ; *Palatine Tonsil/microbiology/virology/pathology ; *Herpesvirus 4, Human/physiology ; Male ; Female ; Child ; *Virus Latency ; *Epstein-Barr Virus Infections/virology/microbiology ; Child, Preschool ; *Microbiota ; *Fusobacterium Infections/microbiology ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Epstein-Barr virus (EBV) acquired in childhood is asymptomatic, with the tonsils as the entry site to infect B lymphocytes and establish latency. Little is known about whether the microbiota influences EBV persistent infection. We aimed to characterize the tonsil microbiome with different EBV latency types. A cohort of 60 children with tonsillar hyperplasia were included. EBV latency types (0/I/II/III) and lytic phase were determined by immunohistochemistry. 16S NGS of lymphoid tonsillar tissue was carried out with the Illumina platform. Bioinformatic analysis was carried out with QIIME2 2023.2 software and the R studio packages Phyloseq and DESeq 2. Absolute quantification of Fusobacterium nucleatum and its subspecies was conducted using qPCR. A minor α-diversity was observed in the latency III group (p < 0.0014). Therefore, the reference employed for differential abundance analysis was the latency III group. Latency III group was characterized by Fusobacterium when compared with non-infected (LFC = 43.81, p = 2.03E-10), latency 0 (LFC = 23.20, p = 2.16E-05); latency I (LFC = 23.21, p = 1.36E-07), and latency II (LFC = 38.03, p = 7.36E-19). In contrast, Prevotella histicola was decreased (LFC = -26.06, p = 0.0004). Latency group III with lytic phase was characterized by Fusobacterium (LFC = 26.74, p = 5.30E-05). Fusobacterium nucleatum subspecies vicentii had a higher copy number within latency group III (p = 0.020). We found that a microbiome signature in lymphoid tonsillar tissue is related to EBV infection, where Fusobacterium nucleatum subspecies could play a crucial role in latency III and the lytic phase of EBV. This study provides the first evidence that the tonsil microbiome varies with EBV stages, a finding relevant to EBV-associated diseases.},
}

Humans
*Fusobacterium nucleatum/genetics/isolation & purification/classification
*Palatine Tonsil/microbiology/virology/pathology
*Herpesvirus 4, Human/physiology
Male
Female
Child
*Virus Latency
*Epstein-Barr Virus Infections/virology/microbiology
Child, Preschool
*Microbiota
*Fusobacterium Infections/microbiology
RNA, Ribosomal, 16S/genetics

@article {pmid41555920,
year = {2025},
author = {Furlan, É and Polizel, GHG and Fernandes, AC and Prati, BCT and Pombo, GDV and Ramírez-Zamudio, GD and Fukumasu, H and Santana, MHA},
title = {The influence of prenatal nutrition on ruminal microbiome of beef cattle.},
journal = {Frontiers in genetics},
volume = {16},
number = {},
pages = {1708543},
pmid = {41555920},
issn = {1664-8021},
abstract = {INTRODUCTION: Maternal nutrition is recognized for inducing long-lasting effects on offspring performance during postnatal life. However, little is known about its potential role in modulating the ruminal microbiota during fetal development, as rumen colonization has traditionally been assumed to occur only at birth. This study aimed to evaluate the long-term effects of maternal nutrition during gestation on the offspring's ruminal microbiota in postnatal life.

METHODS: The experimental design comprised 28 Nellore bulls, offspring of a single sire and born to primiparous heifers. Dams were assigned to two groups and received either mineral supplementation (Control; n = 14; 0.3 g/kg BW) or protein-energy supplementation (Supplemented; n = 14; 5 g/kg BW) throughout gestation, from conception to calving. Calves from both groups were managed identically from birth to slaughter. At the finishing phase, ruminal fluid samples were collected from 10 bulls per treatment. The V4 region of the 16S rRNA gene was sequenced, and amplicon sequence variants (ASVs) were identified using DADA2 and phyloseq for microbial diversity and taxonomic analysis. Pathway over-representation analysis was also conducted using MicrobiomeProfiler.

RESULTS AND DISCUSSION: Maternal nutrition resulted in modest yet significant alterations in the ruminal microbial communities of the offspring. The Supplemented group exhibited higher relative abundance of Fibrobacter and Prevotellaceae UCG-003, with reduced abundance of Xylanibacter. Pathway analysis revealed enrichment of starch and sucrose metabolism, along with modulation of amino acid biosynthesis and nitrogen metabolism, suggesting potential improvements in microbial protein synthesis and nitrogen utilization. In conclusion, maternal nutrition during gestation has long-term effects on the offspring's ruminal microbiota, influencing specific bacterial taxa and metabolic pathways linked to carbohydrate metabolism and nutrient utilization.},
}

@article {pmid41555705,
year = {2026},
author = {Fontaine, F and Turjeman, S and Haib, M and Collado, MC and Callens, K and Koren, O},
title = {Programming the Infant Gut: How Maternal and Early Life Nutrition Shape the Infant Microbiome and Long-term Health-A Narrative Review.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {2},
pages = {e70385},
pmid = {41555705},
issn = {1613-4133},
support = {//Spanish Ministry of Science and Innovation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Female ; Infant ; *Maternal Nutritional Physiological Phenomena ; Pregnancy ; *Infant Nutritional Physiological Phenomena ; Breast Feeding ; Infant, Newborn ; Diet ; },
abstract = {Childhood malnutrition, including undernutrition, obesity, and micronutrient deficiencies, remains a major global health burden. Emerging evidence points to the gut microbiome as a critical mediator linking maternal, prenatal, and early-life nutrition to long-term offspring health outcomes. From conception and through the first years of life, maternal diet, metabolic state, and environmental exposures shape offspring microbial colonization and maturation. Breastfeeding and consumption of fiber-rich and fermented foods (maternal and post-weaning) support beneficial microbiota, while high-fat, high-sugar diets, xenobiotics, and artificial additives may promote dysbiosis. The composition and diversity of the infant microbiome influence immune, metabolic, and neurodevelopmental processes and may also contribute to the intergenerational transmission of malnutrition. While commercial formulas increasingly include "biotics" to mimic human milk, exclusive breastfeeding remains the gold standard. Complementary feeding practices, including timing and diet quality, are known to modulate microbial maturation. Diet-based interventions in pregnancy show promise in improving microbiome function and preventing disease in offspring. Because the microbiome is highly plastic in the first years of life, this window offers unique opportunities for preventive strategies targeting maternal and child nutrition. Integrating microbiome science into public health and dietary guidelines could enhance current approaches to breaking the cycle of malnutrition and promoting lifelong health.},
}

Humans
*Gastrointestinal Microbiome/physiology
Female
Infant
*Maternal Nutritional Physiological Phenomena
Pregnancy
*Infant Nutritional Physiological Phenomena
Breast Feeding
Infant, Newborn
Diet

@article {pmid41555509,
year = {2026},
author = {Kim, JY},
title = {Gut Microbiota, Probiotics, and Aging: Molecular Mechanisms and Implications for Healthy Aging.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2511046},
doi = {10.4014/jmb.2511.11046},
pmid = {41555509},
issn = {1738-8872},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Probiotics ; Animals ; *Aging/physiology ; *Healthy Aging/physiology ; },
abstract = {Recent advances in microbiome research have highlighted that age-related physiological changes are closely shaped by shifts in the gut microbial community rather than by the passage of time alone. Aging is frequently accompanied by a decline in microbial diversity and the loss of short-chain fatty acid-producing taxa, changes that weaken the intestinal barrier and contribute to the persistent low-grade inflammation described as inflammaging. These alterations intersect with immune and metabolic pathways linked to immunosenescence, cellular senescence, and mitochondrial function. In contrast, microbial ecosystems enriched with butyrate-producing and polyamine-generating species have been associated with more stable epithelial integrity, improved metabolic flexibility, and balanced immune activity. Emerging findings also indicate that the gut microbiota communicates with peripheral organs through the gut-skin, gut-muscle, and gut-brain axes, influencing tissue-specific aging processes. Evidence from animal models and human studies shows that dietary modulation, probiotics, and other microbiota-directed approaches can partially restore microbial functions relevant to aging, although responses vary considerably across individuals. Interest is also growing in postbiotic strategies, including microbial metabolites and vesicle-based components, which may offer targeted effects without requiring colonization. By integrating these mechanistic and translational insights, this review outlines how the gut microbiota contributes to aging biology and discusses the potential for microbiome-based interventions to support healthspan.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Probiotics
Animals
*Aging/physiology
*Healthy Aging/physiology

@article {pmid41555501,
year = {2026},
author = {Le Noir de Carlan, C and Verbruggen, E and Colaert-Sentenac, L and Cougnon, M and Sigurðsson, P and Sigurdsson, BD and Debode, J and De Tender, C},
title = {Soil microbiomes conditioned by long-term warming affect plant belowground performance.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70182},
pmid = {41555501},
issn = {1438-8677},
support = {//European Union's Horizon 2020 framework programme for research and innovation under the Marie Skłodowska-Curie grant agreement No. 813114/ ; },
abstract = {Global change affects plant performance, both directly through warming and indirectly through changes in their biotic and abiotic surroundings. Soil microbes can critically influence plant performance, but are vulnerable to warming themselves. Disentangling direct effects of warming on plants from those intermediated by changes in microbial populations is complex under field conditions. To distinguish those effects, we monitored the performance of Agrostis capillaris and Anthoxanthum odoratum grown under uniform and controlled glasshouse conditions in soils inoculated with soil microbiomes conditioned by ambient, medium (14 years; MTW) or long-term (>55 years; LTW) geothermal warming. This was replicated under normal watering or drought conditions to additionally assess stress resistance. Furthermore, we analysed the microbiome of the inocula through metabarcoding to identify root-associated fungi and compare their relative abundance under different warming conditions. We found a decreased belowground biomass of both plant species when grown with LTW-conditioned microbiomes, with an exacerbated effect under drought for Ag. capillaris. We did not observe an associated increase in aboveground biomass, resulting in an increased aboveground biomass:belowground biomass ratio. These changes coincided with concurrent increases in the relative abundance of putative plant pathogens and arbuscular mycorrhizal fungi. We therefore conclude that soil microbes can mediate warming effects on plant performance through reduced belowground biomass.},
}

@article {pmid41555483,
year = {2026},
author = {Sridharan, K and Sivaramakrishnan, G},
title = {Comparative Microbiome Analysis in Ventilator-Associated Pneumonia Across Oral Care Interventions in Intubated Patients: A Systematic Review and Meta-Analysis.},
journal = {American journal of therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1097/MJT.0000000000002103},
pmid = {41555483},
issn = {1536-3686},
}

@article {pmid41555453,
year = {2026},
author = {Orr, RJS and Brynildsrud, O and Bøifot, KO and Gohli, J and Skogan, G and Kelly, FJ and Hernandez, MT and Udekwu, K and Lee, PKH and Mason, CE and Dybwad, M},
title = {Spatial and temporal patterns of public transit aerobiomes.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02303-7},
pmid = {41555453},
issn = {2049-2618},
abstract = {BACKGROUND: Aerobiome diversity is extensive; however, species-level community structure remains poorly resolved. Likewise, microbiomes of public transit systems are of public interest due to their importance for health, though few studies have focused on these ecosystems whilst utilising shotgun metagenomics. Aerosol studies have focused predominantly on individual cities, with limited between-city comparisons suggesting specific community structures. Longitudinal studies show aerobiome diversity as dynamic, fluctuating during seasonal and daily cycles, though interannual cycles remains to be considered. Further, a bacterial bias has limited fungal aerobiome studies, with few considering both fractions collectively. As such, the objective of this study was to examine spatial and temporal patterns in the species diversity of public transit aerobiomes, with an emphasis on bacteria and fungi.

RESULTS: Air samples taken over a 3-year period (2017-2019) from six global cities were subjected to shotgun metagenomic sequencing. Improved classification databases, notably for fungi, applying stringent parameters for trimming, exogenous contamination removal and classification yielded high species-level resolution. Microbial diversity varied substantially among cities, while human and environmental factors, recorded in parallel, were of secondary significance. Bacteria dominated the public transit aerobiome with increased presence in cities with higher population densities. All aerobiomes had complex compositions, consisting of hundreds to thousands of species. Interannual variation had limited significance on the public transit aerobiome diversity and community structure.

CONCLUSIONS: Cities were the most important factor contributing to diversity and community structure, demonstrating specific bacterial and fungal signatures. Further, possible correlation between geographical distance and genetic signatures of aerobiomes is suggested. Bacteria are the most abundant constituent of public transit aerobiomes, though no single species is globally dominant, conversely indicating a large inter-city variation in community structure. The presence of a ubiquitous global species core is rejected, though an aerobiome sub-core is confirmed. For the first time, local public transit aerobiome cores are presented for each city and related to ecological niches. Further, the importance of a robust bioinformatics analysis pipeline to identify and remove exogenous contaminants for studying low-biomass samples is highlighted. Lastly, a core and sub-core definition of contaminant aerobiome species with taxon tables, to facilitate future environmental studies, is presented. Video Abstract.},
}

@article {pmid41555450,
year = {2026},
author = {Ranade, AV and Bernhardt, GV and Srinivas, M and K M, DG and Ahmad, F and Ebby, S and Karim, A and Khan, NA and Jose, J and Ramachandran, G and Marzook, H and Qaisar, R},
title = {Gut microbiome- targeted intervention ameliorates structural and transcriptomic changes in the kidney of hindlimb unloaded mouse model.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {6},
pmid = {41555450},
issn = {2524-4671},
support = {23010901126//University of Sharjah/ ; },
abstract = {The human body is adapted to Earth's gravity, but space microgravity significantly alters kidney function, with the hindlimb unloaded (HU) mouse model serving as a valuable tool for studying these effects. During space travel, changes in gut microbiota can lead to health-related issues. In this study, we explored the protective role of crocodile gut microbiome media on kidney health in a HU mouse model, given the known impact of space travel on gut microbiota and related health issues. Male C57BL/6 mice (four months old) were divided into a ground-based control group (GC), HU mice fed with distilled water (HU), and HU mice fed with crocodile bacterial conditioned media (HU-CP). All groups were maintained in a controlled environment for three weeks. At the end of the experiment, mice were euthanized, kidney tissues were dissected for histopathological examination and transcriptomic analysis. Statistical analysis was performed using one-way ANOVA followed by Tukey's multiple comparison test, with p < 0.05 considered significant. Transcriptomic analysis revealed distinct gene expression profiles across GC, HU, and HU-CP groups, with HU-CP inducing both unique (4325 genes) and differential (975 genes) expression compared to HU group. The treatment partially restored glomerular morphology, reduced inflammation, and reversed gene expression alterations associated with oxidative stress, apoptosis, fibrosis, and inflammation. The crocodile bacterial conditioned media demonstrated potential therapeutic benefits in mitigating renal injury induced by simulated microgravity in HU mice. Further research is needed to elucidate the specific mechanisms involved and explore the potential clinical applications of this approach.},
}

@article {pmid41555417,
year = {2026},
author = {Liu, L and Spaink, HP},
title = {The function of Toll-like receptor 2 in control of transcriptome responses to the microbiome and microbiome composition.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {5},
pmid = {41555417},
issn = {2524-4671},
abstract = {BACKGROUND: Toll-like receptor 2 (TLR2) plays a pivotal role in innate immunity and has recently emerged as a critical regulator of host-microbiome interactions. However, how TLR2 influences host transcriptional responses to colonized microbiome and microbial community dynamics remains largely unclear. A comparison between germ free (GF) and conventionalized zebrafish (Danio rerio) larvae provides a valuable system to investigate how the microbiome influences host transcriptomic responses in a tlr2 mutant versus wild-type control. Vice versa, to understand the role of Tlr2 in regulating the microbiome, we have analyzed microbial community composition in both tlr2 mutant and wild-type zebrafish at larval and adult stages.

RESULTS: RNAseq analysis revealed that approximately 2.6% of the zebrafish genome (827 genes) exhibited transcriptomic alterations in tlr2 mutant larvae compared to the wild type under microbiome-colonized conditions, whereas around 2% of the genome (639 genes) showed differential expression under GF conditions. KEGG enrichment analyses show that under both microbiome-colonized and GF conditions major differences between the tlr2 mutant and wild type are related to metabolism. Furthermore, there is a striking difference in endoplasmic reticulum stress responses, including well-known markers for inflammatory bowel disease which are all downregulated in the mutant under the microbiome-colonized condition. Microbiome colonization elicited a broader transcriptional response in tlr2 wild-type larvae than in the mutant, with specifically the ferroptosis, apoptosis and inflammation related pathways differently regulated. In terms of how Tlr2 influences microbial composition, 16 S rRNA gene sequencing showed large differences in beta diversity between the tlr2 mutant and wild type. The tlr2 mutant exhibited higher microbial alpha diversity during early development, whereas alpha diversity was higher in wild-type adults. For larvae at the genus level, tlr2 mutant larvae showed increased Chryseobacterium and Flectobacillus but reduced Gracilibacteria abundance relative to wild-type controls. For adult gut samples, the relative abundance of Cetobacterium was higher in the tlr2 mutants, indicating a developmental stage-specific restructuring of the microbiome.

CONCLUSIONS: TLR2 not only modulates host transcriptional responses to microbial colonization, but also shapes gut microbial diversity, composition, and metabolic potential. Our findings highlight the critical role of TLR2 in orchestrating immune-metabolic homeostasis and provide new insights into its broader function in maintaining host-microbiota symbiosis across developmental stages.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00502-z.},
}

@article {pmid41555050,
year = {2026},
author = {Nakayama-Imaohji, H and Tada, A and Ogiwara, S and Munyeshyaka, E and Tabassum, N and Mori, T and Fujikawa, R and Suzuki, K and Kuwahara, T},
title = {α-Amylase in Aspergillus oryzae-fermented rice promotes the growth of human symbiotic Faecalibacterium Prausnitzii.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36928-x},
pmid = {41555050},
issn = {2045-2322},
support = {25K14867//Japan Society for the Promotion of Science/ ; },
abstract = {Diet is one of the critical factors that govern the human gut microbiome. Fermented foods provide beneficial effects for human health by supplying diverse nutrients and digestive enzymes. We aimed to investigate the effect of fermented rice extract prepared with Aspergillus oryzae on the growth of human symbiotic Faecalibacterium prausnitzii. After steamed rice was fermented by A. oryzae, a water-soluble fraction was prepared by centrifugation and used as rice-koji extract. The growth of F. prausnitzii in the media supplemented with 1% rice-koji extract was enhanced compared to that in a control medium. Fractionation of the rice-koji extract with an anion-exchange column and mass spectrometry analysis were conducted to identify the growth-promoting factors for F. prausnitzii. LC-MS/MS analysis revealed that the fractions showing a growth-promoting effect were rich in α-amylase from A. oryzae. The addition of purified A. oryzae-derived α-amylase and starch to the culture media increased the growth and butyrate production from F. prausnitzii. These findings suggest that A. oryzae-derived enzymes in fermented rice-koji possess a growth-promoting effect, enabling F. prausnitzii to efficiently uptake and utilize starch degradation products.},
}

@article {pmid41554884,
year = {2026},
author = {Wu, Z and Liu, Z and Wang, W and Zhang, S and Tsai, AY and Lozano-Torres, JL and Sawa, S and Zhang, L and Chen, S and Lv, X and Erb, M and Xu, J and Hu, L},
title = {Root-knot nematode Meloidogyne incognita uses secondary-metabolite-mediated soil microbiome shifts to locate host plants.},
journal = {Nature plants},
volume = {},
number = {},
pages = {},
pmid = {41554884},
issn = {2055-0278},
support = {LR25D010001//Natural Science Foundation of Zhejiang Province (Zhejiang Provincial Natural Science Foundation)/ ; },
abstract = {Plant-parasitic nematodes are among the most destructive soil-dwelling pests, posing severe threats to global agriculture. However, the interplay between plant metabolites, rhizosphere microorganisms and their potential role in guiding pathogenic nematodes to their hosts remains poorly understood. Here we explored this gap by investigating the role of benzoxazinoids (BXs), a class of defensive metabolites of maize plants, in influencing the host-seeking behaviour of root-knot nematodes (RKNs). Our findings revealed that, surprisingly, BXs secreted by maize roots, particularly 6-methoxy-benzoxazolin-2-one, not only enhance RKN infection but also serve as powerful attractants. Remarkably, BX effects were observed only in the presence of a soil matrix. Further analysis demonstrated that 6-methoxy-benzoxazolin-2-one modulates the abundance and composition of rhizosphere bacteria, which in turn play a crucial role in RKN attraction and infection. We discovered that rhizosphere bacteria of BX-producing plants emit volatile compounds such as methyl ketones and 2-phenylethanol, which are then used by RKNs to locate host plants. RKNs detect these volatiles through chemosensory genes, including Mi-odr-1, Mi-odr-7 and Mi-gpa-6. Our study provides mechanistic insights into how RKNs use secondary-metabolite-shaped plant-microbe interactions to enhance their host-seeking behaviour and maximize their performance.},
}

@article {pmid41554846,
year = {2026},
author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Gop, AP and Shravana, KS and Jagannivasan, A and Nair, AV and Sudarsan, KS and Santhosh, B and Ebeneezar, S and Gopalakrishnan, A},
title = {Egg disinfection improves larval survival and shapes the microbial community in snubnose pompano (Trachinotus blochii).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35646-8},
pmid = {41554846},
issn = {2045-2322},
support = {BT/AAQ/3/SP28267/2018//Department of Biotechnology, Government of India/ ; },
abstract = {Early microbial colonization is crucial for immunity and survival in aquatic animals. This study evaluated the impact of egg disinfection on microbial colonization and larval performance in Trachinotus blochii, a high-value mariculture fish. Optimal egg disinfection protocols were initially identified as 20 ppm iodophor for 10 min, 400 ppm H2O2 for 10 min, and 40 ppm glutaraldehyde for 5 min to improve hatchability. Sequential analyses included 16S rRNA amplicon sequencing of larval microbiota at 10-days post hatching (DPH) and assessment of survival and antioxidant status till 25 DPH. Disinfection significantly enhanced hatchability (up to 90.88 ± 2% with 40 ppm glutaraldehyde), larval survival (up to 34.80 ± 1.1% in glutaraldehyde and 31.18 ± 1.5% in H2O2), and catalase activity. Notably, egg disinfection reshaped the larval microbiota, enriching microbial diversity measures and beneficial bacterial taxa, such as Hyphomonadaceae, Halieaceae, Nannocystaceae, and Alteromonadaceae. Improved survival correlated with enhanced taxonomic and functional metagenomic diversity, lower Proteobacteria: Bacteroidota ratio and higher combined proportions of Fusobacteriota, Firmicutes, and Bacteroidota relative to Proteobacteria. The findings suggest that egg disinfection acts as a microbiota programming strategy to promote larval health, offering a practical approach to enhance sustainability in T. blochii aquaculture.},
}

@article {pmid41554833,
year = {2026},
author = {Qi, Y and Huang, Y and Chen, H and Li, J and Liu, M and Xiong, W and Tang, Q and Zhang, Y},
title = {ACE2 expression by colonic epithelial cells is associated with viral infection, immunity, and energy metabolism.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36052-w},
pmid = {41554833},
issn = {2045-2322},
support = {2025A0505080010//Guangdong Province Science and Technology Innovation Strategy Special Fund/ ; 2024A04J3928//Guangzhou Science and Technology fund/ ; 91742109, 31770978, 31722003, 31770925, 31370847, 81770552//Natural Science Foundation of China/ ; 2016YFC0900102//National Key Research and Development Program/ ; 2018ZX10302205//National Science and Technology Major Project/ ; 5001-3001032//Guangzhou Women and Children's Medical Center Fund/ ; },
abstract = {Coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection first emerged in Wuhan, Hubei Province, China, in December 2019 and spread rapidly to other provinces and other countries. Angiotensin I converting enzyme 2 (ACE2) is the receptor for SARS-CoV and has been suggested to be also the receptor for SARS-CoV-2. Paradoxically, ACE2 expression in the lung protects mice from SARS-CoV spike protein induced lung injury by attenuating the renin-angiotensin system. In the intestine, ACE2 also suppresses intestinal inflammation by maintaining amino acid homeostasis, antimicrobial peptide expression and ecology of the gut microbiome. We performed analysis of single cell-RNA sequencing data from control subjects and those with colitis or inflammatory bowel disease (6 controls, 6 colitis cases, 2 ulcerative colitis cases and 3 Crohn's disease cases). The single cell-RNA sequencing data was also used to conduct co-expression analysis and GO enrichment analysis. Multiplex immunofluorescence (mIF) was performed to assess the expression of ACE2, IFNA4, and RSAD2 on colon specimens obtained from patients, including non‑diseased (control) tissue, ulcerative colitis (UC) tissue and Crohn's disease (CD) tissue. We revealed that ACE2 exhibited specific and high expression levels in colonocytes. Furthermore, genes implicated in viral infection and anti-infection immunity were also found to be highly expressed in colonocytes. Additionally, we conducted an analysis of genes co-expressed with ACE2 within colonocytes, and total of 3420 and 2136 genes were identified as being positively and negatively correlated with ACE2 expression. Concurrently, through Gene Ontology (GO) enrichment analysis, it was observed that genes positively associated with ACE2 expression were significantly enriched in pathways related to viral infection, organismal immunity, and energy metabolism. Accordingly, mIF showed a significant increase in IFNA4 and RSAD2 expression in the colonic epithelial ACE2[+] cells of UC and CD patients relative to controls. Integrated data from single cell-RNA sequencing and patient's mIF highlighted the expression profile of ACE2 in colonic epithelial cells, suggesting the possible involvement of ACE2 in the intestinal tract of patients with SARS-CoV-2 pneumonia in enteroviral infection, immunity and energy metabolism functions.},
}

@article {pmid41554808,
year = {2026},
author = {Sugiyama, N and Kato, S and Shimizu, S and Uehara, O and Hasegawa-Nakamura, K and Shirakata, Y and Noguchi, K and Hatae, M and Kakinoki, H and Kamitomo, M and Furuichi, Y and Nagasawa, T},
title = {Association of low progesterone levels and periodontal disease with threatened preterm labor.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35944-1},
pmid = {41554808},
issn = {2045-2322},
support = {#22K10004//Grants-in-Aid for Scientific Research (C)/ ; },
abstract = {Periodontal disease has been reported to increase the risk of threatened preterm labor (TPL). However, studies analyzing the oral, vaginal, and rectal lumen commensal flora in women with TPL are limited. In this study, a total of 60 women were enrolled, including 30 with TPL and 30 without TPL. We assessed periodontal clinical parameters, salivary hormone levels, and the microbiome using next-generation sequencing. Probing pocket depth (PPD) and bleeding on probing were greater in the TPL than in the non-TPL group. The TPL group was associated with lower progesterone levels and an increase in PPD ≥ 4 mm. Significant differences in alpha diversity in only vaginal Faith's phylogenetic diversity, and significant differences in beta diversity at all sites were observed. ANCOM showed decreased Lactobacillales in the saliva and Bifidobacterium in the rectal lumen, and increased Staphylococcus in the oral cavity and vagina in the TPL group. The peptidoglycan synthesis pathway was significantly upregulated in the oral and vaginal tissues in the TPL group. Overall, the TPL group had lower progesterone levels and more severe periodontal disease; furthermore, the low progesterone levels in the TPL group were associated with oral and vaginal dysbiosis of the microbiota.},
}

@article {pmid41554782,
year = {2026},
author = {Holmes, LA and Veiga, PW and Pettis, JS and Guarna, MM and Hoover, SE},
title = {A non-invasive method for profiling the gut microbiome and virome of honey bee queens.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {2318},
pmid = {41554782},
issn = {2045-2322},
abstract = {UNLABELLED: High honey bee colony mortality worldwide has underscored the critical role of queen bee health in colony survival, with poor queen quality frequently linked to colony losses. The gut microbiome plays fundamental roles in immunity, nutrition, and reproduction, making its characterization essential for understanding stressors that impact queen health, longevity, and fecundity, yet its role in mediating stress responses remains poorly understood. Here, we present a novel, non-invasive method for collecting feces from queen honey bees and demonstrate its potential as a powerful tool for profiling the gut microbiome, detecting stressor exposure, and screening for viral infections. This approach permits repeated, longitudinal assessments of individual queens, providing unprecedented insights into how environmental and pathogenic pressures influence queen health, longevity, and reproductive capacity. Beyond research applications, benefits include evaluating queens before colony introduction and mitigating disease transmission risks in international trade, where pathogen spread remains a major regulatory challenge. By enabling non-destructive monitoring of queen health, this method provides a transformative tool for improving colony resilience and advancing sustainable honey bee management in the face of global challenges.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-32053-3.},
}

@article {pmid41554742,
year = {2026},
author = {Li, Y and Yang, L and Xu, H and Bian, X and Shi, D and Wu, W and Li, L},
title = {Restoration of ethanol-induced Bifidobacterium pseudocatenulatum depletion ameliorates alcohol-associated liver disease.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00913-z},
pmid = {41554742},
issn = {2055-5008},
support = {82502783//National Natural Science Foundation of China/ ; LQ22H030013;2022-KY1-001-039//Zhejiang Provincial Natural Science Foundation of China/ ; zz202320//State Key Laboratory for Diagnosis and Treatment of Infectious Disease Independent Project/ ; 2022499572//Young Innovative Talents Support Program of Zhejiang Medical and Health Science and Technology Project/ ; 2024025437,2024ZR152//Young Innovative Talents Support Program of Zhejiang Chinese Medicine Science Technology Project/ ; 2025ZFJH03//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Alcohol-associated liver disease (ALD), characterized by gut barrier disruption and microbial dysbiosis, is associated with significant depletion of the genus Bifidobacterium in patients, as evidenced by our cohort of 127 subjects. Functional screening revealed B. pseudocatenulatum as a protective strain. In a murine ALD model established with a Lieber-DeCarli ethanol diet, oral administration of B. pseudocatenulatum for 8 weeks ameliorated hepatomegaly, steatosis, and serum transaminase levels. Probiotic intervention restored intestinal barrier function, as indicated by reduced lipopolysaccharide-binding proteins and upregulated tight junction protein expression. Microbiome analysis revealed a mitigation of dysbiosis, with a reduction in pathogenic Escherichia-Shigella and Parabacteroides and an enrichment of beneficial Bifidobacterium and Blautia, concomitant with shifts in lipid metabolism. Mechanistically, B. pseudocatenulatum-derived short-chain fatty acids downregulated the expression of hepatic lipogenic genes (Cd36, Fasn, Accα) and pro-inflammatory cytokines (Il-1β, Ccl2, Tnf-α). These results suggest that B. pseudocatenulatum is a promising probiotic candidate for ALD management.},
}

@article {pmid41554738,
year = {2026},
author = {Zheng, J and Zhang, C and Xiang, S and Li, M and Wang, H and Shi, K and Tondrob, D and Han, Y},
title = {Integrated metabolomics and metagenomics uncover pathogenic mechanisms of Fusarium wilt and faba bean defense responses.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-025-00673-8},
pmid = {41554738},
issn = {2396-8370},
support = {31901929//National Natural Science Foundation of China/ ; cstc2021jcyj-msxmX1021//Natural Science Foundation of Chongqing Municipality/ ; },
abstract = {Fusarium wilt diseases pose a huge threat to faba bean (Vicia faba L.) production globally, with significant outbreaks in Chongqing, China. Symptomatic plants showed wilting leaves and rotten roots, ultimately perishing in the advanced stage. Morphological features, multilocus phylogenetic analyses, and pathogenicity tests demonstrated that the primary causal agent was Fusarium oxysporum. Untargeted metabolomics of faba beans revealed substantial metabolic differences in the infected faba bean roots. Plants responded to fungal biotic stress by reprogramming key metabolic pathways, including alanine, aspartate, and glutamate metabolism, the citrate cycle, arginine biosynthesis, and jasmonic acid metabolism, which collectively underscore activated defense responses. Metagenome sequencing showed that Fusarium wilt significantly reshaped the structure of the rhizosphere microbiota and affected the abundance of genes encoding element cycling in soil. This work elucidates the pathogenic mechanisms of F. oxysporum by integrating pathogen identification, host metabolism, and microbiome ecology. Our findings offer biomarkers for disease diagnosis and targets for biocontrol, advancing sustainable management of Fusarium wilt diseases in legumes.},
}

@article {pmid41554476,
year = {2026},
author = {Harariya, K and Singh, TR and Kalra, A and Padhi, S and Ahamed, F},
title = {Letter to Editor regarding "Oral Microbiome Signatures as Potential Biomarkers for Gastric Cancer Risk Assessment".},
journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract},
volume = {},
number = {},
pages = {102339},
doi = {10.1016/j.gassur.2026.102339},
pmid = {41554476},
issn = {1873-4626},
}

@article {pmid41554431,
year = {2026},
author = {Elechi, JOG and de Mendonça, CR and Bandeira, VCA and Da Silva, MSP and de Melo, APR and Guedes, RCA and Hirabara, SM and Cione, E and de Vasconcelos, DAA},
title = {Exploring recent insights on intermittent fasting in regulating glucocorticoid levels and diet-induced metabolic disorders with focus on MAFLD and hepatic outcomes.},
journal = {Molecular and cellular endocrinology},
volume = {614},
number = {},
pages = {112736},
doi = {10.1016/j.mce.2026.112736},
pmid = {41554431},
issn = {1872-8057},
abstract = {Consumers' risky eating behaviours aided by the current food environment have led to an increase in diet-related metabolic disorders. Metabolic (dysfunction)-associated fatty liver disease origin represents a major global health burden that is increasing at an alarming rate on an annual basis. Modifying the timing of calorie consumption, dietary composition, or caloric intake offers a promising therapeutic approach for the management of this condition. The aim of this review was to provide a concise analysis of the impact of intermittent fasting on the regulation of glucocorticoid levels and diet-induced metabolic disorders with a focus on non-alcoholic fatty liver diseases. We found that intermittent fasting primarily regulates hepatic autophagy via nutritional and hormonal pathways, aiding in the maintenance of energy equilibrium, enhancement of mitochondrial function, regulation of liver quality, preservation of cellular homeostasis, protection of cells from harmful factors, mitigation of liver metabolic disorders, and improvement of liver inflammation. Also, the physiological changes induced by intermittent fasting and their metabolic consequences arise through multiple mechanisms, including alterations in hepatic metabolism, hepatic autophagy, inflammatory responses, liver functional enzymes, hepatic steatosis, fibroblast growth factor signalling, White adipoe tissue browning, adipokines, circadian rhythms, lipid profiles, body composition, the adipose tissue-gut microbiome axis, skeletal muscle, and the autophagy process. Interestingly, we identified the complex interplay among glucocorticoids, intermittent fasting, and non-alcoholic fatty liver diseases highlighting the hepatic macrophage glucocorticoid receptor as a pivotal mediator of fasting-induced reprogramming of the macrophage secretome, including fasting-suppressed cytokines. In conclusion, existing data indicates that intermittent fasting in patients with non-alcoholic fatty liver diseases is a viable, safe, and successful strategy for weight reduction, demonstrating notable trends in the amelioration of dyslipidaemia and non-alcoholic fatty liver diseases.},
}

@article {pmid41554330,
year = {2026},
author = {Piñeiro, B and Kue, J and Costa, J and Santiago, A and Msaddi, J and Nuss, K and Yadav, H and Szalacha, L and Menon, U},
title = {Time-restricted eating in patients with metabolic syndrome: A protocol paper for a feasibility clinical trial.},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {108223},
doi = {10.1016/j.cct.2026.108223},
pmid = {41554330},
issn = {1559-2030},
abstract = {Recent studies have evaluated Time-Restricted Eating (TRE) as a promising dietary behavioral intervention for weight loss and cardiometabolic risk factor improvement. Yet the results are mixed. We describe a TRE protocol, a behavioral dietary intervention where all calorie intake is limited to 10-h eating window followed by a 14-h fasting period, without altering diet quality and quantity. This study aims to determine the feasibility and acceptability of a 12-week TRE intervention among patients with metabolic syndrome. Dietary lifestyle changes can decrease risk in metabolic syndrome, but such changes are difficult to implement and sustain. This is a pilot feasibility study with a single-arm group. A total of 40 adult patients with metabolic syndrome are being enrolled. Participants document their daily eating patterns through MyCap app. The primary outcome is to assess the feasibility and acceptability of the intervention, including recruitment, program delivery, adherence and patient satisfaction. Secondary outcome measures include changes in weight, blood pressure, sleep, quality of life, and biological measures including gut microbiome, HbA1c, lipids, and thyroid function. Findings of this pilot study will provide novel insights into improving information health markers in individuals with metabolic syndrome, as well as inform the feasibility and sustainability of this dietary intervention.},
}

@article {pmid41553769,
year = {2026},
author = {Kay, H and Jabbur, ML},
title = {The elusive rhythms of bacterial life.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70287},
pmid = {41553769},
issn = {1873-3468},
support = {101166968/ERC_/European Research Council/International ; BB/Z514937/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; Institute Strategic Programme BRiC BB/X01102X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Circadian clocks are endogenous timekeeping mechanisms that are phylogenetically widespread. Despite the immense diversity of bacterial life, to date, clocks have been identified in few bacterial species. The cyanobacterial clock is understood in great detail, and the roles of its clock proteins in other types of timing mechanisms and in stress resistance are being studied in an ever-growing range of species. Studies of host-associated microbiomes have shown that host and microbial rhythmicity impact one another reciprocally. However, bacterial rhythms have primarily been studied in species in isolation or in host-associated microbiomes. Here, we summarize the state of the field of microbial chronobiology and propose the hypothesis that rhythmicity could be an emergent property of microbial interactions in free-living bacterial communities.},
}

@article {pmid41553656,
year = {2026},
author = {Langgeng, A and Lee, W and Hanya, G and Okamoto, M and MacIntosh, AJJ},
title = {Of hot springs and holobionts: linking hot spring bathing behavior, parasitism, and gut microbiome in Japanese macaques.},
journal = {Primates; journal of primatology},
volume = {},
number = {},
pages = {},
pmid = {41553656},
issn = {1610-7365},
support = {International Primatological Society//International Primatological Society/ ; Ministry of Education, Culture, Sports, Science, and Technology//Ministry of Education, Culture, Sports, Science, and Technology/ ; #20H03333//Japanese Society for the Promotion of Science/ ; },
abstract = {Japanese macaques at Jigokudani Snow Monkey Park, Nagano, exhibit hot spring bathing behavior (HSBB) during the cold season. HSBB is known to aid thermoregulation and reduce stress, but its impact on host-associated biota in nonhuman primates remains unexplored. In this study, conducted between December 2019 and March 2021, we investigated the relationship between HSBB and lice load, gastrointestinal (GI) parasitism, and the gut microbiome in Japanese macaques at Jigokudani. Fecal samples were collected from sixteen adult females (9 bathers and 7 non-bathers) varying by age, reproductive status, and social rank. Nit-picking rates, used to estimate lice load, differed between bathers and non-bathers in submerged and non-submerged areas. We detected four GI helminths and at least one protozoan parasite, but did not observe noticeable differences in the probability of infection or abundance of these endoparasites between bathers and non-bathers. Finally, the alpha and beta diversity of the gut microbiome did not differ between bathers and non-bathers, but we identified four microbial genera that were significantly more abundant in non-bathers. These findings suggest that HSBB may influence host-(micro)organism relationships. Further research is needed to explore potential health outcomes associated with HSBB.},
}

@article {pmid41553570,
year = {2026},
author = {Reinecke, K and Kleynhans, L and Ronacher, K and Loots, DT},
title = {Characterizing the tuberculosis and type 2 diabetes mellitus comorbidity in a South African cohort using untargeted GCxGC-TOFMS metabolomics.},
journal = {Metabolomics : Official journal of the Metabolomic Society},
volume = {22},
number = {1},
pages = {19},
pmid = {41553570},
issn = {1573-3890},
mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology/metabolism/urine ; *Metabolomics/methods ; Male ; Female ; South Africa/epidemiology ; *Tuberculosis/epidemiology/metabolism/urine ; Middle Aged ; Gas Chromatography-Mass Spectrometry/methods ; Adult ; Cohort Studies ; Comorbidity ; Aged ; },
abstract = {INTRODUCTION: Tuberculosis (TB) and type 2 diabetes mellitus (T2DM) are highly prevalent diseases resulting in high mortality rates globally. Furthermore, T2DM increases susceptibility to TB and vice versa, worsening disease outcomes. This comorbidity is, however, not well described nor understood, despite its rising prevalence globally.

OBJECTIVES: This investigation aimed to better characterize the urinary metabolic profiles of patients with the TB and T2DM comorbidity in a South African cohort, to better understand its metabolic basis and associated clinical implications.

METHODS: Using untargeted GCxGC-TOFMS metabolomics, urine samples from 17 patients with TB and T2DM and 34 healthy controls were analyzed and statistically compared to identify significantly altered urinary metabolites.

RESULTS: TB-T2DM comorbid patients were characterized by altered metabolism of: (1) tryptophan and kynurenine (reduced kynurenic acid, anthranilic acid, picolinic acid) associated with changes to NAD[+] synthesis and a redox imbalance, (2) nucleotides (reduced 3-aminoisobutyric acid, orotic acid, thymine, β-alanine, adenine, hypoxanthine), (3) tyrosine (reduced 3,4-dihydroxyphenylglycol, 4-hydroxy-3-methoxyphenylglycol, hydroxyphenylpyruvate), (4) lipids (reduced dec-2-enedioate, adipic acid, methylmalonic acid), (5) reduced concentrations of various glycine conjugates associated with glycine depletion, and (6) reduced urinary concentrations of various gut microbial metabolites indicative of microbial dysbiosis.

CONCLUSION: These results indicate several metabolic disruptions to amino acids, nucleotides, lipids, NAD⁺ homeostasis and the host microbiome, in TB-T2DM patients, mainly driven by inflammation and oxidative stress. Overall, the findings indicate synergistic amplification of metabolic stress, associated with immune suppression and TB-T2DM disease progression, and subsequently suggests how TB increases T2DM susceptibility and vice versa, as foundation for further investigations.},
}

Humans
*Diabetes Mellitus, Type 2/epidemiology/metabolism/urine
*Metabolomics/methods
Male
Female
South Africa/epidemiology
*Tuberculosis/epidemiology/metabolism/urine
Middle Aged
Gas Chromatography-Mass Spectrometry/methods
Adult
Cohort Studies
Comorbidity
Aged

@article {pmid41553492,
year = {2026},
author = {He, Q and Xie, Y and Liu, J and Li, T},
title = {Diosbulbin B attenuates propylthiouracil-induced thyroid enlargement in mice by regulating the gut microbiota-short chain fatty acids-thyroid axis.},
journal = {Naunyn-Schmiedeberg's archives of pharmacology},
volume = {},
number = {},
pages = {},
pmid = {41553492},
issn = {1432-1912},
support = {No. 2025JC-GXPT-005//Shaanxi Provincial Science and Technology Department/ ; },
abstract = {This research investigates Diosbulbin B's capacity to protect against propylthiouracil-induced thyroid enlargement in mice and examines its underlying operative principles. Propylthiouracil was administered to mice by gavage for 15 days to establish a mouse thyroid enlargement model. Meanwhile, Diosbulbin B was administered to the mice as an intervention. After the experiment, biochemical indicators were measured, and, together with non-targeted metabolomics, targeted metabolomics, 16S rDNA sequencing, and Spearman correlation analysis, the alleviating effect of Diosbulbin B on thyromegaly induced by propylthiouracil and its potential mechanism were systematically evaluated. Diosbulbin B decreased thyroid function markers and ameliorated pathological alterations in the thyroid induced by propylthiouracil. Additionally, it alleviated propylthiouracil-induced inflammatory responses and oxidative damage in thyroid tissue. Untargeted metabolomics revealed Diosbulbin B primarily normalized propylthiouracil-disrupted fatty acid metabolism. Crucially, Diosbulbin B reversed the consumption of SCFAs in feces. What is more, 16S rDNA gene sequencing analysis demonstrated that Diosbulbin B successfully rebalanced the gut microbiome by boosting the population of beneficial bacteria while cutting down on harmful microorganisms, effectively bringing the intestinal flora structure back to normal. On top of that, when we looked at the connection between fatty acids and gut bacteria, it became clear that Firmicutes, Bacteroidota, and Verrucomicrobia, along with propionic, butyric, and acetic acids, could be considered key indicators of thyroid enlargement caused by propylthiouracil. Diosbulbin B significantly improved propylthiouracil-induced thyroid enlargement by regulating the intestinal flora, increasing fatty acid production, and reducing inflammation and oxidative stress.},
}

@article {pmid41553090,
year = {2026},
author = {Lei, S and Tong, H and Zhou, Y and Huang, J and Zhou, X and Dai, J and Yu, Z},
title = {Gut microbiota landscape of Haemaphysalis longicornis under Borrelia burgdorferi infection.},
journal = {Insect science},
volume = {},
number = {},
pages = {},
doi = {10.1111/1744-7917.70241},
pmid = {41553090},
issn = {1744-7917},
support = {//the Innovation-Driven Research Programme of Central South University/ ; 32170071//National Natural Science Foundation of China/ ; 32170142//National Natural Science Foundation of China/ ; 32300051//National Natural Science Foundation of China/ ; 2023JJ30651//Natural Science Foundation of Hunan Province/ ; 2025JJ50101//Natural Science Foundation of Hunan Province/ ; },
abstract = {This study aimed to explore the reason for Haemaphysalis longicornis restricting Borrelia burgdorferi colonization and transmission from the perspective of gut microbiota, and to investigate the impact of different infection statuses on the Haemaphysalis longicornis microbiota and its potential role in pathogen transmission. Pathogen-free Haemaphysalis longicornis ticks and IFNAR1[-/-] mice were used to establish infection models. Ticks fed on pathogen-infected mice, and their midguts were analyzed at day 4 and 10 post-feeding. DNA was extracted from the midguts, and the V3-V4 region of bacterial 16S rRNA gene was amplified and sequenced. Analysis of microbiome data were analyzed using QIIME2 and R. After digesting the bloodmeals, the gut microbiota of ticks that ingested bloodmeal with Borrelia burgdorferi exhibited minimal structural changes, while the ticks with uninfected bloodmeal or bloodmeal with Langat virus showed the dysbiosis. The Borrelia group showed minimal temporal shifts in β-diversity, with stable co-occurrence networks and increased core microbial interactions. Neutral model analysis revealed a hybrid niche in the Borrelia group. Potential biomarkers were identified that may suppress Borrelia burgdorferi transmission. Our findings reveal that Borrelia burgdorferi infection is associated with a stabilized and functionally distinct gut microbiota in Haemaphysalis longicornis. The gut microbiota of Haemaphysalis longicornis functions as a barrier against Borrelia burgdorferi colonization and transmission through microbial regulation and resource limitation, thus providing a potential mechanistic explanation for the observed vector incompetence. These findings highlight the potential of microbiome-targeted strategies to block pathogen transmission and offer new insights into vector-borne disease.},
}

@article {pmid41552974,
year = {2026},
author = {Yang, XY and Zhang, ZW and Chen, GD and Yuan, S},
title = {Gut microbiome remodeling induced by microplastic exposure in humans.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2617696},
pmid = {41552974},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Microplastics/adverse effects/toxicity ; *Bacteria/classification/drug effects/genetics/isolation & purification/metabolism ; Dysbiosis/chemically induced/microbiology ; Animals ; },
abstract = {The impact of microplastics (MPs) on the diversity and composition of the gut microbiome has been extensively documented in animal studies, but evidence in humans remains limited. Recognizing the potential differences in MP effects between animal and human gut microbiomes, this review synthesizes current evidence concerning their impact on the human gut microbiota. Furthermore, the potential links between microplastic-induced dysbiosis and the pathogenesis of human diseases were analyzed. Cross-sectional studies have been conducted to explore microplastic exposures (such as in humans who consume hot foods served in disposable plastic tableware) and their associations with gut microbiome functionalities in infants, preschool children and adults. Exposure to MPs increased the abundance of Dethiosulfovibrionaceae, Enterobacteriaceae, Moraxellaceae, Actinomycetota, Pseudomonadota, and Veillonella. On the other hand, MPs decreased the abundances of Bacillota, Bacteroidota, Lactobacillales, Rikenellaceae, Parabacteroides, Roseburia, Coprococcus, Turicibacter, and Eubacterium coprostanoligenes. These changes were associated with a decrease in butyrate production and a decrease in short-chain fatty acid levels. However, for some other bacteria, both inductive (on Oscillospiraceae, Adlercreutzia, Phascolarctobacterium, and Collinsella) and repressive effects (on Streptococcus) have been documented. There are contradictory reports about MP-induced changes in Lachnospiraceae (including the Dorea genus), Alistipes and Faecalibacterium, which may be correlated with obesity, gastrointestinal dysfunction, some cancers, inflammatory bowel disease and Crohn's disease. Potential reasons for these discrepancies are proposed. This review also examines putative mechanisms, with a focus on biofilm formation on selective surfaces, and discusses the inherent limitations of current MP exposure assessments in human gut microbiota studies.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Microplastics/adverse effects/toxicity
*Bacteria/classification/drug effects/genetics/isolation & purification/metabolism
Dysbiosis/chemically induced/microbiology
Animals

@article {pmid41552936,
year = {2026},
author = {Lu, Y and Chang, L and Liu, S and Wang, M and Zhao, Y},
title = {Rutin alleviates dietary advanced glycation end products (AGEs)-induced insulin resistance in mice by modulation of gut microbiota.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo04604a},
pmid = {41552936},
issn = {2042-650X},
abstract = {Dietary advanced glycation end products (AGEs), formed during thermal food processing, are associated with metabolic disorders. This study investigated the efficacy of rutin in alleviating AGEs-induced insulin resistance (IR) in a mouse model. Male C57BL/6 mice were fed a high-AGEs diet for 12 weeks to induce IR, followed by 8 weeks of rutin intervention (100 mg per kg body weight per day). Rutin supplementation markedly ameliorated IR, as indicated by reduced hyperglycemia and dyslipidemia, a reduced homeostasis model assessment of insulin resistance (HOMA-IR) index, an elevated insulin sensitivity (HOMA-IS) index, and upregulation of insulin receptor substrates IRS-1 and IRS-2. Metagenomic analysis demonstrated that rutin intervention restored gut microbial richness and diversity and induced structural shifts in the microbiota composition. Specifically, rutin enriched beneficial genera, including Akkermansia, Bifidobacterium, Faecalibacterium, Lactobacillus, and Coriobacteriales, while reducing populations of IR-associated taxa such as Erysipelotrichaceae, Coprobacillus, Enterococcus, Adlercreutzia, and Allobaculum. Concurrently, rutin increased fecal concentrations of short-chain fatty acids (SCFAs), notably acetic acid and propionic acid. Spearman's correlation analysis confirmed negative associations between rutin-modulated microbiota and IR indicators. These results demonstrate that rutin mitigates AGEs-induced IR by reshaping the gut microbiome and promoting beneficial microbial metabolites.},
}

@article {pmid41552834,
year = {2026},
author = {Close, R and Kremer, S and Mitchem, M and Bellinghiere, A and Nirmalkar, K and Borges, CR and Krajmalnik-Brown, R and Shah, DD},
title = {A sulfotransferase from a gut microbe acts on diverse phenolic sulfate compounds, including acetaminophen sulfate.},
journal = {PNAS nexus},
volume = {5},
number = {1},
pages = {pgaf403},
pmid = {41552834},
issn = {2752-6542},
abstract = {Sulfonation is one of the two main phase II detoxification pathways in eukaryotes which transforms nonpolar compounds into hydrophilic metabolites. Sulfotransferases catalyze these reactions by transferring a sulfo group from a donor to an acceptor molecule. Human cytosolic sulfotransferases use only 3'-phosphoadenosine 5'-phosphosulfate (PAPS) as a donor to sulfonate a variety of chemicals. Less understood are microbial aryl-sulfate sulfotransferases (ASSTs), which catalyze sulfo transfer reactions, without utilizing PAPS as a donor. Currently, the identity of physiological sulfo donor substrates remains unknown and sulfo acceptor substrates are underexplored. With this study, we aim to understand the potential contribution of a gut microbial enzyme to sulfonation chemistry by uncovering its substrate preferences. Here, we show that a sulfotransferase (Bacteroides vulgatus ASST) from the prevalent gut microbe B. vulgatus (now Phocaeicola vulgatus) is a versatile catalyst that utilizes a wide range of phenolic molecules as substrates that are commonly encountered by the host. With this action, it modulates concentrations of donor phenolic sulfates such as acetaminophen sulfate, dopamine sulfate, p-cresol sulfate, and related compounds in vitro and displays broad acceptor flexibility by sulfonating diverse phenolic compounds, including p-coumaric acid, p-cresol, 4-ethylphenol, tyramine, among others. These findings suggest that gut microbial enzymes like ASSTs may contribute to host detoxification of phenolics, a role previously attributed solely to human sulfotransferases. However, further in vivo studies are necessary to understand the potential contributions of ASSTs to host detoxification processes.},
}

@article {pmid41552775,
year = {2026},
author = {Hodes, GE and Kropp, DR},
title = {Acute Estradiol Bridges Gut Microbiome Composition With Cognition.},
journal = {Biological psychiatry global open science},
volume = {6},
number = {2},
pages = {100662},
pmid = {41552775},
issn = {2667-1743},
}

@article {pmid41552724,
year = {2025},
author = {Wu, YC and Chen, BY and Duan, SZ},
title = {Oral microbiota in cardiovascular health and disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1731845},
pmid = {41552724},
issn = {2235-2988},
mesh = {Humans ; *Cardiovascular Diseases/microbiology/etiology ; *Microbiota ; *Mouth/microbiology ; Animals ; },
abstract = {Hundreds of microbial species inhabit the oral cavity and are essential to local and systemic health. Cardiovascular disease (CVD) causes a significant burden on global health, with its etiology and pathogenesis still not fully understood. Growing evidence indicates an association between the oral microbiome and CVD. However, the variability of populations, follow-up durations, and disease severity between various human investigations led to divergent conclusions. Animal studies have focused on the relationship between individual microbial species and CVD, yet gaps remain in the mechanisms between CVD and microbiome. In addition, a comprehensive understanding of the interactions between oral pathogens and the cardiovascular system has not been elucidated. In this Review, we summarize our current knowledge of basic and clinical research on potential mechanisms linking the oral microbiome to CVD and highlight the need for population-based studies with controlled baselines to establish mechanism links between oral microbial pathways and CVD.},
}

Humans
*Cardiovascular Diseases/microbiology/etiology
*Microbiota
*Mouth/microbiology
Animals

@article {pmid41552720,
year = {2025},
author = {Wang, Z and Zhang, T and Liu, Y},
title = {Emerging technologies and current challenges in intratumoral microbiota research.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1685862},
pmid = {41552720},
issn = {2235-2988},
mesh = {Humans ; *Tumor Microenvironment ; *Neoplasms/microbiology ; *Microbiota ; Computational Biology ; Single-Cell Analysis ; Animals ; },
abstract = {Intratumoral microbiota are now recognized as an integral component of the tumor microenvironment, affecting tumor initiation, metastatic potential, immune modulation, and treatment response. However, their extremely low biomass poses significant challenges for accurate detection, functional interpretation, and reproducibility, largely because the detection process is highly susceptible to environmental contamination. Standardization of analytical procedures has not yet been established; consequently, variability in sampling protocols, sequencing workflows, and bioinformatic pipelines further complicates cross-study comparisons and hampers the consolidation of robust evidence in this field. Recent advances in technology have begun to provide opportunities to overcome these barriers. Improved contamination-control strategies and more sophisticated decontamination algorithms have enhanced the reliability of microbial detection in low-biomass tissues. High-resolution approaches, such as single-cell RNA sequencing, spatial transcriptomics and optimized anaerobic cultivation, enable the sensitive identification, spatial localization, and mechanistic study of tumor associated microbes. Parallel developments in genome-resolved and enzyme-level analysis reveal microbial metabolic pathways that shape immune responses, drug resistance, and tumor progression. Organoid-based co-culture models further provide physiologically relevant platforms to dissect host-microbe-immune interactions and interpret microbiota-driven modulation of therapeutic responses. Integrating microbiome data with clinical and multi-omics profiles, assisted by artificial intelligence, is accelerating biomarker discovery and informing microbe-guided therapeutic strategies. Taken together, the standardization of research strategies, combined with the application of advanced detection technologies, is propelling the field beyond descriptive profiling toward mechanistic understanding and clinical translation, thereby unlocking the potential of intratumoral microbiota for precision oncology.},
}

Humans
*Tumor Microenvironment
*Neoplasms/microbiology
*Microbiota
Computational Biology
Single-Cell Analysis
Animals

@article {pmid41552713,
year = {2025},
author = {Rodríguez, ZG and Thome, SKR and Castillejos, RD and García-Reyes, ED and Martínez-Vargas, A and Nájera-Segura, NS and González, EEJ and Nivon-Torres, GF and Mascarua, EAA and Caballero-Sánchez, H and Palacios-Cruz, RL and Solórzano-Mata, CJ and Sosa-Velasco, TA and Zárate-Ortiz, C},
title = {Precision Pediatric Caries Diagnostics: Saliva-Check Mutans versus Culture for High-Density Streptococcus mutans Detection.},
journal = {Discoveries (Craiova, Romania)},
volume = {13},
number = {4},
pages = {e220},
pmid = {41552713},
issn = {2359-7232},
abstract = {The paradigm of dental medicine is shifting from a reactive surgical model to precision pediatric caries diagnostics, emphasizing early detection of pathogenic oral microbiota. Rapid point-of-care assays capable of identifying high-density Streptococcus mutans are critical to enable targeted intervention. This pilot study evaluated the diagnostic validity of a high- threshold monoclonal antibody-based lateral flow assay (Saliva-Check Mutans, SCM) relative to selective culture for identifying clinically meaningful S. mutans loads in children. Stimulated saliva samples were collected from 50 schoolchildren aged 9-13 years in Oaxaca, Mexico. Samples were analyzed using SCM and selective culture on Mitis Salivarius Agar (MSA), with presumptive S. mutans colonies confirmed biochemically. Selective culture identified 46% of participants as positive, whereas SCM detected 18% as positive. Relative to culture, SCM demonstrated 39.1% sensitivity (95% CI: 21.5%-60.1%), 100% specificity (95% CI: 87.5%-100%), and 100% positive predictive value (95% CI: 66.4%-100%), with no false positives observed. The results highlight the assay's rule-in capability for high-density pathogenic loads (>10^5 CFU/mL). The diagnostic discordance reflects divergent analytical thresholds, termed the "Threshold Gap". While SCM exhibits limited sensitivity for low-level colonization, its absolute specificity supports its use as a precision high-threshold triage tool, identifying pediatric patients with clinically significant S. mutans burdens who may benefit from intensified preventive strategies. Integration with culture or molecular approaches can enhance risk stratification and precision dentistry workflows.},
}

@article {pmid41552431,
year = {2026},
author = {Buonaccorsi, A and McMullen, BN and Builder, B and Drummond, K and Halteman, S and See, JC and Thomas, E and Viands, A and Worley, S and Wright, JR and Keeney, J and Lamendella, R},
title = {Metagenomic surveillance of tick-borne pathogens and microbiomes in Huntingdon County, Pennsylvania.},
journal = {One health (Amsterdam, Netherlands)},
volume = {22},
number = {},
pages = {101305},
pmid = {41552431},
issn = {2352-7714},
abstract = {The rise in tick populations across the United States has contributed to a surge in tick-borne diseases, with Pennsylvania ranking among the highest in reported cases. To better understand local pathogen prevalence and microbial community structure, an integrative study of ticks collected from ten recreational trails in Huntingdon County, Pennsylvania during the summer of 2023 was conducted. A total of 96 ticks were sampled, with 33 PCR-positive specimens selected for shotgun metagenomic sequencing. Pathogen screening via qPCR detected Borreliella burgdorferi, Borrelia miyamotoi, Babesia spp., and Anaplasma phagocytophilum. Shotgun metagenomics revealed a broader diversity of tick-borne pathogens, including Rickettsia and Ehrlichia spp., and demonstrated increased sensitivity by detecting low-abundance pathogens in samples that were PCR-negative. Co-infections were common, and multivariate statistical analysis identified significant associations between environmental variables (e.g., humidity, time of day, land cover) and microbial diversity and predicted gene function. Notably, diversity was higher in ticks collected during early afternoon and from northern sites. Co-occurrence network analysis showed Rickettsia as a central taxon with multiple significant positive associations with other microbes while other pathogens were largely absent or peripheral. These findings underscore the enhanced resolution of metagenomic approaches for pathogen detection and the value of combining molecular surveillance with ecological metadata. Our study provides critical insights into local tick microbiomes and pathogen prevalence, which may inform public health interventions and vector management strategies in central Pennsylvania.},
}

@article {pmid41552224,
year = {2025},
author = {Fu, X and Wang, X and Norbäck, D and Zhang, X and Sun, Y},
title = {A Comparative Analysis of Bacterial Communities in Settled Air Dust and Vacuumed Surface Dust From University Dormitories and Associations With Respiratory Health.},
journal = {Cureus},
volume = {17},
number = {12},
pages = {e99514},
pmid = {41552224},
issn = {2168-8184},
abstract = {BACKGROUND: The indoor microbiome significantly impacts human health. Different sampling methods are used to characterize this environment, but it is unclear how these methods affect the resulting microbial profiles and health-related interpretations. This study aimed to compare the bacterial communities captured by two common methods, i.e., passive collection of settled air dust and active vacuuming of surface dust, and to evaluate how sampling choice influences epidemiological associations with respiratory health.

METHODS:  We collected paired settled air dust (n = 86) and vacuumed surface dust (n = 83) samples from 87 university dormitory rooms. The bacterial composition was characterized by sequencing the V3-V4 region of the 16S rRNA gene. We analyzed differences in bacterial diversity, taxonomic composition, predicted functional profiles, and associations with self-reported student health data (rhinitis, asthma, and respiratory infections).

RESULTS:  The two sampling methods captured drastically different bacterial communities (PERMANOVA R² = 0.65, p < 0.001). Vacuumed dust samples were dominated by the genus Pseudomonas (75.1% mean relative abundance), whereas air dust samples were more diverse and primarily composed of Ralstonia (15.6%), Pelomonas (11.3%), and Anoxybacillus (9.3%). Air dust samples exhibited significantly higher alpha diversity (observed taxa: 906.2 ± 179.6) compared to vacuumed dust (345.1 ± 82.3, p < 0.001). These compositional differences led to distinct predicted functional pathways and divergent associations with health outcomes. For asthma, airborne Collinsella was associated with strongly increased odds (OR 2.17, p = 0.003), while Paracoccus was associated with decreased odds (OR 0.062, p = 0.006). By contrast, associations in vacuumed dust were limited to taxa with small effect sizes, such as Peptoclostridium (OR 1.07, p = 0.004). Furthermore, while airborne genera like Slackia were associated with respiratory infections (OR 5.94, p = 0.005), no significant bacterial associations for respiratory infections were found in vacuumed dust.

CONCLUSION:  The choice between sampling settled air dust versus vacuumed surface dust provides profoundly different views of the indoor bacteriome, which can lead to contradictory conclusions in epidemiological studies of asthma and respiratory illness. Our findings underscore that the selection of an environmental sampling strategy is a critical methodological decision that can dictate the outcome and potential health implications of indoor microbiome research. Researchers must align their sampling method with a clear exposure hypothesis to ensure valid health risk assessments. Future indoor air quality standards and epidemiological studies should consider implementing multi-method sampling to capture a comprehensive profile of microbial exposure.},
}

@article {pmid41551989,
year = {2026},
author = {Wu, E and Li, X and Ni, Z and Zhao, F and Jia, C},
title = {Oral microbiome-SASP-aging axis: mechanisms and targeted intervention strategies for age-related diseases.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2616138},
pmid = {41551989},
issn = {2000-2297},
abstract = {BACKGROUND: Global demographic aging is intensifying the burden of age-related diseases. Cellular senescence and the accompanying senescence-associated secretory phenotype (SASP) act as key drivers of disease progression by mediating chronic inflammation. As the second largest microbial community in the human body, the oral microbiome occupies a central position in systemic aging pathologies, and its dysbiosis and interaction with SASP are critical in this process. An imbalanced oral microbiota contributes to systemic chronic conditions via metabolic activities, virulence factor release, and immune system activation, while SASP serves as a central molecular mediator linking microbial dysbiosis to chronic inflammation, with well-recognized involvement in inflammatory bowel disease, bone disorders, and neurodegenerative conditions.

OBJECTIVE: This review aims to examine the mechanism by which oral pathogens directly modulate SASP secretion via microbial metabolites and virulence factors to drive the pathogenesis of age-related diseases, propose a unifying framework of the 'oral microbiome-SASP-aging' axis, summarize therapeutic interventions targeting this axis, and suggest future development directions for precise modulation of the 'microbiome-SASP-aging' cascade.

DESIGN: A narrative review was conducted to synthesize and analyze existing literature on the interplay between the oral microbiome, SASP, and age-related diseases. The review focused on mechanisms of oral pathogen-mediated SASP modulation, therapeutic strategies targeting the 'oral microbiome-SASP-aging' axis, and potential advancements in precise therapeutic delivery and combinatorial therapies.

RESULTS: The 'oral microbiome-SASP-aging' axis serves as a unifying framework for these pathologies. SASP inhibitors, probiotics, and traditional Chinese medicine (TCM) targeting this axis show promise for age-related disease management. Additionally, spatiotemporally precise delivery systems and probiotic-TCM combinatorial therapies are proposed for precise modulation of the 'microbiome-SASP-aging' cascade.

CONCLUSIONS: The 'oral microbiome-SASP-aging' axis is a pivotal pathway driving age-related diseases. Therapeutic strategies targeting this axis hold significant promise for clinical management of these diseases. Future advancements in spatiotemporally precise delivery systems and combinatorial therapies are anticipated to enable precise modulation of the 'microbiome-SASP-aging' cascade, offering novel avenues for the prevention and treatment of age-related diseases.},
}

@article {pmid41551917,
year = {2026},
author = {Ling, C and Chen, X and Yang, J and Zhan, X and White, JC and Kah, M and Shen, Y and Xing, B},
title = {Multiscale Plant Defense Strategies against Ciprofloxacin Stress: From Chloroplast-Centered Adaptation to Microbiome Coordination.},
journal = {Research (Washington, D.C.)},
volume = {9},
number = {},
pages = {1082},
pmid = {41551917},
issn = {2639-5274},
abstract = {Biological stress responses operate across multiple scales, yet the coordination mechanisms remain poorly characterized. Here, we present comprehensive systems-level characterization of coordinated plant and endophytic microbiome responses during xenobiotic stress, integrating ultrastructural analysis, proteomics, and microbiome profiling in rice seedlings exposed to ciprofloxacin. We discovered a sophisticated multi-level defense system with chloroplasts as a key hub within a highly integrated cross-organellar network, comprising 36% of all differentially expressed proteins. The system operates through 3 integrated mechanisms: (a) differential cellular accumulation patterns showing 14-fold tissue-specific differences, (b) reactive-oxygen-species-associated metabolic processes with reduced toxicity of transformation products, and (c) restructuring of endophytic bacterial communities toward stress-resistant genera. This work indicates that biological systems deploy hierarchical, integrated responses spanning from organellar to ecosystem levels. The chloroplast-centered response represents a comprehensive characterization of multicompartmental responses with implications across multiple biological fields. Our findings illustrate how multidisciplinary systems approaches can uncover emergent properties of multiscale biological responses invisible to single-scale analyses, providing a framework for investigating multiscale responses across diverse biological systems.},
}

@article {pmid41551788,
year = {2026},
author = {Song, Q and Li, J and Liu, Y and Li, W and Li, M and Zhang, B and Guo, B},
title = {Metagenomics and volatile metabolomics reveal microbial succession and its correlations with fruity flavor volatile compounds during Mianhua industrial processing.},
journal = {Food chemistry: X},
volume = {33},
number = {},
pages = {103446},
pmid = {41551788},
issn = {2590-1575},
abstract = {Mianhua, a traditional fermentation-type staple food popular in northern China, undergoes dynamic microbial and volatile compound changes during industrial processing. 848 volatile compounds were identified using volatile metabolomics dominated by esters (18.51 %), notably hexanoic acid ethyl ester and octanoic acid ethyl ester, which confer fruity flavors. Metagenomics analysis revealed Proteus (25.93 %), Fructilactobacillus (16.63 %), Lactobacillus (10.16 %) and Companilactobacillus (7.14 %) as dominant genera. Mixing with traditional starters was critical for flavor development, driven by microbial succession and synergistic interactions between Lactobacillaceae (e.g., Fructilactobacillus sanfranciscensis and Lactobacillus helveticus) and Kazachstania during fermentation. Notably, F. sanfranciscensis and L. helveticus were significantly correlated with the formation of key esters with fruity characteristics, elucidating their roles in substrate conversion via carbohydrate metabolism and the esterification pathways. This study clarifies the microbial contributions to fruity flavor and provides insights into volatile-microbiota correlations, laying a foundation for future flavor-oriented research and industrial applications of microbiota regulation in Mianhua production.},
}

@article {pmid41551650,
year = {2025},
author = {Wu, Y and Li, W and Shi, J and Zhang, Z and Jing, C and Sheng, J and Li, Z and Shi, X and Liu, D and He, L and Sun, H},
title = {Microbiome-volatile metabolome analysis reveals aroma regulation driven by microbial niche competition in Jinggang honey pomelo wine.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1725554},
pmid = {41551650},
issn = {1664-302X},
abstract = {INTRODUCTION: Microbial succession in fruit wine has been reported, but the ecological mechanisms linking niche competition to aroma formation remain poorly understood. To test the hypothesis that niche competition between microbial communities significantly influences aroma formation in pomelo wine, the flesh of Jinggang honey pomelo was subjected to semi-inoculation fermentation to produce Jinggang honey pomelo wine.

METHODS: High-throughput amplicon sequencing technology was used to investigate the evolving microbial community during the fermentation process of pomelo wine. The changes in volatile compounds were measured using headspace solid phase microextraction (HS-SPME) coupled with gas chromatography-mass spectrometry (GC-MS).

RESULTS: The dominant taxa in the wine were Weissella, Pediococcus, Lactiplantibacillus, Saccharomyces, Komagataella, Wickerhamomyces, and Aspergillus. The microbiota shifts were associated with dynamic changes in physicochemical properties, and they altered the pH, alcohol content, total soluble solids, and overall acidity. Principal component analysis (PCA), orthogonal partial least squares-discriminant analysis (OPLS-DA), and relative odor activity value analysis identified 17 key volatiles. A correlation network analysis revealed that Lactiplantibacillus and Aspergillus were strongly associated with various flavor molecules.

DISSCUSSION: The present findings suggested that inter-kingdom niche competition between fungi and bacteria plays a pivotal role in shaping the aroma profile of pomelo wine, offering new insights for targeted aroma regulation.},
}

@article {pmid41551598,
year = {2025},
author = {Verbunt, J and Jocken, J and Canfora, E and Barnett, D and Blaak, EE and Savelkoul, P and Stassen, F},
title = {Assessment of the reproducibility of bacterial membrane vesicle isolation and characterization.},
journal = {Extracellular vesicles and circulating nucleic acids},
volume = {6},
number = {4},
pages = {728-741},
pmid = {41551598},
issn = {2767-6641},
abstract = {Aim: This study aimed to evaluate the reproducibility of the isolation and characterization of feces-derived bacterial membrane vesicles. Methods: Human fecal samples (n = 12) stored at -80 °C were thawed, sampled, and then refrozen. From these samples, bacterial membrane vesicles were isolated through ultrafiltration, ultracentrifugation and size exclusion chromatography. Vesicle-associated DNA was characterized by marker [16 ribosomal DNA (rDNA)] sequencing to determine composition. The same fecal samples were thawed again after > 6 months of storage at -80 °C to repeat this procedure. Compositions and other vesicle characteristics were compared to investigate effects of storage and freeze/thawing on sample stability. In addition, for four of the fecal aliquots, the bacteria were subjected to marker gene sequencing alongside their derived membrane vesicles. Results: No significant differences were observed in the pre- and post freeze/thawing composition of feces-derived bacterial membrane vesicles [permutational multivariate analysis of variance (PERMANOVA) P = 0.356] or bacteria (PERMANOVA P = 0.721) as determined by 16S rDNA sequencing. Additionally, no significant differences were observed in vesicle size, concentration, and associated protein or DNA content. These results indicate that, long-term storage of feces at -80 °C and an additional freeze/thawing cycle does not induce compositional or qualitative changes to vesicle repertoires. Conclusion: These reproducibility findings hold great relevance for research on (gut)bacteria derived membrane vesicles. Our results indicate that fecal samples can be stably preserved at -80 °C for bacterial and vesicle isolations as their characteristics remain stable over time.},
}

@article {pmid41551583,
year = {2026},
author = {Chen, T and Huang, R and Huang, Y and Wang, J and Wang, Z and Zhang, X},
title = {Shared signatures of alcohol-associated dysbiosis in humans and non-human primates.},
journal = {Current research in microbial sciences},
volume = {10},
number = {},
pages = {100534},
pmid = {41551583},
issn = {2666-5174},
abstract = {Alcohol use disorder (AUD) is a chronic brain disease with limited therapeutic options. Increasing evidence suggests that the gut microbiome contributes to AUD via the microbiome-gut-brain axis. Here, we conducted a cross-species investigation of gut microbiota alterations in patients with clinically diagnosed AUD and in non-human primates (NHPs) subjected to long-term alcohol (ethanol) self-administration, using metagenomic sequencing. Both cohorts showed reduced microbial diversity and conserved dysbiosis, with consistent depletion of Verrucomicrobia, Actinobacteria, Faecalibacterium, Akkermansia, Intestinibacter, Phascolarctobacterium, and Ruminococcus, alongside increased Blautia and Coprococcus. These microbial shifts correlated with liver function indices, notably positive associations between Ruminococcus and bilirubin levels in both species, suggesting a potential role in liver injury. Functional analyses revealed conserved microbial adaptations, including upregulated DNA repair pathways, fermentative energy metabolism, and downregulated glutamate/glutamine biosynthesis. Together, these results identify evolutionarily conserved microbial and metabolic alterations linking alcohol consumption, gut dysbiosis, and hepatic dysfunction. Our cross-species evidence highlights the gut microbiome as a potential biomarker and therapeutic target for AUD.},
}

@article {pmid41551422,
year = {2026},
author = {Cai, T and Yao, J and Jiang, H and Zou, J and Xia, T and Mou, X and Zhang, S and Tan, X and Tang, J and Xiang, W},
title = {Tetracycline residue alters the nutritional quality and bioactive composition of soybean sprouts: Evidence from transcriptomic and rhizosphere microbiota analyses.},
journal = {Food chemistry. Molecular sciences},
volume = {12},
number = {},
pages = {100345},
pmid = {41551422},
issn = {2666-5662},
abstract = {Antibiotic residues in edible crops have become an increasing food safety concern, yet their impacts on crop nutritional quality and bioactive composition remain poorly understood. Here, we investigated the effects of tetracycline, a widely used antibiotic in soil-vegetable systems, on the growth and nutritional quality and bioactive composition of soybean sprouts. Results showed tetracycline exposure significantly inhibited sprout growth and nutrient accumulation in a dose-dependent manner, with high concentrations reducing vitamin C, total flavonoids, and coumestrol contents by approximately 50 %, 30 %, and 43 %, respectively. Transcriptomic analysis revealed that these related declines were associated with disruptions in carbon, amino acid, and lipid metabolism, as well as in flavonoid and coumestrol biosynthesis pathways. In parallel, rhizosphere microbiota analysis showed that tetracycline reshaped microbial community structure by reducing nitrogen-cycling-related taxa (Dokdonella, Acidibacter) and enriching resistant genera (Acinetobacter), which were significantly correlated with changes in sprout nutritional quality and bioactive composition. Together, these results demonstrate that tetracycline residues drive substantial losses of nutritional and bioactive composition in edible crops through coordinated metabolic and microbiome-mediated mechanisms, revealing an underappreciated pathway by which antibiotic contamination threatens crop nutritional value and food quality.},
}

@article {pmid41551418,
year = {2025},
author = {Wark, G and Kaakoush, NO and Samocha-Bonet, D and Ghaly, S and Danta, M},
title = {Oral Microbial Diversity is Associated with Biologic Treatment and Metabolic Health Status but not with Disease Activity in Patients with Inflammatory Bowel Disease.},
journal = {Crohn's & colitis 360},
volume = {7},
number = {4},
pages = {otaf047},
pmid = {41551418},
issn = {2631-827X},
abstract = {BACKGROUND: Higher diversity of the oral microbiome has been associated with poorer oral health outcomes in the general population. We aimed to characterize the oral microbiota in patients with inflammatory bowel disease (IBD) and compare this with that of healthy controls (HC). We also sought to examine associations between IBD management and disease control, diet and metabolic disease with oral microbial diversity.

METHODS: This prospective case-control study compared participants with IBD in clinical remission with HC. Baseline anthropometry and fasting blood metabolic markers were measured, dietary intake recorded, and oral samples were collected for 16S rRNA gene amplicon sequencing.

RESULTS: There were 57 patients with IBD (Ulcerative colitis (UC) = 26, Crohns Disease (CD) = 31) and 24 HC enrolled. There were no significant differences in oral microbial diversity between the IBD and HC cohorts. Among participants with IBD, oral microbial diversity did not associate with IBD activity nor risk of subsequent disease flare (adj-P = .28), however the use of biologic medications was associated with a lower oral microbial alpha diversity (species richness P = .01). Higher plasma insulin concentrations were associated with a higher oral alpha diversity (species richness adj-P < .01) and with beta diversity (Pseudo-F: 2.05, P = .02).

CONCLUSIONS: Oral microbial diversity is not associated with IBD disease activity or course but is positively influenced by biologic treatment. Higher fasting insulin, however, is associated with more diverse "unhealthy" oral microbiota. Within the limitations of this small study, oral microbiota may be a better marker of metabolic health than of IBD activity.},
}

@article {pmid41551289,
year = {2025},
author = {Zhang, J and Thomas Backet, RV and Sekela, JJ and Zeller, MJ and Sellers, RS and Redinbo, MR and Gulati, AS and Bhatt, AP},
title = {Commercially Purchased and In-House Bred C57BL/6 Mice with Different Gut Microbiota Exhibit Distinct Indomethacin-Induced Toxicities.},
journal = {Gut microbes reports},
volume = {2},
number = {1},
pages = {},
pmid = {41551289},
issn = {2993-3935},
support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R35 GM155168/GM/NIGMS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK122042/DK/NIDDK NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R35 GM152079/GM/NIGMS NIH HHS/United States ; },
abstract = {Non-steroidal anti-inflammatory drug (NSAID)-induced toxicities are a significant clinical problem, yet the factors influencing these outcomes remain incompletely understood. Here, we investigated the impact of mouse vendor on indomethacin-induced injury using C57BL/6 mice from different breeding facilities (in-house "Tar Heel" and commercial Charles River). We found that Tar Heel mice exhibited significantly enhanced susceptibility to indomethacin toxicity, characterized by greater body weight loss, increased ileal ulceration, elevated fecal lipocalin-2 levels, and higher goblet cell numbers in ileum compared to Charles River mice. Importantly, whole genome metagenomic analysis revealed distinct baseline gut microbiomes between the two types of mice. Notably, Tar Heel mice showed higher abundances of β-glucuronidase (GUS)-producing bacteria, particularly those expressing Loop-1 GUS enzymes, and elevated levels of mucolytic enzyme-encoding bacteria. These differences suggest that enhanced indomethacin toxicity observed in Tar Heel mice may be related to functional changes in their gut microbiome, which may predispose to an exaggerated response to NSAID exposure. Together, our findings demonstrate that vendor-specific differences significantly influence NSAID-induced intestinal toxicity and highlight the importance of considering mouse sources and gut microbial compositions in experimental design. Moreover, we highlight potential functional roles that gut microbes play in host-indomethacin interactions.},
}

@article {pmid41551178,
year = {2026},
author = {Esposito, A and Valentino, V and Tagliamonte, S and Sequino, G and Vitaglione, P and Ercolini, D and De Filippis, F},
title = {Development of a synbiotic dietary supplement containing potential Next Generation Probiotics for modulation of the gut microbiome and metabolome.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101289},
pmid = {41551178},
issn = {2665-9271},
abstract = {The term Next Generation Probiotics (NGPs) refers to microbial strains positively impacting on human health, but do not belong to common probiotic species (e.g., lactic acid bacteria, LAB). We characterized genomically and phenotypically 14 strains isolated from the gut microbiome of healthy individuals, to evaluate their ability to produce urolithins, equol and short-chain fatty acids (SCFA). The 4 most promising strains (namely Bacteroides uniformis A4, Bacteroides thetaiotaomicron A14, unclassified Bacteroidaceae A26 and unclassified Lachnospiraceae A49) were used for the production of a synbiotic formulation, containing the strains and the precursors of health-promoting molecules. This dietary supplement was administered for 2 weeks to a continuous mucosal-Simulator of the Human Intestinal Microbial Ecosystem (mSHIME) model inoculated with a faecal sample from a low fiber-consuming donor. We performed Shotgun Metagenome Sequencing on a total of 204 samples collected from lumen and mucosa compartments, and determined the concentration of SCFA, equol and urolithin. Our results highlighted that the potential NGP strains contained in the supplement persisted in the gut ecosystem during 2 weeks of washout (Wilcoxon's rank sum test, p-value <0.05). In addition, the treatment led to an enrichment in beneficial taxa and to an increase in the production of SCFAs (p-value <0.05). This study demonstrated that feeding the gut microbiota with NGPs and dietary prebiotics can modulate both the gut microbiome and metabolome, suggesting a potential beneficial impact on human health. However, further in vivo studies are needed to confirm these results.},
}

@article {pmid41551170,
year = {2026},
author = {Chang, CC and Pak, J and Bae, S and Kim, GD and Son, HS},
title = {Impact of low aging temperature on the microbial and metabolic dynamics of rice wine during long-term storage.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101294},
pmid = {41551170},
issn = {2665-9271},
abstract = {This study investigated the effects of aging temperature and microbial inoculation on the physicochemical, microbiological, and metabolic properties of Korean rice wine (makgeolli) during long-term storage. Samples were aged at three different temperatures (4 °C, -1 °C, and -5 °C) for 180 days and were inoculated with Lactiplantibacillus plantarum or Saccharomyces cerevisiae to examine their respective influences on metabolite shifts during cold storage. Microbial communities were analyzed using amplicon (16S rRNA) and shotgun metagenomic sequencing, and metabolite profiles were determined by GC-MS to provide an integrative understanding of microbial and metabolic stability during long-term cold storage. Lower aging temperatures reduced fluctuations in metabolic and microbial activities, particularly among LAB, thereby contributing to a more stable physicochemical profile and extended shelf life. During rice wine aging, LAB exerted a more pronounced effect on metabolite dynamics than yeast, particularly for pyruvate, γ-aminobutyric acid, and lactic acid, underscoring their role in the aging process. Additionally, sub-zero aging temperatures preserved the initial microbial composition, limited enzymatic degradation, and stabilized organic acid profiles, reflecting enhanced chemical stability of the product during aging. While such chemical stability may have implications for sensory outcomes, this remains a hypothesis that requires direct sensory evaluation in future studies. Overall, the findings suggest that controlled storage temperatures and targeted microbial inoculation can improve the chemical and microbiological stability of rice wine during long-term storage.},
}

@article {pmid41551013,
year = {2025},
author = {Wang, C and Chang, K and Chen, M and Zou, X and Ni, Y and Zhang, Q and Zhao, L and Xing, B and Guo, L and Chen, W and Cao, B},
title = {Enrichment of the commensal microbiome in the lower respiratory tract is associated with improved outcomes following lung transplantation.},
journal = {Chinese medical journal pulmonary and critical care medicine},
volume = {3},
number = {4},
pages = {308-318},
pmid = {41551013},
issn = {2772-5588},
abstract = {BACKGROUND: Alterations in the respiratory microbiome are common following lung transplantation; however, the complex relationship between microbial composition and posttransplant clinical outcomes remains insufficiently characterized. This study aimed to delineate microbial signatures within the lower respiratory tract and to elucidate their associations with posttransplant outcomes in lung transplant recipients (LTRs).

METHODS: Metagenomic sequencing was performed on 138 bronchoalveolar lavage fluid (BALF) samples collected in 2023 from patients who had undergone lung transplantation between 2017 and 2023 at the China-Japan Friendship Hospital. Lung function indices, hematologic parameters, and serum cytokine levels were assessed, and patients were prospectively followed to record adverse clinical events.

RESULTS: The lung microbiome of stable LTRs formed four distinct clusters, exhibiting marked heterogeneity in both α- and β-diversity. The most prevalent cluster, enriched with oral-origin commensals, such as Neisseria subflava (N. subflava), Prevotella melaninogenica, and Streptococcus mitis (S. mitis), demonstrated the highest microbial diversity, and was associated with the lowest C-reactive protein levels, fewest adverse events, and the longest complication-free postoperative duration. In contrast, a virus-enriched cluster characterized by reduced diversity and high abundance of Torque teno virus and Cytomegalovirus human betaherpesvirus 5 was associated with poorer outcomes. BALF samples from infected LTRs exhibited more severe dysbiosis than those from immunocompetent individuals, with reduced diversity and pathogen dominance. Concurrent infections aggravated antibody-mediated rejection-related lung function decline, indicating complex microbiome-immune interactions. Integrative modeling of microbiome, hematologic, and pulmonary function data yielded superior diagnostic performance for infection detection (area under the receiver operating characteristic curve = 0.93).

CONCLUSION: The composition of the lung microbiome may serve as a prognostic biomarker for clinical outcomes after lung transplantation. The presence of diverse, commensal-dominated communities was associated with improved outcomes, whereas viral enrichment correlated with adverse events. These findings underscore the clinical importance of microbiome monitoring in posttransplant management and suggest that targeted modulation of microbial communities could improve long-term graft stability and patient prognosis.},
}

@article {pmid41551009,
year = {2025},
author = {Wang, B and Wang, Y and Ning, K},
title = {Unveiling the role of the respiratory microbiome in long COVID pathogenesis and therapeutics.},
journal = {Chinese medical journal pulmonary and critical care medicine},
volume = {3},
number = {4},
pages = {221-224},
pmid = {41551009},
issn = {2772-5588},
}

@article {pmid41550969,
year = {2026},
author = {Wei, Y and Lu, J and Wu, S and Mo, Z and He, H and Shen, Y and Zou, J and Xing, C and Huang, Y and Jiang, Q},
title = {Comparative Analysis of the Effects of Mogroside V, Epigallocatechin Gallate, and Resveratrol on Growth Performance, Blood Parameters, Rumen Microbiota, and Short-Chain Fatty Acid Metabolism in Heat-Stressed Hu Sheep.},
journal = {Food science & nutrition},
volume = {14},
number = {1},
pages = {e71455},
pmid = {41550969},
issn = {2048-7177},
abstract = {Hu sheep are highly prized for their tender meat, but heat stress (HS) caused by the high temperature and humidity in southern China severely impacts their performance. This study compared the alleviating effects of Mogroside V (Mog V), epigallocatechin gallate (EGCG), and resveratrol (RES) on HS in Hu sheep. Forty male Hu sheep were randomly divided into a control group and three treatment groups (n = 10), each with a pen. The sheep were housed under HS for 60 days. Body weight, feed conversion ratio (FCR), respiratory rate (RR), and rectal temperature (RT) were monitored. Blood physiological parameters, HSPs, antioxidant enzymes, and inflammatory factors were measured. 16S rRNA sequencing and targeted metabolomics were used to analyze the correlation between rumen microbiota and short-chain fatty acid (SCFA) metabolites. Results showed that all three extracts significantly increased final weight, total weight gain, and daily weight gain, while reducing FCR, RR, and RT. They also decreased HSP70/90, MDA, and the inflammatory factors TNF-α, IL-1β, and IL-6, and increased antioxidant enzyme activity. Microbiome and metabolome analysis revealed that RES increased Verrucomicrobia and Fibrobacterium, promoting propionic and butyric acid production; Mog V enriched Firmicutes and Clostridium succinate, promoting energy metabolism; and EGCG regulated acetate metabolism through Lactobacilli, inhibiting pathogenic bacteria. In summary, all three plant extracts alleviated the physiological damage caused by HS and improved production performance, with Mog V showing the most significant effect and possessing high potential for application.},
}

@article {pmid41550964,
year = {2026},
author = {Wang, AYL and Aviña, AE and Liu, YY and Kao, HK},
title = {Microbial allies in skin trauma recovery: from immune modulation to engineered probiotic therapeutics.},
journal = {Burns & trauma},
volume = {14},
number = {},
pages = {tkaf068},
pmid = {41550964},
issn = {2321-3868},
abstract = {Research shows that the microbiome of the skin is present as an active contributor to wound healing processes by moving past its historical infection-related function. The review investigates how commensal and probiotic bacteria affect immunomodulation while accelerating epithelial growth, together with tissue repair processes. Researchers use modern methods to link immunological concepts with material science along with synthetic biological techniques to study engineered probiotics which transform current wound treatments. The research study represents an extensive integration of recent findings concerning probiotic-mediated immunomodulatory operations and engineered approaches that improve probiotic delivery systems and their performance during skin wound healing procedures. Recent genetically engineered Lactobacillus reuteri strains that express chemokines like CXCL12 have been found to promote wound healing to an accelerated rate in animal models, and pre-clinical phases of clinical trials in the setting of diabetic foot ulcers (DFU) has demonstrated safety and therapeutic potential. Simultaneously, another live biotherapeutic product has been validated in terms of regenerative and immunomodulatory properties in animal models and in a clinical trial, a multi-cytokine-integrated strain of Lactococcus cremoris secreting FGF-2, IL-4, and CSF-1 promoted faster wound healing in diabetic mice and healed 83% of subjects in a Phase I DFU study. The range of probiotic therapies for trauma care expands due to advancements in probiotic delivery using materials and membrane vesicles derived from probiotics. This review builds a detailed framework that connects core immune functions with modern engineering methods for developing smart wound healing systems that combine engineered probiotics with bioresponsive materials and real-time monitoring systems. Engineered probiotics promise to become an alternative strategy for treating chronic wounds and infection-related complications that currently create significant medical problems.},
}

@article {pmid41550925,
year = {2025},
author = {Neff, CP and Siebert, J and Karr, M and Lippincott, R and Kvaal, R and Noe, AT and Wall, E and Nusbacher, N and Fiorillo, S and Fennimore, BP and Campbell, TB and Lozupone, C and Palmer, BE},
title = {Gut microbiome composition influences immunologic alterations in the blood and gut of HIV-positive and HIV-negative men who have sex with men.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1707736},
pmid = {41550925},
issn = {1664-3224},
mesh = {Humans ; Male ; *Gastrointestinal Microbiome/immunology ; *HIV Infections/immunology/microbiology/blood ; *Homosexuality, Male ; Adult ; Middle Aged ; Colon/immunology/microbiology ; Immunity, Innate ; },
abstract = {BACKGROUND: HIV infection and factors associated with sexual activity among men who have sex with men (MSM) can dysregulate relationships between the gut microbiome and immune system.

METHODS: To explore these relationships in depth, blood and colonic biopsy samples from HIV+ and HIV- MSM and non-MSM were analyzed using Cytometry by Time of Flight (CyTOF). Immune profiles were then integrated with gut microbiome composition and MSM-related behaviors.

RESULTS: HIV infection status influenced immune cell composition in colonic biopsies, marked by a loss of CD4⁺ CD103⁺ and CD8⁺CD103⁺ tissue-resident T cells and group 3 innate lymphoid cells (ILC3s). In the blood, HIV status was linked to reductions in circulating group 2 innate lymphoid cells (ILC2s), and naïve CD8⁺ T cells, while mucosal-associated invariant T (MAIT) cells were reduced in MSM engaging in high-risk sexual behaviors regardless of HIV status. Network analysis revealed distinct, tissue-specific relationships between immune cell populations and gut microbial taxa, further shaped by both HIV infection and MSM-associated factors.

CONCLUSIONS: These findings provide new insights into host:microbe interactions, with implications for immune regulation, HIV persistence, and transmission among MSM.},
}

Humans
Male
*Gastrointestinal Microbiome/immunology
*HIV Infections/immunology/microbiology/blood
*Homosexuality, Male
Adult
Middle Aged
Colon/immunology/microbiology
Immunity, Innate

@article {pmid41550814,
year = {2026},
author = {Mechshanova, A and Berillo, D and Polyakov, V},
title = {Chemical composition and ecological adaptation of Populus (Salicaceae) species and hybrids depending on soil and environmental conditions.},
journal = {RSC advances},
volume = {16},
number = {4},
pages = {3368-3386},
pmid = {41550814},
issn = {2046-2069},
abstract = {This review synthesizes two decades of research on the interplay between soil properties and genotype in shaping the chemical composition and adaptive traits of hybrid poplars (Populus spp.). The present review is grounded in a comprehensive survey of peer-reviewed literature published from 2000 to 2025. Out of approximately 400 identified documents, 100 were chosen according to their scientific validity, methodological soundness, and pertinence to the study's objectives. The search strategy incorporated databases including PubMed, PubChem, Google Scholar, Scopus, and ResearchGate, using keyword combinations such as Populus species & soil, Populus species & ecological role, and Populus species & pollutant uptake. Unlike previous summaries, it advances the field by highlighting novel insights into genotype soil-metabolite interactions, demonstrating how macro- and micro-nutrient uptake influences the accumulation of flavonoids, salicylates, and other polyphenolic derivatives. It also examines how trees respond to soil pH, organic matter, and contamination, including radionuclides, and how feedback via rhizosphere microbiomes and leaf litter decomposition regulates nutrient cycling and microbial biomass. Beyond integration, the review identifies critical gaps, notably the lack of long-term field validation of soil-microbiome-metabolite linkages and the need for directed breeding of poplar varieties with specific metabolite traits. By outlining how selective breeding, metabolomics, and chemical modification of plant-derived compounds can be harnessed for bio-based materials and pharmaceuticals, and by providing region-specific case studies in urban greening, phytoremediation, bioenergy, and agroforestry, this synthesis establishes a framework for translating biochemical insights into applied strategies for ecosystem restoration and sustainable land use.},
}

@article {pmid41550645,
year = {2025},
author = {Wang, X and Wang, X and Cao, Y and Wang, W and Liu, D and Zhang, J and Chen, Y and Chen, D},
title = {Nanoplatforms in sepsis storm: Multimodal synergy for precision immunomodulation and pathogen neutralizations.},
journal = {Pharmaceutical science advances},
volume = {3},
number = {},
pages = {100087},
pmid = {41550645},
issn = {2773-2169},
abstract = {Sepsis, a severe global health challenge characterized by life-threatening organ dysfunction stemming from a dysregulated immune response to drug-resistant pathogens, imposes a substantial disease burden. The intricate nature of sepsis necessitates meticulous drug administration and underscores the urgency for advanced drug delivery strategies. This paper presents a comprehensive overview of recent advancements in nanotechnology-driven therapeutic interventions for sepsis, emphasizing innovative approaches such as stimulus-responsive and nano-drug delivery systems that have been applied to tackle sepsis and its associated complications. Drawing from various theories and mechanistic insights into sepsis pathogenesis, we explore novel therapeutic avenues and their potential integration with nano-delivery systems, considering factors such as the microenvironment. We demonstrate how these nano-delivery systems can enhance treatment accuracy and diversity. Furthermore, the synergy between nanomedicine and emerging technologies like CRISPR, CAR-T therapy, AI, microfluidics, microbiome research, and immunotherapy holds the promise to revolutionize sepsis diagnosis, treatment, and management strategies. However, overcoming pathogen resistance, precisely modulating excessive immune response/immunosuppression, and achieving efficient targeted delivery of nanocarriers in complex pathological environments remain core challenges. Future research needs to focus on the development of smarter and more responsive nanoplatforms and deeply explore their deep integration with multiple cutting-edge technologies in order to advance the clinical translation of precision sepsis diagnosis and treatment.},
}

@article {pmid41550372,
year = {2025},
author = {Tenea, GN and Jarrin-V, P and Lin, L},
title = {Editorial: Trigger the microbiome changes in foods via metagenomic technologies: from diagnostic to potential changes in product safety or quality risk profiles.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {13},
number = {},
pages = {1766291},
doi = {10.3389/fbioe.2025.1766291},
pmid = {41550372},
issn = {2296-4185},
}

@article {pmid41550264,
year = {2026},
author = {Ali, N},
title = {Interactions between serum uric acid and gut microbiota: implications for metabolic health.},
journal = {Metabolism open},
volume = {29},
number = {},
pages = {100438},
pmid = {41550264},
issn = {2589-9368},
abstract = {Serum uric acid (SUA), the end product of purine metabolism, is a known risk factor for developing gout; however, recent evidence suggests its broader role in metabolic disorders. The gut microbiota, a complex microbial ecosystem, plays a crucial role in influencing purine metabolism and intestinal uric acid (UA) excretion. Recent findings have uncovered a two-way relationship: certain microbes can metabolize purines and UA, while elevated UA can reduce microbial diversity, alter the production of SCFAs, and compromise intestinal barrier function. These interactions are linked to obesity, insulin resistance, T2D, NAFLD, and CVD, connecting purine metabolism with overall metabolic health. This review synthesizes current experimental and clinical evidence on SUA-microbiota interactions, with an emphasis on microbial enzymes, host urate transporters, and microbial metabolites, including bile acids and SCFAs. It also discusses therapeutic implications, spanning urate-lowering drugs to microbiota-targeted strategies, including probiotics, prebiotics, and dietary modulation. Despite progress, significant gaps remain: most human studies are cross-sectional, microbial taxa influencing SUA remain inconsistent, and interindividual microbiome variability limits the translation of findings to personalized care. Future multi-omics and longitudinal approaches are necessary to elucidate causal pathways and identify biomarkers, ultimately informing innovative strategies for the prevention and treatment of metabolic diseases beyond gout.},
}

@article {pmid41550022,
year = {2026},
author = {Sun, R and Chen, Y and Tang, X},
title = {Gut Microbiota-Derived Small Molecules in Atherosclerosis: Biosynthesis, Mechanistic Insights, and Translational Potential.},
journal = {Journal of natural products},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jnatprod.5c01353},
pmid = {41550022},
issn = {1520-6025},
abstract = {Atherosclerosis (AS) is the pathological foundation of most cardiovascular diseases and remains a major cause of global mortality. Increasing evidence implicates gut microbiota-derived small molecules (GMDSMs) as critical chemical modulators of lipid metabolism, vascular inflammation, and thrombosis. In this review, we summarize representative GMDSMs that have been mechanistically linked to AS, including amino acid derivatives, fatty acids, trimethylamine N-oxide, bile acids, and bacterial cell membrane compartments. For each class, we highlight representative biosynthetic enzymes, microbial taxa, and host targets that mediate atherogenic or protective effects. Mechanistic studies have established distinct microbial-host cometabolic pathways linking diet, microbiota composition, and cardiovascular outcomes. We further discuss emerging therapeutic strategies that modulate microbial metabolism or harness beneficial metabolites for AS prevention. Elucidating the biosynthetic diversity and functional logic of these molecules will accelerate the development of microbiome-based diagnostics and interventions for cardiovascular disease.},
}

@article {pmid41549758,
year = {2026},
author = {Ai, T and Sun, K and Jin, LN and Zhu, X and Peng, W and Huang, J and Sun, J and Zhu, L},
title = {Biotransformation of Acetaminophen in Rice Phyllosphere: Xenobiotic-Plant-Microbiota Interactions.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c10295},
pmid = {41549758},
issn = {1520-5118},
abstract = {The biotransformation of acetaminophen, a pharmaceutical contaminant widely found in crop produce, in the rice phyllosphere highlights critical xenobiotic-plant-microbiota interactions. This study investigated acetaminophen uptake, translocation, and transformation in hydroponically exposed rice shoots, revealing accumulation at 8.33 ± 0.82 μg/g and conversion into hydroxylated, glycosylated, methylated, thiomethylated, sulfonated, dimerized, and amino acid-conjugated derivatives. Specifically, these transformations may be driven by plant enzymes (cytochrome P450, glycosyltransferases, sulfotransferases, and methyltransferases) and synergistically by enriched microbial genera (Sphingomonas, Pantoea, and Pseudomonas). Furthermore, acetaminophen stress altered the rice phyllosphere metabolome (elevated linoleic acid and jasmonic acid) and reshaped microbial communities, with enhanced degradation pathways and network complexity indicating adaptive stress mitigation. Overall, this integrated transcriptome, metabolome, and microbiome profiling provides mechanistic insights into the cooperative detoxification role of plant enzymes and phyllosphere microbes, offering perspectives on leveraging plant-microbiota interactions to reduce xenobiotic impacts on crops and food safety.},
}

@article {pmid41549477,
year = {2026},
author = {Muradova, M and Proskura, A and Senty-Segault, V and Boichot, V and Ilina, V and Poirier, N and Gourrat, K and Chaloyard, J and Nadtochii, L and Baranenko, D and Heydel, JM and Canon, F and Lirussi, F and Schwartz, M and Neiers, F},
title = {A Human Oral Bacterial β-Glucosidase Involved in Aroma Release from Glycosides.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c13712},
pmid = {41549477},
issn = {1520-5118},
abstract = {Flavor perception is driven by the interplay of gustation, olfaction, and somatosensory inputs. Among the factors influencing flavor perception, the enzymatic activity of oral bacterial glycosidases plays a role in modulating taste and aroma, generating aroma molecules from glycosidic precursors. This study investigates the in vitro capacity of oral bacterial β-glucosidases to hydrolyze glycosidic aroma precursors. Seven candidate enzymes from oral bacteria were recombinantly produced and screened for glycosidase activity. Among them, only the β-glucosidase from Prevotella sp. (PsBG1) showed hydrolytic activity toward chromogenic substrates and the aroma glucosides tested, leading to the release of salicylaldehyde, hexanol, and octanol, as confirmed by GC-MS. Structural analysis of PsBG1 revealed key residues involved in substrate recognition and catalysis. These results identify a specific oral bacterial enzyme capable of releasing aroma-active compounds from glycosides in vitro, suggesting a potential contribution of oral microbiota enzymatic activity to in-mouth aroma release.},
}

@article {pmid41549467,
year = {2026},
author = {C A M Fernandes, G and Rodeo, SA},
title = {Metabolic Optimization Before Orthobiologic Therapies (MOBOT): A Narrative Review.},
journal = {Sports health},
volume = {},
number = {},
pages = {19417381251409133},
doi = {10.1177/19417381251409133},
pmid = {41549467},
issn = {1941-0921},
abstract = {CONTEXT: The efficacy of orthobiologic therapies, such as platelet-rich plasma (PRP) and concentrated bone marrow aspirate (cBMA), is influenced by not only the biologic product but also the patient's systemic biological milieu. Emerging preclinical and clinical evidence suggests that modifiable metabolic factors, including obesity, insulin resistance, chronic low-grade inflammation, inflammaging, sarcopenia, dysbiosis, poor sleep, and lifestyle behaviors such as smoking and alcohol use, can impair tissue regeneration and reduce the effectiveness of orthobiologics.

EVIDENCE ACQUISITION: A structured approach guided article selection. Searches in PubMed, Embase, and Scopus through July 2025 were supplemented by reference checking. Terms included "metabolic optimization," "obesity," "insulin resistance," "inflammation," "sarcopenia," "dysbiosis," "sleep," "orthobiologics," "PRP," and "bone marrow aspirate." Preclinical and clinical studies, mechanistic reviews, and meta-analyses assessing the impact of metabolic factors on musculoskeletal regeneration and orthobiologic outcomes were included. Only English-language articles relevant to mechanisms, clinical implications, or patient optimization were considered.

STUDY DESIGN: Narrative review.

LEVEL OF EVIDENCE: Level 5.

RESULTS: Evidence-based strategies to optimize metabolic health include targeted exercise, nutritional optimization, pharmacologic interventions, sleep regulation, microbiome support, and behavioral counseling for tobacco and alcohol cessation. While clinical evidence remains limited and of low methodological rigor, preclinical and available clinical studies support the plausibility, safety, and potential efficacy of these interventions. Optimizing metabolic factors can enhance tissue responsiveness, reduce interpatient variability, and improve orthobiologic therapy outcomes.

CONCLUSION: Optimizing metabolic health before orthobiologic therapy improves the biological environment and regenerative outcomes. Screening and managing factors such as insulin resistance, chronic inflammation, and poor sleep are essential. Further randomized controlled trials and biomarker-guided studies are needed to validate strategies and personalize interventions.Strength-of-Recommendation Taxonomy (SORT):C: Supported mostly by preclinical and indirect clinical evidence.},
}

@article {pmid41549355,
year = {2026},
author = {Ye, L and Ruan, M and Xiao, N and Rao, C and Ming, J and Dan, H and Zeng, X and Liu, T and Wang, J},
title = {Oral Microbial Dysbiosis and Pathogenic Functional Shifts in Mucosa-Dominant Pemphigus Vulgaris and Low-Risk Mucous Membrane Pemphigoid.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70207},
pmid = {41549355},
issn = {1601-0825},
support = {82470983//National Natural Science Foundations of China/ ; 82270986//National Natural Science Foundations of China/ ; 82201074//National Natural Science Foundations of China/ ; },
abstract = {BACKGROUND: Mucosal-dominant pemphigus vulgaris (MD-PV) and low-risk mucous membrane pemphigoid (LR-MMP) are autoimmune bullous diseases primarily affecting the oral mucosa, yet their oral microbiome profiles remain inadequately characterized.

METHODS: Using 16S rRNA sequencing of saliva from 21 MD-PV patients, 26 LR-MMP patients, and 14 healthy controls (HC), we analyzed microbial diversity, differential taxa (LEfSe), and functional potential (PICRUSt2/BugBase).

RESULTS: Both patient groups showed significant microbial restructuring without major richness changes, featuring increased Firmicutes and decreased Proteobacteria. Disease-specific signatures included Flavobacteriia enrichment in MD-PV and Coriobacteriia/Actinobacteria in LR-MMP. Shared metabolic alterations involved "Biosynthesis of amino acids," "Phosphotransferase system," and "Ribosome" pathways, while distinct activations included "all-trans-farnesol biosynthesis" in MD-PV and "peptidoglycan biosynthesis" in LR-MMP. Phenotype prediction revealed increased Gram-positive bacteria and reduced pathogenic and stress-tolerant taxa. Microbial dysbiosis scores positively correlated with clinical disease severity.

CONCLUSION: Our study identifies distinct oral microbial dysbiosis patterns in MD-PV and LR-MMP, with conserved functional shifts and disease-specific metabolic adaptations. The microbiota-severity correlation highlights its potential role in disease mechanisms, offering new insights for therapeutic exploration.

TRIAL REGISTRATION: Chinese Clinical Trial Registry (ChiCTR): ChiCTR2500105460.},
}

@article {pmid41549231,
year = {2026},
author = {Novak, SD and Aguirre, KA and Neher, WR and Torres, AM},
title = {Bacterial endophytes journey from the seed to the seedling: an analysis of community structural shifts and bacterial localization during colonization.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08113-9},
pmid = {41549231},
issn = {1471-2229},
}

@article {pmid41549174,
year = {2026},
author = {Lynch, CMK and Knox, EG and Soong, D and Bastiaanssen, TFS and Trontti, K and Tofani, GSS and Ivaschuk, S and Collins, MK and Arafa, D and Nagpal, J and Hovatta, I and Lyons, DA and Clarke, G and Cryan, JF},
title = {The Microbiota Shapes Central Nervous System Myelination in Early Life.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e15671},
doi = {10.1002/advs.202515671},
pmid = {41549174},
issn = {2198-3844},
support = {SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; CRSII5_186346/NMS2068//Saks Kavanaugh Foundation and the Swiss National Science Foundation/ ; 22/PATH-S/10876//Science Foundation Ireland-Irish Research Council Pathway Programme/ ; GOIPD/2019/714//Irish Research Council/ ; 214244/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 108906/Z/15/Z/WT_/Wellcome Trust/United Kingdom ; 133//MS Society Research Centre Award/ ; },
abstract = {Maturation of the gut microbiota coincides with neurodevelopmental processes such as myelination, essential for efficient neural signal transmission. While a role for the microbiome in regulating adult prefrontal cortex (PFC) myelination is known, its effects on early-life myelin formation, growth, and integrity remain unclear. Using a cross-species approach in germ-free (GF) mice and zebrafish, we examined how the microbiota influences early myelination and neural development. Multi-system, multi-level analyses showed that the microbiota impacts glial maturation and myelination across species. In GF mice, we observed sex- and age-dependent alterations in pathways linked to neuronal activity and myelination, with myelin-related transcriptomic changes correlating with functional shifts in neurotransmission- and metabolism-related metabolites over time. Myelin growth and integrity were also affected in a sex- and time-dependent manner. As microglia regulate neuronal activity and engulf myelin, we examined microbiota-microglia interactions and found altered expression of genes involved in microglia maturation and synaptic pruning in both species. In zebrafish larvae, the microbiota influenced the spatial distribution of microglia and oligodendrocytes within the brain and spinal cord. These findings reveal conserved microbiota-mediated modulation of neuronal activity, myelination, and glial maturation in early life, providing a foundation for future studies into these mechanisms.},
}

@article {pmid41549150,
year = {2026},
author = {Negi, R and Sharma, B and Jyothi, RS and Gupta, A and Parastesh, F and Kaur, T and Jhamta, S and Thakur, N and Singh, S and Yadav, N and Yadav, AN},
title = {Phyllosphere microbiome: Exploring the unexplored frontiers for precision agricultural and environmental sustainability.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {50},
pmid = {41549150},
issn = {1573-0972},
mesh = {*Microbiota ; *Agriculture/methods ; Bacteria/classification/metabolism/genetics/isolation & purification ; Fungi/metabolism/classification ; *Plant Leaves/microbiology ; *Plants/microbiology ; },
abstract = {The phyllosphere, encompassing the aerial surfaces of plants, represents one of the largest microbial habitats on Earth and plays a pivotal yet underutilized role in sustainable agriculture and environmental health. Colonized by diverse bacterial, fungal, and yeast communities, the phyllosphere microbiome significantly influences plant growth, disease resistance, nutrient dynamics, and abiotic stress tolerance. These microorganisms engage in complex interactions with host plants, often functioning as biofertilizers, biopesticides, and stress protectants by producing phytohormones, antimicrobial metabolites, and stress-responsive compounds. Importantly, phyllospheric microbes also contribute to atmospheric and ecological balance by participating in carbon and nitrogen cycling, degrading volatile organic compounds (VOCs), and mitigating air pollution. However, despite their immense potential, the practical application of phyllospheric microbes remains limited by challenges such as environmental instability, poor field persistence, and incomplete functional characterization. The highly variable microclimate of the leaf surface poses survival barriers to both native and introduced microbial inoculants. Moreover, the specificity of plant-microbe associations and the complexity of microbial interactions necessitate precision-based approaches for successful deployment. Recent advances in omics technologies, microbial consortia engineering, and nano-enabled delivery systems provide new opportunities to overcome these limitations. A deeper understanding of phyllosphere microbial ecology, combined with innovations in synthetic biology and ecological modeling, can facilitate the development of robust microbial tools tailored to specific crops and climates. Harnessing the potential of phyllospheric microorganisms is not merely an academic pursuit, it is a strategic imperative for transitioning toward climate-resilient, low-input, and ecologically sound agricultural systems.},
}

*Microbiota
*Agriculture/methods
Bacteria/classification/metabolism/genetics/isolation & purification
Fungi/metabolism/classification
*Plant Leaves/microbiology
*Plants/microbiology

@article {pmid41548675,
year = {2026},
author = {Li, D and Wang, Y and Qiang, H and Liu, Z and He, Z and Liu, W and Yue, X and Zhou, A},
title = {Tailoring microbial communities for medium chain fatty acid production from waste activated sludge: comparative performance of endogenous vs. exogenous consortia.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134038},
doi = {10.1016/j.biortech.2026.134038},
pmid = {41548675},
issn = {1873-2976},
abstract = {Optimizing medium chain fatty acid (MCFA) production from waste activated sludge (WAS) requires tailoring microbial communities, yet it remains unclear whether combining substrate sterilization with exogenous caproate-synthesizing bacteria (CSB) can enhance chain elongation. Here, we compared the MCFA production achieved using this strategy with that driven by the endogenous microbiomes in both the solid residue and the supernatant. Among all experimental groups, this strategy achieved the highest MCFA production in the supernatants (3935 ± 21 mg COD/L). This strategy increased CSB abundance in both the solid residue and the supernatant relative to the abundance in the endogenous microbiome systems. Notably, in supernatant systems, this strategy not only enriched acidogens but also led to the highest soluble protein utilization rate, maximal CO2 release/uptake, and an increased gene abundance related to pyruvate generation. Life cycle assessment confirmed economic and environmental benefits. This work provides new insights into optimizing MCFA recovery from WAS.},
}

@article {pmid41548640,
year = {2026},
author = {Chen, Z and Lou, J and Yan, M and Cui, R and Jin, Y and Zhang, M and Zhang, R and Mao, S and Chen, J and Sun, L and Lu, T and Qian, H},
title = {Environmental stress and symbiotic shifts: the impact of perfluorooctanoic acid (PFOA) on soil microbe-plant networks.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {127688},
doi = {10.1016/j.envpol.2026.127688},
pmid = {41548640},
issn = {1873-6424},
abstract = {Perfluorooctanoic acid (PFOA) is a persistent per- and polyfluoroalkyl substance (PFAS) frequently detected at extremely high concentrations in soils near industrial contamination sources, yet plant-microbe responses under such extreme conditions remain poorly understood. Here, Arabidopsis thaliana was exposed to PFOA at concentrations approaching the upper levels reported in contaminated soils (1, 10, and 100 mg/kg) to investigate integrated physiological, transcriptomic, and microbiological responses over a 14-day period. Plant growth was inhibited in a clear concentration-dependent manner, with progressive reductions in fresh biomass, root length, and rosette leaf number, and the strongest suppression observed at 100 mg/kg. PFOA exposure also induced oxidative stress, as indicated by elevated reactive oxygen species (ROS) levels. Transcriptomic analysis revealed distinct dose- and pathway-specific response patterns. Only 37 differentially expressed genes (DEGs) were detected at 1 mg/kg, whereas 2184 and 4999 DEGs were identified at 10 and 100 mg/kg, respectively. 10 mg/kg PFOA exposure predominantly activated antioxidant defense and adaptive stress-response pathways, including glutathione metabolism, phenylpropanoid and flavonoid biosynthesis, MAPK signaling, and plant hormone signal transduction. In contrast, extreme exposure (100 mg/kg) was characterized by widespread repression of primary metabolic pathways, particularly photosynthesis, carbon fixation, oxidative phosphorylation, and glycolysis, indicating metabolic collapse. Rhizosphere microbial communities responded more strongly than bulk soils to PFOA stress, exhibiting reduced α-diversity, enhanced β-diversity separation, enrichment of putatively tolerant taxa (e.g., Pseudomonas, Sphingomonas, Burkholderiaceae, and Ascomycota), and increased network connectivity. Overall, these results demonstrate coordinated plant and rhizosphere microbial responses to severe PFOA contamination, providing ecological insights into PFAS hotspot soils.},
}

@article {pmid41548616,
year = {2026},
author = {Yang, Y and Chang, Y and Cheng, Y and Qian, Z and Zhao, J and Li, C and Zhu, X and Jia, X and Feng, L},
title = {An integrated metabolome-microbiome analysis revealed distinct regulatory effects of Xiaoer Chiqiao Qingre granules in young versus adult rats with acute upper respiratory tract infection.},
journal = {Journal of ethnopharmacology},
volume = {},
number = {},
pages = {121232},
doi = {10.1016/j.jep.2026.121232},
pmid = {41548616},
issn = {1872-7573},
abstract = {Xiaoer Chiqiao Qingre Granules (XECQ), officially recognized in the Chinese Pharmacopoeia (Approval No. Z20123090), represent a widely used traditional Chinese medicine (TCM) formulation for treating acute upper respiratory tract infection (AURTI) across both pediatric and adult patients.

AIM OF THE STUDY: This investigation examined XECQ's divergent regulation of endogenous metabolism and intestinal microbiome in juvenile versus mature rats, serving clinical medication to support pediatric utilization of XECQ.

MATERIALS AND METHODS: AURTI model was constructed, and serum inflammatory cytokine levels, pulmonary histopathology, and immunohistochemical analysis were assessed. Young rats served as pediatric developmental proxies. Integrated serum metabolomics and 16S rDNA sequencing methodologies elucidated XECQ's systemic modulatory actions upon host metabolism and enteric microbial communities.

RESULTS: XECQ manifested anti-AURTI efficacy across both age cohorts. Metabolites quantification identified 37 juvenile-specific and 18 adult-specific serum biomarkers. Additionally, XECQ modulated intestinal microbiome diversity and enhanced community richness across both age groups. Following XECQ treatment, the genera Subdoligranulum, Marvinbryantia, Anaerostipes, Bacillus, and Dubosiella_ag were significantly restored in young rats, while Escherichia-shigella, Parabacteroides, and Subdoligranulum showed notable recovery in adults. Species clustering analysis revealed distinct differences in intestinal microbiome modulation between age groups, with young rats exhibiting markedly different regulatory patterns for genera such as norank_f_Muribaculaceae, norank_f_Eubacterium_coprostanoligenes_group, Clostridium_sensu_stricto_1, and norank_f_Oscillospiraceae. In young rats, XECQ primarily regulated amino acid metabolism, notably pathways involving cysteine and methionine. In adult rats, the therapeutic effects were mainly associated with the modulation of pentose and glucuronate interconversion and purine metabolic pathways. Notably, glycerophospholipid metabolism emerged as a shared pathway across both age groups under normal conditions, during AURTI pathology, and following XECQ treatment.

CONCLUSION: XECQ differentially modulates the serum metabolome and intestinal microbiome between young and adult rats, highlighting the necessity of pediatric-specific studies to support the clinical application of XECQ in children.},
}

@article {pmid41548440,
year = {2026},
author = {Hong, EH and Hyeong, J and Ahn, JH and Han, Y and Kim, S and Kim, SM and Yoo, HH and Jeong, H and Cho, HJ and Park, JH and Chang, SY and Ko, HJ},
title = {Limosilactobacillus reuteri alleviates psoriasis via aryl hydrocarbon receptor-mediated regulation of Interkeukin-17A.},
journal = {International immunopharmacology},
volume = {172},
number = {},
pages = {116194},
doi = {10.1016/j.intimp.2026.116194},
pmid = {41548440},
issn = {1878-1705},
abstract = {BACKGROUND: Psoriasis is a chronic immune-mediated skin disorder characterized by keratinocyte hyperproliferation and interleukin-17A-driven inflammation. Growing evidence highlights the contribution of microbiome-derived factors to cutaneous immune regulation. The study aimed to evaluate the therapeutic efficacy of heat-killed Limosilactobacillus reuteri NCHBL-005 in an imiquimod-induced psoriasis-like mouse model.

RESULTS: Both topical and oral administration of NCHBL-005 significantly alleviated clinical and histological features, including reduced epidermal thickness, improved Psoriasis Area and Severity Index scores, and diminished inflammatory cell infiltration. Mechanistically, NCHBL-005 suppressed interleukin-1 beta and interleukin-17A expression in psoriatic lesions and decreased interleukin-17A-positive RAR-related orphan receptor gamma t-positive T-cells while maintaining regulatory T-cell balance. These effects were retained in Toll-like receptor 2- and nucleotide-binding oligomerization domain-containing protein 2-deficient mice but abolished in aryl hydrocarbon receptor-deficient mice, underscoring the essential role of aryl hydrocarbon receptor signaling. NCHBL-005 directly attenuated inflammatory responses in keratinocytes by suppressing the expressions of interleukin-1 beta, interleukin-17A, and tumor necrosis factor-alpha, and by inhibiting nuclear factor kappa-light-chain-enhancer activation. Liquid chromatography-tandem mass spectrometry profiling identified indole-3-acetaldehyde, indole-3-carbinol, and indole-3-lactic acid as major aryl hydrocarbon receptor ligands derived from NCHBL-005. Among these, indole-3-acetaldehyde most effectively reproduced the therapeutic effects, reducing interleukin-17A-positive cells, epidermal hyperplasia, and nuclear factor kappa-light-chain-enhancer activation.

CONCLUSIONS: NCHBL-005 and its metabolite indole-3-acetaldehyde alleviate psoriatic inflammation through modulation of the aryl hydrocarbon receptor-interleukin-1 beta-interleukin-17A axis, thereby restoring skin immune homeostasis. This study highlights postbiotic intervention in the aryl hydrocarbon receptor-interleukin-1 beta-interleukin-17A axis as a promising therapeutic strategy for psoriasis.},
}

@article {pmid41548201,
year = {2026},
author = {Mirmozaffari, Y and Roca, C and Martin, WJ and Heetderks, KA and Van Dorsten, A and Cook, L and Benaim, EH and Wolfgang, MC and Kimple, AJ},
title = {Species-Level Characterization of the Nasal Microbiome in Various Disease States Utilizing Third-Generation Sequencing.},
journal = {International forum of allergy & rhinology},
volume = {},
number = {},
pages = {},
doi = {10.1002/alr.70103},
pmid = {41548201},
issn = {2042-6984},
}

@article {pmid41547908,
year = {2026},
author = {Kim, YC and Won, SY and Jeong, BH},
title = {Identification of an altered gut microbiome and the protective effect of microbiome changer in prion diseases.},
journal = {Veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13567-025-01699-2},
pmid = {41547908},
issn = {1297-9716},
support = {2022R1C1C2004792//National Research Foundation of Korea/ ; RS-2023-00273199//National Research Foundation of Korea/ ; 2017R1A6A1A03015876//National Research Foundation of Korea/ ; B0080529001944//Gyeongbuk RISE CENTER/ ; 2021R1A6C101C369//Korea Basic Science Institute/ ; },
abstract = {Prion diseases are fatal and contagious brain disorders caused by a pathogenic prion protein (PrP[Sc]) derived from the benign prion protein (PrP[C]). To date, there are no therapeutic substances to completely block prion diseases. Thus, the development of a therapeutic substance is necessary, and the identification of a novel biomarker of prion disease is the first essential step to develop new drugs. In the present study, we carried out a metagenomic analysis to identify microbiome biomarkers for prion disease using next-generation sequencing and bioinformatics tools in intraperitoneally prion-infected mice. In addition, we evaluated the protective effects of epigallocatechin-3-gallate (EGCG), a potent microbiome changer, in prion-infected mice by western blotting and survival analysis. We found a total of 14 differentially abundant taxa between prion-infected and control mice. In addition, we found that prion diseases caused altered microbiome networks and upregulation of DNA repair-related pathways. Furthermore, we observed the protective effect of the microbiome changer EGCG against prion disease in prion-infected mice. Given previous reports of microbiome alterations in prion diseases, we further validated these associations and demonstrated the protective effects of a microbiome-modulating compound.},
}

@article {pmid41547903,
year = {2026},
author = {Hashmi, MA and Verma, S and Math, RGH and Muralidharan, S and Pranesh, G and Sahana, MP and Hariharan, N and N C, M and Kamath, V and Yaligod, V and Hiremath, SA and Jawali, A and Maddipati, T and Chandrasingh, S and Thomas, A and Mallnaik, N and Shanmuganand, VC and George, CE and Thomas, A and Ghosh, TS and Ramanathan, A},
title = {Integrative analysis of plasma small-molecule and gut-microbiome markers of sarcopenia in a pilot study within an Indian cohort.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-35476-8},
pmid = {41547903},
issn = {2045-2322},
}

@article {pmid41547860,
year = {2026},
author = {Castillo-Fernandez, J and Gilroy, R and Jones, RB and Honaker, RW and Whittle, MJ and Watson, P and Amos, GCA},
title = {Waltham catalogue for the canine gut microbiome: a complete taxonomic and functional catalogue of the canine gut microbiome through novel metagenomic based genome discovery.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {25},
pmid = {41547860},
issn = {2049-2618},
mesh = {Animals ; Dogs/microbiology ; *Gastrointestinal Microbiome/genetics ; *Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Feces/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The canine microbiome is a vastly understudied area relative to the importance of dogs in society, particularly given the potential importance of the microbiome in veterinary medicine. This has led to a large knowledge gap in the basic taxonomy and functions of the canine gut microbiome and an overreliance on human databases for canine-specific research. Using a broad sample set, long read sequencing, short read sequencing, and metagenomic assembly approaches, we have produced the most comprehensive microbiome resource in all companion animal research.

RESULTS: Here, we describe the recovery of 240 core species that account for > 80% of the canine gut microbiome when tested on an independent validation dataset. We uncovered > 900 new canine-specific strains, 89 novel species, and 10 novel genera, providing a dramatic increase in previous knowledge of the canine microbiome and allowing for mapping rates of up to 95%, a 70% increase on historic mapping rates of ~ 25% using publicly available resources. Through detailed annotation of function, we demonstrate the potential importance of the novel species and genera to health and nutrition and provide evidence of new canine-adapted strains of existing genera and species previously unknown to inhabit canines that provide important metabolic function to the canine host. We discovered the canine microbiome has an expansive ability to metabolize carbohydrates, providing insight into how canines process diverse carbohydrates given their known limited host genomic potential. We uncovered a range of species with abilities to produce butyrate, propionate, and vitamins, highlighting the importance of the canine microbiome to host nutrition. We describe two novel Peptacetobacter species that could regulate host bile acid metabolism, an important finding in the context of chronic GI disease in pets. We demonstrated all new species and genera had no known virulence, suggesting they are commensal and, finally, provided a baseline for antimicrobial resistance in the microbiota species of healthy pets.

CONCLUSIONS: This work gives entirely new perspectives on the functional capabilities of the canine gut microbiome, suggesting the canine microbiome is distinct, presumably having evolved to its host, diet, and environment over several millennia. Video Abstract.},
}

Animals
Dogs/microbiology
*Gastrointestinal Microbiome/genetics
*Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
Metagenome
Feces/microbiology
Phylogeny
RNA, Ribosomal, 16S/genetics

@article {pmid41547850,
year = {2026},
author = {Naya-Català, F and Domingo-Bretón, R and Matias, RS and Calduch-Giner, JÀ and Belenguer, Á and Gomes, S and Guilhermino, L and Moroni, F and Valente, LMP and Pérez-Sánchez, J},
title = {Dietary rayon microfibers differentially reshape rearing water and host associated microbiomes of farmed European sea bass (Dicentrarchus labrax).},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00851-5},
pmid = {41547850},
issn = {2524-6372},
abstract = {BACKGROUND: Viscose-rayon microfibres (RFs) are cellulosic microfibres widely dispersed throughout aquatic environments. Whether ingested by or suspended in the surrounding environment, these microfibres may impact both wild and farmed animals. A previous study on European sea bass (Dicentrarchus labrax) showed that the increased presence of RFs in aquafeeds (CTRL-no RFs; RF1-0.001 g/kg; RF2-0.01 g/kg; RF3-0.1 g/kg) was linked to an exponential increase of RFs in water, intestine and skeletal muscle. This finding was associated to a fatty liver and tissue-specific transcriptional changes, depicting the up-regulation of hepatic lipogenic enzymes and intestinal/head kidney inflammatory markers. The aim of the present study was to extend this evaluation by investigating changes in associated microbial communities after the ingestion of RFs in the diet, employing a multi-layered approach for the integrative profiling of gut, skin, and environmental water microbiome using the Nanopore platform.

RESULTS: Amplicon-sequencing identified ~2800 taxa across water, skin and gut microbiomes. Gut and skin microbiomes were more similar to each other, but increasing RF exposure shifted the skin community toward the water microbiome. Moreover, RF induced the highest taxonomic variation in water (691 taxa), followed by skin (253) and gut (99), while microbial diversity Shannon and Simpson indexes declined from 4 down to 3.3 under RF2 and RF3 in a dose-dependent manner. Major exponents of this trend were the decrease of Synechococcus and Flavobacteriales in association with the increase of starch- and hydrocarbon-degrading taxa (Ardenticatenaceae and Gracilibacteria). In both gut and skin, bacterial richness decreased in fish fed low to intermediate RF doses, whereas RF3 fish resembled controls. Thus, compositional and discriminant analyses consistently grouped CTRL and RF3 samples, suggesting the existence of a dose threshold occurring in parallel with host counter-regulatory responses. Such feature was reflected by abundant skin-associated bacteria (Exiguobacterium and Planococcus) with at least the genetic potential to be linked to vitamin B6 biosynthesis and host-driven muscle regeneration markers, whereas predominant gut taxa with the same pattern (Microbacterium and Achromobacter) was associated with polysaccharide degradation and correlated with host gene inflammatory mechanisms.

CONCLUSIONS: This study revealed a concomitant dose-dependent and dose-threshold response among the bacterial communities composing the holobiont of European sea bass in response to dietary RFs ingestion, highlighting novel bacterial taxa and pathways through which microplastic exposure may differentially reshape rearing water and host-associated microbial communities.},
}

@article {pmid41547827,
year = {2026},
author = {Cavaliere, S and Fogolari, M and Iuliani, M and Foderaro, S and Cortellini, A and Simonetti, S and Mingo, EC and Calagna, S and Russano, M and Vincenzi, B and Tonini, G and Angeletti, S and Pantano, F},
title = {Salivary microbial signature highlighting actinomyces as a predictor of immune-checkpoint inhibitor monotherapy response in advanced non-small cell lung cancer.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-025-07570-4},
pmid = {41547827},
issn = {1479-5876},
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have improved survival in advanced non-small cell lung cancer (NSCLC), yet reliable biomarkers beyond programmed death-ligand 1 (PD-L1) expression remain limited. Increasing evidence links the gut microbiome to ICI activity, but the predictive value of the salivary microbiome is poorly defined.

METHODS: We prospectively analyzed baseline saliva from 71 stage IV NSCLC patients treated with anti-PD-1/PD-L1 (ICI) monotherapy. After quality control, 70 samples underwent 16 S rRNA gene sequencing of the V1-V3 region. Microbial diversity, differential abundance (LEfSe, Mann-Whitney/Kruskal-Wallis with false discovery rate correction) and survival associations (Kaplan-Meier; Cox proportional-hazards with LASSO-based variable selection and 1000-fold bootstrap validation) were examined. In this cohort, an exploratory genus-level cut-off was derived by receiver operating characteristic (ROC) analysis.

RESULTS: α-diversity and β-diversity did not differ between responders (progression-free survival (PFS) ≥ 12 months; n = 18) and non-responders (n = 52). Differential‑abundance profiling revealed a graded enrichment of the phylum Actinobacteria across all lower ranks, class Actinobacteria, order Actinomycetales, family Actinomycetaceae and genus Actinomyces,in non‑responders (LEfSe LDA > 3.5; p = 0.001 for each level; FDR ≤ 0.049). ROC analysis suggested an Actinomyces relative abundance of 11% (AUC = 0.768; sensitivity 0.94; specificity 0.44) as a data-driven threshold, classifying patients into low (≤ 11%, n = 46) and high (> 11%, n = 24) groups. High abundance was associated with shorter PFS (median 3 vs. 4 months; HR = 2.16, 95% CI 1.21-3.88, p = 0.009) and overall survival (OS) (median 5 vs. 9 months; HR = 2.61, 95% CI 1.48-4.61, p < 0.001) after multivariable adjustment for ECOG status, treatment line, corticosteroid and opioid use, smoking, histology and metastatic sites. Bootstrap validation supported model stability, with median bootstrap HRs of 2.56 (PFS) and 2.63 (OS), with narrow percentile CIs (PFS 1.57-4.49; OS 1.40-6.34) overlapping the original estimates.

CONCLUSIONS: In this exploratory cohort, salivary microbiome signature characterized by high Actinomyces abundance was independently associated with poorer ICI outcomes in NSCLC. Saliva profiling is non-invasive and, if validated in larger and independent cohorts, may complement tumour PD-L1 and clinical factors to refine patient stratification.},
}

@article {pmid41547778,
year = {2026},
author = {Park, SH and Park, SM and Suh, JW and Kim, JY and Sohn, JW and Yoon, YK},
title = {Clinical impact of altered gut microbiota and metabolite profiles on mortality in patients with candidemia: a prospective observational pilot cohort study.},
journal = {Annals of clinical microbiology and antimicrobials},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12941-026-00850-x},
pmid = {41547778},
issn = {1476-0711},
abstract = {BACKGROUND: The gut microbiota plays an important role in defending against infectious diseases. However, data on the clinical implications of the microbiome profiles in patients with candidemia remain limited. In this study, we investigated the association between the intestinal microbiome and mortality in patients with candidemia.

METHODS: This prospective, observational, pilot cohort study enrolled adult patients with culture-confirmed candidemia. Fecal samples were collected within 5 days of diagnosis and analyzed using 16 S ribosomal RNA gene sequencing for microbiota profiling and gas chromatography-mass spectrometry for metabolomic analysis. Multivariate logistic regression was used to identify predictors of in-hospital mortality, defined as death during hospitalization.

RESULTS: Fifty-nine patients with candidemia were analyzed, and the in-hospital mortality rate was 40.7%. The median Shannon diversity index of the gut microbiota was significantly lower in non-survivors than that in survivors (P = 0.009). Linear discriminant analysis revealed 11 bacterial species that differed significantly between the two groups. Among the 111 fecal metabolites, only 3-isopropoxy-hexamethyl-tetrasiloxane differed significantly between the survivors and non-survivors (P = 0.007). Septic shock (adjusted odds ratio: 10.59; 95% confidence interval, 1.70-65.97), underlying malignancy (7.79 [1.41-43.10]), and Shannon diversity index (0.40 [0.19-0.84]) were significant predictors of in-hospital mortality.

CONCLUSIONS: Low gut bacterial diversity is independently associated with mortality in patients with candidemia. These preliminary findings warrant confirmation through larger, well-powered studies.},
}

@article {pmid41547669,
year = {2026},
author = {Isınıbılır, M and Doğan, O and Bilgin, R and Çalıcı, Z},
title = {Microbiome dynamics linked to Aurelia aurita during bloom and post-bloom periods in the Golden Horn Estuary: a snapshot via eDNA metabarcoding.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {41547669},
issn = {1614-7499},
abstract = {Jellyfish blooms are significant events in marine ecosystems, profoundly impacting carbon and nutrient cycles. During these events, decomposing jellyfish release dissolved organic matter (DOM), which fuels bacterial growth and reshapes nutrient cycling. In this study, we employed an environmental DNA (eDNA) metabarcoding approach to capture bacterial communities associated with Aurelia aurita, and in different body parts, as well as its ambient surface water column during bloom (December 2022) and post-bloom (March 2023) periods in the Golden Horn Estuary, İstanbul, Türkiye. The results reveal distinct temporal and regional variations in bacterial diversity, highlighting the pivotal role of jellyfish blooms in reshaping bacterial communities.},
}

@article {pmid41547536,
year = {2026},
author = {Banik, M and Bashyal, S and Ahmed, KA and Banik, K and Dua, K and Choi, JP and Paudel, KR and Majumder, R},
title = {The Gut Microbiome of Australian Cats and Dogs: Dietary Influences, Health Impacts, and Emerging Research.},
journal = {Veterinary journal (London, England : 1997)},
volume = {},
number = {},
pages = {106566},
doi = {10.1016/j.tvjl.2026.106566},
pmid = {41547536},
issn = {1532-2971},
abstract = {The gut microbiome plays a pivotal role in the health, metabolism, and behaviour of companion animals, yet comprehensive syntheses of its composition and functional relevance in cats and dogs in Australia are overlooked and remain limited globally. This review synthesises current knowledge on the gut microbial communities inhabiting the gastrointestinal tracts of dog and cats, with a particular focus on taxonomic diversity, dietary modulation, and associations with disease states within Australian context. Core phyla including Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria dominate the canine and feline gut, but marked interspecies and individual variability is shaped by factors such as feeding practices, living environment, obesity, and chronic disease. Recent studies have elucidated functional signatures linked to conditions ranging from the influence of microplastics to pet gut health, as well as gut-microbiome transmission between pets and their owners, highlighting this area as a promising field of investigation. In parallel, this review contextualizes the broader landscape of pet ownership in Australia, where nearly 70% of households own pets, and significant resources are devoted to nutrition, veterinary care, and preventive health. Emerging evidence also suggests bidirectional influences between pets and their human companions' microbiota, highlighting opportunities for integrated approaches. We identify critical knowledge gaps, including the need for region-specific microbial baselines, standardized methodologies, and controlled intervention trials targeting microbiome modulation and transmission. By consolidating advances across microbial ecology, veterinary medicine, and translational research, this review provides a foundation for future studies that aim to harness the diagnostic and therapeutic potential of the pet microbiome, thereby improving health outcomes for animals and humans alike.},
}

@article {pmid41547455,
year = {2026},
author = {Qu, Q and Gao, H and Gao, X and Li, P and Mou, Y and Kong, X and Tan, X},
title = {Dietary inulin mediates the molecular mechanism of intestinal metabolites to alleviate high salt diet-induced chronic kidney disease in mice.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110269},
doi = {10.1016/j.jnutbio.2026.110269},
pmid = {41547455},
issn = {1873-4847},
abstract = {It is recognized that excessive dietary salt intake is a critical factor contributing to chronic kidney disease (CKD). A high-salt diet (HSD) disrupts the balance of the gut microbiota, but the molecular mechanisms linking gut dysbiosis to target organ damage remain unclear. This study identified dietary prebiotic inulin (INU) as a potent regulator of the gut-short-chain fatty acid-kidney axis, capable of counteracting HSD-induced CKD. Sequencing analysis showed that INU selectively enriched Bifidobacterium and Faecalibaculum while downregulating Desulfovibrio. This microbiome shift restored intestinal tight junction proteins and reduced serum lipopolysaccharide (LPS) levels, thereby inhibiting TLR4/NF-κB-mediated renal inflammation. Notably, the effects of direct SCFA supplementation align with the renal protective effects of INU, confirming the critical role of the gut-kidney axis. Our study reveals INU as a dietary strategy that combats HSD-induced CKD via SCFAs produced by the microbiota, offering new insights into the gut-SCFAs-kidney axis as a therapeutic target.},
}

@article {pmid41547444,
year = {2026},
author = {Shan, Y and Huang, X and Han, X and Yang, Y and Zheng, M},
title = {3'-Sialyllactose ameliorates antibiotic-associated diarrhea by shaping unique gut microbiota and metabolite composition.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27362},
pmid = {41547444},
issn = {1525-3198},
abstract = {3'-Sialyllactose (3'-SL) is a naturally occurring prebiotic in milk, known to regulate intestinal microbiota and prevent diseases. However, the mechanisms through which 3'-SL alleviates antibiotic-associated diarrhea remain poorly understood. In this study, an antibiotic-associated diarrhea model was established through the co-administration of ampicillin and neomycin. The effects of 3'-SL supplementation on diarrhea phenotype, inflammation, intestinal permeability, and barrier function were examined in antibiotic-associated diarrhea-model mice. Moreover, gut microbiota composition, metabolite profiles, and their alterations were analyzed using genomic and metabolomic approaches. The results demonstrate that 3'-SL increased body weight and aquaporin (AQP) 3 and AQP4 levels but reduced diarrhea rate, cecal mass, and fecal water content in the model mice, indicating its therapeutic effect on diarrhea. Furthermore, 3'-SL reduced serum levels of IL-6, tumor necrosis factor (TNF)-α, and IL-1β, while increasing IL-10 levels in the mice. Moreover, 3'-SL reduced intestinal permeability by enhancing both the mechanical barrier (ZO-1 and occludin mRNA expression) and the chemical barrier (MUC2 mRNA and protein expression) in the mice. 16S rRNA analysis revealed that mice in the 3'-SL group exhibited greater abundances of Akkermansia, Bacteroides, and Dubosiella, along with a reduced relative abundance of the diarrhea-associated bacterium Alloprevotella. Furthermore, metabolomics analysis indicated that 3'-SL promoted enrichment of purine metabolism, pyrimidine metabolism, nucleotide metabolism, and the pentose phosphate pathway, which may be associated with diarrhea development, inflammation amelioration, and barrier regulation. In conclusion, our findings suggest that 3'-SL ameliorates antibiotic-associated diarrhea by modulating gut microbiota and metabolite profiles.},
}

@article {pmid41547433,
year = {2026},
author = {Engin, ED and Engin, AB and Engin, A},
title = {Bidirectional effect of intestinal microbiome and host in circadian rhythm disruption: Environmental factors and breast cancer development.},
journal = {Environmental toxicology and pharmacology},
volume = {},
number = {},
pages = {104939},
doi = {10.1016/j.etap.2026.104939},
pmid = {41547433},
issn = {1872-7077},
abstract = {Suppression of nocturnal circadian melatonin signaling amplitude, disruption of the host's circadian clock through diet or phase shifts, and imbalances in the gut microbiome are significant factors that increase the incidence of breast cancer. After host-derived mature microRNAs (miRNAs) are secreted from intestinal epithelial cells, they pass to the microbiota as faecal or exosomal miRNAs and modify the epigenetic profile of the microbiome. Subsequently, the profile of host miRNAs is altered by metabolites, which are derived from intestinal bacteria. Bidirectional epigenetic modulations of host and microbiota trigger the activation of oncogenic transcriptional pathways in extraintestinal tissues. However, the effect of the mutual epigenetic interactions between the gut microbiota and the host on the development of extraintestinal cancer is not clear. The aim of this review is to discuss the factors influencing bidirectional epigenetic regulation mechanisms between microbial dysbiosis and the host in breast cancer.},
}