@article {pmid41879811,
year = {2026},
author = {Kaiser, ME and Parikh, MA and Turitto, G and Grutman, G and Frishman, WH and Peterson, SJ},
title = {Processed Foods and Food Dyes: What Are We Eating and What Is the Cardiovascular Risk?.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000001256},
pmid = {41879811},
issn = {1538-4683},
abstract = {Ultra-processed foods (UPFs) are industrially manufactured products that contain several additives and may contain high levels of added sugar, fat, salt, or little whole food. They also represent an increasing percentage of the world's diet and are increasingly associated with the development of cardiovascular disease (CVD). The findings of several meta-analyses and extensive, population-based longitudinal studies suggest there is a dose-response relationship between UPF consumption and each of the following outcomes: CVD, stroke, and total CVD-related deaths. Some food additives, especially emulsifiers (like carboxymethylcellulose and mono- and diglycerides), preservatives (like carboxymethylcellulose and mono- and diglycerides), and artificial colors (like tartrazine and sunset yellow), have been proven to independently alter the gut microbiome, induce cellular oxidative stress, and enhance chronic low-level low-grade inflammation. A common mechanistic pathway involves activation of the nuclear factor kappa B family of transcription factors, which mediate the production of pro-inflammatory cytokines, induce endothelial dysfunction, and promote atherogenesis. Thus, reducing UPF serves as a modifiable target for CVD prevention, can be incorporated into dietary guidelines and food-labeling practices to influence public health policy.},
}

@article {pmid41879866,
year = {2026},
author = {Finch, JTD and Riegler, M and Cook, JM and Brettell, LE},
title = {Filth Flies, Flowers and Food: Pollination by Flies (Calliphoridae) Does Not Affect the Strawberry Microbiome.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02741-2},
pmid = {41879866},
issn = {1432-184X},
support = {PH16002//Horticultural Innovation Australia Limited/ ; },
}

@article {pmid41879986,
year = {2026},
author = {Couradeau, E and Vanegas, J and Betancurt-Anzola, D and Glass, S and Eckert, K and Bechtold, EK and Ellenbogen, JB and Zaragoza, LR and Wrighton, K and Vanegas, JS},
title = {Soil Microbial Diversity in Páramos Wetland of the Colombian Andes Reveals Novel and Unique Features Within a Global Wetland Database.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02738-x},
pmid = {41879986},
issn = {1432-184X},
support = {2325922//NSF/ ; 7006508//USDA Hatch/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; DE-SC0023084 and DE-SC0023456//DOE/ ; },
abstract = {Tropical wetlands are the largest natural source of methane on Earth, yet they remain the least studied, particularly high-altitude wetlands like those in the Páramo of Chingaza, Colombia. These ecosystems are crucial for water provisioning, carbon sequestration, and biodiversity conservation but are threatened by rapid climate change. While the páramo biome supports thousands of endemic plant species and plays a vital role in balancing carbon inputs and greenhouse gas outputs (CO2 and CH4), its soil microbial diversity and functional roles in soil processes are largely unexplored. To fill this knowledge gap, we conducted amplicon sequencing of the ITS, 16S rRNA, and 18S rRNA genes to examine microbial diversity across three distinct ecosites at Laguna Seca, Chingaza, characterized by different macrotopographies, water-table levels, and vegetation assemblages. Our findings revealed significant variations in microbial community structure, with the peatland ecosite showing the highest diversity across all amplicons. Comparative analysis with global wetland datasets indicated that microbial communities at Laguna Seca share similarities with subarctic Stordalen Mire fen and other peat-forming wetlands. Notably, our targeted assessment identified a diversity of potential methanogens and methanotrophs exclusively within the peatland ecosite, at low but comparable abundance to other wetlands. This suggests that methane cycling in the other ecosites of this wetland may either be less prominent than expected or involve organisms not previously associated with known methane processes. These findings establish a baseline for understanding microbial diversity in tropical high-montane wetlands and underscore the unique ecological significance of páramo peatlands amid climate change.},
}

@article {pmid41880485,
year = {2026},
author = {Gupta, S and Geurkink, B and de Rink, R and Plugge, CM and Muyzer, G},
title = {Enhanced activity and tolerance of sulfide-oxidizing bacteria in a dual reactor haloalkaline biodesulfurization system.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag082},
pmid = {41880485},
issn = {1365-2672},
abstract = {AIMS: Studies on haloalkaline biodesulfurization (BD) systems have depicted the process efficiency and active microbial community. This paper aims to unravel the functional potential of BD system's microbial community by investigating its metabolic potential through molecular and kinetic approaches.

METHODS AND RESULTS: Biomass from all sections of a pilot dual-reactor BD system from six different operations was analysed using kinetic, molecular and genomic approaches. For kinetic analyses, at the end of six runs, biological oxidation (BO) rates of sulfide (0.1-2 mmol L-1), thiosulfate (0.1 to 32 mmol L-1), and biologically formed sulfur in the BD system (Bio-sulfur) (5 mmol L-1) were measured. Highest BO rates were ~ 0.38 µmol O2 mgN-1 sec-1 for sulfide at 1 mmol L-1-S HS- for the run with 0.9 g L-1 sulfide and 10 min HRT (Hydraulic retention time) in anoxic reactor and 0.064 µmol O2 mgN-1 sec-1 at 2 mmol L-1 S2O32--S, for the run with 0.5 0.9 g L-1 sulfide and 10 min HRT in anoxic reactor, cDNA-based qPCR of sqr and fccB genes revealed association with sulfide oxidation efficiency and element sulfur formation. Function predictions via R-based functional prediction tool -Tax4Fun2 indicated a truncated Sox pathway of thiosulfate oxidation.

CONCLUSIONS: Higher sulfide concentrations boosted biological activity and increased tolerance within the active BD microbiome. Both FccAB and Sqr were prevalent, indicating their essential roles in sulfide oxidation. The predicted truncated Sox system suggests thiosulfate dismutation to sulfate and elemental sulfur.},
}

@article {pmid41880538,
year = {2026},
author = {Consuegra-Asprilla, JM and Cuesta-Astroz, Y and González, Á},
title = {Characterization of the vaginal microbiome and its metabolic potential in Colombian patients with recurrent vulvovaginal candidiasis.},
journal = {Medical mycology},
volume = {},
number = {},
pages = {},
doi = {10.1093/mmy/myag026},
pmid = {41880538},
issn = {1460-2709},
abstract = {Recurrent vulvovaginal candidiasis (RVVC) is a multifactorial condition in which vaginal microbiota dysbiosis plays a key role. This study aimed to characterize the vaginal microbiome of patients with RVVC using metagenomic sequencing. Vaginal scraping samples were collected from 34 women aged 20-47 years and classified into three groups: (1) 14 women with RVVC who had experienced 3-7 episodes of VVC in the previous year; (2) 9 women with severe RVVC, defined as ≥8 episodes in the last year; and (3) 11 healthy women as controls. The results revealed an increased relative abundance of bacteria associated with bacterial vaginosis-including Gardnerella vaginalis, Gardnerella swidsinskii, and Prevotella bivia-as well as higher levels of Lactobacillus iners in both RVVC groups. In contrast, healthy women showed greater abundance of Lactobacillus crispatus and Lactobacillus gasseri. Diversity analyses indicated lower α-diversity in the healthy group compared to RVVC patients. Metabolic potential profiling showed a differential increase in sequences related to the phosphotransferase system (PTS), fructose/mannose metabolism, pentose phosphate pathway, and cysteine/methionine and purine metabolism in RVVC groups relative to controls; no significant differences were observed between RVVC groups, indicating that microbial profiles alone do not correlate with the degree of disease severity. These findings provide relevant insights into the taxonomic and functional characteristics of the vaginal microbiome in women with RVVC and may support the development of targeted therapeutic strategies.},
}

@article {pmid41880553,
year = {2026},
author = {Liao, Y and Jiang, R and Zhang, H and Zhang, W},
title = {The dual roles of microorganisms in inflammatory diseases: initiators and regulators.},
journal = {Critical reviews in clinical laboratory sciences},
volume = {},
number = {},
pages = {1-33},
doi = {10.1080/10408363.2026.2637106},
pmid = {41880553},
issn = {1549-781X},
abstract = {Research on the microbiome is reshaping the conceptual foundations of inflammatory diseases. As a dynamic component of the host ecosystem, microbial communities collectively influence inflammatory responses and homeostatic balance through their metabolites, structural signals, and interactions with immune pathways. Dysbiosis can amplify immune activation and metabolic disturbances, leading to persistent inflammation, whereas specific commensal taxa and their metabolites possess the capacity to suppress excessive immune responses and restore homeostasis. This bidirectional regulatory capacity positions the microbiome as a central node that both drives and modulates inflammatory networks. Multi-omics investigations have delineated the systemic architecture of microbe-host interactions, revealing cross-system axes such as the gut-brain, gut-liver, and skin-gut pathways that constitute a signaling framework integrating inflammation and immunity, thereby reshaping our understanding of disease pathogenesis. Within this framework, inflammation is redefined as an adaptive strategy for maintaining systemic stability rather than merely a singular pathological reaction. Therapeutic approaches including fecal microbiota transplantation (FMT), engineered microbial strains, and interventions targeting metabolic signaling are propelling microecological medicine into an era of precision modulation. As systems biology converges with spatial omics, research on the microbiome is shifting from descriptive pathology toward mechanistic control, establishing it as a critical nexus linking immunity, metabolism, and disease evolution. This transformation heralds a paradigm shift in medicine from merely "suppressing inflammation" to actively "reconstructing ecological order."},
}

@article {pmid41880855,
year = {2026},
author = {Bhattacharya, S and Kolandhasamy, P and Mandal, A and Rajaram, R and Darbha, GK},
title = {Biofilm-mediated surface depolymerization of multiple synthetic polymers by mangrove-derived bacterial consortia.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141847},
doi = {10.1016/j.jhazmat.2026.141847},
pmid = {41880855},
issn = {1873-3336},
abstract = {Plastic pollution persists across marine and terrestrial ecosystems largely due to the intrinsic resistance of synthetic polymers to biological attack. Despite growing evidence of microbial interactions with plastics, the mechanistic basis and extent of biofilm-mediated polymer deterioration remain poorly constrained. Here, we investigate the capacity of mangrove-derived bacterial consortia to initiate early-stage degradation of major synthetic polymers (PET, PS, LDPE, HDPE, and PP) under controlled laboratory conditions. Over a 120-day incubation under controlled laboratory conditions, consortium-exposed polymers exhibited differential mass loss, surface erosion, and mechanical weakening, with PS 20.14% and PET 8.33% showing the highest susceptibility. Integrated surface and molecular analyses using confocal laser scanning microscopy, atomic force microscopy, scanning electron microscopy energy dispersive X-ray spectroscopy, and Fourier-transform infrared spectroscopy revealed extensive biofilm formation, nanoscale pitting, oxidative functional group incorporation, and localized polymer chain modification. Tensile testing further demonstrated reductions in mechanical integrity consistent with surface-driven structural weakening. First-order kinetic fits were applied to gravimetric data to provide comparative, non-predictive estimates of degradation dynamics across polymer types. This study provides quantitative and mechanistic evidence that environmentally adapted microbial consortia can promote biofilm-driven surface depolymerization, highlighting mangrove sediments as underexplored reservoirs of plastic-interacting microbes. These findings advance current understanding of early-stage plastic biodegradation and inform future strategies for biotechnological intervention in microplastic-polluted environments.},
}

@article {pmid41881017,
year = {2026},
author = {Zhou, J and Zeng, X and Sun, J and Yang, Y and Wang, J and Xiao, X and Fang, P and Liu, Y and Wang, M and Long, Y and Fu, F and Li, W and Du, J and Liang, Z and Nie, S and Luan, S and Li, X and Zhang, H and Peng, Y and Sun, S and Zhu, W and Zhang, L and Shang, Q and Chen, Y and Xu, Y and Chen, L and Ding, Z and Du, D and Guo, AY and Wei, X and Yuan, Y},
title = {Gut microbiota-derived indole-3-lactic acid suppresses anti-PD-1 efficacy in esophageal squamous cell carcinoma.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.02.019},
pmid = {41881017},
issn = {1934-6069},
abstract = {Esophageal squamous cell carcinoma (ESCC) is a highly aggressive malignancy where the efficacy of anti-PD-1 immunotherapy varies among individuals, possibly influenced by the gut microbiota. Here, we analyze 122 fecal samples from ESCC patients undergoing neoadjuvant immunotherapy and identify an enrichment of Ligilactobacillus salivarius (L. salivarius) in non-responders. Humanized microbiome, orthotopic ESCC mouse models, and single-cell RNA sequencing confirm that L. salivarius-produced indole-3-lactic acid (ILA) suppresses tumor-infiltrating NKG7[+]CD8[+] Tpex cells, impairing anti-tumor immunity. Moreover, ILA-deficient L. salivarius strains abolish ILA production and immune resistance. In vitro assays reveal that ILA targets the aryl hydrocarbon receptor and downregulates nuclear factor κB (NF-κB) signaling in Tpex cells. Pharmacological NF-κB activation restores Tpex function and reverses resistance. Two validation cohorts support the L. salivarius-ILA-NKG7[+]CD8[+] Tpex axis as a resistance mechanism in ESCC patients. These findings highlight L. salivarius and ILA as key modulators of the tumor microenvironment, offering potential strategies for overcoming immunotherapy resistance in ESCC.},
}

@article {pmid41881056,
year = {2026},
author = {Chetruengchai, W and Sriwattanapong, K and Manaspon, C and Fakhruddin, KS and Samaranayake, L and Shotelersuk, V and Porntaveetus, T},
title = {Metagenome and Metabolic Pathways in Plaque Biofilms of Thai ELANE-Associated Neutropenic Patients: An Original Study and Scoping Review.},
journal = {European journal of dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0046-1818559},
pmid = {41881056},
issn = {1305-7456},
abstract = {Congenital neutropenia, particularly ELANE-associated forms, is associated with recurrent oral infections and aggressive periodontitis. While ELANE deficiency compromises oral health, its relationship to plaque biofilm ecology and metabolic function remains unclear. The oral microbiome-metabolome interplay in this condition remains largely uncharacterized globally. Here, we address this gap by characterizing the dental plaque metagenome and inferred metabolic pathways in a defined cohort of Thai neutropenia patients.In this exploratory study, we sequenced dental plaque samples from a defined cohort of nine individuals: three patients with severe congenital neutropenia or cyclic neutropenia (CyN) with confirmed ELANE variants, and six from age- and gender-matched healthy controls. Shotgun metagenomics was used for genomic analysis, followed by comprehensive microbiota examination. Subsequently, MetaCyc, a curated database, was used for in silico analysis and comparisons of the predicted functional pathways between the test and control plaque biofilms.The principal coordinate analysis plot and heat map revealed distinct segregation of microbial profiles between the patients and control groups. A significant variation in the proportions of the five core phyla was noted in patients and controls. Two commensal species, Aggregatibacter sp oral taxon 458 and Leptotrichia sp oral taxon 212, were enriched in the controls. Conversely, four species were significantly enriched in the patients, Selenomonas flueggei, Streptococcus milleri, Kingella oralis, and Actinobaculum sp oral taxon 183; the latter being notably elevated across all patients. The MetaCyc in silico analyses suggested predicted enrichment of functional pathways associated with inflammation and oxidative stress in patients, including L-methionine biosynthesis IV, formaldehyde assimilation III, L-rhamnose degradation, and the superpathway of (R,R)-butanediol biosynthesis pathways.Our study advances the understanding of ELANE-associated periodontitis by moving beyond descriptive microbiota analysis to suggest potential associations between host immune deficiency, microbial dysbiosis, and the microbiota-associated metabolic pathway alterations. These findings provide preliminary insights into targeted periodontal care in neutropenic patients, though further validation in larger cohorts is required.},
}

@article {pmid41881444,
year = {2026},
author = {Kringeland, GD and Tangedal, S and Julian, D and Paytuví-Gallart, A and Sanseverino, W and Bertelsen, RJ and Husebø, GR and Knudsen, KS and Lehmann, S and Nielsen, R and Eagan, TML},
title = {Antimicrobial resistance genes and antibiotic use in chronic lung disease: a bronchoscopy study of the lower airways microbiome.},
journal = {BMJ open respiratory research},
volume = {13},
number = {1},
pages = {},
doi = {10.1136/bmjresp-2025-003864},
pmid = {41881444},
issn = {2052-4439},
mesh = {Humans ; Male ; Female ; Cross-Sectional Studies ; Bronchoscopy ; Middle Aged ; Aged ; *Anti-Bacterial Agents/therapeutic use ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy ; Case-Control Studies ; *Lung Diseases/microbiology/drug therapy ; *Drug Resistance, Bacterial/genetics ; *Drug Resistance, Microbial/genetics ; Chronic Disease ; },
abstract = {BACKGROUND: Antimicrobial resistance genes (ARGs) in the respiratory microbiome are poorly characterised. We compared the presence of ARGs in healthy controls with patients with chronic lung disease in a cross-sectional study, adjusted for time since antibiotic use.

METHODS: Bronchoalveolar lavage was collected from 100 controls, and 93 patients with chronic obstructive pulmonary disease (COPD), 13 with asthma, 34 with sarcoidosis, 12 with idiopathic pulmonary fibrosis (IPF) and 11 patients with unclassifiable interstitial lung disease (uILD). Participants had not used antibiotics 14 days prior to sampling. Shotgun metagenomic sequencing was performed with Illumina NovaSeq. ARGs were identified using the National Database of Antibiotic-Resistant Organisms. Sample reads were normalised to counts per million.

RESULTS: In total, 38% of controls had at least one ARG, compared with 51%, 39%, 65% and 83% of patients with COPD, asthma, sarcoidosis and IPF, respectively (p=0.01). ARGs against tetracycline (33%) were the most common ARG class, followed by beta-lactam and macrolide resistance (both 26%). In a logistic regression analysis adjusted for sex, age, body composition, smoking and antibiotic use, the OR (95% CI) for having ARGs in the lower airways was 1.30 (0.70 to 2.41) in COPD, 1.00 (0.29 to 3.52) in asthma, 3.52 (1.40 to 8.83) in sarcoidosis, 6.40 (1.25 to 32.73) in IPF and 3.27 (0.76 to 14.16) in uILD compared with controls. Overall mean (SD) ARG counts per million were 403.8 (537.7) in the 35 subjects who had used antibiotics ≤3 months before bronchoscopy, compared with 197.6 (355.9) in the 228 subjects without (p=0.02).

CONCLUSION: The presence of ARGs in the lower airways microbiome was significantly higher in patients with sarcoidosis and IPF than in controls. The counts per million for ARGs were significantly associated with recent antibiotic use.},
}

Humans
Male
Female
Cross-Sectional Studies
Bronchoscopy
Middle Aged
Aged
*Anti-Bacterial Agents/therapeutic use
*Microbiota/genetics
Bronchoalveolar Lavage Fluid/microbiology
Pulmonary Disease, Chronic Obstructive/microbiology/drug therapy
Case-Control Studies
*Lung Diseases/microbiology/drug therapy
*Drug Resistance, Bacterial/genetics
*Drug Resistance, Microbial/genetics
Chronic Disease

@article {pmid41881526,
year = {2026},
author = {Vahid, F and Loyola-Leyva, A and Bouzas, C and Tur, JA and Ivanova, Y and Doychinov, B and Nikolov, R and Chikalanov, A and De Magistris, T and Halimi, J and Forberger, S and Stahl, C and Evers, S and Devaux, Y and Malisoux, L and Mendon, P and Celebic, A and Vaillant, M and Gantenbein, M and Skhiri, L and Kallas, Z and Garcia, L and Bohn, T and , },
title = {Empowering healthy lifestyle behaviour through personalised intervention portfolios using a healthy lifestyle recommender system to prevent and control obesity in older adults: pilot study protocols from the HealthyW8 project.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e108771},
doi = {10.1136/bmjopen-2025-108771},
pmid = {41881526},
issn = {2044-6055},
mesh = {Humans ; Pilot Projects ; Aged ; *Obesity/prevention & control ; *Healthy Lifestyle ; Male ; Female ; Exercise ; *Health Promotion/methods ; Europe ; },
abstract = {INTRODUCTION: Obesity prevalence has increased globally, imposing a significant burden on individuals and societies. Innovative solutions are, therefore, essential to mitigate its impact.

METHODS AND ANALYSIS: This protocol outlines the framework of seven independent European pilot studies conducted in Bulgaria, Germany, Luxembourg and Spain, under the EU-Horizon HealthyW8 project. These studies aim to evaluate as primary outcomes feasibility, usage patterns (adherence) and user satisfaction of the Healthy Lifestyle Recommender System (HLRS), a personalised digital tool designed to promote healthy lifestyles through tailored physical activity and meal recommendations, considering emotional aspects. The seven pilot trials will collectively include 240 (around 30 participants/trial) older adults (≥65 years) with overweight (body mass index (BMI) 25.0-29.9 kg/m[2]) over a 3-month period. As a recruitment mitigation strategy, we will extend the age range to include individuals aged ≥55 years and those with normal weight (BMI 18.5-24.9 kg/m[2]). Other parameters collected include anthropometric measurements, questionnaires to survey lifestyle (alcohol and tobacco consumption, sleep quality), dietary patterns (food frequency questionnaire and 24-hour recall) and emotional well-being, as well as data collected from wearable devices (smartwatch, accelerometer) to track 24-hour activity patterns. Additionally, two pilot studies will collect blood, urine, saliva (only one partner) and stool samples to explore biomarkers of inflammation, oxidative stress, gut microbiome and circulating miRNAs.

EXPECTED OUTCOMES: It is hypothesised that participants will use the HLRS consistently enough to assess its feasibility and impact. The findings will contribute to planning and executing long-term trials focused on health outcomes and enhance understanding of the multimodal nature of obesity risk and its comorbidities. This protocol facilitates comparisons across studies in diverse cultural and contextual settings, offering insights into how personal and environmental factors influence the implementation and effectiveness of the HLRS.

ETHICS AND DISSEMINATION: Ethical approval has been obtained in each country independently. Dissemination efforts will prioritise high-impact journal publications.

TRIAL REGISTRATION NUMBER: NCT07011368.},
}

Humans
Pilot Projects
Aged
*Obesity/prevention & control
*Healthy Lifestyle
Male
Female
Exercise
*Health Promotion/methods
Europe

@article {pmid41881738,
year = {2026},
author = {Park, J and Kim, J and Cho, S and Shin, W},
title = {In vitro platforms for reconstructing skin-microbiome interactions.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.02.006},
pmid = {41881738},
issn = {1879-3096},
abstract = {The growing recognition of the skin microbiome in regulating the host's metabolic and immune functions has spurred the development of in vitro platforms designed to recapitulate their intricate interactions, aiding research into both skin-microbiome and microbe-microbe interactions within their distinct niches. Despite these efforts, challenges remain in dissecting skin-microbiome interactions, especially due to the absence of a standardized platform for the long-term coculture of bacterial and mammalian cells. In this review, we highlight the key components in modeling an in vitro skin ecosystem and discuss the therapeutic potential of skin commensals, including recent advances and applications for engineered live biotherapeutics targeting skin diseases, to underscore the translational value of in vitro skin-microbiome interaction studies.},
}

@article {pmid41881804,
year = {2026},
author = {Gutiérrez, J and Vergara-Amado, J and Martorell, C and Navedo, JG and Wille, M and Guajardo-Leiva, S and Castro-Nallar, E and Verdugo, C},
title = {Functional Shifts in the Gut DNA Virome in a Long-Distance Migratory Shorebird During the Pre-Migratory Fattening.},
journal = {Molecular ecology},
volume = {35},
number = {6},
pages = {e70315},
doi = {10.1111/mec.70315},
pmid = {41881804},
issn = {1365-294X},
support = {FONDECYT N°1191769//Agencia Nacional de Investigación y Desarrollo/ ; ANILLO ATE220062//Agencia Nacional de Investigación y Desarrollo/ ; Doctoral scholarship N°21201700//Agencia Nacional de Investigación y Desarrollo/ ; //The Pathogen Watchtower Program (Biotia Inc. & The Rockefeller Foundation)/ ; //Universidad Austral de Chile/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Charadriiformes/virology/physiology ; *Animal Migration ; *Virome/genetics ; Feces/virology ; Metagenomics ; Metagenome ; },
abstract = {Migration represents one of the most energetically demanding phases in the life cycle of long-distance migratory birds. Pre-migratory fattening is a critical preparatory stage characterized by hyperphagia, rapid fat accumulation, organ remodelling, and immune modulation. Although the gut microbiome has been recognized as a key contributor to these physiological adaptations, the role of the gut virome remains poorly understood. In this study, the diversity, functional potential, and temporal dynamics of the gut DNA virome in a trans-hemispheric migratory shorebird, the Hudsonian godwit (Limosa haemastica), were assessed during pre-migratory fattening. Adult individuals were maintained under controlled aviary conditions for 15 weeks during the preparation for northbound migration, and faecal samples were collected at two distinct physiological time points: at the beginning and the end of pre-migratory fattening. Shotgun metagenomic sequencing revealed 798 high-quality viral operational taxonomic units (vOTUs), the majority of which were bacteriophages (92%). Potential functional annotation identified auxiliary metabolic genes (AMGs) associated with nucleotide metabolism, redox balance, and host adaptation. Although overall gut virome diversity did not differ between stages, significant changes in potential functional profiles of phages were observed, especially during the final stage of fattening when energy demands are at their highest. In addition to bacteriophages, we report two divergent adenoviruses potentially associated with the Siadenovirus and Aviadenovirus genera. These findings suggest that dynamic viral communities may play underrecognized roles in supporting host physiology during energetically costly life stages.},
}

Animals
*Gastrointestinal Microbiome/genetics
*Charadriiformes/virology/physiology
*Animal Migration
*Virome/genetics
Feces/virology
Metagenomics
Metagenome

@article {pmid41882002,
year = {2026},
author = {Rumpler, M and van Mierlo, G and Vinten, KT and Giner, MP and Christen, S and Hayat, F and Makarov, MV and Gardeux, V and Russeil, J and Schomakers, BV and van Gijn, L and Hashimi, H and Steiner, C and Giroud-Gerbetant, J and Joffraud, M and Sanchez Garcia, JL and Moco, S and Migaud, ME and Houtkooper, RH and Deplancke, B and Canto, C},
title = {Therapeutic potential of dihydronicotinamide riboside (NRH) on obesity and glucose intolerance in mice.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70965-4},
pmid = {41882002},
issn = {2041-1723},
support = {MSCA-DN-NADIS no. 101073251//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; R21 AAT009908-01//U.S. Department of Health & Human Services | NIH | National Center for Complementary and Integrative Health (NCCIH)/ ; },
abstract = {NAD[+] is a crucial metabolic cofactor whose intracellular levels can influence the progression of multiple metabolic and age-related complications. There is therefore a strong interest in using NAD[+] precursors (vitamin B3s) as therapeutic tools, but most current precursors exhibit either poor bioavailability or adverse effects. This study examines the metabolic impact of chronic dietary supplementation with a newly described NAD[+] precursor, dihydronicotinamide riboside (NRH), in mice using a comprehensive approach including phenotyping tests, RNA sequencing in different tissues and microbiome analyses. We show that chronic NRH administration at 100 mg/(kg*day) is well tolerated, yet has minimal metabolic effects in mice on a regular diet. However, NRH mitigates high-fat diet-induced metabolic complications when used as a preventive or as a treatment strategy, including improvements in glucose tolerance, increased hepatic expression of lipid catabolism genes and fat redistribution. These results highlight the potential of NRH as a therapeutic agent, although further studies are needed to optimize its use, as higher doses reveal signs of toxicity.},
}

@article {pmid41882035,
year = {2026},
author = {Kumar, M and Ansari, WA and Singh, A and Kumar, SC and Zeyad, MT and Chakdar, H and Farooqi, MS and Sharma, A and Srivastava, S and Jha, GK and Srivastava, AK},
title = {Impact of genotype and soil fertility on wheat rhizosphere microbiota under the trans-gangetic plain.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36646-4},
pmid = {41882035},
issn = {2045-2322},
support = {2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; 2020//Centre for Agricultural Bioinformatics/ ; },
abstract = {The effects of genotypes (HD3086 and PBW343) and soil physicochemical properties on the wheat rhizospheric bacterial communities along the trans Indo-Gangetic plains were studied. The trans-Indo-Gangetic Plains of India are one of the areas in the country where wheat is grown the most. Despite the agricultural significance of this region, extensive studies on the rhizosphere microbial abundance and community structure related to wheat cultivation in this area are still lacking. To address this knowledge gap, the present study was undertaken to characterize the rhizosphere microbiome using full-length 16 S rRNA-based metagenomic profiling, implementing universal primers, tailed with PacBio Sequel II barcode sequences, providing new insights into microbial dynamics across this major wheat-producing landscape. Statistical analysis revealed significant differences in both abundance and diversity among the different soil samples and wheat genotypes. Four phyla exhibited significant differences in relative abundance between the genotypes (p < 0.05): Proteobacteria (p = 0.002), Planctomycetes (p = 0.000), Verrucomicrobia (p = 0.000), and Firmicutes (p = 0.030). The number of genera identified in genotype HD3086 across all locations was 421, while it was 322 for genotype PBW343. There were 251 genera found common, with 170 genera exclusively present in HD3086 and 71 in PBW343. Significant differences were observed in the relative abundance of eighteen genera (p < 0.05) between the genotypes; some of them include Luteolibacter, Gemmata, Pseudomonas, Stenotrophobacter, Pseudarthrobacter, Devosia, Lacibacter, Gaiella, Luteimonas, and Nitrosospira. Correlation analysis indicated significant associations between microbial diversity and soil parameters like pH, total and available nitrogen, potassium, phosphorus, iron, and organic carbon for both varieties. Core taxa analysis revealed 27 core taxa across both genotypes. The study highlights significant genotype effects on rhizosphere microbiomes, with implications for soil health and crop management strategies.},
}

@article {pmid41882107,
year = {2026},
author = {Bertolo, A and Wettstein, R and Valido, E and Capossela, S and Buergin, J and Haumer, A and Speck, N and Nyfeler, N and Widmer, A and Pannek, J and Krebs, J and Stoyanov, J},
title = {Microbial and inflammatory profiling of pressure injuries and urinary tract infections in spinal cord injury: a prospective cohort study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45422-3},
pmid = {41882107},
issn = {2045-2322},
support = {Foko_2018_03//Swiss Paraplegic Foundation/ ; Foko_2018_03//Swiss Paraplegic Foundation/ ; Foko_2018_03//Swiss Paraplegic Foundation/ ; },
abstract = {Pressure injuries (PIs) are common in individuals with spinal cord injury (SCI) and increase the risk of infections, including urinary tract infections (UTIs), which may prolong hospitalisation. However, the role of PIs in the development of postoperative UTIs remains unclear. In this exploratory study, we investigated the relationship between the PI microbiome and urinary bacteria, and examined whether perioperative bacteriuria predicts prolonged hospital stay in patients undergoing reconstructive PI surgery. In this cohort study, 21 male patients with SCI and advanced-stage PIs undergoing reconstructive surgery were evaluated. Microbiome and urinary cytokine profiles were analysed at two postoperative time points: day 3 (early postoperative phase) and day 15 (after completion of antibiotic therapy). DNA from skin, PI tissue, and urine was analysed using 16S rRNA gene sequencing. Asymptomatic bacteriuria was present in 48% of patients on day 3 and 38% on day 15. Dominant urinary bacteria included Enterococcus, Klebsiella, Streptococcus, and Escherichia, which were associated with elevated urinary cytokine levels. High bacterial load (≥ 100,000 bacteria/mL) in urine on day 3 correlated with increased UTI incidence and frequency, although hospitalisation duration was unaffected. By day 15, urinary bacterial load was no longer associated with UTI incidence. The microbiota of PIs and adjacent skin were distinct from urinary microbiota, indicating minimal cross-contamination. Early perioperative high bacterial load is associated with increased urinary inflammation and a higher risk of postoperative UTIs in patients with SCI undergoing PI reconstruction. These findings support early infection monitoring and targeted preventive strategies to improve postoperative outcomes.},
}

@article {pmid41882212,
year = {2026},
author = {Noerman, S and Esberg, A and Mack, CI and Ahmed, H and Egert, B and Nordin, E and Brunius, C and Hanhineva, K and Johansson, I and Landberg, R},
title = {Multi-omics analysis of associations between host demographics and saliva metabolome, sugar profiles, and microbiome profiles.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44287-w},
pmid = {41882212},
issn = {2045-2322},
}

@article {pmid41882388,
year = {2026},
author = {Wang, Y and Wang, L and Zheng, Y and Wang, R and Zhen, F and Cheng, ZJ and Sun, B and Tsui, SK and An, C},
title = {Integrated multi-omics analysis of gut microbiome and serum metabolome in unipolar and bipolar depression.},
journal = {European archives of psychiatry and clinical neuroscience},
volume = {},
number = {},
pages = {},
pmid = {41882388},
issn = {1433-8491},
support = {2023YFC2506201//National Key Research and Development Program of China/ ; SG2021189//Hebei Provincial Department of Science and Technology/ ; ZF2025052//Government Funded Clinical Medicine Excellent Talents Training Project of Hebei Province/ ; H2023206925//Beijing Engineering and Technology Research Center of Food Additives/ ; },
}

@article {pmid41882398,
year = {2026},
author = {Addington, E and Gannon, A and Larcombe, DE and Lawaetz, AC and McHugh, RE and Vahtokari, S and Munnoch, JT},
title = {Microbial Biotechnology in Medicine.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {217-250},
pmid = {41882398},
issn = {0079-6484},
mesh = {Humans ; *Biotechnology/methods ; Synthetic Biology/methods ; Microbiota ; Probiotics/therapeutic use ; Animals ; Precision Medicine ; },
abstract = {The convergence of biology, technology, and medicine has revolutionised healthcare, with microbial biotechnology at the forefront. While many microbes are often considered solely for their infectious properties, many are major producers of natural products, including antimicrobials. Now, not only sources of clinically relevant drugs, they are also being directly engineered for advanced applications such as targeted drug delivery, immune modulation, and precision therapeutics. Microorganisms are key sources of novel antimicrobials, immunomodulatory, and anticancer agents, which synthetic biology and genomics mining can exploit. Bioengineering and exploration of underused microbial taxa offer promising solutions to the problem of rising antimicrobial resistance. Microbes also play crucial roles in modern vaccine development, from live attenuated to recombinant antigen production. The human microbiome has emerged as an interesting player in health, driving innovations in diagnostics and therapies that include next-generation probiotics and microbiota transplants. Furthermore, synthetic biology further empowers the design of 'smart' microbes for in situ therapeutic functions like imaging, biosensing, and targeted treatment. While transformative, these innovations also raise critical ethical and regulatory concerns, including biosafety, ecological impact, data privacy, and equitable access. This chapter explores the multifaceted roles of microbes in medical biotechnology-spanning therapeutics, vaccines, microbiome-based interventions, and engineered systems-underscoring their importance in the evolution of sustainable, personalised healthcare.},
}

Humans
*Biotechnology/methods
Synthetic Biology/methods
Microbiota
Probiotics/therapeutic use
Animals
Precision Medicine

@article {pmid41882400,
year = {2026},
author = {Hacioglu, O},
title = {Microbiota and Microbiome.},
journal = {Progress in molecular and subcellular biology},
volume = {62},
number = {},
pages = {307-331},
pmid = {41882400},
issn = {0079-6484},
mesh = {Humans ; *Microbiota ; Dysbiosis/microbiology ; Animals ; Bacteria/genetics ; Host Microbial Interactions ; },
abstract = {The human microbiota represents a complex and dynamic ecosystem composed of microorganisms from various taxonomic groups, including bacteria, viruses, fungi, archaea, and protozoa. These microorganisms inhabit different anatomical regions of the human body, such as the genitourinary system, the gastrointestinal tract, the oral cavity, the skin, and the respiratory tract, exhibiting distinct densities, compositions, and functional characteristics, and interact reciprocally with the host organism. The term microbiota not only defines the diversity and abundance of microorganisms but also encompasses their functional influence on host physiology. At this point, the concept of the microbiome becomes relevant. The microbiome refers to the collective genomic content of all microorganisms comprising the microbiota, that is, their genetic material and the potential biological functions encoded by their genes. Therefore, microbiome analysis enables not only the assessment of microbial diversity, but also of metabolic capacity, signal transduction, immune regulation, and other host-microbe interactions. The microbiota and microbiome play important roles in preserving human health and homeostatic balance. A healthy microbial composition promotes immune system development, aids digestion and nutrient absorption, reduces pathogenic microorganism colonization, and contributes to the integrity of the mucosal barrier. In contrast, dysbiosis, or disruption of microbial equilibrium, has been linked to a variety of pathophysiological illnesses, including inflammatory diseases, metabolic disorders, neurodegenerative diseases, and some neoplasms. Today, microbiome research is not only essential for understanding health and disease mechanisms but also forms the foundation for innovative future medical applications.},
}

Humans
*Microbiota
Dysbiosis/microbiology
Animals
Bacteria/genetics
Host Microbial Interactions

@article {pmid41882509,
year = {2026},
author = {Seo, JH and Ha, JH and Cho, SH and Kim, KN and Lee, HW},
title = {Comparative analysis of fungal microbiomes in Korean and Chinese chili pepper powders.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70611},
pmid = {41882509},
issn = {1097-0010},
support = {//This work was supported by the Ministry of Education, Republic of Korea (DOI: 10.13039/100009950), and the Jeju Special Self-Governing Province. This research was conducted as part of the Regional Innovation System and Education (RISE) program through the Jeju RISE Center (Project No. 2025-RISE-17-001)./ ; //Regional Innovation System and Education (RISE) program through the Jeju RISE center/ ; 2025-RISE-17-001//Ministry of Education (MOE) and the Jeju Special Self-Governing Province, Republic of Korea/ ; },
abstract = {BACKGROUND: Chili pepper powder plays a crucial role in kimchi fermentation; however, its use may result in fungal contamination. Therefore, analyzing its mycobiome is vital to maintain quality control standards. In this study, we used internal transcribed spacer (ITS)2 amplicon sequencing to compare fungal communities in commercially available Korean and Chinese chili pepper powders widely used in Korea (n = 9 per group).

RESULTS: Ascomycota was the predominant phylum in the Chinese and Korean chili pepper powders. Chinese powder samples exhibited higher genus-level diversity and were notably enriched in Vishniacozyma, whereas Korean powders showed relative enrichment in Fusarium and Issatchenkia. Species richness tended to be higher in Chinese than Korean samples (2.20 ± 0.42 vs. 1.82 ± 0.39). Beta diversity analysis revealed a distinct compositional separation between samples based on origin (permutational multivariate analysis of variance, P < 0.01). The distribution of potentially toxin-related genera also varied by origin: Aspergillus and Penicillium were more abundant in Chinese powders, whereas Fusarium predominated in Korean powders. Although detection at the genus level does not directly indicate mycotoxin contamination, origin-specific enrichment patterns suggest distinct toxin risk profiles warranting additional investigation.

CONCLUSION: These findings underscore the importance of systematically monitoring fungal and mycotoxin-producing communities in chili pepper powders and evaluating the impact of kimchi fermentation on mycotoxin persistence and mitigation. Such measures are essential for improving food safety and traceability. © 2026 The Author(s). Journal of the Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid41882531,
year = {2026},
author = {Kullaya, VI and Rofael, S and Heysell, SK and Thomas, TA and Ongeso, N and Gathii, K and Said, B and Mpagama, S and Mmbaga, BT and McHugh, TD},
title = {Gut microbiome disruption in Tanzanian pulmonary tuberculosis patients: links to treatment, nutritional status, and host immunity.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04882-3},
pmid = {41882531},
issn = {1471-2180},
support = {AREF-325-KULL-F-C0956//Africa Research Excellence Fund (AREF)/ ; },
}

@article {pmid41882573,
year = {2026},
author = {Schöttker, B and Kopp-Schneider, A and Biehl, L},
title = {Protocol of the LEONORA randomized clinical trial: Lower gastrointestinal symptom burden by prophylaxis with synbiotics after colorectal cancer surgery.},
journal = {BMC cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12885-026-15903-9},
pmid = {41882573},
issn = {1471-2407},
}

@article {pmid41882673,
year = {2026},
author = {Deng, J and Qiu, Q and Ye, S and Yu, J and Yao, D and Deng, H and Wang, C and Han, L and Deng, Y and Chen, Y and Liu, Y and Liu, C and Shang, X and Fang, X and Lu, C},
title = {Disentangling environmental and disease-specific signatures in the gut microbiome of psoriasis: discovery of Fimenecus sp. as a novel biomarker and characterization of the gut virome.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08013-4},
pmid = {41882673},
issn = {1479-5876},
abstract = {BACKGROUND: The contribution of the gut microbiome to the pathogenesis of psoriasis remains a subject of debate, with inconsistent findings across studies likely confounded by environmental factors. This study aimed to statistically disentangle the effects of a shared household environment from disease-specific microbial signatures in psoriasis. Our objective was to identify novel, multi-kingdom biomarkers, encompassing bacteria and viruses, that hold significant diagnostic and therapeutic potential.

METHODS: We conducted a nested case-control study, performing shotgun metagenomic sequencing on stool samples from 143 participants. The cohort comprised 98 psoriasis patients, 28 healthy cohabiting relatives, and 17 unrelated healthy controls. A comprehensive multi-kingdom analysis of bacteria, viruses, and their associated metabolic pathways was implemented. To ensure the robustness of our findings, a two-stage discovery-validation strategy was employed to identify distinct microbial features associated with psoriasis.

RESULTS: Our analysis revealed that the shared household environment was the predominant factor shaping the overall gut microbiome structure. Despite this strong confounding effect, we successfully identified a novel bacterial species, Fimenecus sp000432435, as a robust biomarker for psoriasis, achieving an area under the curve (AUC) of 0.84. Genomic functional prediction indicated that this species encodes pathways with the potential for B-vitamin and secondary bile acid biosynthesis. Furthermore, characterization of the gut virome identified five disease-associated bacteriophages. Among these, vBin_422 exhibited a significant negative correlation with the abundance of Fimenecus sp000432435, suggesting a potential ecological interaction. Notably, the biotin biosynthesis pathway was negatively correlated with disease severity, whereas specific viral taxa showed a positive correlation with systemic inflammatory markers within the patient cohort.

CONCLUSIONS: Controlling for environmental confounders reveals that psoriasis is associated with sparse but distinctmicrobial signatures rather than broad dysbiosis. Fimenecus sp000432435 is a promising candidate for non-invasive diagnostics, while the characterized virome opens new therapeutic avenues targeting bacteriophage-bacteria interactions in psoriasis management.

TRIAL REGISTRATION: ChiCTR-IOR-17011075. Registered 6 April 2017, http://www.chictr.org.cn/showproj.aspx?proj=17334.},
}

@article {pmid41882707,
year = {2026},
author = {Patel, J and Chaudhary, H and Parekh, B and Joshi, R},
title = {Exploring gut microbiome alterations and hormonal imbalances in polycystic ovary syndrome: insights from a comparative study.},
journal = {Journal of ovarian research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13048-026-02081-2},
pmid = {41882707},
issn = {1757-2215},
support = {ANRF/PAIR/2025/000008//Science and Engineering Research Board/ ; },
}

@article {pmid41882727,
year = {2026},
author = {Liao, X and Song, W and Wan, Y and Zhang, J and Ren, P and Delaplace, P and Chen, Y},
title = {Dual functions of apigenin in suppressing Phytophthora capsici and shaping the pepper microbiome.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02386-w},
pmid = {41882727},
issn = {2049-2618},
support = {ZR2023QC067//Shandong Provincial Natural Science Foundation/ ; SYS202206//Shandong Provincial Natural Science Foundation/ ; No. 202502AQ370001//Yunnan Department of Science and Technology - Development and adoption of innovative 'green' management tools against insect pest and disease on tomato and pepper in Yunnan/ ; 2024CXPT034//Key R&D Program of Shandong Province, China/ ; },
abstract = {BACKGROUND: Plant resistance to soil-borne pathogens is shaped by the interactions among host genetics, root exudates, and rhizosphere microbiomes. Flavonoids are widely recognized for their antimicrobial and signaling functions, yet their role in mediating metabolite-microbiome-pathogen interactions in pepper (Capsicum frutescens) remains poorly understood.

RESULTS: Through integrated microbiome, transcriptome, and metabolome analyses, we compared resistant (CA53) and susceptible (CA476) pepper cultivars under challenge by Phytophthora capsici in the pepper rhizosphere. Resistant plants maintained relatively stable transcriptional and metabolic profiles, whereas susceptible plants exhibited a pronounced suppression of the flavonoid biosynthesis pathway, with a marked decline in apigenin levels. Exogenous application of apigenin significantly enhanced pepper resistance by disrupting sporangial cell membrane integrity and thereby inhibiting zoospore release (95% reduction in zoospore release). In addition, apigenin functioned as a central hub metabolite, selectively enriching disease-suppressive rhizosphere microbes and reinforcing host protection.

CONCLUSION: Our findings uncover a dual role of apigenin in pepper resistance: directly inhibiting pathogen propagation and indirectly reinforcing the recruitment of protective microbiota. These insights highlight the ecological functions of root-derived metabolites in shaping plant-microbiome interactions and provide potential avenues for metabolite-informed strategies in sustainable crop protection. Video Abstract.},
}

@article {pmid41882740,
year = {2026},
author = {Täubel, M and Hill, MS and Allard, S and Gilbert, JA and Valkonen, M and Karvonen, AM and Vepsäläinen, A and Pekkanen, J and Kirjavainen, PV},
title = {Environmental microbiota transfer from forest soil into urban homes: a proof-of-principle study.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {41882740},
issn = {2049-2618},
support = {296814, 296817//Research Council of Finland/ ; 349427//Research Council of Finland/ ; },
mesh = {Humans ; Dust/analysis ; *Soil Microbiology ; Forests ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota/genetics ; Finland ; RNA, Ribosomal, 16S/genetics ; Fungi/genetics/classification/isolation & purification ; Housing ; Adult ; Air Pollution, Indoor/analysis ; Proof of Concept Study ; Infant ; },
abstract = {BACKGROUND: Urban lifestyles are characterized by reduced encounters of environmental microbe stimuli that activate immunoregulatory pathways. This has been linked to an increased risk of inflammatory diseases, asthma, and allergies. A potential preventative solution is to modify indoor microbial exposures toward health-promoting interactions. Here, we test the feasibility of environmental microbiota transfers into urban homes and quantify the spatiotemporal impact on the built environment microbiota.

METHODS: House dust microbiota of six Finnish homes was monitored over a 20-week period by collecting settled dust from infant (IBZs) and adult breathing zones (ABZs) and floor dust from different home locations. Microbiota in dust samples was characterized using qPCR and amplicon sequencing of the bacterial and archaeal 16S rRNA gene and fungal ITS1 region. Microbiota transfers were performed with repeated seeding of forest soil onto rugs placed in the home entryway.

RESULTS: We observed significant, post-intervention increases in the relative abundances of forest soil bacteria in house dust. The magnitude of effect was influenced by building characteristics, spatiotemporal dynamics, and occupant dynamics and was greatest in a home with comparably little additional microbial influx-a home with no pets, low occupancy, and mechanical ventilation. The most pronounced effect was observed in settled dust close to the soil-seeded rugs at IBZ, within the first 2 weeks after each seeding event, though the soil-associated bacterial signal also extended spatially into the living areas of the homes. Increases in bacterial diversity and an asthma protective microbiota index, as well as decreases in the proportion of human-sourced bacteria, were also observed, but only in airborne dust close to the soil-seeded rug. Effects on fungal microbiota or on the bacterial and fungal loads in house dust were inconsistent.

CONCLUSIONS: We demonstrate that a simple soil-to-rug intervention can modify the bacterial microbiota in airborne particulate matter in residential homes. The introduction of specific environmental soil microbes was most pronounced closest to the source, which is relevant when targeting infant inhalation exposure. While this approach is promising, specifically in highly urbanized settings, dosage and composition of environmental microbiota additions to reach health benefits require further study. Video Abstract.},
}

Humans
Dust/analysis
*Soil Microbiology
Forests
*Bacteria/classification/genetics/isolation & purification
*Microbiota/genetics
Finland
RNA, Ribosomal, 16S/genetics
Fungi/genetics/classification/isolation & purification
Housing
Adult
Air Pollution, Indoor/analysis
Proof of Concept Study
Infant

@article {pmid41882801,
year = {2026},
author = {Langlois, A and Duplessis, M and Ronholm, J and Vincent, AT and Poulin-Laprade, D and Petri, RM},
title = {Impact of differential dietary concentrations of cobalt, manganese and zinc on gastrointestinal microbiome and resistome of lactating dairy cattle.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00554-9},
pmid = {41882801},
issn = {2524-4671},
}

@article {pmid41882807,
year = {2026},
author = {McGovern, KC and Silverman, JD},
title = {Scale reliant mixed effects models enhance microbiome data analysis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02377-x},
pmid = {41882807},
issn = {2049-2618},
support = {R01GM148972-01/GM/NIGMS NIH HHS/United States ; R01GM148972-01/GM/NIGMS NIH HHS/United States ; },
abstract = {Linear models, including those used for differential abundance analyses, are frequently used in microbiome research to assess how experimental conditions (e.g., disease state or age) affect microbial abundance. Linear mixed-effects models (MEMs) extend linear models to accommodate complex designs, such as longitudinal sampling or hierarchical study structures. However, when applied to microbiome data, existing MEM approaches suffer from high false positive and false negative rates because sequence counts are compositional - they reflect relative rather than absolute abundances. Current methods attempt to overcome this limitation through normalization, but these approaches rely on strong, often unrealistic assumptions about the unmeasured biological scale (e.g., total microbial load). Here we introduce scale-reliant mixed-effects models (SR-MEM), which extend our earlier scale-reliant inference framework by explicitly modeling uncertainty in the unmeasured scale via user-defined probability distributions. By treating scale as a latent variable rather than fixing it through normalization, SR-MEM enables robust inference for complex experimental designs. SR-MEM can incorporate external scale measurements (e.g., flow cytometry, qPCR) or leverage scale information from independent studies to further improve inference. Across simulations and multiple real-world case studies, SR-MEM consistently controls the false discovery rate while maintaining comparable or higher power than standard approaches relying on normalization or bias correction. In reanalyses of published datasets, SR-MEM yields results that are more reproducible across studies and more consistent with known biological and pharmacological effects. SR-MEM provides a principled and practical framework for mixed-effects modeling of microbiome sequence count data in the presence of unmeasured biological scale. By avoiding normalization-based assumptions and instead propagating scale uncertainty through inference, SR-MEM improves error control and reproducibility in longitudinal and hierarchical studies. An accessible implementation is provided in the ALDEx3 R package.},
}

@article {pmid41883106,
year = {2026},
author = {Parker, G},
title = {A further piece of my mind.},
journal = {Australasian psychiatry : bulletin of Royal Australian and New Zealand College of Psychiatrists},
volume = {},
number = {},
pages = {10398562261438777},
doi = {10.1177/10398562261438777},
pmid = {41883106},
issn = {1440-1665},
abstract = {At the conclusion of my academic career, I was privileged when the University of New South Wales convened a Festschrift. This paper captures a number of themes addressed in my presentation at the Festschrift. I overview a long personal focus on models, involving service delivery, diagnostic criteria and management of psychiatric conditions. I also detail a personal 'triple M' model underlying many research studies taken over my career and composed of modelling, measuring and management phases, optimally logically linked. I also argue for the melding of implicit thinking (or 'gut instinct') and explicit thinking in psychiatric research and practice. While my research time has largely concluded, I suggest that psychiatric theorizing and management may well have a new paradigm in play involving the gut microbiome.},
}

@article {pmid41883130,
year = {2026},
author = {Kuo, M and Lê Cao, KA and Kodikara, S and Mao, J and Sankaran, K},
title = {Phylobar: an R package for multiresolution compositional barplots in omics studies.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag151},
pmid = {41883130},
issn = {1367-4811},
abstract = {SUMMARY: Stacked barplots, though widely used in microbiome studies, can obscure important patterns in microbiome data. They omit rare taxa and can mask shifts that emerge at finer taxonomic levels. To address this issue, we introduce phylobar, an R package that interactively links stacked barplots with overview phylogenetic or taxonomic hierarchies. The interface allows users to collapse or expand subtrees, paint color palettes interactively, and search for specific taxa. This allows comparison across taxonomic resolutions that are hidden in static overviews. phylobar works with any omics data with hierarchical organization, including cell type hierarchies, as we demonstrate in a case study of immune cell composition in COVID-19 patients.

phylobar is available as an R package on GitHub. It uses the htmlwidgets library to link interactive D3 visualizations with R. The interactive plots can be embedded within R Markdown or Quarto notebooks, and views can be exported as vector graphics files. The package is open source and documented at https://mkdiro-O.github.io/phylobar.},
}

@article {pmid41883152,
year = {2026},
author = {Zheng, Q and Zhou, Z and Li, T and Xu, J and Zhou, Y and Cui, Y and Wang, K and Wang, N and Li, M and Zhou, L and Tian, J},
title = {Charting the Evolution of Personalized Nutrition: A Comprehensive Bibliometric Survey of Global Research Landscapes and Future Trajectories.},
journal = {Nutrition research reviews},
volume = {},
number = {},
pages = {1-36},
doi = {10.1017/S0954422426100389},
pmid = {41883152},
issn = {1475-2700},
abstract = {Personalized nutrition has emerged as a revolutionary paradigm in nutritional science, shifting from traditional "one-size-fits-all" approaches to tailored dietary recommendations. We conducted a comprehensive bibliometric analysis through a systematic search strategy capturing various conceptualizations of personalized nutrition. The analysis identified 3,159 publications demonstrating three distinct phases: an inaugural phase with minimal activity, a developmental phase showing gradual growth, and a maturation phase exhibiting exponential growth. Five distinct research clusters emerged: clinical nutrition applications for special populations, nutrigenomics and personalized dietary recommendations, metabolic health and weight management, gut microbiome and functional nutrition, and precision nutrition with multi-omics integration. Temporal analysis revealed a clear evolution from genetic foundations toward microbiome research, metabolomics, and computational approaches. Citation analysis highlighted landmark studies that established individual variability in dietary responses, the gut microbiome's role in personalization, and technology-enabled intervention systems as foundational to the field. The convergence of microbiome research, metabolomics, artificial intelligence (AI), and clinical applications creates promising directions for advancing personalized nutrition science. Future research must bridge the gap between mechanistic elucidation and clinical application, leveraging AI-driven predictive models and precision delivery systems to translate biological insights into effective public health strategies.},
}

@article {pmid41883694,
year = {2026},
author = {Feigl, V and Röhberg, MZ and Masa, K and Hegedűs, H and Janek, Z and Deák, V and Fehér, C and Buda, K and Medgyes-Horváth, A},
title = {Extremophilic microbial isolates and metagenomic analysis of Greek and Hungarian bauxite residues.},
journal = {Biotechnology reports (Amsterdam, Netherlands)},
volume = {50},
number = {},
pages = {e00956},
pmid = {41883694},
issn = {2215-017X},
abstract = {Bauxite residue (BR) is an extreme environment for microorganisms. The aim of the work was to isolate extremophilic microorganisms for further biotechnological applications, such as bioleaching or waste rehabilitation. At the same time, metagenomic analysis was performed to monitor short-term changes in deposited BR. We isolated and identified alkaliphilic and extreme halotolerant strains of Nesterenkonia massiliensis, N. natronophila, Micrococcus luteus, Aspergillus iizukae, Gibellulopsis serrae, and G. nigrescens from Greek and Hungarian BRs. Most strains were siderophore producers, cellulose degraders and produced oxalic and acetic acids. Metagenomic analysis revealed a shift in the most abundant bacterial classes from the freshly produced BR during 1 month and 3 months of storage: from Gammaproteobacteria (29% relative abundance), to Actinomycetes (31%) and Gammaproteobacteria (39%), respectively. Metagenomic analysis showed the presence of Nesterenkonia species. These results highlight the diverse microbiome of BR and underscore its potential as a valuable reservoir of extremophilic microorganisms.},
}

@article {pmid41883716,
year = {2025},
author = {Abu, Y and Roy, S},
title = {Intestinal dysbiosis during pregnancy and microbiota-associated impairments in offspring.},
journal = {Frontiers in microbiomes},
volume = {4},
number = {},
pages = {1548650},
pmid = {41883716},
issn = {2813-4338},
abstract = {The maternal microbiome is increasingly being recognized as a key determinant in various neonatal health outcomes, including offspring immunity, metabolism, brain function, and behavior. While the oral, vaginal, skin, and gut microbiota are significant contributors to the offspring's postnatal gut microbial seeding, the composition and diversity of the maternal gut microbiome during pregnancy seems to be critical in shaping neonatal health outcomes, even prior to birth. Growing evidence suggests that the balance among the microbial groups in the gut and their interactions with the host are crucial for health. Dysbiotic communities in pregnancy and early in life may lead to disease processes in offspring, though the specific processes by which maternal gut microbes affect offspring gut microbial development are unknown. Here, we summarize research examining gut microbial shifts during pregnancy, and their effects on the diversity and composition of the infant microbiome and on early health outcomes. We also discuss current theories for how the maternal gastrointestinal (GI) tract influences neonatal seeding, and how probiotics during the perinatal period may affect offspring health outcomes.},
}

@article {pmid41883788,
year = {2026},
author = {Xu, X and Chen, Y and Ye, Q and Xu, B and Yan, X},
title = {Multi-omics analysis reveals maternal gut microbiota-derived short-chain fatty acids and progesterone are associated with offspring birth weight in sows.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1781673},
pmid = {41883788},
issn = {1664-302X},
abstract = {INTRODUCTION: Piglet birth weight is a key determinant of preweaning survival and subsequent growth performance, yet the role of maternal gut microbiota in relation to offspring birth weight in sows remains incompletely characterized. This study aimed to investigate the association between maternal gut microbiota in late gestation and offspring birth weight in sows.

METHODS: Fecal samples were collected from 260 Landrace × Yorkshire (LY) sows at gestation day 100, and sows were categorized into high birth weight (HBW; 1.41 ± 0.02 kg, 16.25 ± 0.25 piglets/litter, n = 59) and low birth weight (LBW; 1.07 ± 0.02 kg, 12.19 ± 0.22 piglets/litter, n = 52) groups based on the average birth weight of live-born piglets and live litter size. We performed 16S rRNA gene amplicon sequencing and fecal untargeted metabolomics, and quantified fecal short-chain fatty acids (SCFAs) and sex hormones.

RESULTS: Compared with LBW sows, HBW sows showed distinct bacterial community profiles with higher relative abundances of multiple taxa linked to SCFAs production, including Ruminococcus, Oscillibacter, Parabacteroides, and Bacteroides (p < 0.05). Untargeted metabolomics revealed a clear separation between groups and enrichment of pathways related to primary bile acid biosynthesis and steroid hormone biosynthesis in HBW sows (p < 0.05). Consistently, fecal acetate (p = 0.005), propionate (p = 0.034), isobutyrate (p = 0.007), valerate (p = 0.036), as well as progesterone (p = 0.016), were significantly higher in HBW sows, and these indices were also positively correlated with piglet birth weight. Spearman correlation analysis showed that gut bacterial taxa enriched in the HBW group were positively associated with primary bile acids and sex hormone-related metabolites, which were also positively correlated with piglet birth weight.

DISCUSSION: In conclusion, these multi-omics data indicate that higher piglet birth weight is associated with an SCFAs-enriched gut microbial ecosystem accompanied by enhanced bile acid and steroid hormone-related fecal metabolic profiles during late gestation.},
}

@article {pmid41883797,
year = {2026},
author = {Sui, C and Qiao, H},
title = {The Type VI secretion system in enteric pathogen colonization: molecular mechanisms, ecological dynamics, and therapeutic potential.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809019},
pmid = {41883797},
issn = {1664-302X},
abstract = {The Type VI Secretion System (T6SS) is a sophisticated, phage-tail-like contractile nanomachine that mediates contact-dependent protein translocation in a wide range of Gram-negative enteric pathogens. As a primary weapon for interference competition, T6SS enables pathogens like Salmonella and Vibrio cholerae to directly eliminate commensal rivals. This targeted elimination allows pathogens to dismantle microbiota-mediated colonization resistance and seize essential nutritional niches. Beyond interbacterial warfare, the system facilitates "exploitative competition" by secreting effectors for the acquisition of limited micronutrients such as iron and zinc. Furthermore, T6SS acts as a crucial virulence determinant by manipulating host cell signaling, disrupting cytoskeletal integrity, and even enhancing intestinal contractions to physically expel competitors. The expression and activity of T6SS are dynamically regulated by gastrointestinal cues, including bile salts, pH fluctuations, and quorum sensing signals, ensuring its activation is precisely timed during infection. Elucidating these multifaceted roles not only deepens our understanding of microbial ecology in the gut but also highlights T6SS as a promising target for microbiome engineering and the development of customizable, precision antimicrobial therapies.},
}

@article {pmid41883802,
year = {2026},
author = {Qiao, X and Yan, X and Dong, C and Tao, L and Aili, A and Waheed, A},
title = {Correction: From microbiome collapse to recovery: a roadmap for microbiome-informed grassland restoration under global change.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1819081},
doi = {10.3389/fmicb.2026.1819081},
pmid = {41883802},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1741287.].},
}

@article {pmid41883805,
year = {2026},
author = {Liu, F and Shi, L and Yan, S and Zhang, Y and Zhang, M and Han, T and Zhao, X and Li, Z and Niu, N},
title = {Effects of reduced nitrogen on the nifH-harboring soil microbiome in a soybean-maize strip intercropping system.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1770580},
pmid = {41883805},
issn = {1664-302X},
abstract = {INTRODUCTION: Nitrogen (N) is a core limiting factor for crop growth, with approximately 50% of global food production relying on chemical N fertilizer inputs. However, excessive N application results in N use efficiency below 40%, and unabsorbed N triggers environmental problems. Maize-soybean relay strip intercropping (MSSI) enhances vertical resource partitioning, increases land productivity, and optimizes N utilization, but its effects on nifH-marked N-fixing microbiota under reduced N input remain unclear. This study aimed to investigate the abundance and diversity of N-fixing microbiota in response to the MSSI system with reduced N application.

METHODS: A 2-year field experiment was conducted in two soil textures (sandy loam in Wuji and medium loam in Gaocheng) including three cropping systems: monocropping maize, monocropping soybean, and MSSI. To further explore the underlying mechanism, an N gradient experiment with four fertilizer rates was established in Wuji. At the maturation stage, rhizosphere soil samples were collected, and q-PCR, enzyme activity assays, and high-throughput sequencing were used to analyze N cycle-related marker genes, enzyme activities, and nifH gene abundance and diversity.

RESULTS: The MSSI system maintained maize yields comparable to monocropped maize, while soybean yields reached 60.1-69.6% of monocropped levels. MSSI significantly increased nifH gene abundance in soybean rhizosphere soil, but reduced the Chao1, Shannon, Simpson, and observed species indices of N-fixing microbiota. Specifically, MSSI decreased N-fixer diversity (Shannon: -18.2%) and richness (Chao1: -12.5%), whereas the 25% reduced N input treatment (ISN25) enhanced diversity (Shannon: +15.7%) by improving community evenness without altering species richness.

DISCUSSION: Our results demonstrate that the MSSI system significantly alters soil N fertility and the community structure of nifH-marked N-fixing bacteria. The reduced N input combined with MSSI can optimize N utilization by regulating N-fixing microbial communities, providing a theoretical basis for sustainable agricultural practices that balance food security and ecological protection.},
}

@article {pmid41883991,
year = {2026},
author = {Yang, J and Yuan, Z and Mei, S and Liu, H and Xiang, Q and Song, E},
title = {Non-Invasive Techniques for Early Detection of Oral Squamous Cell Carcinoma: A Narrative Review.},
journal = {Cancer management and research},
volume = {18},
number = {},
pages = {569352},
pmid = {41883991},
issn = {1179-1322},
abstract = {Oral squamous cell carcinoma (OSCC) is the most common malignant tumor of the oral cavity, accounting for the majority of oral cancers, and early detection is crucial for improving patient survival rates and prognosis. Traditional diagnostic methods have limitations, including invasiveness and diagnostic delays, and are insufficient for early detection and distinguishing between similar diseases. In recent years, with the rapid advancement of molecular biology and biotechnology, a variety of emerging non-invasive diagnostic approaches have provided new strategies for early screening and precise diagnosis of OSCC. This review summarizes the cutting-edge technologies in OSCC diagnosis in recent years, including biomarker-based detection (such as microRNA, circRNA, gene methylation, and salivary proteomics), oral microbiome analysis, optical imaging technologies combined with artificial intelligence, and more. These emerging methods not only offer non-invasive or minimally invasive advantages but also enable the detection of potential molecular changes in the early stages of the disease, allowing for early intervention. Despite the challenges in standardization, sensitivity, and specificity optimization that these new technologies face in clinical applications, they undoubtedly offer vast prospects for early detection and personalized treatment of OSCC. This review aims to achieve the following objectives: First, to systematically evaluate the latest research evidence on various emerging non-invasive diagnostic technologies; second, to comprehensively compare their advantages and limitations relative to traditional methods; and finally, to attempt constructing a clinical translation assessment framework for early-stage multimodal diagnostic technologies in OSCC, thereby guiding future translational strategies.},
}

@article {pmid41883995,
year = {2026},
author = {Złoch, M and Sibińska, E and Monedeiro, F and Miśta, W and Arendowski, A and Fijałkowski, P and Pietrowska, M and Mrochem-Kwarciak, J and Jędrzejewska, A and Telka, E and Karoń, K and Rabsztyn, M and Pomastowski, P and Gabryś, D},
title = {Adaptation of MALDI-TOF MS Technique for Tracking Changes in the Urinary Microbiome During and After Radiotherapy for Prostate Cancer.},
journal = {Cancer management and research},
volume = {18},
number = {},
pages = {573379},
pmid = {41883995},
issn = {1179-1322},
abstract = {PURPOSE: The urinary microbiome may influence the development of radiation-induced complications in prostate cancer. However, its dynamics during and after radiotherapy (RT) remain unclear. This study aimed to use matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to characterize and monitor urinary microbiome changes during RT for prostate cancer.

PATIENTS AND METHODS: Eighty-eight patients with prostate cancer who underwent RT were included. Midstream urine and blood samples were collected at six time points: before gold fiducial implantation (t1), at the start (t2) and end of RT (t3), and at 1, 4, and 7 months post-RT (t4-t6). Microorganisms were cultured under diverse conditions and identified by MALDI-TOF MS. Statistical analyses were used to assess the associations between microbial profiles, RT stages, and biochemical parameters in the urine and blood.

RESULTS: A total of 1773 microbial isolates were identified in 89% of urine samples, with 79% showing a polymicrobial composition. The microbiota was dominated by Staphylococcus (51.6%), Micrococcus, Enterococcus, Kocuria, and Corynebacterium. Biodiversity decreased at the end of RT but gradually recovered up to seven months post-treatment. Genera such as Actinomyces, Corynebacterium, Staphylococcus, and Streptococcus were significantly correlated with study time course, whereas the abundance of Kocuria rhizophila increased over time. Changes in microbiome composition were strongly associated with glucose levels in urine and blood.

CONCLUSION: RT triggers a dynamic response in the urinary microbiome, with an initial decline in diversity followed by progressive recolonization. Glucose levels in urine and blood significantly affect microbial composition, suggesting that metabolic factors modulate RT-related microbiome shifts. These findings highlight the interplay between RT, host metabolism, and urinary microbiota, supporting the potential value of glucose monitoring to maintain microbial balance after RT.},
}

@article {pmid41884202,
year = {2026},
author = {Kotelevets, SM},
title = {Clinical significance of a possible route of transmission of Candida and Helicobacter pylori associations in gastroduodenal pathology.},
journal = {World journal of gastrointestinal pathophysiology},
volume = {17},
number = {1},
pages = {118294},
pmid = {41884202},
issn = {2150-5330},
abstract = {Fungal and bacterial interactions are widespread in the environment. Such intra-abdominal co-infections may lead to sepsis, potentially resulting in significant mortality. Interactions between invasive fungi (Candida) and pathogenic bacteria [Helicobacter pylori (H. pylori)] appear to be particularly relevant to human infection outcomes. Co-colonization by fungi and bacteria (coinfections) remains a pressing issue among patients with gastrointestinal pathology; however, the transmission routes and pathogenic mechanisms of these microbiome interactions are not yet fully understood. Candida species are known to support the growth of certain bacteria, and studies have observed a significant increase in the colony counts of these bacteria in the presence of fungi. As an opportunistic pathogen, Candida-in association with H. pylori-may contribute to dysbiosis of the oral microflora and other regions of the gastrointestinal tract, potentially facilitating disease progression. Therefore, understanding the interactions between fungi and bacteria is essential for improving early diagnosis and treatment efficacy. Synergistic effects have been identified in the development of resistance to antifungal and antibacterial therapies. Modern treatment strategies should consider focusing on methods to disrupt this synergy, as well as on preventative measures to limit the transmission of Candida-Helicobacter associations between individuals.},
}

@article {pmid41884244,
year = {2026},
author = {Salvadori, M and Rosso, G},
title = {Gut-kidney axis: Dysbiosis and renal disease.},
journal = {World journal of nephrology},
volume = {15},
number = {1},
pages = {115357},
pmid = {41884244},
issn = {2220-6124},
abstract = {According United States renal data system the morbidity rate for chronic kidney disease (CKD) is 2.5 times than patients not affected by CKD and the mortality rate is 144.9 per 1000 persons-years. The gut microbiota is involved in uremic toxins (UTs) production. This fact was demonstrated by experiments in rats, which revealed better survival in CKD rats that were deprived of the gut microbiota. In men, UT levels are low in CKD patients without a colon. Diet may affect the gut microbiota through food additives such as prebiotics, probiotics and post biotics. Conservation processes and food processing may also affect the gut microbiota. Other factors are food quantity and composition. The gut microbiota may be the cause of UTs production and accumulation in the blood. Additionally, there is interplay among different organs such as liver, kidney and gut. Several theories have been formulated to justify the interplay between the metabolic dysfunctions. In particular, the increase of species such as Eggerthelia lenta, Fusobacterium nucleatum and Alistipes shahii leads to an increase of the aromatic amino acids degradation, and secondary bile acids and trimethyamine oxide biosynthesis in the intestine. This fact determines an increase of the levels of UT precursors such as indole, p-cresol, phenol, phenylacetaleyde, benzoic acid and trimethylamine. Recent studies document the following. The human microbiome project revealed that the gut microbiota may play an important role in both human health and diseases, including kidney disease. Recently, several studies have shown a strict correlation between the gut microbiota and CKD. Probiotics, prebiotics and synbiotics are possible therapies. Probiotics are living microorganisms that, consumed in adequate quantities, are beneficial for the patient, and act on the intestinal microbiome equilibrium. Lactobacilli and Bifidobacteria are common examples of probiotics. Prebiotics are generally fibers not absorbed by the gut, representing a selective nutrient for the microbiome already present in the gut, which favors their growth and activity. Inulin, fructo-oligosaccharides and other fibers are examples of prebiotics. The association and synergism between probiotics and prebiotics is symbiotic.},
}

@article {pmid41884347,
year = {2026},
author = {Liu, H and Li, J and Yang, K and Li, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T},
title = {Oral microbiome alterations and their association with long-term heavy metal exposure and early health effects.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2647511},
pmid = {41884347},
issn = {2000-2297},
abstract = {BACKGROUND: Long-term heavy metal exposure poses health risks, and non-invasive biomarkers for early detection are needed.

OBJECTIVE: This study investigated whether oral microbiome alterations can serve as a non-invasive indicator of long-term HMs exposure and associated early biological effects.

DESIGN: Soil, buccal mucosa, blood, and urine samples were collected from contaminated (CA) and uncontaminated (UA) areas. Soil contamination was assessed, and internal biomarkers were measured. Oral bacterial diversity was analyzed using metagenomic sequencing.

RESULTS: Severe Cd and Pb contamination was found in CA soil. Participants in CA had elevated internal Cd levels, renal impairment, and immune alterations. Oral microbiome analysis revealed decreased alpha diversity, reduced network complexity, and a shift from beneficial to pathogenic keystone taxa in CA. Functional analysis showed enrichment of stress-response pathways, suppression of metabolic pathways, and increased pathways linked to human diseases. Specific bacterial taxa correlated with internal biomarker levels.

CONCLUSIONS: There is a close association between long-term HMs exposure and reproducible, multi-faceted shifts in the oral microbiome. The oral microbiome may represent a promising, non-invasive biomarker for assessing environmental exposure and its early biological impacts.},
}

@article {pmid41884457,
year = {2026},
author = {Saeed, NK and Elbeltagi, YM and Al-Beltagi, M},
title = {Unveiling the viral dimension: The paediatric gut virome as a key modulator of gastrointestinal metabolic, and neurodevelopmental health.},
journal = {World journal of virology},
volume = {15},
number = {1},
pages = {118362},
pmid = {41884457},
issn = {2220-3249},
abstract = {Paediatric gut microbiome research has long been bacteriocentric, overlooking the extensive viral component known as the gut virome. Composed of bacteriophages, eukaryotic viruses, and endogenous viral elements, the paediatric gut virome is the most abundant and genetically diverse biological entity in the intestine. Emerging evidence indicates that the virome is a key regulator of microbial ecology, immune maturation, and systemic physiological programming during early life. This narrative review synthesizes current knowledge on the establishment, development, and functional roles of the paediatric gut virome, with emphasis on its interactions with the bacterial microbiome and host immune system. We highlight how early-life viral exposures influence mucosal immune imprinting, epithelial barrier integrity, and immune tolerance, particularly during the first 1000 days of life. Virome dysbiosis is increasingly associated with paediatric gastrointestinal disorders, including inflammatory bowel disease, necrotizing enterocolitis, celiac disease, and functional gastrointestinal disorders. Beyond the gut, the virome also contributes to metabolic regulation, type 1 diabetes risk, and gut-brain axis signaling, influencing neurodevelopment. Mechanistic pathways involving phage-mediated bacterial modulation, innate immune sensing, cytokine signaling, and metabolic intermediates are discussed, positioning the paediatric gut virome as a central regulator of gastrointestinal and systemic homeostasis.},
}

@article {pmid41885217,
year = {2026},
author = {Corbett, GA and Murphy, L and Hokey, E and Brien, MO and McEvoy, A and McDonnell, B and Hill, K and Davis, A and Wilson, Z and Callanan, S and Luethe, L and Corcoran, S and McAuliffe, FM},
title = {Research on Preterm Birth Prevention: The Participant Experience.},
journal = {The Australian & New Zealand journal of obstetrics & gynaecology},
volume = {66},
number = {2},
pages = {e70116},
pmid = {41885217},
issn = {1479-828X},
support = {22/FFP-A/10302/SFI_/Science Foundation Ireland/Ireland ; //National Maternity Hospital Foundation/ ; },
mesh = {Humans ; Female ; *Premature Birth/prevention & control ; Pregnancy ; Prospective Studies ; Adult ; *Patient Satisfaction ; Motivation ; Surveys and Questionnaires ; Young Adult ; *Patient Selection ; },
abstract = {BACKGROUND: Research on spontaneous preterm birth (sPTB) is deeply important to the patients it serves. There is an absence of the patient's voice on the experience of research participation.

MATERIALS/METHODS: This prospective mixed-method study examined the experience of participants of a preterm birth research study. Recruited patients had significant risk factors for spontaneous preterm birth and were offered enrolment in a preterm birth study. Participants enrolled in early pregnancy and continued participation until 6 weeks postpartum. At the postnatal visit, they completed a survey on their experience of participation. Responses were analysed using reflexive thematic analysis.

RESULTS: In total, 112 women completed the study participation survey. Motivations for recruitment included the altruistic goal of protecting other women and families from spontaneous preterm birth (54.5%, 61/112) and interest in the scientific rationale of the study rooted in the microbiome (10.7%, 12/112). 91.0% enjoyed participating in the study. Participant satisfaction with enrolment related to perception of improved clinical care (26.8%, 30/112), continuity of care with the research team (20.5%, 23/112), perceived improved clinical outcome they attributed to study participation (9.8%, 11/112) and symptom benefit from the intervention (1/8%, 2/112).

CONCLUSIONS: Women at risk of spontaneous preterm birth were motivated for study participation by the goal of protecting other women and families from preterm birth. Participant satisfaction related to perceived improved clinical care and continuity of care. Participants had a strong appetite for results dissemination. These findings highlight the willingness of patients to participate in research, even in the setting of a pregnancy at risk of preterm birth.},
}

Humans
Female
*Premature Birth/prevention & control
Pregnancy
Prospective Studies
Adult
*Patient Satisfaction
Motivation
Surveys and Questionnaires
Young Adult
*Patient Selection

@article {pmid41885274,
year = {2026},
author = {Belančić, A and Fajkić, A and Wah Lam, Y and Alić, L and Labriffe, M and Pilipović, K and Džidić-Krivić, A and Yee Sy, H and Jankovic, S},
title = {Microbiome-driven PKs: addressing research gaps and shaping future directions beyond the narrative review.},
journal = {Expert opinion on drug metabolism & toxicology},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/17425255.2026.2650187},
pmid = {41885274},
issn = {1744-7607},
}

@article {pmid41885500,
year = {2026},
author = {Coster, D and Margalit, T and Ben-Ami, R and Boursi, B and Shamir, R},
title = {Demography-dependent variability in the human tumor mycobiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0231025},
doi = {10.1128/spectrum.02310-25},
pmid = {41885500},
issn = {2165-0497},
abstract = {UNLABELLED: Recent studies have shown that the tumor mycobiome may have prognostic and diagnostic significance in cancer patients. We aimed to gain a better understanding of how patient characteristics (age, sex, body mass index [BMI], and race) influence the composition of the tumor mycobiome, using the data of these studies. We first tested the data in view of recent critiques of tumor microbiome data processing procedures and concluded that the batch correction and transformation used on it may produce false signals. Instead, we explored 14 combinations of data transformation and batch correction methods on data of 224 fungal species across 13 cancer types. Propensity scores were utilized to adjust for potential confounders such as histological type and tumor stage. To minimize false outcomes, we identified as positive results only those fungi species that showed significant difference in abundance across a demographic factor within a particular cancer type, using data normalized according to all 14 combinations. We observed significant differences in 24 fungal species abundance within tumors for certain demographic characteristics. A total of 20 of these differences were among races in specific cancers. The findings indicate that there are intricate interactions between the mycobiome, cancer type, and patient demographics. Our study highlights the need to account for race in order to understand the role of the mycobiome in cancer development and treatment response. The study also underscores the importance of data processing techniques.

IMPORTANCE: This study analyzes the demographic-dependent variability of the intratumor mycobiome, providing a novel understanding of fungal abundance across different cancer types and patient demographics. By analyzing over 5,000 tumor samples from The Cancer Genome Atlas, the research identified 24 fungal species with significant abundance variations linked to demographic factors such as race, age, sex, and body mass index. These findings underscore the complexity of the tumor microenvironment and the importance of accounting for demographic diversity in cancer research. The study emphasizes the necessity of using robust data normalization and batch correction techniques to avoid spurious associations in order to ensure the reliability of mycobiome analysis. This work highlights the mycobiome as a new frontier in precision oncology and paves the way for future personalized cancer diagnostics and treatments that account for the influence of demographic factors on tumor biology.},
}

@article {pmid41885558,
year = {2026},
author = {Chen, K and Lin, X and Wei, X and Yin, Y and Ye, M and Yang, S},
title = {Divergence in the tomato rhizosphere microbial community structure driven by three soil types.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0303125},
doi = {10.1128/spectrum.03031-25},
pmid = {41885558},
issn = {2165-0497},
abstract = {UNLABELLED: Loess, calcareous, and laterite soils are common in Guangxi, southern China, where tomatoes are widely cultivated. To understand how these soil types affect tomato growth and the associated microbial communities, we analyzed soil fertility and the rhizosphere microbiome. Tomatoes in calcareous soil exhibited higher β-glucosidase activity and microbial biomass carbon, whereas those in laterite soil showed increased acid phosphatase activity and microbial biomass phosphorus. Actinobacteriota, Proteobacteria, and Acidobacteriota were the dominant bacterial phyla across all soils, while Ascomycota and Basidiomycota predominated among fungi. Each soil type hosted distinct microbial communities: loess was enriched with the bacterial genera Ramlibacter and Bradyrhizobium and the fungus Alternaria; calcareous soil favored the bacterium Rubrobacter and the fungus Fusarium, and laterite supported bacteria such as Bacillus and Sphingobium, along with the fungus Curvularia. Given its higher phosphorus availability and the presence of beneficial microbes like Bacillus, laterite soil appears to provide a more favorable environment for tomato cultivation compared to loess and calcareous soils.

IMPORTANCE: Soil type is a critical but often overlooked factor influencing tomato productivity in southern China, where diverse soils such as loess, calcareous soil, and laterite are extensively cultivated. Understanding how these soils shape rhizosphere microbial communities and soil nutrient dynamics is essential for improving crop performance. This study provides the first comparative assessment of tomato-associated microbiomes across these major soil types in Guangxi. Our findings reveal that each soil fosters distinct microbial assemblages and enzyme activities, with laterite particularly enriched in beneficial taxa such as Bacillus and associated with enhanced phosphorus availability. These insights highlight the importance of soil-specific microbial processes in supporting tomato growth and offer a scientific basis for selecting and managing soils to optimize productivity. The results also contribute to broader efforts to harness rhizosphere microbiomes for sustainable agricultural improvement.},
}

@article {pmid41885716,
year = {2026},
author = {Xu, H and Yang, H and Shi, Y and Hu, X and Zhang, L and Li, P and Ma, Y and Yang, T and Xu, Y and Dong, C and Shen, Q},
title = {Genotype-Dependent Rhizosphere Microbiome Assembly Improves Potassium Use Efficiency in Pear Rootstocks Under Low Potassium Stress.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70499},
pmid = {41885716},
issn = {1365-3040},
support = {32272802//National Science Foundation of China/ ; CARS-28-10//China Agriculture Research System/ ; },
abstract = {Potassium (K) is a vital nutrient for fruit quality in pears (Pyrus spp.), and rhizosphere microbes play a critical role in enhancing plant K uptake and utilization. To investigate the genotype-dependent influences of the rhizosphere microbiome on potassium use efficiency (KUE) in pears, we compared two rootstocks with contrasting KUE (Pyrus betulaefolia and Pyrus ussuriensis) using integrated pot and long-term field experiments, 16S rRNA amplicon sequencing, and metagenomic analyses. Synthetic community (SynCom) inoculation and transcriptome profiling were employed to elucidate the mechanisms underlying enhanced K acquisition. Under low-K conditions, P. betulaefolia recruited distinct microbial communities, which significantly improved K accumulation by upregulating genes (e.g., ATP1A, kdPB, and COG3158) associated with K transport and homoeostasis. Field trials further confirmed that P. betulaefolia-grafted trees sustained higher Bacillaceae abundance, superior fruit quality, and elevated K content than P. ussuriensis under K-deficient conditions. SynComs constructed from five Bacillaceae strains enhanced low-K tolerance by promoting root metabolic activity, stimulating root hair development, modulating K[+] transporter (e.g., NRT2.4) expression, and activating calcium-dependent signalling pathways. Inoculation with SynComs led to substantial improvements under K limitation, including a 105.86% increase in plant biomass, a 164.99% increase in K accumulation, and a 125.91% enhancement in the aboveground K utilisation index. These findings reveal that genotype-driven enrichment of Bacillaceae-dominated microbiomes significantly enhances pear KUE, offering mechanistic insights to guide the development of microbiome-based bioinoculants and breeding of "microbiome-responsive" rootstocks for sustainable fruit production under K-limiting conditions.},
}

@article {pmid41885826,
year = {2026},
author = {Hervé, V and Lambourdière, J and René-Trouillefou, M and Lopez, PJ},
title = {Patterns of microbial diversity in three aquatic ecosystems of a Caribbean island.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag031},
pmid = {41885826},
issn = {1574-6941},
abstract = {The functioning of various aquatic ecosystems is greatly influenced by the composition of their microbial communities. However, the prokaryotic and eukaryotic organisms present in the microbiome remain to be characterized in the waters of various tropical islands. Here, we used DNA metabarcoding to assess differences in the richness and abundance of prokaryotic and eukaryotic microbial communities in coastal, mangrove, and urban surface waters in Guadeloupe (French West Indies). We found that turnover was an important driving force in these three compartments, and that the urban compartment was the most diverse. We identified 119 prokaryotic and 80 eukaryotic OTUs with differential abundance between these three compartments. Furthermore, functional predictions revealed the importance of photosynthetic organisms (including Bacillariophyceae, Chrysophyceae, Chlorophyceae and Cyanobacteria) in the three compartments, and an enrichment of urban waters in chemoheterotrophic prokaryotes and eukaryotic consumers. Interestingly, we detected several putative harmful algal bloom taxa never before described in Guadeloupe. By cataloging the taxa restricted to particular water bodies, this inventory will facilitate analyses of the long-term effects of urbanization and industrialization on the evolution of microbial assemblages in Guadeloupe.},
}

@article {pmid41885829,
year = {2026},
author = {Lewandowski, R},
title = {The gut microbiome as a rainforest: probiotic colonization resistance, functional effects, and next-generation strategies.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag035},
pmid = {41885829},
issn = {1574-6968},
abstract = {Does taking probiotics really matter? The idea is enticing. Swallow a capsule, add helpful microbes, support immunity, and strengthen the gut. Yet the microbiome is not a vacant landscape waiting for reinforcements. It is a densely woven ecosystem that behaves like an old-growth rainforest. Every niche is filled, every interaction balanced through biochemical negotiation, and any newcomer must face strong colonization resistance. With such a fortified system, what impact can a probiotic truly make? Most strains pass through the adult gut without becoming permanent residents. Still, they are not biologically inconsequential. During transit, they can influence epithelial barrier integrity, alter short-chain fatty acid and bile acid profiles, modulate immune signaling, and participate in cross-feeding interactions that reshape metabolic activity. These effects are best understood as functional ripples rather than structural reconfiguration. Accordingly, probiotic efficacy often reflects transient biochemical and host-microbe interactions, although the balance between transient activity and durable colonization depends on strain and formulation, dosing duration, host factors, and the baseline microbiome ecosystem, including recent disturbances such as antibiotics. Probiotic efficacy should therefore be evaluated using outcomes aligned with the intended mechanism, prioritizing clinical endpoints and biomarkers, supported by complementary compositional and functional microbiome readouts.},
}

@article {pmid41885920,
year = {2026},
author = {Wang, J and Zhang, J and Wang, J and Lu, D and Lai, S and Wang, X},
title = {Differences in gut microbiota and faecal metabolomics characteristics in preterm infants with feeding intolerance.},
journal = {Journal of medical microbiology},
volume = {75},
number = {3},
pages = {},
pmid = {41885920},
issn = {1473-5644},
mesh = {Humans ; *Infant, Premature ; Infant, Newborn ; Female ; *Feces/microbiology/chemistry ; *Gastrointestinal Microbiome ; Male ; Metabolomics ; Biomarkers/analysis ; Metabolome ; Bacteria/classification/isolation & purification/genetics ; *Food Intolerance/microbiology/diagnosis ; },
abstract = {Introduction. Feeding intolerance (FI) is one of the most common clinical issues in preterm infants, and there are currently no internationally unified diagnostic criteria.Gap Statement. Screening valuable biomarkers and evaluating their diagnostic value for FI in preterm infants is of great significance.Aim. This study aimed to identify and assess diagnostic biomarkers for feeding intolerance in preterm infants.Methodology. This study included clinical data from 49 preterm infants admitted to a tertiary maternal and child health hospital in Zhejiang's coastal region (January to June 2024). Based on feeding assessments at day 21 postpartum recorded in electronic medical records, infants were divided into feeding-tolerant (FT, n=34) and feeding-intolerant (FI, n=15) groups. Patient data analysis incorporated maternal age, gestational age, parity, antibiotic use, pregnancy complications and neonatal factors (birth weight, Apgar scores, delivery/feeding methods, vomiting, abdominal distension, gastric residuals, kangaroo care and enema use). Faecal samples underwent microbiome and metabolomic profiling to identify diagnostic biomarkers.Results. Baseline data showed no significant differences in maternal-infant characteristics between groups (P>0.05). Dynamic monitoring of feeding tolerance in 21-day-old preterm infants revealed that the incidence of vomiting, abdominal distension, abnormal intestinal morphology and gastric residual volume >30% or >2 ml kg[-1] was significantly higher in the FI group than in the FT group (P<0.001), whereas there was no significant difference in the frequency of nasogastric feeding between the two groups (P>0.05). Microbial analysis revealed enrichment of Escherichia (10.92%) and Klebsiella (6.88%) in FT infants, while FI infants specifically harboured increased Clostridium_P (3.93%), Burkholderia (4.06%) and Limosilactobacillus (4.94%). Metabolomic profiling identified significant pathway differences in ATP-binding cassette transporters (ABC transporters), carbohydrate digestion/absorption and propanoate metabolism. The receiver operating characteristic (ROC) analyses showed that metabolites arginine-proline (Arg-Pro, AUC=0.920), glutamic acid-arginine (Glu-Arg, AUC=0.873), lactaldehyde (AUC=0.900) and genera Clostridium_P (AUC=0.947), Escherichia (AUC=0.765), Staphylococcus (AUC=0.733) and Bifidobacterium (AUC=0.851) exhibited robust predictive value for FI.Conclusion. Our study demonstrates that bacterial genera such as Staphylococcus, Clostridium_P, Bifidobacterium and Escherichia in the gut microbiota, along with metabolites including Arg-Pro, Glu-Arg and lactaldehyde identified in metabolomics, can serve as diagnostic criteria for feeding tolerance in preterm infants. Klebsiella shows a certain degree of diagnostic efficacy but falls into the category of 'low accuracy', requiring comprehensive evaluation considering the research background, sample characteristics and clinical context.},
}

Humans
*Infant, Premature
Infant, Newborn
Female
*Feces/microbiology/chemistry
*Gastrointestinal Microbiome
Male
Metabolomics
Biomarkers/analysis
Metabolome
Bacteria/classification/isolation & purification/genetics
*Food Intolerance/microbiology/diagnosis

@article {pmid41886413,
year = {2026},
author = {Montes-Carreto, LM and Arellano-Hernández, HD and Guerrero, JA and Martinez-Romero, E},
title = {Comparative fecal microbiome analysis of the endangered Volcano rabbit (Romerolagus diazi) reveals a microbial core in contrasting habitats of Central Mexico.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0343260},
pmid = {41886413},
issn = {1932-6203},
mesh = {Animals ; Rabbits/microbiology ; Mexico ; *Feces/microbiology ; *Endangered Species ; *Ecosystem ; Bacteria/genetics/classification/isolation & purification ; *Microbiota ; Archaea/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Fungi/genetics/classification/isolation & purification ; },
abstract = {Herbivores show a larger microbial diversity in their guts than omnivores or carnivores. Bacterial symbionts expand the host digestion capacity by fermenting cellulose and hemicellulose. Comparisons between populations in different distribution areas can reveal how environmental conditions affect microbiota, helping to design conservation strategies. The Volcano rabbit (Romerolagus diazi) is the smallest lagomorph in Mexico. It is classified as endangered by Mexican legislation and as critically endangered by the IUCN, in the Red List. Here we extend our previous microbiome study to another region in Mexico from a high site near an active volcano, the Popocatépetl. In both areas, the most abundant bacterial genera included Acinetobacter, Enterobacter, Streptomyces, Bacteroides, Pseudomonas, Janthinobacterium, Flavobacterium, and Duganella. Among Archaea, Methanosarcina, Halobaculum, Thermococcus, Halorubrum, and Methanobrevibacter were prevalent. Fungal genera such as Fusarium, Ascochyta, Pyricularia, Aspergillus, and Colletotrichum were also identified. Potential functions were identified including carbohydrate, amino acid and nucleotide metabolism. The most abundant enzymes were transferases, hydrolases and oxidoreductases. The PERMANOVA test between areas for Bacteria (p = 0.26), Archaea (p = 0.21) and Fungi (p = 0.48) indicated no significant differences in the taxonomic composition or coding sequences (p = 0.5), although there were differences in relative abundances. Additionally, for archaea, genera that had not been reported previously in Volcano rabbit fecal microbiomes such as Halomicroarcula, Halomicrobium, Haloplanus, and Sulfolobus were identified, with Sulfolobus found exclusive in Izta-Popo. The Volcano rabbit fecal microbiome showed unique bacterial and archaeal profiles. Overall, these microbial communities are likely to contribute to the digestion of plant fibers, phenolic compounds, and other dietary components, underscoring their importance for the health and conservation of these endangered species.},
}

Animals
Rabbits/microbiology
Mexico
*Feces/microbiology
*Endangered Species
*Ecosystem
Bacteria/genetics/classification/isolation & purification
*Microbiota
Archaea/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
Fungi/genetics/classification/isolation & purification

@article {pmid41886872,
year = {2026},
author = {Roger, M and Le Monier, P and Bruzac, S and Noël, C and Akcha, F and Bertucci, A},
title = {Tissue differences and changes in the resident bacteriome composition of the Pacific oyster Magallana gigas in relation to trace metal contamination.},
journal = {Ecotoxicology and environmental safety},
volume = {314},
number = {},
pages = {120064},
doi = {10.1016/j.ecoenv.2026.120064},
pmid = {41886872},
issn = {1090-2414},
abstract = {Symbiotic microbial communities associated with marine organisms may contribute to the biology and the local adaptation of their host, playing a crucial role in the health of the holobiont. The role of the microbiome of bivalves remains poorly understood despite their high economic value and use as sentinel species to biomonitor water quality. In this study, we used 16S (V3-V4) rRNA amplicon sequencing to investigate the resident bacterial communities associated with the digestive gland, the mantle and the gills of Pacific oysters. We analysed oysters collected from six sites along the French coastline to investigate whether chemical stressors can shape the oyster bacteriome in natural conditions. The resident bacteriome of oysters was dominated by the phyla Proteobacteria, Spirochaetota, Firmicutes and Actinobacteriota with some differences between organs. Chemical analysis revealed differences in trace metal concentration among sites and organs. Statistical analysis showed strong positive or negative correlations between the concentration in some metals and bacterial diversity (ASVs abundance). We identified 316 ASVs associated with As, Cr, Cu, Mn and Zn concentrations in digestive glands, 99 ASVs associated with Ni concentrations in gills, and 116 ASVs associated with Cu concentrations in the mantle. Metal contamination mostly affected members of the core microbiota of oysters such as genera Colwellia and Psychrobacter, evidencing the crucial role of marine pollutants, particularly trace metals, as key parameters of the interactions between hosts and their bacterial partners.},
}

@article {pmid41886887,
year = {2026},
author = {Kumar, V and Shukla, R and Gangani, S and Joseph, R and Jain, S and Yadav, H},
title = {Epigenetics and the gut-brain axis: Insights into DNA methylation, aging, and Alzheimer disease.},
journal = {The Journal of pharmacology and experimental therapeutics},
volume = {393},
number = {4},
pages = {104299},
doi = {10.1016/j.jpet.2026.104299},
pmid = {41886887},
issn = {1521-0103},
abstract = {Alzheimer disease (AD) and aging have similar molecular mechanisms that are affected by genetic as well as environmental variables. Based on current research, gut microbiomes contribute to age-specific biological processes and play an essential role in maintaining host homeostasis. Several molecular processes, including the host DNA methylation mechanism, are affected by microbially derived metabolites such as short-chain fatty acids, folate, and choline. This interaction establishes a mechanistic causal relationship that further shapes gene expression, inflammatory balance, and neuronal function in aging and related diseases. In this review, we looked at recent research showing how gut dysbiosis and its associated metabolites impact DNA methylation, which consequently contributes to disease progression in AD and aging. We also talked about how the DNA clock and age-associated methylation drifts can be used for forecasting biological aging. In addition, we discussed recent findings on how microbial and diet-based interventions may restore the methylation patterns that might be involved in aging and neurodegenerative processes. We also implicated the possible use of methylation-based biomarkers in the diagnosis of AD. Additionally, we have also explored the potential therapeutic benefits of using microbiome modulators, dietary modifications, and pharmacological interventions. Next, we highlighted the importance of multiomics and longitudinal studies to build the causal connection underlying methylation dynamics and microbial changes in neurodegeneration. Altogether, this review highlights the potential of the microbiome-methylation axis as an approach to understanding aging and establishing precision strategies to maintain cognitive health. SIGNIFICANCE STATEMENT: This review explores the interplay between DNA methylation and gut microbiota in aging and Alzheimer's disease. It highlights the gut-brain axis and summarizes recent findings on microbiome-driven epigenetic changes and metabolites influencing cognitive decline. The review also emphasizes microbiome-targeted therapeutic strategies for age-related disorders. Overall, it integrates current molecular insights with emerging approaches for the detection, prevention, and management of Alzheimer's disease and associated cognitive challenges.},
}

@article {pmid41887041,
year = {2026},
author = {Huang, J and Fu, Z and Zhou, S and Hu, J and Yu, G and Qin, C and Ma, Z},
title = {Metagenomic insights into sex-specific taxonomic and functional differentiation of epidermal mucus microbiota in the humphead wrasse (Cheilinus undulatus).},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {59},
number = {},
pages = {101810},
doi = {10.1016/j.cbd.2026.101810},
pmid = {41887041},
issn = {1878-0407},
abstract = {The humphead wrasse (Cheilinus undulatus) is a large coral reef fish of high ecological and economic importance, whose epidermal mucus microbiota plays a critical role in host defense, immune regulation, and environmental adaptation. However, the influence of host sex on the structure and functional potential of epidermal mucus microbiota remains poorly understood. In this study, epidermal mucus samples were collected from sexually mature female and male humphead wrasse, and shotgun metagenomic sequencing was performed to systematically compare microbial community composition, diversity, and functional gene profiles between sexes. The results showed no significant differences in alpha diversity (ACE and Shannon indices) between female (FM) and male (M) groups. In contrast, beta diversity analyses and hierarchical clustering revealed clear sex-related separation of microbial community structures at both phylum and genus levels. Although both groups were dominated by Pseudomonadota, Bacillota, Bacteroidota, and Verrucomicrobiota, their relative abundances and sex-specific taxa differed markedly. Functional annotation based on KEGG indicated that female-specific taxa harbored a greater number and broader range of functional genes, mainly associated with carbohydrate, amino acid, energy, and cofactor metabolism, as well as disease-related pathways. Furthermore, Comprehensive Antibiotic Resistance Database (CARD) and the Virulence Factor Database (VFDB) analyses revealed that female-specific taxa exhibited higher diversity of antibiotic resistance genes and virulence factors, whereas male-specific taxa showed a more limited functional repertoire, primarily related to basic metabolism and biofilm formation. Overall, this study demonstrates pronounced sex-associated differences in both the taxonomic composition and functional potential of epidermal mucus microbiota in humphead wrasse, highlighting the importance of host sex in shaping host-microbiome interactions and providing new insights for health management and conservation of coral reef fishes.},
}

@article {pmid41887058,
year = {2026},
author = {Mayr, C and Dankó, E and Antonielli, L and Kostić, T},
title = {Influence of cabbage farming practice and potato peel addition on the endpoint microbial community in sauerkraut fermentation.},
journal = {International journal of food microbiology},
volume = {454},
number = {},
pages = {111742},
doi = {10.1016/j.ijfoodmicro.2026.111742},
pmid = {41887058},
issn = {1879-3460},
abstract = {The microbial dynamics and lactic acid bacteria (LAB) content of sauerkraut are influenced by various factors. Understanding microbial variations and pathogen-exclusion capacity in spontaneously fermented vegetables is essential for reducing risks in home-style fermentation systems. We investigated the effects of conventional versus organic farming practices and potato peel addition on LAB counts and microbial diversity at days 14 and 21 of fermentation. We tested the susceptibility of different fermentations to the proliferation of a human bacterial pathogen modelled by a surrogate challenge test with Listeria innocua. We monitored the presence of Leuconostoc mesenteroides and Lactiplantibacillus plantarum at different fermentation stages. LAB counts were slightly boosted by potato peel addition until day 14. Day 21 sauerkraut samples with added potato peel sourced from conventional farming practice resulted in significantly higher LAB counts than organic samples. PERMANOVA based on Bray-Curtis dissimilarity indicated dissimilar microbiota between organic and conventional sauerkraut, while potato peel addition showed no significant effect. The presence of distinct taxa in certain samples highlights the strong influence of raw material microbiota on the final fermented product. Cultivation-based analysis combined with qPCR assessment revealed a decline of L. mesenteroides and a progressive increase of L. plantarum during sauerkraut fermentation. The contrasting amplicon sequencing results showing the presence of L. mesenteroides at the later fermentation stage underscore the need to combine cultivation with sequencing to accurately track community succession. The surrogate pathogen challenge test showed no recovery of L. innocua.},
}

@article {pmid41887326,
year = {2026},
author = {Alves, ED and Carpena, MX and Bierhals, IO and Matijasevich, A and Barros, AJD and Santos, IS and López-Dominguez, L and Comelli, EM and Bandsma, RHJ and Blum-Menezes, D and Borges, MC and Tovo-Rodrigues, L},
title = {Breastfeeding, early-life feeding practices and adolescent gut microbiota: long-term associations in a birth cohort.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {103101},
doi = {10.1016/j.clnesp.2026.103101},
pmid = {41887326},
issn = {2405-4577},
abstract = {BACKGROUND & AIMS: Breastfeeding plays a critical role in shaping the infant gut microbiome by promoting the growth of beneficial bacteria essential for intestinal health, however, its long-term impact remains poorly elucidated. This study investigates the association between breastfeeding practices and gut microbiota diversity and composition in adolescence.

METHODS: We analyzed data from 350 participants in the birth cohort, with breastfeeding history at three months as the primary exposure. Additional exposures included breastfeeding duration, and timing and type of complementary food introduction. Gut microbiota was assessed at 12 years through 16S rRNA gene sequencing (V3-V4 region) of DNA from fecal samples. Alpha (Chao1, Simpson, Shannon) and beta diversity (weighted and unweighted UniFrac) metrics, alongside relative taxonomic abundances, were evaluated as primary outcomes.

RESULTS: No significant differences were observed in microbial diversity between exclusive breastfed (EBF), mixed feeding and non-breastfed groups at three months. However, relative abundance analyses suggested associations between breastfeeding patterns at three months and specific bacterial taxa. Non-breastfed children exhibited a higher relative abundance of Ruminococcus (β = 0.439; 95% CI: 0.11-0.74) compared to EBF, while those who had mixed breastfeeding showed an association with a higher probability of Alloprevotella detection at age 12 (OR = 2.82; CI 95% 1.14; 6.95). These associations did not remain significant after multiple testing correction. Early introduction of liquids (<6 months) was associated with lower Ruminococcus abundance (β = -0.40; 95% CI: 0.72-0.07), whereas early introduction of semi-solid foods was linked to lower odds of Alloprevotella presence (OR = 0.35; 95% CI: 0.15-0.82).

CONCLUSIONS: Although breastfeeding and early dietary practices may exert lasting effects on adolescent gut microbiota composition, these associations appear modest. Further research with larger cohorts and multi-omics approaches is needed to clarify the underlying mechanisms and clinical implications.},
}

@article {pmid41887353,
year = {2026},
author = {Amalraj, S and Karthick, V and Thamarai, R and Suganya, M},
title = {Exposome-induced dysregulation of glycemic homeostasis: Emerging biomarkers for diabetes risk and progression.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {397},
number = {},
pages = {128012},
doi = {10.1016/j.envpol.2026.128012},
pmid = {41887353},
issn = {1873-6424},
abstract = {Environmental exposures throughout life profoundly influence the development and progression of diabetes mellitus. The exposome, representing the totality of environmental exposures from conception to adulthood, interacts with genetic and metabolic pathways, leaving measurable signatures termed biomarkers. These biomarkers encompass indicators of exposure, biological effect, and susceptibility, providing mechanistic insights into glycemic regulation and disease progression. This review synthesizes current evidence on exposome-linked biomarkers in both Type 1 and Type 2 diabetes, highlighting chemical pollutants, dietary patterns, lifestyle factors, psychosocial stressors, and microbiome-derived metabolites as critical contributors to glycemic dysregulation. Advanced omics technologies, including metabolomics, proteomics, transcriptomics, and epigenomics, have facilitated the identification of these biomarkers, enabling a holistic understanding of environmental impacts on diabetes. Integrating exposomics with biomarker research offers potential for early detection, risk stratification, personalized interventions, and improved management of glycemic control. Knowledge gaps remain, particularly in longitudinal exposure mapping, causal inference, and translation into clinical practice. This review provides a comprehensive framework for understanding how environmental imprints shape metabolic health and identifies future directions for research in precision diabetes medicine.},
}

@article {pmid41887418,
year = {2026},
author = {Zhang, M and Liao, X and Wang, F and Shen, H and Mao, S and Xu, Z},
title = {Decoding skatole: A comprehensive review on biosynthesis, metabolism, and mitigation in livestock production.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134491},
doi = {10.1016/j.biortech.2026.134491},
pmid = {41887418},
issn = {1873-2976},
abstract = {Skatole (3-methylindole) is a potent malodorous compound generated through the microbial degradation of tryptophan in livestock production. Because of its extremely low odor threshold and biological toxicity, skatole is a critical contributor to odor pollution in animal farming systems and poses risks to animal health, product quality, and the surrounding environment. This review synthesizes advances in skatole biosynthesis, absorption and metabolism, migration and regulation mechanisms of skatole, as well as its respective impacts on humans and livestock, with particular emphasis on its dual role as both a pollutant and a potential biomarker of gastrointestinal health. This review systematically examine drivers of skatole formation, including dietary protein, gut microbiota, and environmental conditions. In addition, emerging mitigation strategies, such as nutritional regulation, microbiota-targeted interventions and bioremediation are evaluated. By integrating mechanistic insights with practical applications, this review identifies research gaps to support low-odor, sustainable livestock production.},
}

@article {pmid41887515,
year = {2026},
author = {Zhao, X and Song, L and Li, N and Zhang, J and Zhang, Y and Zhao, S and Zheng, N and Zang, C and Wang, J},
title = {Comparative analysis of fecal microbiome, metabolome, and serum metabolome in cows with different milk urea nitrogen phenotypes.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27914},
pmid = {41887515},
issn = {1525-3198},
abstract = {Milk urea nitrogen (MUN), the primary form of non-protein nitrogen (N) in milk, is an indirect indicator of N metabolism in dairy cows. MUN concentrations are modulated by various factors, including dietary composition, physiological status, and environmental conditions. However, the potential roles of host gut microbiota and metabolome in the development of distinct MUN phenotypes remain insufficiently elucidated. Here, we compared fecal microbiota and fecal/serum metabolomes of high-MUN (HMUN) and low-MUN (LMUN) cows (n = 7 per group) under uniform feeding management using 16S rRNA gene sequencing and LC-MS-based metabolomics. Compared with that of LMUN cows, the feces of HMUN cows exhibited relatively higher abundances of UCG-009, UCG-002, and Christensenellaceae_R-7_group and lower abundances of Succinivibrio, Lachnospiraceae_NK3A20_group, Acetitomaculum, Prevotellaceae_UCG-001, and norank_f__Bifidobacteriaceae. Metabolomic analysis revealed that HMUN cows had relatively lower levels of hydroxypropionic acid, N-myristoyl arginine, and N-eicosapentaenoyl tryptophan in feces, and reduced amounts of L-serine, linoleic acid, and butyrate in serum. KEGG pathway mapping revealed that the metabolites relatively elevated in LMUN cows were primarily involved in the β-alanine metabolism pathway. UCG-009 and Christensenellaceae_R-7_group were positively correlated with MUN, whereas Succinivibrio, Lachnospiraceae_NK3A20_group, Anaeroplasma, and Acetitomaculum were negatively correlated. These microbial taxa were also significantly associated with several fatty and amino acid metabolites, including adipic acid, undecenoic acid, dodecanedioic acid, DL-tryptophan, and L-leucine. Collectively, this study revealed certain differences in the gut microbiota and metabolome between cows with high and low MUN levels. These findings suggest that alterations in gut microbial composition and metabolic profiles may contribute to variations in MUN phenotypes and provide new insights into host factors influencing MUN metabolism in dairy cows.},
}

@article {pmid41887569,
year = {2026},
author = {Plesz, SB and Szűcs, KF and Ágg, B and Makra, N and Ligeti, B and Demeter, ZO and Adlan, LG and Liszli, P and Szabó, D and Ferdinandy, P and Zádori, ZS and Gáspár, R and Horvath, G and Kekesi, G},
title = {The impact of prebiotic supplementation in a triple-hit rat model of schizophrenia.},
journal = {Neuropharmacology},
volume = {},
number = {},
pages = {110946},
doi = {10.1016/j.neuropharm.2026.110946},
pmid = {41887569},
issn = {1873-7064},
abstract = {Schizophrenia is associated with cognitive deficits and higher stress sensitivity, potentially related to gut-brain axis disturbances, partially due to dysbiosis. To ascertain this phenomenon, we aimed to evaluate these behavioral phenotypes in association with microbiota profile in the triple-hit Wisket rat model of schizophrenia. Furthermore, as a bidirectional approach, the effects of clozapine (CLO) and/or prebiotic (galactooligosaccharide, B-GOS) treatment were also investigated. Male Wistar (control) and Wisket rats were treated for 3 weeks: CLO or its vehicle was administered intraperitoneally, while B-GOS or water was provided ad libitum in drinking bottle. The food-rewarded Ambitus test was used to assess cognition-related behaviors before and during the third week of the treatment. Afterwards, fecal samples were collected to analyse microbiota composition, and smooth muscle electromyography was performed to assess immobilization-induced stress response. B-GOS monotreatment resulted in the highest improvement in cognition-related parameters in Wisket model rats; however, it never reached the performance of control animals. Wisket animals showed higher vulnerability to immobilization-induced stress condition. This group-difference disappeared by each pharmacological treatment, with the most prominent effect of the CLO+B-GOS combination treatment. β-diversity analysis revealed an overall compositional difference of fecal microbiota between treatment groups. Several taxa associated with schizophrenia-model or treatment were significantly correlated with behavioral parameters. Consistent with clinical findings, cognitive impairment with increased stress sensitivity were highlighted in Wisket model rats. To our knowledge, this is the first study on B-GOS prebiotic in a triple-hit schizophrenia model, suggesting microbiome-targeted therapy may aid some schizophrenia-related symptoms.},
}

@article {pmid41887859,
year = {2026},
author = {Chen, J and Li, G and Liu, J and Yuan, X and Zhao, G and Yang, X and Huang, S and Zheng, Z},
title = {Comparative assessment of novel nematicide trifluenfuronate and fosthiazate on soil ecosystem: From microbial community structure to KEGG functional pathways.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {409-419},
doi = {10.1016/j.jes.2025.05.033},
pmid = {41887859},
issn = {1001-0742},
mesh = {*Soil Microbiology ; *Soil Pollutants/toxicity ; Soil/chemistry ; *Antinematodal Agents/toxicity ; Ecosystem ; *Microbiota/drug effects ; RNA, Ribosomal, 16S ; Bacteria ; Organophosphorus Compounds ; Thiazolidines ; },
abstract = {In recent years, the increasing demand for environmentally friendly pesticides in agricultural production has driven the development of novel pesticides characterized by high efficiency, low toxicity, and improved environmental compatibility. Simultaneously, greater emphasis is being placed on evaluating their impact on the soil ecosystem to ensure sustainable pesticide use and the stability of agroecosystems. In this study, we employed 16S rRNA gene high-throughput sequencing and metagenomic analysis to compare the effects of the novel nematicide trifluenfuronate and the commonly used nematicide fosthiazate on soil physicochemical properties, bacterial community structure, and metabolic functions in cucumber cultivation soils. Results showed that soil enzyme activity, microbial community structure and diversity exhibited the most significant differences on day 7 following nematicide application but stabilized by day 100. Both nematicide type and concentration were key factors influencing bacterial community structure. Compared to fosthiazate, trifluenfuronate more significantly enhanced soil bacterial community abundance while exerting fewer negative impacts on related enzyme activities and KEGG pathways. In addition, fosthiazate preferentially regulated membrane-associated efflux genes, whereas trifluenfuronate primarily interfered with the transcriptional regulation of target genes to mitigate antibiotic stress. These alterations in microbial community structure and function led to changes in soil nutrient bioavailability. This made the trifluenfuronate treatment group have higher available nitrogen and phosphorus content to supply to cucumber. This research contributes to understanding their ecological effects and paves the way for future sustainable pesticide research.},
}

*Soil Microbiology
*Soil Pollutants/toxicity
Soil/chemistry
*Antinematodal Agents/toxicity
Ecosystem
*Microbiota/drug effects
RNA, Ribosomal, 16S
Bacteria
Organophosphorus Compounds
Thiazolidines

@article {pmid41887904,
year = {2026},
author = {Jin, R and Chen, C and Zhang, J and Li, Y and Wu, Y and Wang, F and Chen, Z and Huang, T and Cheng, Q and Yu, X and Jia, P},
title = {Solid waste dumping differentially impacts soil prokaryotic, fungal, and viral communities: Insights from metagenomics.},
journal = {Journal of environmental sciences (China)},
volume = {163},
number = {},
pages = {867-879},
doi = {10.1016/j.jes.2025.10.021},
pmid = {41887904},
issn = {1001-0742},
mesh = {*Soil Microbiology ; Metagenomics ; *Microbiota ; Fungi ; *Solid Waste ; Soil/chemistry ; Soil Pollutants/analysis ; *Refuse Disposal ; Environmental Monitoring ; },
abstract = {Rapid urbanization and industrialization have dramatically increased global solid waste generation, placing immense pressure on waste management systems. In many developing countries, illegal and uncontrolled dumping remains widespread, yet its ecological impacts, particularly on soil microbial communities, are still poorly understood. To address this knowledge gap, we applied high-throughput amplicon sequencing and metagenomic profiling to analyze soil microbiomes across three categories of solid waste dumping. Our results show that solid waste dumping significantly altered both biotic and abiotic components of soil ecosystems. Soil properties shifted abruptly, with elevated pH and increased concentrations of pollutants such as petroleum hydrocarbons and fluorides. Microbial communities were extensively restructured, exhibiting both taxonomic turnover and functional adaptations. Viral communities displayed greater sensitivity to dumping-induced disturbances than prokaryotic or fungal communities. These findings provide new insights into soil microbiome responses to anthropogenic pollution and highlight taxon-specific adaptation strategies. To our knowledge, this is among the first comparative studies integrating prokaryotic, fungal, and viral responses to solid waste dumping using high-throughput molecular approaches. Our findings present a novel perspective that may guide future monitoring efforts and enhance approaches to environmental damage identification and assessment.},
}

*Soil Microbiology
Metagenomics
*Microbiota
Fungi
*Solid Waste
Soil/chemistry
Soil Pollutants/analysis
*Refuse Disposal
Environmental Monitoring

@article {pmid41887936,
year = {2026},
author = {Han, P and Seneviratne, C and Zhao, Q and Salomon, C and Li, X and Ivanovski, S},
title = {Salivary Microvesicle Methylome and Microbiome Profiles in Periodontitis: An Exploratory Study.},
journal = {Journal of clinical periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jcpe.70114},
pmid = {41887936},
issn = {1600-051X},
support = {534-2019//Australian Dental Research Foundation/ ; 2034591//National Health and Medical Research Council/ ; 82001421//National Natural Science Foundation of China/ ; },
abstract = {AIM: Salivary microvesicles (MVs) are nanosized extracellular vesicles from the host and microbiota whose cargo may mirror the biological state of their parent cells. This cross-sectional study aimed to explore the diagnostic power of host methylome and microbiome profiles of MVs in various periodontal disease states.

MATERIALS AND METHODS: This exploratory study recruited 20 healthy, 16 gingivitis and 26 stage III/IV periodontitis cases. The origins of salivary host-MVs were identified using a multiplex extracellular vesicle (EV) kit. The microbiome and host methylome profiles of MV DNA were analysed using 16S rRNA sequencing and methylated DNA immunoprecipitation sequencing (MeDIP-seq), respectively.

RESULTS: The periodontitis group showed increased CD63+, CD45+, CD29[+] and CD24[+] MV subpopulations (AUC > 0.7), along with significantly higher bacterial outer membrane vesicles (AUC > 0.89) from Treponema, Fretibacterium and Treponema denticola, compared to both healthy and gingivitis groups, as well as the non-periodontitis (combining healthy and gingivitis) group. MeDIP-seq identified 1196 differentially methylated regions across 3' UTRs, CDS, introns and intergenic regions (AUC > 0.9), distinguishing periodontitis from the other groups. These methylated genes were enriched in inflammation-related pathways, including AMP-activated protein kinase (AMPK) and Toll-like receptor 4 (TLR4) pathways.

CONCLUSION: This exploratory study found that host methylome and microbiome profiles in salivary MVs reflect periodontal disease status, and hence supports their potential as non-invasive liquid biopsy biomarkers for periodontitis.},
}

@article {pmid41887962,
year = {2026},
author = {Marjot, T},
title = {The limits of lifestyle in metabolic disease: How the microbiome shapes exercise response.},
journal = {Journal of hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhep.2026.03.007},
pmid = {41887962},
issn = {1600-0641},
}

@article {pmid41887976,
year = {2026},
author = {Kim, MJ and Sonnenberg, GF},
title = {Diet-induced death: microbiome-mediated lipid stress reduces intestinal ILC3s.},
journal = {Trends in immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.it.2026.03.002},
pmid = {41887976},
issn = {1471-4981},
abstract = {Group 3 innate lymphoid cells (ILC3s) promote gastrointestinal health, dynamically interface with diet and microbes, and become impaired during chronic inflammation or metabolic syndrome. Torrico and colleagues uncover a key pathway rapidly disrupting ILC3 homeostasis in the intestines of humans and mice following the consumption of a high-fat diet.},
}

@article {pmid41888026,
year = {2026},
author = {Song, J and Ding, M and Joyce, PWS and Pi, X and Zhang, B and Li, B},
title = {Decoding the HMO‒microbiome axis: bridging maternal milk to infant health outcomes.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2649456},
doi = {10.1080/19490976.2026.2649456},
pmid = {41888026},
issn = {1949-0984},
mesh = {Humans ; *Milk, Human/chemistry/microbiology/metabolism ; *Oligosaccharides/metabolism/chemistry ; Infant, Newborn ; *Gastrointestinal Microbiome ; Female ; *Infant Health ; Infant ; Prebiotics ; },
abstract = {Human milk oligosaccharides (HMO) are unique glycans in breast milk that critically mediate interactions between the microbiome and infant health. This review synthesizes recent advances in understanding HMOs as key connectors of maternal and neonatal microbiomes with health outcomes. HMO composition, shaped by genetic factors (e.g., Secretor/Lewis status), lactation stage, maternal diet, and health, exhibits significant structural diversity. Critically, a bidirectional relationship exists between HMOs and the maternal microbiota: the maternal microbiome influences HMO biosynthesis, while HMOs selectively shape the microbial community within breast milk. In neonates, indigestible HMOs function as prebiotics, driving the assembly of a beneficial gut microbiota dominated by Bifidobacterium. This HMO-guided microbial establishment is fundamental to infant health, conferring protection against pathogenic infections (respiratory, gastrointestinal, and urinary), reducing the risk of necrotizing enterocolitis and allergies, and promoting healthy weight regulation, neurodevelopment, and bone mineralization. The modulation of host‒microbe interactions by HMOs underpins these systemic benefits, highlighting their central role as microbial and immunological regulators. Understanding the HMO-microbiome axis provides a holistic framework for elucidating how breast milk components foster infant development and disease resilience.},
}

Humans
*Milk, Human/chemistry/microbiology/metabolism
*Oligosaccharides/metabolism/chemistry
Infant, Newborn
*Gastrointestinal Microbiome
Female
*Infant Health
Infant
Prebiotics

@article {pmid41888049,
year = {2026},
author = {Khalyfa, A and Zhen, L and Joshi, T and Gozal, D},
title = {Gut Luminal Exosomes in Young and Old Mice: Multi-Omic Characteristics and Regulation of Gut Permeability.},
journal = {Aging cell},
volume = {25},
number = {4},
pages = {e70455},
doi = {10.1111/acel.70455},
pmid = {41888049},
issn = {1474-9726},
mesh = {Animals ; *Exosomes/metabolism ; Male ; Female ; Mice ; Mice, Inbred C57BL ; Permeability ; *Aging/metabolism ; *Gastrointestinal Microbiome ; MicroRNAs/metabolism/genetics ; *Intestinal Mucosa/metabolism ; Multiomics ; },
abstract = {Aging is a multifaceted process impacting physiological, genomic, metabolic, and immune functions. This study investigates the role of luminal fecal exosomes (LFEs) in age-associated metabolic dysfunction. We analyzed LFEs from young (3-month) and old (24-month) male and female C57BL/6 mice to characterize age-related differences in exosomal proteomic and miRNA cargos. To explore interactions between LFEs and the gut microbiome, naïve young mice were gavage fed with LFEs from old donors, followed by 16S rRNA sequencing. Gut permeability in vitro and in vivo and systemic metabolic effects were assessed using ECIS, 3D microfluidic models, and insulin sensitivity assays. Bioinformatic analyses identified specific proteins and miRNAs linked to insulin resistance and barrier dysfunction. Heatmaps and principal component analysis revealed distinct differences in LFE profiles between young and old mice. Notably, LFEs from old mice impaired gut barrier integrity and metabolic function in young recipients, with reciprocal effects noted in older mice when receiving LFEs from young mice. Multi-omics profiling, including proteomics and miRNA sequencing, identified age-dependent and gender-related changes in LFE cargo, encompassing host- and GM-derived proteins and miRNAs. These age-specific profiles were associated with pathways implicated in cancer, neurobehavioral changes, and metabolic dysfunction. Our findings highlight that LFEs from old mice are enriched with proteins and miRNAs involved in insulin resistance and gut barrier disruption. Together, these findings identify gut luminal exosomes as age-dependent mediators of microbiome-host communication that contribute to intestinal barrier dysfunction and metabolic decline.},
}

Animals
*Exosomes/metabolism
Male
Female
Mice
Mice, Inbred C57BL
Permeability
*Aging/metabolism
*Gastrointestinal Microbiome
MicroRNAs/metabolism/genetics
*Intestinal Mucosa/metabolism
Multiomics

@article {pmid41888125,
year = {2026},
author = {Fu, J and Zhang, J and He, R and Dong, Q and Mao, H and Shen, W and Wu, W and Chen, X and Ma, W and Zhai, Q and Chen, L and Zhou, H and Hu, S and He, Y and Qi, C},
title = {A global metagenomic atlas of aging identifies a microbiota phase transition associated with disease risk.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00970-4},
pmid = {41888125},
issn = {2055-5008},
support = {2023A1515012538//Basic and Applied Basic Research Foundation of Guangdong Province/ ; NSFC82300623//National Natural Science Foundation of China/ ; NSFC82272391//National Natural Science Foundation of China/ ; NSFC82302610//National Natural Science Foundation of China/ ; 2019YFA0802300//National Key Research and Development Program of China/ ; },
abstract = {Biological aging has been associated with altered risk of aging-related diseases, but the contribution of the gut microbiota to this process remains poorly understood. Here, we constructed an interpretable gut microbiota age clock using metagenomic data from 8115 fecal samples across five continents. We discovered a key microbial perturbation occurring at 56-60 years of chronological age, which was validated in an independent cohort of 2263 metagenomes. This perturbation was associated with a decline in ecological stability and substantial changes in the abundance of core species. Notably, the association between gut microbiota age and diseases was identified to be significantly altered before and after this inflection time. Moreover, within-species analyses uncovered phylogenetic divergence for seven age-related species, such as Escherichia coli, alongside functional alterations in older individuals, including enhanced cell motility, carbohydrate metabolism and horizontal gene transfer. Overall, our global gut microbiome atlas uncovers a critical age transition phase, highlighting opportunities for microbiota-based therapies and offering novel insights into evolutionary dynamics during aging.},
}

@article {pmid41888318,
year = {2026},
author = {Huang, W and Zhang, J and Shan, J and Shen, W and Du, P and Liu, J and Guo, X and Chen, Z and Zeng, W and Lin, Q and Fan, H},
title = {Lactobacillus paragasseri LPG-9 reduces placental inflammation in intrahepatic cholestasis of pregnancy by regulating TGR5 in mice.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09869-4},
pmid = {41888318},
issn = {2399-3642},
support = {32370139//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32300085//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Intrahepatic cholestasis of pregnancy (ICP), a liver disorder associated with adverse fetal outcomes, is characterized by elevated bile acid levels and placental inflammation by the TGR5. However, the interplay among the gut microbiome, bile acid metabolism, and ICP-associated placental inflammation remains unexplored. We aimed to investigate the role of the gut microbiota in regulating bile acid metabolism and placental inflammation, and to identify potential probiotic-based therapies for ICP in C57BL/6 mice. Immunohistochemical analysis of human placentas revealed significantly higher inflammation and decreased TGR5 expression in ICP compared with controls. In vivo and in vitro assays confirmed the anti-inflammatory effects of TGR5 activation. Using 16S rRNA sequencing and metabolomics, ICP mice exhibited a distinct gut microbiota composition and reduced abundance of bile salt hydrolase (BSH)-producing bacteria (e.g., Lactobacillus), accompanied by a significant decrease in the proportion of secondary bile acids. Transplanting fecal microbiota from ICP donors into healthy mice reproduced the disease phenotype of ICP, confirming the pathogenic role of gut microbiota dysbiosis. Supplementation with BSH-enriched Lactobacillus paragasseri LPG-9 remodeled the bile acid profile, thereby activating placental TGR5 to inhibit TLR4-NF-κB signaling and promoting hepatic bile acid excretion via BSEP.},
}

@article {pmid41888432,
year = {2026},
author = {Marquioni, VM and Hofacker, AC and Villavicencio, JV and Bansept, F},
title = {Modulating microbial intake helps to maintain the gut microbiome diversity.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-09867-6},
pmid = {41888432},
issn = {2399-3642},
abstract = {The animal gut is home to a myriad of microbes whose diversity has a proven impact on the host's health. Indeed, lower values of this metric often correlate with pathological status. In this context, processes involved in the gut microbiome assembly have been studied in the search for optimal nutritional habits and medical interventions. While the nutritional content of food has been extensively investigated, its microbial content has comparatively received little attention as an ecological driver of the gut microbiome. Furthermore, while probiotics use is increasing, the question of optimal dose remains open. Here, we fill these gaps by designing a model that tracks the effect of microbial migration bursts - that result from feeding and/or from probiotics administration - on the gut community alpha-diversity. We find that there is a set of feeding parameters (feeding interval and food microbial content) that maximizes the gut Shannon alpha-diversity, which we call the Maximal Diversity Strategy (MDS). Using a combination of numerical and analytical techniques, we show that for large numbers of microbial types, in the diversity maximization scenario, diversity converges to that of the food, and the feeding rate converges to the average clearance rate. These results remain robust both to the choice of distribution for the parameters that describe microbial dynamics and to weak dispersal noise, thus increasing their theoretical significance and potential for empirical exploration. We believe this work can help evaluate how quantitative ecological control can be used to improve the intake protocols of live biotherapeutic products.},
}

@article {pmid41888636,
year = {2026},
author = {Wang, S and Tong, C and Wang, R and Liu, F},
title = {IL-17A Inhibitors Therapy Affect Oral Fungal and Bacterial Microbiome in Psoriasis.},
journal = {Experimental dermatology},
volume = {35},
number = {4},
pages = {e70237},
doi = {10.1111/exd.70237},
pmid = {41888636},
issn = {1600-0625},
support = {7254353//Beijing Natural Science Foundation/ ; CYJZ202218//Beijing Chao-Yang Hospital Golden Seeds Fundation/ ; },
mesh = {*Psoriasis/drug therapy/microbiology ; *Interleukin-17/antagonists & inhibitors ; *Mouth/microbiology ; *Mycobiome/drug effects ; Humans ; Male ; Female ; Adult ; Middle Aged ; Aged ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Case-Control Studies ; },
abstract = {Psoriasis is a chronic inflammatory skin disease in which the IL-23/Th17/IL-17 axis plays a central pathogenic role while also contributing to antifungal defence. IL-17-targeting biologics such as secukinumab and ixekizumab are increasingly used in its management. This study aimed to characterize changes in the diversity and composition of oral fungal and bacterial communities in psoriasis patients before and after treatment with IL-17 inhibitors. Oral swabs were collected from psoriasis patients at baseline and after 3 months of IL-17 inhibitor therapy, as well as from healthy controls. Direct microscopy and fungal culture were performed. Microbial DNA was extracted and subjected to amplicon sequencing of the fungal ITS1 region and the bacterial 16S rRNA V3-V4 region using the Illumina HiSeq platform. A total of 36 patients and 38 healthy controls were enrolled in this study. Fungal microbiome analysis revealed significantly increased alpha diversity after treatment compared with baseline (p < 0.05), accompanied by markedly elevated beta diversity (p < 0.001). The dominant fungal genera were Blumeria, Pichia and Aspergillus. The relative abundance of Candida was significantly higher in psoriasis patients at baseline than in controls (16.00% vs. 6.43%, p < 0.05) and decreased significantly after therapy (6.12%, p < 0.05). In the bacterial microbiome, beta diversity decreased significantly following treatment (p < 0.001), whereas alpha diversity increased (p < 0.05). The predominant bacterial genera were Streptococcus, Neisseria and Rothia. After treatment, the relative abundance of Haemophilus was significantly lower than at baseline (9.18% vs. 10.14%, p < 0.05). Streptococcus showed a higher trend in patients versus controls (29.74% vs. 16.48%) and declined post-treatment (23.71%). In conclusion, IL-17 inhibitor therapy in psoriasis alters the oral fungal and bacterial microbiota, with notable shifts in Candida, Haemophilus and Streptococcus. These findings provide new insights into the oral microbial changes associated with biologic therapy and may inform clinical monitoring of mucocutaneous microbial imbalance during treatment.},
}

*Psoriasis/drug therapy/microbiology
*Interleukin-17/antagonists & inhibitors
*Mouth/microbiology
*Mycobiome/drug effects
Humans
Male
Female
Adult
Middle Aged
Aged
*Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
Case-Control Studies

@article {pmid41888651,
year = {2026},
author = {Zhang, H and Cong, J and Hu, X and Lu, D and Kollie, SC and Elolimy, AA and Loor, JJ and Yang, Z and Li, M and Mao, Y and Yang, Z},
title = {Investigating the potential role of propionylcarnitine in milk pentadecanoic acid synthesis in Chinese holstein dairy cows using multi-omics analysis.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-12786-9},
pmid = {41888651},
issn = {1471-2164},
support = {YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; YZ2024269//Yangzhou City Policy Guidance Program (International Science and Technology Cooperation) Project in China/ ; },
}

@article {pmid41888669,
year = {2026},
author = {Yang, R and Tao, L and Su, W and Zou, F and Wang, Y and Zhang, G and Chen, H and Zhou, X},
title = {Microbial signatures with diagnostic potential in early gastric cancer: insights beyond H. pylori.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-04981-1},
pmid = {41888669},
issn = {1471-2180},
support = {82100594//National Natural Science Foundation of China/ ; JSPH-MC-2021-10//Jiangsu Province Hospital (the First Affiliated Hospital with Nanjing Medical University) Clinical Capacity Enhancement Project/ ; },
}

@article {pmid41888912,
year = {2026},
author = {Krull, J and Sidhu, C and Solanki, V and Bligh, M and Rößler, L and Singh, RK and Huang, G and Robb, CS and Teeling, H and Seeberger, PH and Schweder, T and Crawford, CJ and Hehemann, JH},
title = {Sulfated mannan of diatoms selects host-specific microbiota in the sunlit ocean.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02379-9},
pmid = {41888912},
issn = {2049-2618},
support = {101029842//MSCA/ ; Project number 570219261//Deutsche Forschungsgemeinschaft/ ; HE 7217/5-1//DFG/ ; 101044738//ERC/ ; },
abstract = {BACKGROUND: Diatoms, a keystone phylum in Earth's ecosystems, are responsible for substantial oxygen production and the fixation of carbon dioxide in the form of carbohydrates that fuel global food webs. They host diverse prokaryotes, yet how diatoms preferentially recruit those with complementary metabolic traits remains unknown.

RESULTS: We discovered that diatoms exude a C6-sulfated α-1,3-mannan that serves as a selective carbon source for adapted Polaribacter. Its structure was resolved using NMR spectroscopy, chromatography, chemical synthesis, and enzymatic dissection. Biochemical, physiological, and structural analyses demonstrated, that specialized Bacteroidota employ a four-enzyme pathway to metabolize this glycan. Metagenomic and transcriptomic data revealed that sulfated mannan utilization loci are globally abundant and actively expressed in surface ocean bacterioplankton. Because this mannan provides only carbon, oxygen, sulfur, and hydrogen, bacteria must obtain other essential elements elsewhere, reinforcing metabolic interdependence.

CONCLUSIONS: Together, these results define a chemically specific interaction between diatoms and specialized bacteria that is mediated by a single sulfated polysaccharide and a dedicated four-enzyme degradation pathway. Presence of this pathway in marine metagenomes and transcriptomes indicates that a sulfated mannan from diatoms exerts selection pressure in the sunlit ocean microbiome.},
}

@article {pmid41888988,
year = {2026},
author = {Khalil, M and Baffy, G and JohnBritto, JS and Mitten, E and Di Ciaula, A and Portincasa, P},
title = {Potential far-reaching metabolic consequences of cholecystectomy.},
journal = {European journal of clinical investigation},
volume = {56},
number = {4},
pages = {e70198},
doi = {10.1111/eci.70198},
pmid = {41888988},
issn = {1365-2362},
support = {//Prima Project: Tradition & Innovation: promoting sustainable Mediterranean diet by Healthy Foods - B4HT, CUP H93C22000950001/ ; 101080329//PAS GRAS project, Horizon Europe Research and Innovation Action. TheHORIZON-HLTH-2022-STAYHLTH-01-05-twostage/ ; },
mesh = {Humans ; *Cholecystectomy/adverse effects ; Bile Acids and Salts/metabolism ; Gastrointestinal Microbiome/physiology ; Dysbiosis/metabolism ; Liver/metabolism ; Colorectal Neoplasms/etiology ; Receptors, Cytoplasmic and Nuclear/metabolism ; Gallstones/surgery ; Gallbladder/metabolism ; Enterohepatic Circulation ; Receptors, G-Protein-Coupled ; },
abstract = {BACKGROUND: Cholecystectomy is one of the most commonly performed abdominal surgical procedures and is considered the gold standard for symptomatic gallstone disease. Removing the gallbladder, however, is not a neutral process. The gallbladder stores and concentrates diluted cholesterol- and bile acid-enriched hepatic bile and is dynamically involved in the daily enterohepatic circulation of bile acids, with critical local and systemic metabolic effects via agonism of nuclear and membrane-associated receptors such as FXR and GPBAR1.

METHODS: We performed a narrative review to discuss the mechanisms driving cholecystectomy-associated dysmetabolism and disruption of the gut-liver axis. We reviewed studies that connect cholecystectomy to bile acid-mediated metabolic effects and examine the pathophysiological processes possibly involved in this scenario.

RESULTS: Experimental and human evidence highlights that cholecystectomy may be linked to several metabolic disorders, also increasing the risk of colorectal cancer. After cholecystectomy, the reservoir and concentrating function of the gallbladder are absent and bile enters the intestine directly. This new anatomical and functional configuration represents a major change in the entero-hepatic circulation of primary and secondary bile acids and in their signalling functions, with altered effects on metabolic receptors and on the gut microbiome. Post-cholecystectomy gut dysbiosis may lead to reduced microbial diversity and diminished capacity to generate beneficial short-chain fatty acids, promoting a pro-inflammatory milieu and altered metabolic homeostasis.

CONCLUSIONS: Cholecystectomy can predispose to metabolic changes leading to type 2 diabetes mellitus, obesity, metabolic dysfunction-associated steatotic liver disease and cardiovascular diseases.},
}

Humans
*Cholecystectomy/adverse effects
Bile Acids and Salts/metabolism
Gastrointestinal Microbiome/physiology
Dysbiosis/metabolism
Liver/metabolism
Colorectal Neoplasms/etiology
Receptors, Cytoplasmic and Nuclear/metabolism
Gallstones/surgery
Gallbladder/metabolism
Enterohepatic Circulation
Receptors, G-Protein-Coupled

@article {pmid41889037,
year = {2026},
author = {Muddiman, KJ and Doble, A and Stephen, AS and Bescos, R and Illsley, CS and Nicholas, TL and Hanks, S and Toit, LD and Brookes, ZLS},
title = {A Pilot Study Assessing the Oral Microbiome in Women of Menopausal Age: Do Oral Nitrate-Reducing Bacteria Play a Role?.},
journal = {International dental journal},
volume = {76},
number = {3},
pages = {109518},
doi = {10.1016/j.identj.2026.109518},
pmid = {41889037},
issn = {1875-595X},
abstract = {INTRODUCTION: The links between oral health and female ageing are poorly understood, but many changes occur in the oral cavity of menopausal women that affect quality of life, and few current oral health interventions consider gender as part of their approach. The aim of this pilot study was to test the hypothesis that the oral microbiome and microenvironment change during female ageing and are thus worthy of further consideration both experimentally and clinically.

METHODS: This observational pilot study retrospectively assessed women aged 18 to 89 years (n = 60) attending a UK primary care dental school facility for blood pressure screening, further analysing the salivary oral microbiome using metagenomics and the biochemical microenvironment using high-performance liquid chromatography. Periodontal health screening (Basic Periodontal Examination [BPE]) was then conducted as part of routine clinical care.

RESULTS: The cross-sectional design classified women into <32 years (n = 18), 40 to 49 years (n = 10), 50 to 59 years (n = 20), and 60+ years (n = 12), but the differences in salivary oestradiol levels between groups were inconclusive. Small numbers were not enough to detect differences in oral microbiome abundance, but nitrate-reducing species (P < .05), nitrate-nitrite-reducing activity (P < .05), and buffering capacity all increased as women aged 60+ years (P < .01), warranting increased numbers. Ageing women also had higher blood pressure (P > .05), were more likely to have periodontal pockets >5.5 mm (BPE4), and had an increased abundance of Porphyromonas (P < .05), but a full periodontal assessment is needed.

CONCLUSIONS: These observations suggest that the composition of the oral microbiome changes as women age, and thus, prospective and longitudinal oral microbiome studies with larger numbers are needed, including concurrent full periodontal assessment, plasma hormonal levels, and salivary flow. However, this study suggests that the oral microbiome in older women may require special consideration, with an increased focus on tailored oral hygiene interventions for this group.},
}

@article {pmid41889114,
year = {2026},
author = {Vlk, L and Odriozola, I and Pergl, J and Větrovský, T and Kvasničková, J and Krüger, C and Petružálková, M and Baldrian, P and Vojík, M and Sádlo, J and Petřík, P and Pyšek, P and Kohout, P},
title = {From pathogens to partners: temporal and biogeographical patterns in fungal associations of alien trees.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71094},
pmid = {41889114},
issn = {1469-8137},
support = {DG16P02M041//Ministerstvo Kultury/ ; EXPRO 19-28807X//Grantová Agentura České Republiky/ ; 21-20802M//Grantová Agentura České Republiky/ ; CZ.02.01.01/00/22_008/0004597//Ministerstvo Školství, Mládeže a Tělovýchovy/ ; },
abstract = {Alien trees reshape belowground fungal communities, but the factors governing the balance between mutualists and pathogens remain unclear. We tested whether residence time, mycorrhizal type, and biogeographical origin shape this balance, and whether alien stands differ from native vegetation. We sampled soils beneath 73 alien tree species in 48 chateau parks and native stands. Using ITS2 metabarcoding with guild assignment, we quantified ectomycorrhizal (ECM) and pathogen fungi and analysed predictors with multivariate models and binomial GLMMs, accounting for spatial structure and covariates. Symbiotic fungal community composition varied with origin, phylogenetic group and mycorrhizal type. With increasing residence time, ECM alien trees showed higher ECM fungal richness and relative abundance; whereas, contrary to enemy accumulation expectations, pathogen richness and relative abundance declined. Alien arbuscular mycorrhizal (AM) trees harboured more pathogens than ECM trees. Alien tree assemblages had a lower ECM fungal share, twice the pathogen relative richness, and threefold higher pathogen relative abundance than native assemblages. Residence time and mycorrhizal type are primary filters shaping belowground trajectories of alien trees, with biogeographical origin patterning community composition. Elevated pathogen loads in alien stands highlight spillover risks to neighbouring vegetation, informing risk assessment and monitoring of alien tree plantings.},
}

@article {pmid41889117,
year = {2026},
author = {Ganjayi, MS and Krauss, TA and Demster, GE and Park, S and Anspach, GB and Anthony, SR and Wang, S and Tranter, M and Helsley, RN and Baumann, CW},
title = {Systemic Consequences of Chronic Ethanol Intake: From Microbiome Shifts to Metabolic Impairment.},
journal = {Comprehensive Physiology},
volume = {16},
number = {2},
pages = {e70132},
doi = {10.1002/cph4.70132},
pmid = {41889117},
issn = {2040-4603},
support = {//Osteopathic Heritage Foundation/ ; 23CDA1051959//American Heart Association/ ; R01DK139147/NH/NIH HHS/United States ; K01DK128022/NH/NIH HHS/United States ; R01HL158671/NH/NIH HHS/United States ; },
mesh = {Animals ; *Ethanol/administration & dosage ; Mice ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice, Inbred C57BL ; *Alcohol Drinking/adverse effects/metabolism ; },
abstract = {Chronic ethanol (EtOH) consumption is a major contributor to multi-organ dysfunction, yet its systemic effects remain incompletely understood. To address this, we utilized a physiologically relevant long-term mouse model, administering 20% EtOH in drinking water for 60 weeks, to investigate the integrated consequences of chronic exposure. EtOH-consuming mice (0.4-0.5 mL/day) exhibited > 30% reductions in chow and fluid intake, resulting in a 12% decrease in total caloric intake compared to controls (p < 0.001). Body mass remained similar until Week 52, after which EtOH-treated mice had lower body mass due to reductions in both lean and fat mass (p ≤ 0.004). Functional assessments revealed impaired treadmill endurance (-17%) and grip strength (-11%) (p ≤ 0.037), while motor coordination remained unaffected (p = 0.203). Chronic EtOH exposure significantly altered gut microbiota composition, reducing Lactobacillus and enriching Faecalibaculum, Clostridium, and Bifidobacterium at the genus level. These changes were accompanied by marked depletion of short-chain fatty acids (p ≤ 0.05). Indirect markers of gut permeability (serum LPS & zonulin) and liver injury (serum ALT & AST, hepatic amyloid content) were elevated, alongside increased total cholesterol and > 62% upregulation of hepatic TNFα, IL-6 & serum amyloid A (p ≤ 0.046). EtOH also induced dyslipidemia and glucose intolerance (p ≤ 0.041), although transcriptomic changes in white adipose tissue were minimal despite elevated free fatty acids. In conclusion, chronic EtOH consumption disrupts energy balance, compromises gut barrier integrity, and impairs hepatic metabolism, collectively driving systemic and metabolic dysfunction. These findings underscore the gut-liver axis as a key mediator of EtOH-induced pathology and highlight the gut microbiome as a promising therapeutic target.},
}

Animals
*Ethanol/administration & dosage
Mice
*Gastrointestinal Microbiome/drug effects
Male
Mice, Inbred C57BL
*Alcohol Drinking/adverse effects/metabolism

@article {pmid41889411,
year = {2026},
author = {Haykal, D and Rossi, A and Kerob, D and Dréno, B},
title = {Post-oncologic skin health: cutaneous recovery and rehabilitation after cancer treatments.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1774381},
pmid = {41889411},
issn = {2234-943X},
abstract = {BACKGROUND: Advances in oncology have markedly improved cancer survival, however, chronic cutaneous sequelae induced by chemotherapy, radiotherapy, targeted therapies, and immunotherapies remain common and may persist long after treatment completion. These long-term skin changes, ranging from xerosis and pruritus to pigmentary alterations, fibrosis, and immune-mediated dermatoses, can substantially impair quality of life and functional recovery.

OBJECTIVE: To define the evolving role of dermatology in post-oncologic skin health and to critically synthesize mechanistic and clinical evidence supporting long-term dermatologic rehabilitation strategies.

METHODS: A structured search of PubMed and MEDLINE (2010-2025) identified clinical and mechanistic studies, consensus guidelines, systematic reviews, and cohort data relevant to post-treatment cutaneous sequelae. Eligible publications included human studies addressing chronic skin changes after cancer therapy or evaluating therapeutic approaches applicable to survivorship dermatology. The search yielded 612 records, of which 148 full-text articles were reviewed and 54 met the inclusion criteria for synthesis.

RESULTS: Post-oncologic skin care extends beyond symptomatic management to encompass restoration of epidermal barrier function, mitigation of chronic inflammation, support of the cutaneous microbiome, and improvement of psychosocial well-being. Mechanistic studies highlight persistent structural, immunologic, molecular, and microbial alterations that underline delayed skin recovery. Within this context, photobiomodulation and selective energy-based modalities may support long-term cutaneous resilience, however robust clinical evidence of their benefit is lacking.

CONCLUSION: Dermatologists play a central role in survivorship care by transitioning cutaneous management from symptomatic treatment toward preventive, restorative, and rehabilitative strategies that improve long-term quality of life.},
}

@article {pmid41889491,
year = {2026},
author = {Zhou, X and Luo, X and Wu, Y and Wang, H and Pan, Z and Wang, J and Xiao, X and Lin, M and Yao, Z},
title = {Co-infection with Pseudomonas aeruginosa and Mycobacterium avium complex in patients with bronchiectasis: coincidence or inevitability?.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1785156},
pmid = {41889491},
issn = {2296-858X},
abstract = {The burden of bronchiectasis is rapidly escalating worldwide, with its airway microbiome shifting from a "single-pathogen" paradigm to "multiple-pathogen coexistence." Both Mycobacterium avium complex and Pseudomonas aeruginosa infections have been demonstrated to exacerbate airway destruction, yet they are rarely examined concurrently. Emerging evidence suggests these pathogens exhibit a long-term coexistence pattern within the same patient, with one dominating when the other recedes. Furthermore, existing studies indicate that the disease burden in coinfected patients is higher than in those with either pathogen alone. However, the specific competitive and synergistic interactions between M. avium complex and P. aeruginosa in bronchiectasis patients remain poorly recognized, posing substantial therapeutic challenges. This review summarizes current understanding of the epidemiology and clinical manifestations of M. avium complex and P. aeruginosa co-infection in patients with bronchiectasis, along with potential mechanisms of microbial interaction between the two pathogens.},
}

@article {pmid41889559,
year = {2026},
author = {Kim, M and Puglisi, CH and Hojjat, A and Nagel, E and Vuong, HE},
title = {Maternal environment during pregnancy shapes offspring neural circuitry and social behaviors.},
journal = {Current opinion in physiology},
volume = {47},
number = {},
pages = {},
pmid = {41889559},
issn = {2468-8673},
abstract = {Social interactions encompass complex behaviors that promote individual and group benefits such as communication and cooperation but can also include negative outcomes including competition and conflict. Neural circuits that facilitate social behaviors begin developing in utero and are informed by the maternal environment which include nutritional status, immune state, stress, and microbiome composition. This relationship between the maternal environment during pregnancy and the programming of social circuits and behaviors suggests a critical window of opportunity for early interventions strategies for social disorders, such as autism spectrum disorders. Here, we review recent causal mechanistic findings on how maternal environmental exposures during pregnancy can shape development and function of circuits implicated in social behaviors.},
}

@article {pmid41889579,
year = {2026},
author = {Vesnupriya, P and Karukuvelraja, R and Rehanaz, N and Shamna, ME and Saranya, N},
title = {Mind gut harmony: psychobiotics effects on the gut-brain axis and harnessing its effects for the mental health.},
journal = {Journal of food science and technology},
volume = {63},
number = {4},
pages = {613-634},
pmid = {41889579},
issn = {0022-1155},
abstract = {The microbiota-gut-brain axis is gaining attention as a potential therapeutic avenue for treating illnesses of the illnesses of the central nervous system. In recent years, there has been a notable increase in literature examining the connection between the gut microbiome and its impact on overall health and wellness. The microbiota-gut-brain axis is a promising therapeutic target for treating central nervous system diseases and reducing drug adverse effects. Probiotics have been shown in pre-clinical and clinical trials to improve health by modulating the microbiota in the gut-brain axis. Psychobiotics are probiotics that modulate the gut-brain axis (GBA) and regulate the central nervous system to improve gastrointestinal function, as well as have antidepressant and anxiolytic properties via neuronal, humoral, and metabolic mechanisms. Some psychobiotic strains have been shown to reduce inflammation and cortisol levels, thereby degenerative and neurodevelopmental illnesses such as Parkinson's disease, Alzheimer's disease, and autism spectrum disorder can be effectively treated with psychobiotics. Alleviating anxiety and depression symptoms. Neurodegenerative and neurodevelopmental illnesses such as Parkinson's disease, Alzheimer's disease, and autism spectrum disorder can be effectively treated with psychobiotics. This review summarizes the psychobiotic potential on the gut-brain axis for the mental health.},
}

@article {pmid41889649,
year = {2026},
author = {Su, R and Ma, J and Li, J and Liu, Y and Ma, T and Wang, J and Mai, Q and Ma, Q and Wang, J and Wang, H and Yang, S and Zhang, X},
title = {Fecal microbiota transplantation ameliorates alcohol-associated liver disease through coordinated restoration of short-chain fatty acid and α-linolenic acid signaling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1744446},
pmid = {41889649},
issn = {1664-302X},
abstract = {BACKGROUND: Alcohol-associated liver disease (ALD) is closely linked to gut microbiota dysbiosis. However, the specific microbial metabolic functions that drive the transition from microbial imbalance to hepatic inflammation and metabolic injury remain unclear, limiting the development of mechanism-based therapeutic strategies.

METHODS: This study integrated human microbiome analysis with fecal microbiota transplantation (FMT) experiments in an ALD mouse model. Multi-omics approaches, including 16S rRNA gene sequencing, untargeted metabolomics, and immunological profiling, were employed to systematically characterize the interactions among gut microbiota composition, microbial-derived metabolites, and host immune responses.

RESULTS: We observed that ALD progression was characterized by an early shift in microbial composition followed by a marked decline in microbial diversity, culminating in an ecological collapse of the gut microbiota. FMT from healthy donors significantly improved liver histopathology and serum biochemical parameters, accompanied by restoration of gut microbial diversity and key metabolic functions. Metabolomic analyses revealed enhanced short-chain fatty acid (SCFA) production and activation of α-linolenic acid (ALA)-related metabolic pathways following FMT. These metabolic improvements were associated with reduced inflammatory responses and improved immune homeostasis.

CONCLUSION: Our findings demonstrate that FMT from healthy donors ameliorates ALD by restoring critical microbial metabolic functions, particularly SCFA production and ALA-related pathways. These results highlight microbial metabolic function as a promising therapeutic target for microbiome-based interventions in ALD.},
}

@article {pmid41889654,
year = {2026},
author = {Yu, G and Han, Y and Liu, J and Zhang, Y and Hao, H and Li, M},
title = {Straw-returning of Triticale to field improved the yield of foxtail millet efficiently by modulating soil physicochemical traits and fungal microbiome assembly.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1791055},
pmid = {41889654},
issn = {1664-302X},
abstract = {Green manure-crop rotation systems are effective management practices for maintaining soil health and enhancing crop yield. However, the influence of various green manure-millet rotation systems on soil properties, fungal community structure, and millet yield in the North China Plain remains undetermined. In this study, three types of green manures with foxtail millet rotation experiment were conducted. The physico-lchemica indexes, millet yield and soil fungal community characteristic were detected. Our findings suggest that three green manure-millet rotation systems increased millet yield compared to millet-winter fallow (Si-Le). Among them, the Triticale-millet rotation (Si-Ts) showed the highest yield increase, with a rise of 46.16% in 2021 and 85.7% in 2022. In 2021, compared with Si-Le, the organic matter (OM) in Si-Ts increased by 17.86%, and the available phosphorus (AP) rose by 113.82%. In 2022, in contrast to Si-Le, the alkali-hydrolyzed nitrogen (AHN) in Si-Ts increased by 17.68%, the available phosphorus (AP) by 37.56%, and the available potassium (AK) by 12.56%. Additionally, Si-Ts exhibited the highest diversity of soil fungi and the greatest relative abundance of beneficial genera from the dominant phylum Ascomycota and Mortierellomycota. Moreover, Green manure rotations (particularly Si-Ts) alleviate these constraints by simultaneously augmenting microbial diversity (driven by OM/AK/AHN) and crop yield (driven by AP/OM). Overall, the Triticale-millet rotation is a feasible practice for improving soil conditions, maintaining soil microbial balance, and ensuring high yields of millet. Our findings offer theoretical support for green manure-crop rotation in influencing the soil environment and the sustainable development of the millet industry in the North China Plain.},
}

@article {pmid41889668,
year = {2026},
author = {Hong, J and Song, H and Jeong, S and Kim, JS and Choi, H and Kim, C},
title = {Gut and fecal microbiome profiles of the electric eel (Electrophorus varii) revealed by 16S rRNA amplicon sequencing.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112661},
pmid = {41889668},
issn = {2352-3409},
abstract = {We report a 16S rRNA gene amplicon sequencing dataset describing gut and fecal microbiota of the electric eel Electrophorus varii, a freshwater electrogenic fish lacking baseline microbiome references. Fecal and gut samples (n = 3 per group) from an individual eel were analyzed to characterize genus-level taxonomic composition and alpha diversity. The gut samples were strongly predominated by Cetobacterium, whereas the fecal samples contained more heterogeneous community structures. Principal component analysis (PCA) based on Hellinger-transformed relative abundances was applied to primarily separate gut and fecal microbiota samples along the first principal component (PC1) axis (92.8 %). Shannon alpha diversity was significantly higher in fecal microbiota compared with gut microbiota. Although the present dataset is based on triplicate samples from a single individual, expanded studies incorporating multiple electrogenic species and species-level comparisons will be necessary to determine whether electric discharge environments are associated with significant shifts in freshwater fish gut microbiome structure.},
}

@article {pmid41889698,
year = {2026},
author = {Almatrafi, R and Alasiri, A and Almuneef, G and Al-Hazzani, AA and Alghoribi, MF and Hakami, M and Arafah, AM and Alotibi, RS and Alrabiah, S and Alqurainy, N and Ajina, R and Aldriwesh, MG},
title = {First metagenomic analysis of age-associated changes in the gut microbiome among healthy Saudi adults: SAMS pilot study.},
journal = {Frontiers in aging},
volume = {7},
number = {},
pages = {1733638},
pmid = {41889698},
issn = {2673-6217},
abstract = {INTRODUCTION: The gut microbiome undergoes dynamic changes with aging across diverse healthy populations. However, data from Saudi Arabia remain limited. This pilot study investigated age-related variations in the gut microbiome among healthy Saudi adults to characterize region-specific microbial signatures and identify taxa potentially associated with aging in a healthy population.

METHODS: We established the Saudi Aging and Microbiome Study (SAMS) to investigate age-related changes in fecal microbiome of Saudi adults. In this pilot phase, 145 healthy participants aged 19-69 years were enrolled. Shotgun metagenomic sequencing was performed to profile fecal microbiome at the species level. Microbial diversity and taxonomic composition were compared across five age groups. Spearman and confounder-adjusted partial Spearman correlation were applied to identify taxa significantly associated with chronological age.

RESULTS: We analyzed fecal microbiome of 145 healthy adults distributed among five age groups: G1 (19-29 years, n = 33; 22.7%), G2 (30-39 years, n = 30; 20.7%), G3 (40-49 years, n = 27; 18.6%), G4 (50-59 years, n = 31; 21.4%), and G5 (60-69 years, n = 24; 16.6%). Of these, 75 (51.7%) were male, and 70 (48.3%) were female. Alpha diversity increased from young to older adulthood for observed richness and Shannon indexes (all q < 0.05). Beta diversity also varied significantly with age (PERMANOVA R [2] = 0.13, q = 0.023), indicating distinct microbial community structures in healthy older adults. At the phylum level, Firmicutes significantly increased with age (FC = 1.35; q = 0.026), whereas Bacteroidota decreased (FC = 0.59; q = 0.01). Consistent with these trends, Blautia obeum showed positive correlations, while Bacteroides thetaiotaomicron and Phocaeicola vulgatus showed negative correlations with chronological age.

CONCLUSION: In healthy Saudi adults, increasing age was associated with higher microbial diversity and compositional shifts at phylum and species levels. These age-associated microbial taxa might represent biomarkers of healthy aging and suggest an enhanced community capacity for short-chain fatty acids (SCFAs) production, a hypothesis warranting validation through future functional analyses.},
}

@article {pmid41889714,
year = {2026},
author = {Rojas-Rodríguez, AL and Jaramillo-Romero, V},
title = {The role of the gut microbiota during the first 2 years of life in the early programming of obesity, type 2 diabetes, and hypertension.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1772889},
pmid = {41889714},
issn = {2296-861X},
abstract = {The first 2 years of life constitute a critical window for the establishment of the gut microbiota and the early programming of cardiometabolic risk. The aim of this review was to analyze the influence of the gut microbiota during the first 2 years of life and its association with obesity, type 2 diabetes, and arterial hypertension. The reviewed studies suggest that early dysbiosis is associated with increased cardiometabolic vulnerability, linked to low-grade inflammation and alterations in energy metabolism. Associations are described between maternal metabolic conditions (such as obesity or gestational diabetes) and a less favorable initial intestinal ecosystem in the child, characterized by lower microbial diversity and reduced abundance of bacteria considered protective. In childhood obesity, longitudinal studies indicate that less mature microbiomes during the first year of life are associated with a higher risk of overweight, particularly when early antibiotic exposure and unhealthy dietary patterns coexist. In contrast, exclusive breastfeeding is associated with more functional microbial profiles. Regarding arterial hypertension, the findings suggest an influence mediated by microbial metabolites such as short-chain fatty acids and mechanisms involved in vascular regulation. Overall, the first 1,000 days represent a priority axis for promoting early-life practices that support a balanced gut microbiota as a potential strategy for cardiometabolic disease prevention.},
}

@article {pmid41703607,
year = {2026},
author = {Li, L and Sun, W and Tan, T and Xu, J and Chen, Y and Chen, Y and Gao, G and Ai, X and Zhou, J and Li, Y and Zhang, D and Lei, S},
title = {Limonin attenuates hyperlipidemia by regulating the gut microbiota-bile acid-farnesoid X receptor axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {},
pages = {},
pmid = {41703607},
issn = {1479-5876},
support = {2024ZD0532700//National Major Science and Technology Projects of China/ ; 2023AFB302//Natural Science Foundation of Hubei Province/ ; Q20234308//Youth Project of Scientific Research Project of Hubei Provincial Department of Education/ ; 2018YFZD025//Key science and technology project of Jingmen under Grant/ ; 2023YFZD043//Key science and technology project of Jingmen under Grant/ ; 2024ZDYF006//Key science and technology project of Jingmen under Grant/ ; WJ2023M173//Health and Family Planning Commission of Hubei Province/ ; 2022BCE060//Hubei Province key R & D project under Grant/ ; },
abstract = {BACKGROUND: Hyperlipidemia is an established risk factor for cardiovascular disease. Limonin, a natural tetracyclic triterpenoid compound found in the traditional Chinese herb Tangerine peel and citrus fruits, has been shown to ameliorate hyperlipidemia, although the underlying mechanisms of action are unknown. The present study employed a comprehensive approach integrating to assess the efficacy of Limonin in the treatment of hyperlipidemia and to explore its molecular mechanisms.

METHODS: Hyperlipidemia model was induced by high-fat diet (HFD). The effects of Limonin on hyperlipidemia were evaluated through serum, liver lipid, and Hematoxylin & eosin (H&E). Then, the mechanism of Limonin alleviates hyperlipidemia was explored by network pharmacology. Targeted metabolism was used to measure bile acids (BAs)’ changes in serum and fecal, and 16 S rDNA sequencing of gut microbiota. Finally, the expression of genes and proteins about FXR/FGF15, ASBT, and FGF15/FGFR4 signaling pathways in the distal ileum or liver was detected by qPCR, immunohistochemistry, and Western blotting.

RESULTS: The results confirmed the significant anti-hyperlipidemia effect of Limonin. Network pharmacology analysis revealed that Limonine alleviates hyperlipidemia is possibly closely pertaining to BAs metabolism. In a mouse model of hyperlipidemia, Limonin altered the colonic BAs profile, especially in terms of elevated levels of conjugated BAs. Limonin reshaped the structure of the gut microbiome by decreasing bile salt hydrolase (BSH)-producing genera, including Lactobacillus, Bacteroides, Clostridium, Streptococcus, and Adlercreutzia. Decreased BSH activity increased levels of conjugated BAs, which inhibited activation of ileum FXR, facilitated BAs synthesis and fecal BAs excretion. The decreased FXR activity resulted in lower expression of FGF15 and ASBT in the distal ileum, lower expression of FGF15 and its receptor in the liver, and increased expression of CYP7A1 in the liver.

CONCLUSION: Limonin remodels the gut microbiota to reduce BSH activity and to activate BAs synthesis pathways, thereby ameliorating dyslipidemia. These results provide a theoretical basis for clinical investigations into the use of Limonin in anti-hyperlipidemia therapies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07826-7.},
}

@article {pmid41709254,
year = {2026},
author = {Parlak, HM and Ozkul, C and Akman, AC and Guncu, GN and Ergunay, K and Akyon, Y},
title = {Submucosal microbiota profile in peri-implant health, peri-implant mucositis, and different severity levels of peri-implantitis.},
journal = {BMC oral health},
volume = {26},
number = {},
pages = {},
pmid = {41709254},
issn = {1472-6831},
abstract = {BACKGROUND: The unique and complex peri-implant microbiota harbors many species, mostly bacteria, and dysbiotic shift in microbiota induces peri-implant diseases. The aim of the study was to investigate the compositions and differences in submucosal microbial profiles in subject with different peri-implant heath statues, from peri-implant healthy (PH) to advanced peri-implantitis (PI).

METHODS: Submucosal plaque samples were obtained from 78 individuals with PH, peri-implant mucositis (PM), early, moderate, and advanced PI (PH:16, PM:16, PI-early: 14, PI-moderate: 16, and PI-advanced:16) and analyzed using sequencing of 16S rRNA gene. Differences of submucosal microbiome profiles between groups were evaluated with taxonomic abundances and microbial diversity using the alpha-diversity metrics (observed features, Shannon index, and Chao1 index), beta-diversity metrics (Bray–Curtis dissimilarity, unweighted, and weighted UniFrac distance), and linear discriminant analysis effect size analysis.

RESULTS: According to alpha-diversity and beta-diversity analysis, the submucosal microbiota diversity showed no difference in the PI, PM, and PH sites. Prevotella, Fusobacterium, Bacteroides, Treponema, Porphyromonas, Fretibacterium, and Veillonella genera showed high abundance in the PI groups. At the genus-level, compositional differences between two distinct clinical groups were found. Pseudoramibacter was significantly enriched in PM and PI groups compared to PH. Fretibacterium was the most discriminative taxa between PI-early and PH.

CONCLUSIONS: Despite similar overall microbial diversity, distinct compositional shifts in the submucosal microbiota were observed across peri-implant health and disease. Specific genera, particularly Fretibacterium and Pseudoramibacter, were associated with disease conditions and may serve as potential candidates for future biomarker research. These findings suggest that microbial composition, in addition to diversity, could be relevant to understanding peri-implant disease processes and may inform the development of diagnostic and preventive strategies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-026-07942-2.},
}

@article {pmid41714986,
year = {2026},
author = {Lu, S and Zhou, N and Song, X and Song, X and Qiao, X},
title = {Comparison of severe and general Mycoplasma pneumoniae pneumonia in children: a targeted next-generation sequencing based study.},
journal = {BMC infectious diseases},
volume = {26},
number = {},
pages = {},
pmid = {41714986},
issn = {1471-2334},
abstract = {BACKGROUND: The incidence and severity of Mycoplasma pneumoniae pneumonia (MPP) in children have increased after the pandemic of COVID-19, raising public concern. However, factors that affect the severity of MPP have not been well described. This study aimed to investigate the influence of Mycoplasma pneumoniae characters, respiratory co-existing pathogens, and host response on the severity of MPP.

METHODS: Clinical characteristics of 288 children hospitalized for MPP between November 2023 and July 2024 were analyzed retrospectively. Patients were divided into severe MPP (SMPP) and general MPP (GMPP) groups according to disease severity. Targeted next-generation sequencing (tNGS) was employed to analyze the respiratory pathogens of patients.

RESULTS: Of 288 cases, there were 113 SMPP and 175 GMPP. Compared with GMPP group, children with SMPP had significantly higher levels of neutrophil percentage, Neutrophil to Lymphocyte Ratio (NLR), C-Reactive Protein (CRP), Alanine aminotransferase (ALT), Lactic dehydrogenase (LDH) and D-D dimer (all P < 0.05), which reflected a higher host immune response in SMPP group. Meanwhile, tNGS based pathogen analysis showed that Mycoplasma pneumoniae characters (A2063G mutation or not, pathogen concentration) were not associated with the severity of MPP (P > 0.05). Furthermore, co-existing pathogens analysis showed that the SMPP group had a lower number of co-detected pathogens, children with human respiratory syncytial virus (RSV) co-existing were more frequent in the SMPP group (all P < 0.05). Multivariate analysis showed that lower number of co-detected pathogens (decreased microbial diversity), RSV co-existing, elevated CRP, and LDH were independent risk factors for SMPP.

CONCLUSION: Collectively, our data showed that respiratory microbiome and host response may play important roles in the pathology of MPP, decreased microbial diversity, RSV co-existing, CRP, and LDH level can predict the severity of MPP.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-026-12914-6.},
}

@article {pmid41872963,
year = {2026},
author = {Kim, B and Kim, HN and Cheong, HS and Jeong, S and Kim, J and Park, DI and Joo, EJ},
title = {Fecal microbiota from hepatitis B-infected individuals alters triglyceride metabolism and microbial pathways in mice.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00825-5},
pmid = {41872963},
issn = {1757-4749},
support = {RS-2023-KH135855//Korea Health Industry Development Institute/Republic of Korea ; NRF-2021R1A2C4002454//National Research Foundation of Korea/ ; },
}

@article {pmid41873297,
year = {2026},
author = {Katsanos, A and Benekos, K and Karavasili, M and Gorgoli, K and Kostoulas, C and Gartzonika, K and Christodoulou, DK and Katsanos, K and Georgiou, I},
title = {Intestinal Microbiome of Newly Diagnosed Patients With Neovascular Age-Related Macular Degeneration: A 16S rRNA Gene Sequencing Study.},
journal = {Cureus},
volume = {18},
number = {2},
pages = {e103984},
pmid = {41873297},
issn = {2168-8184},
abstract = {BACKGROUND: This study aims to explore differences in the intestinal microbiome between patients with newly diagnosed neovascular age-related macular degeneration (AMD) and controls using 16S rRNA gene sequencing.

METHODOLOGY: In this cross-sectional study, stool samples from newly diagnosed White patients with neovascular AMD and controls were used for the assessment of the intestinal microbiome. The DNeasy PowerSoil Pro Kit (QIAGEN, Hilden, Germany) was used to extract microbial DNA before sequencing the V3-V4 hypervariable region of the 16S rRNA gene on the Illumina MiSeq system (Illumina, San Diego, CA). Bioinformatic analysis was performed on the Nephele platform using the DADA2 pipeline in R (ClinicalTrials.gov identifier: NCT05757674).

RESULTS: Thirty-three patients (age: 75 ± 7 years, 17 women) and 34 age- and sex-matched controls (age: 73 ± 7 years, 18 women) were analyzed. No differences in height, weight, body mass index, smoking, or systemic comorbidities were noted between the groups. The most prevalent phyla in both groups were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. The most prevalent genus was Bacteroides in both groups. Neither alpha nor beta diversity was different among the groups. The differential abundance analysis using Analysis of Compositions of Microbiomes with Bias Correction 2 (ANCOM-BC2) showed that some Amplicon Sequence Variants (ASVs) from the Coprococcus genus were more abundant in controls than in patients with AMD, whereas several ASVs from Bacteroides were more abundant in the AMD group.

CONCLUSIONS: In our sample, the intestinal microbiome of newly diagnosed patients with neovascular age-related AMD showed some small but noteworthy differences compared to matched healthy controls. Some Bacteroides ASVs were enriched in AMD patients, while certain Coprococcus ASVs were more abundant in controls.},
}

@article {pmid41873486,
year = {2026},
author = {Pulaski, M and Weber, HC},
title = {Microbiome-derived signaling molecules and the brain-gut axis: emerging mechanisms and clinical implications.},
journal = {Current opinion in endocrinology, diabetes, and obesity},
volume = {},
number = {},
pages = {},
pmid = {41873486},
issn = {1752-2978},
abstract = {PURPOSE OF REVIEW: Recent advances in metabolomics, multi-omics integration, and neurogastroenterology have fundamentally reshaped understanding of the human gut microbiome. Rather than microbial composition alone, emerging evidence highlights microbial secretory and signaling activity as a central regulator of brain-gut communication. Understanding how microbiome-derived molecules interact with epithelial, immune, endocrine, and neural pathways is essential for advancing mechanistic insight and precision interventions in disorders of gut-brain interaction (DGBI).

RECENT FINDINGS: Recent studies demonstrate that the gut microbiome functions as a metabolic and endocrine signaling system, producing compounds such as short-chain fatty acids, bile acids, tryptophan-derived metabolites, polyamines, and lipid mediators that act on enteroendocrine cells, immune circuits, mechanosensory pathways, and vagal afferents. These signals are integrated centrally through brainstem and cortical networks, shaping gastrointestinal motility, visceral sensitivity, stress responsiveness, and affective processing. Functional dysbiosis and altered microbial signaling - rather than consistent taxonomic changes - appear to be primary modulators of brain-gut axis dysregulation.

SUMMARY: Emerging data calls for a reframing of gut-brain disorders as conditions of disrupted microbial signaling. Clinically, they support mechanism-based stratification and targeted dietary, microbiome-directed, and neuromodulatory therapies. The findings identify a need for functional biomarkers and targeted molecular approaches to advance precision medicine in DGBIs.},
}

@article {pmid41873937,
year = {2026},
author = {Wang, X and Liu, X and Zhou, G and Miao, Y and Zhao, X and Cao, Y and Wang, Z and Deng, D},
title = {A Watermelon-Like Micro/Nano Hierarchical Delivery Platform for Ulcerative Colitis by Regulating Redox Homeostasis and Remodeling Gut Microbiota.},
journal = {Advanced healthcare materials},
volume = {},
number = {},
pages = {e05873},
doi = {10.1002/adhm.202505873},
pmid = {41873937},
issn = {2192-2659},
support = {2022YFF1100303//National Key R&D Program of China/ ; 82172085//National Natural Science Foundation of China/ ; CPU2022QZ14//Double FirstRate Construction Plan of China Pharmaceutical University/ ; BK20190028//Distinguished Young Scholars/ ; },
abstract = {Ulcerative colitis (UC) is a refractory inflammatory bowel disease marked by mucosal barrier damage, immune dysregulation, and microbial imbalance. Current treatments are limited by systemic toxicity and inadequate targeting. Drawing inspiration from the "watermelon seed and watermelon" concept, this study employs microfluidic technology to encapsulate chondroitin sulfate (CSU) based nanoparticles (NPs) loaded with the antioxidant quercetin (Qu@CSCP) within hyaluronic acid/calcium alginate (HACM) hydrogel microspheres. This process yields a "watermelon-like" micro/nano hierarchical hydrogel microsphere system (QC@HACM) specifically designed for targeted combination therapy of UC. The HACM shell protects Qu@CSCP from the harsh gastrointestinal (GI) environment and enables targeted accumulation in inflamed colon tissue. Owing to its colon-adhesive properties, QC@HACM enhances the expression of tight junction proteins and reshapes the gut microbiota, enriching beneficial probiotics. Upon localized release, Qu@CSCP NPs activate the Nrf2/HO-1 antioxidant pathway, induce M2 macrophage polarization, and modulate the Bax/Bcl-2 ratio to suppress epithelial apoptosis. This dual mechanism effectively relieves oxidative stress and promotes mucosal healing. The therapeutic efficacy of these microspheres was further validated in a murine model of UC, as evidenced by reduced levels of pro-inflammatory cytokines accompanied by restoration of gut microbiota homeostasis. Consequently, this oral delivery platform represents a promising stepwise therapeutic strategy for comprehensive UC management.},
}

@article {pmid41873970,
year = {2026},
author = {Valenzuela-Diaz, S and Dikareva, E and Hickman, B and Kiljunen, S and Kolho, K-L and de Vos, W and Salonen, A and Korpela, K},
title = {Impact of phage enrichment on the observed infant gut phageome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0215325},
doi = {10.1128/spectrum.02153-25},
pmid = {41873970},
issn = {2165-0497},
abstract = {The human gut microbiota, particularly during infancy, plays a pivotal role in shaping long-term health outcomes. While research on the bacterial microbiota has advanced rapidly, the infant gut virome-dominated by bacteriophages-remains underexplored due to technical challenges in viral DNA detection and recovery. To address this, we optimized a polyethylene glycol (PEG)-based protocol for phage DNA enrichment tailored to the constraints of infant fecal samples, focusing on maximizing viral yield from minimal input material. We validated the optimized protocol on fecal samples from 41 infants at 1, 6, and 12 months of age and assessed the impact of phage enrichment on the observed gut phageome. The results demonstrate that the optimized protocol improves viral DNA recovery and significantly alters the observed virome composition, especially in older infants. Without appropriate enrichment, key features of the gut virome may be underrepresented or missed entirely. These findings underscore the importance of protocol optimization in virome studies and provide a scalable, cost-effective method for robust infant gut virome profiling.IMPORTANCEUnderstanding the viral component of the infant gut microbiome is essential for uncovering its role in early-life health, yet technical limitations have hindered its study. This work presents a systematically optimized and validated protocol for enriching viral DNA from infant stool samples, designed specifically for low-input material typical of early life. By adapting polyethylene glycol-based precipitation methods, we achieved consistent and scalable recovery of viral DNA across infants of different ages. Application of this protocol revealed key age- and delivery mode-specific differences in phage diversity and replication strategies that were undetectable using standard approaches. Our findings demonstrate that careful protocol optimization is critical for accurate virome profiling in infants and offer a practical solution to overcome longstanding methodological challenges in the field.},
}

@article {pmid41874128,
year = {2026},
author = {Yıldırım, S and Zhu, W and Cope, E and Lindemann, S and Suez, J and Shade, A},
title = {Sex-specific microbiome-host interactions: from infection to chronic disease-call for papers.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0015626},
doi = {10.1128/msystems.00156-26},
pmid = {41874128},
issn = {2379-5077},
}

@article {pmid41874175,
year = {2026},
author = {Ibarguren-Quiles, C and Blasco, L and López-Causape, C and Bleriot, I and Fernández-García, L and Arman, L and Barrio-Pujante, A and Ortiz-Cartagena, C and Aracil, B and Menéndez-Rodriguez, O and Mariñas-Pardo, L and Cantón, R and Oliver, A and Tomás, M},
title = {Identification and functional insights into new phage tail-like bacteriocins targeting Pseudomonas aeruginosa as new antimicrobials.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0289425},
doi = {10.1128/spectrum.02894-25},
pmid = {41874175},
issn = {2165-0497},
abstract = {The current health crisis caused by multidrug-resistant (MDR) pathogens is one of the health problems of most concern globally. Infections caused by these pathogens, such as Pseudomonas aeruginosa, lead to high rates of complications, particularly in compromised patients such as cystic fibrosis (CF) patients. The need to counteract and minimize the forecast future impact has led to the rescue of phage therapy. The use of bacteriophages has important advantages, including highly specific targeting, self-amplification at the infection site, minimal disruption of the microbiome, safety, and biocompatibility. However, the capacity of bacteria to escape these entities results in a form of resistance that compromises the effectiveness of the therapy. This involves the search for potential alternatives, such as the phage tail-like bacteriocins (PTLBs), also named as tailocins. These high-molecular-weight particles resemble the tail structure of bacteriophages and are characterized by the absence of genetic material, avoiding the development of resistance, one of the major handicaps associated with phage therapy. In this study, we detected 34 different PTLBs in 75 P. aeruginosa genomes, with different serotypes and sequence types, 11 of which were characterized as novel F-type PTLB subtypes (F13-F24). Furthermore, we report that four selected PTLBs (R1, F15, F19, and R3-F24) can deal with bacterial infection, with the R1 and the F15 PTLBs being the most efficient in clearing infection in vitro, yielding a survival rate of more than 75% in the Galleria mellonella larvae in vivo model. This reaffirms the potential of PTLBs to control P. aeruginosa infections, which can cause chronic infections in some patients, such as people with CF, due to its strong impact as a MDR bacterium.IMPORTANCEThe 75 Pseudomonas aeruginosa genomes from people with cystic fibrosis in the study collection included at least one phage tail-like bacteriocins (PTLB) cluster. From the 34 different PTLBs detected in the study collection, 7 were R-type, 10 were complex (R- and F-type encoded), and 14 were F-type PTLBs. Eleven new F-type PTLBs were described in the P. aeruginosa collection under study. An association between the O-antigen present on the surface of the P. aeruginosa isolate and the encoded PTLB subtype was detected. The R1 and F15 PTLB subtypes display high antimicrobial activity both in vitro and in vivo (Galleria mellonella).},
}

@article {pmid41874177,
year = {2026},
author = {Poursalavati, A and Laforest-Lapointe, I and Fall, ML},
title = {SS-VIME: a single-source virome-microbiome extraction protocol toward comprehensive soil community analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0332325},
doi = {10.1128/spectrum.03323-25},
pmid = {41874177},
issn = {2165-0497},
abstract = {Integrated analysis of soil microbiomes and their associated viromes is critical for understanding ecosystem function, yet is hampered by the profound spatial heterogeneity of soil, which introduces significant bias when using separate extraction workflows and/or subsampling strategies to capture fungal, bacterial, and viral communities. Here, we present single-source extraction for unified soil virome-microbiome profiling (SS-VIME), a protocol that overcomes this limitation. Based on extended cellulose column chromatography, this method sequentially elutes distinct DNA and double-stranded RNA (dsRNA) fractions from a single soil lysate. We validated the protocol using sterilized soil co-spiked with a ZymoBIOMICS microbial community standard and a synthetic viral dsRNA fragment. Sequencing confirmed that the DNA fraction accurately recovered the theoretical bacterial (16S rRNA gene) and fungal (ITS) community profiles, while the dsRNA fraction demonstrated highly specific recovery of the target viral signature. The protocol was then successfully applied to characterize the complex native communities in environmental soil samples. The SS-VIME protocol provides a streamlined approach for isolating high-quality nucleic acids suitable for downstream applications. By using dsRNA as a proxy for viral activity and eliminating subsample bias, this method provides a robust, accessible, and unified platform to investigate virus-host dynamics in situ, paving the way for a more holistic understanding of the soil microbiome.IMPORTANCEThe study of soil microbes and their viruses, which are central to ecosystem health, is fundamentally limited by technical barriers. Separate extraction workflows for each group introduce sampling bias, obscuring the true ecological relationships within soil's spatially complex micro-environments. Our single-source virome-microbiome extraction (SS-VIME) protocol directly overcomes this by efficiently recovering both microbial DNA and viral double-stranded RNA (dsRNA) from one sample. This unified approach is not only cost-effective but, by using dsRNA as a signature of viral activity, captures a more accurate and representative profile of the soil active virome. SS-VIME provides the foundation for robustly investigating how viruses modulate soil health, carbon cycling, and agricultural productivity, moving the field from correlational studies toward a direct, integrated view of the soil ecosystem.},
}