@article {pmid41699596,
year = {2026},
author = {Hu, S and Chen, T and Liu, X and Wu, Z and Wang, X},
title = {Effects of aerobic exercise on inflammation and gut microbiota in obese mice: a metagenomic and metabolomic analysis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41699596},
issn = {1479-5876},
support = {2025AFB925//Natural Science Foundation of Hubei Province/ ; XZ202501ZR0140//Key project of Natural Science Foundation of Tibet Autonomous Region/ ; SNSBJKJJHXM2024023//Shannan Science and Technology Plan Project/ ; Yz2024179//National Resource Center for the First-Year Experience and Students in Transition, University of South Carolina/ ; JY2024066//the University-level teaching and research project of Yangtze University/ ; (25Y117)//Philosophical and Social Science Research Project of the Education Department of Hubei Province/ ; 2025csz005//Key Project of Social Sciences Fund of Yangtze University/ ; },
abstract = {BACKGROUND: Aerobic exercise can ameliorate insulin resistance (IR). However, the mechanism by which aerobic exercise regulates the gut microbiome to ameliorate IR and obesity remains unexplored.

METHODS: Obese models were established by feeding C57BL/6 male mice a high-fat diet. A total of 26 mice were randomly divided into control group (group A, N = 8) and high-fat diet group (HFD group, N = 18). Successfully modeled mice were further assigned to model group (group B, N = 8) and exercise group (group C, N = 8). Group C underwent a 6-week treadmill exercise program (12 m/min, 60 min per day, 5 days per week). After intervention, colon tissue morphology was observed through hematoxylin-eosin staining, serum lipids and inflammatory indicators levels were detected by ELISA. The changes in the intestinal microbiota of the mice were also examined using metagenomic sequencing and UPLC-MS non-targeted metabolomics.

RESULTS: Compared with the group A, the body weight, TC, TG, LDL-C, blood glucose, insulin, and IR in the group B significantly increased (P < 0.01), while the levels of pro-inflammatory cytokines TXNIP, TNF-α, NLRP3, IL-1β, and IL-18 significantly increased (P < 0.05 or P < 0.01). Compared with the group B, aerobic exercise reduced the body weight, TC, blood glucose, insulin, IR, TXNIP, TNF-α and other indicators in obese mice (P < 0.05 or P < 0.01). Moreover, aerobic exercise can regulate the imbalance of the intestinal flora in obese mice and ameliorate the disorder of metabolites. The metabolic pathways including arachidonic acid metabolism and histidine metabolism showed the most significant differences after the intervention of aerobic exercise.

CONCLUSIONS: In conclusion, aerobic exercise can ameliorate glucose and lipid metabolism, IR, inflammatory response, and regulate the intestinal microecology and metabolic disorders in obese mice. The mechanism may be closely related to enhancing the diversity of intestinal flora, regulating the metabolism of arachidonic acid and histidine.},
}

@article {pmid41807420,
year = {2026},
author = {de Oliveira Ignacio, MA and Marconi, C and Bidinotto, LT and Balsanelli, E and Belleti, R and da Silva, MG and Duarte, MTC},
title = {Characteristics associated with Lactobacillus-depleted vaginal microbiota in women with different sexual behavior.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41807420},
issn = {2045-2322},
support = {2018/14770-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2015/04224-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {UNLABELLED: The aim of this study was to compare the vaginal microbiome of women with different sexual behaviors and to examine characteristics associated with Lactobacillus-deprived community state type IV. In this prospective study performed in a community-based population in a city of approximately 150,000 inhabitants in Southeast region of Brazil, vaginal swabs were obtained of 109 participants, including women who only had sex with women (n = 54) and women who only had sex with man (n = 55). Sociodemographic data, sexual and intimated hygiene practices of the participants were also assessed. Vaginal microbiota was assessed by sequencing the hypervariable regions V3 and V4 of 16 S ribosomal nucleic acid gene (Illumina 250 PE). Alpha diversity (Shannon index) was compared between the two groups by the Mann-Whitney test. Logistic regression analyses were performed to estimate odds ratios (OR) and 95% confidence intervals (CI) for the association between covariates with the Lactobacillus-deprived community state type IV. Results showed that overall distribution of vaginal CSTs did not differ between the two study groups (P = 0.19). However, alpha diversity was increased in women that only have sex with women (P = 0.0018). Lactobacillus-deprived community state type IV was associated with lower income (OR: 4.15, 95% CI: 1.04–16.46) and use of sex toys (OR: 3.97, 95% CI: 1.09–14.45). In conclusion, nearly one-third of women that only have sex with women had a sub-optimal vaginal microbiome and show evidence of sex transmissibility of CST-IV associated organisms.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-025-34977-2.},
}

@article {pmid41868365,
year = {2026},
author = {Li, J and Li, Q and Wang, M and Xu, S and Zhang, D},
title = {Crop rotation-driven changes in secondary metabolites of potato rhizosphere soil exert stronger regulation on soil microbial community.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768797},
pmid = {41868365},
issn = {1664-302X},
abstract = {INTRODUCTION: Crop rotation promotes ecological effects and production by regulating belowground processes, particularly the shaping of the rhizosphere soil microbiome. Rhizosphere metabolites are a key driver of belowground processes and play a crucial role in shaping soil microbial community composition. However, the rhizosphere metabolites of different potato rotations have rarely been reported, and the regulation of key metabolites on the rhizosphere soil microbiome remains unclear.

METHODS: This study measured agronomic traits of potatoes, collected potato rhizosphere soils from three crop rotations, including potato monoculture (P-P), maize (Zea mays)-potato rotation (M-P), cowpea (Vigna unguiculata)-potato rotation (V-P), to determine rhizosphere soil metabolites and analyze defense metabolites, and assess the soil bacterial and fungal diversity and community composition.

RESULTS: Compared to monoculture, the potato rotations had positive effects on growth and yield. Potato rotations had more primary metabolites, such as amino acids and carbohydrates and conjugates, but significantly reduced secondary metabolites with defensive functions in rhizosphere soils including phenols and other benzene derivatives, flavonoids, alkaloids and other N-containing compounds, and terpenoids. Potato rotation systems supported higher diversity of bacteria and fungi and enriched beneficial bacteria such as biocontrol, nitrogen fixation, C degradation, denitrification, and pollutant degradation bacteria, while suppressing pathogenic fungi in the rhizosphere soils. Rhizosphere soil metabolites strongly correlated with the microbial community composition. The secondary metabolites, which are predominantly alkaloids, terpenoids, and flavonoids, exerted a dominant regulatory effect on the composition of soil microbial community.

DISCUSSION: These results demonstrate the important regulation of rhizosphere metabolites on soil microbial community composition, deepening our understanding of the benefits of crop rotation via the belowground effect.},
}

@article {pmid41868371,
year = {2026},
author = {Bel Mokhtar, N and Stathopoulou, P and Asimakis, E and Augustinos, A and Salgueiro, J and Alleck, M and Sookar, P and Dembilio, Ó and Segura, DF and Tsiamis, G},
title = {Evolutionary dynamics of type VI secretion systems in fruit fly-associated Enterobacter.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755534},
pmid = {41868371},
issn = {1664-302X},
abstract = {Species in the genus Enterobacter are widely distributed and occupy diverse ecological niches. Although many species within this genus have been extensively isolated and characterized, their symbiotic associations with Tephritidae fruit flies remain understudied, particularly through comparative genomic analyses. To address this gap, we conducted a whole-genome comparative analysis of thirteen Enterobacter strains isolated from the most economically significant fruit fly species: Anastrepha fraterculus, Bactrocera dorsalis, Bactrocera zonata, Ceratitis capitata, and Zeugodacus cucurbitae. The results revealed that different fruit flies harbor distinct Enterobacter species, with Enterobacter hormaechei being the most prevalent across hosts. Notably, distinct E. hormaechei subspecies were associated with specific hosts, suggesting a potential host-driven adaptation and coevolution. Pangenome analysis highlighted a dynamic genetic structure among these strains, with significant differences in the core, shell, and species-specific gene composition. The high proportion of metabolism-related genes in the core genome suggests a conserved role in essential biological functions, whereas the enrichment of mobile genetic elements (prophages and transposons) and cell motility genes within the shell and species-specific genomes highlights the genomic plasticity and potential host-specific adaptations. Three distinct subtypes of T6SS (type VI secretion systems) gene clusters, T6SS_C1, T6SS_C2, and T6SS_C3, were detected across Enterobacter strains. T6SS_C1 and T6SS_C2 were identified in most Enterobacter strains, whereas T6SS_C3 cluster was restricted to a single isolate. Although these clusters contained thirteen core T6SS genes, they were characterized by different gene synteny and effector/immunity gene content, suggesting that different Enterobacter strains may utilize distinct mechanisms for interbacterial interactions, host manipulation, and environmental adaptation. Overall, our findings reveal the genetic basis of the symbiosis between Enterobacter species and fruit flies, shedding light on their evolutionary dynamics, diversity of T6SS, and functional traits. These results open new avenues for developing microbiome-based strategies for pest management, including the targeted manipulation of microbial communities to enhance sterile insect technique (SIT) outcomes.},
}

@article {pmid41868375,
year = {2026},
author = {Gao, Y and Wang, Z and Cheng, J and Fu, Y and Wang, Y and Sun, Y and Geng, G and Sun, Y},
title = {Effects of Sphingomonads on sugar beet growth and rhizosphere microbiota under continuous cropping.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1793515},
pmid = {41868375},
issn = {1664-302X},
abstract = {INTRODUCTION: Sugar beet is a crucial sugar crop, and its yield and quality are vulnerable to the adverse effects of continuous cropping. Plant growth-promoting rhizobacteria function as biological control agents and exhibit high potential for crop growth promotion.

METHODS: In this study, soil subjected to continuous sugar beet cropping was selected as the experimental substrate to evaluate the effects of Sphingobium abikonense strain W2, Sphingomonas panni strain W9, Sphingomonas sp. strain W13, and their mixed bacterial suspension on sugar beet seedling growth and soil properties using pot experiments. High-throughput sequencing was used to characterize changes in the rhizosphere soil microbial community structure.

RESULTS: The results indicated that Sphingomonads inoculation significantly improved the agronomic performance of sugar beet seedlings, as evidenced by increased plant height, stem diameter, aboveground and root fresh weight, and enhanced nitrogen and phosphorus uptake. In addition, inoculation increased soil pH, available potassium content, and sucrase activity. Microbial community analysis revealed that all inoculation treatments markedly altered the diversity and composition of the rhizosphere microbiome. Compared with the continuous cropping control, the inoculated soils exhibited a significantly higher abundance of Pseudomonadota, exceeding that observed under crop rotation. Moreover, beneficial genera (e.g., Pseudomonas, Cupriavidus, Massilia, and Novosphingobium) were enriched. Functional prediction demonstrated a significant enhancement of key metabolic processes, including ureolysis and xylanolysis.

CONCLUSION: Overall, Sphingomonad inoculation effectively regulated the structure and function of the rhizosphere microbial community, improved soil enzyme activity and nutrient availability, and promoted sugar beet seedling growth. This study provides a theoretical foundation and potential biocontrol strategy for mitigating continuous cropping obstacles in sugar beet cultivation.},
}

@article {pmid41868536,
year = {2026},
author = {Liu, Y and Wang, S and Liu, Y and Yu, D and Wang, Q and Tian, Y and Ma, L},
title = {Impact of Dupilumab on the Skin Microbiome in Children Aged 6-12 years with Moderate-to-Severe Atopic Dermatitis.},
journal = {Journal of asthma and allergy},
volume = {19},
number = {},
pages = {570878},
pmid = {41868536},
issn = {1178-6965},
abstract = {PURPOSE: We aimed to investigate alterations in the skin microbiome following treatment and discontinuation of dupilumab in children with atopic dermatitis (AD).

METHODS: In all, 24 pediatric AD patients and 10 pediatric health volunteers (HVs) were included. AD patients were treated with dupilumab for 16 weeks and following by a 12-week discontinuation. Cutaneous samples were collected from HVs, and AD patients at baseline and during dupilumab application period (Week 2, Week 4, Week 8, Week 12, and Week 16) and discontinuation period (Week 22 and Week 28) to conduct sequencing targeting the 16s rRNA V3-V4 regions. Clinical severity was assessed using the Eczema Area and Severity Index (EASI), Individual Signs Score (ISS), Children's Dermatology Life Quality Index scores (CDLQI), Patient Oriented Eczema Measure (POEM), and peak pruritus Numerical Rating Scale (NRS itch).

RESULTS: Dupilumab treatment significantly improved AD characteristics, with reductions in EASI, ISS, CDLQI, POEM, and NRS itch scores (all P < 0.01). Concurrently, 16s rRNA sequencing indicated decline in Staphylococcus aureus abundance and increase in microbial diversity. These changes began to reverse upon treatment discontinuation, coinciding with a trend toward worsening EASI scores. Moreover, a dupilumab-responsive reduction in other bacterial genera such as Aggregatibacter, and Megasphaera were observed; and these alterations could be reversed after treatment cessation.

CONCLUSION: We provided a dynamical pattern of skin bacterial community during and after dupilumab therapy in pediatric AD patients. Our findings suggest that the therapeutic action of dupilumab may extend to modulating a wider range of bacteria than previously recognized. The roles of our identified candidate microbial taxa require further investigation in larger and functional studies.},
}

@article {pmid41868611,
year = {2026},
author = {Jimenez-Arenas, P and Ferrer, M and Ruiz-Rivera, M and Júlvez, J and Bustamante, M and Gascon, M},
title = {The relationship between the gut microbiota and neuropsychological development and behaviour during childhood and adolescence: a systematic review of epidemiological studies.},
journal = {Brain, behavior, & immunity - health},
volume = {53},
number = {},
pages = {101212},
pmid = {41868611},
issn = {2666-3546},
abstract = {Mounting evidence suggests that early-life microbial colonization might shape cognitive development and behaviour. This systematic review summarizes current research on the relationship between the gut microbiota and neuropsychological development and behaviour in children and adolescents (0-18 years). Following PRISMA guidelines, we conducted a comprehensive search across MEDLINE, Scopus, and Web of Science, identifying 78 eligible studies covering both clinical neurodevelopmental disorders and general-population neuropsychological outcomes. We observed a high heterogeneity across studies regarding study design, statistical analyses and the consideration of confounding factors (e.g., diet, medication use), gut microbiota determinations and the assessment of neurobehavioural outcomes. Only 42% of studies used longitudinal designs, and confounding factors were frequently unaddressed. Microbiome alterations in autism spectrum disorder (n = 23 studies) included community structure shifts, elevated Clostridium and Sutterella, and reduced Blautia, Lactobacillus, and Bifidobacterium. Functional and metabolomic analyses suggest immunomodulatory and neuroactive processes as main contributors, including elevated levels of the short-chain fatty acids propionate and valerate. For attention-deficit/hyperactivity disorder (n = 7) findings were less consistent. Associations were modest in the general paediatric population, with Veillonella and Bifidobacterium appearing across multiple studies being more abundant in children with enhanced neuropsychological development. Overall, the evidence highlights potential microbial signatures associated with neurodevelopment, yet methodological limitations constrain causal inference. Most of the studies were of poor to fair quality, often due to technical shortcomings in microbiome assessment and statistical limitations. Future research should prioritize standardized exposure/outcome assessment protocols and multi-omics integration, while underlining the potential of methodological rigour in translating findings into clinically actionable knowledge.},
}

@article {pmid41868718,
year = {2026},
author = {Jia, S and Liu, P and Zhang, H and Zeng, H and Chen, G and Zhao, L},
title = {Why the COPD Microbiome Matters: How Airway Microbes Shape Disease Severity and Treatment Response.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {21},
number = {},
pages = {531521},
pmid = {41868718},
issn = {1178-2005},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy/diagnosis/physiopathology/immunology/drug therapy ; *Microbiota ; *Lung/microbiology/drug effects/physiopathology/immunology ; Dysbiosis ; *Bacteria/drug effects/immunology/pathogenicity/growth & development/classification ; Severity of Illness Index ; Treatment Outcome ; Host-Pathogen Interactions ; Disease Progression ; *Respiratory System/microbiology ; },
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is a heterogeneous disease caused by multiple factors, with diverse clinical manifestations leading to varying treatment outcomes. Dysbiosis of the respiratory microbiome is one of the key contributors to this variability.

OBJECTIVE AND METHODS: Due to differences in microbial detection technologies and sample collection methods, studies on the characteristics of respiratory prokaryotic microbiota and how these microbes influence host functions in COPD patients have yielded variable results. In this review, we conducted a comprehensive search of relevant literature from PubMed, ScienceDirect, and Elsevier, summarizing studies on the characteristics and functional analyses of prokaryotic microbiota under various technical approaches. The goal was to identify common patterns of microbiota changes in COPD across different disease states, as well as individual microbial influences on host functions.

RESULTS: Compared with healthy adults, in stable-phase COPD patients, the relative abundance of Prevotella species in the Bacteroidetes phylum is significantly reduced. During acute exacerbations, the predominant microbiota is composed of Moraxella, Haemophilus, and Streptococcus species from the Proteobacteria and Firmicutes phyla. Clinical indicators in COPD patients are correlated with the abundance of Streptococcus (Firmicutes) and Prevotella (Bacteroidetes) species. Furthermore, the different phyla of respiratory prokaryotic microbiota are associated with innate immunity, metabolism, and inflammation factors related to COPD.

CONCLUSION: This review summarizes evidence on dynamic changes in the airway prokaryotic microbiome during COPD progression. It highlights the dual role of these microbial changes as biomarkers of disease progression and modifiable targets for personalized care. Observed patterns-such as reduced Prevotella abundance in stable disease and the dominance of Moraxella, Haemophilus, and Streptococcus during acute exacerbations-provide a basis for stratifying patients and designing individualized treatment plans. Microbiome analysis may aid in early identification of high-risk patients for preventive strategies, guide pathogen-specific antimicrobial or immunomodulatory therapy, and allow treatment response to be monitored through microbial shifts. By linking distinct microbial profiles to host immune and inflammatory pathways, this approach supports the development of tailored interventions to restore microbial balance. These strategies could improve clinical outcomes and advance precision medicine in COPD management.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/therapy/diagnosis/physiopathology/immunology/drug therapy
*Microbiota
*Lung/microbiology/drug effects/physiopathology/immunology
Dysbiosis
*Bacteria/drug effects/immunology/pathogenicity/growth & development/classification
Severity of Illness Index
Treatment Outcome
Host-Pathogen Interactions
Disease Progression
*Respiratory System/microbiology

@article {pmid41868793,
year = {2026},
author = {Yan, N and Zhang, Y and Wang, S and Hu, S and Ruan, L and Wang, Y and Feng, W and Xiong, W and Zhang, W and Wei, Y and Yao, C},
title = {CAMK1D as a potential therapeutic target for gut microbiota-driven promotion of lung adenocarcinoma development.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e20985},
pmid = {41868793},
issn = {2167-8359},
mesh = {Humans ; *Adenocarcinoma of Lung/genetics/microbiology ; *Gastrointestinal Microbiome/genetics ; *Lung Neoplasms/genetics/microbiology ; Genome-Wide Association Study ; Polymorphism, Single Nucleotide ; *Calcium-Calmodulin-Dependent Protein Kinase Type 1/genetics/metabolism ; Mendelian Randomization Analysis ; },
abstract = {BACKGROUND: The gut microbiome is closely associated with malignant tumors; however the specific mechanisms by which it contributes to the development of lung adenocarcinoma remain unclear. In this study, we performed a two-sample bidirectional Mendelian randomization (MR) analysis to assess the causal relationship between the gut microbiome and lung adenocarcinoma. By identifying single nucleotide polymorphism markers linked to gut microbiome species, we aimed to discover potential biomarkers for lung adenocarcinoma. These findings may offer new insights into the role of the gut microbiome in the prevention and treatment of lung adenocarcinoma.

METHODS: We used genome-wide association study (GWAS) summary statistics to assess the association between the gut microbiome and lung adenocarcinoma through two-sample MR analysis. Sensitivity analyses were performed to confirm the robustness of the findings. Reverse MR analysis and GWAS data integration were employed to identify potential genetic and therapeutic targets. Bioinformatics analysis and quantitative Real-Time PCR (qRT-PCR) were utilized to validate gene expression and explore the underlying mechanisms of key genes.

RESULTS: Our analysis identified two bacterial taxa, Prevotella9 and Parabacteroides, as being causally associated with lung adenocarcinoma, both showing positive causal relationships. Sensitivity analyses confirmed the robustness of these associations. The reverse MR analysis revealed no evidence of reverse causality. GWAS data identified 15 genes (DNAH1, PDE10A, DOCK2, INSYN2B, DNAI3, SUOX, LINC01505, SULT4A1, NT5ELP, LINC02895, calcium/calmodulin dependent protein kinase 1D (CAMK1D), ENSG00000253557, BCAS3, C18orf63, MYO18B) that passed the summary-data-based MR test. The transcriptomic data revealed that five genes (CAMK1D, BCAS3, DNAH1, PDE10A, and C18orf63) were differentially expressed between lung adenocarcinoma patients and healthy individuals. Through qRT-PCR validation, the CAMK1D gene was markedly upregulated in lung adenocarcinoma cell lines, whereas BCAS3, DNAH1, PDE10A, and C18orf63 genes exhibit ed substantially reduced expression.

CONCLUSION: Our study identified specific gut microbial taxa as risk factors for lung adenocarcinoma and proposes CAMK1D as a microbiota-related candidate biomarker and potential therapeutic target that may inform personalized treatment and drug development strategies in the future.},
}

Humans
*Adenocarcinoma of Lung/genetics/microbiology
*Gastrointestinal Microbiome/genetics
*Lung Neoplasms/genetics/microbiology
Genome-Wide Association Study
Polymorphism, Single Nucleotide
*Calcium-Calmodulin-Dependent Protein Kinase Type 1/genetics/metabolism
Mendelian Randomization Analysis

@article {pmid41868872,
year = {2026},
author = {Kyrochristou, I and Kyrochristou, G and Fousekis, F and Katsanos, K and Schizas, D and Vlachos, K and Lianos, GD},
title = {Determinants of the healthy gut microbiome: core features, modifying factors and normal functions.},
journal = {Annals of gastroenterology},
volume = {39},
number = {2},
pages = {191-201},
pmid = {41868872},
issn = {1108-7471},
abstract = {The human gut microbiome represents a complex and dynamic ecosystem that is central to maintaining health and preventing disease. Defining a "normal" gut microbiome remains challenging, given the significant variability arising from host physiology, lifestyle, genetics, geography and environmental exposures. This review synthesizes current evidence regarding the composition and functions of the gut microbiota in healthy individuals from diverse populations. At the taxonomic level, healthy gut microbial communities are typically dominated by the phyla Firmicutes and Bacteroidetes, with additional contributions from Actinobacteria and Proteobacteria. However, substantial inter-individual and regional differences are observed, such as a higher prevalence of Prevotella in populations consuming fiber-rich Eastern diets, and greater Bacteroides abundance in Western cohorts. Anatomical location and health status also influence alpha-diversity, underscoring the need to interpret diversity metrics within context. Furthermore, the gut microbiome performs essential functional roles across multiple organ systems, including fermentation of dietary fibers into short-chain fatty acids, regulation of immune responses, modulation of the gut-brain axis, maintenance of intestinal barrier integrity, and support of cardiovascular and hepatic functions. These findings support the conceptualization of the microbiome as a multifunctional organ system that integrates host and environmental signals. In summary, a healthy gut microbiome is best understood as a dynamic equilibrium, characterized by functional resilience and adaptability, rather than a fixed microbial profile. Interpreting this variability is crucial for developing targeted interventions to prevent disease.},
}

@article {pmid41869364,
year = {2026},
author = {Wang, B and Zhang, Y and Lin, L and Wang, S and Yang, S},
title = {Psoriasis: microbiome dysbiosis and pathogenic mechanisms.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1714515},
pmid = {41869364},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Psoriasis/microbiology/immunology/etiology/therapy ; *Gastrointestinal Microbiome/immunology ; Animals ; *Microbiota/immunology ; Skin/immunology/microbiology ; },
abstract = {Psoriasis is a chronic immune-mediated inflammatory disease whose pathogenesis is a triad of genetic predisposition, immune dysregulation, and environmental triggers. This review provides a novel, in-depth synthesis arguing that microbial dysbiosis is not merely an associative phenomenon but a central regulatory node within this triad, actively shaping immune responses and clinical phenotypes. We move beyond cataloging microbial shifts to construct a detailed mechanistic framework of the gut-skin axis. Gut dysbiosis; characterized by reduced diversity, a diminished Bacteroidetes/Firmicutes ratio, and depleted SCFA producers, compromises intestinal barrier integrity, reduces systemic immunoregulatory tone via diminished SCFA signaling, and promotes Th17 polarization. This systemic inflammation is directly communicated to the skin. Concurrently, cutaneous dysbiosis, featuring Staphylococcus aureus dominance and fungal alterations, disrupts the local barrier, provides chronic antigenic stimulation, and amplifies IL-17-driven inflammation, creating a self-sustaining loop. Crucially, we analyze how specific infections (HCV, H. pylori, Streptococcus) act as environmental triggers by sharing or activating these very pathways. The bidirectional relationship with therapy is dissected: while biologics induce drug-specific microbiome shifts that often correlate with clinical normalization, they also carry infection risks that must be strategically managed. Emerging microbiome-targeted interventions like specific probiotics show promise but are hampered by methodological inconsistencies. This review uniquely highlights the causality gap and proposes that future breakthroughs require a shift from correlation to mechanism. We conclude that the microbiome is a dynamic interface between genes and environment in psoriasis; its successful integration into diagnostic and therapeutic paradigms demands standardized multi-omics approaches, functional validation, and personalized medicine strategies that target this critical axis.},
}

Humans
*Dysbiosis/immunology/microbiology
*Psoriasis/microbiology/immunology/etiology/therapy
*Gastrointestinal Microbiome/immunology
Animals
*Microbiota/immunology
Skin/immunology/microbiology

@article {pmid41869707,
year = {2026},
author = {Wang, Z and Fu, Y},
title = {Bacteria weigh up costs and benefits of mobile weapons.},
journal = {eLife},
volume = {15},
number = {},
pages = {},
pmid = {41869707},
issn = {2050-084X},
mesh = {*Gastrointestinal Microbiome ; Humans ; *Bacteria/genetics/metabolism ; },
abstract = {Gaining the ability to kill rival microbes is not always an advantage for bacteria in complex gut microbiomes.},
}

*Gastrointestinal Microbiome
Humans
*Bacteria/genetics/metabolism

@article {pmid41869810,
year = {2026},
author = {Zhang, C and Sun, Z and Lin, Y and Long, W and Zhang, R and Huang, H and Liang, W},
title = {Pulmonary mucoid Pseudomonas aeruginosa infection and association with higher species richness and stronger inflammatory immune response.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0229525},
doi = {10.1128/spectrum.02295-25},
pmid = {41869810},
issn = {2165-0497},
abstract = {The mucoid phenotype of Pseudomonas aeruginosa (PA) is regarded as a comprehensive adaptive stress response to difficult environmental circumstances. However, there is little knowledge about the relationship between the prevalence of mucoid PA and species richness and immune inflammatory response. A case-control study was conducted in hospitalized patients with pulmonary infections caused by mucoid and non-mucoid PA. Sputum samples were subjected to 16S rDNA sequencing to characterize microbial diversity and taxonomic composition, while serum levels of TNF-α, IL-6, IL-8, IL-10, and IL-17 were measured using enzyme-linked immunosorbent assays. Subsequent statistical analysis using R 4.0 revealed significant correlations between differentially abundant microbial taxa and cytokine profiles. Compared to the non-mucoid PA group, the mucoid PA group demonstrated significantly higher α-diversity indices in terms of species richness, as indicated by the Chao1 (P = 0.0015) and Observed-species metrics (P = 0.0014). Furthermore, distinct β-diversity patterns were observed between the two groups (P < 0.05). LefSe analysis revealed significant enrichment of Veillonella spp., Haemophilus spp., Porphyromonas spp., Prevotella spp., Actinomyces spp., Lactobacillus spp., and Rothia spp. in the mucoid PA group, while Stenotrophomonas spp., Acinetobacter spp., Parvimonas spp., and Serratia spp. dominated in the non-mucoid PA group. The mucoid PA infections showed marked elevation of IL-8 (P = 0.0137), TNF-α (P = 0.0048), IL-10 (P = 0.0042), IL-17 (P = 0.0220), and IL-6 (P = 0.0001). Spearman correlation revealed Veillonella spp./Rothia spp./Porphyromonas spp./Prevotella spp. positively correlated with IL-10/TNF-α/IL-17/IL-6, whereas Haemophilus spp. showed a negative relationship with IL-17. Stenotrophomonas spp. exhibited strong negative correlations with IL-10/IL-6, and Serratia spp. was inversely associated with TNF-α in non-mucoid PA infections. Clinically distinct microbial ecosystems in mucoid PA correlate with exacerbated inflammation. This phenotype-driven dichotomy provides actionable biomarkers for stratified antimicrobial/immunomodulatory therapies in chronic lung disease.IMPORTANCEThis study holds significant clinical and scientific importance, as it elucidates the critical differences between mucoid and non-mucoid Pseudomonas aeruginosa (PA) infections in pulmonary patients. By demonstrating that mucoid PA infections are associated with distinct microbial ecosystems (higher species richness and different taxonomic compositions) and more severe inflammatory responses (elevated TNF-α, IL-6, IL-8, IL-10, and IL-17), the research provides crucial insights into phenotype-specific pathogenesis. The identified correlations between specific bacterial species (e.g., Veillonella/Rothia with pro-inflammatory cytokines) offer potential biomarkers for clinical stratification. These findings are particularly valuable for developing targeted therapeutic strategies, as they suggest mucoid PA infections may require different antimicrobial/immunomodulatory approaches compared to non-mucoid variants. The study bridges an important knowledge gap in understanding how bacterial phenotypic adaptation influences host-microbiome interactions and disease outcomes in chronic lung infections.},
}

@article {pmid41869813,
year = {2026},
author = {Mancabelli, L and Palomba, E and Magni, F and Chatenoud, L and Olgiati, I and Buracchi, C and Bugarin, C and Gaipa, G and Abbruzzese, C and Filippini, M and Forastieri, A and Fumagalli, R and Geraldini, F and Picetti, E and Terranova, L and Vaschetto, R and Zoerle, T and Ventura, M and Citerio, G and Gori, A and Bandera, A and Alagna, L and Turroni, F},
title = {Microbial signatures and host immune responses associated with the development of ventilator-associated pneumonia among patients with neurological injuries.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0319325},
doi = {10.1128/spectrum.03193-25},
pmid = {41869813},
issn = {2165-0497},
abstract = {Ventilator-associated pneumonia (VAP) remains a leading complication in mechanically ventilated patients, yet the contribution of the respiratory microbiota remains poorly understood. The PULMIVAP study is a multicenter, longitudinal cohort investigation of respiratory microbiota composition and host immune responses in critically ill adults intubated for non-pulmonary conditions. A total of 146 intubated adult patients were enrolled across eight Italian ICUs, forming matched groups of 73 with VAP and 73 without. Oropharyngeal swabs and endotracheal aspirates were collected at intubation and either at VAP diagnosis or at a matched point in controls for a total of 584 biological samples. Metataxonomic analyses revealed substantial temporal shifts in microbial communities across both upper and lower respiratory compartments, with a trend toward reduced microbial richness in patients who developed VAP. Several genera, such as Corynebacterium, were more abundant in no-VAP patients, whereas Escherichia-Shigella and Peptoniphilus were enriched in VAP samples. Cytokine-microbiota correlation analysis suggested a pro-inflammatory signature in VAP patients, with Citrobacter positively associated with IFN-γ and TNF-α, while several commensal genera were inversely correlated with inflammatory mediators. Additionally, taxa associated with VAP correlated with lower PaO2/FiO2 ratios, implicating them in disease severity. Consistently, several bacteria, such as Corynebacterium, appeared to be linked to better respiratory outcomes, suggesting protective or risk-associated microbial profiles. Overall, these findings highlight the complex interplay between microbial communities and mucosal immunity in the pathogenesis of VAP. The identification of condition-associated microbial and immunological signatures may inform future strategies for risk stratification and targeted prevention.IMPORTANCEVentilator-associated pneumonia (VAP) remains a major complication of mechanical ventilation, yet most microbiome studies have focused on late-stage infection or single airway compartments, limiting insight into early microbial dynamics associated with VAP risk. By longitudinally characterizing upper and lower airway microbiota before and during VAP development, this study provides new insights into microbial and immune patterns associated with susceptibility and disease severity in humans. These findings contribute to the current understanding of VAP pathogenesis by suggesting a role for early airway dysbiosis and local immune responses alongside clinical factors. Remarkably, the identification of taxa associated with risk or protection supports the potential for microbiota-informed monitoring and future risk stratification strategies during mechanical ventilation.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT04849039.},
}

@article {pmid41869814,
year = {2026},
author = {Yang, K and Yang, Z and Li, H and Liu, H and Cao, S and Bao, Y and Feng, L and Zhang, L and Niu, J and Tian, T},
title = {Effects of heavy metal exposure on oral microbial communities in women with different menopausal status.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0312325},
doi = {10.1128/spectrum.03123-25},
pmid = {41869814},
issn = {2165-0497},
abstract = {This study investigates the effects of long-term heavy metal exposure on the oral mucosal microbiota in women. By measuring both external environmental heavy metal exposure and internal heavy metal exposure indicators in the human body, it aims to elucidate the complex interactions between external environmental exposure and internal exposure, as well as their potential association with menopausal status. We analyzed oral microbial composition, function, and co-occurrence networks in 47 women from polluted and control areas. Heavy metal exposure significantly altered oral microbial diversity and functional pathways, with molybdenum (Mo) exhibiting a uniquely strong influence. Key metabolic pathways related to cardiovascular disease and carbohydrate metabolism were enriched in specific groups. Network analysis revealed a loss of keystone species and structural simplification in postmenopausal women from the polluted area. These findings suggest that heavy metal exposure alters oral microbial communities, and these alterations correlate with shifts in host metabolic pathways that are known to be associated with menopausal hormonal changes, potentially impacting women's health during this transition.IMPORTANCEThis study reveals, for the first time, how chronic heavy metal exposure and menopause interact to disrupt the female oral microbiome. We identify Mo as a key metal, correlating strongly with specific bacteria and linked to downregulated cardiovascular and metabolic pathways. Critically, postmenopausal women in polluted areas exhibit a severe loss of keystone species and a collapsed microbial network structure. These findings position the dysregulated oral microbiome as a potential mechanistic link between environmental metal exposure and the heightened systemic risks-such as metabolic disorders and chronic inflammation-observed in postmenopausal women, highlighting new targets for preventive health strategies.},
}

@article {pmid41869817,
year = {2026},
author = {Chong, Q and Cheng, M and Cao, Q and He, J and Xiao, M and Li, Y and Wang, Z and Wang, J and Zhang, K and Gou, H},
title = {Systematic evaluation of phage cocktail-ciprofloxacin combination therapy against multidrug-resistant Salmonella Typhimurium induced gut dysbiosis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0264025},
doi = {10.1128/spectrum.02640-25},
pmid = {41869817},
issn = {2165-0497},
abstract = {Phage therapy, despite its promise as a novel therapeutic alternative for multidrug-resistant (MDR) bacterial infections, is hampered by clinical limitations such as narrow host range and therapeutic inconsistency. This research has engineered a phage-antibiotic synergistic therapy enabling precision eradication of drug-resistant Salmonella Typhimurium (S. Typhimurium). From slaughterhouse wastewater and fecal samples, three Felixounavirus phages (TSP_TW2, TSP_SW1, and TSP_SJ5) were isolated. Compared to the clinical phage repository, these phages demonstrated more superior broad-spectrum activity, successfully lysing over 85% of the tested wild-type isolates. The in vitro study, validated by laser confocal fluorescence imaging demonstrates that compared to solitary phage, phage cocktail delays the emergence of resistance to 24 h while also achieving effective biofilm eradication. In the murine intestinal infection model, the experimental group treated with phage cocktail in combination with ciprofloxacin (CIP) demonstrated significant therapeutic effects, reaching 90% survival rate, restoring the CD4[+]/CD8[+] T cell balance, and decreasing the levels of pro-inflammatory factors, which were significantly superior to those of phage or CIP alone. In addition, the susceptibility of S. Typhimurium to β-lactams, quinolones, and observed four- to eightfold reduction in tetracycline minimal inhibitory concentration (MIC) demonstrated effective restoration of antibacterial activity after therapeutic intervention. 16S rRNA high-throughput sequencing showed that the index of intestinal flora diversity of mice in the treatment group was not significantly difference to healthy control group, while specifically promoting the growth of beneficial microbial populations such as Lactobacillus spp. The innovative phage-antibiotic combination therapy established in this study demonstrated dual therapeutic advantages: effective clearance of antimicrobial-resistant strains and maintenance of enteric microbiome homeostasis, thereby offering a clinically promising strategy for controlling infections caused by antimicrobial-resistant S. Typhimurium.IMPORTANCEFoodborne Salmonella infections threaten global public health, as conventional antibiotics accelerate resistance and disrupt microbial balance. We pioneer a synergistic phage-ciprofloxacin cocktail strategy that overcomes multidrug-resistant Salmonella infection through three key advances: First, it delays resistance evolution while eradicating biofilm matrices; second, the therapy synergistically enhances antibiotic sensitivity to restore efficacy of critical drugs; and third, the combined approach maintains optimal gut microbiota balance during pathogen clearance. By using environmentally derived phages with minimized antibiotic dosing, this strategy achieves targeted removal of resistant pathogens-including invasive biofilms-without collateral damage to commensal flora. Crucially, it prevents systemic inflammation and preserves intestinal barrier function. This ecologically sustainable paradigm provides a dual-defense mechanism against infections and microbiome dysbiosis, positioning phage-antibiotic synergy as a transformative tool for containing foodborne disease threats.},
}

@article {pmid41869825,
year = {2026},
author = {Mehta, A and Stebliankin, V and Mathee, K and Narasimhan, G},
title = {MEditome: Computational Detection of RNA Edit Sites Using de Novo Assembly in Microbiomes.},
journal = {Journal of computational biology : a journal of computational molecular cell biology},
volume = {},
number = {},
pages = {15578666261428562},
doi = {10.1177/15578666261428562},
pmid = {41869825},
issn = {1557-8666},
abstract = {RNA editing is a post-transcriptional modification that alters single-nucleotide sites within RNA strands, thus diversifying transcriptomes and proteomes and modulating gene expression. While better characterized in eukaryotes and in a few microbes, the study of RNA editing in entire microbiomes remains unexplored. Recent studies have demonstrated that A-to-I RNA editing contributes to bacterial adaptation and pathogenicity. Previously, we developed MetaEdit, a reference-based computational pipeline to detect RNA edit sites in microbiomes. While MetaEdit successfully identified RNA edit sites in Escherichia coli within the context of the human gut microbiome, including previously reported loci, it relied primarily on aligning reads to reference genomes of target bacteria. This dependence on reference genomes introduced potential biases, as editing can only be identified in reference genomes, while editing in novel microbial strains missing from the reference databases could be overlooked. Even for reference genomes, the search for edit sites is inefficient since it would have to be conducted one reference genome at a time.Here, we introduce MEditome, employing de novo assembly to overcome these limitations. This crucial change enables the detection of RNA edit sites across all microbial organisms in the microbiome, including novel bacterial strains for which comprehensive reference genomes are unavailable. Using sequencing data from the Integrative Human Microbiome Project, MEditome identified 2,295 unique RNA editing sites across diverse bacterial taxa. Several of these overlaps with previously identified edits in E. coli detected by MetaEdit in hok/gef gene family and arginine-associated genes, providing in silico validation of accuracy. We observed taxon-specific editing patterns and gene-level differential editing associated with inflammatory bowel disease, highlighting RNA editing as a potential regulatory mechanism influencing microbial adaptation and host-microbe interactions.},
}

@article {pmid41869845,
year = {2026},
author = {Suk, K and Lee, WH},
title = {Peptidoglycan recognition proteins in the brain: Role in neuroinflammation and behavioral consequences.},
journal = {Histology and histopathology},
volume = {},
number = {},
pages = {25064},
doi = {10.14670/HH-25-064},
pmid = {41869845},
issn = {1699-5848},
support = {RS-2024-00408736//National Research Foundation of Korea (NRF), Korean government/ ; },
abstract = {Peptidoglycan recognition proteins (PGRPs) constitute an evolutionarily conserved family of pattern recognition molecules that detect bacterial peptidoglycan. While their antimicrobial functions have been well characterized in peripheral immunity, recent discoveries have unveiled critical roles for PGRPs in central nervous system inflammation and behavior. Among the four mammalian PGRP family members, PGLYRP1 exhibits unique expression in brain microglia and demonstrates potent pro-inflammatory properties in neurological contexts. Recently, PGLYRP1 has been shown to function as a key amplifier of neuroinflammation through a novel TREM1-Syk-Erk1/2-Stat3 signaling axis, establishing a positive feedback loop with TNF-α that perpetuates microglial activation. This review synthesizes current understanding of PGRP biology in the nervous system, with particular emphasis on molecular mechanisms of PGLYRP1, cellular sources, and behavioral consequences. We examine the structural basis of peptidoglycan recognition, cell-type-specific expression patterns, signaling pathways, and integration with other innate immune systems. Furthermore, we explore emerging connections between gut microbiome-derived peptidoglycan, blood-brain barrier penetration, and neuropsychiatric disorders. Critical knowledge gaps remain regarding physiological versus pathological roles of PGLYRP1, therapeutic targeting strategies, and translational potential. Understanding PGLYRP1-mediated neuroinflammation provides novel mechanistic insights into microbiome-brain communication and offers promising therapeutic avenues for neuroinflammatory and neurodegenerative diseases.},
}

@article {pmid41869887,
year = {2026},
author = {Wang, Z and Guo, S and Li, J and Huang, Q and Ning, J and Xia, B and Lv, X and Liu, X and Gao, Z and Li, J and Liu, L and Song, M and Wang, J},
title = {Identifying Cytokine Motif-Containing, Immunomodulatory Bacterial Proteins in Human Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e20332},
doi = {10.1002/advs.202520332},
pmid = {41869887},
issn = {2198-3844},
support = {2025YFA1309200//National Key Research and Development Program of China/ ; 2023KF-05//Open funding project of State Key Laboratory of Pharmaceutical preparation/ ; },
abstract = {Accumulating evidence emphasizes the importance of microbiota-immune interactions in health and disease development, and identified bacteria-derived small-molecule metabolites as well as macromolecules such as peptides and proteins as promising therapeutic approaches. Here, we identify cytokine motif-containing, immunomodulatory bacterial proteins (CMCPs) as a special category of bacterial proteins in both bacterial genomes and gut metagenomes using Hidden Markov Models (HMMs). We further find eight colorectal cancer‑associated CMCPs differentially enriched in patients or healthy controls. Engineered E. coli Nissle 1917 (EcN) expressing selected CMCPs administered to Apc[min/+] mice selectively colonize intestinal tumors, deliver functional CMCPs in situ, and elicit significant antitumor immune responses while reducing tumor burden. In vitro, purified CMCPs modulate mouse splenic T cells, bone marrow‑derived macrophages and dendritic cells. Our findings indicate that bacterially encoded CMCPs can directly modulate tumor immunity and serve as microbiota‑derived proteins as candidate immunomodulators, which can further be applied in microbiome-mediated immune therapies for CRC.},
}

@article {pmid41869963,
year = {2026},
author = {Zhong, X and Chen, W and Sun, Q and Zhang, S and Yang, J and Min, W and Li, W},
title = {Crisaborole Reduced the Staphylococci but Increased Cutibacterium on the Skin Microbiome of Children with Atopic Dermatitis.},
journal = {Dermatitis : contact, atopic, occupational, drug},
volume = {},
number = {},
pages = {17103568261431028},
doi = {10.1177/17103568261431028},
pmid = {41869963},
issn = {2162-5220},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a common, recurrent skin disease in children, associated with an imbalance in the skin microbiome. Topical corticosteroids (TCS) cream is the first-line drug for treating AD. However, its long-term use is prone to the development of adverse reactions. Crisaborole, a nonsteroidal medication, is effective and well-tolerated for long-term maintenance treatment and flare reduction in adult and pediatric patients with mild-to-moderate AD. However, the effect of crisaborole on the skin microbiome remains unknown.

OBJECTIVE: The study aimed to compare the effects of topical crisaborole treatment and TCS treatment on microbial abundance and diversity in AD lesions.

METHODS: A cross-sectional study was conducted involving 30 children with mild-to-moderate AD and 10 healthy controls. Patients with AD were divided into three groups (untreated, TCS, and crisaborole; n = 10 each) based on baseline status. Skin samples were collected directly from the healthy child, the untreated lesions, and after a 2-week treatment period. The skin microbiome was analyzed using 16S rRNA gene sequencing.

RESULTS: Compared to the untreated AD group, both TCS and crisaborole treatments significantly reduced the relative abundances of Staphylococcus and Pseudomonas, while increasing the abundances of Streptococcus and Cutibacterium (formerly Propionibacterium). Alpha diversity of the skin microbiome was significantly increased after both treatments. However, the microbial profile of the crisaborole group was more distinct from the healthy control group than the TCS group was. Furthermore, the crisaborole group showed significant enrichment of taxa from the phylum Actinobacteria, including the genus Cutibacterium and species acnes.

CONCLUSIONS: Although the efficacy of crisaborole in treating mild-to-moderate AD in children is not equivalent to that of TCS, crisaborole could still remarkably improve the clinical symptoms of patients and partially restore the microbial diversity on the skin surface of children with AD.},
}

@article {pmid41869966,
year = {2026},
author = {Yu, T and Fan, H},
title = {Host-microbiota interactions: a novel insight into the aryl hydrocarbon receptor in Parkinson's disease.},
journal = {Postgraduate medical journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/postmj/qgag017},
pmid = {41869966},
issn = {1469-0756},
abstract = {BACKGROUND: Parkinson's disease (PD) is regarded as the second most common neurodegenerative disease. Accumulating evidence suggested an emerging effect of the dysregulation of the gut-brain axis in the neurodegenerative disease pathogenesis, mediated particularly by microbiota-derived metabolites in PD. The aryl hydrocarbon receptor (AHR) is of great importance in regulating central nervous system inflammation by sensing microbiota-derived metabolites.

STRATEGY: AHR is a transcription factor activated by ligands, which can be activated locally or remotely by endogenous microbial metabolites. AHR signaling suppressed inflammation by activating anti-inflammatory and immunosuppressive responses, promoting intestinal host-microbiome homeostasis. The pathogenesis of PD is related to the activation of microglia and the occurrence of neuroinflammation. There is increasing attention that alterations in the intestinal flora and decreased AHR activity were closely associated with PD.

CONCLUSION: The AHR-gut microbiota axis garnered increasing attention in PD research. In this review, we synthesize current clinical and preclinical evidence linking the AHR-gut microbiota axis to PD pathogenesis, and we highlight that pharmacological targeting of this pathway represents an emerging therapeutic strategy for PD.},
}

@article {pmid41870062,
year = {2026},
author = {Weingarten, EA and Fernando, BM and Freitas, MR and Indest, KJ},
title = {Cave microbial communities are structured by environmental matrix and depth and can be characterized with field-portable assays.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0031226},
doi = {10.1128/aem.00312-26},
pmid = {41870062},
issn = {1098-5336},
abstract = {UNLABELLED: Terrestrial caves are unique ecosystems characterized by environmental stability, nutrient limitation, and absence of light, yet they host diverse microbial communities with ecological and public health relevance. Microbiome studies of caves have typically been limited in scope, sampling only select environments or cave depths. We conducted a broad survey of microbial diversity in three natural limestone caves and two abandoned mines spanning continental, subtropical, and arid climates in the United States. Using amplicon sequencing of 382 samples composed of soil, rock, water, air, and bat and rodent feces, microbiome composition was found to be primarily structured by cave location, followed by environmental matrix (soil, water, air, etc.), and transect distance from the cave entrance. Significant heterogeneity was observed both between and within caves, underscoring the need for spatially explicit and multi-matrix sampling to capture representative community profiles. Portable DNA extraction and quantitative PCR (qPCR) technologies for onsite detection of microbial pathogens were further validated, demonstrating comparable results to laboratory-based workflows and reducing sample-to-result turnaround time from several days to less than 2 h. Pathogen panels detected zoonotic and waterborne agents of human health concern, including Salmonella and Legionella, directly from cave environments. Collectively, our findings establish a methodological framework for robust microbiome characterization in subterranean ecosystems and highlight the feasibility of field-deployable genetic tools for both biodiversity mapping and rapid pathogen surveillance. These approaches will enable more systematic monitoring of cave environments, with applications for ecology, conservation, and public health.

IMPORTANCE: Caves and mines represent extreme and isolated environments that harbor unique microbial communities, yet they remain among the least studied environments on Earth. Understanding how these communities are structured across different habitats and locations is essential for both ecological research and public health monitoring. In this study, we surveyed microbiomes across multiple caves and environmental materials to reveal how location, substrate type, and depth shape microbial diversity. We also demonstrated that portable DNA extraction and analysis tools can be used in the field to rapidly detect microorganisms, including potential pathogens, without the need for laboratory infrastructure. These results provide new insight into how microbial life is distributed in subterranean ecosystems and establish practical methods for monitoring microbial diversity and detecting pathogens in remote environments.},
}

@article {pmid41870087,
year = {2026},
author = {Wang, X and Wu, W and Yang, B and Liu, Y and Xu, Y and Wang, L and Lv, X and Gao, J and Lu, M and Yu, A and Li, N and Chen, Q and Lu, L and Zhao, D},
title = {Additive effects of fecal microbiota transplantation and infliximab on gut microbiome and metabolome in refractory inflammatory bowel disease patients.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0077425},
doi = {10.1128/msystems.00774-25},
pmid = {41870087},
issn = {2379-5077},
abstract = {UNLABELLED: Fecal microbiota transplantation (FMT) is an emerging therapy for inflammatory bowel disease (IBD), yet its efficacy in patients refractory to conventional treatments and its underlying mechanisms require further elucidation. We studied 37 IBD patients (15 ulcerative colitis [UC], 22 Crohn's disease [CD]) refractory to conventional therapies and 16 healthy donors. FMT monotherapy from a single donor induced week-4 clinical response in 12 UC and 9 biologic-naïve CD patients, with all responders sustaining remission and most achieving endoscopic remission by week 14. Integrated multi-omics revealed FMT restored microbial diversity and profoundly reorganized host-microbiota-metabolite networks. In nine refractory CD patients (7 infliximab [IFX] non-responders, 2 FMT non-responders), IFX-FMT combination led to week-4 response in 6 patients, all of whom attained clinical and endoscopic remission by week 14, with more complete microbial-metabolic restoration than monotherapy. Our findings establish that FMT induces remission in refractory IBD via ecosystem network rewiring, and that IFX-FMT exhibits additive effects, supporting further trials of microbiome-directed adjunctive strategies.

IMPORTANCE: This study provides mechanistic and clinical insights into the therapeutic effects of fecal microbiota transplantation (FMT) in inflammatory bowel disease (IBD), particularly when combined with the anti-tumor necrosis factor (anti-TNF) biologic infliximab (IFX). While both FMT and IFX achieve response in approximately 60% of IBD patients, their combined influence on the gut microbial and metabolic landscape in refractory disease has been poorly understood. Here, we demonstrate that FMT monotherapy restores gut microbial diversity and reconfigures host-microbiota-metabolite networks, correlating with clinical and endoscopic remission in patients refractory to conventional treatments. Furthermore, in Crohn's disease patients unresponsive to either therapy alone, combined IFX-FMT induced more complete microbial and metabolic normalization and achieved remission where monotherapy had failed. These findings reveal ecosystem-level network rewiring as a central mechanism of FMT efficacy and establish the additive potential of combining microbiome-targeted and immunomodulatory therapies. This work supports the development of microbiome-informed adjunctive strategies for severe or refractory IBD, highlighting an actionable path toward personalized, mechanism-based treatment regimens.

CLINICAL TRIALS: This study is registered with ClinicalTrials.gov as NCT07149441.},
}

@article {pmid41870088,
year = {2026},
author = {Park, J-Y and Yoon, CK and Lee, J-J and Shin, YJ and Kim, B-S},
title = {Potential role of the ocular surface microbiome in dry eye: microbial interactions and symptom alleviation.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0010426},
doi = {10.1128/msystems.00104-26},
pmid = {41870088},
issn = {2379-5077},
abstract = {Dry eye is a prevalent ocular disorder characterized by tear film instability, inflammation, and ocular discomfort. Although the ocular surface (OS) microbiome contributes to immune regulation and pathogen defense, its role in dry eye pathophysiology remains unclear. Therefore, the present study aimed to characterize alterations in the OS microbiome of patients with dry eye undergoing cyclosporin A or NewHyalUni treatment and to identify their potential roles related to clinical improvement. Patients with dry eye were treated with either cyclosporin A and NewHyalUni drop combination or NewHyalUni alone. OS samples were collected before and after treatment, and the microbiome was analyzed by whole metagenome sequencing. Potential contaminants were removed before downstream analysis to account for the low-biomass nature of OS samples. Clinical evaluations included symptom scores and the assessment of meibomian gland dysfunction (MGD). No significant differences in the overall microbial composition were observed between the treatment groups. Nevertheless, both groups demonstrated symptomatic improvement. OS microbiome alterations were strongly correlated with improvements in MGD scores. Moreover, microbial interactions were found to shift following treatment. Key species (Staphylococcus epidermidis, Staphylococcus pseudintermedius, Streptomyces lividans, and Edwardsiella tarda) were identified as potential mediators of MGD score improvement by modulating microbiome functions and suppressing inflammation-associated species. Although distinct treatment regimens did not lead to divergent microbiome profiles, symptomatic improvement was associated with alterations in a specific microbiome. These findings highlight the OS microbiome's potential role in dry eye and support the development of microbiome-based therapeutic strategies.IMPORTANCEDry eye is a common ocular disorder with complex pathophysiology that extends beyond tear deficiency and inflammation. Despite growing evidence of host-microbiome interactions at mucosal surfaces, the contribution of the ocular surface (OS) microbiome to dry eye remains poorly understood. Our findings in this study reveal that shifts in specific taxa and ecological interactions correlate with improvements in meibomian gland function and dry eye symptoms, even in the absence of major changes in overall microbiota. By identifying microbial signatures potentially linked to clinical improvement, we provide systems-level insight into the role of low-biomass microbiomes in ocular health. This work expands the current understanding of microbiome-host dynamics in non-gut environments and supports future development of microbiome-informed therapeutic strategies.CLINICAL TRIALSThis study is registered with ClinicalTrials.gov as NCT06936462.},
}

@article {pmid41870192,
year = {2026},
author = {Ranga, A and Malhotra, AG and Singh, J and Pandey, KM},
title = {Genomic Sequencing from Sanger to Next-Generation Sequencing: Historical Context, Comparative Advances, and Prospects for Next-Generation Phenomics.},
journal = {Omics : a journal of integrative biology},
volume = {},
number = {},
pages = {15578100261433762},
doi = {10.1177/15578100261433762},
pmid = {41870192},
issn = {1557-8100},
abstract = {DNA sequencing has revolutionized biological and biomedical research, offering profound insights into genome organization, function, and variability. From the pioneering Sanger capillary electrophoresis method to the advent of next-generation sequencing, the field has evolved toward unprecedented speed, scalability, and cost decreases over the years. These advancements have enabled diverse applications across genomics, transcriptomics, metagenomics, epigenomics, and precision medicine, powering global initiatives such as the Human Genome Project, the Human Microbiome Project, and the 1000 Genomes Project. Bioinformatics has also advanced in data processing, variant detection, and functional annotation, helping transform raw sequencing data into biologically meaningful insights and knowledge. Although highly advanced, sequencing technologies still encounter challenges, including accuracy trade-offs and the need for efficient management of rapidly increasing volumes of data. Leveraging the genomic revolution, this review explores the shifts toward next-generation phenomics (NGP), an archetype that uses artificial intelligence that integrates multi-omics data with digital phenotyping, the Internet of Things, and real-time analytics. The goal of NGP is to integrate genotypic and phenotypic data to support predictive modeling of health, disease, and environmental interactions. By tracing history, advances in sequencing technologies, and future perspectives on NGP, this article offers a comprehensive overview for researchers and clinicians, highlighting how the integration of omics and digital data will drive the generation of personalized and systems-level biology.},
}

@article {pmid41870248,
year = {2026},
author = {Deng, Y and Zhen, X and Xia, R and Zhu, R and Zhang, G and Chen, P and Lai, J and Tao, R},
title = {Integrated Microbiome and Metabolome Analysis for Characterization and Discrimination of Saliva, Semen, Vaginal Secretions, and Their Mixtures.},
journal = {Analytical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.analchem.5c05356},
pmid = {41870248},
issn = {1520-6882},
abstract = {Body fluid identification (BFID) and estimation of time since deposition (TsD) are valuable yet challenging in forensic practice. Previous studies have demonstrated that integrating microbial and metabolomic profiles provides complementary biological insights. Therefore, this study performed untargeted metabolomic profiling and full-length 16S rRNA sequencing on fresh saliva (SA), semen (SE), vaginal secretions (VF), and their mixtures (SA-VF and SE-VF), with additional microbial analysis after 15 and 30 days of indoor exposure. Results showed the single-fluid samples exhibited specific dominant bacterial taxa, whereas the two mixture samples contained detectable bacterial signatures from both constituent fluids. Untargeted UHPLC-QTOF/MS analysis revealed unique metabolic signatures for each body fluid, enriched in biologically relevant pathways like steroid and bile acid metabolism. Moreover, we putatively identified characteristic metabolites, including α-solanine, candicidin, and megalomicin C1, some of which are rare microbial antibiotics. Owing to the exploratory nature and associated constraints of nontargeted approaches, these results serve as a provisional reference for identifying potential candidates. Integration of metabolomic and microbiome data uncovered strong metabolite-microbe correlations, highlighting microbially influenced metabolic networks unique to each body fluid type. Using differential microbes and metabolites individually as input features, the random forest model achieved BFID accuracies of 80 and 83.1%, respectively; however, integrating both sets of features increased accuracy to 100%. In contrast, microbial-based TsD prediction performed well for single-fluid samples but showed reduced effectiveness for mixed samples. Overall, our research highlights the powerful predictive potential and improved predictive accuracy of the integration of microbiome and metabolome data in BFID.},
}

@article {pmid41870398,
year = {2026},
author = {Handoko, C and Singh, A and Dharmage, SC and Hu, YJ and Dashper, SG and Bertelsen, RJ and Lowe, AJ and Lopez, DJ},
title = {The Impact of Early Childhood Caries on Asthma Trajectories During the First 15 Years of Life.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70307},
pmid = {41870398},
issn = {1398-9995},
support = {//Australian Institute of Family Studies/ ; },
}

@article {pmid41870630,
year = {2026},
author = {da Costa, JP and Fraiz, GM and Bonifácio, DB and Milagro, FI and Bressan, J},
title = {Sex-specific differences in salivary microbiota composition and their associations with metabolic health in adults with excess body weight: a secondary cross-sectional analysis.},
journal = {Clinical oral investigations},
volume = {30},
number = {4},
pages = {},
pmid = {41870630},
issn = {1436-3771},
abstract = {OBJECTIVES: Growing evidence links the oral microbiome to obesity-related outcomes, yet the influence of sex-related biological differences on salivary microbial profiles remains insufficiently explored. This exploratory study aimed to characterize the composition, abundance, and diversity of the salivary microbiota in Brazilian men and women with excess body weight and to examine its associations with cardiometabolic markers.

MATERIALS AND METHODS: This cross-sectional secondary analysis of a randomized controlled trial (REBEC: RBR-9832wsx) included 59 adults with excess body weight. Salivary microbiota was profiled through amplification of the 16 S rRNA V4 region, and bioinformatics analyses were performed using the Microbiome Analyst (v2.0). Associations between microbial taxa and clinical variables were assessed using Spearman’s correlation.

RESULTS: Men exhibited greater alpha diversity at the family level by higher Shannon (p = 0.015, rrb = 0.4) and Simpson (p = 0.003, rrb = 0.5) indices. Sex-specific microbial differences were identified: men showed higher levels of genera Tannerella, Lachnoanaerobaculum, and Actinomyces, as well as the putative species-level taxons Tannerella serpentiformis and Lachnoanaerobaculum umeaense, whereas women demonstrated greater abundance of genera Campylobacter, Granulicatella, Moryella, and Scardovia. Among women, Granulicatella genera was positively associated with triglycerides and the TyG index.

CONCLUSION: Men and women with excess body weight exhibited distinct salivary microbiota profiles, with differences in both diversity and taxonomic composition.

CLINICAL RELEVANCE: Sex-specific differences in salivary microbiota composition may be associated with variations in metabolic markers. These findings are exploratory and hypothesis-generating, providing insight into sex-related patterns in the oral microbiome and may help inform future research exploring personalized approaches to cardiometabolic risk assessment.},
}

@article {pmid41870676,
year = {2026},
author = {Božac, E and Žučko, J and Braut, A and Špalj, S and Peršić Bukmir, R and Toplak, N and Hladnik, M and Vitezić, BM},
title = {Supragingival dental biofilm microbiomes of tobacco heating system smokers, cigarette smokers and non-smokers.},
journal = {Clinical oral investigations},
volume = {30},
number = {4},
pages = {},
pmid = {41870676},
issn = {1436-3771},
mesh = {Humans ; *Biofilms ; Cross-Sectional Studies ; Male ; Female ; Adult ; *Microbiota ; *Smokers ; RNA, Ribosomal, 16S ; *Non-Smokers ; Middle Aged ; *Gingiva/microbiology ; DNA, Bacterial ; Heating ; },
abstract = {OBJECTIVES: The study compared the bacterial composition of supragingival dental biofilm (SDB) among smokers and non-smokers (NS).

MATERIALS AND METHODS: This cross-sectional study included 60 subjects allocated into three groups: tobacco heating system smokers (THSS), cigarette smokers (CS) and NS. SDB samples were collected, and bacterial DNA was extracted and prepared for next generation sequencing of the 16s rRNA gene hypervariable regions. Bioinformatic pipelines were applied to assess microbial diversity and taxonomic composition.

RESULTS: No significant differences were observed in alpha diversity (Observed taxa and Shannon index) or beta diversity (Bray-Curtis index) among groups. In contrast, significant differences in microbiome bacterial composition were identified across multiple taxonomic levels. At the genus level, Alysiella (p = 0.016) and Propionibacterium (p = 0.025) were most abundant in THSS, whereas Actinobaculum (p = 0.004), Avibacterium (p = 0.015) and Haemophilus (p = 0.030) predominated in NS. At the species level: Alysiella filiformis (p = 0.006) and Streptococcus thermophilus (p = 0.025) were most abundant in THSS, Streptococcus lactarius (p = 0.05) in CS, and Prevotella multiformis (p = 0.016) and Lactobacillus salivarius (p = 0.018) in NS group.

CONCLUSIONS: Distinct differences in bacterial composition of SDB were observed among THSS, CS and NS. The increased abundance of anaerobic bacteria with cariogenic potential in THSS and CS suggests a more dysbiotic profile and increased pathogenic potential compared to NS.

CLINICAL RELEVANCE: Variations in SDB bacterial composition may influence the pathological potential of dental biofilms in smokers and non-smokers.},
}

Humans
*Biofilms
Cross-Sectional Studies
Male
Female
Adult
*Microbiota
*Smokers
RNA, Ribosomal, 16S
*Non-Smokers
Middle Aged
*Gingiva/microbiology
DNA, Bacterial
Heating

@article {pmid41870852,
year = {2026},
author = {Ellis, JR and Powell, EJ and Tomasovic, LM and Warman, A and Chien, A},
title = {The cutaneous microbiome as a dynamic photoprotective interface against solar radiation.},
journal = {Photochemical & photobiological sciences : Official journal of the European Photochemistry Association and the European Society for Photobiology},
volume = {},
number = {},
pages = {},
pmid = {41870852},
issn = {1474-9092},
}

@article {pmid41871006,
year = {2026},
author = {Londoño-Sierra, DC and Restrepo-Mesa, SL and Costa Antunes, AE and Sivieri, K and Martínez-Galán, JP},
title = {Enhancing the microbiome in the maternal-infant dyad: Perspectives from maternal and infant nutrition.},
journal = {Archivos argentinos de pediatria},
volume = {},
number = {},
pages = {e202510860},
doi = {10.5546/aap.2025-10860.eng},
pmid = {41871006},
issn = {1668-3501},
abstract = {Establishing the microbiome is an important milestone for infant health. The type of delivery, gestational age, antibiotic use, and infant feeding practices significantly impact this process. However, interest in the effects of maternal diet and nutrition has grown. The objective of this review is to present an update on the microbiota in the mother-child dyad and the role of maternal nutritional status and diet in its modulation. Scientific articles in electronic databases were reviewed. Adherence to established dietary guidelines during pregnancy and lactation, as well as otherrecommendations based on the study of foods that are sources of fiber, unsaturated fatty acids, and fermented foods, is a good starting point for promoting a healthy microbiome from the early years of life.},
}

@article {pmid41871143,
year = {2026},
author = {Nguyen, AT and Kim, A and Fernando, C and Kularatne, BMDN and Palmer, DRJ and Hill, JE},
title = {Ligand-binding properties of substrate binding proteins of a maltose uptake system in Gardnerella swidsinskii.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {3},
pages = {},
pmid = {41871143},
issn = {1465-2080},
mesh = {*Maltose/metabolism ; *Bacterial Proteins/metabolism/genetics/chemistry ; Oligosaccharides/metabolism ; Glycogen/metabolism ; Operon ; Ligands ; Protein Binding ; Gene Expression Regulation, Bacterial ; Substrate Specificity ; *Maltose-Binding Proteins/metabolism/genetics ; },
abstract = {Glycogen and its breakdown products, maltose and malto-oligosaccharides, are important carbon sources for vaginal bacteria including Gardnerella species. MusEFGKI transport systems for maltose and malto-oligosaccharides have been identified in all Gardnerella species; however, unlike in other species, the Gardnerella swidsinskii operon encodes two substrate-binding proteins (SBPs) (MusE1345, MusE1346, ~60% amino acid identity). Two SBPs could allow binding of additional ligands, providing a competitive advantage to G. swidsinskii relative to other species with only one SBP. Our objectives were to determine if both genes are expressed in G. swidsinskii and compare the specificity and affinity of G. swidsinskii MusE SBPs for glycogen breakdown products. Gene expression analysis showed the presence of a polycistronic transcript spanning both SBP encoding genes; however, musE1346 transcripts were more abundant, likely due to the presence of an additional promoter identified in the intergenic region. No difference in the relative expression of either gene was observed in isolates grown in media supplemented with glycogen or maltotriose. Predicted structures of both SBPs were highly similar and characteristic of previously characterized maltose-binding proteins. Both proteins had a high affinity for maltose, maltotriose and maltotetraose (K d 10[-6] to 10[-7] M) and much lower affinities to maltopentaose and maltohexaose (K d 10[-3] to 10[-4] M). Our results demonstrate that the affinities of G. swidsinskii MusE SBPs for maltose and malto-oligosaccharides are similar under the same experimental conditions.},
}

*Maltose/metabolism
*Bacterial Proteins/metabolism/genetics/chemistry
Oligosaccharides/metabolism
Glycogen/metabolism
Operon
Ligands
Protein Binding
Gene Expression Regulation, Bacterial
Substrate Specificity
*Maltose-Binding Proteins/metabolism/genetics

@article {pmid41871593,
year = {2026},
author = {von Seth, E and Karlsen, TH and Tanaka, A and Ponsioen, C and Bergquist, A},
title = {Primary sclerosing cholangitis.},
journal = {Lancet (London, England)},
volume = {},
number = {},
pages = {},
doi = {10.1016/S0140-6736(25)02582-6},
pmid = {41871593},
issn = {1474-547X},
abstract = {Primary sclerosing cholangitis is a rare, chronic cholestatic liver disease characterised by biliary inflammation and fibrosis. Inflammatory bowel disease co-occurs in 50-80% of individuals with primary sclerosing cholangitis and there is an increased risk for hepatobiliary and colorectal cancers. Primary sclerosing cholangitis presentation is highly variable but there is usually a slowly progressive fibrosis of the bile ducts with strictures, development of liver fibrosis and cirrhosis, and eventually a need for liver transplantation, after which primary sclerosing cholangitis can reoccur. Primary sclerosing cholangitis is diagnosed mostly at the asymptomatic stage but, as the disease advances, people often have itching, fatigue, upper right abdominal pain, recurrent cholangitis, or complications related to portal hypertension. There are few treatment options and its exact cause and pathogenesis remain unclear. It is widely believed that both genetic and environmental factors are important, with the intestinal microbiome increasingly recognised as crucial to disease development, progression, and outcomes. This Seminar explores the clinical features of primary sclerosing cholangitis, summarises the current understanding of its pathogenesis, and gives insights into the challenges and opportunities in managing the disease.},
}

@article {pmid41871875,
year = {2026},
author = {Zhang, Y and Xu, X and Wang, S and Yin, X and Zhang, B and Zhu, Z and Ji, R and Zhu, J and He, H and Cheng, S and Han, Z and Xie, T and Zhang, X and Wang, Y and Shen, S and Kou, Y and Bao, S and Liu, Y and Cao, B and Bonny, C and Guo, X and Segal, E and Tan, Y and Shen, L and Peng, Z},
title = {Fecal microbiota transplantation combined with anti-PD-1 therapy in refractory microsatellite-stable gastric cancer: a phase I feasibility and safety study.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {3},
pages = {},
doi = {10.1136/jitc-2025-013823},
pmid = {41871875},
issn = {2051-1426},
mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; Male ; Female ; *Stomach Neoplasms/therapy/drug therapy ; Middle Aged ; Aged ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Feasibility Studies ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Adult ; },
abstract = {BACKGROUND: The discovery and therapeutic application of immune checkpoint inhibitors (ICIs) have significantly improved clinical outcomes in cancer treatment. However, the response rate is still low in gastrointestinal (GI) cancers. The gut microbiome's impact on immune modulation is a promising area for overcoming resistance to immunotherapy.

METHODS: This study (NCT04130763) is an open-label, single-arm, single-center, phase I study assessing the safety and efficacy of fecal microbiota transplantation (FMT) from healthy donors in 10 patients with advanced GI cancer resistant to anti-programmed death-ligand 1 (PD-(L)1) treatment. 10 patients with histologically confirmed, unresectable, or metastatic GI cancers (8 gastric, 2 colorectal) who were refractory to anti-PD-(L)1 treatment were enrolled. Patients received initial FMT treatment via oral capsules (60 capsules), followed by a combination therapy phase, where maintenance FMT (10 capsules per treatment) was paired with nivolumab at 3 mg/kg every 2 weeks for six cycles. Serial biomarker assessments were conducted through both fecal and blood sampling.

RESULTS: The combination of FMT and anti-PD-1 treatment was well tolerated with no serious adverse events. The objective response rate was 20% and the disease control rate was 40%. Clinical benefits were associated with colonization of donor-derived immunogenic microbes, and an activated immune status reflected by peripheral immune cell populations. Moreover, microbial signatures were identified for anti-programmed cell death protein-1 (PD-1) responsiveness and validated in an independent cohort.

CONCLUSIONS: This phase I study demonstrates the feasibility and safety of combining FMT with anti-PD-1 therapy in patients with ICI-refractory gastric cancer. The observed preliminary efficacy signals and identified microbial signatures generate hypotheses for future trials to investigate microbiome-based approaches to enhance immunotherapy efficacy.

TRIAL REGISTRATION NUMBER: NCT04130763.},
}

Humans
*Fecal Microbiota Transplantation/methods
Male
Female
*Stomach Neoplasms/therapy/drug therapy
Middle Aged
Aged
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Feasibility Studies
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Adult

@article {pmid41871943,
year = {2026},
author = {Awoniyi, M and El Hag, M and Hernandez, J and Yang, Q and Evans, N and Nemet, I and Ngo, B and Coskuner, D and Zhou, J and Farmer, M and Su, L and Zhou, H and Roach, J and Stappenbeck, T and Sartor, RB},
title = {Dysbiotic microbiota trigger colitis-associated colorectal cancer and imprint a distinctive bile acid profile in a PSC-IBD model.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-336675},
pmid = {41871943},
issn = {1468-3288},
abstract = {BACKGROUND: Primary sclerosing cholangitis-associated UC (PSC-UC) carries excess colorectal neoplasia despite often mild-appearing endoscopy, implicating persistent microscopic inflammation and microbiota-bile acid (BA) dysfunction.

OBJECTIVE: To test whether PSC-UC neoplasia is driven by transferable microbiota-mediated inflammation linked to secondary BA loss.

DESIGN: Surveillance colonoscopies (2012-2022) from PSC-UC (n=251) and UC-only (n=8839) were compared for segmental endoscopic/histological activity and dysplasia. We generated multidrug resistance protein 2 (MDR2)[-/-] × interleukin (IL)-10[-/-] double-knockout (DKO) mice and used germ-free (GF) derivation, faecal microbiota transplantation (FMT), antibiotic conditioning and cohousing with shotgun metagenomics and liquid chromatography-tandem mass spectrometry BA profiling.

RESULTS: PSC-UC showed greater inflammatory activity and a right-shifted dysplasia burden versus UC-only. Under specific-pathogen-free conditions, DKO mice developed early right-predominant colitis and multifocal dysplasia progressing with age. DKO communities were depleted of 7α-dehydroxylation capacity with near absence of deoxycholic and lithocholic acids and no enrichment of canonical bacterial genotoxins. GF DKO mice were protected, whereas live DKO donor FMT reinstated severe colitis and dysplasia; sterile-filtered stool supernatant was inactive. IL-10[-/-] donor FMT or cohousing attenuated colitis and increased recipient secondary BA, whereas wild-type/MDR2[-/-] donor transfers were non-colitogenic. In GF DKO mice, direct deoxycholic acid repletion caused hepatotoxicity.

CONCLUSION: PSC-UC neoplasia associates with transmissible microbiota-dependent inflammation and secondary BA deficiency. Controlled restoration of BA-transforming microbial functions, rather than indiscriminate secondary BA replacement, is a rational translational direction.},
}

@article {pmid41871945,
year = {2026},
author = {Vázquez-Castellanos, JF and Yoon, SJ and Won, SM and Raes, J and Kwon, HC and Si, J and Suk, KT},
title = {Stage-dependent gut microbiome and functional signatures across the liver disease spectrum: an integrative multicohort study.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337436},
pmid = {41871945},
issn = {1468-3288},
abstract = {BACKGROUND: The gut-liver axis plays a critical role in liver disease progression; however, how gut microbial ecology and function vary across disease stages remains unclear.

OBJECTIVE: To define stage-specific microbial and functional signatures and evaluate their diagnostic potential.

DESIGN: We analysed faecal samples from 1168 individuals spanning healthy controls, fatty liver, hepatitis, cirrhosis and hepatocellular carcinoma by 16S rRNA sequencing, with a subset (n=141) profiled by shotgun metagenomics. To increase statistical power and enable external validation, 2376 publicly available metagenomic datasets, including 734 liver-related, were integrated. Machine learning-based multicohort analysis was used to identify microbial biomarkers, assess risk factors and classify disease stages.

RESULTS: Microbial diversity declined and a low-richness enterotype expanded with disease severity. Machine learning revealed a discordance in hepatitis, which lacked taxonomic markers but was defined by a conserved functional signature of biosynthetic upregulation. In contrast, advanced stages featured consistent markers like Ligilactobacillus and Veillonella, with strain-level evidence confirming oral-gut transmission. Functional profiling delineated a metabolic continuum from anabolic precursor synthesis in hepatitis to virulence factor production in cirrhosis and putrefactive metabolism in carcinoma. Comparative analysis confirmed that these signatures were distinct from those in non-liver metabolic and oncologic disorders. Importantly, the expansion of oral-derived Veillonella spp and the low-richness enterotype were significantly associated with increased mortality.

CONCLUSION: This large-scale study delineates stage-dependent ecological and functional remodelling of the gut microbiome across liver diseases. These findings highlight the potential of microbiome-based markers for non-invasive diagnosis and prognostic risk stratification in liver diseases.},
}

@article {pmid41872049,
year = {2026},
author = {Carpay, NC and Kamphorst, K and van Elburg, RM and Vlieger, AM},
title = {Antibiotics in the first week of life are not associated with functional gastrointestinal disorders at 9-12 years of age.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70402},
pmid = {41872049},
issn = {1536-4801},
support = {//None/ ; },
abstract = {OBJECTIVES: Dysbiosis due to early-life antibiotics may contribute to the development of functional gastrointestinal disorders (FGIDs). This follow-up study of a birth cohort primarily investigates the association between antibiotic treatment in the first week of life and the presence of FGIDs at 9-12 years. Secondarily, it examines whether a history of infantile colic or current food allergy is associated with FGIDs.

METHODS: A prospective observational birth cohort of 436 term-born infants was followed up at the age of 9-12 years; 151 received intravenous antibiotics in the first week of life due to suspected early onset sepsis (AB+) and 285 did not (AB-). Participants filled out questionnaires on the presence of FGIDs (Rome IV questionnaire) and food allergies, and FGID diagnoses were reported by general practitioners. Statistical analyses included chi-squared tests and multivariable logistic regression.

RESULTS: 306 of 388 eligible participants (79.5%) participated in the follow-up study: 109 (35.6%) AB+ and 197 (64.4%) AB-. FGID prevalence at 9-12 years was similar in AB+ and AB- (any FGID: odds ratio [OR] 1.083, 95% confidence interval [CI] 0.608-1.932). Infantile colic was not significantly associated with FAPDs after adjusting for confounders (adjusted OR 2.007, 95% CI 0.978-4.003, p = 0.051). Children with a food allergy were more likely to have a functional abdominal pain disorder (FAPD) (adjusted OR 4.028, 95% CI 1.532-10.286).

CONCLUSIONS: No statistically significant association was observed between first-week antibiotics or infantile colic and FGIDs at 9-12 years of age, but FAPDs were significantly more prevalent in children with food allergies.},
}

@article {pmid41872068,
year = {2026},
author = {Ben-Assa, N and Naddaf, R and Carasso, S and Dagan, O and Sason, A and Gefen, T and Geva-Zatorsky, N},
title = {Intra-species competition combats vancomycin-resistant enterococci.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2647529},
pmid = {41872068},
issn = {1949-0984},
mesh = {Animals ; *Vancomycin-Resistant Enterococci/physiology/virology/drug effects/genetics/growth & development ; Mice ; *Enterococcus faecalis/physiology/virology/drug effects/genetics/growth & development ; *Gram-Positive Bacterial Infections/microbiology/therapy ; Anti-Bacterial Agents/pharmacology ; Bacteriophages/genetics/physiology ; Humans ; *Antibiosis ; Vancomycin/pharmacology ; Female ; },
abstract = {Vancomycin-resistant Enterococcus (VRE) is a leading cause of multidrug-resistant infections in hospitalized patients, yet no reproducible microbiota therapies exist to selectively displace it. Here we harness intra-species competition within Enterococcus to suppress VRE colonization. Through in vitro screening and mouse colonization models, we identified a single antibiotic-susceptible strain, E. faecalis X98, that significantly reduced VRE burden both in vitro and in mouse experiments, whereas multi-strain consortia failed due to competitive interference among consortium members. In parallel, we subjected the vancomycin-sensitive strain E. faecalis OG1RF to phage selection, which produced a prophage-integrated derivative with convergent glycosyltransferase mutations that secreted a VRE-killing factor, conferring enhanced antagonism even without exogenous phage. These findings reveal ecological and evolutionary principles for selecting strains as targeted microbial therapeutics. Exploiting intra-species antagonism and phage-driven evolution provides a practical framework for developing microbiota-based interventions that minimize collateral damage to the microbiome while addressing antibiotic-resistant pathogens.},
}

Animals
*Vancomycin-Resistant Enterococci/physiology/virology/drug effects/genetics/growth & development
Mice
*Enterococcus faecalis/physiology/virology/drug effects/genetics/growth & development
*Gram-Positive Bacterial Infections/microbiology/therapy
Anti-Bacterial Agents/pharmacology
Bacteriophages/genetics/physiology
Humans
*Antibiosis
Vancomycin/pharmacology
Female

@article {pmid41872195,
year = {2026},
author = {DeVito, VL and Karamched, BR},
title = {Signed, sealed, delivered: a generalizable model for living biotherapeutic dosing and metabolism.},
journal = {NPJ systems biology and applications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41540-026-00685-4},
pmid = {41872195},
issn = {2056-7189},
abstract = {Living Biotherapeutic Products (LBPs) offer a promising therapeutic strategy for metabolic disorders rooted in gut microbiome dysfunction, yet quantitative frameworks for predicting their efficacy remain underdeveloped. We introduce the Bacterial Compartment Absorption and Transit (BCAT) model, a pharmacokinetic-pharmacodynamic framework that couples probiotic transit, endogenous microbiome metabolism, and enzymatic transformation within a unified dose-optimization setting. Building on the classical CAT model, BCAT incorporates mechanistically-derived colon compartments and treats dosing time as a control variable. We validate BCAT against clinical data for native choline metabolism and SYNB1618 probiotic trials, achieving 5% mean prediction error compared to ~30% for prior two-compartment models. Applying BCAT to trimethylaminuria (TMAU), we predict that ~10[9] CFU of engineered probiotic, administered 3-4 h before meals, achieves 95% reduction in systemic trimethylamine, matching healthy hepatic clearance. Global sensitivity analysis identifies enzyme expression level as the dominant design parameter, enforcing the broad applicability of this model. The BCAT framework generalizes to any gut microbiome-mediated metabolic disorder and provides quantitative dosing targets to guide live biotherapeutic development.},
}

@article {pmid41872294,
year = {2026},
author = {Vaughn, SN and Pavlovsky, JC and Heiman, JA and Jackson, CR},
title = {Contrasting spatial and temporal structuring of seawater and sediment bacterial communities in coastal environments.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45076-1},
pmid = {41872294},
issn = {2045-2322},
}

@article {pmid41872423,
year = {2026},
author = {Papagiannidou, A and Mitropoulou, M and Papantzikos, K and Petropoulou, D and Tsilingiris, D and Magkos, F and Dalamaga, M},
title = {Hypomagnesemia: A Clinical and Nutritional Update.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {},
pmid = {41872423},
issn = {2161-3311},
abstract = {PURPOSE OF REVIEW: Hypomagnesemia, defined as low serum/plasma magnesium concentration, is a highly prevalent yet underrecognized electrolyte disorder with extensive clinical, metabolic, and nutritional implications. This review provides an updated synthesis of magnesium physiology, dietary determinants, homeostatic regulation, diagnostic challenges, and therapeutic strategies, with particular emphasis on recent meta-analyses and large-scale epidemiological evidence linking hypomagnesemia to multisystem disease.

RECENT FINDINGS: Accumulating evidence has shown consistent associations between low serum or dietary magnesium and increased risk of cardiometabolic disorders (hypertension, type 2 diabetes mellitus, metabolic syndrome, and cardiovascular disease), neuropsychiatric conditions (migraine, depression, cognitive impairment, and dementia), osteoporosis, immune dysregulation, and adverse outcomes in hospitalized, critically ill, and chronic kidney disease patients. Mechanistic studies have clarified the roles of TRPM6/7 channels, tight junction claudins, and basolateral magnesium transporters in intestinal and renal magnesium handling, elucidating pathways underlying both inherited and acquired deficiencies. Research has also highlighted the contribution of modern dietary patterns, food processing, mineral-depleted drinking water, medication use (notably proton pump inhibitors, diuretics and chemotherapeutic agents), and gut microbiome alterations to widespread subclinical deficiency. Meta-analyses of RCTs indicate that magnesium supplementation confers modest but clinically relevant improvements in blood pressure, glycemic control, inflammatory markers, endothelial function, migraine frequency, and depressive symptoms, particularly in individuals with baseline hypomagnesemia. However, serum magnesium remains an insensitive biomarker of total body magnesium status, and consensus on optimal diagnostic thresholds and replacement strategies is lacking.

SUMMARY: Magnesium deficiency contributes to a wide spectrum of multisystem disorders, and is driven by dietary insufficiency, gastrointestinal and renal losses, medication use, chronic disease, and altered microbiome function. Meta-analytic evidence supports its role as a modifiable risk factor across cardiovascular, metabolic, neurological, skeletal, and immune disorders. Dietary modification, optimized supplementation, and correction of underlying causes of deficiency remain central to management. Future research should focus on improved diagnostic tools, personalized dosing approaches and long-term outcomes of magnesium repletion. Enhancing clinical awareness and integrating magnesium evaluation into routine care may reduce the growing burden of hypomagnesemia.},
}

@article {pmid41872585,
year = {2026},
author = {Gokalp, S and Dinleyici, EC and Muluk, C and Inci, A and Aktas, E and Okur, I and Ezgu, F and Tumer, L},
title = {Alterations in gut microbiota composition in children with methylmalonic acidemia, propionic acidemia, and maple syrup urine disease.},
journal = {European journal of clinical nutrition},
volume = {},
number = {},
pages = {},
pmid = {41872585},
issn = {1476-5640},
support = {TGA-2021-7036//Gazi Üniversitesi (Gazi University)/ ; },
abstract = {AIM: Methylmalonic acidemia (MMA), propionic acidemia (PA), and maple syrup urine disease (MSUD) are rare monogenic disorders that are described as intoxication-type inborn errors of metabolism (IEMs). They usually present in early life, and long-term management requires strict dietary protein restriction, which may significantly alter gut microbiota composition. Despite growing interest in microbiome research, limited data exist on gut microbiota in these disorders, and no study is available for MMA and MSUD. We aimed to describe the gut microbiota compositions in children with MMA, PA, and MSUD.

METHOD: A total of eight patients (Five MMA, one PA, and two MSUD), and 11age-matched healthy controls were enrolled. All patients were following a medically supervised, protein-restricted diet. Fecal sample was collected from each participant, and gut microbiota composition was evaluated with 16S rRNA sequencing.

RESULTS: Patients with MMA, PA, and MSUD exhibited significantly altered gut microbiota composition compared to healthy controls. Alpha diversity analysis revealed reduced microbial richness in patients, with significantly lower Chao1 and observed OTU indices (p < 0.05). Beta diversity metrics demonstrated distinct clustering between groups, indicating significantly different microbial community structures. Higher relative abundances of opportunistic or dysbiotic taxa have been seen in patient group, while controls were enriched in beneficial taxa like Faecalibacterium prausnitzii, Ruminococcus, and Lactobacillus. LEfSe analysis identified 17 taxa enriched in patients-including members of Proteobacteria, Sphingobacteriia, and Streptococcus anginosus-and 6 taxa enriched in controls, notably Faecalibacterium prausnitzi.

DISCUSSION: This is the first descriptive study of the gut microbiota composition of MMA, PA, and MSUD patients. These findings indicate an association between long-term dietary management and altered microbiota composition, although causality cannot be inferred due to the cross-sectional study design. The observed alterations suggest that the gut microbiota may represent a novel therapeutic target in the management of IEMs.},
}

@article {pmid41872600,
year = {2026},
author = {Segev, T and Barak, D and Zahavi, L and Godneva, A and Rein, M and Krongauz, D and Samocha-Bonet, D and Rossman, H and Weinberger, A and Segal, E},
title = {Diet-microbiome associations in 10,068 individuals from the Human Phenotype Project to guide personalized nutrition.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41872600},
issn = {1546-170X},
abstract = {Diet is a major environmental factor influencing the human gut microbiome. However, the effects of specific foods and dietary patterns on microbial composition, diversity and function is not fully understood, limiting progress toward personalized dietary strategies. Here, leveraging 10,068 participants from the Human Phenotype Project with app-based diet logs and shotgun metagenomics, we predicted diet-microbiome associations at species-level resolution. Diet significantly predicted microbial diversity (richness r = 0.26, Shannon Index r = 0.24), the relative abundance of 669 of 724 species tested (92.4%, false discovery rate <0.05), and 313 of 320 pathways (97.8%, false discovery rate <0.05). Feature attribution identified distinct food-microbe links, including coffee with Lawsonibacter asaccharolyticus (r = 0.43), yogurt with Streptococcus thermophilus (r = 0.42) and milk with Bifidobacterium species (r = 0.31-0.36). In parallel, broader dietary patterns, especially the degree of food processing, emerged as predictors of microbial diversity and composition. We also show that diet-microbiome associations persist over four years, with 82.5% of species exhibiting significant longitudinal tracking between predicted and observed abundances. Finally, we developed an exploratory analysis for simulating personalized dietary interventions with predicted microbiome shift effects that are associated with improvements in cardiometabolic health. Our findings demonstrate that diet is strongly associated with microbiome composition, diversity and function, and highlight its potential for guiding personalized interventions.},
}

@article {pmid41872622,
year = {2026},
author = {Lee, H and Oh, Y and Seo, TW and Choi, YB and Kim, S and Cheon, S and Lee, DG and Kang, S and Han, K and Heo, YM and Mun, S},
title = {Exploring Cyclo (-Gly-Pro) for inflammation modulation in atopic dermatitis: a study on streptococcal postbiotics.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41872622},
issn = {2092-9293},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by intense itching and eczematous lesions, significantly affecting quality of life. Complex interactions involving genetic predispositions, environmental factors, and immune dysregulation contribute to AD pathogenesis, with impaired skin barriers and Staphylococcus aureus playing critical roles. Recent interest in postbiotics, beneficial compounds derived from probiotics, has opened potential therapeutic avenues.

OBJECTIVE: This study investigates the postbiotic solution derived from three human skin-derived Streptococcus isolates, to identify a core bioactive compound and its therapeutic role in AD.

METHODS: Using GC-MS and GC-FID, we quantified Cyclo (-Gly-Pro) and assessed its impact on inflammatory biomarkers in an AD-like keratinocyte cell model. The effect of different incubation temperatures on the compound's production was also analyzed. Furthermore, 16S V3-V4 amplicon sequencing was performed to analyze changes in the skin microbiome of AD patients following treatment.

RESULTS: Cyclo (-Gly-Pro) was consistently present across all strains, with production inversely related to incubation temperature, peaking at 25 °C. Our findings suggest that optimized production conditions and potential synergistic effects with other postbiotic components could enhance therapeutic efficacy.

CONCLUSION: These results support further in vivo research to elucidate the mechanisms and validate the compound's role in AD treatment strategies, potentially leading to novel dermatological therapies.},
}

@article {pmid41872902,
year = {2026},
author = {Rojas, CA and Smith, R and Oliver, R and Jospin, G and Corral, I and Ganz, HH},
title = {Temporal variability is an inherent feature of the healthy canine microbiome assessed by full-length 16S rRNA gene sequencing.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00546-9},
pmid = {41872902},
issn = {2524-4671},
}

@article {pmid41872951,
year = {2026},
author = {Matei, DE and Rosser, EC},
title = {The gut-joint axis in juvenile idiopathic arthritis.},
journal = {Arthritis research & therapy},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13075-026-03786-x},
pmid = {41872951},
issn = {1478-6362},
support = {KENN 21 22 09//Kennedy Trust for Rheumatology Research/ ; KENN 21 22 09//Kennedy Trust for Rheumatology Research/ ; 094//FOREUM/ ; },
}

@article {pmid41865111,
year = {2026},
author = {Oliveira, AGG and Dias, MF and Haq, IU and Ferreira, JFG and Silva, CP and Moreira, M and da Silva Lanna, MC and Santos Rodrigues, LD and de Mâcedo Farias, L and Magalhães, PP},
title = {Seasonal and Source-Associated Microbiome Dynamics in Brazilian Drinking Water.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02735-0},
pmid = {41865111},
issn = {1432-184X},
}

@article {pmid41865193,
year = {2026},
author = {Mathkor, DM and Aldairi, AF and Faidah, H and Babalghith, AO and Johargy, AK and Ahmad, F and Haque, S and Bantun, F},
title = {The role of breastfeeding in modulating antimicrobial resistance in neonates: a systematic review.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41865193},
issn = {1530-0447},
abstract = {Antimicrobial resistance (AMR) is a growing health concern in neonates. Breastfeeding potentially plays a pivotal role in modulating neonatal gut microbiota, thereby influencing the acquisition and transmission of AMR genes (ARGs). This systematic review evaluates the links between breastfeeding and the origin of neonatal gut microbiota and AMR. Selection of pertinent studies published between 2015 and 2025 focusing on major outcome measures of neonatal AMR and ARG transfer was performed on scholarly databases. Following quality assessment, 22 studies met the inclusion criteria for further consideration. Evidence consistently demonstrates that breast milk is an active contributor to the microbial and genetic landscape of the neonatal gut microbiome. Further, studies implicated breast milk as a source of ARG transfer in neonates. Other reports indicated that exclusive breastfeeding and human milk-associated bioactive compounds promoted the colonization of beneficial commensals, limited colonization of multidrug-resistant species, and suppressed horizontal transfer of ARGs. Interestingly, maternal factors, such as maternal antibiotic history, lifestyle, and overall health status, appeared to influence the links between breast milk and transmission and impact of ARGs in neonates. In conclusion, while breastfeeding-based strategies are important to neonatal AMR mitigation, further mechanistic studies are required to establish causal pathways. IMPACT: Breastfeeding has an active role in altering neonatal gut microbiota and influences antimicrobial resistance (AMR) acquisition. This review synthesizes evidence from 2015-2025 indicating that breastfeeding is both a source of antimicrobial resistance genes (ARGs) and contains bioactive components that suppress ARG transmission and promote beneficial colonization. Maternal factors, such as antibiotic exposure, lifestyle, and overall health, potently influence these links. Mechanistic comprehension of the links between breastfeeding, neonatal microbiome, and AMR acquisition may allow identification of prevention strategies against neonatal infections. The analyses underscore the need for longitudinal, mechanistic studies to determine causal relationships and long-term effects of breastfeeding on neonatal AMR.},
}

@article {pmid41865545,
year = {2026},
author = {Yu, F and Feng, H and Yu, Z and Jiang, J and Li, S and Meng, J},
title = {Dissolved nitrogen and phosphorus trigger Euglena sanguinea blooms via Burkholderiaceae enrichment and extracellular polymeric substance stimulation.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129428},
doi = {10.1016/j.jenvman.2026.129428},
pmid = {41865545},
issn = {1095-8630},
abstract = {As representative landscape water bodies, urban park ponds are typically shallow and hydrologically isolated, making them highly susceptible to algal blooms. This study focused on recurrent summer-autumn blooms of Euglena sanguinea in Hefei Binhu Forest Park. These blooms form thin, red, oil-slick-like surface scums that severely suppress aquatic photosynthesis. We investigated phytoplankton community succession and its drivers by collecting surface biofilm, mid-depth water, and bottom sediment samples from three representative ponds during the 2024 bloom season. Results revealed extensive E. sanguinea blooms in July-August, with surface cell density reaching 9.86 × 10[6] cells/L (42% of total) and biomass attaining 98.61 mg/L (94% of total). This bloom peak coincided with a 2.5-fold increase in surface dissolved total nitrogen (DTN) and phosphorus (DTP). Concurrently, the surface biofilm exhibited a peak extracellular polymeric substance (EPS) concentration of 43.92 mg/L and a film-forming rate of 90.73%, structurally supported by the predominance of large algal-bacterial aggregates (>64 μm), which accounted for nearly 80% of the particulate composition. The bounding EPS (BEPS), rich in tryptophan-like proteins, corresponded with peak biofilm hydrophobicity. Critically, this nutrient-enriched microenvironmental transformation selected for a low-diversity, high-dominance microbiome. Burkholderiaceae dominated the August biofilm (23%), contrasting sharply with sediment communities (dominated by Steroidobacteraceae, 7%) and post-bloom October biofilms (dominated by Sporichthyaceae, 21%). Mechanistic path analysis revealed that DTN and DTP stimulated bloom expansion not by directly promoting algae, but by enriching Burkholderiaceae and stimulating EPS production. These findings elucidate a microbially mediated pathway linking nutrient enrichment to E. sanguinea bloom formation, challenging the conventional direct nutrient-bloom paradigm. The study provides mechanistic blueprint for targeted, microbiome-informed management of urban landscape water blooms.},
}

@article {pmid41865546,
year = {2026},
author = {Fan, X and Wang, Y and Liang, W and Ma, X and Zhang, W and Yu, C},
title = {Organic fertilizers reduce N2O and NH3 emissions by regulation soil nitrogen pool and microbiome.},
journal = {Journal of environmental management},
volume = {404},
number = {},
pages = {129432},
doi = {10.1016/j.jenvman.2026.129432},
pmid = {41865546},
issn = {1095-8630},
abstract = {Organic fertilizers are generally considered beneficial towards maintaining long term soil health, yet they could elevate N2O and NH3 emissions which raise concerns regarding air pollution and climate change. In this study, four types of organic fertilizers (raw sheep manure, RSM; composted sheep-manure organic fertilizer, OF; biochar-amended organic fertilizer, CharOF; sterilized OF, SOF) were applied onto three kinds of soils in microcosm cultivation to explore their effects on N2O and NH3 emissions and the underlining mechanisms. The results showed that traditional organic fertilizers (RSM and OF) significantly increased N2O and NH3 emissions from the soils, whereas CharOF reduced by as much as 23.0% in N2O and 18.4% in NH3 from that of RSM/OF peaks. Both OF and SOF significantly increased soil total nitrogen (TN) and organic nitrogen (Org-N), while CharOF significantly improved soil NO3[-]-N, NH4[+]-N and microbial biomass nitrogen (MBN). Metagenomic sequencing showed that RSM and OF significantly increased denitrification genes norB and narI, dissimilatory nitrate reduction genes nasA, napA and nirB, and mineralization gene ureC, while CharOF slightly suppressed denitrification genes nirS and narI, dissimilatory nitrate reduction genes nasA/B, napA, nirB and NR, and mineralization gene ureC. RDA analysis revealed that NO3[-]-N, NH4[+]-N, MBN and pH were the environmental factors affecting NC relevant genes and gas emissions. PLS-PM model revealed that soil nitrogen pool correlated stronger to the NH3 and N2O emissions than that of nitrogen cycle (NC) relevant genes. This study provides a theoretical foundation for the promotion of low-pollution fertilization practices in green agriculture, and contributes to the advancement of agricultural sustainability. Additionally, it offers fresh perspectives on organic fertilizer production and its role in enhancing socio-economic systems for public benefits.},
}

@article {pmid41865576,
year = {2026},
author = {Wu, Y and Qin, L and Zhang, Y and Jia, Y and Lü, Y and Wang, N and Zheng, H and Li, L and Zhang, Z},
title = {Co-exposure to polystyrene microplastics and glyphosate induces gut microbiota dysbiosis and cognitive impairment in honeybees.},
journal = {Journal of hazardous materials},
volume = {507},
number = {},
pages = {141796},
doi = {10.1016/j.jhazmat.2026.141796},
pmid = {41865576},
issn = {1873-3336},
abstract = {Microplastics, as emerging persistent environmental contaminants, can act as vectors for the absorption of other pollutants in ecosystems, such as pesticide residues. However, the combined toxicological effects of microplastics and pesticides on pollinators remain poorly understood. Here, we evaluated the toxicity of polystyrene microplastics (PS) and glyphosate (GLY), both individually and in combination, in honeybees (Apis mellifera). While no significant changes in body weight gain or food consumption were observed after 20 days of exposure, co-exposure to PS and GLY significantly increased bee mortality and induced midgut damage and microbial dysbiosis. In the gut, pathways associated with cell proliferation and differentiation, along with genes related to oxidative stress, detoxification, and immunity, were significantly downregulated. Furthermore, the combination of PS and GLY impaired sucrose responsiveness, a key cognitive behavior in bees. Brain transcriptomics indicated a downregulation of serotonergic synapse-related genes, which were correlated with shifts in core gut bacteria such as Snodgrassella and Lactobacillus. Our findings demonstrate that co-exposure to PS and GLY exacerbates gut homeostasis disruption and impairs cognitive behavior, suggesting a potential role of the gut-brain axis. This study extends our understanding of the combined ecological risks posed by multiple environmental contaminants to bees as insect pollinators and emphasizes the need for comprehensive hazard assessments in insect conservation.},
}

@article {pmid41865725,
year = {2026},
author = {Wang, S and Sun, H and Lv, X and Li, J and Du, D and Guo, F and Zhang, C},
title = {Ultrasound-assisted extraction optimization of Fructus Tribuli polysaccharides: How stir-frying processing alters structures and enhances antihypertensive efficacy.},
journal = {Ultrasonics sonochemistry},
volume = {128},
number = {},
pages = {107829},
doi = {10.1016/j.ultsonch.2026.107829},
pmid = {41865725},
issn = {1873-2828},
abstract = {Fructus Tribuli (FT), the dried ripe fruit of Tribulus terrestris L., is recognized for its antihypertensive properties, which are enhanced by stir-frying without adjuvants. However, research on its polysaccharides with therapeutic potential remains limited. This study optimized the ultrasound-assisted extraction (UAE) of FT polysaccharides (FP) using response surface methodology, yielding a maximum extraction yield of 2.182 ± 0.29% under the conditions of liquid-solid ratio 20:1 mL/g, 51 min, 62 °C, and precipitation ethanol concentration of 95%. Subsequently, FP and stir-fried FT polysaccharides (SFP) were isolated, and their structural differences and antihypertensive effects were systematically compared. Structural analysis revealed notable differences between FP and SFP. Furthermore, the extraction resulted in a higher polysaccharide yield for SFP. In spontaneously hypertensive rats, both FP and SFP attenuated hypertension and vascular injury, modulated gut microbiota, increased short-chain fatty acids, and enhanced intestinal barrier function effects that were more pronounced with SFP. Mechanistically, both polysaccharides inhibited the aortic TLR4/MyD88 pathway. These results suggest that stir-frying modifies polysaccharide structure, thereby improving gut microbiome regulation, barrier protection, and vascular outcomes, highlighting the value of processing in enhancing polysaccharide efficacy. Thus, stir-frying amplifies therapeutic effects through bioactive macromolecular remodeling, advancing the understanding of Traditional Chinese medicine processing principles.},
}

@article {pmid41865866,
year = {2026},
author = {Wang, Y and Wang, D and Wang, H},
title = {Comparative analysis of the gut microbiome and bile acid profiles in sympatric Rana chensinensis and Fejervarya multistriata tadpoles.},
journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology},
volume = {},
number = {},
pages = {111996},
doi = {10.1016/j.cbpa.2026.111996},
pmid = {41865866},
issn = {1531-4332},
abstract = {Environmental temperature is an essential exogenous factor influencing the gut microbiota of amphibians, which exerts profound physiological impacts on the host by modifying bile acids (BAs). Even sympatric amphibians often have considerably different optimal breeding temperatures. However, the effect of different developmental temperatures on gut microbiota and BA profiles in sympatric amphibians remains unclear. To address this deficiency, morphological, histological, metagenomics and metabolomics information were compared between Rana chensinensis (R. chensinensis) and Fejervarya multistriata (F. multistriata) tadpoles. Morphological and histological results showed that body mass index (BMI), intestinal mass to body mass ratio (IM/BM), and enterocyte height (EH) were higher in F. multistriata, whereas body mass (BM), total length (TL), and intestine mass (IM) were higher in R. chensinensis. Metagenomics analysis revealed the relative abundance of microorganisms (Bacteroides, Clostridium, and Enterococcus) producing bile salt hydrolase (BSH) is higher in F. multistriata, whereas the relative abundance of microorganisms (Dorea spp, Extibacter muris, Clostridium leptum, and Proteocatella sphenisci) possessing the BAI operon is higher in R. chensinensis. Comparative metabolomic analysis identified that F. multistriata has a higher ratio of unconjugated to conjugated BAs (CA/TCA, CDCA/TCDCA, and DCA/TDCA), which may suppress the abundance of pathogen (e.g., Clostridioides difficile). Additionally, the lower TDCA content in F. multistriata may be potentially linked to its stronger absorptive capacity. In contrast, R. chensinensis exhibits a higher ratio of DCA to CA, which probabaly enhance their cold tolerance. Overall, this study elucidated the potential impacts of developmental temperature-driven differences in gut microbiota and BAs on sympatric amphibians' physiological metabolism.},
}

@article {pmid41865944,
year = {2026},
author = {Zou, C and Liang, L and Zhao, M and Lin, L},
title = {Chlorogenic acid enhances gut microbiota regulatory effect and anti-inflammatory of Lycium barbarum polysaccharide by simulated fermentation.},
journal = {International journal of biological macromolecules},
volume = {356},
number = {},
pages = {151538},
doi = {10.1016/j.ijbiomac.2026.151538},
pmid = {41865944},
issn = {1879-0003},
abstract = {The intricate interplay between dietary components, the gut microbiome, and host immunity is a core of intestinal immune research. Lycium barbarum polysaccharide (LBP)-chlorogenic acid (CGA) complex exhibits proliferative activity of Bacteroides and strong inhibitory effect on Staphylococcus aureus, but lacks of the microbial fermentation characteristics and immunomodulatory effect. Herein, in vitro fecal bacteria microbiota and macrophages models were employed to investigated the regulatory capacity of the LBP-CGA complex on intestinal microbiota and immunomodulatory activities of its metabolites. Results showed that LBP and LBP-CGA both readily fermentable. Fermentation led to significant molecular weight and pH reductions, nearly 85% polysaccharide degradation. Notably, LBP-CGA complex was more favorable to increase the relative abundance of Sutterella, Veillonella, Faecalibacterium and contents of SCFAs than LBP. Interesting, LBP fermentation product possessed the potential for immune-enhancing, with the polysaccharide fraction was the key active component. Conversely, LBP-CGA complex fermentation product elicited the potential for immune-suppressive response, with dihydrocaffeic acid of CGA metabolites was critical contributors. The data further indicated LBP-CGA exhibited better immunomodulatory of intestinal microbiota probably due to the proliferation of Bacteroides. Bacteroides may improve the bio-transformation of CGA and produce more dihydrocaffeic acid, which may in turn potentiate the immunosuppressive activity of the LBP-CGA complex fermentation product. To summarize, the results revealed that CGA elevated the ability of LBP to regulate the intestinal microbiota and to potential exert immunosuppression. This study offers profound insights into the development of LBP-CGA complex as a prebiotic with excellent anti-inflammatory effect.},
}

@article {pmid41866241,
year = {2026},
author = {Chauhan, S and Kumari, P and Deepa, N and Chanotiya, J and Trivedi, PK and Singh, A},
title = {Proteomic insights into plant-endophyte interactions: advancing understanding of mutualistic symbiosis and plant resilience.},
journal = {Critical reviews in biotechnology},
volume = {},
number = {},
pages = {1-20},
doi = {10.1080/07388551.2026.2618190},
pmid = {41866241},
issn = {1549-7801},
abstract = {Endophytic microorganisms are a vital part of the plant microbiome, contributing significantly to the plant's growth, development, and stress tolerance. Proteomics investigations have significantly enhanced our comprehension of the interactions between plants and endophytes, illuminating the complex molecular mechanisms that govern these mutually beneficial relationships. The review aims to integrate the latest developments in proteomic research concerning endophyte-plant interactions, emphasizing on elucidating the molecular mechanisms that underlie the benefit imparted to the host plant by the symbionts. The special focus of the review is to discuss the proteome level changes happening at the early recognition events, primary and secondary metabolism, signaling pathways, and defense mechanisms. By underscoring critical proteomic signatures, the review aspires to offer insights into how these interactions enhance plant health, increase stress resilience, and promote overall growth. The article discusses the potential applications of proteomics in agriculture and environmental sciences, emphasizing its role in crop resilience against biotic and abiotic stresses, optimizing biocontrol strategies, and improving nutrient use efficiency. The article also highlights that despite the advancements, critical gaps persist including the necessity for a deeper understanding of the temporal dynamics of proteomic responses, the specificity of protein-protein interactions, and the influence of environmental factors on the proteome induced by the endophytes. The review concludes by proposing future directions for proteomics research in plant-endophyte interactions for developing a more comprehensive understanding of the intricate molecular dialogues for developing a more sustainable and resilient agricultural systems.},
}

@article {pmid41866413,
year = {2026},
author = {Berkelmann, D and Zuñiga-Umaña, JM and Chaverri, P and Solano, W and Gatica-Arias, A},
title = {Fungal diversity associated with coffee leaf rust (Hemileia vastatrix) pustules based on ITS1 amplicon sequencing.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866413},
issn = {1573-0972},
support = {111-C1-472//Vicerrectoría de Investigación, Universidad de Costa Rica/ ; },
mesh = {*Plant Diseases/microbiology ; *Coffea/microbiology ; Plant Leaves/microbiology ; *Basidiomycota/genetics/classification/isolation & purification ; DNA, Fungal/genetics ; Costa Rica ; Phylogeny ; Sequence Analysis, DNA ; Biodiversity ; *Fungi/genetics/classification/isolation & purification ; Coffee/microbiology ; DNA, Ribosomal Spacer/genetics ; },
abstract = {Coffee leaf rust (CLR), caused by Hemileia vastatrix, is one of the biggest economic challenges for coffee cultivation and leads to high economic losses each year. Co-occurring fungal microbial communities and their diversity in the presence of CLR are widely understudied but may harbor potential agents or indicators to reduce CLR infections. In this study, the fungal communities associated with CLR pustules in Coffea arabica L. plants across different regions of Costa Rica were analyzed. To this end, individual pustules were excised from infected leaf tissue and used as source material for DNA extraction and subsequent amplification and sequencing of the fungal taxonomic marker region ITS1. Effects of altitude and location on fungal community structure were also observed. High taxonomic variance within regions and a large proportion of unclassified taxa were detected as well as similar community structures across regions, possibly reflecting small effects of the analyzed regions on the identified taxa. However, altitude was a significant factor on the detected community structure, indicating either less favorable growth conditions for the pathogen in higher regions or favorable conditions for co-occurring taxa. This emphasizes that taxonomic identification of co-occurring fungi and their ecological relevance (e.g., potential mycoparasites) during CLR infection requires further research. This study provides a foundational framework for global coffee research by emphasizing the untapped potential of fungal community analyses to develop innovative, microbiome-informed strategies for managing coffee leaf rust and improving crop resilience.},
}

*Plant Diseases/microbiology
*Coffea/microbiology
Plant Leaves/microbiology
*Basidiomycota/genetics/classification/isolation & purification
DNA, Fungal/genetics
Costa Rica
Phylogeny
Sequence Analysis, DNA
Biodiversity
*Fungi/genetics/classification/isolation & purification
Coffee/microbiology
DNA, Ribosomal Spacer/genetics

@article {pmid41866421,
year = {2026},
author = {Mathur, S and Prasad, M and Kumar, S and Chaurasia, A and Ranjan, R},
title = {A metagenomic survey of the rhizosphere bacterial community of P. longum from the herbal garden, Dayalbagh Educational Institute (D.E.I), Agra, India.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41866421},
issn = {1573-0972},
}

@article {pmid41866543,
year = {2026},
author = {Lu, Q and Chen, S and Shan, B and Wei, A and Luo, Y and Wu, L and Jiang, Q and Chen, Z},
title = {Rhizosphere microbiome dynamics and hormonal interactions regulating tiller development in sugarcane cultivars.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-38474-y},
pmid = {41866543},
issn = {2045-2322},
support = {32201392//National Natural Science Foundation of China/ ; 2024GXNSFBA010329//Natural Science Foundation of Guangxi Province/ ; Guike AA24263045//Guangxi Major Science and Technology Program/ ; },
abstract = {Sugarcane tillering is a key determinant of crop productivity, yet the integrated roles of rhizosphere microbiome dynamics, nutrient status, and hormone signaling in regulating tiller development remain poorly understood. Here, we compared rhizosphere microbial communities, endogenous hormone profiles, and nutrient element concentrations in sugarcane cultivars with contrasting tillering capacities. High-tillering varieties exhibited significantly greater microbial diversity and more complex co-occurrence network structures in the rhizosphere, characterized by enrichment of Acidobacteriota, Chloroflexi, and Planctomycetes and functional pathways related to nitrogen fixation, phosphorus solubilization, and auxin biosynthesis. In contrast, low-tillering varieties harbored simplified, stress-adapted microbial consortia and prioritized pathways linked to oxidative stress response and heavy metal detoxification. Hormonal analysis revealed that high-tillering cultivars maintained higher levels of growth-promoting hormones-particularly auxin (IAA) and active cytokinins-in tiller buds while low-tillering cultivars accumulated elevated abscisic acid (ABA) and inactive cytokinin conjugates. Nutrient analysis indicated that high-tillering genotypes possessed higher nitrogen and phosphorus contents, supporting vigorous axillary bud activation and shoot proliferation, whereas low-tillering varieties accumulated more zinc and manganese, potentially reflecting stress adaptation. Network-level integration of microbial, hormonal, and nutrient profiles underscored genotype-specific feedback between rhizosphere microbiota and plant physiological states, highlighting modular associations that link microbial hubs with tissue-specific nutrient and hormone signatures. Our findings reveal a systems-level mechanism by which rhizosphere microbial community structure and function interact with plant-nutrient-hormonal status to regulate tillering in sugarcane. These insights provide a basis for microbiome-informed strategies to enhance sugarcane productivity through integrated nutrient-hormonal-microbe management.},
}

@article {pmid41866581,
year = {2026},
author = {Halo, BA and Aljabri, YAS and Glick, BR and Yaish, MW},
title = {Metagenomic and functional insights into root endophytic bacteria associated with drought stress in cowpea.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-45459-4},
pmid = {41866581},
issn = {2045-2322},
support = {IG/SCI/BIOL/24/03//Sultan Qaboos University, College of Science, Oman/ ; },
}

@article {pmid41866722,
year = {2026},
author = {Chen, SJ and Wayne, CD and Jacobs, TH and Besner, GE},
title = {Rethinking probiotic delivery: new hope for preventing necrotizing enterocolitis.},
journal = {Expert opinion on drug delivery},
volume = {},
number = {},
pages = {},
doi = {10.1080/17425247.2026.2648748},
pmid = {41866722},
issn = {1744-7593},
abstract = {INTRODUCTION: Necrotizing enterocolitis (NEC) is a devastating disease of the gastrointestinal tract that mainly affects premature newborns, with mortality rates exceeding 50% in the most severe cases. Despite decades of research the disease persists, there is no known cure, and treatment consists of supportive care only. Dysbiosis of the gut microbiome has been implicated as a contributing factor to the development of NEC. With a deepening understanding of the therapeutic efficacy of probiotics in reversing intestinal dysbiosis, a potential avenue to prevent this disease has emerged.

AREAS COVERED: Through review of the literature related to probiotics in NEC and novel oral delivery methods for probiotics, we will discuss what is known about preventing NEC with commercially available probiotics. We will discuss the challenges imposed on probiotic therapy by the September 2023 FDA warning on probiotic administration to premature babies. We will also examine novel delivery methods for probiotics that can enhance their beneficial capabilities.

EXPERT OPINION: By obtaining approval for novel oral probiotic delivery technologies including biofilm formation and prebiotic co-ride, the risk of NEC in premature infants could be significantly decreased.},
}

@article {pmid41866998,
year = {2026},
author = {Ebigbo, N},
title = {The esophageal microbiome: mechanisms and clinical implications.},
journal = {Current opinion in gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOG.0000000000001170},
pmid = {41866998},
issn = {1531-7056},
abstract = {PURPOSE OF REVIEW: Interest in the esophageal microbiome has expanded rapidly, yet its functional and clinical relevance remains incompletely defined. This review synthesizes emerging evidence on host-microbe interactions in esophageal diseases, with a focus on mechanistic pathways and translational potential.

RECENT FINDINGS: Recent studies demonstrate that esophageal microbes influence epithelial differentiation, barrier integrity, and inflammatory signaling in conditions such as eosinophilic esophagitis and Barrett's esophagus. Microbial metabolism, particularly bile acid transformation, links microbial composition to epithelial stress responses and neoplastic progression. In esophageal cancer, tumor-associated microbes modulate epigenetic regulation and suppress antitumor immunity. Integrative multiomics approaches have further identified microbial signatures associated with disease progression and treatment response.

SUMMARY: The esophageal microbiome influences disease pathogenesis and has potential for risk stratification and therapeutic targeting. Future progress will depend on longitudinal studies, improved functional resolution, and integration of microbial data with epithelial and immune biology to enable clinical translation.},
}

@article {pmid41867064,
year = {2026},
author = {Nikam, R and Pax, K and Beverly, ML and Kumar, PS},
title = {Mapping the subgingival HerBiome and HisBiome over the human healthspan.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70098},
pmid = {41867064},
issn = {1943-3670},
support = {/DE/NIDCR NIH HHS/United States ; },
abstract = {BACKGROUND: Understanding the intricate relationship between sex, age, and the oral microbiome is crucial for deciphering the onset and progression of numerous age-related oral and systemic diseases.

METHODS: Subgingival plaque was collected from 781 periodontally and systemically healthy females and 160 males spanning 0 to 80 years. 16S amplicon sequencing was performed. 80 million sequences were annotated and analyzed through the QIIME pipeline, principal components analysis (PCA) used for dimensionality reduction, LefSe to identify driver species, beta dispersion to measure inter-subject variability, and machine learning algorithm (RandomForest package in R [RF]) to validate the results. Causal mediation models were implemented to investigate the influence of aging on the male and female microbiomes.

RESULTS: PCA demonstrated significant class separation based on sex (p < 0.001, permutational multivariate analysis of variance [PERMANOVA]). Males demonstrated higher alpha diversity (p < 0.001, Wilcoxon signed-rank test of the Shannon diversity index), but also higher inter-subject heterogeneity p < 0.001, ANOVA). RF identified males with 0.99 sensitivity, 0.15 specificity, and accuracy of 85%. Age exerted an almost complete mediation effect, with significant differences in the trajectory and pattern of aging between males and females. Females > 30 demonstrated a lower microbial diversity (p < 0.001) and higher levels of Fusobacterium nucleatum (p < 0.001), while the male microbiome remained highly personalized throughout the lifespan, without defined patterns of aging.

CONCLUSIONS: Sex and age interact to influence the subgingival microbiome. These findings might explain differing disease susceptibilities in either sex, as well as informing personalized prevention and intervention based on age and sex. Further studies using granular -omics approaches are needed to advance our knowledge.

PLAIN LANGUAGE SUMMARY: Periodontal (gum) diseases are caused by a breakdown in the intricate balance between bacteria that live under the gumline and the local immune response. Since periodontal diseases have been reported to be more common in men than in women, we set out to investigate whether these bacterial communities are intrinsically different between the 2 sexes, and whether these differences are sustained over the lifespan. Using deep-sequencing technology to analyze the microbiomes of 941 individuals, we discovered that sex at birth is indeed a determining factor in the types of bacteria that live under the gums. Aging trajectories and patterns also differ between men and women, with women demonstrating a distinct shift after 30 years of age, and men showing no definite age-based change. These findings have important implications for the cause of periodontitis in either sex, as well as the potential to personalize therapy based on age and sex.},
}

@article {pmid41867134,
year = {2026},
author = {Piraccini, BM and Micali, G and Fulgione, E and Guida, S and Caldarola, G},
title = {Experts' view on the management of scalp seborrheic dermatitis in Italy.},
journal = {The Journal of dermatological treatment},
volume = {37},
number = {1},
pages = {2644012},
doi = {10.1080/09546634.2026.2644012},
pmid = {41867134},
issn = {1471-1753},
mesh = {Humans ; *Dermatitis, Seborrheic/diagnosis/drug therapy ; Italy ; Antifungal Agents/administration & dosage/therapeutic use ; Algorithms ; *Scalp Dermatoses/diagnosis/drug therapy ; *Dermatologic Agents/administration & dosage/therapeutic use ; Severity of Illness Index ; Acne Vulgaris/drug therapy/diagnosis/complications ; Adolescent ; Diagnosis, Differential ; },
abstract = {BACKGROUND: Acne vulgaris is a common skin disorder that negatively affects adolescents' quality of life. Recent evidence suggests that combining isotretinoin with desloratadine may enhance treatment outcomes.

OBJECTIVES AND METHODS: This study aimed to develop a practical algorithm for SSD management in Italy, by gathering insights from Italian dermatology experts on diagnosis, treatment and long-term management of SSD.

RESULTS: According to literature review and clinical experience, accurate diagnosis of SSD requires medical history, clinical evaluation, disease severity assessment and trichoscopy. The differentiation of SSD from psoriasis, eczema, and tinea capitis is essential to guide appropriate treatment, which should counteract the main pathogenic mechanisms underlying the disease and be tailored to the severity of clinical manifestations. Topical antifungals are the first-line treatments due to their efficacy in reducing Malassezia colonization. The use of topical anti-inflammatory agents, including corticosteroids, is useful for moderate-to-severe cases, but should be limited due to potential adverse effects. Selenium disulfide may be a useful option for both acute symptom control and long-term maintenance because of its antifungal, sebostatic, keratolytic, and microbiome-restoring properties, associated with a high degree of patient satisfaction. Systemic antifungals may be considered in refractory cases.

CONCLUSION: This experts' view provides a structured approach to SSD management in Italy, integrating clinical experience and scientific evidence.},
}

Humans
*Dermatitis, Seborrheic/diagnosis/drug therapy
Italy
Antifungal Agents/administration & dosage/therapeutic use
Algorithms
*Scalp Dermatoses/diagnosis/drug therapy
*Dermatologic Agents/administration & dosage/therapeutic use
Severity of Illness Index
Acne Vulgaris/drug therapy/diagnosis/complications
Adolescent
Diagnosis, Differential

@article {pmid41867523,
year = {2026},
author = {Kanno, N and Ohtani, T and Oda, N and Kato, S and Ohkuma, M and Shigeto, S},
title = {Domain-Level Classification of Archaea and Bacteria Using AI-Assisted Single-Cell Raman Spectroscopy.},
journal = {ACS omega},
volume = {11},
number = {10},
pages = {16913-16921},
pmid = {41867523},
issn = {2470-1343},
abstract = {Archaea and Bacteria are two fundamentally distinct domains of life that share prokaryotic traits, yet differ markedly in molecular and cellular architecture. While many archaeal species identified thus far have been found in extreme environments, recent metagenomic studies have revealed their widespread presence in moderate habitats, including soils, oceans, and even the human microbiome. However, archaea remain less well characterized than bacteria, largely due to the technical challenges associated with culturing and identifying these microorganisms. In this study, we present a culture-independent method for discriminating archaea from bacteria at the single-cell level using Raman spectroscopy combined with machine learning. We constructed a Raman spectral data set comprising 22 prokaryotic species (11 archaea and 11 bacteria) and developed a domain-level Archaea-Bacteria (AB) classifier using the LightGBM tree-based machine learning algorithm. Our AB classification model achieved an average classification accuracy of 89.1% and a sensitivity of 98.1% on eight representative species (including two independent held-out test species) with minimal data size and preprocessing. We also compared its performance to convolutional neural networks with transfer learning, a widely used deep learning approach. Our method provides a robust analytical framework for archaeal detection and represents a valuable addition to the microbiological toolkit, particularly for studying unculturable or low-abundance archaeal populations in complex microbial communities.},
}

@article {pmid41867679,
year = {2026},
author = {Biagioli, V and Matera, M and Cavecchia, I and Illiceto, M and Pennazzi, L and Luongo, G and Lugli, S and Striano, P},
title = {Beyond breastfeeding: a One Health Decalogue for nurturing the infant microbiota.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1784544},
pmid = {41867679},
issn = {2296-861X},
abstract = {BACKGROUND: Early-life nutrition is a key determinant of infant gut microbiota development, immune maturation, and long-term health outcomes. Although breastfeeding is widely recognized as the optimal feeding strategy, many mothers are unable to breastfeed, underscoring the need for practical, evidence-based guidance to support infant health beyond breastfeeding. A One Health approach enables the integration of nutritional, microbial, clinical, environmental, and socio-cultural factors that influence maternal-infant dyads.

METHODS: A narrative review of the literature was conducted using PubMed, Scopus, and Google Scholar, focusing more on works published from 2020 to 2026. Evidence was synthesized on maternal and infant nutrition, breast milk bioactive components, infant formula feeding, gut microbiota development, and short- and long-term health outcomes in non-breastfed infants. Based on this interdisciplinary evidence, a translational "One Health Decalogue" was developed for mothers who are unable to breastfeed.

FINDINGS: The reviewed literature highlights that infant nutrition, particularly in the absence of breastfeeding, significantly influences gut microbiota composition, immune programming, metabolic regulation, and neurodevelopment. Key modifiable factors include formula composition, feeding practices, maternal health status, environmental exposures, caregiver education, and psychosocial support. The proposed One Health Decalogue synthesizes these elements into 10 actionable principles aimed at supporting microbial resilience, promoting healthy development, and reducing health inequalities when breastfeeding is not possible.

CONCLUSION: Translating scientific evidence into practical tools is essential to support infants who cannot be breastfed. The One Health Decalogue presented in this review provides a comprehensive, interdisciplinary, and translational framework for healthcare professionals, families, and public health policies, fostering informed nutritional choices and holistic strategies to optimize infant health beyond breastfeeding.},
}

@article {pmid41867689,
year = {2026},
author = {Zhong, L and Qing, Y and Liu, J},
title = {The role of enteral nutrition and parenteral nutrition in the management of inflammatory bowel disease: a bibliometric analysis (1999-2025).},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1767514},
pmid = {41867689},
issn = {2296-861X},
abstract = {OBJECTIVES: As a chronic disease often accompanied by malnutrition, Inflammatory Bowel Disease (IBD) has encountered many difficulties in long-term management. Enteral nutrition (EN) and parenteral nutrition (PN) are important methods to help improve nutritional status and support the remission of the disease. However, although increasing attention has been directed toward this kind of nutritional therapy, there is still a lack of detailed and accurate bibliometric analysis in this field. Therefore, the goal of this study is to find out the research trends and hot spots, and provide reference for future academic exploration and clinical practice.

METHODS: On November 26th, 2025, publications concerning EN, PN in IBD published from 1999 to 2025 were retrieved from two databases: Web of Science Core Collection and Scopus. In this study, R software, Microsoft Excel, VOSviewer and CiteSpace are used to measure and visually analyze the articles.

RESULTS: A total of 3,245 documents were reviewed, indicating a trend of power-law growth. The USA and UK lead in global collaboration, with China being third in volume but with less cooperative intensity. The study identifies a clear progression from early "total parenteral nutrition" and "corticosteroids" to "exclusive enteral nutrition". Citation bursts occurring in the years 2020 to 2025 included "Mediterranean diet," "gut microbiome," and "Crohn's disease exclusion diet," pointing to an emerging focus in personalized, whole-food-based therapies and microbiome modification.

CONCLUSION: The research on nutritional therapy of IBD demonstrates a rapid increase, which shows that it is becoming more and more important in helping patients control their illness. In the future, we need more high-quality research to turn these data into useful and multidisciplinary treatment guidelines.},
}

@article {pmid41867705,
year = {2026},
author = {Barrodia, P and Saw, AK and Jeter-Jones, SL and Chang, CC and Shao, J and Arslan, E and Singh, AK and Satpati, S and Jenq, RR and Rai, K and Piwnica-Worms, H},
title = {Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.06.710208},
pmid = {41867705},
issn = {2692-8205},
abstract = {UNLABELLED: Fasting enhances small intestinal regeneration after radiation but the contribution of the gut microbiome to this process remains uncharacterized. We identify Akkermansia muciniphila (AKK) as a key mediator of this response. AKK was enriched in fasted mice and its antibiotic depletion abrogated radioprotection whereas reintroduction restored both organismal survival and intestinal integrity. Fasting elevated propionic acid, consistent with AKK 's metabolic output. AKK -conditioned medium and propionate induced histone H3 acetylation in intestinal stem cell cultures while in vivo fasting induced AKK -dependent H3K27ac and H3K9ac, remodeling promoter-enhancer landscapes in crypt epithelial cells. Epigenetic profiling revealed a rewired core regulatory program enriched for pioneer transcription factors (Foxa, Gata, Klf), architectural organizers (Ctcf, Boris), and lineage-defining and metabolic regulators (Cdx2, Hnf4). This program supports expansion of a population of persister stem cells characterized by open chromatin accessibility at key stem and regenerative-associated loci including Clu , Olfm4 , Lgr5, Ascl2, Lrig1, Sox9, Rnf43, and Axin2. These findings define a fasting-induced microbiome-metabolite-chromatin axis that epigenetically primes highly plastic persister stem cells for rapid regeneration of the intestinal epithelium following radiation-induced injury.

SIGNIFICANCE STATEMENT: Fasting changes the gut microbiome, but how these changes help the body recover from damage is not well understood. We found that fasting increases a helpful bacterium, Akkermansia muciniphila , which produces propionate, which drives epigenetic changes by modifying histones and regulating gene activity. These changes promote the expansion of persister stem cells that help the intestine recover after radiation. This study shows how fasting and gut bacteria work together to protect healthy tissue and suggests that diet or microbial treatments could help reduce side effects of cancer radiotherapy.},
}

@article {pmid41867794,
year = {2026},
author = {Alviter-Plata, A and Ahmari, N and Gadient, J and Brammer-Robbins, E and Martyniuk, CJ and Zubcevic, J},
title = {Loss of Bone Marrow β1/β2-Adrenergic Receptors Reprograms Host-Microbiota Interactions and Protects Against Diet-Induced Obesity.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.03.05.707516},
pmid = {41867794},
issn = {2692-8205},
abstract = {The gut ecosystem is shaped by multiple factors with the immune system being one of the major determinants in shaping its composition in health and disease. On the other hand, the immune system regulates its responses through the action of the sympathetic nervous system (SNS) in part through beta-adrenergic receptors 1/2 (ADRB1/2). In the past years, a clear link has been established between the immune system, SNS, and the modification of nutrient absorption by the gut microbiota in the development of diet-induced obesity. We have previously shown in male mice transplanted with bone marrow cells ADRB1/2 knock-out mice (KD) showed mild immunosuppression and microbiota changes. Post-recovery, mice were challenged with high-fat diet (HFD) for two weeks ad libitum . Our findings show that KD mice are protected against diet-induced adiposity and weight gain. Additionally, these mice showed an increase in residual calorific values and a decreased expression of the fatty acid transporter FAT/CD36. Suggesting a decreased absorption of lipids in the KD mice. Gut microbiota analysis showed that KD microbiota composition on a HFD remained stable with a significant enrichment in the Bacteroidetes phylum , which is depleted in obesity. This was associated with a switch from triglycerides to diglyceride fecal profile. Moreover, microbiome culture showed a decrease in triglycerides after an incubation with 0.1% of HFD lipid extract. Suggesting a potential role of the Bacteroidetes phylum in the metabolism of these lipids. Our findings demonstrate not only that the gut microbiota can modify nutrient absorption and susceptibility to diet-induced obesity but also that the immune system contributes to selective depletion of microbial members that would otherwise thrive on dietary lipids. Revealing a novel mechanism by which host immunity sculpts the gut ecosystem in ways that influence metabolic outcomes.},
}

@article {pmid41867919,
year = {2026},
author = {Morrin, ST and Buck, RH and Hill, DR},
title = {A unique blend of five human milk oligosaccharides supports recovery of infant microbiome composition and function after ex vivo antibiotic use.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1765159},
pmid = {41867919},
issn = {2296-2360},
abstract = {Human milk oligosaccharides (HMOs) are the third most abundant solid component of human breast milk, with well-established prebiotic and immunomodulatory functions. HMOs serve as selective substrates to support the growth of beneficial microbes in the developing gastrointestinal tract. At the same time individual HMOs have been shown to also exert selection against pathogens via direct anti-adhesive mechanisms. A longstanding hypothesis has held that HMOs act in concert and with other bioactive components of milk, and that this complex matrix of milk components collectively accounts for both the benefits to microbiome development and reduced risk of infectious disease associated with breastfeeding. The prebiotic activity of a diverse blend of fucosylated, acetylated, and sialylated HMOs was examined using microbiota cultured in an ex vivo model of the infant gastrointestinal tract before, during and after the supplementation of common childhood antibiotics. The anti-adhesive activity of this blend against infant-prevalent bacterial pathogens was tested using in vitro cultured intestinal epithelial cells. Taken together, this data suggests that a blend of 5 specific HMOs acts through multiple selection mechanisms to shape the development of the microbiota and interrupt opportunistic microbial pathogenesis.},
}

@article {pmid41868041,
year = {2026},
author = {Yu, S and Shu, W and Zhang, J and Cheng, S and Shen, X and Chen, G and Zhang, T and Dong, K and Zhang, J and Wang, H},
title = {Gut Microbiota-Immune Interactions in Endometrial Cancer: Causal Mediation and Subtype-Specific Mechanisms.},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {583327},
pmid = {41868041},
issn = {1179-1411},
abstract = {PURPOSE: In this study, we applied two-sample Mendelian randomization (MR) to explore the causal effects between gut microbiota (GM), immune cells, and endometrial cancer (EC) subtypes and to assess whether immune cells mediate the impact of GM on EC.

PATIENTS AND METHODS: Using two-sample Mendelian randomization and mediation analysis, we analyzed GWAS data: GM (Dutch Microbiome Project; N=7738), EC subtypes (IEU Open GWAS; N=331,588), and immune traits (N=3757). We assessed the effects of the causal gut microbiota on EC subtypes and immune trait mediation.

RESULTS: Subtype-specific causal relationships were identified.Overall EC: Four positive (e.g. genus Erysipelotrichaceae noname) and three negative (e.g. species Bacteroides faecis) microbial causal effects; three mediated by immune traits (e.g. Ruminococcus obeum via CD86+ myeloid DC AC). Endometrioid EC: Five negative (e.g. class Bacilli) and two positive (e.g. species Aspergillus senegalensis) effects; three immune-mediated (e.g. Bacilli via IgD+ CD38br % lymphocytes). Non-endometrioid EC: Two positive (e.g. species Bacteroides stercoris) and one negative (species Ruminococcus bromii) effect; one mediated (Ruminococcus bromii via CD8br NKT % lymphocytes).

CONCLUSION: Immune traits significantly mediated causal pathways from GM to EC development. It also highlighted the distinct causal relationships and immune-mediated mechanisms across the three major EC subtypes (overall, endometrioid, and non-endometrioid). These subtype-specific insights into the gut-immune-cancer axis provide novel perspectives for developing therapeutic strategies targeting GM and the immune microenvironment in different EC subtypes.},
}

@article {pmid41868135,
year = {2026},
author = {Wen, P and Zhuo, X and Xue, S},
title = {Fatty acid-related immune network in psoriasis: metabolic regulation of innate and adaptive immunity.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1731683},
pmid = {41868135},
issn = {1663-9812},
abstract = {Psoriasis is a chronic inflammatory skin disorder driven by dysregulation of the Treg/Th17 axis, where enhanced Th17 activity promotes keratinocyte proliferation and inflammation, while impaired Treg function exacerbates immune dysregulation. Emerging evidence highlights peroxisome proliferator-activated receptor γ (PPARγ) as a key regulator of fatty acid oxidation (FAO), a metabolic pathway critical for Treg differentiation and function. PPARγ activation enhances FAO via upregulation of CD36, CPT1, and AMPK signaling, while suppressing glycolysis, thereby skewing the Treg/Th17 balance toward immune tolerance. Concurrently, short-chain fatty acids (SCFAs), microbial metabolites with immunomodulatory properties. ameliorate psoriatic inflammation by promoting Treg expansion, inhibiting Th17 polarization, and modulating innate immune cells (neutrophils, dendritic cells, and macrophages). SCFAs exert their effects through receptor-dependent signaling and epigenetic mechanisms (HDAC inhibition), while derivative compounds and probiotic interventions enhance therapeutic potential. This review summarizes mechanistic insights into PPARγ-driven FAO and SCFA-mediated immunomodulation, proposing novel metabolic and microbiome-targeted strategies for psoriasis treatment.},
}

@article {pmid41868170,
year = {2026},
author = {Zhang, J and Zhang, M and Wu, X and Jing, H and Li, P and Wang, W and Guo, X and Zhao, Z and Zhu, S and Wang, Y},
title = {Circulating Butyrate Attenuates Cetuximab Efficacy in Colorectal Cancer Through EGFR and AMPK-Wip1 Signaling.},
journal = {Drug design, development and therapy},
volume = {20},
number = {},
pages = {574116},
pmid = {41868170},
issn = {1177-8881},
mesh = {*Colorectal Neoplasms/drug therapy/pathology/metabolism ; *Cetuximab/pharmacology ; Humans ; ErbB Receptors/metabolism/antagonists & inhibitors ; Signal Transduction/drug effects ; *AMP-Activated Protein Kinases/metabolism ; *Butyrates/pharmacology/blood ; Animals ; Mice ; Cell Proliferation/drug effects ; Drug Screening Assays, Antitumor ; *Adaptor Proteins, Signal Transducing/metabolism ; *Antineoplastic Agents, Immunological/pharmacology ; Neoplasms, Experimental/drug therapy/pathology/metabolism ; Dose-Response Relationship, Drug ; Mice, Nude ; Tumor Cells, Cultured ; },
abstract = {BACKGROUND: Cetuximab is an approved therapy for metastatic colorectal cancer (CRC) with wild-type RAS and BRAF; however, additional resistance mechanisms beyond genetic mutations remain poorly understood. Butyrate, a key metabolite produced by the gut microbiome and present in the circulatory system, has been reported to supply cellular energy and modulate the epidermal growth factor receptor (EGFR) downstream signaling pathway. However, whether butyrate affects the resistance to cetuximab is still unknown.

METHODS: In this work, Cell Counting Kit-8 (CCK-8) and colony formation assays were used to evaluate the efficacy of cetuximab. Glycolysis/oxidative phosphorylation (OXPHOS) Assay Kit was applied to assess metabolic activity. Human Phospho-Kinase Array and RNA sequencing were employed to screen targets of butyrate. Overexpression plasmids and short hairpin RNAs (shRNAs) targeting these molecules were transfected into cells for further validation. Subcutaneous tumor and pulmonary metastasis models were used for in vivo studies.

RESULTS: The findings showed that physiological concentrations of butyrate increased cetuximab resistance in KRAS wild-type cells only. Further investigation found that butyrate upregulated EGFR signaling through facilitating the binding reaction between epidermal growth factor (EGF) and EGFR. In parallel, butyrate activated AMP-activated protein kinase (AMPK)-wild-type p53-induced phosphatase 1 (Wip1) signaling, leading to suppression of p53 and p38 mitogen-activated protein kinase (p38 MAPK)-mediated pro-apoptotic signaling. These two mechanisms are the reason that butyrate attenuates the efficacy of cetuximab. Results of subcutaneous tumor and pulmonary metastasis models exhibited a similar conclusion to in vitro experiments.

CONCLUSION: Butyrate reduces cetuximab efficacy in KRAS wild-type colorectal cancer through EGFR and AMPK-Wip1 signaling, and may represent a candidate predictive biomarker for treatment response.},
}

*Colorectal Neoplasms/drug therapy/pathology/metabolism
*Cetuximab/pharmacology
Humans
ErbB Receptors/metabolism/antagonists & inhibitors
Signal Transduction/drug effects
*AMP-Activated Protein Kinases/metabolism
*Butyrates/pharmacology/blood
Animals
Mice
Cell Proliferation/drug effects
Drug Screening Assays, Antitumor
*Adaptor Proteins, Signal Transducing/metabolism
*Antineoplastic Agents, Immunological/pharmacology
Neoplasms, Experimental/drug therapy/pathology/metabolism
Dose-Response Relationship, Drug
Mice, Nude
Tumor Cells, Cultured

@article {pmid41868349,
year = {2026},
author = {Liang, J and Huang, T and Li, J and Yang, Z and Ni, J and Wang, Y},
title = {The chemistry of the nitrate-nitrite-nitric oxide pathway: regulating muscle oxygenation and exercise performance.},
journal = {RSC advances},
volume = {16},
number = {17},
pages = {15723-15735},
pmid = {41868349},
issn = {2046-2069},
abstract = {Nitric oxide (NO) is a pleiotropic signaling molecule fundamentally involved in regulating skeletal muscle physiology, including blood flow, contractility, and metabolism. For decades, the synthesis of NO was attributed solely to the l-arginine-dependent nitric oxide synthase (NOS) enzymes. However, the discovery and characterization of the nitrate-nitrite-NO pathway have revealed an alternative, NOS-independent mechanism for NO generation. This pathway is particularly significant under hypoxic and acidic conditions, which are characteristic of exercising skeletal muscle. Dietary inorganic nitrate, abundant in green leafy vegetables and beetroot, is sequentially reduced to nitrite and then to bioactive NO. This review critically examines the intricate chemistry underpinning this pathway, from the initial enzymatic reduction of nitrate by both mammalian and microbial reductases to the diverse chemical routes of nitrite reduction to NO within the muscle milieu. We delve into the specific roles of key proteins such as xanthine oxidoreductase, deoxyhemoglobin/deoxymyoglobin, and mitochondrial complexes in catalyzing these transformations. Furthermore, we explore how NO generated via this pathway modulates muscle oxygenation through vasodilation and regulation of mitochondrial respiration. The ergogenic potential of dietary nitrate supplementation is discussed in the context of human exercise performance, highlighting the significant controversies, methodological challenges, and sources of inter-individual variability, including genetics and the microbiome. This review aims to provide a comprehensive, chemistry-focused perspective on the nitrate-nitrite-NO pathway, bridging fundamental biochemical mechanisms with their physiological consequences in exercise.},
}

@article {pmid41868361,
year = {2026},
author = {Zhang, Y and Pang, Y and Tan, H and Xian, R and Liang, J and Wen, Q and Li, Z and Yan, L and Xie, Z and Li, J and Fu, W and Zhou, P},
title = {Electroacupuncture alleviates comorbid obesity and depression via the gut-brain axis: orchestrating SCFA-producing bacteria and hippocampal synaptic plasticity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1772788},
pmid = {41868361},
issn = {1664-302X},
abstract = {INTRODUCTION: Comorbid obesity and depression (COMBD) represents a complex metabolic-neuropsychiatric challenge with limited therapeutic options. While Electroacupuncture (EA) is effective for both metabolic and mood disorders, the systemic mechanisms-particularly the interplay between the gut microbiome and hippocampal plasticity-remain elusive.

METHODS: We established a COMBD rat model using a high-fat diet combined with chronic unpredictable mild stress (CUMS). An integrated multi-omics approach comprising 16S rDNA sequencing, LC-MS/MS serum metabolomics, and hippocampal transcriptomics was utilized to decipher the therapeutic mechanisms of EA.

RESULTS: EA treatment significantly attenuated body weight gain and reversed depressive-like behaviors. Crucially, EA restructured the dysbiotic gut microbiota, specifically increasing the abundance of short-chain fatty acid (SCFA)-producing bacteria. This microbial restoration was strongly correlated with a reprogrammed serum metabolic profile. In the hippocampus, transcriptomic analysis identified Cd74 as a pivotal upstream regulator modulated by EA. Furthermore, EA mitigated hippocampal oxidative stress and restored synaptic plasticity, evidenced by increased dendritic spine density and upregulated synaptic protein expression.

CONCLUSION: Our findings suggest that EA ameliorates COMBD via a coordinated "Microbiota-Metabolism-Brain" axis. Specifically, EA creates a neuroprotective milieu by promoting beneficial SCFA-producing bacteria and regulating metabolic signals, which subsequently targets hippocampal Cd74 to restore synaptic plasticity. This study provides a novel mechanistic basis for the clinical application of EA in treating complex metabolic-mood comorbidities.},
}

@article {pmid41868364,
year = {2026},
author = {Yin, J and Wang, H and Cui, Y and Zhou, X and Zhang, S and Yin, H},
title = {Bacteriophage-mediated gut microbiota regulation: a bibliometric landscape analysis (2005-2024).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1768117},
pmid = {41868364},
issn = {1664-302X},
abstract = {OBJECTIVE: This study systematically evaluates the current situation, knowledge structure and development trend of bacteriophage-mediated intestinal microbiota regulation research from 2005 to 2024 through literature measurement analysis.

METHOD: Retrieve relevant research from the Web of Science core collection, Scopus and PubMed databases. After screening according to inclusion criteria, CiteSpace, VOSviewer, and R-bibliometrix were employed for bibliometric and visualization analysis. This systematically mapped publication trends, collaboration networks among countries/institutions/authors, core journals, and research hotspots.

RESULTS: Thousands of relevant studies were included. From 2005 to 2024, the number of papers published in microbiology journals showed a step-by-step increase, reaching a peak of 355 articles in 2022. The United States and China are the main contributors. University College Cork in Ireland and San Diego State University in the United States have become core research institutions, and Colin Hill is listed as the most influential author. The Frontiers in Microbiology has published the largest number of papers, and Microbiome and Nature Communications have become platforms for the publication of high-impact research results. The research focus has shifted from the description of early bacteriophage-bacterial binary interaction to exploring the ternary relationship of "bacteriophage-microbiota-host health." In recent years, short-chain fatty acids, microbiota disorders and clinical intervention have become the core research directions. This study included 16 clinical trials on phage-mediated gut microbiota regulation, 14 of which were based on moderate to high-quality clinical evidence, indicating that research design in this field has advanced from the initial observational stage to the intervention verification stage.

CONCLUSION: This research systematically sorts out the research progress of 20 years in the field of bacteriophage-mediated intestinal microbiota regulation through the method of literature metrology. The research clearly outlines the evolutionary trajectory of this field from basic description to mechanism exploration to clinical transformation. Future research should focus on the following directions: clarifying the molecular mechanism of the interaction of core diseases, establishing a standardized research framework, and carrying out large-scale multi-center clinical trials to promote the transformation of this field from basic research to clinical application.},
}

@article {pmid41859031,
year = {2026},
author = {Motlak, M and Gill, C and Guzzardi, E and Barlow, S and Guilarte, G and Choudhary, S},
title = {Alcohol Use and Hidradenitis Suppurativa: An Unclear Relationship.},
journal = {Skin appendage disorders},
volume = {},
number = {},
pages = {},
pmid = {41859031},
issn = {2296-9195},
abstract = {BACKGROUND: Hidradenitis suppurativa (HS) may be linked to behavioral factors that exacerbate inflammation, gut microbiome, and healing.

SUMMARY: This review evaluates current evidence on the relationship between alcohol consumption and HS. Emerging studies show high incidences of alcohol and substance use disorders in HS patients. However, observational studies remain inconsistent: HS patients may experience higher alcohol-related burden, yet its association to disease progression and baseline severity remains unclear. Limitations of existing studies include self-reported exposures of alcohol, heterogeneous outcome measures, and potential confounding factors, such as stress.

KEY MESSAGES: Biologic plausibility remains, as alcohol can promote dysbiosis, inflammation, and oxidative stress that may influence disease activity and healing. This review highlights the need for larger, controlled trials that determine whether the reduction or elimination of alcohol may improve HS outcomes.},
}

@article {pmid41859075,
year = {2026},
author = {Chen, M and Zhang, J and Yang, H and Lei, L and Yang, L and Wang, S and Yu, H},
title = {JK5G postbiotics modulate gut microbiota and metabolome to alleviate cancer-related pain: a randomized controlled trial with multi-omics integration.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1764491},
pmid = {41859075},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Metabolome/drug effects ; Male ; Middle Aged ; Female ; *Probiotics/administration & dosage ; *Cancer Pain/metabolism/microbiology/therapy/etiology ; Quality of Life ; Double-Blind Method ; Adult ; Metabolomics/methods ; Aged ; Feces/microbiology ; Multiomics ; },
abstract = {INTRODUCTION: Cancer-related pain remains a critical clinical challenge, with existing opioid-based therapies often yielding inadequate relief and significant side effects. This study investigates the therapeutic potential of JK5G postbiotics-a formulation of inactivated Lactobacillus strains and metabolites-in modulating the gut-microbiome-immune axis to alleviate pain in cancer patients.

METHODS: This study employs a randomized, double-blind, placebo-controlled trial design involving 149 participants divided into two groups: a control group receiving patient-controlled subcutaneous analgesia (PCSA) plus placebo, and an experimental group receiving PCSA plus JK5G postbiotics. The primary outcomes were changes in gut microbiota composition assessed by 16S rRNA gene sequencing, and quality of life (QoL). The secondary outcomes included fecal metabolomics, adverse effects (AEs), blood inflammatory cytokines, and lymphocyte subsets. This study was registered at www.chictr.org.cn(ChiCTR2500108811).

RESULTS: JK5G supplementation significantly improved pain scores, QoL, and cognitive and social functioning compared to controls. Microbiome analysis revealed enrichment of beneficial taxa such as Akkermansia muciniphila and Bifidobacterium, alongside suppression of pathogenic Escherichia-Shigella. Machine learning identified five core microbial biomarkers (Akkermansia muciniphila, Bifidobacterium, Escherichia-Shigella, Blautia, Streptococcus), with SHAP analysis highlighting Akkermansia muciniphila and Bifidobacterium as top contributors. Metabolomic profiling demonstrated upregulation of 236 metabolites, including kynurenic acid and butyric acid, with tryptophan and butyrate metabolism emerging as key altered pathways. Immune profiling showed elevated CD3[+]CD4[+] T cells and reduced TNF-α levels, while MIMOSA2 analysis linked microbial taxa to metabolic shifts, such as correlations between Ruminococcus torques and butyric acid.

CONCLUSION: These findings suggest that JK5G may contribute to the amelioration of cancer-related pain by reshaping gut microbiota, modulating host metabolism, and enhancing immune responses. This study highlights the potential of JK5G postbiotics as an adjunct therapy, supporting the need for further validation in larger cohorts and mechanistic investigations to advance its clinical translation.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/showproj.html?proj=285304, identifier ChiCTR2500108811.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Metabolome/drug effects
Male
Middle Aged
Female
*Probiotics/administration & dosage
*Cancer Pain/metabolism/microbiology/therapy/etiology
Quality of Life
Double-Blind Method
Adult
Metabolomics/methods
Aged
Feces/microbiology
Multiomics

@article {pmid41859112,
year = {2026},
author = {Chen, H and Lou, G and Meng, F and Zhang, Y and Kuang, H and Yang, D},
title = {Critical role of reproductive tract microbiota and derived metabolites in inflammation, tumor immunity, and tumorigenesis of gynecological cancers: a narrative review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1734792},
pmid = {41859112},
issn = {1664-3224},
mesh = {Humans ; Female ; *Genital Neoplasms, Female/metabolism/immunology/microbiology/therapy/etiology ; Animals ; *Microbiota/immunology ; *Carcinogenesis/immunology ; Inflammation/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; *Genitalia, Female/microbiology/immunology ; },
abstract = {Gynecological malignancies, including ovarian, cervical, and endometrial cancers, present significant clinical challenges due to the epidemiological complexity and limitations in current therapeutic strategies. Emerging evidence highlights the critical role of the microbiome and its metabolites in modulating tumor initiation, progression, and treatment responses. This review explores the intricate mechanisms through which gut and reproductive tract microbiota influence gynecological cancers via immune regulation, metabolic reprogramming, and epigenetic modifications. Key microbial metabolites, such as short-chain fatty acids, bile acids, and estrogen-metabolizing intermediates, serve as molecular bridges in host-microbe communication, impacting chemotherapy resistance and immunotherapy efficacy. Furthermore, we discuss the translational potential of microbiome-targeted interventions, including probiotics, fecal microbiota transplantation, and precision microbial therapies, as innovative approaches for diagnosis, prognosis, and treatment. Understanding the microbiota-reproductive axis offers novel insights into overcoming therapeutic resistance and improving patient outcomes in gynecologic oncology.},
}

Humans
Female
*Genital Neoplasms, Female/metabolism/immunology/microbiology/therapy/etiology
Animals
*Microbiota/immunology
*Carcinogenesis/immunology
Inflammation/immunology/metabolism/microbiology
*Gastrointestinal Microbiome/immunology
*Genitalia, Female/microbiology/immunology

@article {pmid41859191,
year = {2026},
author = {Su, Y and Xia, Y},
title = {Gut microbiota dysbiosis and depression: Bidirectional interactions, mediating pathways, and microecological therapeutics.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101372},
pmid = {41859191},
issn = {2665-9271},
abstract = {The microbiota-gut-brain axis (MGBA) is increasingly recognized as a key target for ameliorating major depressive disorder (MDD). This review systematically synthesizes evidence on the bidirectional relationship between gut microbiota dysbiosis and MDD, and delineates the core mechanisms-such as neuroinflammation, neurotransmitter metabolism, and hypothalamic-pituitary-adrenal (HPA) axis dysregulation-through which this axis influences depressive pathogenesis. Further, the intestinal microbiota characteristics related to MDD, the main regulatory pathways, and the potential efficacy of microbiome-targeted intervention measures-including psychobiotics, prebiotics, fecal microbiota transplantation (FMT), and dietary strategies-were sorted out. In the clinical assessment and drug research of depression, the assessment tools are mainly divided into two categories: clinician-rated and self-reported. These two types are often used together to provide multi-dimensional evidence of therapeutic efficacy. Evidence suggests that stress-related intestinal permeability may initiate gut dysbiosis, which in turn can impair barrier function, promote neuroinflammation, disrupt neurotransmitter synthesis, and overactivate the HPA axis, potentially exacerbating depressive symptoms. Interventions targeting the gut microbiota may help reshape microbial communities, increase short-chain fatty acids (SCFAs) and 5-Hydroxytryptamine (5-HT), and dampen inflammatory and stress responses, thereby offering a promising, non-pharmacological avenue for alleviating MDD. This review not only offers a theoretical foundation for microbiota-based therapeutics in MDD but also highlights pathways toward developing safe, effective non-pharmacological strategies for depression management.},
}

@article {pmid41859194,
year = {2026},
author = {Armah, J and Alzahid, S and Pei, Q and Cousin, L and Fanfan, D and Heldermon, C and Lyon, D},
title = {Associations among physical activity, diet, non-lifestyle characteristics and the gut microbiome of cancer patients: A scoping review and network analysis.},
journal = {Oncoscience},
volume = {13},
number = {},
pages = {85-103},
pmid = {41859194},
issn = {2331-4737},
abstract = {Lifestyle factors, such as physical activity and dietary modifications can beneficially modulate the gut microbiome of cancer patients, however their effects are often shaped by non-modifiable variables. This review and network analysis aims to synthesize current evidence on how both lifestyle and non-lifestyle factors affect the gut microbiome in cancer patients. A systematic search was conducted on Scopus, CINAHL, PubMed and Web of Science to produce 51 eligible studies for this review. A chi-square test of independence indicated that the distribution of gut bacteria function categories was significantly associated with the category of influencing factor (Χ[2] = 390.87, p = 0.032). Across studies, high physical activity and healthy diets were associated with increased abundances of saccharolytic/short-chain fatty acids and lactic acid-producing bacteria, alongside decreased abundances of pathogenic or opportunistic bacteria. However, these associations may also be influenced by non-lifestyle characteristics such as chemotherapy, age, and cancer type or stage which could mask the benefits of lifestyle interventions. This study highlights the limited but growing evidence linking physical activity, diet and the gut microbiome in cancer populations. Progress in this field will require larger, more integrative designs that account for non-lifestyle confounders and apply advanced analytical approaches to capture complex interactions.},
}

@article {pmid41859443,
year = {2026},
author = {Whitaker, BK and Gdanetz, K and Vaughan, MM and McCormick, S and Becker, T},
title = {Wheat mycobiome dynamics driven by interseasonal crop-crop transfer and Fusarium head blight.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1778987},
pmid = {41859443},
issn = {1664-302X},
abstract = {INTRODUCTION: Fusarium head blight (FHB) is a devastating disease of wheat that causes mycotoxin contamination in grains. Diseases like FHB have traditionally been managed with integrated strategies; but this has led to a proliferation of fungicide-resistant pathogens and soil erosion while full disease control has remained elusive. Leveraging the microbiome for more sustainable management is an alternative, however, translation of promising strategies is hampered by our limited understanding of crop microbiome differences across plant development and tissue types.

METHODS: We characterized fungal communities using amplicon sequencing across five developmental timepoints in wheat leaves and wheat heads, as well as in maize debris from the previous growing season. Samples were collected from two locations in Illinois, USA. We assessed how tissue type, site, developmental stage, and wheat variety contributed to mycobiome composition. Source-sink relationships among debris, leaves, and heads were evaluated, and taxa associated with high and low FHB conditions were identified. Network analyses were used to determine the roles of key fungal taxa in wheat head and maize debris microbiomes.

RESULTS: Mycobiome composition varied strongly by tissue type, though site and developmental timepoint were also important contributors. Host variety conditionally explained mycobiome variation in wheat heads, but not in leaves or debris. We also identified debris as a major fungal source to leaves early in development, but not later-and found that leaves were never a large inoculum source to head mycobiomes at either developmental stage tested. Taxa enriched under high FHB conditions in wheat heads belonged to the Ascomycota (Cladosporium, Pseudopithomyces), while taxa enriched under low FHB conditions primarily belonged to the Basidiomycota (Filobasidium, Sporobolomyces, Tilletiopsis, Entyloma). Fusarium spp. were important nodes in wheat head and maize debris microbiome networks.

DISCUSSION: This work shows that fungal movement from crop to crop across seasons, and between plant tissues within a season, shape phyllosphere microbiome dynamics and can indicate potential disease outcomes in the FHB pathosystem. As microbiome-based disease management develops alongside rapid growth in the biologicals industry and increased recognition of microbial roles in agriculture, this work highlights several promising directions. These include identifying basidiomycetous yeasts associated with low FHB, pinpointing taxa correlated with Fusarium in wheat heads and maize debris, and demonstrating that applying biocontrols to wheat leaves is unlikely to affect pathogen spread to heads. Future research should focus on controlled tests of microbe-microbe interactions and their impacts on plant immunity, disease suppression, and yield.},
}

@article {pmid41859445,
year = {2026},
author = {Huang, Y and Liang, Q and Shen, Y and Chen, J and Xu, W},
title = {Oral microbiome dysbiosis in autism spectrum disorder: the oral-gut-brain axis and future perspectives: a narrative review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1783810},
pmid = {41859445},
issn = {1664-302X},
abstract = {Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with a steadily increasing global prevalence, yet its etiology remains largely unclear. Emerging evidence suggests that oral microbiome dysbiosis may contribute to the pathogenesis of ASD, potentially through the oral-gut-brain axis, although the exact role and causality remain to be fully established. In this narrative review, we synthesize recent clinical and metagenomic evidence on oral microbiome alterations in ASD and critically evaluate the potential pathways through which these microbial imbalances may impact neurodevelopmental outcomes. We summarize the key host-microbe interactions, including inflammatory signaling, epithelial barrier disruption, and immune-neural crosstalk, while emphasizing that direct causal evidence is still limited. Dysbiosis in individuals with ASD is characterized by altered microbial communities, including increased Streptococcus and decreased Prevotella, which correlate with clinical symptom severity. Moreover, metagenomic profiling has indicated the presence of potential biomarkers in the oral microbiome, which may serve as promising noninvasive diagnostic tools for ASD. While the clinical applications of oral microbiome diagnostics are still in the early stages, we explore the challenges and opportunities for developing these biomarkers for risk stratification. Finally, we outline future research directions that could enhance the understanding of the oral microbiome's role in ASD and facilitate the development of personalized intervention strategies.},
}

@article {pmid41859446,
year = {2026},
author = {Bai, L and Wang, Z and Wang, H and Ma, B},
title = {Comprehensive evaluation of environment adaptability in wild and captive lenok (Brachymystax lenok): from the perspective of antioxidant capacity, immune response and gut microbiome.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1764670},
pmid = {41859446},
issn = {1664-302X},
abstract = {INTRODUCTION: The intestinal microbiota is considered an adaptive trait closely associated with reintroduction success and may contribute to the ecological fitness of B. lenok.

METHODS: In this study, intestinal morphology, digestive enzyme activity, immune parameters, and gut microbiota composition were compared between wild and farmed B. lenok to elucidate differences in intestinal and hepatic health under distinct aquatic environments.

RESULTS: Histological analysis showed that villi in the hindgut of wild individuals were longer and denser than those of farmed ones. Although the intestinal structure of farmed B. lenok remained intact, their villus morphology and density differed significantly from those of the wild group. Compared with the farmed group, wild B. lenok showed higher hepatic immune/antioxidant activity (elevated alkaline phosphatase (AKP), acid phosphatase (ACP), lysozyme (LYZ), and catalase (CAT), as well as glutathione (GSH) content) and up-regulated liver immune-related genes (c3, foxo1, igM, il-10, lyz, etc.), while farmed fish displayed higher intestinal stress markers (CAT, malondialdehyde (MDA) and a pro-inflammatory signature (il-6, il-1β upregulated). Microbiota profiling revealed higher abundance of Firmicutes and Bacteroidetes but a trend of decreasing Proteobacteria in the wild group.

DISCUSSION: Collectively, these findings demonstrate significant differences in intestinal morphology, digestive function, and microbial community composition between wild and farmed B. lenok. This study provides new insights for improving post-stocking adaptability in reintroduction programs and proposes novel conservation strategies for biodiversity restoration.},
}

@article {pmid41859449,
year = {2026},
author = {Han, Y and Huang, H and Zhang, Z and Li, X and Li, T and Zong, S},
title = {Microbiome and metabolome dynamics in phloem and rhizosphere of Pinus tabuliformis against Dendroctonus valens infestation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1754801},
pmid = {41859449},
issn = {1664-302X},
abstract = {Microbial communities play essential roles in mediating plant defenses against insect pests. However, how host-associated microbiota and metabolites jointly respond to bark beetle infestation remains largely unexplored. Here, we integrated microbiome and metabolome profiling to elucidate how Pinus tabuliformis regulates its phloem and rhizosphere responses under varying levels of Dendroctonus valens infestation. Both bacterial and fungal diversity, as well as the relative abundance of dominant taxa such as Erwinia and Pseudoxanthomonas, shifted significantly with infestation intensity. Concurrently, key plant defense metabolites-including terpenoids, jasmonates, and polyphenols-were markedly elevated. Pathway enrichment analysis indicated that the phloem was characterized by enhanced phenylpropanoid and flavonoid biosynthesis, whereas the rhizosphere soil accumulated terpenoids and polyketides, implicating both compartments in resistance modulation. In the phloem, differential bacterial and fungal taxa displayed distinct positive and negative correlations with phenylpropanoid intermediates and downstream derivatives, while in the rhizosphere, bacteria from Bacillota and fungi such as Candida and Ogataea were strongly linked to diterpenoids, sesquiterpenoids, flavonoids, and indole derivatives. These findings demonstrate that P. tabuliformis mounts a compartment-specific, microbiome-associated metabolic response to D. valens infestation, providing new insights into the ecological roles of symbiotic microbiota in plant defense and offering a mechanistic foundation for microbe-based pest management strategies.},
}

@article {pmid41859450,
year = {2026},
author = {Jia, J and Chen, L and Liu, Q and Wang, K and Zhao, K and Ren, X and Gao, X and An, J},
title = {Correction: Enhancement of soil microbial community stability by earthworms and collembolans in soil from abandoned coal mine land.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1803716},
doi = {10.3389/fmicb.2026.1803716},
pmid = {41859450},
issn = {1664-302X},
abstract = {[This corrects the article DOI: 10.3389/fmicb.2026.1636784.].},
}

@article {pmid41859452,
year = {2026},
author = {Jia, C and Zhu, W and Yuan, Y and Xie, Q},
title = {How gut microbiota contribute to neuropsychiatric disorders: evidence from neuroimaging studies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1760096},
pmid = {41859452},
issn = {1664-302X},
abstract = {The interaction between the gut microbiota and central nervous system (CNS) diseases has emerged as a major focus in neuroscience and microbiome research. Accumulating evidence shows that gut microbiota influence the pathogenesis of neurodevelopmental, neurodegenerative, autoimmune, and psychiatric conditions via the microbiota-gut-brain axis. However, the underlying mechanisms are complex and not yet fully elucidated. Advances in multimodal magnetic resonance imaging, positron emission tomography, and diffusion tensor imaging, now enable in vivo visualization of associations between gut microbial alterations and abnormalities in brain structure and function, providing new perspectives for understanding the role of gut microbiota in CNS pathology. This review systematically reviews neuroimaging-based research linking gut microbiota to neurological diseases (e.g., Alzheimer's disease, multiple sclerosis, traumatic brain injury), and psychiatric disorders (e.g., schizophrenia, and autism spectrum disorder). It highlights the mediating roles of microbial metabolites, immune-inflammatory responses, and neuroimmune pathways, and discusses future directions integrating multi-omics data with neuroimaging technologies, as well as their potential clinical applications. What distinguishes this review from its predecessors in the same field is its explicit neuroimaging-driven framework rather than general mechanistic discussion.},
}

@article {pmid41859467,
year = {2026},
author = {Szydłowicz, M and Zajączkowska, Ż and Chabowski, M and Nowicki, M and Łukianowski, B and Gajdzis, P and Kváč, M and Calderón, EJ and Le Gal, S and Kicia, M},
title = {Multi-site screening for Pneumocystis jirovecii in lung cancer: possible tumour tissue colonization.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1755638},
pmid = {41859467},
issn = {2235-2988},
mesh = {Humans ; *Lung Neoplasms/microbiology/complications/pathology ; *Pneumocystis carinii/isolation & purification/genetics ; Male ; Female ; Middle Aged ; Aged ; Genotype ; Aged, 80 and over ; *Pneumonia, Pneumocystis/microbiology/diagnosis ; DNA, Fungal/genetics ; Lung/microbiology ; Adult ; *Pneumocystis Infections/microbiology/diagnosis ; Polymerase Chain Reaction ; },
abstract = {OBJECTIVES: Recent studies suggest that various tumour types can be colonized by different microorganisms, but data on unusual opportunistic fungus - Pneumocystis jirovecii - remain scarce. Lung cancer patients are considered one of the risk groups for its infection. Since P. jirovecii tends to distribute focally within the lungs, this study aimed to determine whether it can be detected in lung tumour tissue.

METHODS: Fragments of neoplastic tissue (NPL), normal adjacent tissue (NAT) and respiratory secretions (RS) were collected from 70 patients with histologically confirmed primary lung cancer. DNA was extracted and analysed by nested-PCR targeting the mtLSU rRNA and CYB loci, followed by genotyping.

RESULTS: Pneumocystis jirovecii was detected in fourteen samples derived from 8/70 individuals (11.4%): two NPL, six NAT and six RS. In two patients, Pneumocystis was detected in all three specimen types; both were diagnosed with the same histological malignancy grade (G3, P=0.036). The genotype distribution varied across sample types in most cases.

CONCLUSIONS: The ability of Pneumocystis to colonize NPL may be linked to the stage of tumour advancement, suggesting that local tumour-related factors could influence its colonization. These findings support further investigation of the lung microbiome in the context of tumour-associated microenvironments and their potential utility as complementary biomarkers in lung cancer.},
}

Humans
*Lung Neoplasms/microbiology/complications/pathology
*Pneumocystis carinii/isolation & purification/genetics
Male
Female
Middle Aged
Aged
Genotype
Aged, 80 and over
*Pneumonia, Pneumocystis/microbiology/diagnosis
DNA, Fungal/genetics
Lung/microbiology
Adult
*Pneumocystis Infections/microbiology/diagnosis
Polymerase Chain Reaction

@article {pmid41859469,
year = {2026},
author = {Zafeiropoulou, K and Hageman, IL and Mu, T and Davids, M and Li Yim, AYF and Joustra, VW and Hakvoort, TBM and Satsangi, J and Chronas, K and Koelink, PJ and Wildenberg, ME and van den Wijngaard, RM and D'Haens, GR and de Jonge, WJ},
title = {Colonic biopsy-associated microbial signatures are predictive of response to anti-TNFα biological therapy in Crohn's disease.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1741002},
pmid = {41859469},
issn = {2235-2988},
mesh = {Humans ; *Crohn Disease/drug therapy/microbiology/pathology ; Male ; Female ; Adult ; *Gastrointestinal Microbiome/drug effects ; *Colon/microbiology/pathology ; Biopsy ; Middle Aged ; *Tumor Necrosis Factor-alpha/antagonists & inhibitors ; Treatment Outcome ; Adalimumab/therapeutic use ; Antibodies, Monoclonal, Humanized/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Infliximab/therapeutic use ; Ustekinumab/therapeutic use ; Intestinal Mucosa/microbiology/pathology ; Biological Therapy ; },
abstract = {INTRODUCTION: Crohn's disease (CD) is commonly treated with biologic therapies, including anti-TNFα agents, vedolizumab (VDZ), and ustekinumab (USTE), yet only a subset of patients respond to these treatments. This study aimed to evaluate the potential of the gut microbiome to predict treatment response.

METHODS: Adult CD patients initiating anti-TNFα (infliximab or adalimumab), VDZ or USTE were enrolled. Pre-treatment ileal and/or colonic biopsies were collected endoscopically. Treatment response after 26-52 weeks was defined by ≥50% reduction in the simple endoscopic score for CD and either a corticosteroid-free clinical response (≥3-point HBI decrease or remission [HBI ≤4] without systemic steroids) or a biochemical response (≥50% or ≤5 mg/L CRP reduction and ≥50% or ≤250 μg/g faecal calprotectin reduction) versus baseline. Mucosal microbiota was profiled by 16S rRNA gene sequencing of biopsies. Machine learning models predicting treatment response were trained using ASV-level count data. The impact of heat-killed bacteria on anti-TNFα-induced CD14[+]CD206[+] macrophages was tested in mixed lymphocyte reactions (MLRs).

RESULTS: A total of 125 patients were included: 39 on anti-TNFα, 47 on VDZ, and 39 on USTE. Clinical features were similar between responders and non-responders, aside from sex (USTE-colon) and CRP (USTE-ileum). No major microbial differences were observed in VDZ, USTE ileal or colon samples. However, in colonic biopsies, anti-TNFα responders had significantly higher pre-treatment α-diversity, and 3.9% of β-diversity variation associated with response. Among six models, the anti-TNFα colonic model performed significantly better than random (AUC = 0.90) to predict response. Mediterraneibacter gnavus ASVs associated with non-response, whereas Blautia ASVs associated with response, to anti-TNFα. When tested in MLRs, pretreatment with M. gnavus and B. luti led to a reduction in macrophage polarization, with a significantly stronger effect observed for M. gnavus compared with B. luti.

DISCUSSION: Taken together, this study demonstrates that the colonic mucosal microbiome prior to anti-TNFα treatment can distinguish responders from non-responders in CD, supporting its potential as a predictive biomarker.},
}

Humans
*Crohn Disease/drug therapy/microbiology/pathology
Male
Female
Adult
*Gastrointestinal Microbiome/drug effects
*Colon/microbiology/pathology
Biopsy
Middle Aged
*Tumor Necrosis Factor-alpha/antagonists & inhibitors
Treatment Outcome
Adalimumab/therapeutic use
Antibodies, Monoclonal, Humanized/therapeutic use
RNA, Ribosomal, 16S/genetics
Infliximab/therapeutic use
Ustekinumab/therapeutic use
Intestinal Mucosa/microbiology/pathology
Biological Therapy

@article {pmid41859568,
year = {2025},
author = {Adnan, D and Engen, PA and Villanueva, M and Raeisi, S and Ramirez, V and Naqib, A and Green, SJ and Bishehsari, F and Barnes, LL and Keshavarzian, A and Dhana, K and Voigt, RM},
title = {Oral microbiome brain axis and cognitive performance in older adults.},
journal = {NPJ dementia},
volume = {1},
number = {},
pages = {},
pmid = {41859568},
issn = {3005-1940},
support = {R01 AG052583/AG/NIA NIH HHS/United States ; R01 AG056653/AG/NIA NIH HHS/United States ; },
abstract = {The human oral microbiota is a community of microorganisms that reside in the oral cavity, including lingual, buccal, and saliva, each niche with a distinct microbial composition. Alterations in oral microbiota have been associated with an increased risk of Alzheimer's disease (AD). This study used data from 143 older adults in the MIND trial to evaluate the association between oral microbiome and cognitive function. Oral niche-specific differences (saliva, buccal, and lingual), as well as the microbiome composition differences (α and β diversity), were associated with cognitive function. A lower abundance of Gemella and a higher abundance of anaerobic pro-inflammatory bacteria (e.g., Parvimonas, Treponema, Dialister) were linked to a lower Cognitive Z Score. Porphyromonas, previously linked to AD, was not associated with cognition. The outcomes suggest that oral microbiota may be a biomarker for cognitive function. Further research is required to assess whether oral microbiota-directed strategies can positively impact cognitive decline.},
}

@article {pmid41859724,
year = {2025},
author = {Fei, Y and Lei, Z and Wang, Y and Joshua, M and Guo, L and Li, L},
title = {Overview of multi-omics approaches for pulmonary sarcoidosis.},
journal = {EC pulmonology and respiratory medicine},
volume = {14},
number = {1},
pages = {},
pmid = {41859724},
support = {R21 ES036375/ES/NIEHS NIH HHS/United States ; },
abstract = {PURPOSE: Here, we review recent findings in the transcriptome, proteome, metabolomics, and microbiome of pulmonary sarcoidosis and highlight differentially expressed genes, specific pathways, mechanisms, microorganisms, metabolites, and targeted therapeutics in the field.

RECENT FINDINGS: The transcriptome and proteome of pulmonary sarcoidosis have been widely studied in recent years. Many differentially expressed genes and signaling pathways have been identified. Several proteins have been identified as potential molecular markers of pulmonary sarcoidosis. The microorganisms and metabolites of patients with sarcoidosis also have certain specificity. We compared pulmonary sarcoidosis with other diseases, such as idiopathic pulmonary fibrosis, tuberculosis, and chronic beryllium disease, and found some differential diagnoses. Based on the identified pathways and mechanisms, targeted therapeutic strategies have been proposed.

SUMMARY: Many differentially expressed genes have been identified, including CBX8, CCL5, CXCL9, CXCL11, GBP1, GBP5, LINC01278, MMP12, PSMB9, STAT1, and TLE3, as well as the related enriched pathways, such as the IFN-γ, IL-1, IL-17, MHC, T-cell receptor, TNF, Th1, and Th2 signaling pathways. Proteins such as ABCG1, Apo A-I, CXCR5, MMP12, PD-1, PPARγ, and vitamin D-binding protein, together with the Fc galactosylation status of IgG4, are potential molecular markers for pulmonary sarcoidosis. Many specific microorganisms and metabolites in patients with sarcoidosis have also been found. Targeted drugs such as infliximab, nintedanib and rituximab have been proposed according to the discovered pathways and mechanisms.},
}

@article {pmid41859763,
year = {2026},
author = {Qin, YF and Zhang, WR and Wang, L and Wang, YF and Lin, D and Cai, TG and Li, HZ and Huang, QS and Rillig, MC and Zhu, D},
title = {Extracellular vesicles drive stress-induced antibiotic resistance spread in soil.},
journal = {Environmental science and ecotechnology},
volume = {30},
number = {},
pages = {100681},
pmid = {41859763},
issn = {2666-4984},
abstract = {Antimicrobial resistance threatens millions of lives annually, yet its acceleration by non-antibiotic pollutants remains poorly understood. Artificial sweeteners, now ubiquitous in soils and waters, are known individually to promote conjugative transfer of resistance genes, but real environments contain complex mixtures whose collective impact is unknown. Extracellular vesicles (EVs) released by stressed bacteria serve as protected, long-range vectors for antibiotic resistance genes (ARGs), yet whether sweetener diversity modulates this pathway has never been tested. Here we show that increasing artificial-sweetener diversity dramatically enriches ARGs, virulence factors and mobile genetic elements inside soil-derived Evs, driving compositional shifts in 30.5% of EV-associated genera while leaving the bulk microbiome largely undisturbed. EVs originate from a small, fast-growing Pseudomonadota subset that upregulates vesicle-biogenesis genes in response to oxidative and membrane stress; these vesicles selectively package chromosomal resistance traits and transfer phenotypic resistance to recipient Escherichia coli. This stress-induced decoupling reveals EVs as rapid, hidden mediators of resistome mobilization that community-level surveys miss. By demonstrating that pollutant diversity itself drives resistance dissemination through nanoscale vectors, our findings establish EVs as a critical new indicator within the One Health framework and call for revised environmental risk models that account for chemical complexity rather than single-compound exposures.},
}

@article {pmid41859944,
year = {2026},
author = {Jiang, M and Gomez, A and Seelig, DM and Gallaher, DD},
title = {Prune (dried plum) consumption does not reduce colonic tumor formation but drives beneficial changes in the gut microbiome of rats.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo03398e},
pmid = {41859944},
issn = {2042-650X},
abstract = {Previous research has highlighted the potential benefits of prune consumption, including a changed gut microbiome composition and a reduction in colon cancer risk factors. This study investigated whether prune consumption reduced colon tumor development and led to positive changes in the large intestinal microbiome in a chemically induced colon cancer model in rats. Male Wistar rats were fed one of three diets: 5% (by energy) prune, 10% prune, or a prune-free control. Rats were fed the diets for 32 weeks. Rats received weekly injections of 1,2-dimethylhydrazine for 15 weeks to induce colon tumorigenesis. Colonic tumor number or size did not differ among the diet groups. However, there was a trend toward fewer small intestinal tumors in the 10% prune diet group (p < 0.1). Groups fed prune had heavier cecum tissue, indicating greater large intestinal fermentation. The prune diets increased taxonomic richness and altered bacterial species composition. Specifically, prune consumption was associated with increased abundance of Methanosphaera genus and taxa from the Lachnospiraceae family, such as Blautia and Coprococcus. Prune diets also increased total cecal SCFA amount, notably butyrate. However, 24 hour fecal excretion of p-cresol, indole, and total bile acids did not differ significantly among the groups. While prune consumption did not show a significant reduction in colonic tumor formation, potential benefits were noted in a trend towards reducing small intestine tumors, increasing large intestinal fermentation and SCFA production, and increasing microbial richness, suggesting prune consumption may provide other health benefits.},
}

@article {pmid41859980,
year = {2026},
author = {Akebota, N and Ma, RF and Yang, HQ and Li, YD and He, K and Liu, HY and Tang, KY and Zhu, Y},
title = {Behavioral smearing and physiological secretions drive divergent microbiome assembly during breeding in the crested ibis.},
journal = {Zoological research},
volume = {47},
number = {2},
pages = {361-373},
doi = {10.24272/j.issn.2095-8137.2025.407},
pmid = {41859980},
issn = {2095-8137},
mesh = {Animals ; *Microbiota/physiology ; *Birds/physiology/microbiology ; RNA, Ribosomal, 16S/genetics ; Feathers/microbiology ; Seasons ; Reproduction/physiology ; Bacteria/classification/genetics ; },
abstract = {Host-microbiota interactions represent a key axis in animal adaptation, especially in species displaying pronounced seasonal variation in behavior and physiology. In avian species, behavioral processes associated with reproduction may influence symbiotic microbial communities, yet the underlying mechanisms remain poorly resolved. The endangered crested ibis (Nipponia nippon) exhibits a distinctive seasonal transition in plumage coloration, shifting from white in the non-breeding period to gray during breeding, a change linked to smearing behavior and deposition of black secretions from the neck region. In the present study, 16S rRNA sequencing across three body sites was performed to profile body surface microbiomes during breeding (gray-feather) and non-breeding (white-feather) stages. Breeding individuals exhibited lower microbial diversity, consistent with an influence of black neck secretions on microbiome structure. Microbial communities were differentiated more strongly by season than by body site, and microbial similarity among body sites increased during breeding, supporting redistribution of microbes through smearing behavior. Community assembly also showed clear season- and site-specific variation. Neck feathers exhibited a 36.5% better fit to the neutral model, indicating a stronger contribution of stochastic assembly, likely associated with microbial dispersal during smearing of black secretions. In contrast, neck skin showed a 36.3% lower neutrality and 11.87% more host-selected variants, indicating stronger deterministic selection associated with breeding-related secretions. These findings support a dual regulatory framework during breeding, in which behavioral smearing promotes microbial dispersal while physiological secretion strengthens host filtering. Such coordinated regulation likely drives seasonal microbiome variation and contributes to seasonal adaptation. Overall, this work provides novel insight into the integration of behavior and physiology in shaping host-microbiota interactions during critical life stages and establishes a microbiome-based perspective for crested ibis conservation.},
}

Animals
*Microbiota/physiology
*Birds/physiology/microbiology
RNA, Ribosomal, 16S/genetics
Feathers/microbiology
Seasons
Reproduction/physiology
Bacteria/classification/genetics

@article {pmid41859990,
year = {2026},
author = {Szczepanik, K and Kierończyk, B and Szymkowiak, P and Taciak, M and Barszcz, M and Tuśnio, A and Gawin, K and Dobrowolski, P and Świątkiewicz, M},
title = {Effects of Hermetia illucens larvae full-fat meal and astaxanthin on the microbiome and histomorphology of the large intestine in piglets.},
journal = {Polish journal of veterinary sciences},
volume = {29},
number = {1},
pages = {17-29},
doi = {10.24425/pjvs.2026.158497},
pmid = {41859990},
issn = {2300-2557},
mesh = {Animals ; Swine/microbiology/anatomy & histology ; *Animal Feed/analysis ; Larva ; *Gastrointestinal Microbiome/drug effects ; Diet/veterinary ; Xanthophylls/pharmacology/administration & dosage ; *Intestine, Large/anatomy & histology/microbiology/drug effects ; Animal Nutritional Physiological Phenomena ; *Diptera ; },
abstract = {This study evaluated the effects of Hermetia illucens (HI) larvae full-fat meal and astaxanthin (AST) on large intestine histomorphometry, microbiota activity, and composition in pigs. Forty-eight pigs (8.7 kg) were divided into six groups: control (0HI), 2.5% HI (2.5HI), 5% HI (5HI), 2.5% HI + AST (2.5HI+AST), 5% HI + AST (5HI+AST), and AST alone (AST). The experiment lasted from 35 to 70 days of age. HI meal increased mucosal thickness (p<0.01), crypt depth (p<0.05), and width (p<0.05). Goblet cell counts increased in the 2.5HI (p<0.05), while enterocyte numbers decrease in the AST group (p<0.01). Dietary HI meal reduced concentrations of total short-chain fatty acids (SCFA), including butyrate (p<0.05), whereas AST increased acetic acid levels in multiple intestinal regions (p<0.05). Both additives modified microbial populations: AST increased total bacterial counts (p<0.001), while 2.5% HI meal reduced the abundance of the Bacteroides-Prevotella cluster (p<0.001). Significant interactions were detected for Lactobacillus/Enterococcus spp. and Enterobacteriaceae (p<0.001). HI meal decreased p-cresol concentrations in the middle colon (p<0.05), whereas AST reduced phenol in the distal colon (p<0.05) and indole in the middle colon (p<0.05). AST increased ammonia levels in the proximal colon (p=0.001). These findings suggest that HI meal and AST modulate intestinal fermentation, exhibit anti-inflammatory effects, and regulate microbial populations, potentially reducing harmful metabolites and odor emissions. Their dietary combination may have positive implications for intestinal health.},
}

Animals
Swine/microbiology/anatomy & histology
*Animal Feed/analysis
Larva
*Gastrointestinal Microbiome/drug effects
Diet/veterinary
Xanthophylls/pharmacology/administration & dosage
*Intestine, Large/anatomy & histology/microbiology/drug effects
Animal Nutritional Physiological Phenomena
*Diptera

@article {pmid41860010,
year = {2026},
author = {Medenica, S and Prelević, V and Zanković, N and Maggio, V and Rizzo, M},
title = {Cardiorenometabolic medicine as a new subspecialty in the light of novel pharmaceuticals with dual or triple benefits.},
journal = {Expert opinion on drug safety},
volume = {},
number = {},
pages = {},
doi = {10.1080/14740338.2026.2648248},
pmid = {41860010},
issn = {1744-764X},
abstract = {INTRODUCTION: There is a lack of clinical models which include comprehensive and holistic care of patients with cardiorenometabolic diseases and isolated care of those patients usually leads to poor clinical outcomes. Cardiometabolic diseases, encompassing conditions like type 2 diabetes, obesity, and atherosclerotic cardiovascular disease, represent a major global health burden. Their frequent coexistence due to shared mechanisms necessitates an integrated care approach, reflecting a critical paradigm shift. Therefore, necessity for a new integrated clinical model which include all those specialties should be the focus of a new, modern interdisciplinary approach.

AREAS COVERED: This review synthesizes mechanistic insights, safety data, and emerging interventions for cardiorenometabolic disease management. It examines cornerstone therapies like SGLT2 inhibitors and GLP-1 receptor agonists, highlighting their profound cardiovascular, renal, and metabolic benefits. Newer dual/triple incretin therapies are also discussed for their potential in weight loss and cardioprotection. Safety considerations, including genitourinary infections and gastrointestinal intolerance, are addressed. Additionally, emerging research on gut microbiota - derived metabolites and sleep optimization as modifiable risk pathways is explored. The literature search included papers published as of July 2025, identified using PubMed.

EXPERT OPINION: We advocate a holistic, risk-adapted approach integrating pharmacologic, behavioral, and metabolic dimensions to optimize patient outcomes and truly transform cardiometabolic care.},
}

@article {pmid41860216,
year = {2026},
author = {Chatman, CC and Olson, EG and Ricke, SC and Majumder, EL-W},
title = {Exposure to known and emerging groundwater contaminants significantly alters poultry microbiome and metabolome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0246925},
doi = {10.1128/aem.02469-25},
pmid = {41860216},
issn = {1098-5336},
abstract = {UNLABELLED: The exposome encompasses all lifetime environmental exposures affecting health. Its complexity and high data dimensionality make it challenging to link specific exposure combinations to adverse health outcomes. Establishing relevant exposome criteria is key to addressing current knowledge gaps. This study evaluated contaminant levels in Wisconsin groundwater and their effects on host health. We focused on three co-occurring chemicals that were detected at concentrations exceeding groundwater standards: nitrate, atrazine, and imidacloprid, and the emerging contaminant, microplastics. In this study, broilers were exposed to a low-dose chemical mixture (35,000 ppb nitrate + 1.7 ppb atrazine + 0.58 ppb imidacloprid) and high-dose chemical mixture (100,000 ppb nitrate + 3,000 ppb atrazine + 3,000 ppb imidacloprid) or polyethylene microplastics (PE MPs) for 49 days. Both contaminant types significantly altered the cecal microbiomes as determined by the enrichment of the genera Fournierella and Ruminococcus and an unclassified Coriobacteriaceae genus. Untargeted metabolomics revealed distinct but convergent patterns of metabolic reprogramming across exposures. Chemical mixtures modulated pathways linked to xenobiotic metabolism, pyruvate and thiamine metabolism, and other cofactor-dependent processes, consistent with a shift from oxidative, biosynthetically intensive metabolism toward glycolysis, fermentation, and detoxification. In contrast, PE fibers selectively suppressed oxidative and cofactor/vitamin pathways while perturbing bile acid, sphingolipid, and aromatic compound metabolism, indicating a simplified, maintenance-oriented energy state. Despite these pronounced metabolomic shifts, histopathology revealed no overt intestinal or systemic lesions in any treatment group, highlighting altered microbial activity despite the absence of gross pathological lesions and supporting a silent dysbiosis phenotype.

IMPORTANCE: Environmental contaminants in groundwater are increasingly common, yet their combined effects on animal health remain poorly understood. The current study shows that even low-level exposure to agricultural chemical mixtures and microplastics can alter the gut microbial metabolism in broiler chickens without intestinal damage. These subclinical shifts, characterized by altered energy pathways, cofactor scarcity, and microbial restructuring, highlight a form of silent dysbiosis. Our findings emphasize the need to integrate microbiome- metabolic endpoints into environmental risk assessments to predict earlier, more meaningful, functionally relevant impacts.},
}

@article {pmid41860224,
year = {2026},
author = {Bintarti, AF and Sulesky-Grieb, A and Colovas, J and Marolleau, B and Boureau, T and Simonin, M and Barret, M and Shade, A},
title = {Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0301925},
doi = {10.1128/spectrum.03019-25},
pmid = {41860224},
issn = {2165-0497},
abstract = {Drought is a critical risk for staple crops like common bean (Phaseolus vulgaris L.). We conducted an experiment to understand the legacy effects of repeated drought exposure across plant generations on the root and rhizosphere microbiome of the common bean, hypothesizing that a legacy of exposure improves overall plant microbiome resilience. We profiled the bacterial microbiome using marker gene amplicon sequencing over two plant generations in a complete factorial design for two common bean genotypes, Red Hawk and Flavert. We performed parallel experiments for Red Hawk in two different countries using soils of Pays de la Loire, France, and Michigan, USA. Despite the clear and relatively consistent drought effects on the plant phenotypes, there was neither a strong response of the Red Hawk microbiomes to drought nor a notable legacy of drought exposure. For Flavert, there was a minor legacy drought effect for the second generation in the rhizosphere microbiome beta diversity, while its root had no legacy effect observed. This study demonstrates that below-ground plant microbiomes can be resistant to drought stress and that cross-generational legacy depends on soil origin and host genotype. Such parallel experiments across countries are useful to inform generalities and build theory toward prediction on microbiome responses to global change.IMPORTANCEDrought remains an important challenge in crop agriculture because of climate change, and plant microbiome management has potential to support plant resilience to drought. Here, we investigated the impact of drought and drought legacy across two generations on the root and rhizosphere microbiomes of the drought-susceptible legume common bean, a key staple food crop with production widely distributed across the Americas, Africa, Europe, and Asia, and which is of critical importance for food security in many of its production regions. Despite host plant decline with drought, the effects of drought on the microbiomes were either not observed, inconsistent, or weak, suggesting overall microbiome resistance and limited drought legacy. This work provides insights into how the stability of the below-ground plant microbiome can be driven by stress resistance, offering a different perspective on how the microbiome could be managed to support crops facing drought.},
}

@article {pmid41860424,
year = {2026},
author = {Guo, Y and Liu, W and Qiu, K and Si, H and Zhang, Y and Huang, Y and Yang, Y and Xie, Y},
title = {Linking Bacterial Diversity to Rhizosphere Ecological Stoichiometry and Nutrient Availability in a Clonal Desert Plant.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag076},
pmid = {41860424},
issn = {1365-2672},
abstract = {AIMS: This study aimed to examine the relationships between rhizosphere (RS) microorganisms of the desert pioneer plant Psammochloa villosa and soil nutrient availability, with the goal of clarifying microbial mechanisms supporting its persistence in desertified regions and identifying potential targets for microbiome-based management.

METHODS AND RESULTS: Using absolute quantification of 16S rRNA gene and ITS sequencing, microbial communities in the RS of P. villosa were compared with those in bulk soil (BS). The results showed that the rhizosphere of P. villosa had significantly lower total phosphorus (TP) but higher carbon-to-phosphorus (C/P) and nitrogen-to-phosphorus (N/P) ratios than BS, while the available nitrogen-to-available phosphorus ratio (AN/AP) was 4-5 times higher than N/P. This pattern suggests that the RS experiences stronger phosphorus limitation than BS. A lower fungi-to-bacteria (F/B) ratio in the RS relative to BS was positively associated with TP and negatively associated with soil C/P and N/P ratios, indicating a bacterial-dominated community under phosphorus-limited conditions. Structural equation modeling further indicated that rhizobacterial diversity strongly promoted the acquisition of available nutrients by significantly affecting soil organic carbon (SOC), TP, and stoichiometric balance.

CONCLUSIONS: These results indicate that bacterial diversity is tightly linked to the regulation of ecological stoichiometry and nutrient availability under P-limited conditions in the rhizosphere of P. villosa.},
}

@article {pmid41860558,
year = {2026},
author = {Bloom, P and Khanna, S},
title = {Fecal microbiota transplantation in chronic liver disease: Current and future state of the art.},
journal = {Hepatology communications},
volume = {10},
number = {4},
pages = {},
pmid = {41860558},
issn = {2471-254X},
mesh = {*Fecal Microbiota Transplantation/methods/trends/adverse effects ; Humans ; Gastrointestinal Microbiome ; *Liver Diseases/therapy ; Chronic Disease ; },
abstract = {Chronic liver diseases are associated with changes in gut microbiome composition and function. Early data suggest that fecal microbiota transplantation (FMT) may treat several chronic liver diseases, especially cirrhosis, hepatic encephalopathy, and alcohol-associated liver disease. Well-powered and multisite studies are needed to better understand which indications and subpopulations hold promise for FMT. At present, there is variability in the screening, processing, and administration of FMT. Some of this variability is inherent to the nature of FMT, but some of the variability could be standardized to optimize safety and efficacy. Ultimately, we may find that narrowed and donor-independent microbiome therapeutics are superior tools to provide a consistently effective result in chronic liver disease. Regulation of FMT for chronic liver disease indications in the United States will continue to require the rigid regulatory framework of other drugs, requiring an Investigational New Drug (IND) application.},
}

*Fecal Microbiota Transplantation/methods/trends/adverse effects
Humans
Gastrointestinal Microbiome
*Liver Diseases/therapy
Chronic Disease

@article {pmid41860619,
year = {2026},
author = {Fu, X and Chen, Y and Wang, Y and Chen, B and Chen, M and Lyu, J and Sun, H and Wang, Z and Xu, J and Li, GL and Ren, D},
title = {Microbiota in Chronic Suppurative Otitis media: association with Postoperative Tympanic membrane outcomes.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {41860619},
issn = {1432-0614},
mesh = {Humans ; *Otitis Media, Suppurative/microbiology/surgery ; *Microbiota ; Female ; Male ; Chronic Disease ; Middle Aged ; Adult ; *Tympanic Membrane/microbiology/surgery ; Pseudomonas aeruginosa/isolation & purification/genetics ; Biomarkers ; Bacteria/classification/genetics/isolation & purification ; Aged ; Tympanic Membrane Perforation/microbiology ; Anti-Bacterial Agents/therapeutic use ; },
abstract = {Chronic suppurative otitis media (CSOM) is a prevalent condition with global health implications due to its impact on hearing and quality of life. Conventional treatments often fail because of bacterial biofilms and antimicrobial resistance. Effective treatment of CSOM depends on the precise determination of the middle ear microbiota; however, current microbial detection methods do not meet this need. Postoperative reperforation may compromise surgical outcomes. If the risk of perforation can be predicted immediately after surgery, sensitive antibiotics could be administered proactively for early intervention to optimize treatment efficacy. This study introduces 2b-RAD sequencing for the microbiome (2b-RAD-M), a novel technology designed to provide a comprehensive profile of the CSOM microbiota and identify diagnostic biomarkers that predict postoperative outcomes. We analyzed ear swabs from patients with postoperative perforation (PO), nonperforation (NPO), and otosclerosis (CON) using microbial diversity, relative abundance, and composition analyses. Bacillus_A_bombysepticus and Pseudomonas aeruginosa were identified as potential biomarkers, with Bacillus_A_bombysepticus demonstrating superior diagnostic accuracy (area under curve (AUC) = 0.92) compared to P. aeruginosa (AUC = 0.25). Functional predictions revealed that biological activities related to gene regulation, substance metabolism, and DNA repair were more prominent in the PO group. This study offers new insights into CSOM pathogenesis and progression, proposing Bacillus_A_bombysepticus as a novel biomarker for predicting postoperative outcomes that can indicate an increased risk of tympanic membrane reperforation for the first time. KEY POINTS: 2b-RAD-M technology enables comprehensive CSOM microbiota profiling and biomarker identification. Bacillus_A_bombysepticus (AUC = 0.92) outperforms Pseudomonas aeruginosa in diagnostic accuracy. Bacillus_A_bombysepticus predicts postoperative tympanic membrane reperforation via functional activity analysis.},
}

Humans
*Otitis Media, Suppurative/microbiology/surgery
*Microbiota
Female
Male
Chronic Disease
Middle Aged
Adult
*Tympanic Membrane/microbiology/surgery
Pseudomonas aeruginosa/isolation & purification/genetics
Biomarkers
Bacteria/classification/genetics/isolation & purification
Aged
Tympanic Membrane Perforation/microbiology
Anti-Bacterial Agents/therapeutic use