@article {pmid42761814,
year = {2026},
author = {Meng, X and Li, L and Hao, R and Lin, Z and Liu, K and Chi, G and Ren, J and Liu, R and Gao, Y and Yu, X and Tong, X},
title = {Shared oral microbiome signatures linking periodontitis and autoimmune thyroiditis: NHANES 2009-2012.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2728750},
pmid = {42761814},
issn = {2000-2297},
abstract = {OBJECTIVE: To examine the association between periodontitis severity and autoimmune thyroiditis (AIT) in a nationally representative US sample and to explore oral microbiome features shared between the two conditions.

METHODS: We analyzed adults from NHANES 2009-2012 with complete periodontal examinations, thyroid autoantibodies, and oral microbiome data (n = 1,346). Periodontitis was classified using CDC/AAP case definitions. AIT was defined as positivity for thyroid peroxidase antibodies (TPOAb ≥ 9 IU/mL) and/or thyroglobulin antibodies (TgAb ≥ 4 IU/mL). Survey-weighted multivariable logistic regression estimated adjusted odds ratios (aORs) and 95% confidence intervals (CIs). Oral microbiome diversity and differentially abundant genera were compared between groups.

RESULTS: In the fully adjusted model, mild and severe periodontitis were associated with higher odds of AIT compared with periodontally healthy individuals (mild: aOR 2.15, 95% CI 1.20-3.84; severe: aOR 2.77, 95% CI 1.22-6.28), whereas moderate periodontitis was not significantly associated (aOR 1.47, 95% CI 0.63-3.43). Genera enriched in both AIT and periodontitis included Fusobacterium, Bergeyella, Johnsonella, and Prevotella_2. Fusobacterium abundance increased across periodontal severity categories and showed a weak inverse correlation with TPOAb, whereas TT3 and FT3 showed weak positive correlations with Fusobacterium.

CONCLUSION: Periodontitis severity was associated with AIT in this cross-sectional NHANES analysis, and Fusobacterium emerged as a shared genus associated with both periodontal status and thyroid autoimmunity. Longitudinal and interventional studies are warranted to assess causality.},
}

@article {pmid42761980,
year = {2026},
author = {Assaf, S and Lio, P},
title = {The Active Shelf: A Clinician's Guide to Active Dermatologic Care for Atopic Dermatitis.},
journal = {The Journal of clinical and aesthetic dermatology},
volume = {19},
number = {7},
pages = {33-37},
pmid = {42761980},
issn = {1941-2789},
abstract = {Key therapeutic options for dermatologic care frequently extend beyond prescription medications to include evidence-based, over-the-counter (OTC) topicals that meaningfully influence disease pathophysiology. We introduce the concept of active dermatologic care (ADC), which encompasses nonprescription topical products with biologically active compounds that support and modulate key skin disease processes and can be routinely incorporated into comprehensive dermatologic care plans. We expand upon the recent concept of categorizing OTC active ingredients for acne based on their mechanisms of action and apply it to atopic dermatitis. The pathophysiologic pillars of itch, barrier dysfunction, acid mantle disruption, dysbiosis, and inflammation are each considered as potential therapeutic targets for ADC.},
}

@article {pmid42762145,
year = {2026},
author = {Yi, TW and Kumar, P and Karwasra, R and Sharma, N and Behare, MH and Linkang, X and Abdelkarim Maki, MA and Khanna, K},
title = {Biopolymeric Approaches for Colon Cancer Treatment: A Comprehensive Review of Polysaccharide-based Delivery Systems.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {235},
pages = {},
doi = {10.3791/70872},
pmid = {42762145},
issn = {1940-087X},
mesh = {Humans ; *Polysaccharides/chemistry/administration & dosage ; *Colonic Neoplasms/drug therapy ; *Drug Delivery Systems/methods ; Animals ; *Antineoplastic Agents/administration & dosage/chemistry ; Drug Carriers/chemistry ; },
abstract = {Globally, colon cancer remains one of the leading causes of mortality. Multidrug resistance, systemic toxicity, and poor tumor selectivity significantly limit conventional chemotherapy. This review highlights the need for localized therapy to increase efficacy and minimize systemic side effects. Colon-targeted drug delivery systems (CDDS) are designed and developed to overcome these challenges. Both natural and synthetic polysaccharides act as carriers in CDDS because of their biodegradability, biocompatibility, pH- and enzyme-responsiveness, and mucoadhesive properties. Polysaccharides such as chitosan, dextran, pectin, alginate, and hyaluronic acid have been formulated into nanoparticles, microparticles, and hydrogels, enabling controlled and site-specific delivery. These carriers deliver chemotherapeutics, nucleic acids, and immunotherapeutics, as well as theranostic agents that combine imaging and therapy. Preclinical evidence demonstrates significant translational potential for polysaccharide-based CDDS. However, clinical trials remain limited, which highlights the gap between laboratory findings and clinical applications. Major challenges in colon-targeted drug delivery include variability in polysaccharide sources and quality, difficulties in large-scale manufacturing, and regulatory challenges. Addressing these challenges will be essential to move towards commercialization and clinical adoption. Personalized therapy through microbiome profiling, integration with nanotechnology and bioinformatics, and smart, biosensor-responsive carriers will be the focus going forward. Polysaccharide-based CDDS provide safer, more effective, and more personalized treatment with continued research to optimize delivery and overcome existing limitations.},
}

Humans
*Polysaccharides/chemistry/administration & dosage
*Colonic Neoplasms/drug therapy
*Drug Delivery Systems/methods
Animals
*Antineoplastic Agents/administration & dosage/chemistry
Drug Carriers/chemistry

@article {pmid42762163,
year = {2026},
author = {Silva-Magaña, MA and Mora-Flores, LP and Pita-Galeana, MA and Hernández-Lemus, E and de Anda-Jáuregui, G},
title = {A network dynamical simulation model for the study of antibiotic resistance in microbial communities.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2734703},
doi = {10.1080/19490976.2026.2734703},
pmid = {42762163},
issn = {1949-0984},
mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota/drug effects ; *Bacteria/drug effects/genetics ; Computer Simulation ; Models, Biological ; *Drug Resistance, Bacterial ; *Drug Resistance, Microbial ; },
abstract = {Antibiotic resistance emerges from ecological and evolutionary processes occurring within complex microbial communities. Interactions among microorganisms can shape the pathways through which resistance traits spread and persist, yet many theoretical approaches treat microbial populations as homogeneous compartments. Here we present a simulation-based network dynamical model that represents microbial communities as ecological association networks. In this formulation, nodes correspond to bacterial populations, metapopulations, or taxon-level ecological units, while resistant counterparts represent state-expanded subpopulations associated with the same ecological unit. Edges represent co-occurrence-based ecological proximity rather than direct physical contacts or confirmed horizontal gene transfer events. Using stochastic simulations across multiple network topologies, we explore how structural properties of microbial communities influence the emergence and persistence of resistance. Parameter sweeps across transmission probability, initial resistance fraction, and antibiotic intervention timing allow us to characterize regimes in which resistance either remains localized or spreads through the community. The model produces time series of resistant and susceptible states and snapshots of evolving network configurations, enabling qualitative comparison across simulation scenarios. Our results show that network structure strongly modulates resistance dynamics. Highly clustered networks tend to trap resistance within local neighborhoods, whereas heterogeneous networks with hub nodes facilitate rapid dissemination. Antibiotic perturbations can either suppress resistance or paradoxically accelerate its expansion depending on network topology and intervention timing. These findings should be interpreted as qualitative results from a minimal proof-of-concept model, not as a direct reconstruction of plasmid transfer, species replacement, or patient-specific microbiome responses.},
}

*Anti-Bacterial Agents/pharmacology
*Microbiota/drug effects
*Bacteria/drug effects/genetics
Computer Simulation
Models, Biological
*Drug Resistance, Bacterial
*Drug Resistance, Microbial

@article {pmid42762368,
year = {2026},
author = {Cirak, S and Grieshaber, V and Müller, P and Chao, CM},
title = {The lung microbiome in childhood-onset severe neuromuscular disease with respiratory insufficiency: rationale, current evidence, and opportunities for oxford nanopore long-read sequencing.},
journal = {Molecular and cellular pediatrics},
volume = {13},
number = {1},
pages = {},
pmid = {42762368},
issn = {2194-7791},
abstract = {In severe childhood-onset neuromuscular disease (NMD), ventilatory muscle weakness and ineffective airway clearance drive recurrent infections and chronic colonization that is often culture-negative, polymicrobial, or both. The lung microbiome framework offers a unifying model: altered microbial immigration, elimination, and growth can produce dysbiosis with pathobiont expansion and antimicrobial resistance (AMR). We propose that pediatric NMD may follow a distinct developmental trajectory in which early-life secretion stasis, viral insults, and frequent antibiotics perturb immune-microbiome crosstalk during lung growth, potentially "imprinting" long-term community structure. However, NMD-specific airway microbiome data remain sparse because most studies rely on culture or upper-airway sampling. Oxford Nanopore Technologies (ONT) long-read sequencing enables real-time metagenomics with AMR gene detection and can deliver same-day profiles (as short as ~ 6 h from sample to result in optimized workflows), but requires robust low-biomass controls and, in some settings, polishing or hybrid strategies to mitigate higher per-read error. A major limitation of metagenomic sequencing of respiratory samples is the high proportion of host DNA, bacterial reads may account for only about 1-5% of the total sequencing reads. We review microbiome principles relevant to pediatric NMD, summarize current evidence, and outline ONT-enabled study designs and translational priorities.},
}

@article {pmid42762400,
year = {2026},
author = {Cunha, B and Alter, A and Berschback, M and Park, S and Gold, S and Schneider, Y},
title = {Rethinking Restrictive Diets in IBD: Toward an Inclusion-Focused Nutritional Paradigm.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42762400},
issn = {1534-312X},
mesh = {Humans ; *Inflammatory Bowel Diseases/diet therapy ; Elimination Diets ; Diet, Mediterranean ; Diet, Carbohydrate-Restricted ; Diet, Gluten-Free ; FODMAP Diet ; },
abstract = {PURPOSE OF REVIEW: Patient-initiated elimination diets are widely adopted by those with inflammatory bowel disease (IBD), yet the evidence supporting their long-term use remains limited and their risks are increasingly recognized. Some common elimination diets utilized by patients include the specific carbohydrate diet (SCD), low-FODMAP diet, and gluten-free and dairy-free diets. This narrative review critically examines the role of self-initiated restrictive dietary strategies in IBD management, evaluating the evidence for and against common elimination-based approaches, and contrasts these with emerging data supporting more inclusive dietary patterns.

RECENT FINDINGS: Sustained elimination diets carry meaningful risks: malnutrition, micronutrient deficiency, sarcopenia, gut microbial dysbiosis, food anxiety, and avoidant/restrictive food intake disorder (ARFID). Current evidence demonstrates that the Mediterranean diet performs comparably to more restrictive approaches in inducing symptomatic remission, and generally is not associated with adverse nutritional and psychosocial consequences. Contemporary recommendations from several gastrointestinal societies discourage long-term elimination diets and favor inclusive, nutritionally adequate patterns, particularly the Mediterranean diet, as a preferred dietary framework for most patients with IBD, though supporting evidence remains largely observational and randomized controlled trial data are limited. We propose a paradigm shift from dietary exclusion toward inclusion, diversity, and nutritional adequacy, with registered dietitians as essential partners in IBD care. When elimination is clinically indicated, it should be time-limited, goal-directed, and followed by structured food reintroduction. Moving beyond restriction represents not a retreat from dietary focus, but its maturation, aligning nutritional guidance with the principles of patient-centered, evidence-based disease management.},
}

Humans
*Inflammatory Bowel Diseases/diet therapy
Elimination Diets
Diet, Mediterranean
Diet, Carbohydrate-Restricted
Diet, Gluten-Free
FODMAP Diet

@article {pmid42762419,
year = {2026},
author = {Negi, R and Sharma, B and Darshani, P and Thakur, SS and Ratnasari, A and Barwant, MM and Tomar, P and Yadav, N and Yadav, AN},
title = {Revitalization of plant growth-promoting plant allied microbes: an eco-friendly approach for agricultural and environmental sustainability.},
journal = {Biologia futura},
volume = {},
number = {},
pages = {},
pmid = {42762419},
issn = {2676-8607},
abstract = {Plants are increasingly recognized as metaorganisms because they harbor diverse and dynamic microbial communities that establish intricate symbiotic associations and collectively regulate plant growth, development, and adaptation to changing environmental conditions. Plant-associated microorganisms colonize distinct ecological niches, including the rhizosphere, phyllosphere, endosphere, and surrounding soil, where they contribute to nutrient acquisition, phytohormone production, disease suppression, and tolerance to biotic and abiotic stresses. These multifunctional interactions have positioned plant growth-promoting (PGP) plant-allied microbes as promising alternatives to chemical fertilizers and pesticides for sustainable agriculture. However, despite significant advances in plant microbiome research, information on the diversity, functional mechanisms, agricultural applications, emerging technologies, and translational challenges of PGP microbes remains dispersed across the literature, limiting a comprehensive understanding of their potential for sustainable crop production. To address this gap, this review synthesizes recent advances in the ecology, functional mechanisms, and agricultural significance of plant growth-promoting plant-allied microbes, with particular emphasis on their roles in improving nutrient availability, enhancing crop productivity, suppressing phytopathogens, and increasing plant resilience to environmental stresses. The review further discusses recent developments in microbial consortia, microbiome engineering, omics-based technologies, and advanced bioformulation strategies, while critically evaluating challenges associated with commercialization, formulation stability, environmental variability, regulatory frameworks, and farmer adoption. Finally, future research priorities and technological innovations required for the successful integration of microbial-based solutions into climate-resilient agricultural systems are highlighted. This review provides a comprehensive and up-to-date perspective that supports the development and sustainable implementation of plant-allied microbial technologies for environmentally responsible agriculture and long-term food security.},
}

@article {pmid42762752,
year = {2026},
author = {Gomes, BPFA and Francisco, PA and Lima, AR and Godoi-Jr, EP and Fagundes, PIG and Passini, MRZ and Bronzato, JD and Lopes, EM and Chen, T and Paster, BJ},
title = {Unraveling microbial heterogeneity in post-treatment endodontic infections via 16S rRNA gene profiling.},
journal = {Archives of oral biology},
volume = {192},
number = {},
pages = {106767},
doi = {10.1016/j.archoralbio.2026.106767},
pmid = {42762752},
issn = {1879-1506},
abstract = {OBJECTIVES: This study aimed to characterize the intraradicular bacteriome of post-treatment endodontic infections using high-throughput 16S rRNA gene sequencing and to assess inter-individual microbial heterogeneity through a disaggregated ecological analysis.

DESIGN: Endodontic samples were collected from single root canals of 10 female patients requiring retreatment. The V3-V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Amplicon sequence variants were generated using DADA2-based processing. Microbial communities were characterized using relative-abundance profiles, Bray-Curtis, Hellinger, and CLR-transformed Aitchison distances, together with Local Contribution to Beta Diversity (LCBD), Species Contribution to Beta Diversity (SCBD), and Baselga's abundance-based beta-diversity partitioning.

RESULTS: Proteobacteria and Firmicutes predominated, although their relative contributions varied substantially among individuals, with greater heterogeneity at genus and species levels. Desulfobulbus predominated in R3, R10, R17, and R19, Enterococcus in R5 and R11, Haemophilus in R15 and R22, and Streptococcus in R21, whereas R20 showed a more distributed polymicrobial profile. Streptococcus oralis subsp. dentisani clade 398 showed the highest mean relative abundance, while Parvimonas micra had the highest prevalence despite relatively low abundance. R21, R22, and R20 showed the greatest beta-diversity contributions. Community differences were driven predominantly by balanced changes in taxon abundance rather than abundance gradients. The species-level core was limited and threshold-dependent.

CONCLUSION: Post-treatment endodontic infections exhibited highly individualized microbial profiles and substantial inter-individual variation, with a limited species-level core. These findings highlight the ecological complexity of microbial communities present after endodontic treatment and support comprehensive infection control during retreatment.},
}

@article {pmid42762890,
year = {2026},
author = {Ibrahim, F},
title = {Rapidly Fermentable Prebiotic Substrates: Benefits, FODMAP Effects and Host Tolerance.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {105130},
doi = {10.1016/j.clnesp.2026.105130},
pmid = {42762890},
issn = {2405-4577},
abstract = {Rapidly fermentable prebiotic substrates occupy a contradictory position in human nutrition. In microbiome and functional-food research, low molecular weight non-digestible carbohydrates such as inulin, fructo-oligosaccharides, galacto-oligosaccharides are added to foods and supplements to promote bifidogenic, metabolic and gastrointestinal benefits. In parallel, clinical nutrition often restricts the same substrates as FODMAPs to reduce symptoms in irritable bowel syndrome and related disorders of gut-brain interaction, while food-science research seeks to reduce raffinose-family oligosaccharides because of their flatulence-producing and antinutritional effects. This review examines these contradictory framings and asks whether the same rapidly fermentable substrates should be understood as beneficial prebiotics, symptom-provoking FODMAPs, or tolerance-limiting food components. It argues that the physiological effects of these substrates are not fixed properties of the compounds alone but also arise from interactions between intrinsic fermentability and host context. Rapidly fermentable substrates may support beneficial microbial and metabolic responses in tolerant individuals, but may contribute to gas production, osmotic effects, luminal distension, symptom generation or even immune activation in susceptible contexts. Future research should move beyond defining prebiotic efficacy primarily by enrichment of selected bacterial taxa. Instead, each substrate should be tested through dose-response studies that establish both beneficial and tolerance thresholds across healthy individuals and clinically relevant phenotypes. Future studies should also examine prebiotics within a host-ecology framework, testing whether benefit depends less on maximising microbial stimulation and more on maintaining a controlled, spatially contained and clinically tolerable microbiome.},
}

@article {pmid42762960,
year = {2026},
author = {Fukuda, T and Takagaki, M and Nakamura, H and Ozaki, T and Kadono, Y and Kawabata, S and Terada, E and Nakagawa, R and Matsumura, T and Teranishi, K and Yamazaki, H and Kishima, H},
title = {Role of gut microbiome modulation in the attenuation of aging-related neuroinflammation in early brain injury after subarachnoid hemorrhage.},
journal = {Brain research},
volume = {},
number = {},
pages = {150559},
doi = {10.1016/j.brainres.2026.150559},
pmid = {42762960},
issn = {1872-6240},
abstract = {Early brain injury (EBI) critically determines post-subarachnoid hemorrhage (SAH) outcome, with worse prognosis in older patients. Aging confers exaggerated inflammation, possibly via gut microbiome (GM) alterations. We investigated whether GM alterations contribute to aging-related worsening of post-SAH EBI and whether GM modulation can reduce this inflammatory vulnerability. Young (8-12 weeks) and aged (17-20 months) male C57BL/6 mice underwent experimental SAH. Neurological scores, brain water content, neuronal degeneration, blood-brain barrier permeability, and inflammation were assessed. A combined GM modulation protocol consisting of antibiotic pretreatment, fecal microbiota gavage from young donors, and subsequent co-housing with young mice was performed in aged recipient mice. Compared to young mice, aged mice exhibited higher mortality, worse neurological scores, increased neuronal degeneration, and enhanced neutrophil infiltration, neutrophil extracellular trap (NET) formation, and microglial TNF-α expression. Absolute brain water content was lower in aged mice than in young mice, with a similar age-related difference also observed in sham animals. GM analysis revealed reduced diversity, decreasedFirmicutes, and increasedProteobacteriain aged mice. The GM modulation intervention shifted the GM composition toward that of young mice and was associated with reduced neuronal injury, neutrophil infiltration, NET formation, and microglial inflammation; however, neurological scores and brain water content did not improve at 24 h. These findings indicate that aging is associated with greater post-SAH vulnerability and enhanced neuroinflammation, while GM modulation reduces specific neuroinflammatory and neurodegenerative components of EBI without demonstrating improvement in overall functional outcome at 24 h. The gut-brain axis constitutes a potential therapeutic target for improved SAH outcomes in older adults.},
}

@article {pmid42763148,
year = {2026},
author = {De Troyer, T and De Windt, K and Pomian, B and De Paepe, E and Plekhova, V and Vanhaecke, L},
title = {Design of experiments-driven optimization of dual ultra-high-performance liquid chromatography high resolution mass spectrometry for integrated fecal metabolomics and lipidomics.},
journal = {Analytica chimica acta},
volume = {1422},
number = {},
pages = {346087},
doi = {10.1016/j.aca.2026.346087},
pmid = {42763148},
issn = {1873-4324},
mesh = {*Feces/chemistry ; Chromatography, High Pressure Liquid/methods ; *Metabolomics/methods ; *Lipidomics/methods ; Liquid Chromatography-Mass Spectrometry/methods ; *Lipids/analysis ; Mass Spectrometry ; Humans ; },
abstract = {Recently, feces has gained increased attention in metabolomics and lipidomics research due to its ability to reflect complex diet-host-microbiome interactions. Traditionally, these analyses rely on separate workflows, resulting in longer analysis times and increased instrument load. To address these limitations, we present a dual ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry (dual UHPLC-HRMS) approach. As a first step, two previously validated single UHPLC-HRMS methods for metabolomics and lipidomics, each demonstrating robust chromatographic separation of compounds, covering a broad physicochemical range (LogP -5.30 to 21.90), were selected. To integrate both workflows into the dual platform, thirteen critical LC-MS parameters were systematically optimized using a Design of Experiments (DoE). The parameters encompassed ion generation, transmission and detection, injection-related factors, unified column oven conditions, and source geometry. This approach enabled a robust dual workflow, achieving a 21% reduction in analysis time. Targeted evaluation demonstrated consistent detection of 287 metabolites (260 with CV<20%) and 162 lipids (144 with CV<20%), thereby outperforming the single methods, which detected 272 metabolites (232 with CV<20%) and 145 lipids (116 with CV<20%), respectively. Untargeted analysis further demonstrated increased coverage, with an additional 1652 metabolite and 3966 lipid features detected with the dual method without compromising repeatability of the feature signal intensities (79.4% vs. 81.2% for metabolomics and 87.4% vs. 82.7% for lipidomics, with CV<30%). Our novel dual UHPLC-HRMS workflow enhances analytical throughput, while also improving fecal metabolome and lipidome coverage and repeatability, offering a robust and cost-effective solution for large-scale studies.},
}

*Feces/chemistry
Chromatography, High Pressure Liquid/methods
*Metabolomics/methods
*Lipidomics/methods
Liquid Chromatography-Mass Spectrometry/methods
*Lipids/analysis
Mass Spectrometry
Humans

@article {pmid42763326,
year = {2026},
author = {Shirazi Nia, R and Lu, J and De Vega, D and Poudine, N and Pan, C and Zhou, F and Ji, J and Giamas, G},
title = {Beyond the blood-brain barrier: humanised mice, the missing link in glioblastoma research.},
journal = {Oncogene},
volume = {},
number = {},
pages = {},
pmid = {42763326},
issn = {1476-5594},
abstract = {Glioblastoma (GBM) remains a major challenge in neuro-oncology, associated with a high rate of mortality despite decades of intensive research and therapeutic advancements, underscoring the urgent need for innovative preclinical platforms that can more accurately recapitulate the biological and pathological features of human disease. While conventional animal models have contributed to our understanding of GBM biology and the evaluation of treatment efficacy, they fail to capture the full complexity and heterogeneity of the tumour microenvironment (TME). Ex vivo models are associated with certain advantages in this context; however, they can not mirror the complex dynamic and multicellular interactions present in living organisms, particularly the critical treatment barriers unique to the central nervous system: the blood-brain barrier (BBB), blood-cerebrospinal fluid barrier (BCSFB) and blood-meningeal barrier (BMB). In response to these limitations, humanised mouse models have emerged as an advanced platform capable of faithfully mimicking the molecular, pathological and immunological features of human GBM. These models enable the replication of complex in vivo crosstalk between the immune system and the TME, while preserving the relevant treatment barriers that govern drug delivery to the brain. Accumulating evidence indicates that humanised mouse models closely reproduce the infiltration of human immune components into the TME, enabling the study of clinically relevant interactions that contribute to therapeutic resistance and treatment failure in GBM. This review aims to provide a comprehensive and systematic overview of the currently employed humanised mouse models in GBM research, highlighting their applications and comparative advantages. Finally, we evaluate the opportunities and challenges associated with each model and discuss future directions to increase the translational relevance and predictive power of preclinical GBM research. Humanised mouse models provide a valuable translational platform combining the human immune system and PDX orthotopic engraftment. Compared to conventional models and ex vivo models, these models can reproduce the complex cross-talk between tumour cells and the immune system, tumour heterogeneity, immunosuppressive TME, as well as complex in vivo interactions such as brain-specific barriers, including BBB, BCSFB and BMB. Future implementation of the human gut microbiome in these models has the potential to further increase translational relevance and precision in GBM research. Created in BioRender.com.},
}

@article {pmid42763356,
year = {2026},
author = {Kasprowicz-Furmańczyk, M and Chmielnicki, W and Zdanowska, N and Owczarczyk-Saczonek, A},
title = {The Role of the Microbiome in Lichen Sclerosus: Pathophysiological Insights and Therapeutic Implications.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42763356},
issn = {2193-8210},
abstract = {Lichen sclerosus (LS) is a chronic inflammatory and fibrotic dermatosis of unclear etiology, traditionally considered an autoimmune disorder. Emerging evidence suggests that microbiome dysbiosis may contribute to disease pathogenesis by modulating local immune responses and tissue remodeling. This narrative review synthesizes current data on the skin, genital, and gut microbiome in LS, focusing on potential mechanistic links between microbial imbalance and immune activation. Available studies consistently show alterations in microbial composition; however, findings remain heterogeneous because of the small sample sizes, methodological variability, and predominantly cross-sectional designs. Despite these limitations, accumulating data indicate that microbial dysbiosis may influence key immunological pathways involved in LS, including T-cell activation and chronic inflammation. In particular, mucosa-associated invariant T (MAIT) cells are proposed as a potential mechanistic bridge between microbial-derived signals and immune dysregulation, although their role in LS remains unclear. These observations support a conceptual model of LS as a microbiome-modulated inflammatory and fibrotic disorder rather than a purely autoimmune condition. Clinically, microbiome profiling and targeted modulation may offer novel diagnostic and therapeutic opportunities. Future research should prioritize longitudinal and interventional studies, ideally incorporating multi-omics approaches, to clarify causality and facilitate translation into clinical practice.},
}

@article {pmid42763436,
year = {2026},
author = {Alberdi, A and Ramirez, J and Gaun, N and Horisberger, Z and Wang, B and Trivedi, U and Bogri, A},
title = {LMDmapper: an open-source desktop tool for spatial mapping of laser microdissection samples.},
journal = {Open research Europe},
volume = {6},
number = {},
pages = {257},
pmid = {42763436},
issn = {2732-5121},
abstract = {Laser microdissection (LMD) enables researchers to isolate targeted microsamples from microscopy slide specimens for downstream molecular analyses. While traditionally employed for isolating eukaryotic cells from complex tissues, LMD is starting to be used for micro-scale spatial microbiome analyses, which require the precise location of the microsamples to be tracked for downstream spatial analyses. To address this need, we present LMDmapper, an open-source desktop application that allows designing, tracking and logging micron-scale spatial microsample data and metadata from LMD sessions. The software parses Leica Database LIF image files (containing stage coordinates), imports laser microdissection CSV exports (containing image pixel coordinates), transforms and maps image pixel coordinates into stage coordinates, and presents the resulting cut points together with user-defined plate layouts and collection metadata. LMDmapper supports a variety of microdissection designs, including multiple slides, specimens, collection plates and plate layouts. The application is implemented in TypeScript using Electron, React, Vite, and fast-xml-parser. LMDmapper outputs include a metadata CSV linking microsample identifiers to plate positions, collection information, image labels, pixel coordinates and stage coordinates, as well as the possibility to create overview images of the specimens, and automatically calculating distances between cutting points and regions of interest. With these capabilities, LMDmapper is intended as a practical bridge between microscope-side laser microdissection records and downstream spatial omics sample tracking.},
}

@article {pmid42763526,
year = {2026},
author = {Palanivel, M and Narayana, JK and Chotirmall, SH},
title = {Axial Connectivity of the Lung Microbiome: A Review of Interorgan Crosstalk.},
journal = {Comprehensive physiology},
volume = {16},
number = {5},
pages = {e70269},
pmid = {42763526},
issn = {2040-4603},
abstract = {The classic organ-centric model of human physiology is rapidly giving way to a unified approach embracing the human body as an integrated network of bidirectional interorgan communication. The human microbiome serves as a fundamental mediator of this shift, regulating immune homeostasis, barrier integrity and metabolic signaling across organs. While the lung maintains a characteristic low-biomass microbiome in dynamic equilibrium, any disruption primes local and systemic immune responses contributing to disease. Beyond the well-described gut-lung axis, crosstalk between the lung and other distal organ systems is lesser recognized; however, increasingly acknowledged as a key under-appreciated contributor to respiratory disease including extrapulmonary complications. This review synthesizes current established evidence on axial connectivity of the lung microbiome across the gut, brain, skin, heart, kidney, and liver, and finds that such crosstalk is predominantly, though not exclusively gut-mediated. Direct lung-organ interactions are described for several axes; however, they remain preliminary. Across these lung-axial systems, common pathophysiological mechanisms emerge, including dysbiosis-induced depletion of microbial metabolites, immunomodulation, and barrier perturbations, all linking pulmonary disease with neuroinflammation, gastrointestinal deficits, and cardiac, renal, hepatic, and dermatological abnormalities. We assess how therapeutic modulation of interorgan systems offers promising avenues for improved risk stratification and novel therapeutics. Recognizing microbiome-mediated pulmonary-organ crosstalk represents an emerging conceptual framework in respiratory medicine, repositioning microbial communities as key modulators of extrapulmonary disease.},
}

@article {pmid42764218,
year = {2026},
author = {Huang, QY and Xiang, HR and Tu, HK},
title = {[Current research status of the intratumoral microbiome and evolution of detection technologies].},
journal = {Zhonghua zhong liu za zhi [Chinese journal of oncology]},
volume = {48},
number = {9},
pages = {1124-1138},
doi = {10.3760/cma.j.cn112152-20260303-00105},
pmid = {42764218},
issn = {0253-3766},
support = {82574197//National Natural Science Foundation of China/ ; K20230085//Healthy Zhejiang One Million People Cohort/ ; },
mesh = {Humans ; *Microbiota ; *Tumor Microenvironment ; *Neoplasms/microbiology/pathology ; Metagenomics ; Bacteria/isolation & purification ; },
abstract = {As a core functional component of the tumor microenvironment, the regulatory role of intratumoral microbiome in tumorigenesis and progression has become as a frontier research direction in oncology. Microorganisms such as bacteria, fungi, and viruses participate in the regulation of tumor biological mechanisms through multiple pathways, including metabolite secretion, induction of genomic instability, and remodeling of the immune microenvironment; their species composition and abundance characteristics exhibit distinct cancer-type specificity, and their impact on patient prognosis is highly context-dependent. Current detection systems for the intratumoral microbiome mainly encompass in situ detection technologies, metagenomic sequencing, and computational pathology-driven intelligent detection, each with its own advantages and limitations, among which intelligent detection centered on deep learning is gradually overcoming the technical bottlenecks of identifying low-abundance microbial signals, achieving accurate quantification, and resolving spatial distribution. In the future, with the deep integration of three-dimensional pathological imaging, spatial omics, and multi-modal foundation models, intratumoral microbiome research will advance toward the in-depth development of multi-dimensional data integration, providing innovative ideas and technical pathways for elucidating the regulatory mechanisms between microorganisms and the host and for developing precision diagnostic and treatment strategies based on individual microecological characteristics.},
}

Humans
*Microbiota
*Tumor Microenvironment
*Neoplasms/microbiology/pathology
Metagenomics
Bacteria/isolation & purification

@article {pmid42764315,
year = {2026},
author = {Shao, Y and Zhang, RF and Wang, Z and Gan, J and Jiang, XJ and Yang, L},
title = {From Dysbiosis to Blood-Brain Barrier Disruption: The Metabolite-Mediated Gut-Brain Axis in Alzheimer's Disease.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42764315},
issn = {1559-1182},
mesh = {Humans ; *Blood-Brain Barrier/metabolism/pathology ; Animals ; *Alzheimer Disease/metabolism/pathology/microbiology ; *Dysbiosis/metabolism ; *Gastrointestinal Microbiome/physiology ; *Brain-Gut Axis/physiology ; *Brain/metabolism ; },
abstract = {Alzheimer's disease (AD) is not merely a central nervous system disorder; rather, it is a systemic condition profoundly influenced by the peripheral internal environment. Recent research has revealed that imbalances in the gut microbiota (GM) and metabolite disturbances contribute to AD onset and progression. Clinical and animal studies have indicated that AD patients commonly exhibit reduced GM diversity, decreased populations of short-chain fatty acid (SCFA)-producing and indole-producing bacteria, disrupted bile acid (BA) profiles, and elevated levels of trimethylamine N-oxide (TMAO) and kynurenine pathway (KP) activity. These alterations not only reflect gut dysbiosis, but also impair blood-brain barrier (BBB) integrity and amplify neuroinflammation by modulating tight junction proteins and inflammatory signaling through their effects on receptors and transporters such as G protein-coupled receptors(GPR41/43), aryl hydrocarbon receptor(AhR), Farnesoid X receptor(FXR)/ Takeda G protein-coupled receptor 5(TGR5), L-type amino acid transporter 1(LAT1), and Major Facilitator Superfamily Domain containing 2A(MFSD2A). From an integrative perspective, these changes -including short-Chain Fatty Acids (SCFAs) deficiency, elevated TMAO and toxic BA levels, overactivation of the KP, and Lipopolysaccharides (LPS) leakage-often act synergistically, collectively forming key pathological nodes in the "metabolic network-BBB-AD" axis. GM-targeted strategies such as dietary interventions, probiotics and fecal microbiota transplantation (FMT) have demonstrated potential in improving metabolite profiles and BBB homeostasis. Future research should utilize induced pluripotent stem cell-derived organoids and multi-omics integration approaches to elucidate the spatiotemporal dynamics of metabolites within the gut-brain axis (GBA), thereby laying the foundation for precise microbiome-based interventions in AD.},
}

Humans
*Blood-Brain Barrier/metabolism/pathology
Animals
*Alzheimer Disease/metabolism/pathology/microbiology
*Dysbiosis/metabolism
*Gastrointestinal Microbiome/physiology
*Brain-Gut Axis/physiology
*Brain/metabolism

@article {pmid42764380,
year = {2026},
author = {Li, L and Lei, S and Ngan, C},
title = {Pathogen-oriented mNGS is not equivalent to microbiome profiling: interpreting BALF mNGS diversity in ARDS.},
journal = {Journal of intensive care},
volume = {14},
number = {1},
pages = {},
pmid = {42764380},
issn = {2052-0492},
support = {25LCYJ34//Health Commission of Sichuan Province Medical Science and Technology Program/ ; },
abstract = {Gao et al. provide valuable data-linking bronchoalveolar lavage fluid metagenomic next-generation sequencing with inflammatory subphenotypes of acute respiratory distress syndrome. We highlight three issues relevant to interpretation: an apparent inconsistency concerning exclusion of samples with no micro-organisms detected, use of a pathogen-oriented workflow for community-level ecological inference, and the distinction between detection yield and diagnostic performance without an independent reference standard. Clarification of sample eligibility, sensitivity analysis including technically valid samples reported as negative by sequencing, and confirmation that sequencing and bioinformatic procedures are validated for quantitative microbiome analysis would strengthen interpretation.},
}

@article {pmid42764750,
year = {2026},
author = {Holmes, A and Matilla, MA},
title = {Toward Sustainable Crop Production in a Changing Climate: Microbiomes, Pathogens, Biostimulants and Biocontrol Innovations.},
journal = {Microbial biotechnology},
volume = {19},
number = {9},
pages = {e70442},
doi = {10.1111/1751-7915.70442},
pmid = {42764750},
issn = {1751-7915},
support = {JHI-A1-1//Scottish Government Environment, Natural Resources and Agriculture Research Program/ ; JHI-A1-2//Scottish Government Environment, Natural Resources and Agriculture Research Program/ ; JHI-D3-1//Scottish Government Environment, Natural Resources and Agriculture Research Program/ ; PID2023-146281NB-I00//Spanish Ministry for Science, Innovation and Universities/ ; },
mesh = {*Climate Change ; *Microbiota ; *Crops, Agricultural/microbiology/growth & development ; Biological Control Agents ; Soil Microbiology ; Biotechnology/methods ; *Crop Production/methods/trends ; Agriculture/methods ; Plant Diseases/microbiology/prevention & control ; },
abstract = {Climate change is recognised as one of the most pressing global challenges, with profound consequences for plant health, agricultural productivity, and food security worldwide. In this opinion article, we discuss recent advances in how climate change affects plant-microbe interactions, soil antibiotic resistance, and plant-associated microbiomes, including shifts in the distribution of plant pathogens. We also examine the influence of land-use practices, including integrated agricultural management, on the physicochemical and microbiological properties of soils under changing climatic conditions. In addition, we critically discuss emerging biological and biotechnological strategies aimed at enhancing plant health and resilience under climate change. These approaches include the rational design of synthetic microbial communities (SynComs), bacteriophage therapy, mycovirus-based biocontrol, antibiotic-producing microbial biocontrol agents, (nano-enabled) microbiome engineering, and extracellular vesicle-mediated RNA delivery systems. Challenges involved in translating laboratory-based discoveries into effective field applications are also discussed. Collectively, current advances highlight the growing potential of microbial biotechnology to reduce reliance on chemical pesticides and fertilisers, while supporting sustainable and integrated crop management under climate-change scenarios.},
}

*Climate Change
*Microbiota
*Crops, Agricultural/microbiology/growth & development
Biological Control Agents
Soil Microbiology
Biotechnology/methods
*Crop Production/methods/trends
Agriculture/methods
Plant Diseases/microbiology/prevention & control

@article {pmid42764800,
year = {2026},
author = {Ruiz, D and Robinson, V and Doucoure, M and Cheema, AR and Ramirez Cabal, C and Saleef Abdul Salam, A and Younes, RA and Song, W and Ibrahim, SA and Ariyo, O and Gupta, RD},
title = {Role of the Reproductive Tract Microbiome in Infertility and Assisted Reproductive Technologies: A Comprehensive Review.},
journal = {Cureus},
volume = {18},
number = {8},
pages = {e114891},
pmid = {42764800},
issn = {2168-8184},
abstract = {The female reproductive tract microbiome has emerged as a potential factor associated with reproductive health, infertility, and outcomes of assisted reproductive technologies (ARTs). Growing interest in host-microbiome interactions has highlighted the potential roles of microbial communities in implantation, immune regulation, and endometrial receptivity. This comprehensive narrative review summarizes current evidence on the reproductive tract microbiome and its relationship with infertility and ART outcomes. Relevant literature was identified from MEDLINE, Embase, and Web of Science from database inception through March 2026, with emphasis on observational, interventional, and mechanistic studies involving human participants or human-derived samples. The review examines microbial communities of the vagina, cervix, endometrium, and fallopian tubes and their associations with infertility, recurrent pregnancy loss, implantation failure, and ART outcomes. Proposed biological mechanisms, including alterations in epithelial barrier integrity, immune modulation, inflammatory signaling, and hormonal-microbial interactions, are also discussed. In addition, the review evaluates emerging microbiome-based diagnostic approaches and potential therapeutic strategies, including antibiotics, probiotics, micronutrient supplementation, and vaginal microbiota transplantation. Current evidence suggests that the reproductive tract microbiome may be associated with reproductive health and fertility outcomes and represents a promising area of translational research. However, substantial methodological heterogeneity, limited high-quality interventional evidence, and the lack of standardized diagnostic criteria currently restrict clinical implementation. Well-designed prospective studies and randomized clinical trials are needed to clarify causal relationships, evaluate microbiome-targeted interventions, and determine whether microbiome-based approaches can improve infertility and ART care.},
}

@article {pmid42764836,
year = {2026},
author = {Dong, C and Tai, J and Ma, Y and Wang, Y and Yang, J},
title = {Anti-inflammatory dietary patterns and cognitive aging in older adults: a scoping review of mechanistic, clinical, and nursing implications.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1952047},
pmid = {42764836},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary patterns with lower inflammatory potential may support cognitive aging, but Mediterranean, Dietary Approaches to Stop Hypertension (DASH), Mediterranean-DASH Intervention for Neurodegenerative Delay (MIND), and dietary inflammatory scores represent non-equivalent exposures, and observational findings have not been consistently confirmed in randomized trials. This scoping review mapped evidence linking whole-diet patterns and dietary inflammatory indices with cognitive aging, measured biological pathways, and clinical interpretation and potential nursing implications.

METHODS: PubMed, Embase, Web of Science Core Collection, and Scopus were searched from inception to 30 June 2026. Eligible studies evaluated dietary patterns or validated inflammatory indices in older adults or cohorts assessed in later life and reported cognitive, dementia, mechanistic, neuroimaging, neuropathological, or implementation outcomes. Evidence was synthesized narratively, with observational and interventional findings considered separately.

RESULTS: Thirty-eight reports were included: 27 longitudinal observational studies, seven randomized intervention reports, three cross-sectional biomarker or neuroimaging studies, and one post hoc analysis. Mediterranean- and MIND-oriented patterns and lower dietary inflammatory potential were recurrently associated with more favorable cognitive outcomes, but findings varied across definitions, populations, measures, and follow-up. Randomized evidence was mixed and not definitive. Fourteen reports measured inflammatory, proteomic, microbiome, neuroimaging, cerebrospinal-fluid, spectroscopy, or neuropathological outcomes, supporting selected biological links without establishing a complete diet-neuroinflammation-cognition pathway. No study evaluated a complete nurse-led or nurse-supported dietary pathway; the nursing framework is author-derived and untested.

CONCLUSION: The evidence is epidemiologically suggestive and biologically plausible, but does not establish that any specific diet prevents dementia. Dietary improvement may be incorporated into individualized multidomain risk reduction, provided that nutritional adequacy, frailty, cultural fit, affordability, and sustained adherence are addressed. Better-contrasted trials, temporally ordered mechanistic studies, and prospective implementation evaluations are needed.},
}

@article {pmid42764917,
year = {2026},
author = {Li, B and Yang, Q and Li, M and He, J and Zhang, Z and Wan, X and Mo, Z and Li, R and Li, S and Xu, W and Gu, M and Huang, H and Li, W and Huang, Z and Yang, H and Chen, WH and Liu, Z},
title = {Gut microbiota-derived 5-HTP penetrates the host blood-brain barrier and ameliorates autism symptoms.},
journal = {Acta pharmaceutica Sinica. B},
volume = {16},
number = {9},
pages = {6168-6184},
pmid = {42764917},
issn = {2211-3835},
abstract = {Autism spectrum disorder (ASD), a highly prevalent neurodevelopmental condition, is increasingly recognized for its strong association with the intestinal microbiome. However, the development of gut microbiota-targeted therapies has been impeded by a limited understanding of the molecular mechanisms underlying interactions between commensal bacteria and the host nervous system. In this study, shotgun metagenomic sequencing and UPLC-MS/MS targeted metabolic analyses identified altered tryptophan metabolites in the gut microbiota of both human ASD patients and ASD mouse models. Notably, we demonstrate that commensal bacteria-derived 5-hydroxytryptophan (5-HTP), metabolite of tryptophan, ameliorates anxiety, stereotypical and repetitive behaviors, as well as social deficits in these mouse models. Furthermore, 5-HTP is capable of crossing the blood-brain barrier and inhibits the overexpression of receptor tyrosine kinase (RTK) ligands, thereby suppressing the downstream RTK/MAPK/ERK signaling cascade. This inhibition subsequently normalizes the excessive stabilization of dendritic spines in the hippocampus in MeCP2 mouse. Our research demonstrates that gut microbiota producing 5-HTP improves ASD symptoms in various ASD animal models, elucidates the molecular mechanisms between gut microbiota and the onset and treatment of ASD, and provides a promising therapeutic approach for ameliorating ASD through the expression of neuron-regulated small molecules by gut indigenous bacteria.},
}

@article {pmid42765047,
year = {2026},
author = {Guo, Q and Liang, F and Chen, P and Zhang, Y and Xie, M and Wan, X and Mao, J and Chen, H and Wu, W and Jiang, D and Wu, S},
title = {Microbiota-Host Interactions in Perimenopausal Syndrome: Mechanisms and Therapeutic Strategies (Review).},
journal = {International journal of women's health},
volume = {18},
number = {},
pages = {631942},
pmid = {42765047},
issn = {1179-1411},
abstract = {BACKGROUND: Perimenopausal syndrome (PMS) is common, with more than 70% of perimenopausal women experiencing symptoms such as hot flashes and anxiety. As a key regulator of host physiology, the gut microbiota may play an important role in the pathogenesis of PMS.

OBJECTIVE: This review aimed to synthesize clinical and preclinical evidence on alterations in the gut microbiota during perimenopause, elucidate the potential mechanisms underlying host-microbiota interactions, and summarize and critically evaluate current therapeutic strategies targeting the gut microbiota.

METHODS: A targeted literature search of PubMed and Web of Science was conducted for relevant studies published through July 15, 2026. Search terms covered perimenopause, menopause, gut microbiota, estrobolome, gut-brain axis, metabolomics, female microbiome, ovarian function, probiotics, and fecal microbiota transplantation. Human studies were prioritized, with high-quality animal and mechanistic studies included when clinical evidence was limited.

RESULTS: Few studies have directly examined women with PMS. Findings on gut microbial diversity and changes in specific taxa have been inconsistent across studies, and no reproducible pattern of gut dysbiosis specific to PMS has been established. Current evidence suggests that ovarian aging and fluctuations in sex hormones may reshape the gut microbial ecosystem. In turn, microbial enzymes and metabolites may interact bidirectionally with host endocrine changes by influencing the enterohepatic circulation of estrogens, immune and inflammatory responses, ovarian function, and gut-brain communication. Lifestyle interventions are supported by a relatively substantial body of evidence for symptom improvement, although whether their effects are mediated by the gut microbiota remains unclear. Certain strain-specific probiotics have shown preliminary clinical promise. However, evidence supporting prebiotics, synbiotics, traditional Chinese medicine, acupuncture, plant-derived products, and fecal microbiota transplantation is derived mainly from small clinical studies or preclinical experiments. By distinguishing direct clinical evidence from PMS populations from indirect evidence derived from other populations and experimental studies, this review reveals a central paradox in current research that strong biological plausibility coexists with insufficient clinical causal evidence.

CONCLUSION: The gut microbiota may contribute to the pathogenesis and progression of PMS through the "gut microbiota-estrogen-ovary-immune-brain axis". However, current evidence primarily supports bidirectional associations and biological plausibility. Although microbiota-targeted interventions have potential therapeutic value, the available evidence remains insufficient to support their routine clinical use. Future research should include longitudinal cohort studies using standardized menopausal staging and multicenter randomized controlled trials. Confounding factors such as age, diet, medication use, and hormone therapy should be adequately controlled. Integrated analyses of multiple omics datasets should also be combined with mechanistic studies to establish the causal role and clinical translational potential of the gut microbiota.},
}

@article {pmid42765490,
year = {2026},
author = {Milano, M and Hiram Guzzi, P},
title = {Differential analysis of microbial interaction networks.},
journal = {Briefings in bioinformatics},
volume = {27},
number = {5},
pages = {},
doi = {10.1093/bib/bbag522},
pmid = {42765490},
issn = {1477-4054},
support = {//OFIDIAPlus (Operational Fire Danger preventIon plAtform Plus)/ ; },
mesh = {*Microbiota ; Humans ; Inflammatory Bowel Diseases/microbiology/genetics ; *Gene Regulatory Networks ; *Microbial Interactions ; *Diabetes Mellitus, Type 2/microbiology/genetics ; Female ; Atherosclerosis/microbiology/genetics ; Computational Biology/methods ; },
abstract = {Microbiome studies increasingly indicate that disease-associated shifts cannot be understood from compositional changes alone. The functional architecture of microbial communities-encoded in patterns of association among microbial gene families-may reveal how these systems reorganize across biological conditions. Here, we present a network-based framework for characterizing microbiome rewiring across conditions. The approach combines condition-specific network inference, differential network analysis, and pathway-level network analysis to identify associations that are gained, lost, or altered between groups, with a specific focus on sex-dependent differences. We apply the framework to inflammatory bowel disease, type 2 diabetes, and atherosclerotic cardiovascular disease (ACVD), comparing male and female-specific microbial gene family networks within each disease context. Across these settings, differential networks flag large numbers of candidate rewired associations; however, permutation testing (sex labels shuffled, group sizes preserved, 500 permutations for gene-family networks, and 1000 for pathway networks) shows that the global amount of apparent rewiring is not greater than expected under the null at the global or edge level in any cohort, and that most edges exclusive to one group are induced by group-specific feature filtering rather than by a genuine change in association ($\sim $80%-83% in ACVD). We therefore present the method as a rigorously validated framework and a cautionary case study: the differential-network machinery is sound, but the headline biological signal in a naive analysis is largely a property of correlation thresholding and, for the longitudinal inflammatory bowel disease (IBD) cohort, of pseudoreplication. The only non-null result across all validations is a SOHPIE-DNA per-taxon test in the IBD disease arm (15 taxa at FDR $< 0.05$), which we report as a single nominal finding requiring independent replication. Code, data, and supplementary information are available at https://github.com/mmilano87/NetMicrobiome.},
}

*Microbiota
Humans
Inflammatory Bowel Diseases/microbiology/genetics
*Gene Regulatory Networks
*Microbial Interactions
*Diabetes Mellitus, Type 2/microbiology/genetics
Female
Atherosclerosis/microbiology/genetics
Computational Biology/methods

@article {pmid42765517,
year = {2026},
author = {Ward, GD and Ruiz-Tabas, Á and Altea-Manzano, P},
title = {Metastatic niche shaped by host factors influences disseminated cancer cell fate.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70471},
pmid = {42765517},
issn = {1873-3468},
support = {DGP_PIDI_2024_02725//Consejería de Universidad, Investigación e Innovación, Junta de Andalucía/ ; //Federation of European Biochemical Societies/ ; PID2023-152426OA-I00//Agencia Estatal de Investigación/ ; ERC-StG-101116912//European Union/ ; },
abstract = {Metastasis is responsible for the vast majority of cancer-related deaths, yet organ selectivity and the fate of disseminated cancer cells remain incompletely understood. While tumor-intrinsic programs have been extensively characterized, increasing evidence indicates that host-related extrinsic factors critically modulate the molecular and cellular landscape of metastatic niches. Aging, dietary habits, microbiome, physical activity, smoking, air pollution, and chronic stress may reshape systemic inflammation, immune surveillance, vascular permeability, stromal composition, extracellular matrix remodeling, and metabolic signaling in organs commonly targeted by metastasis, including bone, lung, liver, and brain. These host-dependent alterations influence disseminated cancer cell homing, extravasation, dormancy, and proliferative outgrowth by reprogramming tissue-resident and recruited cell populations, as well as niche-derived soluble and mechanical cues. In this review, we describe a framework in which metastasis is dynamically codetermined by tumor cell plasticity and host systemic state, contextualized by recent mechanistic insights into how lifestyle and physiological states rewire organ microenvironments to become either permissive or restrictive to metastatic colonization. Understanding these interactions may reveal actionable targets for metastasis prevention and highlight modifiable behaviors as biological determinants of organ susceptibility to metastatic disease.},
}

@article {pmid42765534,
year = {2026},
author = {Gabrielli, M and Bredel, A and Paoli, L and Robinson, SL},
title = {Advancing biosynthetic pathway discovery through short-read-directed long-read sequencing.},
journal = {Natural product reports},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6np00020g},
pmid = {42765534},
issn = {1460-4752},
abstract = {Time span of literature: 2020-todayMetagenomic methods have rapidly advanced, enabling the identification of biosynthetic pathways directly from complex microbiome data. Short-read sequencing, while accurate and cost-effective, often generates fragmented assemblies that can lead to incomplete biosynthetic gene cluster (BGC) recovery. Although long-read sequencing offers a solution to the fragmentation problems, technical requirements and higher costs have limited its scalability. Here, we examine BGC fragmentation in short-read sequencing data across large databases of metagenome-assembled genomes (MAGs) and estimate the targeted genome contiguity required to recover 'complete' biosynthetic gene clusters. We argue that the increasing availability of MAGs recovered from short-read metagenomes with recent advancements in ultra-low input DNA amplification for high-fidelity PacBio sequencing-now requiring as little as nanograms of DNA-can be used sequentially to boost biosynthetic pathway discovery. We demonstrate how natural products researchers can benefit from using short-read MAG comparisons to guide targeted long-read re-sequencing efforts with low amounts of input DNA and/or limited financial resources. Our analysis provides strategic recommendations for the broader scientific community on how to best leverage the strengths of short- and long-read sequencing data to efficiently allocate resources and accelerate natural product discovery.},
}

@article {pmid42765606,
year = {2026},
author = {Zhang, J and Xu, S and Chen, C and Wang, Z and Du, W and Hong, L and Asiegbu, FO and Wang, K},
title = {Synthetic microbial community promotes seedling growth of Chinese fir via dissolving phosphorus and modifying rhizosphere microbial community.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag135},
pmid = {42765606},
issn = {1758-4469},
abstract = {Phosphorus (P) is an essential nutrient for plant growth, yet its availability in soil is severely constrained by fixation into insoluble forms that plants cannot directly utilize. Although phosphate-solubilizing microorganisms (PSM) represent a promising strategy to mobilize soil P, the functional potential of endophytic PSM and their synthetic consortia in promoting tree growth remains largely underexplored. In this study, endophytic bacteria were isolated from the roots of Chinese fir (Cunninghamia lanceolata). Among them, 42 isolates were screened for phosphate-solubilizing activity on media containing calcium phosphate, iron phosphate, aluminum phosphate, and organic phosphorus. Six strains with strong solubilizing capacity and no antagonistic interactions were selected to construct a synthetic microbial community (SynCom-P6), which was then applied to local soil and Chinese fir seedlings. Soil available P content initially decreased but subsequently increased from day 7 to day 21 after SynCom-P6 inoculation, indicating effective mobilization of insoluble P in soil. Inoculation with SynCom-P6 significantly enhanced root elongation and biomass accumulation, with both root fresh and dry weights showing marked increases compared to the control. Absolute quantification 16S amplicon and metagenomic sequencing revealed that SynCom-P6 reshaped the rhizosphere bacterial community, enriching beneficial genera such as Massilia and Dyadobacter, and altered functional profiles, including upregulation of hormone signaling and nitrogen fixation related genes. These results demonstrated that the synthetic community not only improved soil P availability but also promoted root growth and modified the rhizosphere microbiome in a beneficial direction. Our findings highlight the potential of endophytic phosphate-solubilizing SynCom-P6 as a promising bio-inoculant for sustainable forestry, reducing the need for chemical P fertilizers while enhancing Chinese fir productivity. Future research should focus on field validation and mechanistic exploration of microbial interactions and functional gene expression.},
}

@article {pmid42765627,
year = {2026},
author = {Liu, W and Ding, J and Sun, Y and Yan, B and Wang, Z and Wang, C and Shu, C and Zhou, JG and Yu, G and Peng, Y and Wang, S},
title = {Composable Visualization of High-Dimensional Biological Data with ggalign.},
journal = {Current protocols},
volume = {6},
number = {9},
pages = {e70453},
doi = {10.1002/cpz1.70453},
pmid = {42765627},
issn = {2691-1299},
support = {//National Natural Science Foundation of China/ ; },
mesh = {*Software ; *Computer Graphics ; *Data Visualization ; Humans ; *Computational Biology/methods ; Multiomics ; },
abstract = {ggalign is an R/CRAN package for creating flexible and composable multi-panel data visualizations. The package extends the ggplot2 grammar of graphics by introducing an integrative framework that supports both data-free and data-aware composition. After five years of continuous development, ggalign has evolved into a comprehensive solution that handles diverse data types and layout structures, including quad, circular, and stack layouts. It was originally designed for general-purpose composable visualization and has been expanded to support multi-omics data integration, extending the application of ggalign to pan-cancer analysis, single-cell transcriptomics, and microbiome studies. This article presents eight basic protocols for constructing complex visualizations using the declarative syntax of ggalign. Basic Protocol 1 describes data-free composition for flexible arrangement of multiple plots; Basic Protocol 2 describes data-aware quad layout for integrating a central plot with surrounding annotations; Basic Protocol 3 describes data-aware circular layout for visualizing ring-structured data; Basic Protocol 4 describes stack layout and nested composition for coordinated display of multi-track graphics; Basic Protocol 5 describes visualization of gene expression matrix heatmaps; Basic Protocol 6 describes visualization of somatic mutation landscapes using ggoncoplot(); Basic Protocol 7 describes circular visualization based on chromosome data, and Basic Protocol 8 describes cross-connection visualization between genes and pathways. The complete package reference is available at https://yunuuuu.github.io/ggalign/, with comprehensive documentation and tutorials at https://yunuuuu.github.io/ggalign-book/, and a gallery of example figures at https://yunuuuu.github.io/ggalign-gallery/. © 2026 Wiley Periodicals LLC. Basic Protocol 1: Data-free composition Basic Protocol 2: Aligning data-aware with quad layouts Basic Protocol 3: Aligning data-aware with circular layouts Basic Protocol 4: Stack layouts and nested composition Basic Protocol 5: Visualizing heatmap of gene expression matrix Basic Protocol 6: Visualizing somatic mutation landscapes using ggoncoplot() Basic Protocol 7: Visualizing circos plots with ggalign Basic Protocol 8: Visualizing observational connections.},
}

*Software
*Computer Graphics
*Data Visualization
Humans
*Computational Biology/methods
Multiomics

@article {pmid42765732,
year = {2026},
author = {Hammer, AJ and Kasschau, KD and Davis Ii, EW and Hoffman, P and Johnson-Camacho, K and Alexiev, A and Anderson, K and Shannon, J and Marriott, LK and Sharpton, TJ},
title = {Polycyclic aromatic hydrocarbons, gut microbiome composition, impulsivity, and attention covary in a human cohort.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0078326},
doi = {10.1128/spectrum.00783-26},
pmid = {42765732},
issn = {2165-0497},
abstract = {Polycyclic aromatic hydrocarbons (PAHs) are pervasive environmental pollutants linked to adverse neurobehavioral outcomes, yet the biological pathways coupling exposure to behavior are poorly defined. The gut microbiome is both sensitive to PAH exposure and a modulator of central nervous system function, suggesting it may mediate how PAH exposure influences neurobehavior. We tested whether PAH exposure, gut microbiome composition, and neurobehavioral function covary in a statewide sample of 34 adults stratified into high-impulsivity/poor-attention (HH) and low-impulsivity/fast-attention (LL) groups. Participants wore silicone wristbands for 30 days to passively sample PAH exposure and provided a single fecal sample for 16S rRNA profiling at the end of the wear period. Higher PAH exposure was associated with HH group membership in a sex-dependent manner, with the largest elevations among HH males. At the community level, PAH exposure profiles correlated with microbiome dissimilarity, and HH membership was associated with increased alpha-diversity and altered community composition relative to LL members. At the taxon level, 22 genera were significantly associated with 14 PAH compounds (FDR < 0.1). No individual genera were significantly associated with neurobehavioral group after multiple testing correction. Nevertheless, cross-referencing PAH-responsive genera (FDR < 0.1) against those with nominal neurobehavioral associations (P < 0.05) identified two candidate genera-Hydrogenoanaerobacterium and Methanobrevibacter-whose abundance covaries with both PAH exposure and neurobehavioral phenotype. Both have been independently linked to cognitive or neurological outcomes in prior work. These findings support a three-way relationship among environmental chemical exposure, gut microbiome composition, and neurobehavioral function, establishing an empirical foundation for testing microbiome-mediated links between PAH exposure and neurobehavioral outcomes.IMPORTANCEPolycyclic aromatic hydrocarbon (PAH) exposure is widespread and is associated with impulsivity and attention problems, but how exposure translates into neurobehavioral risk is unclear. The gut microbiome is a plausible intermediary: gut microbes biotransform environmental chemicals and produce metabolites that influence brain function. In a statewide adult cohort, higher PAH exposure associated with with greater impulsivity and poorer attention in a sex-dependent manner, and both PAH exposure and neurobehavioral phenotype were associated with distinct gut microbiome features at the community and taxon levels. We identify candidate genera at the intersection of PAH exposure and neurobehavioral group whose biology independently implicates them in cognitive and neurological function. Because their associations with neurobehavioral phenotype are nominal, we present these genera as hypothesis-generating candidates for future study. By showing that all three domains covary within a single cohort, this work moves beyond pairwise associations toward testable microbiome-targeted and exposure-reduction strategies for PAH-related neurobehavioral risk.},
}

@article {pmid42765765,
year = {2026},
author = {Benot, AO and Waldschmidt, G and Gilvarg, SC and Legge, EOL and Okyere, IJ and Tiyapun, C and Lucas, SK and Vander Yacht, AL and Goff, JL},
title = {Prescribed burns drive lasting changes in soil nitrogen cycling and microbial function.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0085226},
doi = {10.1128/msystems.00852-26},
pmid = {42765765},
issn = {2379-5077},
abstract = {Fire is a major pulse disturbance to soil microbial communities, with broad implications for nutrient cycling; however, regular burning is also a natural and often-essential process maintaining biodiversity in unique and imperiled fire-dependent ecosystems. Prescribed fire is widely used to promote this biodiversity and simultaneously reduce wildfire risk. Although such repeated burning is known to alter surface biodiversity, belowground soil geochemistry, and soil microbial community structure, the functional consequences (i.e., the metabolic capabilities that underlie the ecosystem services soil microorganisms provide) remain underexplored. Here, we examined the effects of 30 years of repeated prescribed fire at the Albany Pine Bush-a fire-dependent, inland pitch pine barren ecosystem of the northeastern United States. Compared with the control stands, we observed that this long-term fire management has led to substantial depletion of inorganic soil nitrogen, specifically nitrate. We found no meaningful differences in the higher-level taxonomic composition of soil prokaryotic or fungal communities; however, analysis of metagenome-assembled genomes assembled from these soils revealed several differentially abundant populations. Furthermore, our metagenomic analysis revealed significant changes in the nitrogen-cycling functional potential, specifically decreased dissimilatory nitrate reduction and denitrification potential in repeatedly burned soils. These functional shifts have important implications for both nutrient cycling and emissions of trace nitrogen gases from these soils. Our results suggest that functionally meaningful changes in the soil microbiome can persist between burn events, even when higher-order community membership appears stable. This may imply that repeated fire can deplete reactive nitrogen emissions from soils by lowering the functional capacity of nitrogen-reducing microbes.IMPORTANCEPrescribed fire is widely used by land managers to reduce wildfire risk and promote biodiversity. While the effects of fire on aboveground processes are well understood, much less is known about how repeated burning influences soil biological properties-including the functional role that soil microorganisms play in nutrient cycling and greenhouse gas production. We addressed this gap by studying soils from the Albany Pine Bush, a rare and endangered ecosystem that has experienced regular prescribed fires for 30 years. Long-term fire management significantly altered soil chemistry, specifically lowering the amount of nitrogen in the soil. In addition, we found that fire management decreased the genetic potential of the soil microbial community to produce nitrogen oxides-potent contributors to climate change. Thus, prescribed fire's contribution to greenhouse gas emissions may involve a complex relationship between direct fire-driven emissions, increased fire resilience of promoted vegetation, and-as suggested by our results-the reduced ability of soil microbes to produce greenhouse gases.},
}

@article {pmid42765877,
year = {2026},
author = {Bonanno, S and Sheta, R and Ramu, T and Verenkar, S and Kim, D and Bessette, E and Pierre, P and Joshi, NS},
title = {Modulating innate immune responses to curli fibers through protein engineering.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0039426},
doi = {10.1128/iai.00394-26},
pmid = {42765877},
issn = {1098-5522},
abstract = {Curli fibers produced by Escherichia coli are functional amyloids that activate Toll-like receptor 2 (TLR2), initiating innate immune responses at mucosal surfaces. While microbiome-derived curli contribute to host-microbe interactions, their intrinsic immunostimulatory activity limits their utility as programmable scaffolds for engineered probiotic systems, and dysregulated TLR2 activation has been associated with inflammatory bowel disease, systemic lupus erythematosus, neurodegeneration, and sepsis. Here, we engineered E. coli Nissle 1917 to produce modified curli fibers designed to reduce TLR2 signaling through two mechanistically distinct strategies: steric shielding via silk-elastin-like protein sequences and direct receptor antagonism via a known TLR2 antagonist, staphylococcal superantigen-like protein 3 (SSL3). Both engineered variants assembled into structurally intact amyloid fibers and exhibited significantly reduced intrinsic TLR2-dependent NF-κB activation in reporter cells. In competitive inhibition assays against structurally diverse TLR2 agonists, the SSL3 fusion achieved near-complete attenuation of TLR2-dependent signaling, maintained under rising agonist load, while steric shielding provided moderate, agonist class-dependent inhibition. In primary human monocyte-derived dendritic cells, the SSL3 fusion robustly attenuated IL-8 secretion and transcriptional induction of IL-8, IL-6, and IL-1β, whereas steric shielding produced only partial attenuation that did not translate to broad inflammatory suppression. These results establish engineered curli as a tunable platform for receptor-specific modulation of innate immune signaling and highlight the broader potential of modular microbial amyloids as programmable interfaces for engineering host-microbe interactions at mucosal surfaces.},
}

@article {pmid42765916,
year = {2026},
author = {Wang, G and Liu, X and Wang, Z and Tian, H and Li, Y and Luo, Y},
title = {Exploring Cervical Cancer-Associated Vaginal and Cervical Microbiota via 16S rRNA Sequencing.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70412},
doi = {10.1002/mbo3.70412},
pmid = {42765916},
issn = {2045-8827},
support = {320.6750.2021-25-5//Wu Jieping Medical Foundation Special Funding for Clinical Research/ ; },
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Middle Aged ; *Vagina/microbiology ; *Cervix Uteri/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Sequence Analysis, DNA ; DNA, Bacterial/genetics/chemistry ; Aged ; China ; DNA, Ribosomal/genetics/chemistry ; Phylogeny ; Lactobacillus/genetics/isolation & purification ; Prevotella/genetics/isolation & purification ; Computational Biology ; },
abstract = {Although the etiology of cervical cancer has been partially established, its pathogenesis remains a key research focus. Specific studies on the genital tract microbiota of cervical cancer patients in Southern China are still scarce. To address this research gap, the present study collected genital tract microbial samples from 16 cervical cancer patients and 16 healthy women. Analysis of cervical cancer-specific microbiota was conducted via 16S rRNA gene sequencing. The study included 32 women (16 cervical cancer patients and 16 healthy controls) aged 45-65 at enrollment. Total genome DNA from samples was extracted using the hexadecyltrimethylammonium bromide (CTAB) CTAB method. The vaginal and cervical microbiota composition was determined by sequencing barcoded 16S rDNA gene fragments (V3-V4), and a comparative bioinformatics analysis of the microbiome was performed. The study revealed a homogeneous microbial composition dominated by Lactobacillus in healthy women, whereas cervical cancer patients exhibited increased diversity with reduced Lactobacillus and enriched Prevotella. No significant differences were observed between sampling sites within each group. Functional predictions linked the cancer-associated microbiota to metabolic pathways and the AEROBACTIN-SYN-PWY pathway. In conclusion, our findings suggest that these specific key microbial taxa and their related metabolic pathways contribute to the pathogenesis of cervical cancer and may serve as promising targets for clinical treatment and intervention.},
}

Humans
Female
*Uterine Cervical Neoplasms/microbiology
*RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
Middle Aged
*Vagina/microbiology
*Cervix Uteri/microbiology
*Bacteria/classification/genetics/isolation & purification
Sequence Analysis, DNA
DNA, Bacterial/genetics/chemistry
Aged
China
DNA, Ribosomal/genetics/chemistry
Phylogeny
Lactobacillus/genetics/isolation & purification
Prevotella/genetics/isolation & purification
Computational Biology

@article {pmid42765918,
year = {2026},
author = {Gregory, CL and Radja, K and Haak, DC and Bradford, EL and Fell, RD and Walke, JB and Belden, LK},
title = {A metagenomic survey reveals widespread antibiotic resistance genes in honey bee (Apis mellifera) gut bacteria across the United States.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0075526},
doi = {10.1128/aem.00755-26},
pmid = {42765918},
issn = {1098-5336},
abstract = {Antibiotic use has contributed to antibiotic resistance genes (ARGs) accumulating in many environments, including host-associated microbiomes. Managed honey bee gut bacteria may accumulate ARGs, as honey bees are sometimes treated with antibiotics and often live in agricultural landscapes contaminated with antibiotics. We describe the occurrence and distribution of ARGs in honey bee bacterial gut symbionts from 13 apiaries in a transect across the USA from Washington to Virginia. Using metagenomic sequencing, we detected 55 unique ARGs conferring resistance to 14 classes of antibiotics. Of these, 11 ARGs encoded multidrug resistance. ARGs varied among sites, and ARG composition in hives shifted across the transect. Among honey bee gut bacterial genera, ARG occurrence varied, with Gilliamella and Frischella containing the highest proportions of ARGs despite their low relative abundance in the gut community, suggesting specific genera may serve as ARG reservoirs. As tetracycline is the most used antibiotic in beekeeping, we compared the frequency and abundance of tetracycline resistance genes across apiaries. All hives contained tetracycline resistance genes, with tetB and tetM present at all apiaries. Based on qPCR, tetB and tetM abundance varied significantly among apiaries. TetB was higher overall and declined in abundance from Washington to Virginia. We demonstrate that honey bee gut bacteria possess a diversity of ARGs, not all of which are consistent with antibiotic use in beekeeping, ARG frequency varies among bacterial genera in the honey bee gut, and certain ARGs are associated with hive geographic location.IMPORTANCEThe spread of antibiotic resistance genes (ARGs) to bacterial pathogens is a critical issue facing global health. Gut bacterial symbionts of managed honey bees make good bioindicators for ARGs because honey bees interact with potential environmental reservoirs of ARGs and are broadly distributed across the USA, including in both urban and rural environments. Based on our transect across the USA, ARGs were diverse and widely distributed among honey bee gut symbionts, although certain bacterial genera had a higher propensity for accumulating ARGs. Tetracycline resistance genes were most common, and varied in occurrence and abundance across the transect. The abundance of tetB, in particular, increased from east to west along the sampled transect. These large-scale patterns of ARG distribution within a widely dispersed host-associated microbiome system provide a foundation from which to examine the underlying factors driving differences in ARG occurrence and abundance.},
}

@article {pmid42766112,
year = {2026},
author = {Shang, J and Li, L and Dong, C and Wei, Y},
title = {Bacteriophage-bacteria coevolution: from molecular arms races to ecological and applied perspectives.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42766112},
issn = {1432-072X},
mesh = {*Bacteriophages/genetics/physiology ; *Bacteria/virology/genetics ; *Biological Coevolution ; Gene Transfer, Horizontal ; Host-Pathogen Interactions ; CRISPR-Cas Systems ; *Biological Evolution ; Evolution, Molecular ; },
abstract = {Bacteriophages are the most abundant biological entities, driving bacterial evolution through long-term coevolution. Bacteria have evolved diverse defense strategies against phage, including receptor modification, restriction-modification systems, CRISPR-Cas, abortive infection systems, and newly discovered systems such as BREX, DISARM, CBASS, Thoeris, and Zorya. In response, phages deploy countermeasures such as receptor-binding diversification, anti-CRISPR proteins, DNA modification, and inhibitors targeting host immunity. These interactions generate distinct evolutionary dynamics-arms race and fluctuating selection-shaping microbial population structure and ecological stability. Phage-host coevolution promotes microbial diversity, horizontal gene transfer, and regulates community composition across ecosystems. Understanding these processes is critical for applications like phage therapy, microbiome engineering, and biotechnology. This review summarizes molecular mechanisms of bacterial defense and phage counter-defense, discusses coevolutionary models, highlights ecological and applied implications, and outlines future research directions.},
}

*Bacteriophages/genetics/physiology
*Bacteria/virology/genetics
*Biological Coevolution
Gene Transfer, Horizontal
Host-Pathogen Interactions
CRISPR-Cas Systems
*Biological Evolution
Evolution, Molecular

@article {pmid42766174,
year = {2026},
author = {Palanisamy, M and Thalavaipandian, L and Selvaraj, D and Rajamani, K and Babalola, OO and Ramalingam, S},
title = {Unlocking the hidden potential of the genus Salvia through a systematic review of endophytic bacterial and fungal diversity and biotechnological prospects.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42766174},
issn = {1432-072X},
support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; },
mesh = {*Endophytes/classification/genetics/physiology/metabolism/isolation & purification ; *Salvia/microbiology/chemistry/growth & development ; Biotechnology ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Fungi/classification/genetics/isolation & purification/metabolism ; Biodiversity ; },
abstract = {The genus Salvia is one of the largest and the most pharmacologically important genera within the family Lamiaceae, which is known for its rich diversity of bioactive compounds, including phenolics and terpenoids. Recent studies have shown that endophytic fungi and bacteria associated with Salvia play important roles in plant growth, development, and chemical composition, which in turn contribute to species adaptability. This review presents a comprehensive, PRISMA-guided systematic review that emphasises the diversity and biotechnological potential of these endophytes. Available evidence indicates that although Salvia-associated endophytes have been widely studied, most research has focused on a single species, namely Salvia miltiorrhiza, with comparatively limited attention to other species and their associated endophytic communities. This review compiles comprehensive, current knowledge on endophyte diversity, tissue-specific distribution, and ecological roles, along with their biotechnological applications related to plant growth promotion, stress tolerance, biocontrol activity, and the production of bioactive compounds. It also highlights the role of endophytes in enhancing host secondary metabolite accumulation, with appropriate citations. Despite significant advances, gaps remain in understanding endophyte diversity across different Salvia species and in linking microbial functions to host-associated metabolic outcomes. This review identifies key knowledge gaps and outlines future directions to advance our understanding of plant-endophyte interactions and to support their effective application in sustainable agriculture and biotechnology.},
}

*Endophytes/classification/genetics/physiology/metabolism/isolation & purification
*Salvia/microbiology/chemistry/growth & development
Biotechnology
*Bacteria/classification/isolation & purification/genetics/metabolism
*Fungi/classification/genetics/isolation & purification/metabolism
Biodiversity

@article {pmid42766561,
year = {2026},
author = {Chen, X and Lei, M and Tang, J and Wang, H and Chen, J and Liu, Y and Li, S and Liu, F and Wang, Y and Li, Z and Dai, Z},
title = {Efficacy, safety, and feasibility of youth-derived fecal microbiota transplantation among adults with type 1 diabetes mellitus: A protocol of Pilot Randomized Controlled Trial.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0343078},
doi = {10.1371/journal.pone.0343078},
pmid = {42766561},
issn = {1932-6203},
mesh = {Humans ; *Diabetes Mellitus, Type 1/therapy/microbiology ; *Fecal Microbiota Transplantation/methods/adverse effects ; Pilot Projects ; Adult ; Double-Blind Method ; Female ; Glycated Hemoglobin/metabolism/analysis ; Male ; Feasibility Studies ; Young Adult ; Randomized Controlled Trials as Topic ; Treatment Outcome ; Blood Glucose ; Adolescent ; Continuous Glucose Monitoring ; Gastrointestinal Microbiome ; Insulin/therapeutic use ; },
abstract = {BACKGROUND: Dysbiosis of gut microbiota plays a key role in type 1 diabetes mellitus (T1DM). Fecal microbiota transplantation represents a novel therapeutic avenue. We hypothesize that youth-derived fecal microbiota transplantation (yFMT) can remodel the gut microecosystem and improve clinical outcomes. This pilot trial aims to assess the feasibility, safety, and preliminary efficacy of yFMT in adults with T1DM.

METHODS AND ANALYSIS: This single-center, randomized, double-blind, placebo-controlled pilot study will enroll adults with T1DM who have suboptimal glycemic outcomes (glycated hemoglobin [HbA1c] of 7.0-14.0% or time in range [TIR] <70%). Following a 17-day run-in period for insulin optimization, continuous glucose monitoring (CGM) wearing, baseline assessments and bowel preparation, participants will be randomly allocated (1:1) to take yFMT or placebo capsules for 6 consecutive days, alongside their standard insulin therapy, and then complete a 12-week follow-up. The primary efficacy endpoint is the change from baseline in the rate of achieving the composite target of TIR > 70% and time below range <4% at 12 weeks post-randomization. Secondary efficacy endpoints include: (1) the change from baseline in the same composite achievement rate at 4 weeks post-intervention; (2) changes from baseline at Weeks 4 and 12 in other glycemic metrics (including HbA1c, fasting plasma glucose, 2-hour postprandial glucose, and additional CGM metrics), C-peptide, immune responses, infection markers, and gut microbiota composition; and (3) changes from baseline at Week 12 in serum metabolomic profiles (bile acids, short-chain fatty acids, and other related metabolites). Feasibility will be assessed through recruitment rate, retention rate, intervention adherence, and acceptability. Safety endpoints include the incidence of adverse events and serious adverse events.

DISCUSSION: Our findings will offer new insight into the feasibility and effects of oral yFMT capsules in adults with T1DM and provide the necessary evidence to power a subsequent multicenter large-scale study. Exploratory biomarker analyses conducted within this study may further pave the way for future individualized microbiome‑based therapeutics.

TRIAL REGISTRATION: Chinese Clinical Trial Registry identifier: ChiCTR2500111955 (November 7, 2025).},
}

Humans
*Diabetes Mellitus, Type 1/therapy/microbiology
*Fecal Microbiota Transplantation/methods/adverse effects
Pilot Projects
Adult
Double-Blind Method
Female
Glycated Hemoglobin/metabolism/analysis
Male
Feasibility Studies
Young Adult
Randomized Controlled Trials as Topic
Treatment Outcome
Blood Glucose
Adolescent
Continuous Glucose Monitoring
Gastrointestinal Microbiome
Insulin/therapeutic use

@article {pmid42761475,
year = {2026},
author = {Yu, Q and Zheng, Y and Li, Y and Li, S and Wu, W and Lan, L and Mao, J and Fang, K and Chen, Z and Gao, YD},
title = {Supragingival plaque microbiome features in allergic rhinitis and allergic asthma and their association with dental caries: a cross-sectional study.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2732753},
pmid = {42761475},
issn = {2000-2297},
abstract = {BACKGROUND: Allergic rhinitis (AR) and allergic asthma (AS) are associated with increased risk of dental caries, potentially associated with alterations in the oral microbiome.

OBJECTIVE: To characterize supragingival plaque microbiome features and their associations with caries severity in allergic adults.

DESIGN: This cross-sectional study enrolled patients with cat dander-induced AR or AS, along with age- and sex-comparable normal controls (NC). Supragingival plaque was collected for 16S rRNA gene sequencing. Microbial diversity, ANCOM-BC2 with multiple-testing correction and pseudo-count sensitivity analysis and LEfSe exploratory analysis were performed. Factors of caries severity (DMFT/DMFS) were examined with a random forest model and multivariable negative binomial regression.

RESULTS: A total of 89 participants (32 AR, 46 AS and 11 NC) were included. Allergic patients exhibited significantly higher α-diversity than NC. ANCOM-BC2 analysis identified 24 taxa with an omnibus FDR threshold; a family-resolved, genus-unclassified Prevotellaceae passed the pseudo-count sensitivity analysis. LEfSe analysis identified Treponema and Bacteroidota as AR-enriched taxa, and Actinobacteriota as AS-enriched taxa. Treponema was the top-ranked random forest feature. Among allergic patients, regular dental check-ups were associated with lower DMFT (IRR = 0.47, 95% CI: 0.30-0.75) and DMFS (IRR = 0.34, 95% CI: 0.17-0.69). Corynebacterium abundance was inversely associated with DMFT (IRR = 0.56, 95% CI: 0.31-0.98), and Actinomyces abundance was positively associated with DMFS (IRR = 2.96, 95% CI: 1.07-8.19).

CONCLUSIONS: Plaque microbial communities differed across groups, and selected taxa were associated with caries severity among allergic adults. Future investigations are needed to evaluate temporality and mechanisms.},
}

@article {pmid42761666,
year = {2026},
author = {Berggren, A and Farrell, M and Sun, L and Neilands, J},
title = {Orally ingested Lactobacillus crispatus VPC177 enhances total vaginal Lactobacillus counts-a cross-over exploratory study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1894758},
pmid = {42761666},
issn = {1664-302X},
abstract = {INTRODUCTION: The vaginal microbiome plays a crucial role in vaginal health, and disturbances in the microbial balance can negatively affect female wellbeing. In recent years, there has been growing interest in the use of probiotics and prebiotics to support a healthy vaginal microbiota. However, effects are often strain-specific and should be clinically demonstrated to influence the vaginal microbiota. This study aimed at evaluating the ability of four different orally administered probiotic strains to affect the fecal, and more specifically, the vaginal microbiota in healthy women.

METHODS: In this open-label, cross-over, exploratory study 35 women age 20-63 years consumed four different strains, Lactobacillus crispatus VPC111, Lactobacillus gasseri VPG44, L. crispatus VPC177 and Lactiplantibacillus plantarum HEAL9[®] for 14 days each with a washout period of 14 days between each intervention period. Levels of lactobacilli were assessed in fecal and vaginal samples following each intervention period.

RESULTS: VPC111, VPC177, and HEAL9 all resulted in significant increases in fecal lactobacilli after 14 days intervention compared to baseline (p < 0.05). VPC177 significantly increased vaginal lactobacilli (p = 0.001), whereas VPC111, VPG44, and HEAL9 showed no significant vaginal effects. Post hoc characterization of L. crispatus VPC177 demonstrated that it produces both D- and L-lactate at high levels (9.31 and 4.58 g/L, respectively) and possesses genes associated with bacteriocin production, glycogen utilization, and mucosal adhesion, supporting its potential for antimicrobial activity, carbohydrate metabolism, and colonization of the vaginal environment.

DISCUSSION: These findings demonstrate that probiotic effects on the vaginal microbiota are strain-specific, and that an increase in fecal lactobacilli does not necessarily translate into corresponding changes in the vaginal microbial community. Among the strains evaluated, VPC177 was the most promising candidate for supporting vaginal health through oral probiotic administration.},
}

@article {pmid42761778,
year = {2026},
author = {Cheney, C and Page, E and Yeung, D and White, D},
title = {Clinical evidence and biological mechanisms linking obesity to adverse outcomes in pediatric and adolescent acute lymphoblastic leukemia.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1918955},
pmid = {42761778},
issn = {2234-943X},
abstract = {This review critically evaluated the relationship between obesity and survival outcomes in Acute Lymphoblastic Leukemia (ALL), highlighting key evidence gaps and exploring the biological mechanisms that may contribute to this association. In patients with ALL, obesity is consistently associated with a higher incidence of severe treatment-related toxicities, increased frequency of therapy delays, and reduced event-free survival. This connection is most pronounced in pediatric and adolescent ALL populations, whereas evidence supporting a similar effect in adults remains limited. Proposed biological mechanisms underlying these adverse outcomes include increased bone marrow adiposity, chronic low-grade inflammation, dysregulated insulin signaling and obesity-associated alterations in the gut microbiome. The current body of evidence identifies obesity as a clinically significant risk factor that defines a vulnerable subgroup of ALL patients, supporting the need for enhanced toxicity surveillance, individualized treatment strategies, and optimized supportive care interventions. Elucidation of the biological pathways linking obesity to adverse ALL outcomes may also inform the development of novel therapeutic approaches aimed at mitigating obesity-driven morbidity and mortality in this high-risk population.},
}

@article {pmid42761784,
year = {2026},
author = {Yu, M and Wu, Y and Wang, A and Wang, M and Chen, Y and Ren, H and Zhang, Y and Liu, Y and Wang, S and Fan, X},
title = {Chronic low-grade inflammation drives skeletal aging and neurocognitive decline: inflammaging as a central hub coupling bone-brain aging.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1874465},
pmid = {42761784},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Aging/immunology ; *Inflammation/immunology/metabolism ; *Brain/immunology/metabolism/pathology ; *Cognitive Dysfunction/immunology/metabolism ; *Bone and Bones/metabolism/immunology ; cGAS-STING Signaling Pathway ; Senescence-Associated Secretory Phenotype ; Inflammasomes/metabolism ; },
abstract = {BACKGROUND: Global population aging has driven a marked rise in the co-prevalence of osteoporosis and cognitive impairment, and a bidirectional epidemiological association between the two conditions is now supported by multiple meta-analyses. The shared biological mechanisms underlying this comorbidity, however, remain incompletely defined, and the two disorders continue to be managed within largely separate clinical disciplines.

AIM AND SCOPE: This review consolidates existing evidence into an integrative immunopathological framework in which inflammaging-the chronic, low-grade, sterile systemic inflammatory state driven by senescent cells and their senescence-associated secretory phenotype (SASP)-is examined as a shared upstream driver that concurrently reconfigures skeletal remodeling and central neuroimmune dynamics through the bone-brain axis. We do not claim to identify novel molecular targets; rather, we synthesize an integrative perspective that has been treated in disciplinary silos.

KEY MECHANISTIC THEMES: At the molecular level, persistently elevated SASP-derived cytokines (IL-6, IL-1β, TNF-α) engage RANKL-dependent osteoclastogenesis in bone and prime microglial neuroinflammation in the central nervous system. Chronic NF-κB signaling and NLRP3 inflammasome activation, amplified in preclinical models by mitochondrial DNA release via the cGAS-STING axis, sustain this dual pathological output. Within the bone-brain axis, bone-derived endocrine signaling is remodeled during aging: osteocalcin (OCN) secretion declines, while osteocyte-derived sclerostin (SOST) rises and may antagonize Wnt/β-catenin signaling in both compartments. Blood-brain barrier disruption and peripheral immune-cell infiltration further amplify central neuroinflammation.

BALANCED APPRAISAL: We explicitly distinguish (i) conceptual hypotheses, (ii) preclinical (cellular and rodent) findings, and (iii) validated human data. Several widely cited mechanisms-including OCN-GPR158-mediated neuroprotection, cGAS-STING-driven neuroinflammation, and microbiome-based longevity signatures-rest predominantly on murine models or single cohorts and require independent human validation. Microglial responses in the aging brain reflect a heterogeneous state space rather than a uniform pro-inflammatory conversion.

THERAPEUTIC IMPLICATIONS: Candidate bone-brain dual-targeting interventions-senolytics (dasatinib plus quercetin), NLRP3 inhibitors, cGAS-STING blockade, GLP-1 receptor agonists, and microbiota-targeted strategies-are discussed with explicit reference to current evidence level, safety concerns, and translational limitations, rather than as established co-therapies. Dual-endpoint randomized trials enriched for elevated inflammaging biomarkers are needed before any of these agents can be positioned for clinical use in bone-brain comorbidity.

CONCLUSION: The inflammaging-centered framework advanced here provides a testable integrative pathophysiological perspective on bone-brain aging comorbidity and a rationale for interdisciplinary "bone-brain integrated" clinical evaluation in older adults, which we frame as an aspirational, hypothesis-generating model rather than an evidence-based standard of care.},
}

Humans
Animals
*Aging/immunology
*Inflammation/immunology/metabolism
*Brain/immunology/metabolism/pathology
*Cognitive Dysfunction/immunology/metabolism
*Bone and Bones/metabolism/immunology
cGAS-STING Signaling Pathway
Senescence-Associated Secretory Phenotype
Inflammasomes/metabolism

@article {pmid42761811,
year = {2026},
author = {Le, Q},
title = {Restructuring the gut microbiota in obesity: molecular mechanisms linking dysbiosis to systemic inflammation and therapeutic opportunities.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1902756},
pmid = {42761811},
issn = {1664-042X},
abstract = {Obesity is characterized by a chronic low-grade inflammatory state that contributes to insulin resistance, type 2 diabetes, and metabolic syndrome. The gut microbiota has emerged as a critical mediator of this inflammatory process through multiple interconnected mechanisms including metabolic endotoxemia, short-chain fatty acid dysregulation, and intestinal barrier dysfunction. This review synthesizes current evidence on the structural and functional alterations of the gut microbiome in obesity, examines the mechanistic pathways linking dysbiosis to systemic inflammation, and critically evaluates therapeutic strategies aimed at restructuring the obese gut microbial community. We focus on three major intervention approaches: fecal microbiota transplantation, probiotic and prebiotic supplementation, and next-generation targeted microbial therapies. Analysis of clinical and preclinical studies reveals that successful microbial restructuring requires not only compositional shifts but also functional restoration of microbial metabolite production, particularly short-chain fatty acids. The evidence supports a model wherein obesity-associated dysbiosis perpetuates chronic inflammation through increased lipopolysaccharide translocation, reduced butyrate production, and compromised intestinal barrier integrity. Restoring microbial eubiosis through targeted interventions offers a promising avenue for resolving chronic low-grade inflammation and improving metabolic health outcomes in obese individuals.},
}

@article {pmid42758536,
year = {2026},
author = {Gracia Alvira, JB and Migotti, S and Tian, X and Nolte, V and Schlötterer, C},
title = {Environmental temperature is a strong driver of subspecies competition in the Drosophila microbiome.},
journal = {eLife},
volume = {15},
number = {},
pages = {},
pmid = {42758536},
issn = {2050-084X},
support = {10.55776/W1225//Austrian Science Fund/ ; 10.55776/PAT7786824//Austrian Science Fund/ ; 10.55776/F91//Austrian Science Fund/ ; Achadapt/ERC_/European Research Council/International ; },
mesh = {Animals ; *Microbiota ; *Temperature ; *Drosophila/microbiology ; *Drosophila simulans/microbiology ; Symbiosis ; },
abstract = {Most microbiome research focuses on the taxonomic composition at the species level to understand the impact of environmental factors, but intraspecific diversity has largely been ignored. To address this significant knowledge gap, we took advantage of the simple, culturable microbiome of Drosophila. First, we documented that natural populations of D. simulans harbor three diverged clades of Lactiplantibacillus plantarum, a key nutritional symbiont. We studied the distinct ecological roles of these three clades by exposing flies with their native microbiome to two temperature regimes in the laboratory. Tracking the three clades within the complete Drosophila microbiome over a period of more than 10 years at two temperatures, we identified strikingly distinct dynamics in response to the selection regime. We confirmed the functional differentiation of the three clades using in vitro growth measurements and in vivo mono-association assays. Our results highlight that environmental selection operates at the subspecies level. Therefore, we conclude that the functional diversification of the microbiome can only be understood when intra- and interspecific diversity is considered.},
}

Animals
*Microbiota
*Temperature
*Drosophila/microbiology
*Drosophila simulans/microbiology
Symbiosis

@article {pmid42758655,
year = {2026},
author = {Ball, RAW and Mohammed, AD and Jolly, A and Johnson, K and Sklenicka, S and Kucherina, M and Peacock, T and Liu, E and Hogan, KM and Baird, M and Peña, MMO and Nagarkatti, P and Nagarkatti, M and Kubinak, JL},
title = {IgA deficiency reveals a microbiota-dependent pathway to gluten sensitivity.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2724175},
doi = {10.1080/19490976.2026.2724175},
pmid = {42758655},
issn = {1949-0984},
mesh = {Animals ; *Glutens/adverse effects/immunology ; Mice ; Mice, Knockout ; *IgA Deficiency/microbiology/immunology ; *Gastrointestinal Microbiome ; Immunoglobulin A/genetics ; Intestinal Mucosa/pathology/immunology/microbiology ; Mice, Inbred C57BL ; Intestine, Small/pathology/immunology/microbiology ; Th17 Cells/immunology ; Diet, Gluten-Free ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Celiac Disease/microbiology/immunology ; Ileum/pathology/immunology/microbiology ; },
abstract = {Selective IgA deficiency (sIgAD) is the most common primary immunodeficiency and increases susceptibility to gluten-related enteropathies, but the underlying mechanisms of pathogenesis are unknown. Utilizing IgA[-/-] mice and wild-type controls, we investigated how dietary gluten shapes susceptibility to small intestinal inflammation. We found that IgA[-/-] mice developed gluten-induced villus blunting in the ileum and enhanced Th17 responses. Exposure to a gluten-free diet prevented villus blunting in IgA[-/-] mice. Dietary gluten promoted the expansion of Streptococcus and Desulfovibrio species, depletion of members of the order Lactobacillales, and shifts in microbial metabolic pathways related to lipid metabolism. Next, to determine if gluten sensitivity is microbiota-dependent, germ-free colonization experiments were performed using complete microbiota transfers or mono-colonization with a single Streptococcus species (Streptococcus lutetiensis), both of which were sufficient to recapitulate gluten-sensitive enteropathy. Our findings demonstrate that dietary gluten promotes small intestinal inflammation and mucosal remodeling in IgA-deficient mice through microbiota-dependent mechanisms. This work highlights a key role for sIgA in maintaining immune homeostasis at the diet-microbiota interface and reveals a novel microbial pathway underlying gluten sensitivity.},
}

Animals
*Glutens/adverse effects/immunology
Mice
Mice, Knockout
*IgA Deficiency/microbiology/immunology
*Gastrointestinal Microbiome
Immunoglobulin A/genetics
Intestinal Mucosa/pathology/immunology/microbiology
Mice, Inbred C57BL
Intestine, Small/pathology/immunology/microbiology
Th17 Cells/immunology
Diet, Gluten-Free
Bacteria/classification/genetics/isolation & purification/metabolism
*Celiac Disease/microbiology/immunology
Ileum/pathology/immunology/microbiology

@article {pmid42758711,
year = {2026},
author = {Emfietzoglou, M and Bantounou, MA and Osmani, S and Narimatsu, T and Baroutis, KG and Varsamidaki, A and Skondra, D and Papaconstantinou, D and Theodossiadis, P and Chatziralli, I and Miller, JW and Vavvas, DG},
title = {Shotgun metagenomic profiling of the fecal microbiome in Lamp2 knockout mice reveals limited genotype-associated differences under standard housing.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0357009},
doi = {10.1371/journal.pone.0357009},
pmid = {42758711},
issn = {1932-6203},
mesh = {Animals ; *Feces/microbiology ; Mice ; Male ; Mice, Knockout ; *Metagenomics/methods ; *Lysosomal-Associated Membrane Protein 2/genetics ; Genotype ; *Gastrointestinal Microbiome/genetics ; Shotgun Sequencing ; Metagenome ; },
abstract = {BACKGROUND: Lysosomal pathways influence host-microbe interactions, but the microbiome consequences of lysosomal dysfunction remain incompletely defined. LAMP2 is required for autophagosome-lysosome fusion, and pathogenic variants in LAMP2 cause Danon disease. Whether Lamp2 loss alters the gut microbiome in vivo has not been systematically evaluated using methods that profile both taxonomic composition and microbial functional potential, such as shotgun metagenomics.

METHODS: We performed shotgun metagenomic sequencing on 50 fecal samples from male Lamp2 knockout (Lamp2KO) mice and wild-type (WT) littermates sampled at 3, 6, 9, and 12 months under single-genotype cages or mixed-genotype cohousing. Two low-depth libraries (<3 × 105 classified genus-level reads) were excluded from primary inference (primary set: n = 48). We analyzed genus-level alpha diversity, beta diversity, and differential abundance using compositional, cage-aware mixed-effects models and cage-blocked permutation testing. We analyzed functional pathway profiles using copies-per-million abundances with centered-log-ratio transformation and mixed-effects modeling. We controlled multiple testing using the Benjamini-Hochberg false discovery rate.

RESULTS: In the primary set (48 samples from 27 cages), Lamp2KO and WT mice showed similar genus-level alpha diversity and overall community composition (PERMANOVA using Aitchison and Bray-Curtis distances). Primary mixed-effects models detected no genera with differential abundance after false discovery rate correction. Taxonomic profiles were broadly similar between genotypes and were dominated by Bacteroidota and Bacillota. Exploratory within-cage (paired) analyses identified consistent directional differences in a small set of genera, but these signals were not supported by the primary mixed-effects models. Functional pathway profiles were similar between genotypes; one pathway (dTDP-β-L-rhamnose biosynthesis) showed an exploratory association (FDR q < 0.10) within the 50 most abundant pathways.

CONCLUSIONS: In this controlled mouse cohort, we did not detect robust, cage-independent shifts in fecal microbiome composition or inferred functional pathway profiles associated with Lamp2 deficiency under standard SPF husbandry and chow; given the sample size, smaller or compartment-specific effects cannot be excluded.},
}

Animals
*Feces/microbiology
Mice
Male
Mice, Knockout
*Metagenomics/methods
*Lysosomal-Associated Membrane Protein 2/genetics
Genotype
*Gastrointestinal Microbiome/genetics
Shotgun Sequencing
Metagenome

@article {pmid42758728,
year = {2026},
author = {Imrich, CN and Backman, LRF and Allworth, AP and Andorfer, MC and Paris, JC and Greeley, NM and Fu, B and Balskus, EP and Drennan, CL},
title = {The structural basis of malodorant skatole formation by the glycyl radical enzyme indoleacetate decarboxylase.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {38},
pages = {e2618341123},
doi = {10.1073/pnas.2618341123},
pmid = {42758728},
issn = {1091-6490},
support = {GM126982//HHS | NIH (NIH)/ ; T32ES007020//HHS | NIH (NIH)/ ; 1122374//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; 1144152//NSF | NSF Graduate Research Fellowship Program (GRFP)/ ; Gilliam//HHMI (HHMI)/ ; Gates Faculty Scholar Award (OPP1158186)//HHMI (HHMI)/ ; Waterman CHE-20380529//NSF (NSF)/ ; GM145910//HHS | NIH (NIH)/ ; Investigator//HHMI (HHMI)/ ; },
mesh = {*Carboxy-Lyases/metabolism/chemistry ; *Skatole/metabolism/chemistry ; Catalytic Domain ; Models, Molecular ; Cryoelectron Microscopy ; Decarboxylation ; *Bacterial Proteins/chemistry/metabolism ; },
abstract = {Glycyl radical enzymes (GREs) catalyze challenging chemical reactions using a posttranslationally installed glycyl radical cofactor. One such enzyme, indoleacetate decarboxylase (IAD), performs the radical-based decarboxylation of indole-3-acetate (I3A) to form the malodorant molecule skatole. In addition to being an odor nuisance, skatole is a human and livestock lung toxin, a suspected carcinogen, and a mosquito attractant, all of which impact human health, agriculture, food production, and wastewater treatment. Here, we use cryogenic electron microscopy to solve a 2.45-Å resolution structure of IAD from the gut bacterium Olsenella uli. We observe IAD in a homotetrameric form with the substrate I3A bound in all four protomers. The positioning of I3A in the active site is unexpected and is more consistent with a Kolbe-type decarboxylation mechanism, i.e., a decarboxylation initiated by a 1-electron oxidation of the carboxylate moiety rather than being initiated by hydrogen atom transfer (HAT). Previously, a high deuterium content in skatole from IAD assays in D2O was used to support a HAT mechanism over a Kolbe-type mechanism. However, we show here that deuterium content does not necessarily inform on mechanism as IAD can catalyze the exchange of skatole's 3'-methyl hydrogens postturnover. Structural comparisons show that both IAD and hydroxyphenylacetate decarboxylase display structural features that are not found in other characterized GREs, suggesting that they represent a distinct GRE-subclass. Collectively, these insights will inform IAD inhibitor design aimed at decreasing skatole production.},
}

*Carboxy-Lyases/metabolism/chemistry
*Skatole/metabolism/chemistry
Catalytic Domain
Models, Molecular
Cryoelectron Microscopy
Decarboxylation
*Bacterial Proteins/chemistry/metabolism

@article {pmid42758777,
year = {2026},
author = {Briard, M and Guillon, B and Venot, E and Grauso, M and Hennequet-Antier, C and Bruneau, A and Fenaille, F and Castelli, F and Thomas, M and Lezmi, G and Leite-de-Moraes, M and Adel-Patient, K and Saint-Criq, V},
title = {A microbiome-metabolome signature associated with pediatric severe asthma.},
journal = {PloS one},
volume = {21},
number = {9},
pages = {e0358560},
doi = {10.1371/journal.pone.0358560},
pmid = {42758777},
issn = {1932-6203},
mesh = {Humans ; *Asthma/microbiology/metabolism ; *Microbiota ; *Metabolome ; Female ; Child ; Male ; Bronchoalveolar Lavage Fluid/microbiology ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Severity of Illness Index ; Case-Control Studies ; Adolescent ; },
abstract = {BACKGROUND: Severe asthma is a heterogeneous condition encompassing multiple phenotypes. Understanding lung-specific mechanisms in children with severe asthma may enable the development of more precise therapeutic strategies. We previously reported that immune components in bronchoalveolar lavages (BALs) differentiate children with severe asthma from non-asthmatic disease-controls and, frequent from non-frequent exacerbators, among children with severe asthma.

OBJECTIVE: To identify a local signature of severe asthma using complementary multi-omics analyses of BALs. A secondary objective was to evaluate whether bacterial taxa and metabolites discriminate severe asthma subtypes associated with distinct phenotypes or endotypes.

METHODS: BAL microbiome and metabolome were investigated in 20 children with severe asthma and 10 non-asthmatic children using 16S rRNA gene amplicon sequencing and liquid chromatography coupled to high-resolution mass spectrometry (LC-HRMS), respectively. Data were analysed separately and through integrative multi-omics approaches.

RESULTS: Compared with controls, BALs from children with severe asthma showed increased alpha-diversity, higher relative abundances of Actinobacteriota, Streptococcus, Moraxella, Corynebacterium, Tropheryma, and Treponema, and an altered polyamine pathway characterized by reduced arginine and increased spermine and spermidine levels. Integrated analyses revealed significant associations between Streptococcus and both spermine and spermidine. Independently, each dataset discriminated severe asthma phenotypes, notably exacerbation frequency and co-occurring atopic dermatitis. Unsupervised clustering of microbiome profiles identified four distinct clusters that may reflect severe asthma endotypes.

CONCLUSIONS: This study identifies a distinct airway microbiome-metabolome signature associated with pediatric severe asthma. Enrichment of specific bacterial taxa, particularly Streptococcus, together with altered polyamine metabolic pathway, highlights microbial-metabolic interactions potentially involved in disease pathophysiology. The ability of microbiome and metabolome profiles to independently and jointly discriminate clinical phenotypes underscores the relevance of multi-omics approaches for diagnosis and follow-up of severe asthma. Our findings support the importance of airway-level profiling to improve mechanistic understanding of severe asthma and inform on future targeted therapeutic strategies.},
}

Humans
*Asthma/microbiology/metabolism
*Microbiota
*Metabolome
Female
Child
Male
Bronchoalveolar Lavage Fluid/microbiology
RNA, Ribosomal, 16S/genetics
Multiomics
Severity of Illness Index
Case-Control Studies
Adolescent

@article {pmid42759240,
year = {2026},
author = {Xu, J and Song, Y and Wu, W and Zhou, H and Wu, Y and Li, C},
title = {The impact of maternal gestational diabetes mellitus on the microbiome of offspring: A systematic review.},
journal = {Journal of reproductive immunology},
volume = {178},
number = {},
pages = {104965},
doi = {10.1016/j.jri.2026.104965},
pmid = {42759240},
issn = {1872-7603},
abstract = {Gestational diabetes mellitus (GDM) adversely affects maternal and offspring health, and the early-life microbiome is implicated in developmental programming. This systematic review quantitatively evaluated the association between maternal GDM and alterations in the gut and oral microbiomes of offspring. We systematically searched PubMed, Web of Science, and Embase (up to August 2025) for eligible studies adopting high-throughput sequencing techniques. Random-effects meta-analysis was performed for alpha diversity metrics, while findings on beta diversity and microbial taxonomy were summarized narratively. Twenty-one studies were included. The meta-analysis revealed no statistically significant differences in gut microbial alpha diversity between infants exposed to maternal GDM and unexposed controls. Beta diversity exhibited substantial inter‑study heterogeneity, with no consistent shifts observed. In infants born to mothers with GDM, several microbial taxa including Gammaproteobacteria, Enterobacteriaceae, Micrococcaceae, Propionibacteriaceae, Rikenellaceae, Megasphaera, Staphylococcus, Collinsella, Rothia, Pelomonas, Veillonella, Shewanellaceae and Prevotella tended to decrease in abundance, whereas Escherichia tended to increase. Notably, no microbial taxon presented consistent abundance changes in three or more studies, and these repeated findings were based on limited evidence. Delivery mode appeared to have minimal influence on offspring gut alpha diversity. Collectively, maternal GDM may not be strongly linked to shifts in offspring gut or oral microbial alpha diversity. However, the consistent dysregulation of specific microbial taxa in GDM-exposed offspring may exert potential impacts on offspring immune and metabolic development. Further longitudinal multicenter investigations are warranted to elucidate the causal relationships and long-term health implications of GDM-induced microbial alterations in children.},
}

@article {pmid42759465,
year = {2026},
author = {Yang, W and Zhu, X and Zhang, J and Chen, Y and Liu, S and Si, T and Zhang, L},
title = {Silicon nanoparticles and jasmonic acid synergistically enhance cadmium phytoextraction by Sedum alfredii via coordinated metal acquisition and stress tolerance.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143556},
doi = {10.1016/j.jhazmat.2026.143556},
pmid = {42759465},
issn = {1873-3336},
abstract = {Cadmium (Cd) phytoextraction requires efficient metal acquisition and translocation without compromising plant growth and detoxification. We investigated the effects of silicon nanoparticles (Si-NPs) and jasmonic acid (JA), applied alone or together, on Cd phytoextraction by Sedum alfredii. The combined treatment increased shoot biomass and total Cd accumulation by 32.6% and 67.4%, respectively. Si-NPs-containing treatments increased rhizosphere available Cd by 5.4-5.9%, promoted Cd uptake and root-to-shoot translocation, and induced Cd- and Si-transport-related genes. JA strengthened antioxidant enzyme activities. The combined treatment further increased phytochelatin and glutathione levels by 152% and 48.7%, respectively, while reducing malondialdehyde by 38.5%. These responses indicate enhanced thiol-mediated detoxification and oxidative protection. Metabolomic and microbiome analyses further revealed compartment-specific responses. The rhizosphere was associated with Cd-mobilization-related metabolites and enrichment of potentially beneficial genera, including Polycyclovorans and Ramlibacter. In contrast, leaves showed enhanced sulfur-thiol metabolism, redox regulation, and secondary metabolism. Multiblock integration linked Cd phytoavailability and accumulation with detoxification and biomass production. Overall, Si-NPs and JA exhibited asymmetric functional complementarity, integrating enhanced Cd acquisition and transport with thiol-centered detoxification and growth maintenance. This accumulation-compatible tolerance strategy provides a mechanistic framework for improving assisted Cd phytoextraction by coordinating Cd flux with whole-plant detoxification capacity.},
}

@article {pmid42759480,
year = {2026},
author = {Hu, F and Liu, X and Zhang, Y and Tan, S and Wang, J and Xia, M and Lu, F and Zhang, Q},
title = {Polylactic acid microplastics enhance copper bioavailability and host-microbiome toxicity during black soldier fly bioconversion of food waste: Mechanisms and multi-level impacts.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143654},
doi = {10.1016/j.jhazmat.2026.143654},
pmid = {42759480},
issn = {1873-3336},
abstract = {Biodegradable microplastics are increasingly entering food waste (FW) streams, yet their effects on heavy metal behavior during black soldier fly larvae (BSFL) bioconversion remain unclear. This study investigated the combined effects of polylactic acid microplastics (PLA-MPs, 1% w/w) and Cu (100-300 mg/kg ww) in a BSFL-based FW conversion system. The 100-200 mg/kg treatments represented upper-range Cu exposure scenarios relevant to Cu-rich food residues. PLA-MPs increased Cu accumulation in larvae by 14-32% and shifted Cu toward more bioactive fractions in larvae and frass, indicating enhanced Cu mobility and bioavailability. Co-exposure intensified oxidative and detoxification responses, depleted glutathione, increased lipid peroxidation, and altered energy metabolism. Transcriptomic analysis indicated activation of xenobiotic metabolism, glutathione-related detoxification, and immune-associated pathways. PLA-MPs and Cu also reshaped gut and frass microbial communities, increased community stochasticity, suppressed dissolved organic matter humification, and reduced substrate stabilization and bioconversion performance. Partial least squares path modeling further linked Cu activation and migration, host physiological stress, and microbial dysbiosis to reduced bioconversion efficiency. Overall, PLA-MPs enhanced Cu bioavailability and amplified multi-level toxicity during BSFL-mediated FW treatment, highlighting potential risks to the safe valorization of contaminated organic waste.},
}

@article {pmid42759613,
year = {2026},
author = {Klingler, AM and Vidyant, S and Pyakurel, S and Viel, KCMF and Good, A and Rochman, Y and Brusilovsky, M and Caldwell, JM and Rothenberg, ME and Azouz, NP},
title = {Loss of kallikrein 5 expression exacerbates allergic skin inflammation including impairing filaggrin processing, promoting Th2 differentiation and inducing dysbiosis.},
journal = {Mucosal immunology},
volume = {},
number = {},
pages = {100404},
doi = {10.1016/j.mucimm.2026.100404},
pmid = {42759613},
issn = {1935-3456},
abstract = {Atopic dermatitis (AD) is a chronic allergic skin disease with T helper 2 (Th2) cell predominance and epithelial barrier impairment. The serine protease kallikrein (KLK) 5 has an essential role in regulating keratinocyte desquamation and skin renewal. Increased expression and activity of KLK5 is sufficient to induce skin inflammatory responses including AD. We examined the consequences of Klk5 deficiency following exposures to the type 2-provoking agent calcipotriol in mice. Loss of KLK5 exacerbates a spectrum of AD-like responses including increased accumulation of skin eosinophils and langerhans cells, over-expression of an array of cytokines in the skin and exacerbated scratching behavior. Klk5[-/-] mice demonstrated microbiome dysbiosis with enriched actinobacteria and reduced firmicutes in the skin, alteration in skin metabolites involved in the acetyl-CoA pathway and decreased expression of mature filaggrin monomers. Cutaneous application of Cis-Urocanic acid (cUCA) attenuated inflammatory responses highlighting barrier dysfunction as primary mechanism. We reveal an unappreciated role for KLK5 in inhibiting type 2 responses, acting through its roles in filaggrin processing and modulation of the skin microbiome and metabolome. Though KLK5 overactivation is known to contribute to several inflammatory skin disorders, our findings demonstrate that complete loss of KLK5 is also pathogenic in AD-like responses in mice.},
}

@article {pmid42759845,
year = {2026},
author = {Glenn, E and Titus, C and Kasthuriarachchi, T and Burke, K and Chow, D and Lin, C and Liu, E and Zhang, H and Zhang, T and Li, Y},
title = {Maternal-offspring microbiome interface contributes to the impact of maternal use of central nervous system-active drugs on offspring neurodevelopment.},
journal = {Journal of pharmaceutical sciences},
volume = {},
number = {},
pages = {104509},
doi = {10.1016/j.xphs.2026.104509},
pmid = {42759845},
issn = {1520-6017},
abstract = {The prevalence of maternal central nervous system-active medication use has increased over the last two decades, raising questions regarding potential neurodevelopmental consequences for offspring. While most of these substances are known to cross the placenta and enter breast milk, their developmental impact remains unclear. This review synthesizes current evidence identifying the maternal-offspring microbiome interface as a possible conduit for neurodevelopmental programming. We examine how the maternal gut, placental, and breast milk microbiomes establish the foundation for the offspring's early microbial ecosystem, how drug-induced dysbiosis may disrupt these interactions, and how these may impact offspring neurodevelopment. However, isolating specific drug-induced microbial effects from the influence of underlying maternal psychiatric conditions and identifying specific microbial signatures that correlate with resilience or susceptibility in offspring remain a substantial challenge. Current literature relies heavily on preclinical models, highlighting an urgent need for longitudinal human studies to better inform risk-benefit analyses for maternal pharmacotherapy.},
}

@article {pmid42759892,
year = {2026},
author = {Halmi, MFA and Edinur, HA},
title = {Two decades of microbiome forensics: Bibliometric insights into publication trends, applications and methodological advancements.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107716},
doi = {10.1016/j.mimet.2026.107716},
pmid = {42759892},
issn = {1872-8359},
abstract = {Microbiome forensics focuses on complex microbial communities for use as unique identification methods for forensic inferences. They include individual identification, crime scene reconstruction, and estimation of post-mortem intervals. This study adopts a bibliometric approach to assess the global scientific output and knowledge structure of the microbiome forensics, applications and methodological advancement in microbiome forensics. A total of 220 documents spanning two decades (2005 to 2024) were retrieved from the Web of Science Core Collection using related keywords. Of the total number of scientific publications, 6306 citations were found, with an average of 28.66 citations per publication. The United States dominated this domain with the most publications, followed by China, Australia, England, and Germany. Although Michigan State University had the highest number of citations, but the works produced by the Centre National de la Recherche Scientifique in Paris, France, had the highest research impact. Research trend mapping of keyword co-occurrence revealed five major clusters of forensic microbiome research: i. post-mortem interval estimation, ii. human identification, iii. Body fluid identification, iv. geolocation and provenance, and v. computational methods. Subsequent analyses indicated that forensic microbiome research has evolved from the use of culture-based and polymerase chain reaction (PCR) amplification of 16S rRNA for microbial identification before 2017 to the application of next generation sequencing (NGS) coupled with machine learning and bioinformatics from 2018 onwards. The findings of this study may be used to strategically inform knowledge gaps and key areas for future investigations in this field. In addition, building partnerships between forensic societies is needed not only to effectively move the field forward through the development of standardised protocols and quality assurance but also in exchanging expertise with developing countries, where knowledge is urgently needed to resolve crime cases.},
}

@article {pmid42759909,
year = {2026},
author = {Hou, J and Li, Q and Li, Y and Liu, M and Xue, M and An, Y and Yao, Y and Xu, H},
title = {Intraspecific Rice Intercropping Reduces the Rhizosphere Resistome in Association with Organic Acid and low-ARG-burden Microbiota Enrichment.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129180},
doi = {10.1016/j.envpol.2026.129180},
pmid = {42759909},
issn = {1873-6424},
abstract = {Antibiotic resistance genes (ARGs) in agricultural soils are an emerging environmental concern. However, sustainable strategies for reducing ARG in crop rhizospheres remain limited. Here, we investigated associations among rhizosphere metabolites, microbial communities, and ARG profiles in an intraspecific rice intercropping system. Compared with monoculture, intraspecific intercropping reduced the relative abundances of total ARGs and ARGs assigned to the Ranks I and II. Intercropping also altered rhizosphere metabolite profiles, with increased organic acid abundance, and was associated with convergent changes in microbial community composition. Nitrospirales, particularly Candidatus Sulfobium, was enriched under intercropping. MAGs assigned to this lineage contained relatively few annotated ARGs, which were predominantly classified as ARGs assigned to the Rank IV. Exogenous supplementation reproduced this field-associated pattern: citric acid treatment reduced total ARG and ARGs assigned to the Ranks I and II abundance and concurrently increased the relative abundance of Candidatus Sulfobium. These results support an association among rhizosphere organic acids, low-ARG-burden taxa, and reduced ARG abundance. Collectively, these findings highlight intraspecific rice intercropping as a low-input, source-control approach for cleaner rice production and ARG-risk mitigation.},
}

@article {pmid42760068,
year = {2026},
author = {Toufiq, R and Shahid, A and Zahra, R and Lankapalli, AK and Oduwo, J and Owinoh, EO and Aftab, S and Hassan, B and Thomson, K and Walsh, TR and Sands, K},
title = {Cohort profile: Infant Gut Bacterial Study in Pakistan (INBUGS-P) longitudinal birth cohort.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e120775},
doi = {10.1136/bmjopen-2026-120775},
pmid = {42760068},
issn = {2044-6055},
mesh = {Humans ; Pakistan ; Female ; Infant ; Longitudinal Studies ; Infant, Newborn ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Male ; Breast Feeding/statistics & numerical data ; Anti-Bacterial Agents/therapeutic use ; Birth Cohort ; Adult ; Milk, Human/microbiology ; },
abstract = {PURPOSE: The Infant Gut Bacterial Study in Pakistan (INBUGS-P) was established to characterise the longitudinal development of the infant gut microbiome and resistome during the first year of life in a low- and middle-income country setting. The influence of early-life exposures, including mode of delivery, antibiotic use and infant feeding practices on gut bacterial diversity and antimicrobial resistance gene (ARG) profiles is being evaluated.

PARTICIPANTS: A total of 107 mother-infant pairs were recruited at the Pakistan Institute of Medical Sciences between December 2023 and June 2024. Follow-up was conducted at 10 predefined timepoints from birth to 12 months, during which 921 infant stool samples, 158 maternal rectal swabs, 246 breast milk samples and 2171 environmental swabs were collected. Sociodemographic, clinical, cultural and biological data were collected at enrolment and at each follow-up visit using Research Electronic Data Capture.

FINDINGS TO DATE: Baseline characteristics of 98/107 mother-infant dyads are included in the analysis. The cohort reflects an urban low-income population: median household income was PKR 30,000 per month (approximately US$170 per capita per month). Caesarean section accounted for 55% (54/98) of deliveries; 13.0% of infants were late preterm, and 10.0% had low birth weight (<2500 g). Breastfeeding was the predominant feeding mode though only 24 infants were exclusively breastfed from birth to 6 months. Antibiotics were prescribed to almost all mothers following delivery, and 19 infants received antibiotics during follow-up, most commonly amikacin combined with ceftazidime.

FUTURE PLAN: Shotgun metagenomic sequencing of infant stool samples is underway to enable species-level and plasmid-level profiling of microbial communities and ARGs. Subject to funding, hybrid long- and short-read sequencing and extended follow-up to 24 months are planned.},
}

Humans
Pakistan
Female
Infant
Longitudinal Studies
Infant, Newborn
*Gastrointestinal Microbiome/genetics
Feces/microbiology
Male
Breast Feeding/statistics & numerical data
Anti-Bacterial Agents/therapeutic use
Birth Cohort
Adult
Milk, Human/microbiology

@article {pmid42760112,
year = {2026},
author = {Dendooven, E and Genouw, E and Aerts, O},
title = {Smelly Pig Manure: A Hypothetical Explanation for Sodium Metabisulphite Contact Allergy Mimicking Atopic and Seborrheic Dermatitis.},
journal = {Contact dermatitis},
volume = {},
number = {},
pages = {},
doi = {10.1111/cod.70248},
pmid = {42760112},
issn = {1600-0536},
}

@article {pmid42760157,
year = {2026},
author = {Shin, HR and Kim, TY and Min, K and Park, UH and Oh, SW and Kim, JK},
title = {Epigenetic determinants of GLP-1 responsiveness: Integrating dietary modulation beyond genetics.},
journal = {Obesity research & clinical practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.orcp.2026.09.004},
pmid = {42760157},
issn = {1871-403X},
abstract = {Glucagon-like peptide-1 receptor (GLP-1R) agonists have become major therapeutic agents for obesity and type 2 diabetes, yet clinical responses vary substantially among individuals. Although genetic variation contributes to this heterogeneity, it does not fully explain differences in glycemic control, body weight reduction, or broader metabolic outcomes. This narrative review discusses diet-driven epigenetic regulation as a potential framework linking modifiable nutritional exposures to GLP-1 physiology and variability in GLP-1R agonist responsiveness. Endogenous GLP-1 biology and the pharmacological targeting of incretin signaling are first summarized, followed by genetic determinants of GLP-1 responsiveness and their limitations. Major diet-sensitive regulatory mechanisms are then examined, including one-carbon metabolism and DNA methylation, histone modification and chromatin remodeling, microbiome-derived metabolites, and RNA-mediated or epitranscriptomic regulation. These mechanisms may influence endogenous GLP-1 secretion and degradation, GLP-1R expression, β-cell functional capacity, and the broader metabolic or inflammatory context in which incretin signaling occurs. However, direct clinical evidence linking diet-induced epigenetic changes to GLP-1R agonist therapeutic response remains limited. Therefore, diet-epigenome interactions should be interpreted as plausible modifiers of GLP-1-related metabolic biology rather than established determinants of pharmacological efficacy. Future studies integrating dietary assessment, gut hormone profiling, microbiome analysis, epigenomic markers, and multidimensional therapeutic outcomes are needed to determine whether diet-sensitive molecular signatures can support precision nutrition strategies alongside GLP-1-based therapy.},
}

@article {pmid42760326,
year = {2026},
author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C},
title = {Publisher Correction: Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41588-026-02788-4},
pmid = {42760326},
issn = {1546-1718},
}

@article {pmid42760420,
year = {2026},
author = {Wang, Y and Nie, J and Lin, G and He, X and Zhou, H},
title = {Genetic and microbial regulation of NOD2 signaling in homeostasis and disease.},
journal = {MedScience},
volume = {},
number = {},
pages = {},
pmid = {42760420},
issn = {3091-4981},
abstract = {Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) is a key intracellular pattern recognition receptor that senses bacterial peptidoglycan-conserved motifs, and has long been implicated in initiating immune responses. Loss-of-function mutations in NOD2 have been identified as the strongest genetic risk factor for Crohn's disease (CD), a primary subtype of inflammatory bowel disease (IBD), underscoring its significance in the gut homeostasis. Recent advancements extend our understanding of NOD2, revealing how gut microbiota variation impacts NOD2 signaling and broadening its pathological significance far beyond CD. This review highlights the transition from focusing on genetic mutations in NOD2 to examining its dynamic regulation by the gut microbiome. This new perspective not only deepens our understanding of NOD2 in diverse health contexts, but also paves the way for innovative therapeutic strategies targeting the gut microbiota-NOD2 axis.},
}

@article {pmid42760588,
year = {2026},
author = {Abdelhamid, M and Padhi, P and Gifani, M and Beck, JS and Thomas, JP and Khadse, G and Kudela, C and Phillips, GJ and Kanthasamy, AG and Counts, SE},
title = {Bioengineered microbiotic levodopa therapy improves cognition and reduces pathology in a rat model of Alzheimer's disease.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70670},
pmid = {42760588},
issn = {1476-5381},
support = {R01AG060731//National Institutes of Health (NIH)/ ; U01AG074960//National Institutes of Health (NIH)/ ; //Johnny Isakson Endowed Chair, Coach Mark Rich Endowment/ ; //Georgia Research Alliance Eminent Scholar funds/ ; },
abstract = {BACKGROUND AND PURPOSE: Degeneration of the pontine noradrenergic and midbrain dopaminergic systems contributes to cognitive-behavioural disturbances during the prodromal stages of Alzheimer's disease (AD). We developed a genetically engineered, programmable probiotic Escherichia coli Nissle 1917 strain (EcN[rha] L-DOPA) capable of producing L-3,4-dihydroxyphenylalanine (L-DOPA) in a sustained and titratable manner, thus offering a novel gut-brain delivery mechanism to increase brain levels of noradrenaline and dopamine during the early stages of AD.

EXPERIMENTAL APPROACH: We replicated locus coeruleus (LC) projection system degeneration in AD by administering dopamine-β-hydroxylase IgG-saporin immunotoxin into the prefrontal cortex of 6-months-old Tg344-19 AD rats. The animals then received EcN[rha] L-DOPA/benserazide or placebo by daily gavage for 6 weeks. We assessed cognitive-behavioural function prior to postmortem assessments of amyloid-β plaque load, glial cell activation and neuronal and synaptic markers. Gut colonization, along with plasma and brain L-DOPA, dopamine, noradrenaline and metabolite levels, were also measured.

KEY RESULTS: EcN[rha] L-DOPA displayed stable gut colonization and resulted in sustained therapeutic levels of L-DOPA in plasma and brain, resulting in increased cortical and hippocampal noradrenaline levels. EcN[rha] L-DOPA reduced anxiety-like behaviour improved spatial and working memory. The treatment reduced forebrain Aβ plaque and MHC-II antigen-presenting microglial load. Additionally, EcN[rha] L-DOPA increased protein levels of the dendritic spine marker PSD95.

CONCLUSIONS AND IMPLICATIONS: This translational study suggests that EcN[rha] L-DOPA modifies AD by boosting brain catecholamine production, reducing Aβ accumulation and neuroinflammation, promoting synaptic health, and enhancing cognitive function. Collectively, these results highlight EcN[rha] L-DOPA as a promising preclinical engineered gut microbiome-based therapeutic strategy for early-stage AD.},
}

@article {pmid42760760,
year = {2026},
author = {Parmar, P and Couts, KL},
title = {Mucosal Melanoma: Clinical and Biological Implications of Anatomic Site.},
journal = {Pigment cell & melanoma research},
volume = {39},
number = {5},
pages = {e70120},
doi = {10.1111/pcmr.70120},
pmid = {42760760},
issn = {1755-148X},
mesh = {Humans ; *Melanoma/pathology/therapy/genetics/immunology ; *Mucous Membrane/pathology ; Animals ; Female ; },
abstract = {Mucosal melanoma is a rare and aggressive malignancy arising from anatomically distinct mucosal sites that share a common melanocytic origin but differ in their clinical presentation, biology, and management. Accumulating evidence indicates that the anatomic site of origin fundamentally shapes clinical presentation, immune and microbial microenvironments, molecular drivers, and therapeutic vulnerabilities. In this review, we integrate epidemiologic, clinical, genomic, immunologic, microbiome, and translational data to systematically compare mucosal melanomas arising from the sinonasal tract, oral cavity, anorectal region, and vulvovaginal tract. We highlight striking site-specific differences in patterns of presentation and metastasis, immune and microbiome composition, enrichment of actionable molecular alterations, and responses to therapies. We further discuss how current preclinical models often fail to account for this biologic diversity, limiting translational progress. Collectively, these data support viewing mucosal melanoma as a unified disease entity with clinically meaningful heterogeneity shaped by anatomic site of origin, with important implications for classification, clinical management, and trial design.},
}

Humans
*Melanoma/pathology/therapy/genetics/immunology
*Mucous Membrane/pathology
Animals
Female

@article {pmid42760956,
year = {2026},
author = {Dai, Q and Fang, C and Du, Y and Sun, H and Duan, Z},
title = {Psychobiotic, nutritional, and behavioral interventions targeting the microbiome-gut-brain axis in depression, anxiety, and stress: a scoping review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1856471},
pmid = {42760956},
issn = {2296-861X},
abstract = {Probiotics and psychobiotics are increasingly investigated as microbiome-gut-brain axis (MGBA)-targeted strategies for managing depression, anxiety, and stress-related symptoms, but human evidence remains fragmented across intervention types and biomarker domains. We conducted a scoping review of human intervention studies to map MGBA-targeted psychobiotic, nutritional, dietary, and behavioral interventions, with a specific focus on symptom-biomarker bridging evidence. Searches of major biomedical and multidisciplinary databases combined key terms for the microbiome/gut-brain axis, depression/anxiety/stress, probiotics/psychobiotics, dietary or behavioral interventions, and biomarker domains. The search yielded 1,390 records; 72 full-text reports were assessed; 32 original reports were retained after report-level adjudication; and, after study-family consolidation, 30 independent human studies were included in the study-level synthesis. Studies were classified as direct bridge, parallel evidence, or no bridge according to whether biomarker changes were statistically linked to emotional outcomes. Most included studies focused on probiotic or psychobiotic interventions, with fewer studies examining prebiotics, synbiotics, short-chain fatty acid approaches, dietary interventions, or mind-body/behavioral strategies. Across the 30 studies, 9 were classified as direct bridge, 18 as parallel evidence, and 3 as no bridge. The most frequently examined biomarker domains were gut microbiota, microbial metabolites, and inflammation/immune markers, with common specific readouts including BDNF, 5-HT/serotonin-related markers, IL-6, TNF-α/CRP, cortisol/CAR, and SCFA/metabolite measures. Overall, MGBA-related nutritional and psychobiotic interventions may contribute to mood-symptom management by modulating microbial, metabolic, immune, neuroendocrine, and neurotrophic pathways, but robust symptom-biomarker bridging evidence remains limited. Future trials should predefine bridge hypotheses, standardize core biomarker domains and sampling time points, and clearly distinguish primary trial reports from linked secondary publications.},
}

@article {pmid42761134,
year = {2026},
author = {Otero Ramírez, ID and Sánchez Trujillo, SM and Paz Narvaez, IE and Hoyos Concha, JL},
title = {Effect of a bioformulation with native Bacillus subtilis and Bacillus thuringiensis strains on the control of Fusarium oxysporum and the rhizosphere microbiome of strawberry (Fragaria × ananassa).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1932414},
doi = {10.3389/fmicb.2026.1932414},
pmid = {42761134},
issn = {1664-302X},
abstract = {INTRODUCTION: Strawberry (Fragaria × ananassa) is an economically important fruit crop whose production has increased substantially in recent years. However, its productivity is severely affected by a wide range of pathogens, including Fusarium oxysporum, the causal agent of wilt. Although chemical control remains widely used, biological strategies have gained increasing attention because of their environmental benefits and contribution to sustainable agriculture. The objective of this study was to evaluate the biocontrol potential of native bacterial bioformulations against F. oxysporum in strawberry under field conditions.

METHODS: Bacteria isolated from rhizosphere soil and root samples collected from eight producing farms in Cauca, Colombia, were screened for antagonistic activity, and the most effective isolates were identified by 16S rRNA gene sequencing. Bioformulations based on Bacillus subtilis UCBF11 and Bacillus thuringiensis UCBF2 were developed as microbial "bioinputs" and evaluated under open-field conditions in strawberry crops inoculated with F. oxysporum. Agronomic variables such as root growth and biomass, biomass promotion indexes, and the bioinput efficiency index were determined. Additionally, the effect of the treatments on the rhizosphere microbiota was analyzed using high-throughput sequencing of the 16S rRNA and ITS regions.

RESULTS AND DISCUSSION: A total of 350 isolates were obtained. B. subtilis UCBF11 and B. thuringiensis UCBF2 showed high antagonistic activity against F. oxysporum, with inhibition percentages of 79.72% and 84.95%, respectively. Field application of these bioinputs significantly increased root length and biomass compared to the control treatments, with B. subtilis UCBF11 showing the most outstanding performance. Metataxonomic analysis showed modifications in the structure of bacterial and fungal communities among treatments, and bioinput application was associated with a lower increase in the relative abundance of F. oxysporum. These results demonstrate the potential of B. subtilis UCBF11 and B. thuringiensis UCBF2 as biological control agents against F. oxysporum in strawberry crops.},
}

@article {pmid42761166,
year = {2026},
author = {Li, M and Zhao, X and Zhang, B and Cao, R and Wang, Z and Huang, Z and Cheng, C and Lu, S and Jiang, X},
title = {Gut microbiome-metabolome signatures of osteosarcopenia in fracture patients in China.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1863988},
doi = {10.3389/fendo.2026.1863988},
pmid = {42761166},
issn = {1664-2392},
mesh = {Humans ; Female ; Male ; Middle Aged ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Prospective Studies ; *Fractures, Bone/metabolism/microbiology/complications/epidemiology ; Aged ; China/epidemiology ; *Metabolome ; *Sarcopenia/microbiology/metabolism/epidemiology ; Multiomics ; Metabolomics ; Metagenomics ; },
abstract = {BACKGROUND: Osteosarcopenia, defined as the coexistence of low bone mass and sarcopenia, is a disabling musculoskeletal condition, yet its gut microbial and metabolic characteristics in clinical populations remain incompletely understood. Integrative multi-omics approaches may help clarify species-metabolite networks associated with this condition, particularly in fracture patients.

METHODS: In this single-center, prospective cross-sectional study, 69 fracture patients aged ≥50 years were classified into four phenotypes: Normal (n = 18), isolated low bone mass (Bone, n = 18), isolated sarcopenia (Muscle, n = 19), and osteosarcopenia (Both, n = 14). Fecal samples were analyzed using shotgun metagenomics and untargeted metabolomics, yielding paired multi-omics data for 52 participants.

RESULTS: The Bone group had the highest mean age (66.6 ± 9.46 years), whereas the mean ages of the other groups ranged from 60.6 to 61.8 years (overall p = 0.029), while sex, BMI, lifestyle factors, and comorbidities did not differ significantly. Neither α-diversity nor overall β-diversity showed marked differences across phenotypes, suggesting that broad community replacement was not observed. A multi-stage, multi-method strategy yielded a 17-species consensus feature set associated with differences among musculoskeletal phenotypes. Taxonomic patterns were consistent with a candidate fiber/short-chain fatty acid (SCFA)-associated module, whereas exploratory microbe-metabolite correlations suggested a candidate lipid/sterol-associated module. The latter included correlations linking Firmicutes bacterium CAG:24053_14 with putatively annotated cholesterol and N-acylethanolamines.

CONCLUSIONS: Osteosarcopenia in fracture patients was associated with unadjusted differences in selected gut microbial taxa and fecal metabolites within a broadly shared microbial community. These findings are hypothesis-generating and require validation in larger independent cohorts before clinical or biomarker application.},
}

Humans
Female
Male
Middle Aged
Cross-Sectional Studies
*Gastrointestinal Microbiome
Prospective Studies
*Fractures, Bone/metabolism/microbiology/complications/epidemiology
Aged
China/epidemiology
*Metabolome
*Sarcopenia/microbiology/metabolism/epidemiology
Multiomics
Metabolomics
Metagenomics

@article {pmid42761183,
year = {2026},
author = {Kim, J and Son, B and Yoo, W and Shin, H},
title = {Gut microbiome-immune-metabolic axis in fatigue: mechanistic insights and food science approaches.},
journal = {Food science and biotechnology},
volume = {35},
number = {12},
pages = {3449-3463},
doi = {10.1007/s10068-026-02282-x},
pmid = {42761183},
issn = {2092-6456},
abstract = {Fatigue is a heterogeneous symptom associated with lifestyle, infection, exercise, and chronic disease, but its biological links with the gut microbiome remain incompletely defined. This review summarizes clinical and mechanistic evidence connecting gut microbiome alterations with fatigue-related phenotypes, focusing on myalgic encephalomyelitis/chronic fatigue syndrome, post-acute COVID-19 syndrome, general adult fatigue, and exercise-induced fatigue. Evidence was interpreted according to fatigue-related phenotype, microbiome function, microbial metabolite, gut barrier marker, inflammatory response, and food-based intervention. Current studies suggest that reduced short-chain fatty acid production, impaired butyrate-producing capacity, gut barrier dysfunction, microbial translocation, low-grade inflammation, altered tryptophan metabolism, host energy imbalance, and gut-brain/gut-muscle axis signaling may contribute to fatigue-related physiological vulnerability. Food components/ingredients, including dietary fiber, fermented food, prebiotic, probiotic, postbiotic, polyphenol, and polysaccharide, may support microbiome-mediated recovery pathways. Further controlled, phenotype-specific, multi-omics intervention studies are required.},
}

@article {pmid42761216,
year = {2026},
author = {Corral-Jara, KF and Ramayo-Caldas, Y and Bernard, L and Martin, C and Tournayre, J and Morgavi, DP and Popova, M},
title = {Species-specific rumen microbial responses to dietary inhibition of methanogenesis in cows and goats.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852812},
doi = {10.3389/fmicb.2026.1852812},
pmid = {42761216},
issn = {1664-302X},
abstract = {INTRODUCTION: Methane, a greenhouse gas, is produced in the rumen microbiome of ruminants. Various nutritional strategies can reduce enteric methane (CH4) emissions from livestock, but it is unclear whether diet affects rumen microbiome similarly across ruminant species. The objective of this study was to determine whether cows and goats differ in their rumen microbial functional responses to dietary strategies based on starch and/or lipid supplementation, and whether these differences explain diet-associated variation in CH4 emissions under comparable experimental conditions.

METHODS: Experiments were conducted simultaneously, and both species received the same diet based on grassland hay and concentrate as the Control diet (CTL) or supplemented with corn oil and wheat starch (COS), marine algae powder (MAP) or hydrogenated palm oil (HPO). To identify biologically relevant features from the rumen microbial metatranscriptomes, we followed a five-step integrative statistical and network analysis pipeline, combining a network-based approach with clustering and supervised model fitting to associate differentially expressed genes and taxa with CH4 emissions in the rumen.

RESULTS: The COS diet lowered CH4 emissions in both cows and goats and altered their rumen microbiomes. However, the number of differentially expressed KEGG orthologs and differentially abundant OTUs identified in the COS vs CTL comparison was greater in cows than in goats. Moreover, clustering analysis revealed differences in network topology between ruminant species. In goats, CH4 emission reduction was strongly associated with genes involved in carbohydrate metabolism and methylotrophic and hydrogenotrophic pathways of methanogenesis; whereas in cows, hydrogenotrophic pathways were prominent. Additionally, sparse Partial Least Squares (sPLS) analysis identified species-specific discriminant microbial features.

DISCUSSION: Overall, these results show that host species modulates rumen microbial responses to diet and suggest that microbial interactions underlying CH₄ mitigation differ between cows and goats, although validation in independent studies involving larger sample sizes is required.},
}

@article {pmid42761239,
year = {2026},
author = {Matera, M and Besostri, A and Cavecchia, I and Illiceto, MT and Lenzi, MB and D'Ambrosio, T and Baldassarre, ME and Biagioli, V},
title = {Developmental ecology of the infant oral ecosystem: a framework for early childhood caries.},
journal = {Frontiers in oral health},
volume = {7},
number = {},
pages = {1956432},
doi = {10.3389/froh.2026.1956432},
pmid = {42761239},
issn = {2673-4842},
abstract = {BACKGROUND: Early childhood caries (ECC) has traditionally been regarded as a biofilm-mediated disease driven by sugar exposure and acidogenic microorganisms. However, this perspective primarily captures the final stage of a much longer biological process. We propose the Developmental Ecology of the Infant Oral Ecosystem as a conceptual framework in which ECC represents the clinical manifestation of a disrupted developmental ecology of the infant oral ecosystem, resulting from altered host-microbe-environment interactions that operate from the prenatal period through the first 1,000 days of life with maternal, nutritional, inflammatory, immune, metabolic, microbial, and environmental influences shaping early developmental trajectories.

METHODS: This narrative review synthesizes current evidence into an integrated developmental ecological framework encompassing maternal microbial transmission, infant oral microbiome assembly, breastfeeding, complementary feeding, dietary ecology, tooth eruption, biofilm maturation, and the oral-gut axis. These processes are interpreted within the One Health and Developmental Origins of Health and Disease (DOHaD) paradigms to provide a comprehensive ecological perspective on ECC development.

FINDINGS: The reviewed evidence supports a developmental-ecological interpretation in which interconnected early-life ecological processes shape microbial succession, oral ecosystem resilience, and susceptibility to dysbiosis. Rather than acting as the primary cause of disease, the cariogenic biofilm is interpreted within the proposed framework as the ecological endpoint of disrupted developmental trajectories that impair the establishment and maintenance of oral homeostasis.

CONCLUSIONS: Reframing ECC as a developmental ecological disorder complements established preventive approaches, including fluoride use, dietary sugar control, oral hygiene, and regular dental care, while highlighting the importance of maternal health, early-life nutritional ecology, and microbiome-informed preventive strategies aimed at preserving oral ecosystem resilience from the earliest stages of life. The proposed framework is intended to generate testable hypotheses for future longitudinal and interventional research.},
}

@article {pmid42761274,
year = {2026},
author = {Xie, C and Wu, J and Song, P and Xiao, X and An, X and Wu, H and Sun, Z},
title = {Early-stage intercropping modulates rhizosphere soil properties, microbiome composition, and photosynthetic physiology of Phellodendron chinense: a comparative analysis of five cultivation systems.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1882609},
doi = {10.3389/fpls.2026.1882609},
pmid = {42761274},
issn = {1664-462X},
abstract = {INTRODUCTION: Phellodendron chinense is an important medicinal plant in China. However, continuous monoculture has caused soil degradation and physiological constraints, which have become a key bottleneck limiting its sustainable production. Intercropping with companion plants is an effective approach to break this dilemma.

METHODS: We selected five representative cultivation systems commonly practiced of Phellodendron chinense and systematically measured their rhizosphere soil properties, microbial community composition, and leaf gas-exchange traits. The overarching goal was twofold: (i) to characterize the intercropping-induced variations in these three dimensions (soil properties, microbial communities, and photosynthetic physiology, and (ii) to elucidate the coupling relationships among these three dimensions.

RESULTS AND DISCUSSION: The results demonstrated that total nitrogen(N), total sodium(Na), and magnesium(Mg) contents in the T4 and T2 patterns were significantly higher than those in other patterns. The T2 and T4 patterns significantly enhanced microbial community α-diversity. In contrast, the T3 pattern caused significant soil acidification (pH 4.69) and elevated the relative abundance of the tolerant phylum Chloroflexi. T4 and T2 patterns significantly alleviated stomatal limitations in P. chinense, achieving optimal net photosynthetic rate(Pn) and stomatal conductance(Gs). Correlation analysis showed that Pn was significantly and positively correlated with soil P and Mg contents, while Gs was significantly and positively correlated with soil Na content, and N and Na were the critical factors affecting the structural variation of bacterial and fungal communities. Overall, this study demonstrates that intercropping promote soil nutrient accumulation enhances rhizosphere microbial diversity to facilitate the alleviation of photosynthetic physiological limitations. Intercropping P. chinense with bamboo or tea synergistically mitigates the host's photosynthetic physiological limitations through a belowground positive feedback pathway. These findings provide an important theoretical basis for the efficient and sustainable cultivation of this rare medicinal plant.},
}

@article {pmid42761306,
year = {2026},
author = {Kumar, R and Pakbin, B and Singh, MR and Muruganantham, B},
title = {Editorial: Unlocking the potential of the microbiome in cancer therapy.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1950129},
doi = {10.3389/fmicb.2026.1950129},
pmid = {42761306},
issn = {1664-302X},
}

@article {pmid42761415,
year = {2026},
author = {Yu, M and Shi, X and Li, D and Li, Y and Sun, M},
title = {Spatial niches of the colorectal cancer microbiome: differences, interrelationships, and clinical implications of fecal, mucosal, and intratumoral microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1904188},
doi = {10.3389/fcimb.2026.1904188},
pmid = {42761415},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/pathology/diagnosis ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Intestinal Mucosa/microbiology ; *Microbiota ; Animals ; },
abstract = {Colorectal cancer (CRC) is one of the most common malignancies worldwide and a leading cause of cancer-related mortality. The gut microbiome has attracted growing attention because of its involvement in CRC initiation and progression, early detection, prognostic evaluation, and therapeutic response. However, CRC microbiome studies continue to face inconsistent findings and limited reproducibility, partly because of differences in specimen type. Directly comparing microbial signals from fecal, mucosal, and intratumoral samples may therefore bias mechanistic interpretation and mislead clinical translation. From a spatial-niche perspective, this review summarizes the distinct characteristics, formation mechanisms, interrelationships, and clinical implications of fecal, mucosal, and intratumoral microbiota during CRC progression. We further propose a "seed bank-colonizers-specialized populations" model to conceptualize the continuous but non-equivalent hierarchy among these niches. By providing a clearer spatially stratified framework, this review aims to help move CRC microbiome research beyond descriptive associations toward precision-oriented applications supported by mechanistic interpretability, reproducible evidence, and clinical translatability.},
}

Humans
*Colorectal Neoplasms/microbiology/pathology/diagnosis
*Feces/microbiology
*Gastrointestinal Microbiome
*Intestinal Mucosa/microbiology
*Microbiota
Animals

@article {pmid42761444,
year = {2026},
author = {Zou, Z and Liu, H and Hu, Y and Ge, X and Zhang, J and Li, X},
title = {Gut microbiota and microbiota-derived metabolites in radiation-induced injury: mechanisms and therapeutic opportunities.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1923929},
doi = {10.3389/fmicb.2026.1923929},
pmid = {42761444},
issn = {1664-302X},
abstract = {Radiation-induced injury is a complex pathological process involving DNA damage, oxidative stress, inflammatory amplification, epithelial barrier disruption, immune dysregulation, metabolic remodeling, and impaired tissue repair. Accumulating evidence indicates that the gut microbiota is not merely altered by irradiation but may also modify host radiation responses and tissue recovery; however, direct causal support remains confined to selected microbes, metabolites, and pathways, predominantly in preclinical models. Irradiation is frequently associated with reduced microbial diversity, depletion of selected commensals, expansion of opportunistic pathobionts, and altered microbial metabolic output; selected experimental studies further indicate that these changes can modify intestinal injury and host recovery. Conversely, defined microbes and metabolites have improved radiation outcomes in preclinical intervention models by supporting epithelial, immune, and metabolic homeostasis. In this review, we summarize current advances in understanding the gut microbiota-metabolite axis in radiation-induced injury. We first discuss radiation-induced gut dysbiosis and the major microbial metabolites involved, including short-chain fatty acids, tryptophan-derived metabolites, bile acids, lipid metabolites, polyamines, and other bioactive molecules. We then highlight the key mechanisms by which gut microbiota and microbial metabolites mitigate radiation injury, including suppression of oxidative stress, inhibition of inflammatory signaling, restoration of epithelial barrier integrity, promotion of intestinal stem cell-mediated regeneration, regulation of immune homeostasis, and modulation of lipid peroxidation-associated ferroptosis. Finally, we evaluate microbiota-targeted intervention strategies, including probiotics, prebiotics, postbiotics, fecal microbiota transplantation, antibiotic modulation, natural products, engineered probiotics, and nanomedicine-assisted delivery systems. Overall, the gut microbiota-metabolite axis represents a biologically plausible and increasingly testable target for radioprotection and mitigation, although its clinical utility remains to be established. Future studies should move beyond descriptive microbiome profiling toward causal, function-oriented, and multi-omics-driven investigations, with particular emphasis on the microbiota-lipid metabolism-ferroptosis axis and precision microbiome therapeutics. Carefully validated microbiota-targeted approaches may provide future opportunities to reduce normal-tissue toxicity and improve recovery without compromising tumor control.},
}

@article {pmid42761446,
year = {2026},
author = {Li, S and Wan, J and Liang, Z and Li, J and Jiang, H and Luo, L and Li, Y and Luo, S and Huang, H},
title = {Gypenosides ameliorate polycystic ovary syndrome via gut microbiota modulation: An integrated gut microbiome and ovarian transcriptome study.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117478},
doi = {10.1016/j.isci.2026.117478},
pmid = {42761446},
issn = {2589-0042},
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder with complex metabolic and reproductive manifestations. Gut microbiota dysbiosis has emerged as a key factor in PCOS, yet the causal role of microbiota-targeted interventions remains to be fully defined. In a letrozole-induced rat model, we show that gypenosides (GPs)-bioactive saponins from Gynostemma pentaphyllum-alleviate weight gain, hormonal imbalance, and estrous cycle disruption, alongside reducing systemic oxidative stress and inflammation. Integrated ovarian transcriptomics and gut microbiome 16S rRNA sequencing reveal that GPs modulate ovarian gene expression related to inflammation and cellular function while reshaping gut microbiota by enriching beneficial genera including Lactobacillus and Romboutsia. Fecal microbiota transplantation (FMT) establishes causality: PCOS-derived microbiota transfers disease traits to normal recipients, whereas GPs-conditioned microbiota alleviates PCOS phenotypes in recipients. These findings demonstrate that GPs act through a "gut microbiota-oxidative stress-ovary" axis, supporting GPs as a promising microbiota-targeted intervention for PCOS management.},
}

@article {pmid42761474,
year = {2026},
author = {Anand, S and Verma, A},
title = {Response to the Letter to the Editor Entitled "Promising Urinary Microbiome Signals in Congenital Anomalies of the Kidney and Urinary Tract, but not yet Ready for Clinical Risk Stratification".},
journal = {Kidney international reports},
volume = {11},
number = {10},
pages = {107022},
doi = {10.1016/j.ekir.2026.107022},
pmid = {42761474},
issn = {2468-0249},
}

@article {pmid42752812,
year = {2026},
author = {Colares, HC and Silva, TNL and Tarabal, VS and Meira, HGR and Cardoso, JF and Parreira, AG and da Silva, JA and da Silva, GR and de Magalhães, JT and Gonçalves, DB and Granjeiro, PA},
title = {Weissella paramesenteroides M4: Optimization of bioprocesses, antioxidant property, and a potentially probiotic strain with in vitro activity against Cutibacterium acnes.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42752812},
issn = {1874-9356},
abstract = {The skin microbiota is linked to conditions such as acne. As antibiotic resistance limits the effectiveness of conventional treatments, microbiome-based strategies are needed. This study aimed to optimize the biomass production of Weissella paramesenteroides M4, evaluate its antioxidant properties, and assess its efficacy in a topical gel formulation against Cutibacterium acnes. Growth dynamics were established, followed by biomass optimization using fractional factorial and central composite rotatable designs with deproteinized whey as a sustainable substrate. Optimization increased biomass production by 974% (reaching 8.7 × 10[10] CFU/mL, equivalent to 2.031 g/L dry weight under validated conditions); significant variables included yeast extract, peptone, and MnSO4. Antioxidant assays showed activities of 80% (intact cells) and 61% (lysed cells), with 82% relative growth under 1.0 mM H2O2 oxidative stress (estimated spectrophotometrically). Notably, W. paramesenteroides M4 selectively inhibited the pathogen C. acnes ATCC 6919 in vitro without affecting the commensal S. epidermidis ATCC 12,228 in vitro. A cosmetic gel containing the strain maintained antimicrobial efficacy and stability for 15 days at 4 °C. W. paramesenteroides M4 demonstrates high bioprocess efficiency, robust antioxidant potential, and selective in vitro antimicrobial activity. The formulated gel containing the candidate probiotic strain retained antimicrobial activity under refrigeration during storage and shows potential for innovative topical applications, providing a preliminary foundation for alternative acne management. This research provides a sustainable framework for high-yield probiotic production using industrial by-products and introduces a potentially probiotic lactic acid bacterium with selective in vitro activity, representing a promising candidate for alternative acne treatment, addressing a significant gap in current dermatological therapies.},
}

@article {pmid42753081,
year = {2026},
author = {Goyal, MK and Goyal, O and Sehgal, T and Vuthaluru, AR and Goyal, K and Sood, A},
title = {What is new in Rome V?: Redefining diagnostic criteria and clinical pathways in disorders of gut-brain interaction.},
journal = {Indian journal of gastroenterology : official journal of the Indian Society of Gastroenterology},
volume = {},
number = {},
pages = {},
pmid = {42753081},
issn = {0975-0711},
abstract = {The Rome-V criteria represent a major evolution in the conceptualization and clinical application of disorders of gut-brain interaction (DGBIs). Building upon the biologically grounded framework established in Rome IV, Rome V moves beyond rigid symptom-based definitions toward a multi-dimensional, clinically operational model that integrates symptom patterns, temporal characteristics, physiological testing and psycho-social context. A central advance is the transition from categorical classification to dimensional phenotyping, recognizing the continuum and overlap inherent to DGBIs. The recalibration of diagnostic thresholds, most notably the re-introduction of abdominal discomfort and the requirement for symptom intermittency in irritable bowel syndrome, restores diagnostic sensitivity while improving mechanistic specificity. Rome V further introduces Rome Clinical Criteria, addressing the substantial sub-diagnostic population and enabling earlier, context-driven diagnosis in routine practice. Across organ systems, diagnostic definitions are refined to align more closely with underlying pathophysiology and clinical decision-making. This is exemplified by the integration of physiological frameworks in esophageal disorders, temporal stratification in gastroduodenal syndromes, the redefinition of centrally mediated abdominal pain and the incorporation of motor-sensory phenotyping in anorectal disorders. In parallel, Rome V emphasizes harm reduction in biliary disorders and introduces greater continuity across pediatric and adult frameworks. Despite these advances, challenges remain, including the absence of validated biomarkers, variability in global applicability and the need for further validation of new constructs. Overall, Rome V represents a shift from static diagnostic criteria to dynamic clinical pathways, providing a robust platform for mechanism-informed and increasingly individualized care in DGBIs.},
}

@article {pmid42753220,
year = {2026},
author = {Garma, LD and Pernas, S and Vicente Baz, D and García Campelo, R and Terrasa, J and Nasarre, B and Vera García, R and Bermejo, B and González Santiago, S and Fullana, B and Rodríguez-Pérez, M and Fernandez Bruno, M and Reboredo Rendo, C and Perelló, A and Jiménez, D and Guerra, JA and Arrazubi, V and de la Cruz, S and Cejalvo, JM and Tebar, C and Núñez Berrueco, E and Hernández-Marín, B and Rogado, J and Olmos, PM and Arbaizar, LP and Villalba Oliva, MA and Madrid, Y and Sanz-Landaluze, J and Moreno-Martín, G and Morillas, A and Lopez-Alonso, A and Rodríguez-Patón, A and Colomer, R and Artés-Rodríguez, A and Quintela-Fandino, M},
title = {Longitudinal Clinical, Physiological, and Molecular Profiling of Female Patients With Metastatic Cancer: Protocol and Feasibility of a Multicenter High-Definition Oncology Study.},
journal = {JCO precision oncology},
volume = {10},
number = {9},
pages = {e2501185},
doi = {10.1200/PO-25-01185},
pmid = {42753220},
issn = {2473-4284},
mesh = {Humans ; Female ; Feasibility Studies ; Prospective Studies ; *Breast Neoplasms/pathology/genetics ; Neoplasm Metastasis ; Multicenter Studies as Topic ; Longitudinal Studies ; Middle Aged ; Adult ; *Lung Neoplasms/pathology/genetics ; *Colorectal Neoplasms/pathology/genetics ; Pilot Projects ; Aged ; },
abstract = {PURPOSE: A substantial proportion of patients receiving genomically matched therapies do not achieve clinical benefit, underscoring the influence of nongenetic factors on cancer outcomes. High-Definition Oncology (HDO) proposes integrating longitudinal, multimodal patient data-spanning clinical, molecular, physiological, and behavioral domains-to enable truly individualized cancer care. This manuscript describes the HDO study design, framework, and feasibility results in women with metastatic cancer.

METHODS: We initiated a prospective, multicenter observational study (HDO study; ClinicalTrials.gov identifier: NCT06590506) enrolling 300 female patients with newly diagnosed metastatic breast, lung, or colorectal cancer. Here, we report the study design, standardized workflows, prespecified feasibility criteria, and early internal pilot results. Eleven data modalities are collected longitudinally, including tumor and germline genomics, germline epigenomics, gut microbiome, blood and stool metabolomics and proteomics, exposome characterization, wearable-derived physiological monitoring, digital footprint assessment, medical imaging, and patient-reported outcomes. Standardized workflows govern clinical procedures, data acquisition, biospecimen processing, and quality control across all participating sites.

RESULTS: Feasibility was evaluated in the first 30 participants (10% of planned accrual). Patients completed 100% of scheduled clinical visits, 97.4% of planned plasma collections, 80.7% of stool samples, and all tumor biopsies. Wearable devices captured activity, heart rate, sleep, and blood oxygen saturation data during 95.0%, 84.2%, 90.6%, and 70.7% of total patient-days, respectively. Biospecimens met predefined quality control metrics across all molecular modalities. Engagement with mobile applications for pain and emotion reporting exceeded 80%.

CONCLUSION: The HDO study demonstrates the feasibility of comprehensive, longitudinal, multimodal data collection in women with metastatic cancer. This internal pilot establishes an integrated framework for future analyses aimed at characterizing disease trajectories, defining molecular and physiological determinants of outcomes, and developing patient-specific computational models.},
}

Humans
Female
Feasibility Studies
Prospective Studies
*Breast Neoplasms/pathology/genetics
Neoplasm Metastasis
Multicenter Studies as Topic
Longitudinal Studies
Middle Aged
Adult
*Lung Neoplasms/pathology/genetics
*Colorectal Neoplasms/pathology/genetics
Pilot Projects
Aged

@article {pmid42753230,
year = {2026},
author = {Zhang, Y and Giovannucci, EL},
title = {Ultra-processed Foods, Cancer, and Early-onset Cancer: A Comprehensive Review.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgag068},
pmid = {42753230},
issn = {1460-2180},
abstract = {The classification of foods according to their degree of processing, and particularly the concept of ultra-processed foods, is relatively new. Consumption of ultra-processed foods has increased markedly worldwide in recent decades. Their growing consumption has coincided with a rising global burden of cancer, including marked increases in several cancers diagnosed before age 50 years. In this comprehensive review, we summarize trends in ultra-processed food consumption and the sociodemographic, psychological, and behavioral characteristics associated with higher intake. We further review the epidemiological evidence linking ultra-processed foods with cancer incidence and mortality, with particular attention to the limited but emerging evidence relevant to early-onset cancer. Potential mechanisms linking ultra-processed foods to cancer include unfavorable nutrient displacement, changes in body composition and fat deposition, and increased exposure to additives, processing by-products, and other chemicals. These influences may converge on a range of biological pathways, including metabolic dysfunction, chronic inflammation, immune dysregulation, gut microbiome disruption, DNA damage and genomic instability, and epigenetic alterations. Substantial uncertainties remain, including heterogeneous exposure definitions and classification practices, limitations in dietary assessment and temporal exposure capture, residual confounding, and the complexity of putative biological mechanisms. We conclude by highlighting key research challenges and future directions, along with considerations related to policy, regulation, and industry practices.},
}

@article {pmid42753294,
year = {2026},
author = {Saleh, ZH and El Enbaawy, MI and Kamal, MA and Mahmoud, H and Hassan, M},
title = {Heat stress, respiratory dysbiosis, and poultry pathobiome: A comprehensive review of chronic respiratory disease in chickens.},
journal = {Veterinary microbiology},
volume = {322},
number = {},
pages = {111225},
doi = {10.1016/j.vetmic.2026.111225},
pmid = {42753294},
issn = {1873-2542},
abstract = {The poultry respiratory microbiome is increasingly recognized as a critical determinant of poultry health, mucosal immunity, and host resistance to opportunistic pathogens. Chronic Respiratory Disease (CRD) exerts a severe economic toll on the global broiler industry. While conventionally attributed to specific etiological agents such as Mycoplasma gallisepticum, disease progression is fundamentally tied to broad ecological dysbiosis within the respiratory tract. This comprehensive review synthesizes current knowledge on the functional roles and compositional dynamics of the poultry respiratory microbiome in both healthy and diseased states. Notably, we acknowledge the emerging threat of climate change, elucidating how heat stress physically and immunologically disrupts the respiratory mucosal microenvironment, acting as a primary catalyst for microbiome destabilization and CRD susceptibility. By shifting the paradigm from a single-pathogen model to a comprehensive pathobiome perspective, we detail the microbial shifts that characterize CRD. Furthermore, because investigating this low-biomass environment presents unique analytical challenges, we critically evaluate current technical methodologies. We address critical bottlenecks in sample collection, DNA extraction biases, and the comparative efficacy of 16S rRNA amplicon versus shotgun metagenomic sequencing. Ultimately, this synthesis provides a foundational framework for optimizing diagnostic methodologies and developing microbiome-targeted interventions -such as next-generation probiotics- to mitigate CRD in an era of escalating environmental stressors.},
}

@article {pmid42753435,
year = {2026},
author = {Xue, P and Huang, B and Wang, Y and Zhao, L and Mao, L},
title = {Environmental fate and risk of diverse oxygenated isomeric prothioconazole biotransformation products in soil.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143509},
doi = {10.1016/j.jhazmat.2026.143509},
pmid = {42753435},
issn = {1873-3336},
abstract = {Isomeric biotransformation products (TPs) of organic pesticides substantially expand structural diversity and may exhibit distinct environmental behaviors compared with their parent compounds. However, the formation mechanisms and ecological risks of such isomers (regioisomers) in soil remain poorly understood. In this study, the triazole fungicide prothioconazole (PTC) was incubated in agricultural soil, and 21 isomeric TPs were identified and classified into six structural groups using high-resolution mass spectrometry (HR-MS) based on diagnostic fragmentation patterns. These secondary oxygenated isomeric TPs were derived from three primary intermediates (PTC-desthio, PTC-dehydrated, and PTC-S-methyl) via site-selective oxygenation. Toxicity predictions indicated substantial variability among isomers, with certain hydroxylated derivatives exhibiting higher predicted ecotoxicity than others, challenging the assumption that biotransformation necessarily leads to detoxification. Metagenomic analysis showed that PTC exposure significantly altered the soil microbial community, enriching genes associated with xenobiotic degradation and central carbon metabolism. Notably, functional microbial shifts, particularly involving the genus Acinetobacter, were strongly associated with specific isomer profiles. These results suggest a potential link between microbial metabolic responses and the formation of structurally diverse isomeric TPs. The widespread occurrence of such isomers highlights that assessments based solely on parent compounds may underestimate the environmental fate and risks of PTC in agroecosystems.},
}

@article {pmid42753826,
year = {2026},
author = {Li, B and Li, X and Deng, Y and Luo, Y and Huang, Y and She, D and Li, H and Ji, S and Liu, G and Wang, Y and Zu, M and Kundu, SC and Zhang, P and Lv, P and Shi, X and Xiao, B},
title = {Ultrasound-driven plant lipid vesicles amplify oncolytic virotherapy in colorectal cancer.},
journal = {Journal of controlled release : official journal of the Controlled Release Society},
volume = {},
number = {},
pages = {115368},
doi = {10.1016/j.jconrel.2026.115368},
pmid = {42753826},
issn = {1873-4995},
abstract = {Colorectal cancer (CRC) remains a highly aggressive malignancy, and its treatment with oncolytic virotherapy is hindered by multiple delivery barriers and delayed therapeutic kinetics. To address these challenges, we developed a plant lipid-based vesicular system (P-M@Ce6-OVs) co-encapsulating oncolytic viruses (OVs) and sonosensitizer chlorin e6 (Ce6), enabling ultrasound (US)-guided, spatiotemporally controlled delivery to deep colorectal tumors. Under US exposure, the system enhanced mucus infiltration, tumor penetration, and lysosomal escape, while activating sonodynamic therapy to rapidly induce tumor ablation and compensate delayed viral oncolysis. In CRC mouse models, rectal administration of P-M@Ce6-OVs with US exposure achieved a 10.3-fold reduction in tumor burden compared with the control (without treatment), markedly outperforming monotherapies. Importantly, combination with αPD-L1 not only suppressed primary CRC and re-challenged tumors mimicking metastatic relapse, but also induced durable systemic immune protection. This triple combination further potentiated systemic and mucosal antitumor immunity, restoring cytotoxic T-cell function and reinforcing humoral and gut-localized immune responses. Notably, this treatment reshaped gut microbiota by enriching nucleoside-metabolizing bacteria (e.g., Lactobacillus taiwanensis) and altering microbial metabolic profiles, including the pathways related to pyrimidine catabolism and arachidonic acid oxidation. These microbiota and metabolic changes were associated with immune remodeling and tumor suppression. Collectively, this platform integrated US-enabled delivery, sonodynamic activation, and microbiome remodeling to synergistically suppress CRC and re-challenged tumor progression, amplifying virotherapy and antitumor immunity.},
}

@article {pmid42753985,
year = {2026},
author = {Sun, Y and Phipatanakul, W and Lai, PS},
title = {Reframing the asthma microbiome: Multikingdom, multisite, and multiomic perspectives.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.08.026},
pmid = {42753985},
issn = {1097-6825},
abstract = {The field of asthma microbiome research has shifted rapidly in recent years. Advances in sequencing technology have led to an increased ability to characterize multikingdom microbial species and integration with host -omics profiling to enhance future translational applications. Traditional bacteria-centric, cross-sectional studies are giving way to mechanistic frameworks that incorporate fungi, viruses, and host-immune interactions. In this state-of-the-art review of emerging concepts in microbiome asthma research, we first propose a structured framework to consider microbiome studies across 5 major domains-microbial kingdom, site of sampling, integration with host -omics, clinical outcome domain, and translational relevance-in order to synthesize recent high-impact human microbiome studies in asthma. We highlight emerging evidence that fungal and viral communities contribute independently to asthma risk and that human microbial communities are linked to distinct inflammatory and immune pathways shaped by host genetic susceptibility.},
}

@article {pmid42753987,
year = {2026},
author = {Benech, N and Guarino-Vignon, P and McLellan, P and Campidelli, C and Sergeant, M and Joubert, F and Truong, S and Barbier, P and Sandoz, E and Ruffié, P and Sedda, D and Delmeule, A and Pradat, P and Landman, C and Bourrier, A and Marchand, L and Alric, L and Scanzi, J and Cassir, N and Dureault, A and Piet, E and Gallet, S and Botelho-Nevers, E and Roussel-Gaillard, T and Cuerq, C and Ader, F and Guillet, M and Rolhion, N and Grill, JP and Lamaziere, A and Chatel, JM and Pechine, S and Langella, P and Sokol, H},
title = {Faecalibacterium prausnitzii EXL01 Strain for the prevention of multiple-recurrent Clostridioides difficile Infection.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.09.002},
pmid = {42753987},
issn = {1528-0012},
abstract = {BACKGROUND AND AIMS: Recurrent Clostridioides difficile infection (rCDI) results from persistent microbiome dysfunction and impaired colonization resistance. Although fecal microbiota transplantation (FMT) is effective, defined and scalable alternatives are needed. We evaluated whether a single commensal strain could restore key microbiome functions and prevent recurrence.

METHODS: We assessed Faecalibacterium prausnitzii EXL01 in a murine CDI model and a multicenter, open-label single-arm phase I trial including adults with ≥3 CDI episodes. Following vancomycin preconditioning, patients received oral EXL01 for 8 weeks with 8-week follow-up. Primary endpoint was safety. Secondary endpoints included recurrence at week 8. Longitudinal stool samples underwent shotgun metagenomics and metabolomics. Outcomes were benchmarked against matched FMT cohorts. Additional in vitro and murine studies of EXL01 were performed.

RESULTS: In mice, EXL01 reduced C. difficile burden and intestinal inflammation in an antibiotic-disrupted murine model. Six patients were treated; no treatment-related serious adverse events occurred. Five of six patients (83.3%) remained recurrence-free at week 8, comparable to matched FMT cohorts. EXL01 was detectable in stool up to 8 weeks post-treatment. Multi-omics analyses showed that EXL01 engraftment was correlated with restoration of bile acid metabolism, including reduced primary bile acids and increased secondary bile acids, and increased short-chain fatty acid production, particularly butyrate, despite limited taxonomic recovery. EXL01 selectively deconjugated bile acids in vitro.

CONCLUSIONS: A single, well-characterized bacterial strain was associated with restoration of key microbiome functions and low recurrence rates in high-risk rCDI. These findings support precision microbiome therapeutics targeting ecosystem function rather than taxonomic complexity. Controlled trials are ongoing. (clinicaltrials.gov; NCT06306014).},
}

@article {pmid42754090,
year = {2026},
author = {Zuccaro, V and Asperges, E and Bruno, R},
title = {Beyond eradication: a microbiome approach to the management of bacterial vaginosis during pregnancy.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.09.003},
pmid = {42754090},
issn = {1469-0691},
}

@article {pmid42754113,
year = {2026},
author = {Tang, X and Guo, Y and Liu, Y and Wu, Z and Zhang, H and Li, S and Yang, Y and Yao, W and Cai, B and Ge, J},
title = {Organic phosphorus activation by functional bacterial consortium promotes lead immobilization in contaminated soil.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135850},
doi = {10.1016/j.biortech.2026.135850},
pmid = {42754113},
issn = {1873-2976},
abstract = {Microbial remediation of lead (Pb)-contaminated soil through phosphate-mediated stabilization is often hindered by limited microbial stress tolerance and phosphorus availability. To address these limitations, directional enrichment, microcosm experiments, high-throughput sequencing, and functional gene microarray analysis were combined to develop a composite functional consortium with Pb tolerance and phosphate-solubilizing capacity. The results revealed that the co-enrichment strategy produced a composite functional consortium with strong Pb resistance and high capacities for inorganic phosphorus solubilization and organic phosphorus mineralization. After inoculation, soil acid phosphatase and phytase activities significantly increased, thereby promoting organic phosphorus activation and Pb immobilization. Moreover, Pb leachability, mobility, and bioaccessibility decreased by 50%, 67%, and 55%, respectively, relative to their corresponding initial values on day 0. Functional gene microarray analysis revealed a significant decrease in pbrT abundance and enrichment of genes associated with the czc efflux system, cadA, and mobile genetic elements. This pattern suggests a potential shift in microbial Pb resistance strategies from intracellular uptake to extracellular efflux. Partial least squares path modeling further revealed distinct but complementary association patterns among microbial guilds. Specifically, passivators were mainly associated with phosphorus-mediated Pb stabilization, while tolerators were more closely linked to Pb-stress adaptation and extracellular polymeric substance-mediated Pb binding. These findings provide a theoretical basis for microbiome-based remediation of heavy metal-contaminated soils using native organic phosphorus pools.},
}

@article {pmid42754150,
year = {2026},
author = {Nilsson, JK and Walker, SVM and Prescott, SL and Ireland, DJ and Perrella, SL and Palmer, DJ},
title = {Infant formula introduced within 24 hours of birth increases egg allergy risk.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2026.08.040},
pmid = {42754150},
issn = {2213-2201},
abstract = {BACKGROUND: Breast secretions of colostrum precede milk production in the first few days after birth, providing nutrition and playing a critical role in shaping the newborn's gut microbiome and immune system development. Infants fed commercial milk formula in the first few days consume less colostrum, and previous studies have found an associated increased risk of food allergy.

OBJECTIVE: To determine the risk of food allergen sensitization and IgE-mediated food allergy development in infants who received any formula during their first 3 days of life.

METHODS: In a high-risk (defined by family history) cohort of 563 infants, born at 37 weeks' gestation or later, early-life infant feeding practices data were prospectively collected. At age 1 year, infant IgE-mediated food allergy, food allergen sensitization, and medically diagnosed eczema were assessed.

RESULTS: In their first 3 postnatal days, 36.8% (207 of 563) of infants received formula, with 21.8% (123 of 563) of infants receiving formula within 24 hours of birth. Overall, 3.4% of infants developed egg allergy, despite timely egg introduction in the infant diet at age 6 months. There was an increased risk of egg allergy (adjusted odds ratio, 3.62; 95% CI, 1.29-10.16; P = .014) and egg sensitization (adjusted odds ratio, 2.50; 95% CI, 1.09-5.74; P = .031) following formula introduction within 24 hours of birth. No associations were found with other food allergies or sensitization, but there were only a few cases.

CONCLUSIONS: Along with timely infant diet food allergen introduction, avoiding formula supplementation especially within 24 hours of birth is another potential food allergy prevention strategy that warrants further investigation in randomized trials.},
}

@article {pmid42754202,
year = {2026},
author = {Zhu, H and Jia, L and Li, C and Shi, H and Xu, M and Fan, W and Yang, J},
title = {Rhizosphere microbiome-mediated aluminum detoxification in acidic soils: From microbial mechanisms to microecology-based management.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129188},
doi = {10.1016/j.envpol.2026.129188},
pmid = {42754202},
issn = {1873-6424},
abstract = {Aluminum (Al) toxicity in acidic soils severely constrains global crop production. Classical mechanisms of plant Al tolerance, established primarily in sterile laboratory systems, have centered on organic acid secretion. However, such mechanisms do not capture the critical contributions of rhizosphere microorganisms under field conditions. This review synthesizes current advances in microbe-mediated Al detoxification, aiming to reinterpret classical tolerance mechanisms from a microbial perspective and explore strategies for translating these insights into sustainable field applications. Microorganisms alleviate Al stress through direct mechanisms including proton buffering, adsorption, precipitation, and metabolic cross-feeding, as well as indirect mechanisms such as improving phosphorus nutrition, remodeling root cell wall architecture via brassinosteroid signaling, and activating systemic plant defenses. Fungi further contribute through hyphal filtration and cross-kingdom cooperation. Revisiting classical tolerance mechanisms in a microbial context reveals that organic acid exudation, cell wall binding, and stress signaling function as integrated plant-microbe processes. Recent methodological advances in multi-omics, synthetic microbial community (SynCom) construction, and in situ visualization now enable mechanistic validation. Nevertheless, field application remains constrained by poor inoculant colonization, necessitating a shift from single strains to functionally complementary consortia. Future progress will require integrating plant genotype-microbiome interactions into breeding programs and developing closed-loop strategies that couple mechanistic discovery with field deployment. Critically, such strategies must be evaluated not only for short-term yield gains but also for their capacity to restore soil health, enhance ecosystem multifunctionality, and maintain functional resilience under climate-induced environmental stresses, thereby ensuring sustainable agriculture on acidic soils.},
}

@article {pmid42754330,
year = {2026},
author = {Na, SI and Kim, J and Kim, SY and Park, J and Cho, YJ},
title = {SimpleMicrobiome: An integrated web-based platform for streamlined microbiome data analysis and visualization.},
journal = {Journal of microbiology (Seoul, Korea)},
volume = {},
number = {},
pages = {},
doi = {10.71150/jm.2606011},
pmid = {42754330},
issn = {1976-3794},
abstract = {Microbiome studies require multiple analytical steps after initial sequence processing. These steps commonly include data harmonization, preprocessing, taxonomic profiling, diversity analysis, differential abundance testing, predictive modeling, network inference, and preparation of publication-ready outputs. Although robust packages are available for many of these tasks, routine use often depends on command-line workflows, repeated data reformatting, and method-specific scripting. These requirements can limit accessibility for experimental researchers and complicate consistent analysis across interdisciplinary teams. We developed SimpleMicrobiome, a web-based R Shiny platform that integrates established microbiome analysis methods into a single interactive downstream workflow. The application accepts standard abundance, taxonomy, and metadata tables, supports interactive preprocessing and sample filtering, and provides modules for taxa profile visualization, alpha and beta diversity analysis, ANCOM-BC2 and MaAsLin2 differential abundance testing, Random Forest modeling with SHAP-based interpretation, microbial association network inference using SparCC and SPIEC-EASI through NetCoMi, correlation heatmaps, and dbRDA/CAP-style association biplots. The platform is implemented as a modular Shiny application so that preprocessing choices are propagated across downstream analyses, results can be exported as figures and tables, and the same application can be run through the public server, source-code installation, or a Docker image. SimpleMicrobiome consolidates major downstream microbiome analysis tasks in an accessible browser-based environment while retaining links to established analytical frameworks. The platform may reduce technical barriers for non-programming users, improve consistency across exploratory and reporting-oriented analyses, and support collaborative microbiome research. The public application is available at https://simplemicrobiome.mglab.org, the source code is available at https://github.com/yjcho2252/SimpleMicrobiome, and a Docker image for local deployment is available at https://hub.docker.com/r/mglab2252/simplemicrobiome.},
}

@article {pmid42754368,
year = {2026},
author = {Khan, SA and Hegelmaier, T and Wegner, F and Höllerhage, M and Peters, M and Duscha, A and Desel, C and Haghikia, A and Klietz, M},
title = {Gut microbiome dysbiosis, short-chain fatty acid depletion and implications for neuroinflammation in atypical parkinsonian syndromes - a systematic review of patient cohorts.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X261485793},
doi = {10.1177/1877718X261485793},
pmid = {42754368},
issn = {1877-718X},
abstract = {IntroductionAtypical parkinsonian syndromes (APS) such as progressive supranuclear palsy (PSP), multiple system atrophy (MSA) and corticobasal syndrome (CBS) pose a major clinical challenge due to their progressive disease course, reduced life expectancy and resistance to dopaminergic therapy. The gut microbiome has gained increasing attention as a potential contributor to APS etiology and progression.AimThe literature analysis aims to systematically evaluate alterations in the gut microbiome in APS, their correlation with clinical symptoms and their potential diagnostic and therapeutic relevance.Material and methodsPubMed and Web of Science were searched separately for ''progressive supranuclear palsy'', ''multiple system atrophy'' and ''corticobasal syndrome'', each combined with "gut microbiome" AND "human". Inclusion criteria were ≥ 10 subjects per group, clinically confirmed APS and gut microbiome analysis in a case-control, cross-sectional, longitudinal or randomized controlled trial study design. 7 studies met the inclusion criteria (1 PSP, 1 PSP/MSA, 5 MSA). No studies with CBS patients could be included.ResultsThe gut microbiome is altered in APS compared to healthy controls, with several alterations correlating with clinical symptoms in individual studies. A reduction of short-chain fatty acid (SCFA) producing bacteria and an enrichment of pro-inflammatory taxa were observed, alongside impaired markers of intestinal barrier integrity.Discussion and conclusionAPS are associated with dysbiosis that correlates with clinical symptoms, although causality remains to be established. Generalizability is limited due to the lack of geographic heterogeneity in the included studies. Longitudinal studies with larger cohorts are required to identify robust microbial markers and therapeutic potential.},
}

@article {pmid42754660,
year = {2026},
author = {Plazzo, AP and Filz, V and Prothiwa, M and Lambrecht, R and Delgado, ME and Fleming, JR and Duschek, J and Pilgram, E and Friedrich, J and Eisenring, R and Kurtz, L and Stemmer, K and Stenman, LK and Amaya Garcia, F and Unterlass, M and Mayans, O and Böttcher, T and Brunner, T},
title = {Microbiome-host communication via vaccenic acid modulates LRH-1/NR5A2 activity and ameliorates metabolic liver disease.},
journal = {EMBO molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42754660},
issn = {1757-4684},
support = {BR 3369/4-2//Deutsche Forschungsgemeinschaft (DFG)/ ; },
abstract = {Interactions between microbiota and the host can profoundly affect human health. In particular, microbiota-derived metabolites influence liver physiology and contribute to the development of metabolic diseases, yet the molecular mechanisms underlying microbiome-host communication remain incompletely understood. Here, we identify bacterial lipids as modulators of the nuclear receptor Liver Receptor Homolog-1 (LRH-1/NR5A2), a regulator of hepatic metabolism. Lipid extracts from multiple bacterial species, including the probiotic Bifidobacterium animalis subsp. lactis B420[TM], activated LRH-1, leading to the identification of the long-chain fatty acid vaccenic acid (VA) as a previously unrecognized endogenous LRH-1 ligand. VA directly bound the LRH-1 ligand-binding domain and stimulated receptor-dependent transcriptional activity. In high-fat diet-induced obese and hyperglycemic mice, VA-mediated LRH-1 activation improved glucose homeostasis and attenuated metabolic liver disease. Transcriptomic analyses revealed suppression of hepatic de novo lipogenesis as a principle downstream response to LRH-1 activation. Together, these findings establish a microbiota-LRH-1 signaling axis that links bacterial lipid metabolism to host metabolic regulation, identify VA as a functional LRH-1 agonist, and provide a mechanistic rationale for targeting LRH-1 in metabolic liver disease.},
}

@article {pmid42754709,
year = {2026},
author = {Selten, G and Lamouche, F and Gómez-Repollés, A and López, JL and Zhang, XM and Smart, C and Blahovska, Z and Zarate Camargo, G and Kelly, S and de Jonge, R and Radutoiu, S},
title = {Functional capacities drive recruitment of bacteria into plant root microbiota.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42754709},
issn = {2058-5276},
support = {OPP11772165//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; NNF24SA0096909//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF24SA0096909//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF19SA0059362//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 024.004.14//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; },
abstract = {Root-associated microbiomes are shaped by the plant, yet vary across environments and hosts, challenging prediction and engineering. Here, to uncover principles of bacterial selection at the root-soil interface, we applied a systems-level approach using reconstitution studies with communities of isolates from Arabidopsis, barley and Lotus grown in soil. Functional divergence among the microbiota of the host plants reflected distinct strategies: in Arabidopsis and barley, recruitment was primarily shaped by inoculum, while Lotus root environment favoured fewer, functionally diverse isolates, akin to a 'Swiss army knife' strategy. Despite taxonomic variability, root microbiomes encoded overlapping functions. Across major taxa, isolates with broad but distinct functional repertoires within their families were consistently more abundant. Using a genome-to-function framework that is function centric, taxonomically inclusive and host-context aware, we identified 266 functions enriched across all root microbiomes. This functional backbone emerged as a core signature of plant-associated bacteria, providing a solid foundation for microbiome engineering in agriculture.},
}

@article {pmid42754770,
year = {2026},
author = {Petri, RM and Ricci, S and Jelinski, M and Hund, A},
title = {Observational study of the microbiome of perforated abomasal ulcers in unweaned beef calves in Canada.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42754770},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Abomasum/microbiology/pathology ; *Cattle Diseases/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *Stomach Ulcer/veterinary/microbiology ; Canada ; Bacteria/classification/genetics/isolation & purification ; Male ; *Microbiota ; },
abstract = {In western Canada, perforating abomasal ulcers (AU) are generally diagnosed postmortem in beef calves up to 2 months of age. Certain microbes have been associated with AU, but the evidence is circumstantial. Thus, analyzing the abomasal microbiome in calves with and without AU may provide insight into the etiology of the disease. Using 16S rRNA gene sequencing, abomasal tissues from Western Canadian beef calves, with (n = 27) and without AU (n = 17), were analyzed for microbial diversity. No significant differences were seen between microbiomes of AU and CON calves despite numerical differences in abundance. Therefore, a subsample of 18 tissues (12 AU, 6 CON) were analyzed using untargeted metagenomic sequencing for determination of phylogeny, and the presence of antimicrobial resistance genes (ARGs). Staphylococcaceae (1.5%), Campylobacteraceae (1.4%) and Enterobacteriaceae (1.4%) were seen across all samples. Differential abundance analysis revealed Streptomyces spp. REN17 to be less abundant in AU calves, suggesting a potential association between Streptomyces spp. and calf gut health. An ARG associated with polymyxin resistance was found to be differentially abundant in calves with a history of antimicrobial therapy. Although differences were observed in the predicted metabolic functions among groups, none reached statistical significance. In our study, no consistent microbial signature associated with AU was identified, despite the differential abundance of individual taxon, nor did prior antimicrobial therapy associate to the growth of specific microbiota. To better understand the potential role of the abomasal microbiota in AU etiology and the impact of early life interventions in beef calves, a larger sample size is needed.},
}

Animals
Cattle
*Abomasum/microbiology/pathology
*Cattle Diseases/microbiology
RNA, Ribosomal, 16S/analysis/genetics
*Stomach Ulcer/veterinary/microbiology
Canada
Bacteria/classification/genetics/isolation & purification
Male
*Microbiota

@article {pmid42754802,
year = {2026},
author = {Silva de Avó Freixo, H and Miot, HA and Ogawa, MM and de Castro Martins, IM and Leite E Silva, VR and Andreo Filho, N and Lopes, PS and Filho, RM and Bagatin, E},
title = {Urban Exposome and Skin Microbiome in Atopic Dermatitis: A Comparative Study Between Two Brazilian Municipalities.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42754802},
issn = {2193-8210},
support = {Vichy Exposome Grant 2022//Fondation L'Oréal/ ; },
abstract = {INTRODUCTION: Atopic dermatitis (AD) is thought to arise from the interplay of skin barrier dysfunction, type 2 immune dysregulation, and cutaneous dysbiosis, the last of these characterized by reduced bacterial diversity and predominance of Staphylococcus aureus. The urban exposome, including air pollution and reduced environmental microbial diversity, may modulate this dysbiosis. We hypothesized that patients with AD residing in a metropolitan area with a higher pollutant burden would show greater skin dysbiosis, reflected by a higher relative abundance of S. aureus, than patients residing in a municipality with a lower pollutant load and greater environmental biodiversity.

METHODS: This cross-sectional, comparative study enrolled ten children (6-12 years) and ten adults (20-31 years) with active AD, without specific treatment in the preceding 30 days, residing in the metropolitan region of São Paulo or in Botucatu, an interior municipality of São Paulo State, Brazil. Skin swabs were collected from eczematous lesions and characterized by 16S ribosomal RNA (rRNA) gene (V3-V4) sequencing. Alpha and beta diversity and the relative abundance of S. aureus, S. epidermidis, and S. hominis were compared between municipalities and age groups using generalized linear models, Bray-Curtis dissimilarity, principal coordinates analysis (PCoA), and permutational multivariate analysis of variance (PERMANOVA).

RESULTS: The sample (n = 20) had a predominance of male sex (60%) and moderate AD severity (75%). A total of 658 taxa were identified. Alpha diversity did not differ by municipality or age group, and PERMANOVA revealed no global difference in bacterial community composition (p > 0.1). However, participants residing in the metropolitan municipality showed a significantly higher relative abundance of S. aureus and higher proportions of S. aureus relative to total bacteria and to other staphylococci than those residing in the interior municipality.

CONCLUSION: Despite similar overall microbial diversity, patients with AD living in a metropolitan municipality showed selective enrichment of S. aureus compared with those in a less polluted interior municipality. These exploratory findings generate the hypothesis that the urban exposome contributes to cutaneous dysbiosis in AD and warrant confirmation in larger studies with objective exposure measurement.},
}

@article {pmid42754908,
year = {2026},
author = {Kaufhold, G and Bartolomaeus, TUP and Schütte, K and Schütte, T and Kamboj, S and Löber, U and Rahn, G and McParland, V and Braun, L and Markó, L and Mammadli, M and Krannich, A and Bahr, LS and Gutmann, F and Paul, F and Ducarmon, QR and Zeller, G and Mesnage, R and Wilck, N and Zernecke, A and Oefner, PJ and Gronwald, W and Müller, DN and Forslund-Startceva, SK and Bähring, S and Bartolomaeus, H and Siebert, N},
title = {Machine learning identifies microbiome and clinical predictors of sustained weight loss following prolonged fasting.},
journal = {Genome medicine},
volume = {18},
number = {1},
pages = {},
pmid = {42754908},
issn = {1756-994X},
mesh = {Humans ; *Fasting ; Female ; *Machine Learning ; Male ; Adult ; *Weight Loss ; *Gastrointestinal Microbiome ; Middle Aged ; Feces/microbiology/chemistry ; Body Mass Index ; Metabolome ; Body Composition ; Multiomics ; *Microbiota ; Predictive Learning Models ; Intermittent Fasting ; },
abstract = {BACKGROUND: Prolonged fasting may improve metabolic health, but controlled data in healthy adults with longer follow-up and multi-omics profiling are limited. We investigated the immediate and 12-week follow-up effects of a 5-day fasting intervention on body composition, gut microbiome, and circulating and fecal metabolites, and assessed whether baseline characteristics predict individual weight-loss response.

METHODS: In a randomized, waitlist-controlled trial, 38 healthy adults completed a 5-day fasting intervention with 12-week follow-up (LEANER study). Outcomes included body mass index and body composition, gut microbiome composition, and plasma and fecal metabolites. Changes over time and between groups were evaluated using regression-based models and paired non-parametric tests, as appropriate. Additionally, permutation-based multivariate testing was performed on microbiome and metabolome data. Twelve-week body weight response was predicted using data-driven machine learning with cross-validation, followed by external validation in three independent cohorts undergoing prolonged fasting protocols.

RESULTS: Fasting reduced body mass index acutely, predominantly driven by loss of fat mass, and these improvements partially persisted at 12 weeks. Fasting induced marked shifts in gut microbiome composition and in plasma and fecal metabolites. Post-fasting and longer-term changes in microbial diversity were associated with baseline microbiome diversity. A model combining baseline microbiome and clinical variables predicted body mass index response at 12 weeks; prominent predictors included an unclassified Faecalibacterium species, Oscillibacter sp. 50_27, low-density lipoprotein cholesterol, and systolic blood pressure. The model generalized to three independent cohorts, including individuals with metabolic syndrome, patients with multiple sclerosis exposed to repeated fasting, and healthy volunteers fasting for 6-12 days.

CONCLUSIONS: In healthy adults, a 5-day prolonged fasting intervention produces robust short-term metabolic changes with partial persistence and consistent remodeling of the gut microbiome and metabolite profiles. Baseline microbiome and clinical characteristics can help stratify expected longer-term responses, supporting the development of individualized fasting-based interventions.

TRIAL REGISTRATION: ClinicalTrials.gov, NCT04452916. Prospectively registered on June 29, 2020.},
}

Humans
*Fasting
Female
*Machine Learning
Male
Adult
*Weight Loss
*Gastrointestinal Microbiome
Middle Aged
Feces/microbiology/chemistry
Body Mass Index
Metabolome
Body Composition
Multiomics
*Microbiota
Predictive Learning Models
Intermittent Fasting

@article {pmid42754913,
year = {2026},
author = {Bajiya, RK and Agabi, R and García, JO and Torreno, VP and Armengaud, J and Grenga, L},
title = {From functional annotation to functional meaning in microbiome research.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42754913},
issn = {2524-6372},
support = {23002679//Région Occitanie Pyrénées-Méditerranée/ ; FoodMap//ANSES - CEA/ ; 101225682//Marie Skłodowska-Curie Actions Doctoral Networks programme/ ; 101225682//Marie Skłodowska-Curie Actions Doctoral Networks programme/ ; ANR-24-CE15-7400-01//Agence Nationale de la Recherche/ ; },
abstract = {Microbiome research has moved from cataloging community composition to asking what these communities do, but "function" is often used to describe fundamentally different levels of evidence. Functional claims may refer to functional capacity (what is encoded), functional realization (what molecular functions are actively engaged under specific conditions), or functional impact (the resulting consequences for hosts, microbial communities, or ecosystems). In this Perspective, we examine how functional annotations in microbiome research generate biological meaning and why current approaches support different kinds of inference. We propose a framework that distinguishes three levels of functional inference: capacity, realization, and impact. Homology-based, domain-centric, pathway-based, machine learning-driven, and multi-omics approaches each contribute differently to these levels, but none alone captures microbiome function in full. We argue that microbiome function should be interpreted as a hierarchy of inferences rather than a single property. Recognizing this distinction should improve how functional findings are interpreted, reported, and compared across microbiome studies. Accordingly, functional studies should explicitly state whether their conclusions concern capacity, realization, or impact, thereby clarifying the evidential basis of functional claims and improving their interpretation and comparison across microbiome studies.},
}

@article {pmid42755070,
year = {2026},
author = {Zhang, R and Niu, CE and Shi, HN and An, XJ and Li, Q and Geng, ZG and Zhang, JX and Xu, ZF and Yue, YJ},
title = {Comparative analysis of four compound stomachs development, fermentation dynamics, and microbiome structure in Hu sheep and its crossbred combinations.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.260416},
pmid = {42755070},
issn = {2765-0189},
abstract = {OBJECTIVE: This study was conducted to investigate the differences in fermentation parameters, epithelial development, and microbial composition across the four stomach compartments between Hu sheep and its crossbreds.

METHODS: Forty-eight approximately 3-month-old male lambs, assigned to three genetic groups (HH:♂Hu×♀Hu, n=16; DH:♂Poll Dorset×♀Hu, n=16; SH:♂Southdown×♀Hu, n=16), were raised under uniform nutritional and management conditions for 95 days. Feed intake was determined daily and body weight were measured every 20 days. At the end of the trial, six sheep per group close to the average weight were slaughtered. Samples of digesta and tissue from the four stomachs were collected. Fermentation parameters, epithelial development, and microbial community structure were analyzed.

RESULTS: Compared with the HH group (acetate: 25.8, 21.8, and 6.36 mmol/kg; propionate: 6.8, 5.60, and 3.65 mmol/kg; butyrate: 3.66, 3.19, and 1.38 mmol/kg), the DH group exhibited significantly higher acetate concentrations (45.3, 33.7, and 12.9 mmol/kg), propionate (14.3, 11.1, and 5.94 mmol/kg), and butyrate (12.9, 6.69, and 4.52 mmol/kg) in the rumen, reticulum, and omasum, respectively (p<0.05), indicating enhanced fermentation capacity, a significantly thicker rumen mucosal epithelium (p<0.05) suggesting a greater capacity for VFA absorption. Taxonomic analysis showed that Firmicutes and Bacteroidota were the predominant phyla in four stomachs. Differential analysis identified that the DH group had significantly enriched taxa associated with fiber degradation (e.g., Fibrobacterota, Spirochaetota) in the forestomachs. Conversely, the rumen of HH group was enriched with Anaerolineae, associated with complex plant fiber degradation. PICRUSt2 functional prediction indicated that differentially microbes in the DH group were primarily linked to the biosynthesis of lysine and arginine, whereas those in the HH group were enriched in degradation pathways such as amino acid degradation.

CONCLUSION: The DH group markedly elevated VFA production by modulating the forestomach microbial structure. Combined with adaptive improvements in rumen epithelial, this effect potentially enhanced energy utilization and growth performance.},
}

@article {pmid42755168,
year = {2026},
author = {Jassey, VEJ and Lafont Rapnouil, T and Le Geay, M and Walcker, R and Gandois, L and Barret, M and Fanin, N and Robroek, BJM and Lauga, B and Andrews, LO and Greuza, AB and Bakker, MR and Bertrand, G and Birkwald, T and Borges, PAV and Branfireun, B and Brearley, FQ and Brousseau, C and Bu, ZJ and Carrias, JF and Coffinet, S and Corbarra, B and Dias, EMF and Dorrepaal, E and Francez, AJ and Fu, Y and Gabriel, M and Gabriel, R and Gerin, S and Gilbert, D and Gogo, S and Granath, G and Gray, E and Heffernan, L and Heger, TJ and Juutinen, S and Kardol, P and Karofeld, E and Klimkowska, A and Küttim, M and Küttim, L and Kuuri-Riutta, O and Lacourse, T and Lamentowicz, M and Le Roux, G and Lindo, Z and Mackenzie, R and Marcisz, K and Mazei, YA and Mazei, NG and Mendes, CMF and Mitchell, EAD and Mora-Gomez, J and Müller, R and Pouliot, K and Purre, AH and Quaiser, A and Río, BR and Rober, AR and Rochefort, L and Rodríguez, AC and Sannel, ABK and Seemann, F and Servière, L and Strack, M and Swindles, GT and Talbot, J and Tsyganov, AN and Tuittila, ES and Tveit, AT and Väliranta, MM and Wyatt, KH and Ylänne, H and Yu, Z and Zarov, EA and Hamard, S},
title = {Tipping Points in Bacterial Richness Amplify Extracellular Enzyme Activities in Northern Peatlands.},
journal = {Global change biology},
volume = {32},
number = {9},
pages = {e71099},
doi = {10.1111/gcb.71099},
pmid = {42755168},
issn = {1365-2486},
support = {ANR-17-CE01-0007//Agence Nationale de la Recherche/ ; ANR-23-ERCC-0001-01//Agence Nationale de la Recherche/ ; ANR-24-CE02-6475//Agence Nationale de la Recherche/ ; },
mesh = {*Soil Microbiology ; *Bacteria/enzymology/classification ; *Biodiversity ; *Wetlands ; Sphagnopsida/microbiology ; Carbon Cycle ; Carbon/metabolism ; *Microbiota ; },
abstract = {Bacterial communities are vital to northern peatlands' carbon and nutrient cycling, one of the Earth's largest terrestrial carbon stores. However, their diversity and ecological roles at broad geographic scales remain partially understood, limiting our ability to predict their response to global change. Here, we combine a trans-Holarctic survey across 171 Sphagnum-dominated peatlands (SDPs) with a continental-scale reciprocal transplantation experiment to quantify how bacterial diversity shapes carbon and nutrient cycling across bioclimatic gradients. We show that bacterial diversity and composition differ markedly among peatland bioclimatic regions and are primarily structured by the universal abiotic drivers of northern ecosystems: minimum temperature, snow cover, and soil water content. Ecological models further revealed that deterministic processes accounted for approximately 80% of bacterial community assembly, highlighting the strong influence of environmental filtering. Biodiversity-Ecosystem Function analyses identified bacterial richness as a key driver of carbon and nutrient cycling. Using moving-window structural equation models, we identified a critical bacterial richness threshold, below which extracellular enzyme activities increased by ~60%. This transition coincided with stronger environmental filtering and shifts towards bacterial communities with a greater predicted potential for extracellular nutrient acquisition and heterotrophic metabolism. Together, these findings demonstrate that bacterial richness underpins peatland biogeochemical functioning and suggest that biodiversity loss may accelerate carbon turnover, weakening the capacity of northern peatlands to retain carbon. As climate change threatens this unique microbiome, safeguarding bacterial diversity will be critical for maintaining ecosystem resilience and the stability of this globally important carbon sink.},
}

*Soil Microbiology
*Bacteria/enzymology/classification
*Biodiversity
*Wetlands
Sphagnopsida/microbiology
Carbon Cycle
Carbon/metabolism
*Microbiota

@article {pmid42755253,
year = {2026},
author = {Gupta, KH and Israni, AK and Onyeaghala, G},
title = {Gut microbial metabolism of immunosuppressive drugs: from metagenomic associations to functional enzyme biomarkers.},
journal = {Current opinion in organ transplantation},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOT.0000000000001314},
pmid = {42755253},
issn = {1531-7013},
abstract = {PURPOSE OF REVIEW: Inter-individual variability in immunosuppressant exposure remains a major challenge in transplantation. Pharmacogenomics and host-related factors contribute to this variability, with increasing evidence suggesting that the gut microbiome is also an important determinant of drug metabolism. This review summarizes recent advances in microbiome-mediated metabolism of immunosuppressive drugs like tacrolimus and mycophenolate and highlights emerging functional approaches to identify clinically relevant microbial enzymes.

RECENT FINDINGS: Microbial β-glucuronidases contribute to the enterohepatic recirculation of mycophenolic acid by deconjugating mycophenolic acid glucuronide, influencing systemic exposure and gastrointestinal toxicity. In parallel, gut bacteria such as Faecalibacterium prausnitzii can directly metabolize tacrolimus into less active metabolites, potentially contributing to variability in drug exposure and dose requirements. Recent studies further demonstrate that metaproteomic and enzyme activity-based approaches provide greater functional resolution than metagenomics alone for identifying microbiome-associated drug metabolism pathways.

SUMMARY: Current evidence supports a significant role for the gut microbiome in immunosuppressant pharmacokinetics and functional microbial enzymes represent promising biomarkers of immunosuppressant disposition. Moving beyond gene-level associations toward the functional characterization of microbial enzymes through the integration of metaproteomics, metabolomics, and enzyme activity assays with pharmacokinetic modeling may facilitate development of microbiome-based biomarkers and microbiome-guided precision dosing strategies in transplantation. Future integration of microbiome-derived functional data into therapeutic drug monitoring and pharmacokinetic models may improve individualized immunosuppressive therapy and transplant outcomes.},
}

@article {pmid42755267,
year = {2026},
author = {Sampath, V and Lee, K and Kim, SJ and Kim, IH},
title = {Partial Replacement of Molasses with Monosodium Glutamate-Condensed Molasses Soluble enhance growth performance by maintaining gut health in finishing pigs.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag298},
pmid = {42755267},
issn = {1525-3163},
abstract = {A 10-week growth trial was conducted using three groups of 70 finishing pigs [210 head (Landrace × Yorkshire × (Duroc) with initial BW 53.92 ± 2.24 kg] to determine the effect of Monosodium Glutamate-Condensed Molasses Soluble (MSG-CMS) as a replacement for molasses on growth performance, nutrient digestibility, blood profiles, fecal microbiome composition, and meat quality in finishing pigs. For this, the pens of pigs (5 pigs/pen- 3 ♀and 2 ♂) were randomly allocated into 1 of 3 treatment groups in a completely randomized design with 14 replications/treatment. The dietary treatments were: TRT1, 4% Molasses; TRT2, 2% Molasses + 2% MSG-CMS; TRT3, 4% MSG-CMS. The test diets were fed in two phases: Phase 1, from week 0-5 and Phase 2, from week 5-10. Pigs fed the diet containing 4% MSG-CMS showed higher (P < 0.05) average daily gain and average daily feed intake during phases 1, 2, and the overall period compared with other treatments. However, final BW, gain-to-feed ratio, nutrient digestibility, backfat thickness, and lean meat percentage were not affected by dietary treatments. At week 10, pigs that received 4% MSG-CMS exhibited significantly higher (P < 0.05) blood insulin concentration, whereas no differences were detected in meat quality or carcass characteristics. Also, no differences were observed in alpha diversity indices among treatment groups. However, beta diversity analysis using unweighted UniFrac and Bray-Curtis PCoA demonstrated partial separation of microbial communities, with TRT3 showing a clearer clustering pattern. At the phylum level, TRT3 exhibited higher abundances of Firmicutes and Bacteroidota and a lower abundance of Proteobacteria. At the genus level, Prevotella and Lactobacillus were more abundant in TRT1, whereas Clostridium sensu stricto 1 was reduced in TRT3. LefSe analysis revealed enrichment of several fiber- and fermentation-associated taxa in TRT3, including unclassified Selenomonadaceae, Muribaculaceae, Treponema, and unclassified Ruminococcaceae. In summary, complete replacement of molasses with 4% MSG-CMS improved growth performance, without adversely affecting nutrient digestibility, gut microbial diversity, meat quality, or carcass characteristics, suggesting that MSG-CMS could serve as a potential alternative feed ingredient for improving the growth performance of finishing pigs.},
}

@article {pmid42755378,
year = {2026},
author = {Yuan, X and Li, N and Zhu, S and Zuo, T},
title = {Bacteriophages in humans: From discovery and mechanisms to therapeutic promise in combating disease.},
journal = {Chinese medical journal},
volume = {},
number = {},
pages = {},
pmid = {42755378},
issn = {2542-5641},
abstract = {Since the discovery of bacteriophages over a century ago, bacteriophages have evolved from fundamental biological models into promising therapeutic agents, especially in the era of antimicrobial resistance and in the treatment of human diseases. This article systematically reviews the key milestones in phage research and application at both international and Chinese fronts. It examines the evolving understanding of phage-bacterium interactions, which provides the development of targeted phage-based biocontrol and therapeutic strategies. Particular emphasis is placed on recent advances linking phages to human diseases, including their potential roles in gut microbiota modulation and chronic disease contexts. Despite promise, substantial challenges remain. The article concludes by discussing critical future directions, emphasizing the need for identifying key microbial targets in diseases, integrating phage therapy with emerging technologies to accelerate clinical translation, and exploring dietary phage interventions for disease prevention.},
}

@article {pmid42755487,
year = {2026},
author = {Hu, Y and Teng, C and Zhang, D},
title = {Global trends and emerging frontiers in cancer immunotherapy and gut microbiota-derived metabolites: a bibliometric analysis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1876450},
pmid = {42755487},
issn = {2235-2988},
mesh = {Humans ; *Bibliometrics ; *Immunotherapy/trends/methods ; *Neoplasms/therapy/immunology ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {OBJECTIVES: Cancer immunotherapy has achieved remarkable clinical success; however, therapeutic resistance remains a major challenge. Increasing evidence suggests that gut microbiota-derived metabolites play a critical role in modulating host immune responses and influencing treatment outcomes. This study aimed to systematically characterize the global research landscape and identify emerging trends in this field using bibliometric approaches.

METHODS: Publications were retrieved from the Web of Science Core Collection (WoSCC) and Scopus databases based on predefined search strategies. Only English-language articles and reviews were included. Bibliographic records were integrated and deduplicated using the bibliometrix R package. Descriptive analyses were performed to evaluate publication outputs, countries, institutions, authors, and journals. CiteSpace was used for reference burst detection, and VOSviewer was applied to construct keyword co-occurrence networks.

RESULTS: A total of 2,979 publications from 1973 to March 2026 were included, comprising 1,593 reviews and 1,386 original articles. China contributed the largest number of publications (1,121; 37.63%), followed by the United States (499; 16.75%). Notably, the United States exhibited the highest H-index and centrality, indicating its leading role in global research impact and collaboration networks. Sichuan University was the most productive institution (115 publications), with six of the top ten institutions located in China. Laurence Zitvogel (28 publications) and Guido Kroemer (22 publications) were the leading authors in this field. Frontiers in Immunology published the highest number of relevant articles (277). Keyword and temporal analyses indicated a shift from descriptive microbiome profiling toward mechanism-oriented and translational research. Recent hotspots include "immunomodulation", "the gut-liver axis", "intratumoral microbiota", and "microbial metabolites".

CONCLUSIONS: Microbial metabolites have emerged as key functional mediators shaping responses to cancer immunotherapy, reflecting a shift from microbiome composition toward metabolite-centered mechanisms. This field is undergoing a transition from descriptive profiling to mechanism-oriented and translational research. These findings provide important insights for developing microbiota-targeted strategies to enhance the efficacy of cancer immunotherapy.},
}

Humans
*Bibliometrics
*Immunotherapy/trends/methods
*Neoplasms/therapy/immunology
*Gastrointestinal Microbiome
Animals

@article {pmid42755519,
year = {2026},
author = {Schröttner, P and Harb, H},
title = {Editorial: Reviews in bacteria and host.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1961702},
doi = {10.3389/fcimb.2026.1961702},
pmid = {42755519},
issn = {2235-2988},
}