@article {pmid42809026,
year = {2026},
author = {Akanmu, AM},
title = {Beyond the Rumen: Current Evidence and Knowledge Gaps in Microbial Diversity and Function Across the Bovine Gastrointestinal Tract.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42809026},
issn = {1432-0991},
mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Tract/microbiology ; Rumen/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; Biodiversity ; },
abstract = {The bovine gastrointestinal tract (GIT) is a spatially organised microbial ecosystem, but the evidence supporting a whole-tract interpretation is highly uneven. This critical review distinguishes well-established rumen biology from emerging observations in the reticulum, omasum, abomasum, small intestine and hindgut. Comparative studies show strong regional filtering of microbial communities, yet most available datasets are cross-sectional, use digesta rather than mucosa, and infer function from DNA. Consequently, the presence of genes or taxa cannot be equated with active metabolism. Early life provides an important developmental dimension: microbial succession during the milk-to-solid-feed transition accompanies rumen maturation and region-specific immune development, although durable effects on adult productivity remain incompletely demonstrated. Across adult cattle, foregut fermentation supplies most microbially derived energy, whereas downstream compartments support residual fermentation, epithelial interactions and barrier-related processes whose quantitative contributions are less certain. Methanogenesis is therefore treated as one outcome among nutrition, immune function, pathogen resistance and gut integrity. Metagenomics, metatranscriptomics, metaproteomics and metabolomics are complementary rather than interchangeable; coordinated sampling is required to connect functional potential to activity and host phenotype. Priority should be given to longitudinal, multi-compartment, mucosa-and-digesta studies with absolute microbial measurements, metabolite fluxes and transparent causal inference. A tract-wide framework is valuable not because all compartments are equally understood, but because it makes the present evidence imbalance explicit and identifies where microbiome-targeted nutrition can be tested responsibly.},
}

Animals
Cattle/microbiology
*Gastrointestinal Tract/microbiology
Rumen/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
Biodiversity

@article {pmid42809046,
year = {2026},
author = {Dwivedi, S and Kumar, A and Upreti, D},
title = {Reconstructing bovine disease trajectories through integrative multi-omics: molecular decision nodes, predictive biomarkers and precision intervention.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42809046},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Multiomics ; Biomarkers ; *Cattle Diseases/genetics/diagnosis ; Genomics ; },
abstract = {Bovine diseases arise from dynamic interactions among genetic susceptibility, regulatory responses, immune activity, metabolism, microbial ecology and tissue function. Although individual omics studies have identified numerous disease-associated molecular signatures, many remain context-dependent and poorly reproducible across animals, breeds, disease stages and biological matrices. Integrative multi-omics extends beyond parallel profiling of individual molecular layers by connecting genomic variation with epigenetic regulation, transcriptional activity, protein and metabolite states, and microbial ecology to reconstruct coordinated mechanisms underlying disease development and recovery. This review synthesizes integrative multi-omics data across a trajectory from pre-disease vulnerability through active disease to persistence or functional recovery, while examining ecological destabilization as a process that may arise at different points along this continuum. Across diseases, integration of multiple molecular layers identifies recurrent associations among genetic regulation of disease-response pathways, inflammatory activation, immune-metabolic and redox imbalance, tissue-barrier dysfunction and microbiome-metabolite feedback. These interacting processes have the potential to provide greater biological and predictive information than isolated molecular alterations. We therefore propose that robust biomarker development should prioritize reproducible cross-omics signals and compact panels integrating three complementary components: disease burden or causal trigger, host-response state and functional consequence. Such biomarkers require validation across independent populations, breeds, disease stages and field conditions before clinical deployment. By linking molecular layers rather than cataloguing individual signatures, multi-omics can support more reliable disease prediction, mechanistically informed diagnostics, targeted intervention and selection for improved disease resistance and resilience in cattle.},
}

Animals
Cattle
*Multiomics
Biomarkers
*Cattle Diseases/genetics/diagnosis
Genomics

@article {pmid42809189,
year = {2026},
author = {Toda, M and Wangorsch, A and Yajima, Y and Guo, Y and He, C and Vieths, S and Scheurer, S},
title = {Immunomodulatory Function of Soluble Dietary Fiber: Toward Application for Prevention and Treatment of Food Allergies.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42809189},
issn = {1534-6315},
mesh = {Humans ; *Dietary Fiber/metabolism ; *Food Hypersensitivity/prevention & control/immunology/diet therapy ; Animals ; Gastrointestinal Microbiome/immunology ; Receptors, Pattern Recognition/metabolism ; beta-Glucans ; Immunomodulation ; },
abstract = {PURPOSE OF REVIEW: Gastrointestinal dysbiosis is implicated in the disruption of immune homeostasis and the pathogenesis of food allergies. Consequently, dietary fibers have gained attention as key molecules modulating microbial balance and immunity. This review aims to explore the immunomodulatory functions of dietary fibers commonly found in the human diet, including pectin, inulin, β-glucan, and mannan.

RECENT FINDINGS: Dietary fibers affect the immune system through two primary pathways: direct interaction with pattern recognition receptors and indirect action via microbial metabolism. In the indirect pathway, the gut microbiome utilizes these fibers as an energy source to produce a diverse range of metabolites. Notably, these fiber-derived processes exhibit a dual nature in food allergies, showing potential to either suppress or, in some cases, promote allergic inflammation. Understanding the unique physicochemical and physiological characteristics of individual types of fibers is important for the rational development of dietary-based prevention and treatment strategies in food allergies.},
}

Humans
*Dietary Fiber/metabolism
*Food Hypersensitivity/prevention & control/immunology/diet therapy
Animals
Gastrointestinal Microbiome/immunology
Receptors, Pattern Recognition/metabolism
beta-Glucans
Immunomodulation

@article {pmid42809217,
year = {2026},
author = {Timsit, JF and Roberts, JA and Kanj, S and Bassetti, M and Canton, R and Dark, P and Fowler, R and Huttner, A and Kollef, MH and Micek, ST and Sawyer, RG and Thy, M and Yahav, D and Daneman, N},
title = {Duration of antibiotic therapy in sepsis and severe infections in critically ill patients.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag458},
pmid = {42809217},
issn = {1535-4970},
abstract = {Antibiotic treatment duration in critically ill patients has undergone major reevaluation. Historically concerns for short therapy included a lower cure rate and emergence of resistance, whereas prolonged courses raised risks of microbiome disruption, superinfection, Clostridioides difficile colitis, and resistance. Defining optimal duration of therapy in sepsis and severe infections remains challenging due to heterogeneity in host immunity, pathogen virulence, infection site and source control. Mechanistic insights from microbiology and PK/PD highlight how bacterial inoculum, biofilms, mutant selection windows and altered drug distribution in critical illness influence bacterial clearance and resistance selection. Experimental models and PK-optimized dosing strategies underscore the potential to shorten therapy by accelerating pathogen eradication. Across a range of serious infections, randomized trials consistently show that short course therapy (<7 days) is noninferior to longer courses, including bacteremia, intra-abdominal infections and ventilator-associated pneumonia. Biomarker guided strategies-particularly procalcitonin-based algorithms-might further individualize duration of therapy and safely reduce exposure. Uncertainty remains for S. aureus bacteremia, infections caused by non-fermenting Gram-negative bacilli, difficult to treat multidrug-resistant organisms, invasive candidiasis and immunocompromised patients. Robust evidence supports markedly reduced duration of therapy for uncomplicated bloodstream infections after effective source control, intra-abdominal infections and ventilator-associated pneumonia. Infections involving retained prosthetic material or devices often require prolonged therapy or long-term suppressive regimens. Future research must include adequately powered trials across diverse populations, and evaluate rapid diagnostics, host-response profiling, and individualized response-guided strategies. Optimizing antibiotic duration in critically ill patients ultimately requires integrating mechanistic understanding, individual clinical evolution, and stewardship principles to balance potential efficacy and potential harm.},
}

@article {pmid42809314,
year = {2026},
author = {Dritsa, C and Hoffmann, S and Hulme, H and Lynch, C and Taylor, V and Burchmore, R and Cole, J and Goodwin, RJA and Wall, DM},
title = {Mapping gene expression across the microbiome-gut-brain axis of germ-free and specific pathogen-free mice.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {9},
pages = {},
pmid = {42809314},
issn = {1465-2080},
mesh = {Animals ; Mice ; *Brain/metabolism ; *Gastrointestinal Microbiome/genetics ; Germ-Free Life ; Specific Pathogen-Free Organisms ; Gene Expression Profiling ; Mice, Inbred C57BL ; Male ; },
abstract = {Perturbation of the gut microbiota has been implicated in neurological diseases via communication across the microbiome-gut-brain axis. As a result, the discovery of mechanisms underlying interaction across this axis is becoming increasingly important. The germ-free (GF) mouse model has enabled an improved understanding of the influence of the gut microbiota on brain development and function. By utilizing an advanced spatial profiling approach, we determined transcriptional changes in the brain, improving our understanding of how brain cells function and interact within their microenvironment in the absence of microbiome influence. Targeted regions of interest were selected based on brain regions implicated in neurological disease or reported structural differences between GF mouse brains and those of colonized mice. In the hippocampus, 276 differentially expressed genes (DEGs) were identified, 345 DEGs in the thalamus and 21 DEGs in the pons. Contrastingly, we identified only 2 DEGs in the midbrain and 4 in the medulla oblongata, with no DEGs in the cerebellum or corpus callosum. These data provide an overview of gut microbiota influence on gene expression in the brain, highlighting multiple genes of interest for further investigation in the context of microbiome influence on brain function and their potential relevance to neurological disease.},
}

Animals
Mice
*Brain/metabolism
*Gastrointestinal Microbiome/genetics
Germ-Free Life
Specific Pathogen-Free Organisms
Gene Expression Profiling
Mice, Inbred C57BL
Male

@article {pmid42809341,
year = {2026},
author = {Cao, S and Wang, T and Cao, L and Xu, F and Dong, Y and Zou, Z},
title = {The role of gut microbiota-immune axis in swallowing dysfunction and nursing interventions.},
journal = {Acta microbiologica et immunologica Hungarica},
volume = {},
number = {},
pages = {},
doi = {10.1556/030.2026.02927},
pmid = {42809341},
issn = {1588-2640},
abstract = {Dysphagia constitutes a growing global health burden, particularly among geriatric and post-stroke populations. Although traditionally managed through biomechanical interventions, emerging evidence underscores the microbiota-immune axis as a critical modulator of systemic resilience and clinical outcomes. This review delineates how dysphagia drives systemic dysbiosis via three primary mechanisms: dietary modification, descending migration of oral pathogens along the oral-gut-lung axis, and iatrogenic pharmacological effects. A core pathological consequence is the depletion of microbial metabolites, especially short-chain fatty acids (SCFAs), which undermines neurological recovery and musculoskeletal integrity through the gut-brain and gut-muscle axes. Such dysbiosis further weakens intestinal barrier function, precipitating endotoxin translocation, chronic systemic inflammation, and elevated risk of life-threatening complications like aspiration pneumonia. Consequently, nursing practice should integrate microbiome-targeted strategies. Key interventions encompass nutritional modulation with specific probiotics (e.g., Lactobacillus rhamnosus GG) and prebiotics to restore SCFA levels, enhanced oral care to minimize pathogen reservoirs, and pharmacological stewardship to mitigate iatrogenic microbial disruption. Adopting these tailored approaches, these can transit nursing care from compensatory support to actively promoting physiological recovery and immune resilience in dysphagia patients.},
}

@article {pmid42809429,
year = {2026},
author = {He, DS and Liao, F and Chen, HL and Zhang, Q and Wei, MX and Guo, DM},
title = {Gut Microbial Function and Immune Aging: An Evidence-Graded Framework Linking Microbial Metabolites to Healthspan and Age-Related Disease.},
journal = {Aging and disease},
volume = {},
number = {},
pages = {},
doi = {10.14336/AD.2026.0884},
pmid = {42809429},
issn = {2152-5250},
abstract = {This narrative review examines how the metabolic output of the intestinal microbiota, rather than its taxonomic composition alone, relates to immune aging and to clinically meaningful geroscience outcomes. We organise the evidence around four questions: which microbial features are reproducibly associated with older age, which host pathways plausibly mediate their effects, how strong the evidence is for each mechanistic step, and what this implies for intervention. Three points structure the synthesis. First, the microbiota of older adults is not a single "dysbiotic" state: much of the reported difference between younger and older cohorts is attributable to frailty, multimorbidity, polypharmacy, residential setting, diet, physical activity, bowel transit and geography rather than to chronological age, and healthy-longevity phenotypes frequently diverge from the frail-elderly phenotype. Second, the dominant mediators-short-chain fatty acids (SCFAs), bile acids, tryptophan and polyphenol derivatives, polyamines and trimethylamine N-oxide (TMAO)-are context-dependent rather than uniformly protective or harmful, their host effects varying with local versus systemic concentration, receptor distribution, immune state, hepatic and renal clearance, and measurement platform. Third, most human data are cross-sectional; causal inference rests largely on rodent transfer experiments whose translational relevance to human healthspan is unresolved. We therefore label the evidence type supporting each major claim, compare cardiometabolic, neurodegenerative, hepatic, musculoskeletal and oncological domains, and appraise microbiota-targeted interventions with attention to strain, dose and formulation specificity, replication failure, endpoint heterogeneity, and safety in frail or immunocompromised older adults. We conclude by proposing an evidence-graded framework mapping defined microbial functions onto discrete features of immune aging and onto validated geroscience endpoints, and by identifying the designs required to move from association to intervention. The causal and clinical evidence base remains limited, and changes in microbiome composition should not be equated with gains in healthspan.},
}

@article {pmid42809656,
year = {2026},
author = {Qin, Y and Han, B and Wang, W and Xu, H and Zhou, H and Ji, X and Liu, W},
title = {Black soldier fly and uric acid-degrading bacteria contribute to bioconvert duck manure in an efficient manner.},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag297},
pmid = {42809656},
issn = {1938-291X},
abstract = {Duck manure, a major pollutant of intensive poultry production, is characterized by high organic load and nutrient content. However, the high water content of duck manure virtually impedes effective manure management. Here, we report the suitability of duck manure as a rearing substrate for larvae of black soldier fly Hermetia illucens L. (Diptera: Stratiomyidae), achieving a corresponding reduction in organic liquid waste. First, duck manure efficiently sustains the development and growth of black soldier fly larvae and is optimized to rear black soldier fly larvae by appropriately adding corn stalk powders. More importantly, the microbiome plays a key role in promoting black soldier fly larvae to bioconvert the duck manure nutrients into insect biomass. Finally, the larval frass exhibited suppressive effects against the plant pathogen Ralstonia solanacearum (Burkholderiales: Burkholderiaceae). Overall, black soldier fly larvae and the microbiome contribute to valorize and bioconvert duck manure in an efficient and environmentally friendly manner, supporting a circular economy.},
}

@article {pmid42809711,
year = {2026},
author = {Burke, BI and Valentino, TR and Ismaeel, A and Wen, Y and McCarthy, JJ},
title = {Microbial-Derived Exerkines as a Model of Drug Discovery.},
journal = {American journal of physiology. Cell physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpcell.90006.2026},
pmid = {42809711},
issn = {1522-1563},
support = {R01AR084282/AR/NIAMS NIH HHS/United States ; R00AR081367/AG/NIA NIH HHS/United States ; P20GM156679/GM/NIGMS NIH HHS/United States ; R01AR084282/AR/NIAMS NIH HHS/United States ; R00AR081367/AG/NIA NIH HHS/United States ; P20GM156679/GM/NIGMS NIH HHS/United States ; },
abstract = {There has been a growing interest in the utilization of the gut microbiome as a therapeutic tool. The relationship between the gut microbiome and exercise provides a unique opportunity to maximize the therapeutic capacity of the gut microbiome. Here, we summarize the potential of leveraging the gut microbiome to confer the health benefits of exercise through a novel class of microbial metabolites termed microbial-derived exerkines (MDEs). We identify multiple candidate and established MDEs described in the literature (e.g., pipecolic acid, succinate, short-chain fatty acids, indole-3-propionic acid, 3-hydroxyphenylacetic acid) and explore their implications in conditions such as inflammatory bowel disease, aging, skeletal muscle atrophy, cancer, diabetes, cardiovascular disease, and Alzheimer's disease. Given the beneficial effects of exercise on numerous diseases, we anticipate MDEs will be a productive avenue for drug discovery and therapeutic progress.},
}

@article {pmid42809968,
year = {2026},
author = {Nyamjav, I and Lee, E and Kim, HR and Sung, BH and Suh, DE and Lee, S},
title = {Enzymatic biotransformation of polystyrene: Interfacial oxidative modification by a serine hydrolase from Pseudomonas aeruginosa.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143724},
doi = {10.1016/j.jhazmat.2026.143724},
pmid = {42809968},
issn = {1873-3336},
abstract = {Polystyrene (PS) is highly resistant to biodegradation, and the enzymatic processes capable of initiating its environmental transformation remain poorly defined. This study investigates the previously underexplored association between a purified serine hydrolase (SH) from Pseudomonas aeruginosa, a bacterium isolated from the gut microbiome of PS-fed Zophobas atratus, and the early-stage oxidative modification of PS at the polymer-water interface. Under aqueous conditions, SH-treated high-molecular-weight PS films exhibited pronounced nanoscale surface alterations and progressive oxygen functionalization, as demonstrated by field-emission scanning electron microscopy (FE-SEM), Fourier transform infrared spectroscopy (FT-IR), and X-ray photoelectron spectroscopy (XPS). These surface chemical changes were accompanied by a modest reduction in number-average molecular weight (Mn) from 36.7 ± 0.5 kDa to 33.8 ± 0.2 kDa, while the weight-average molecular weight (Mw) remained largely unchanged, indicating limited molecular weight reduction without extensive polymer depolymerization. AEBSF inhibition further supported the involvement of SH activity in the observed PS surface modification. Gas chromatography-mass spectrometry (GC-MS) detected signals tentatively assigned to low-molecular-weight aromatic compounds, including oxygenated species, consistent with chemical transformation associated with SH treatment. Structural modeling and molecular docking suggested that SH adopts a conserved α/β-hydrolase fold with a surface-accessible aromatic binding cavity, potentially facilitating interactions with styrenic motifs at the polymer-water interface. Collectively, these findings reveal a novel association between SH activity and interfacial PS modification, highlighting enzyme-associated surface oxygenation as a potential early-stage process in plastic aging with implications for the environmental fate and potential chemical risks of persistent plastic pollutants.},
}

@article {pmid42810054,
year = {2026},
author = {Ghorbani, Y and Schwenger, KJP and Maughan, H and Teterina, A and Lou, W and Comelli, EM and Fischer, SE and Jackson, TD and Okrainec, A and Allard, JP},
title = {Multi-omic profiling and pathways related to changes in liver histology after Roux-en-Y gastric bypass: a longitudinal study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106498},
doi = {10.1016/j.ebiom.2026.106498},
pmid = {42810054},
issn = {2352-3964},
abstract = {BACKGROUND: Roux-en-Y gastric bypass (RYGB) improves metabolic dysfunction-associated steatotic liver disease (MASLD). However, the impact of RYGB on hepatic transcriptome, faecal microbiome and serum/faecal metabolome remain understudied. Our objective was to investigate the change in these omics and their relationships with changes in liver histology.

METHODS: In this prospective cohort study, patients undergoing RYGB were recruited between 2013 and 2020 and followed for 12 months. Anthropometrics, biochemistry, hepatic transcriptome, faecal microbiome (shotgun metagenomics) and serum/faecal metabolomes were measured. Liver histology and NAFLD Score (NAS) were assessed.

FINDINGS: Thirty-eight patients completed the study. Anthropometrics, biochemical and histological parameters improved post-RYGB (p < 0.05). Hepatic transcriptome analysis revealed a co-expression module enriched in fatty acid metabolism which correlated with changes in NAS post-RYGB (ρ = 0.38, p = 0.019). The core enrichment genes in this pathway were involved in mitochondrial and peroxisomal β-oxidation (ACADVL, ACOX1, and EHHADH) and the tricarboxylic acid (TCA) cycle (SUCLG2, SDHC, and SERINC1). There was an increase in TCA cycle gene expression associated with the resolution of ballooning, while upregulation of β-oxidation genes correlated with less reduction in NAS, ballooning, and inflammation. Metabolomic changes related to the identified co-expression module and pathways reveal a significant increase in faecal acylcarnitines, likely due to malabsorption from RYGB, with a significant reduction in circulating acylcarnitines which correlated positively with SUCLG2 expression and resolution of ballooning. Additionally, the increase in faecal acylcarnitines positively correlated with the bacterial species utilising acylcarnitines. In network analysis, ballooning of hepatocytes was associated with faecal/serum acylcarnitines and TCA metabolites while SUCLG2 was the hub gene associated with these changes.

INTERPRETATION: These findings provide insight on how post-RYGB changes in the transcriptome, metabolome, and microbiome could be associated with improvement in liver histology and may inform the development of future strategies for MASLD management.

FUNDING: Canadian Institutes of Health Research and American College of Gastroenterology.},
}

@article {pmid42810090,
year = {2026},
author = {Hossain, ME and Amin, NB},
title = {How close are modern broilers to their physiological ceiling? Have genetic, nutritional, and precision technologies reached biological limits? A systems biology perspective through physiological ceiling theory.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107849},
doi = {10.1016/j.psj.2026.107849},
pmid = {42810090},
issn = {1525-3171},
abstract = {This review examines the hypothesis that modern broiler chickens may be approaching a multidimensional physiological limit to further productivity improvement and evaluates the extent to which current evidence supports this proposition. Over the past century, genetic selection, nutritional optimization, health management, and technological innovations have dramatically enhanced growth rate, feed conversion efficiency, and carcass yield. However, these gains have increasingly been accompanied by physiological trade-offs, including skeletal abnormalities, muscle myopathies, metabolic disorders, reduced thermal tolerance, and welfare challenges. Rather than assuming the existence of a definitive biological ceiling, this review introduces the concept of a "broiler productivity ceiling" as a systems-based conceptual framework for interpreting the interaction between productivity gains and emerging biological constraints. Evidence relating to gastrointestinal capacity, mitochondrial bioenergetics, skeletal integrity, cardiovascular and respiratory function, immune competence, microbiome dynamics, and environmental adaptability is critically evaluated to assess whether these systems may act as limiting factors to future performance improvement. The review further examines the roles of metabolic heat production, nutrient utilization efficiency, oxygen delivery capacity, and muscle hypertrophy-associated disorders as potential indicators of increasing physiological strain. Advances in omics technologies, precision nutrition, microbiome modulation, and digital livestock systems are discussed as tools for identifying, monitoring, and potentially alleviating biological constraints. Overall, current evidence suggests the emergence of important physiological trade-offs and diminishing returns in some productivity traits but remains insufficient to conclusively demonstrate that an absolute biological ceiling has been reached. Future progress will likely depend on enhancing resilience, robustness, and system-wide biological efficiency rather than pursuing growth acceleration alone.},
}

@article {pmid42810292,
year = {2026},
author = {Pujara, DS and Casteel, CL},
title = {Non-coding RNAs: cross-kingdom regulators of plant-virus-vector interactions in complex agroecosystems.},
journal = {Current opinion in virology},
volume = {77},
number = {},
pages = {101585},
doi = {10.1016/j.coviro.2026.101585},
pmid = {42810292},
issn = {1879-6265},
abstract = {Plant viruses depend on insect vectors for dissemination in complex agroecosystems and often exploit plant and insect physiology to enhance transmission. This review synthesizes recent advances in understanding cross-kingdom exchange of non-coding RNAs (ncRNAs) as a central mechanism shaping plant-virus-vector interactions and broader agroecosystem dynamics. ncRNAs are exchanged among plants, insect vectors, and viruses via the phloem, insect saliva, and external plant surfaces through exudates. These molecules can suppress plant antiviral and anti-insect plant responses, modulate vector biology and behavior, and shape associated microbial communities, including endosymbionts and the plant microbiome. Despite rapid progress, key gaps remain in validating functional targets, identifying transport mechanisms, and demonstrating the ecological relevance of ncRNA exchange in agricultural and natural systems. Elucidating these processes will inform intervention strategies, including RNAi-based vector control and microbiome engineering approaches.},
}

@article {pmid42810338,
year = {2026},
author = {Yang, L and Singh, V and Gawey, BJ and Sinnwell, JP and Johnson, S and Billings, EC and Van Gorp, TM and Harrington, JJ and Slama, MQ and Till, LM and Singh, M and Samineni, TR and Zhu, M and Kalari, KR and Farrugia, G and Chen, J and Mars, RAT and Kashyap, PC},
title = {Microbiome signatures linked to cancer and treatment adverse events in a real-world cohort.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.09.009},
pmid = {42810338},
issn = {1097-4172},
abstract = {The gut microbiome has emerged as a key contributor to cancer biology. Prior studies have focused on individual cancers and often overlook comorbidities, obscuring whether reported associations are specific to a cancer type. Here, we present findings from a real-world mixed-cancer cohort (Mayo Clinic Cancer Microbiome), comprising 1,364 cancer patients and 287 healthy controls. By applying a framework to account for non-specific microbiome associations with cancer, comorbidities, and demographic and clinical variables, we identified 341 cancer-associated species across five cancer classes that represent the most plausible contributors to cancer pathogenesis. Within cancer classes, we found lower levels of fecal bile acids and C. scindens in early-onset breast cancer and elevated lactate and Veillonella parvula in early-onset colorectal cancer. Additionally, Anaerostipes hadrus encoding dihydropyrimidine dehydrogenase was protective against 5-fluorouracil-induced diarrhea. These findings demonstrate the strength of our cohort and provide a foundational resource for the discovery of cancer-specific microbiome signatures and predictive biomarkers.},
}

@article {pmid42810465,
year = {2026},
author = {Benktander, J and Estensoro, I and Sitjà-Bobadilla, A and Piazzon, MC and Lindén, SK},
title = {Gilthead seabream (Sparus aurata) mucus core O-glycosylation changes in Enteromyxum leei parasitized intestine.},
journal = {Fish & shellfish immunology},
volume = {179},
number = {},
pages = {111741},
doi = {10.1016/j.fsi.2026.111741},
pmid = {42810465},
issn = {1095-9947},
abstract = {The gilthead seabream, Sparus aurata, is an important fish within the aquaculture industry. Enteromyxum leei causes chronic enteritis, resulting in reduced nutrient absorption and growth, cachexia and/or death of the fish. There are currently no applied treatments for this disease. To investigate the first barrier pathogens encounter, the mucus, we characterized the gilthead seabream intestinal mucus glycome from five control and five E. leei infected gilthead seabream using mass spectrometry and investigated the link between identified glycans and infection parameters, gene expression and microbiome. We identified 110 O-glycans and 9 N-glycans, whereof the latter constituted 12% of the mucus glycome and did not differ between infected and control fish. The most pronounced O-glycome change detected was decreased levels of Core 4 O-glycans in E. leei infected intestines. The variance of the O-glycosylation was also larger in infected fish compared to the control fish. The relative abundance of Core 4 glycans correlated with the expression levels of muc13 and imuc as well as with key genes in type I immune responses. Furthermore, the decrease in Core 4 glycans was also linked to decreased abundances of Streptococcus, Staphylococcus and Corynebacterium. This work presents the most probable key players in these complex interactions and provides a platform for further studies aiming to identify how the mucosal glycosylation protects the fish from infection.},
}

@article {pmid42810587,
year = {2026},
author = {Hervé, HAAS and Olivier, HAASFERRUA and Sébastien, HAASFERRUA},
title = {Symbiotoxicity and infectious diseases: A proposed conceptual framework linking the exposome, microbiome, resistome, and infection risk.},
journal = {Infectious diseases now},
volume = {},
number = {},
pages = {105356},
doi = {10.1016/j.idnow.2026.105356},
pmid = {42810587},
issn = {2666-9919},
abstract = {Symbiotoxicity refers to the capacity of environmental stressors to alter not only the host organism, but also the microbiomes with which it lives in symbiosis. Applied to infectious diseases, this concept suggests that drug, chemical, or environmental exposure could promote certain infections by disrupting the protective functions of the microbiome. Intestinal, respiratory, skin, and vaginal microbiomes contribute to colonization resistance, maintenance of epithelial barriers, maturation of anti-infective immunity, and structuring of the resistome. Antibiotics provide the best-established model, particularly through recurrent Clostridioides difficile infection, alteration of the neonatal microbiome, and enrichment of the resistome. More recent data suggest that non-antibiotic drugs, industrial or agricultural contaminants, metals, air pollutants, and plasticizers may likewise modify microbial communities. This issue is particularly relevant in newborns and preterm infants, whose microbiome, barriers, and immune system are still maturing. Intestinal colonization preceding some neonatal bloodstream infections illustrates a possible continuum from ecological disruption to pathobiont dominance and invasive infection. However, infectious symbiotoxicity should be regarded as a conceptual framework rather than an established diagnostic entity. It represents an integrative approach linking the exposome, microbiome, resistome, immune maturation, and infection risk, which remains to be confirmed by longitudinal, mechanistic, and interventional studies.},
}

@article {pmid42810699,
year = {2026},
author = {Johnston, CJ and Thompson, SL},
title = {GLT-1 and alcohol.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.alcohol.2026.09.007},
pmid = {42810699},
issn = {1873-6823},
abstract = {Glutamate transporter 1 (GLT-1) is responsible for the uptake of glutamate from the extracellular space, predominantly into astrocytes that insulate glutamatergic synapses. This transport is the primary method by which glutamate is removed from the synapse, as, unlike several other neurotransmitters, there is very little reuptake of glutamate by presynaptic neurons following release. As such, GLT-1 is crucial for homeostatic functioning of glutamatergic synapses, with disruptions such as excessive downregulation contributing to excitotoxicity. Alcohol is one example of an exogenous agent that can downregulate GLT-1 expression with chronic exposure in a brain region-specific manner, which is thought to underlie, in part, the dysregulated glutamatergic signaling observed in alcohol use disorder. This reduction in GLT-1 is thought to, in turn, modulate alcohol use behaviors. The pharmacological agents that restore GLT-1 expression and reduce alcohol intake, most notably the beta-lactam antibiotics, typically also modify peripheral systems, such as immune signaling and makeup of the gut microbiome, suggesting linkage between the central and peripheral effects of chronic alcohol. However, the direct role of GLT-1 in alcohol drinking, and how modulation of GLT-1 is driven by peripheral versus central mechanisms, is not completely understood. Here, we summarize the literature on effects of alcohol on GLT-1 across species and paradigms, how GLT-1 modulation impacts alcohol-related behaviors, and putative mechanisms including an emphasis on peripheral systems. We discuss the inconsistencies in GLT-1 effects between studies and the skewed distribution of experimental designs in this field. We highlight outstanding gaps in knowledge and potential clinical implications, particularly how modulation of GLT-1 expression, especially through peripheral mediators, may present treatment targets for disorders marked by glutamatergic dysfunction such as alcohol use disorder.},
}

@article {pmid42810811,
year = {2026},
author = {Zhang, X and Li, Z and Hua, H and Song, H and Qian, S and Huang, X and Ye, G and Huang, Y and Wang, Q and Zheng, B and Xu, X and Li, Y and Zhu, Y and Yu, L and Hong, Y and Yuan, H and Zhang, J},
title = {Screening of known gut microbiome-derived metabolites in anti-tumor immunity of colorectal cancer.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {9},
pages = {},
doi = {10.1136/jitc-2026-015554},
pmid = {42810811},
issn = {2051-1426},
mesh = {Humans ; *Colorectal Neoplasms/immunology/metabolism/drug therapy/pathology ; Animals ; Mice ; *Gastrointestinal Microbiome/immunology ; Female ; Immunotherapy/methods ; Male ; },
abstract = {BACKGROUND: Most colorectal cancers (CRCs) patients with microsatellite stability (MSS) have minimal benefit from immune checkpoint inhibitor monotherapy, and even after PD-1/PD-L1 blockade, T cell function remains inadequately restored, highlighting the importance of PD-1 downstream signaling events. SHP-2 is a critical effector of PD-1 downstream signaling and plays a key role in establishing the immunosuppressive tumor microenvironment in CRC. Gut microbial metabolites are emerging as regulators of anti-tumor immunity, but their role in modulating the PD-1/SHP-2 interaction remains unknown.

METHODS: We established a split-luciferase complementation screening system based on the PD-1/SHP-2 interaction and systematically screened a library of human gut microbial metabolites (n=480). The effect of candidate metabolites on T cell function was assessed in vitro using flow cytometry, confocal microscopy, and cell viability assays. Using a mouse colon cancer model, we further investigated the role of taurocholic acid (TCA) and glycodeoxycholic acid (GDCA) in the tumorigenesis and immunotherapy of CRC. Finally, the clinical relevance of metabolite-producing bacterium was examined in tumor specimens from CRC patients (n=53) using fluorescence in situ hybridization and real-time PCR assays.

RESULTS: We identified the conjugated bile acids TCA and GDCA as enhancers of the PD-1/SHP-2 interaction. Mechanistically, TCA and GDCA stabilized the PD-1/SHP-2 complex through an allosteric mechanism by promoting PD-1 phosphorylation. Functionally, two metabolites suppressed CD8[+] T cell activation, proliferation, and cytotoxicity in a PD-1/SHP-2-dependent manner, thereby accelerating tumor progression in vivo. Conversely, pharmacological depletion of TCA and GDCA using the bile acid sequestrant cholestyramine (CHO) effectively reversed their immunosuppressive effect and synergized with anti-PD-1 antibody therapy to inhibit the tumorigenesis of CRC. Clinical sample analysis revealed that the abundance of Clostridium scindens, the primary bacterial source of TCA and GDCA, was inversely correlated with CD8[+] T cell infiltration in tumor tissues from CRC patients.

CONCLUSIONS: This study reveals a "Bile acid-associated metabolites-Immune checkpoint" regulatory axis that drives immunosuppression in CRC. The identification of TCA and GDCA as endogenous enhancers of PD-1 signaling provides a mechanistic rationale for targeting these metabolites to overcome immunotherapy resistance.},
}

Humans
*Colorectal Neoplasms/immunology/metabolism/drug therapy/pathology
Animals
Mice
*Gastrointestinal Microbiome/immunology
Female
Immunotherapy/methods
Male

@article {pmid42811102,
year = {2026},
author = {Noonan, AJC and Moriniere, L and Rivera-López, EO and Patel, K and Pena, M and Svab, M and Kazakov, A and Deutschbauer, A and Dudley, EG and Mutalik, VK and Arkin, AP},
title = {Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes using machine learning.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42811102},
issn = {2058-5276},
support = {DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; 2220735//NSF | Directorate for Biological Sciences (BIO)/ ; 2220735//NSF | Directorate for Biological Sciences (BIO)/ ; 2220735//NSF | Directorate for Biological Sciences (BIO)/ ; PEN4826//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by challenges related to selection of phages infecting specific bacterial strains. Here we present a phylogeny-agnostic machine-learning framework predicting strain-level phage-host interactions across diverse bacterial genera from genome sequences alone. Systematically optimizing the workflow over 13.2 million training runs across six datasets (115,037 interactions, 949 bacterial strains, 518 phages), we achieved performance matching species-specific methods (AUROC 0.67-0.94) while eliminating phylogenetic constraints. Experimental validation of 1,240 predicted E. coli phage-host interactions confirmed generalizability (AUROC 0.84), while genome-wide RB-TnSeq screens verified that 68.6% of experimentally identified infection mediators were captured computationally. Model-guided cocktail design achieved up to 97.5% bacterial coverage with five phages, and up to a 3.1-fold improvement in single-phage selection over promiscuity-based selection. This platform enables rational phage-therapy design and precision microbiome engineering with applications across clinical, agricultural and industrial contexts.},
}

@article {pmid42811155,
year = {2026},
author = {Gao, W and Wang, X and Shi, Y and Wu, G and Zhou, M and Lin, X},
title = {Association of gut microbiota composition and microbe-host interactions with response to chemoimmunotherapy in gastric cancer.},
journal = {Genes and immunity},
volume = {},
number = {},
pages = {},
pmid = {42811155},
issn = {1476-5470},
abstract = {Immune checkpoint inhibitors combined with chemotherapy have improved outcomes for advanced gastric cancer, yet only a subset of patients derive benefit, and the contribution of the gut microbiome remains incompletely defined. To identify microbial signatures associated with chemoimmunotherapy response, we performed 16S rRNA gene sequencing on 90 fecal samples collected from 30 patients at baseline, one month after treatment initiation, and at the end of therapy. Patients were stratified by RECIST1.1 criteria into partial response (PR), stable disease (SD), and progressive disease (PD). While overall microbial composition and alpha diversity remained stable over time, immunotherapy enriched Lachnospiraceae and Bacteroidaceae. Notably, baseline microbiota differed significantly among response groups: Senegalimassilia and Lactobacillus were overrepresented in PR patients, whereas Parvimonas, Intestinibacter, and Catenibacterium characterized the SD and PD groups. By integrating public databases, we constructed microbe-metabolite-target and microbe-host interaction networks, indicating that response-associated genera may modulate host genes such as IFNG, IL12B, CXCL6, and DUOX2, thereby influencing CD8[+] T cell infiltration. These findings identify gut microbial signatures as predictive biomarkers and provide mechanistic insight into microbiome-mediated chemoimmunotherapy efficacy in gastric cancer.},
}

@article {pmid42811337,
year = {2026},
author = {Detman-Ignatowska, A and Schiro, G and Filip, R and Samborowska, E and Karczmarski, J and Jarmakiewicz-Czaja, S and Jakubowska, K and Williams, A and Hickman, NR and Laubitz, D and Sikora, A},
title = {Fecal microbiota fermenting simple organic carbon substrates in vitro as microbial factories capable of distinguishing Crohn's disease from healthy states.},
journal = {Microbial cell factories},
volume = {25},
number = {1},
pages = {},
pmid = {42811337},
issn = {1475-2859},
support = {MG-2/21-18//Institute of Biochemistry and Biophysics Polish Academy of Sciences/ ; },
mesh = {Humans ; *Feces/microbiology ; Fermentation ; *Crohn Disease/microbiology/diagnosis ; Lactic Acid/metabolism ; Butyrates/metabolism ; *Gastrointestinal Microbiome ; Acetates/metabolism ; Bacteria/metabolism/classification ; Glucose/metabolism ; },
abstract = {BACKGROUND: Crohn's disease (CD) is characterized by low microbial richness and diversity of the gut microbiome, shifts in the abundance of specific taxa, reduced presence of C2-C6 organic acid producers, especially butyrate-forming bacteria, and alterations in gut metabolites. This study aimed to demonstrate differences in the dynamics and fermentation activity of the fecal microbiota of CD patients and healthy individuals (HIs) grown in vitro on glucose or a mixture of acetate and lactate (fecal microbiota batch cultures). Glucose was used as a substrate for glycolytic fermentation, whereas a mixture of acetate and lactate supported related pathways leading to the production of C2-C6 organic acids, particularly butyrate via the conversion of lactate and acetate.

RESULTS: HI fecal microbiota cultures produced butyrate mainly through lactate and acetate transformation rather than via glucose fermentation. This pathway was impaired in the CD fecal microbiota cultures, which exhibited reduced synthesis of butyrate, valerate, caproate and propionate, and excessive production of ethanol and certain amino acids. These distinct fermentation activities stemmed from differences in the original CD and HI fecal microbiota composition that were further accentuated in batch cultures. The number of beneficial commensal bacteria (e.g., Coprococcus catus, Ruminococcus torques, Gemmiger formicilis, Eubacterium rectale, Fusicatenibacter saccharivoransi, Faecalibacterium prausnitzii) were significantly lower in the CD fecal microbiota cultures and correlated with reduced butyrate, valerate and caproate levels. Conversely, an overabundance of the recognized CD dysbiosis-associated bacteria, such as Escherichia coli, was reflected in elevated ethanol and amino acid levels in post-fermentation liquids. Metabolic potential analysis further indicated an enrichment of genes encoding enzymes involved in ethanol and amino acid biosynthesis in CD fecal microbiota cultures and highlighted the metabolic versatility of E. coli.

CONCLUSIONS: Fermentation patterns of fecal microbiotas in batch cultures can distinguish CD-associated dysbiosis from a healthy microbiome, with particular emphasis on lactate and acetate conversion to butyrate as a key pathway of butyrate production. The differences are observed under standardized in vitro conditions without the need to reconstruct the intestinal environment. These findings, pending further validation, may offer novel diagnostic opportunities and have implications for strategies aimed at restoring a healthy gut microbiome.},
}

Humans
*Feces/microbiology
Fermentation
*Crohn Disease/microbiology/diagnosis
Lactic Acid/metabolism
Butyrates/metabolism
*Gastrointestinal Microbiome
Acetates/metabolism
Bacteria/metabolism/classification
Glucose/metabolism

@article {pmid42811470,
year = {2026},
author = {Ye, X and Xu, C and Yao, S and Shen, J and Li, Z and Zhang, Y and Wu, F and Li, X and Ji, Y and Zhang, L and Huang, Y and Li, Z and Qin, H and Cui, Z},
title = {Enhanced Endophytic Colonization of Flavobacterium Promotes Plant Resistance to Fusarium Wilt.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77725},
doi = {10.1002/advs.77725},
pmid = {42811470},
issn = {2198-3844},
support = {32370119//National Natural Science Foundation of China/ ; 32371730//National Natural Science Foundation of China/ ; 32170123//National Natural Science Foundation of China/ ; 202505AF350062//Academician and Expert Workstation of Yunnan/ ; 2025GG1201//Key Technologies R & D Program of Tiemenguan/ ; },
abstract = {Microbial taxa in the soil microbiome with specific ecological functions play crucial roles in plant health. Flavobacterium is found closely associated with physiological functions that promote plant growth and enhance disease resistance. While cooperative interactions mediated by metabolite exchange can stabilize microbial consortia, the specific interactions between these consortia and plants remain understudied, particularly regarding their application in plant disease control. Here, we isolate a natural microbial consortium comprising Achromobacter, Flavobacterium, and Bacillus strains from cucumber rhizosphere soil, and identify the Flavobacterium strain as a methionine auxotroph. This study reveals the metabolic interactions among strains within a cross-feeding-based consortium. The Achromobacter and Bacillus primarily metabolize carbon and nitrogen sources, respectively, whereas the relevant genes in the Flavobacterium are significantly downregulated. The consortium develops significantly enhanced biofilms with a distinct stratified architecture, facilitating root endophytic colonization by Achromobacter and Flavobacterium. Endophytic Flavobacterium induces systemic resistance in plants, thereby enhancing resistance against phytopathogenic fungal infections. Our findings reveal a novel ecological strategy employed by auxotrophic Flavobacterium species for both microbial interactions and root endophytic colonization and provide a theoretical foundation for microbial consortium-based microbial inoculants in plant disease management.},
}

@article {pmid42811616,
year = {2026},
author = {Molina, L and González-Pagán, L and Segura, A},
title = {The Plant-Microbe Alliance for Environmental Restoration: From Nature-Inspired Solutions to Engineered Ecological Recovery.},
journal = {Microbial biotechnology},
volume = {19},
number = {10},
pages = {e70454},
doi = {10.1111/1751-7915.70454},
pmid = {42811616},
issn = {1751-7915},
mesh = {*Plants/microbiology/metabolism ; *Environmental Restoration and Remediation/methods ; Ecosystem ; *Microbiota ; Biotechnology/methods ; },
abstract = {According to the United Nations, up to 40% of the world's terrestrial ecosystems are degraded and in need of ecological restoration. Here, we argue that ecosystem restoration requires not only the reintroduction of plant species but also the recovery of the biological interactions that sustain ecosystem functioning. Plants and their associated microbiomes form integrated functional units in which microorganisms contribute to nutrient cycling, stress tolerance, contaminant degradation and ecosystem resilience. These plant-microbe partnerships therefore represent a new opportunity for environmental biotechnology. Advances in microbiome engineering, multi-omics and artificial intelligence are enabling the identification, design and management of microbial communities with complementary functions adapted to specific restoration contexts. However, the complexity of environmental microbiomes, the technical limitations of multi-omics in contaminated environments and the gap between computational predictions and ecological performance highlight the need for experimental and field-scale validation. In this context, we propose Holobiont Engineering for Ecosystem Restoration (HEER) as a conceptual framework that treats plants and their microbiomes as functional units and makes ecological interactions explicit targets of restoration. This perspective positions microbial biotechnology at the interface between ecological restoration and environmental engineering, supporting a shift from species-focused approaches towards the recovery of ecosystem functions.},
}

*Plants/microbiology/metabolism
*Environmental Restoration and Remediation/methods
Ecosystem
*Microbiota
Biotechnology/methods

@article {pmid42811751,
year = {2026},
author = {Su, H and Liu, H and Tao, J and Qu, Z and Wang, Q and Lu, P and Tian, X and Yu, S and Li, K and Shi, H and Zuo, M and Xiang, B and Wu, J and Cao, P and Jin, J},
title = {Host Genetic Variation Is Associated with Root-Associated Microbiome Assembly and Resistance to Fusarium oxysporum in Tobacco.},
journal = {Plant physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/plphys/kiag727},
pmid = {42811751},
issn = {1532-2548},
abstract = {Plant-microbe interactions are essential for plant health, yet the genetic basis of host control over root-associated microbiome assembly in Nicotiana tabacum remains unclear. We integrated whole-genome resequencing, amplicon sequencing, and metabolomics across 50 tobacco cultivars, together with microbial genome-wide association and mediation analyses, to investigate host-microbiome covariation. Host genotype significantly influenced the diversity and composition of root-associated microbial communities, particularly in the rhizosphere. Several host loci were associated with heritable microbial taxa linked to nutrient acquisition and stress responses. Mediation analysis suggested that associations between host genetic variation and Pseudomonadaceae abundance were partly transmitted through secondary metabolites variation, particularly terpenoids, whereas this mediating effect was less pronounced for other taxa. Functional assays further showed that several genotype-associated bacterial isolates antagonized Fusarium oxysporum. Among them, Pseudomonas aeruginosa FZ1 suppressed pathogen growth, enhanced host defense responses, and reduced disease severity in greenhouse experiments. These findings suggest that host genetic variation is associated with shifts in the tobacco root microbiome and that secondary metabolites may contribute to the assembly of specific microbial taxa. The study provides a basis for future mechanistic and breeding-oriented investigations of microbiome-associated traits.},
}

@article {pmid42811780,
year = {2026},
author = {Shoarishoar, SS and Seifollahi Marbini, M},
title = {Human Papillomavirus (HPV) and Cervical Cancer: An Exploratory Systematic Review of Heterogeneous Evidence on Epidemiology, Vaccination, Screening, and Molecular Advances.},
journal = {Cancer investigation},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07357907.2026.2740708},
pmid = {42811780},
issn = {1532-4192},
abstract = {This systematic review evaluated evidence on HPV epidemiology, vaccination, screening, and factors associated with cervical cancer and other HPV-related malignancies. Fourteen heterogeneous studies published between 2010 and 2025 were included. HPV16 remained the most frequently reported genotype, while several studies indicated increasing prevalence of other high-risk genotypes, supporting the potential value of the 9-valent HPV vaccine. Population-based evidence demonstrated reduced cervical cancer incidence among women vaccinated before adolescence. Limited studies also investigated HPV persistence, viral load, microbiome alterations, and vaccine awareness. Considering the small number and diversity of studies, findings should be interpreted cautiously and considered exploratory.},
}

@article {pmid42811786,
year = {2026},
author = {Rahman, MA and Azam, RMU and Hossain, MS and Momtaz, S and Begum, A and Sultana, M},
title = {First Report of blaCTX-M-15 in a Marine Thermotolerant Enterobacter Isolate From Bangladesh: Genomic Insights Into Halotolerance and Antimicrobial Resistance.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70425},
doi = {10.1002/mbo3.70425},
pmid = {42811786},
issn = {2045-8827},
support = {//The Chromosome Research Centre, University of Dhaka, Bangladesh/ ; },
mesh = {Bangladesh ; *beta-Lactamases/genetics ; *Enterobacter/genetics/isolation & purification/drug effects/enzymology/classification ; *Seawater/microbiology ; Phylogeny ; Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Thermotolerance ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; },
abstract = {Marine ecosystems are becoming important reservoirs for antimicrobial resistance (AMR). However, genomic data on ESBL (Extended-Spectrum Beta-Lactamase)-producing Enterobacter species from marine environments are limited. The widespread blaCTX-M-15 gene, usually found in clinical and wastewater settings, has not been reported in marine Enterobacter from Bangladesh. A thermotolerant, lactose-fermenting isolate (LB01) from the Bay of Bengal seawater near Laboni Beach, Cox's Bazar, was isolated and identified as Enterobacter kobei based on > 99.4% average nucleotide identity and phylogenetic clustering. Its 4.62 Mb genome (55.05% GC) encoded 4410 genes, including blaCTX-M-15, blaACT-9, and qnrS1, with blaCTX-M-15 located next to an ISEc9-like insertion sequence, indicating a mobilizable resistance locus. The genome also contained efflux systems (acrAB, mdtABC, oqxAB), adhesion and iron uptake genes (fim, flh, ent, fep, chu), and comprehensive halotolerance modules (proVWX, betT, nhaA, kdpABC, mscL/S) consistent with its growth in up to 7% NaCl. This is the first genomic characterization of a marine E. kobei carrying blaCTX-M-15 resistant determinant in Bangladesh, showing convergence of resistance, virulence, and halotolerance traits that support persistence in saline, human-impacted environments. The findings broaden the ecological scope of clinically relevant ESBL genes and highlight the importance of coastal ecosystems as overlooked nodes in the global AMR network within a One Health framework.},
}

Bangladesh
*beta-Lactamases/genetics
*Enterobacter/genetics/isolation & purification/drug effects/enzymology/classification
*Seawater/microbiology
Phylogeny
Anti-Bacterial Agents/pharmacology
Genome, Bacterial
Thermotolerance
Microbial Sensitivity Tests
Drug Resistance, Bacterial
Drug Resistance, Multiple, Bacterial/genetics

@article {pmid42811970,
year = {2026},
author = {Qiu, G and Ran, J and Shi, J and Yuan, L and Dai, W and Jin, J and Zhang, P and Wang, X and Chen, X and Li, C and Xi, Y},
title = {Multi-Organ Metatranscriptomics Establishes Organ-Specific Functional Baselines in the Crested Ibis (Nipponia nippon).},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {9},
pages = {53784},
doi = {10.31083/FBL53784},
pmid = {42811970},
issn = {2768-6698},
support = {ZJXRDQ-2024-JC64//Deqing County Ecological Forestry Comprehensive Service Center/ ; },
mesh = {Animals ; *Transcriptome ; Organ Specificity/genetics ; *Fishes/genetics/microbiology ; Liver/metabolism/microbiology ; Gene Expression Profiling ; },
abstract = {BACKGROUND: The crested ibis (Nipponia nippon) is an iconic East Asian species on the International Union for Conservation of Nature's (IUCN) Red List, with recurrent stress-related sudden death reported in captivity and in the wild. However, the mechanisms underlying stress responses remain poorly characterized.

METHODS: Using opportunistic post-mortem samples, we generated, to our knowledge, the first organ-resolved metatranscriptomic reference dataset for this species in a stress-associated context. Matched libraries from small intestine, liver, spleen, and lung were sequenced and processed using a unified pipeline; microbial transcriptional activity was quantified following host and rRNA removal and stringent detection criteria, enabling concurrent readouts of community composition and functional gene expression.

RESULTS: Transcriptional activity was intestine-centric, whereas liver, spleen, and lung harbored low-load communities with limited taxon sharing. The small intestine was dominated by the aquatic-associated Cetobacterium somerae (~54.8%), consistent with fish-based feeding, while Romboutsia was scarce, suggesting a weak butyrate-producing guild. Functionally, transcripts were enriched for small-molecule metabolism, nucleotide/cofactor turnover, central carbon conversion, and membrane/envelope-associated precursor pathways. Stratified pathway analysis further resolved uneven classified contributions: Paraclostridium bifermentans spanned the broadest classified pathway repertoire, Cetobacterium somerae contributed more strongly to nucleotide-linked functions, and Clostridium perfringens retained a more distinctive inositol-related branch. Antimicrobial resistance (AMR)-linked transcripts in the intestine were dominated by target-site mechanisms (elongation factor Tu (EF-Tu), RNA polymerase β' subunit (rpoC) and DNA gyrase subunit A (gyrA)) with a low-level ErmQ-associated macrolide-lincosamide-streptogramin (MLS) resistance signature, consistent with background expression of core targets.

CONCLUSIONS: This organ-resolved dataset provides a practical baseline for microbiome, pathogen, and resistance surveillance in captive crested ibis, and a reference for future comparisons among captive, wild, and reintroduced populations. AMR signals are best read as contextual markers rather than phenotypic resistance and can serve as auxiliary sentinels alongside composition and function. Overall, the dataset provides a reusable framework for health assessment and conservation planning.},
}

Animals
*Transcriptome
Organ Specificity/genetics
*Fishes/genetics/microbiology
Liver/metabolism/microbiology
Gene Expression Profiling

@article {pmid42812023,
year = {2026},
author = {Yildirim, EA and Laptev, GY and Tiurina, DG and Filippova, VA and Ilina, LA and Brazhnik, EA and Novikova, NI and Sokolova, KA and Ponomareva, ES and Zaikin, VA and Klyuchnikova, IA and Korochkina, EA and Bolshakov, VN and Griffin, DK and Romanov, MN},
title = {Insight Into the Complex Dynamics of Diverse Endometrial Microbial Communities in Dairy Cows During the Transition Period: Normal Condition Versus Pathology.},
journal = {Frontiers in bioscience (Elite edition)},
volume = {18},
number = {3},
pages = {46742},
doi = {10.31083/FBE46742},
pmid = {42812023},
issn = {1945-0508},
support = {24-16-00131//Russian Science Foundation/ ; },
mesh = {Animals ; Female ; Cattle ; *Endometrium/microbiology/pathology ; *Microbiota ; Postpartum Period ; *Endometritis/microbiology/veterinary ; Dairying ; },
abstract = {BACKGROUND: Dysbacteriosis of the reproductive tract is a risk factor for the development of postpartum endometritis in cows. Understanding the complex dynamics of diverse endometrial microbial communities in dairy cows during the transition period, when healthy and compared to with a pathology, is crucial for developing the appropriate measures to control postpartum endometritis depending on the livestock farming system used. The aim of this study was to analyse the endometrial microbiome changes in cows during the transition period in two separate experiments on an industrial (IF) and an organic farm, or eco-farm (EF).

METHODS: Samples were taken on Days 20 (D-20) and 10 (D-10) before calving, at calving (D0), and on Days 3 (D+3), 5 (D+5) and 20 (D+20) postpartum. On IF, the samples were divided into three groups: healthy (IF1H), subclinical (IF2S) and purulent-catarrhal endometritis (IF3E) animals. To investigate the abundance of microbial operational taxonomic units (OTUs) and dynamics of endometrial microbiota composition, quantitative real-time PCR was used. The obtained macroecological time series data was additionally analyzed using the Hurst exponent approach.

RESULTS: In Group IF0, one of the total bacterial count peaks was observed on D0, reaching an average of 5.0 × 10[6] DNA copies/mL, which was 100-fold higher than on D-20 (p < 0.001) and 38.4-fold higher than on D-10 (p < 0.01). Abundance of Fusobacterium, Sneathia and Leptotrichia were 125 times higher in Group IF3E compared to Group IF1H. On IF, a high concentration of Aspergillus was also observed. On EF, these micromycetes were present only at the time of calving. Variability in the number of micromycetes Aspergillus and Fusarium spp. differed depending on the state of the reproductive system. The Hurst exponent-based analysis suggested a somewhat more persistent tendency in the short-time shifts observed in endometrial microbial communities in cows from EF.

CONCLUSIONS: During the transition period, the endometrial microbiome on both farms underwent macroecological changes associated with the state of reproductive health and temporal fluctuations in microbiota abundances. The results of the study can be used to develop strategies for the prevention and treatment of postpartum endometritis in cows.},
}

Animals
Female
Cattle
*Endometrium/microbiology/pathology
*Microbiota
Postpartum Period
*Endometritis/microbiology/veterinary
Dairying

@article {pmid42812093,
year = {2026},
author = {Syal, A and Pasula, R and Mortezaei, K and Panayiotou, I and Kumari, G and Derk, C},
title = {Gastrointestinal Manifestations of Systemic Sclerosis: Screening and Management to Improve Outcomes.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {87},
number = {9},
pages = {52377},
doi = {10.31083/BJHM52377},
pmid = {42812093},
issn = {1759-7390},
mesh = {Humans ; *Scleroderma, Systemic/complications/physiopathology ; *Gastrointestinal Diseases/therapy/etiology/diagnosis/physiopathology ; Gastroesophageal Reflux/etiology/therapy/diagnosis ; Blind Loop Syndrome/etiology/therapy ; Gastroparesis/etiology/therapy ; },
abstract = {Gastrointestinal (GI) involvement is among the most common and clinically important manifestations of systemic sclerosis (SSc), affecting up to 90% of patients and substantially contributing to morbidity and reduced quality of life. SSc-related GI disease results from microvascular injury, enteric nervous system dysfunction, and progressive smooth muscle atrophy with fibrosis, producing widespread dysmotility throughout the gastrointestinal tract. Clinical involvement can extend from the oral cavity to the anorectum, with esophageal dysfunction, gastroesophageal reflux disease (GERD), gastroparesis, small intestinal bacterial overgrowth (SIBO), and intestinal pseudo-obstruction among the major manifestations. Recent diagnostic advances, including high-resolution esophageal manometry (HRM), ambulatory pH-impedance monitoring, and improved imaging, have strengthened early detection and characterization of GI involvement. Treatment remains largely supportive and symptom-directed, including acid suppression, prokinetic therapy, nutritional optimization, and endoscopic or surgical management of complications. Growing evidence on the gut microbiome, immune-mediated mechanisms, and the gut-brain axis is expanding understanding of disease pathophysiology and may guide future targeted therapies. This review synthesizes current evidence on the epidemiology, pathophysiology, clinical manifestations, and management of gastrointestinal involvement in systemic sclerosis, emphasizing early recognition and multidisciplinary care. We conclude by outlining persistent management challenges and future directions to improve diagnostic precision, therapeutic development, and patient-centered outcomes.},
}

Humans
*Scleroderma, Systemic/complications/physiopathology
*Gastrointestinal Diseases/therapy/etiology/diagnosis/physiopathology
Gastroesophageal Reflux/etiology/therapy/diagnosis
Blind Loop Syndrome/etiology/therapy
Gastroparesis/etiology/therapy

@article {pmid42812196,
year = {2026},
author = {Liu, J and Qi, Z},
title = {Intratumoral microbiota: implications for colorectal cancer pathogenesis and therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1832875},
pmid = {42812196},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/therapy/microbiology/immunology/etiology ; Animals ; Tumor Microenvironment/immunology ; *Gastrointestinal Microbiome/immunology ; *Microbiota ; },
abstract = {CRC is the third most prevalent malignancy worldwide and the second leading cause of cancer-related mortality. According to GLOBOCAN 2022 estimates, approximately 1.93 million new CRC cases and 900,000 CRC-related deaths occur annually worldwide. Incidence rates continue to rise in developing countries, driven by the westernization of dietary patterns, sedentary lifestyles, and increasing obesity prevalence, with a notable trend toward younger-onset disease. In recent years, mounting evidence has implicated the microbiota as a critical contributor to CRC initiation and progression. Distinct from the fecal microbiome, the intratumoral microbiome constitutes an independent, low-biomass microbial community predominantly composed of bacteria, with additional fungal, viral, and archaeal components. Microbial communities within the TME promote CRC development and progression by modulating host immune responses, metabolic pathways, and tumor cell proliferation and metastasis. Fusobacterium nucleatum, ETBF, polyketide synthase genotoxicity island-harboring Escherichia coli and Parvimonas micra represent the most well-substantiated candidate oncomicrobes, whose carcinogenic activities involve multiple intertwined pathways, including chronic inflammation, genotoxic DNA damage, immune evasion, metabolic reprogramming, and non-coding RNA regulation. Furthermore, intratumoral microbiota may serve as early diagnostic biomarkers for CRC, offer novel therapeutic targets, and provide potential biological rationale for prognostic prediction. Microbiome-based diagnostic biomarkers, such as multi-bacterial fecal/tissue panels, have demonstrated sensitivity comparable to or superior to the fecal immunochemical test in select retrospective cohorts; however, large-scale, multicenter, prospective validation remains necessary. Strategies targeting intratumoral bacteria - including antibiotics, bacteriophages, phage-guided nanocarriers, and FMT - remain predominantly in the preclinical stage. Although phase I/II trials of FMT for immunotherapy sensitization have yielded encouraging results, small sample sizes and substantial heterogeneity preclude its near-term adoption as a standard-of-care recommendation. This review systematically summarizes the latest advances in understanding the relationship between intratumoral microbiota and CRC, critically appraises the strength of evidence across different hierarchical levels, evaluates the consistency and controversies surrounding major mechanistic hypotheses, addresses methodological challenges inherent to low-biomass microbiome research, and discusses the translational potential in CRC diagnosis, therapy, and prognostic prediction.},
}

Humans
*Colorectal Neoplasms/therapy/microbiology/immunology/etiology
Animals
Tumor Microenvironment/immunology
*Gastrointestinal Microbiome/immunology
*Microbiota

@article {pmid42812233,
year = {2026},
author = {Wang, L and Zhang, L and Liu, X and Li, S and Shen, J and Zhao, X and Zhao, J and Zhu, FX},
title = {Omega-3 PUFAs Mitigate Polytrauma-Induced Gut-Liver-Lung Inflammation and Organ Dysfunction via GPR120/PPAR-γ.},
journal = {Journal of inflammation research},
volume = {19},
number = {},
pages = {613659},
pmid = {42812233},
issn = {1178-7031},
abstract = {BACKGROUND: Severe polytrauma frequently triggers a systemic inflammatory response, culminating in fatal Multiple Organ Dysfunction Syndrome (MODS). Although Omega-3 polyunsaturated fatty acids (PUFAs) possess well-documented anti-inflammatory properties, their role in modulating the gut-liver-lung inflammatory axis following polytrauma remains to be fully elucidated. This study investigated whether targeted Omega-3 PUFA administration could mitigate post-traumatic MODS, alongside concurrent changes in intestinal homeostasis and the GPR120/PPAR-γ signaling axis linked to TLR4/NLRP3-associated hyper-inflammation.

METHODS: Male Sprague-Dawley rats were randomly assigned (computer-generated randomization, n = 6 per group) to Sham, Polytrauma (blunt abdominal trauma + tibial-fibular fracture), and Omega-3 group (300 mg/kg/day via oral gavage). The therapeutic intervention commenced 24 h post-injury and continued daily for 7 consecutive days, with endpoint measurements performed at Day 7. Histological assessments were conducted by investigators blinded to group allocation. We assessed organ injury markers, histological integrity, pro-inflammatory cytokine profiles, colonic GPR120-associated signaling pathways, and the fecal microbiome via 16S rRNA sequencing (n = 6 fecal samples per group).

RESULTS: Omega-3 PUFA administration attenuated polytrauma-induced organ dysfunction (n = 6 per group). Specifically, treatment reduced serum ALT by 51.4% (51.3 ± 8.2 vs 105.6 ± 12.4 U/L in Model group, P = 0.008), AST by 42.4% (141.2 ± 18.5 vs 245.1 ± 22.3 U/L in Model group, P = 0.009), and CK by 48.2% (854.5 ± 112.4 vs 1650.3 ± 156.8 U/L in Model group, P < 0.001). Histological analysis confirmed alleviation of lung injury (score: 2.1 ± 0.2 vs 3.5 ± 0.3; P = 0.012), liver injury (1.7 ± 0.3 vs 3.2 ± 0.2; P = 0.005), and intestinal damage (Chiu's score: 1.6 ± 0.3 vs 3.2 ± 0.2; P = 0.008), alongside preserved goblet cell counts and ZO-1 expression. 16S rRNA sequencing (n = 6 per group) further revealed recovery in microbial alpha-diversity. Compared with the Model group, the Omega-3 group exhibited increased Shannon index (4.02 ± 0.18 vs 3.41 ± 0.32, P = 0.008) and Chao1 index (442.6 ± 41.5 vs 368.2 ± 39.1, P = 0.006). Taxonomic differences across groups were determined using Linear Discriminant Analysis Effect Size (LEfSe). Western blot and qRT-PCR analyses indicated that these protective phenotypic changes were associated with reduced expression of TLR4, NLRP3, and p-p65/total p65 ratio, as well as upregulation of GPR120 and PPAR-γ.

CONCLUSION: Targeted Omega-3 PUFA administration may mitigate polytrauma-induced systemic inflammation and multi-organ dysfunction. These protective effects appear to be associated with maintained intestinal barrier integrity, altered gut microbiota composition, and shifts in GPR120/PPAR-γ pathway activity. These findings suggest that Omega-3 PUFAs warrant further preclinical and translational evaluation as a potential immunonutritional strategy for traumatic MODS management.},
}

@article {pmid42812282,
year = {2026},
author = {Vishwakarma, A and Patil, A and Saini, D and Shankar, A and Shukla, SK and Kushwaha, K and Choudhary, M and Bhardwaj, M and Gupta, V and Yadav, CP and Kumar, P},
title = {A systematic review and meta-analysis reveals enrichment of pro-inflammatory and bacterial immunity-modulating taxa in oral squamous cell carcinoma.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1913744},
pmid = {42812282},
issn = {1664-3224},
mesh = {Humans ; *Mouth Neoplasms/microbiology/immunology ; *Microbiota/immunology ; *Carcinoma, Squamous Cell/microbiology/immunology ; *Bacteria/immunology/classification/genetics ; Dysbiosis/immunology/microbiology ; },
abstract = {INTRODUCTION: Oral squamous cell carcinoma (OSCC) is a major concern due to high recurrence, therapeutic resistance, and mortality. Increasing evidence indicates that oral microbiome dysbiosis contributes to OSCC development, yet comprehensive multi-cohort evaluations are limited. A systematic review and meta-analysis of the oral microbiome was conducted to identify conserved taxa in patients with OSCC.

METHODS: A systematic review and meta-analysis was conducted according to PRISMA guidelines, using data from PubMed, Embase, Web of Science, and Google Scholar. Raw 16S rDNA sequences were processed in QIIME 2 (v2024.10) for quality control, taxonomic classification, and diversity analysis. Linear Discriminant Analysis Effect Size (LEfSe) analyses and machine learning were used for the identification of conserved taxa.

RESULTS: Significant microbial shifts were observed between OSCC and healthy groups. OSCC samples showed enrichment of taxa, which further identified as conserved taxa such as Porphyromonas, Fusobacterium, Campylobacter, Catonella, Prevotella, Selenomonas, and Veillonella, with species including Campylobacter showae, Capnocytophaga granulosa, Capnocytophaga leadbetteri, Prevotella loescheii, Streptococcus anginosus, Streptococcus pneumoniae, and Treponema medium. Healthy individuals exhibited higher levels of Actinobacillus, Corynebacterium, Escherichia-Shigella, and Haemophilus, particularly H. parainfluenzae, Rothia aeria, R. dentocariosa, and Selenomonas spp. Bray-Curtis beta-diversity analysis confirmed significant compositional differences between groups. Sample type and geography-based comparisons revealed additional variation: Geographically, Lautropia and Haemophilus were common across regions, whereas Cutibacterium, Escherichia-Shigella, Gracilibacteria, and several species appeared specific to India. Functional predictions revealed enrichment of pathways related to environmental and genetic information processing, as well as cellular processes in OSCC. Notably, significant enrichment of genes involved in inflammation, ABC transporters, and bacterial immunity was observed in OSCC groups.

CONCLUSION: Overall, this study demonstrates the enrichment of microbial taxa associated with chronic inflammation and carcinogenesis, along with a depletion of protective commensal microbes in patients with OSCC. These findings highlight distinct taxonomic and functional microbiome signatures associated with OSCC and emphasize the influence of sample type and geography on oral microbial composition. The enrichment of predicted inflammatory genes, transport-associated genes, and bacterial immune-related genes suggests the potential contribution of microbial communities to chronic inflammation and tumor progression.},
}

Humans
*Mouth Neoplasms/microbiology/immunology
*Microbiota/immunology
*Carcinoma, Squamous Cell/microbiology/immunology
*Bacteria/immunology/classification/genetics
Dysbiosis/immunology/microbiology

@article {pmid42812373,
year = {2026},
author = {Wu, Y and Wang, S and Ma, X and Lou, X and Zheng, N and Shao, W and Meng, L and Chen, H and Wang, C and Zhao, Y},
title = {Microbial diversity of camel milk production environments in Xinjiang, China: a full-length 16S rRNA survey of farm environmental matrices across Altay and Hami regions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1937458},
pmid = {42812373},
issn = {1664-302X},
abstract = {INTRODUCTION: Camel milk production in Xinjiang, China is predominantly managed under extensive pastoral systems, yet the taxonomic and functional profiles of key production-associated environmental matrices remain poorly characterized.

METHODS: This study employed PacBio Single-Molecule Real-Time (SMRT) full-length 16S rRNA gene sequencing to characterize microbial communities across five environmental matrices (bedding, feces, teat skin, feed, and soil) from camel breeding farms in the Altay and Hami regions of Xinjiang.

RESULTS: After removing chloroplast and mitochondrial sequences, the dominant phyla across all samples were Firmicutes (43.20%), Proteobacteria (20.12%), and Actinobacteriota (12.02%). Alpha diversity analysis revealed significantly higher richness in fecal and feed microbial communities in Altay compared to Hami (Padj < 0.05). Beta diversity analyses (PCoA, NMDS, PERMANOVA) confirmed distinct taxonomic profiles between the two regions, driven by both regional and sample-type effects. Functional profiling indicated conserved metabolic potentials across regions, with enrichment of pathways related to amino acid transport and energy conversion.

DISCUSSION: This study establishes a foundational baseline of the camel farm environmental microbiome in Xinjiang, informing targeted hygiene interventions and future studies investigating environmental contributions to raw camel milk quality. A key limitation is the absence of raw milk samples, precluding direct inference of microbial transmission routes to milk.},
}

@article {pmid42812418,
year = {2026},
author = {Elsayim, R and Alqahtani, MSM and Alosaimi, MM and Alameen, AA and Al Sarar, D and Abdullah, EM and Abudouleh, E},
title = {Genome-guided prebiotic fermentation generates anti-virulence metabolites against Pseudomonas aeruginosa.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1948465},
pmid = {42812418},
issn = {1664-302X},
abstract = {BACKGROUND: The rise of multidrug-resistant Pseudomonas aeruginosa has heightened interest in microbiome-based anti-virulence strategies that mitigate pathogenicity without directly affecting bacterial survival. This study examined whether the fermentation of Arabic gum and baobab by probiotic bacteria produces metabolites that reduce P. aeruginosa virulence.

METHODS: The carbohydrate-active enzyme profiles of Bifidobacterium longum, Lactiplantibacillus plantarum, and P. aeruginosa were compared to predict their ability to utilize plant glycans. Probiotic growth, viable counts, and acidification were measured following supplementation with Arabic gum, baobab, or glucose. The effects of untreated, neutralized, and pH-matched cell-free supernatants on P. aeruginosa growth, biofilm formation, adhesion, and twitching motility were evaluated.

RESULTS: L. plantarum and B. longum exhibited 54 and 53 glycoside hydrolases, respectively, compared to 29 in P. aeruginosa, suggesting a superior probiotic capacity for plant-glycan utilization. Arabic gum at 2% significantly enhanced B. longum viability by approximately 0.27 log10 CFU mL[-1] (P = 0.0058) and resulted in the greatest pH reduction, whereas glucose increased L. plantarum growth by approximately 0.58 log10 CFU mL[-1] (P = 0.0019). Supernatants derived from Arabic gum exhibited the strongest activity, nearly completely inhibiting biofilm formation, reducing adhesion by approximately 54%, and significantly suppressing twitching motility. Baobab demonstrated measurable but generally weaker prebiotic and anti-virulence effects. These findings indicate that the biological effects were contingent on the fermented substrate and the resulting metabolite profile. Neutralization reduced several inhibitory effects, while pH-matched controls largely replicated the growth suppression observed with the corresponding CFS. This indicates that fermentation-associated acidification was a primary determinant of antibacterial activity. The residual activity observed in certain neutralized CFS preparations suggests that additional non-acidic factors may contribute under specific conditions.

CONCLUSION: Genome-informed glycan-utilization predictions identified substrates capable of producing probiotic metabolites that attenuate multiple P. aeruginosa virulence phenotypes. Arabic gum shows particular promise for microbiome-based control of multidrug-resistant P. aeruginosa.},
}

@article {pmid42812431,
year = {2026},
author = {Zhang, J and Ying, W and Liao, L and Jing, X and Zhou, Y and Yue, L and Zhang, B},
title = {From disease to syndrome pattern: a study on the differentiation of traditional Chinese medicine syndrome patterns in asthma using multi-omics characterization.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1922660},
pmid = {42812431},
issn = {1664-3224},
mesh = {Humans ; *Asthma/diagnosis/metabolism/microbiology ; Multiomics ; *Medicine, Chinese Traditional/methods ; Microbiota ; Diagnosis, Differential ; Biomarkers ; Proteomics/methods ; Female ; Metabolomics ; Male ; Transcriptome ; Gene Expression Profiling ; Syndrome ; },
abstract = {BACKGROUND: Bronchial asthma is a highly heterogeneous chronic inflammatory airway disorder. Syndrome differentiation-guided Traditional Chinese Medicine (TCM) treatment for asthma delivers distinct advantages, including fewer adverse reactions and superior anti-inflammatory efficacy. Nevertheless, the intrinsic biological mechanisms underlying TCM asthma syndromes remain largely uncharacterized, restricting the objective and standardized differentiation of TCM subtypes.

METHODS: We integrated transcriptomic, proteomic, metabolomic and oral microbiome data from asthma patients and healthy controls to map asthma molecular and microbiome landscapes. Two representative TCM subtypes-Phlegm-Dampness Obstructing the Lungs (PZLP) and Lung-Qi Deficiency (LQD)-were stratified and compared via differential analysis, WGCNA, LEfSe and random forest machine learning to dissect shared asthma-related molecular features, subtype-specific molecular disparities and potential objective diagnostic biomarkers.

RESULTS: Comprehensive multi-omics and oral microbiome comparisons revealed correlational molecular discrepancies between asthma patients and healthy individuals. Our omics data suggest that asthma-related molecular alterations are tightly associated with three core pathological cascades: dysregulated glycerophospholipid metabolism, potential excessive activation of the NF-κB inflammatory signaling pathway, and impaired phagosome function. Beyond the universal disease-associated molecular signatures of asthma, prominent metabolic and inflammatory phenotypic divergences were detected between the two TCM subtypes. The PZLP subtype showed correlational omics signatures suggestive of elevated lipogenic activity, aberrant MAPK inflammatory pathway activation, and massive intracellular lipid accumulation. In contrast, the LQD subtype exhibited correlated downregulation of lipid transporter genes (e.g., ABCA13), which hypothetically implies compromised lipid transport capacity and disrupted cell membrane homeostasis. Oral microbiota profiling demonstrated profound structural remodeling in asthmatic patients. Although PZLP and LQD patients shared analogous overall microbial community structures, their microbial functional pathways diverged substantially: the LQD group was enriched in methane and glycerol metabolic pathways, whereas the PZLP group displayed overrepresentation of serotonergic and dopaminergic synaptic regulatory pathways. A diagnostic classification model built on differential microbial biomarkers achieved an area under the receiver operating characteristic curve (AUC) of 0.889, demonstrating robust discriminative capacity for distinguishing the two TCM syndromes.

CONCLUSION: This study delineates correlational immunometabolic and oral microbiome signatures of asthma and uncovers potential subtype-specific molecular and microbial markers for two classic TCM asthma patterns. These observations provide testable mechanistic hypotheses for interpreting the molecular pathogenesis of asthma and could supply a preliminary theoretical foundation for objective TCM syndrome differentiation, personalized intervention and targeted asthma therapeutic development.},
}

Humans
*Asthma/diagnosis/metabolism/microbiology
Multiomics
*Medicine, Chinese Traditional/methods
Microbiota
Diagnosis, Differential
Biomarkers
Proteomics/methods
Female
Metabolomics
Male
Transcriptome
Gene Expression Profiling
Syndrome

@article {pmid42812539,
year = {2026},
author = {Napier, EG and Cinco, IR and Malherbe, DC and Stuart, EV and Davies, MH and Leach, CN and Damron, E and Gokmen, M and Leestemaker-Palmer, A and Nuss, S and Bumgardner, C and Kohama, SG and Bermudez, L and Winthrop, KL and Fuss, C and Spindel, ER and Messaoudi, I},
title = {Lung microbial dysregulation and TNF inhibition are associated with worsened nontuberculous mycobacterial lung disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1923035},
pmid = {42812539},
issn = {1664-302X},
abstract = {INTRODUCTION: Nontuberculous mycobacteria (NTM) are ubiquitous bacteria that cause a spectrum of diseases, most notably pulmonary disease (NTMPD). The host factors contributing to the heightened susceptibility and severity of NTMPD in elderly individuals are poorly understood. Prior studies have reported increased incidence of NTMPD in individuals receiving immune modulatory biologics such as anti-TNF and JAK-STAT inhibitors. Moreover, we recently described that age-related changes in the lung microbiome, notably the loss of a main commensal Tropheryma species, may contribute to increased severity. Therefore, in this study we explore the hypothesis that TNF-inhibition and a disrupted lung microbiome are key factors associated with poor NTMPD outcomes.

METHODS: Young (4-7 years old) rhesus macaques were either pretreated with: (1) nebulized amikacin and vancomycin to disrupt the lung microbiome; (2) the TNF inhibitor Inflectra to suppress Th1 responses; or (3) left untreated. Animals were subsequently inoculated with M. avium subsp. hominissuis (MAH) in the right lung. Bacterial load, radiographic changes, immune responses, and microbiome composition were monitored longitudinally.

RESULTS AND DISCUSSION: Antibiotic-treated animals experienced significant microbiome compositional shifts including the depletion of Tropheryma from the lung microbiome. One antibiotic-treated animal developed and resolved cavitary disease after the lung microbiome returned to homeostasis. One Inflectra-treated animal developed chronic granulomatous disease. No control animals showed granulomas. These data suggest that lung microbiome disruption and TNF inhibition are associated with increased susceptibility to NTM granulomatous disease.},
}

@article {pmid42812589,
year = {2026},
author = {Han, X and Dan, Z and Mo, Q and Rao, X and Chen, Y and Jiang, Y and Li, C and Tang, G},
title = {Identifying the key microbiome associated with lumbar discherniation in Chinese patients.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1942642},
pmid = {42812589},
issn = {2296-634X},
abstract = {BACKGROUND: Inflammation and subsequent fibrotic remodeling-characterized by extracellular matrix deposition and myofibroblast activation-are hallmark processes in various degenerative disorders. Lumbar disc herniation (LDH) involves local inflammation and disruption of extracellular matrix organization; however, the role of systemic modulators such as gut microbiota and their metabolites remains poorly understood, particularly in the Han Chinese population.

METHODS: A total of 69 LDH patients and 69 healthy controls were enrolled in this study. Fecal samples were subjected to 16 S rRNA sequencing, and untargeted metabolomics was performed to compare microbial diversity, taxonomic composition, and metabolic profiles between the two groups. A random forest model was constructed to evaluate the diagnostic predictive value of identified microbial and metabolic features.

RESULTS: LDH patients exhibited significant gut microbial dysbiosis, characterized by reduced alpha and beta diversity and markedly decreased abundances of Faecalibacterium and Bacteroides. These microbial alterations were associated with chronic inflammation driven by elevated proinflammatory factors, suppression of glutamatergic and GABAergic neuronal signaling, and dysregulation of pathways involved in mannan degradation and cytoskeleton assembly-processes closely linked to cell-matrix interactions and fibrotic tissue remodeling. Metabolites including phenylalanine and beta-alanine were identified as potential regulatory molecules. The random forest model incorporating microbial pathways and metabolites demonstrated good diagnostic accuracy for distinguishing LDH patients from healthy controls.

CONCLUSION: These findings suggest that gut microbiota may contribute to intervertebral disc degeneration by promoting chronic inflammatory responses and fibrotic structural remodeling. This study provides new insights into the inflammation-fibrosis continuum underlying spinal degeneration and identifies candidate biomarkers with potential for future translational applications.},
}

@article {pmid42812778,
year = {2026},
author = {Iddrisu, AM and Özgen, İ},
title = {Auxin-rhizomicrobiome interactions as a driver of climate-resilient root architecture: a conceptual framework for sustainable agriculture.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1839892},
pmid = {42812778},
issn = {1664-462X},
abstract = {Abiotic stresses such as drought and salinity represent major constraints to global crop productivity, necessitating innovative strategies for enhancing plant resilience. As a critical regulator of root system architecture, auxin (specifically indole-3-acetic acid (IAA)) functions as a vital cross-kingdom signaling molecule that mediates dynamic interactions between plants and auxin-synthesizing rhizosphere microorganisms. This review explores the role of auxin as a cross-kingdom signaling molecule mediating interactions between plants and the rhizosphere microbiome. Auxin-producing plant growth-promoting rhizobacteria (PGPR) such as Pseudomonas, Bacillus, and Azospirillum can modify root system architecture by stimulating lateral root formation, root hair development, and root elongation. These structural changes enhance soil exploration, improving water and nutrient acquisition under stress conditions. In addition, root exudates released by plants recruit beneficial microbial communities, establishing a feedback loop that stabilizes plant-microbe interactions in the rhizosphere. While previous studies have largely treated plant hormonal signaling and rhizosphere ecology as separate domains, this review bridges these silos by proposing the Auxin-Rhizomicrobiome-Root Architecture (ARRA) model; an integrative framework demonstrating how microbial hormone production and plant signaling networks jointly program adaptive root traits under climate stress. Ultimately, the ARRA framework provides a conceptual and practical blueprint for deploying auxin-producing bioinoculants and engineered rhizomicrobiome consortia, offering a scalable strategy to enhance crop resilience and sustainable food security under accelerating climate scenarios.},
}

@article {pmid42812810,
year = {2026},
author = {Zhang, Y and Cao, Y and Wu, W and Guo, Z},
title = {Neuro-Instructive Hydrogels - A Key to Sensory Innervation in Oral Tissues: A Comprehensive Review.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {631162},
pmid = {42812810},
issn = {1178-2013},
mesh = {Humans ; *Hydrogels/chemistry/pharmacology ; Animals ; *Nerve Regeneration/drug effects/physiology ; Tissue Engineering/methods ; *Mouth/innervation ; Bioprinting ; Schwann Cells ; *Guided Tissue Regeneration/methods ; },
abstract = {Current treatments for oral tissue defects restore structure but rarely restore sensory nerves. Tissues without innervation lose protective reflexes and long-term stability. This review examines neuro-instructive hydrogels designed to guide nerve regeneration in oral tissues. We discuss four design mechanisms: physical cues that direct axon growth, spatiotemporal release of neurotrophic signals, regulation of oral stem cells and Schwann cells, and immunomodulation that supports a pro-regenerative niche. We then map these mechanisms onto three clinical scenarios: regeneration of the dentin-pulp complex, reconstruction of innervated jawbone, and repair of oral mucosal nerves. The oral environment imposes specific constraints (saliva, chewing forces, and a rich microbiome) that call for wet-adhesive, antibacterial, and mechanically adaptable designs. Bioprinting offers a route to patient-specific constructs with controlled architecture, and emerging tools such as stimuli-responsive release and machine learning guided formulation may further improve precision. Key next steps include scalable production under Good Manufacturing Practice, large-animal validation, and objective clinical endpoints for sensory recovery. The central goal is to move oral tissue repair from structural filling toward restoration of sensation.},
}

Humans
*Hydrogels/chemistry/pharmacology
Animals
*Nerve Regeneration/drug effects/physiology
Tissue Engineering/methods
*Mouth/innervation
Bioprinting
Schwann Cells
*Guided Tissue Regeneration/methods

@article {pmid42812837,
year = {2026},
author = {Ruiz-Pozo, VA and Tamayo-Trujillo, R and Cadena-Paredes, AS and Guevara-Ramírez, P and Cadena-Ullauri, S and Paz-Cruz, E and Zambrano, AK},
title = {Gut and skin microbiome-metabolome pathways in vitiligo: from dysbiosis to immune activation and melanocyte dysfunction.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1952635},
pmid = {42812837},
issn = {1664-3224},
mesh = {Humans ; *Vitiligo/metabolism/immunology/microbiology ; *Dysbiosis/immunology/metabolism ; Animals ; *Melanocytes/immunology/metabolism ; *Skin Microbiome/immunology ; *Gastrointestinal Microbiome/immunology ; *Metabolome ; *Skin/microbiology/immunology/metabolism ; },
abstract = {Vitiligo is an autoimmune depigmenting disorder driven by genetic susceptibility, oxidative stress, immune dysregulation, and progressive melanocyte loss. Emerging microbiome-metabolome evidence suggests that gut and skin dysbiosis may contribute to disease progression through the gut-skin axis. This review integrates current evidence linking microbial imbalance with immune activation and melanocyte dysfunction in vitiligo. Studies in patients and experimental vitiligo models show altered gut and skin microbial diversity, enrichment of inflammation-associated taxa, depletion of commensal bacteria, impaired short-chain fatty acid biosynthesis, and disruption of tryptophan-indole, kynurenine, bile acid, taurine, riboflavin, and oxidative stress-related metabolic pathways. These alterations may weaken epithelial barrier integrity, impair immune tolerance, promote systemic low-grade inflammation, and increase melanocyte vulnerability to mitochondrial dysfunction, reactive oxygen species accumulation, impaired melanogenesis, apoptosis, and autoantigen exposure. Dysbiosis-associated metabolic remodeling may affect key immunometabolic pathways, including AhR-mediated tryptophan-kynurenine signaling, SCFA-dependent GPCR/HDAC regulation, IFN-γ-JAK/STAT-CXCL9/CXCL10 inflammatory amplification, and NF-κB/inflammasome-mediated innate immune priming. Together, these mechanisms may enhance dendritic cell activation, Th1/Th17 polarization, autoreactive CD8+ T-cell recruitment, and persistence of melanocyte-specific resident memory T cells. Current evidence supports a biologically plausible link between microbiome-metabolome disruption and autoimmune melanocyte loss in vitiligo. However, causality remains unproven. Longitudinal, multi-omics, and functional studies are required to define whether microbial and metabolic signatures act as biomarkers, mechanistic drivers, or therapeutic targets in vitiligo.},
}

Humans
*Vitiligo/metabolism/immunology/microbiology
*Dysbiosis/immunology/metabolism
Animals
*Melanocytes/immunology/metabolism
*Skin Microbiome/immunology
*Gastrointestinal Microbiome/immunology
*Metabolome
*Skin/microbiology/immunology/metabolism

@article {pmid42812883,
year = {2026},
author = {Sahu, BK and Debta, P and Patra, SK and Sahu, MC and Mohanta, TK and Panda, SK},
title = {Molecular mechanisms, pathogenesis and therapeutic advances of Candida albicans in oral candidiasis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1918424},
pmid = {42812883},
issn = {2235-2988},
mesh = {Humans ; *Candida albicans/pathogenicity/drug effects/physiology/genetics ; Biofilms/growth & development/drug effects ; Antifungal Agents/therapeutic use/pharmacology ; *Candidiasis, Oral/microbiology/therapy/drug therapy ; Virulence Factors/metabolism ; Drug Resistance, Fungal ; Virulence ; Signal Transduction ; Host-Directed Therapy ; Quorum Sensing ; Immune Evasion ; Photochemotherapy ; },
abstract = {Oral candidiasis (OC), caused mainly by Candida albicans, is a common opportunistic fungal infection and typically affects immunocompromised individuals. The rise in antifungal resistance, biofilm-associated persistence, and immune evasion mechanisms has complicated OC management. This review examines in depth the molecular pathogenesis of C. albicans in OC, including virulence factors associated with adhesion, morphogenesis, quorum sensing, immune evasion, and biofilm formation. The review highlights the central roles of the cAMP-PKA, MAPK, Rim101, and TOR signaling pathways in regulating yeast-to-hyphal transition, virulence, stress adaptation, and biofilm development. In particular, dysregulation of these pathways promotes filamentation and biofilm maturation, contributing to persistent infection and reduced antifungal susceptibility. Conventional antifungal therapies, including azoles, polyenes, and echinocandins, remain important for OC management; however, biofilm-associated tolerance and emerging resistance can limit their effectiveness, emphasizing the need for complementary therapeutic approaches. Emerging strategies, including host-directed therapies, probiotics, photodynamic therapy (PDT), phytotherapeutics, essential oils, phenolic compounds, nanoparticles, and antimicrobial peptides, show promising antibiofilm and adjunctive potential. Clinical and experimental evidence indicates that PDT can reduce Candida burden, while probiotics may reduce oral Candida colonization and interfere with biofilm development. Furthermore, natural products, nanoparticles, and antimicrobial peptides may enhance conventional antifungal activity through complementary mechanisms. The reviewed evidence suggests that targeting fungal virulence and biofilm-associated mechanisms alongside conventional antifungal therapy may provide a more effective strategy for recurrent and drug-resistant OC. Future research should prioritize standardized clinical evaluation of antibiofilm therapies, microbiome-directed interventions, personalized treatment approaches, and combination therapies to improve therapeutic outcomes.},
}

Humans
*Candida albicans/pathogenicity/drug effects/physiology/genetics
Biofilms/growth & development/drug effects
Antifungal Agents/therapeutic use/pharmacology
*Candidiasis, Oral/microbiology/therapy/drug therapy
Virulence Factors/metabolism
Drug Resistance, Fungal
Virulence
Signal Transduction
Host-Directed Therapy
Quorum Sensing
Immune Evasion
Photochemotherapy

@article {pmid42812898,
year = {2026},
author = {Puspitasari, IM and Putra, DS and Deliyana, AN and Adiputri, NI and Octovia, LI and Paramita, SA and Sinuraya, RK},
title = {Recent Studies on the Effectiveness and Safety of Anti-Obesity Medications: A Scoping Review.},
journal = {Diabetes, metabolic syndrome and obesity : targets and therapy},
volume = {19},
number = {},
pages = {626279},
pmid = {42812898},
issn = {1178-7007},
abstract = {Obesity remains a major global public health challenge associated with increased morbidity, mortality, and reduced quality of life, necessitating effective treatment strategies beyond lifestyle modifications. The present scoping review aimed to synthesize recent evidence on the effectiveness and safety of anti-obesity medications (AOMs). A structured literature search was conducted in PubMed and Scopus in May 2025 to identify original studies published within the previous five years involving individuals with overweight or obesity receiving pharmacological interventions. A total of 42 articles representing 41 unique studies, predominantly randomized controlled trials (RCTs), were included in the evidence synthesis. The review encompassed glucagon-like peptide-1 receptor agonists (GLP-1 RA), including semaglutide, liraglutide, exenatide, and orforglipron; multi-receptor incretin agonists, including tirzepatide, retatrutide, and survodutide; amylin-based combination therapy (cagrilintide plus semaglutide); established non-incretin AOMs (orlistat, phentermine, phentermine/topiramate, and naltrexone/bupropion); microbiome-targeted therapies; and nutraceutical-based interventions. Among these, GLP-1 RA consistently demonstrated substantial weight-loss efficacy, with semaglutide achieving approximately 10-16% weight loss, while tirzepatide produced approximately 15-21% weight reduction over treatment durations of 20-70 weeks. Emerging multi-receptor incretin agonists also demonstrated promising efficacy, whereas established non-incretin AOMs, microbiome-targeted therapies, and nutraceutical-based interventions generally produced modest or more heterogeneous outcomes. Gastrointestinal adverse events (AEs) were the most frequently reported across incretin-based therapies. Overall, incretin-based therapies currently provide the greatest weight-loss benefit, although evidence for several emerging pharmacotherapies, microbiome-targeted therapies, and nutraceutical-based interventions remains limited. Further well-designed comparative trials, mechanistic studies, and long-term real-world investigations are needed to better establish the durability, safety, and clinical applicability of emerging AOMs.},
}

@article {pmid42813007,
year = {2026},
author = {Haga, SB},
title = {Menopause-associated gut microbiome remodeling and pharmacomicrobiomics: emerging mechanisms influencing drug response.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1953547},
pmid = {42813007},
issn = {2813-4338},
abstract = {Menopause is accompanied by profound hormonal changes that alter the composition and function of the gut microbiome, potentially influencing microbial drug metabolism and therapeutic response. At the same time, medication use increases substantially during midlife, creating a dynamic bidirectional relationship in which medications modify the gut microbiome while microbiome remodeling may influence medication efficacy, toxicity, and interindividual differences in drug response. This narrative review examines current evidence linking menopause-associated changes in the gut microbiome with medication response and explores the biological mechanisms that may underlie these interactions. The review summarizes microbiome-mediated pathways including microbial β-glucuronidase activity, direct microbial drug metabolism, altered bile acid metabolism, microbial metabolite signaling, and changes in intestinal barrier function and immune regulation that may influence pharmacokinetics and pharmacodynamics. Although direct evidence connecting menopause-associated microbiome remodeling with altered drug response remains limited, substantial evidence supports independent effects of menopause on the gut microbiome and of the gut microbiome on drug metabolism. Together, these findings provide a conceptual framework for understanding how menopause-associated microbial changes may contribute to variability in pharmacotherapy and highlight important priorities for future research, including incorporation of menopausal status into pharmacokinetic studies and clinical trials to advance microbiome-informed precision medicine for women.},
}

@article {pmid42813060,
year = {2026},
author = {Liu, Q and Zhang, Y and Zhang, R and Zhou, J},
title = {Global change-driven plant adaptive strategies and interspecific interaction networks: from molecular regulation to ecological management.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1904136},
pmid = {42813060},
issn = {1664-462X},
abstract = {Global change drivers, including climate warming, elevated CO2, nitrogen deposition, extreme climate events, heavy metal pollution, and biological invasions, interact in complex ways to reconfigure terrestrial ecosystems. This review synthesizes recent advances to develop a framework linking plant molecular responses to ecosystem management. We first examine how abiotic stressors reshape plant physiology and traits through defense signaling, secondary metabolite synthesis, and life-history adjustments. We then analyze how these plant-level changes cascade upward to restructure interspecific networks, focusing on plant-insect and plant-microbe dynamics mediated by altered chemical communication and resource competition. The mediating role of soil biogeochemistry and plant-soil feedback is also considered. Building on this mechanistic understanding, we propose that global change does not uniformly facilitate plant invasion; rather, it differentially filters invasive lineages along three axes: resource availability (elevated CO2, nitrogen deposition), disturbance regime (extreme drought-rewetting, warming amplitude), and life-history strategy (annual vs. perennial, sexual vs. clonal). Seed functional traits and climate-driven shifts in reproductive phenology operate as the upstream drivers that preconfigure interspecific network structure. Finally, we outline a management framework organized around four invader mechanism types: resource-acquisitive, plasticity-dependent under warming, drought-rewetting adapted, and microbiome-dependent, each matched with empirically validated, scenario-specific interventions. Integrating functional trait data with species distribution models enables quantitative forecasting of distribution shifts and identification of ecologically vulnerable zones. Such predictive outputs provide the data basis for full-cycle ecological management, from risk warning to targeted habitat regulation, offering a scientific foundation for biodiversity conservation and ecosystem restoration under global change.},
}

@article {pmid42813110,
year = {2026},
author = {Liu, P and Mao, R and Li, N and Guo, J and Wang, J and Mao, J},
title = {Beyond a universal obesity microbiome signature: pre-intervention heterogeneity and a framework for baseline profiling.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1921813},
pmid = {42813110},
issn = {2296-861X},
abstract = {Unlike previous reviews that primarily summarize obesity-associated microbial alterations, this review reframes the recurrent inconsistency of human obesity microbiome findings as an informative consequence of pre-intervention heterogeneity rather than merely failed replication or analytical noise. We integrate biological and contextual determinants of baseline microbiota variation with methodological and analytical sources of heterogeneity into a unified framework for interpreting why microbial diversity, taxonomic composition, and functional signals differ across individuals, populations, and studies. We critically synthesize evidence on baseline microbial diversity, community structure, host characteristics, regional dietary exposure, metabolic heterogeneity, and the potential relevance of pre-intervention microbiota to subsequent treatment outcomes. We also examine how cohort definition, stool sampling, laboratory processing, bioinformatic reconstruction, and statistical analysis shape the microbiome profiles that are ultimately observed. On this basis, we propose a baseline heterogeneity framework built on three linked principles: obesity-associated microbial signals are context-dependent; observed microbiota profiles are method- and pipeline-dependent; and their interpretation must be temporally anchored to the pre-intervention state. This framework positions baseline microbiota profiling not as descriptive cataloging or a search for a universal obesity-specific signature, but as a prerequisite for identifying confounding and effect modification, improving cross-population interpretation, and establishing the microbial and host context from which intervention begins. Future studies should integrate microbiota data with comprehensive characterization of relevant biological and contextual domains and evaluate the robustness of findings across analytical choices and independent populations. This conceptual shift provides a more rigorous foundation for region-specific baseline profiling and future longitudinal, mechanistic, and precision obesity research.},
}

@article {pmid42813250,
year = {2026},
author = {Kjærup, RB and Vimon, S and Højmark, M and Dalgaard, TS and Engberg, RM},
title = {Dietary inclusion of a fermented rapeseed-seaweed blend alters immunity and intestinal microbial activity but not Ascaridia galli burden in laying hens.},
journal = {British poultry science},
volume = {},
number = {},
pages = {1-12},
doi = {10.1080/00071668.2026.2704214},
pmid = {42813250},
issn = {1466-1799},
abstract = {1. Dietary components that are pre-fermented with lactic acid bacteria have recently attracted attention and may positively affect performance and gut health in poultry. This study investigated whether a commercial feed ingredient (EP199), containing fermented rapeseed meal, wheat bran and seaweed, could control worm burden, intestinal microbiota profiles and intestinal fermentation patterns, as well as immune profiles of layers infected with Ascaridia galli.2. A total of 192, 20 week old Bovans Brown laying hens were randomly allocated into four treatment groups; control diet vs. EP199 diet and experimentally infected (EXP) vs. naturally infected (NAT). The EP199 diet partly replaced rapeseed cake at 6%. The infected hens were either naturally exposed to A. galli contaminated litter or received oral administration of 764 embryonated A. galli eggs per hen at 20 weeks of age for 12 weeks.3. Performance was unaffected by EP199 or infection. However, hens fed the EP199 diet had a significantly lower egg production 3-12 weeks post-infection (pi) compared to the control group (86.1% vs. 90.1%, P=0.044). There was no effect on intestinal worm burden (x=7.98 worms per hen) or immune competence, as assessed by mitogen activation of peripheral blood mononuclear cells (PBMC). Despite similar nutrient profiles of the two diets, the hens fed the EP199 diet had significantly higher caecal levels of specific short chain fatty acids: acetic acid (79.8 vs. 71.0 mmol/kg digesta; P=0.020), propionic acid (35.0 vs. 30.1 mmol/kg digesta; P=0.005) and n-butyric acid (17.3 vs. 14.7 mmol/kg digesta; P=0.015).4. Compared to the control group, hens fed EP199 had a lower humoral A. galli-specific immune response, in terms of IgY serum titres at 10 weeks (2812 vs. 5291; P=0.002) and 12 weeks (10546 vs. 17668; P=0.025) pi. Hens fed the EP199 diet showed a significantly higher frequency of activated CD4+CD8+ T cells (28.7% vs. 21.9%; P=0.045).5. Feeding EP199 at 6% did not have an effect on severity of A. galli infection. However, EP199 showed an immunomodulatory effect and altered caecal microbial activity. Infection method (experimental vs. natural) influenced both the worm burden and immune parameters.},
}

@article {pmid42813343,
year = {2026},
author = {Sun, LJ and Chen, H and Fan, WJ and Shi, ZY and Zhao, YJ and Wang, Y and Nie, YZ},
title = {Gut Microbiota-Bile Acid Axis Correlates With Colonic Inflammation and Behavioral Deficits in Cirrhosis.},
journal = {Journal of digestive diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-2980.70072},
pmid = {42813343},
issn = {1751-2980},
support = {82470583//National Natural Science Foundation of China/ ; 82473582//National Natural Science Foundation of China/ ; 2026SF-YBXM-297//Key R&D Project in Shaanxi Province/ ; },
abstract = {OBJECTIVES: Hepatic encephalopathy (HE) is one of the common complications of cirrhosis. Gut-derived signals, including microbiota and bile acids, have been found to be involved in the gut-brain axis in cirrhosis. We aimed to explore the impact of the gut-microbiota-bile acid axis on behavioral deficits in cirrhosis.

METHODS: Mice were colonized with gut bacteria obtained from cirrhotic patients with or without HE via fecal microbiota transplantation. Serum bile acid profiles, intestinal histological features, and behaviors were assessed to evaluate the impacts of gut microbial disturbance on bile acids and gut-brain axis. Additionally, rodent cirrhotic models were induced by bile duct ligation (BDL), and the mice were treated with obeticholic acid (OCA) or rifaximin to evaluate the impact of bile acid remodeling on gut bacteria, gut injury, and behaviors. The 16S rRNA sequencing and LC-MS/MS were carried out to analyze gut microbiota composition and bile acid spectrum.

RESULTS: Gut bacteria transplanted from cirrhotic patients caused reduced levels of total and secondary bile acids in mice, which was accompanied by increased colonic lymphocytic infiltration, decreased exploratory behaviors, and higher expression of IBA-1. OCA intervention improved gut dysbiosis, alleviated liver injury and exploratory behavior impairment in the cirrhotic mouse model, accompanied by increased Farnesoid X receptor (FXR) expression and decreased ASBT, IBABP, and OSTα levels.

CONCLUSION: Gut microbiota-bile acid axis correlates with colonic inflammation and behavioral deficits in cirrhosis.},
}

@article {pmid42813435,
year = {2026},
author = {Zhang, Y and Liang, S and Xia, H and Zhong, X and Zheng, Y},
title = {Effects of Antibiotic and Temperature Treatments on Phycosphere Bacterial Communities of Kelp Gametophytes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70425},
doi = {10.1111/1758-2229.70425},
pmid = {42813435},
issn = {1758-2229},
support = {2017N3015//Regional Development Project of Fujian Province/ ; FZHJ03//Demonstration Project on Innovative Development of Marine Economy in the 13th Five-Year Plan of the State Oceanic Administration/ ; },
mesh = {*Temperature ; *Microbiota/drug effects ; *Bacteria/drug effects/classification/genetics/isolation & purification ; *Anti-Bacterial Agents/pharmacology ; *Kelp/microbiology/drug effects/growth & development ; },
abstract = {Microbiome dysbiosis represents a critical bottleneck in sustainable kelp aquaculture, yet the distinct regulatory mechanisms of antibiotics and temperature remain poorly characterized. This study systematically elucidates the divergent effects of penicillin-streptomycin exposure and temperature gradients on Saccharina japonica gametophytes and their epiphytic microbiota. Antibiotic treatment significantly reduced Proteobacteria from 93.02% to 49.70% and increased Bacteroidetes from 6.98% to 49.20%, replacing beneficial Sulfitobacter and Colwellia with opportunistic Kordia and Klebsiella, indicating severe dysbiosis driven by the creation of unoccupied ecological niches. In contrast, temperature variation did not alter dominant phyla: Proteobacteria remained predominant, but Vibrio peaked at 15°C (44.11%) alongside the maximal gametophyte specific growth rate of 5.21% per day, concurrently elevating pathogenic loads of Vibrio and Pseudomonas. These findings reveal that antibiotics disrupt core community architecture, whereas temperature modulates metabolic rates within stable taxonomic frameworks. Consequently, we propose a stratified preservation strategy: short-term seedling cultivation at 15°C requires stringent antimicrobial measures to mitigate disease risk, while lower temperatures are preferable for long-term germplasm storage to minimize contamination potential. This framework provides essential insights for precision microbial management, balancing growth promotion with disease control in kelp aquaculture systems.},
}

*Temperature
*Microbiota/drug effects
*Bacteria/drug effects/classification/genetics/isolation & purification
*Anti-Bacterial Agents/pharmacology
*Kelp/microbiology/drug effects/growth & development

@article {pmid42813505,
year = {2026},
author = {Huang, S and Sun, S and Zhao, Z and Gao, D and Zhang, W and Zhou, N and Jin, Y and Jin, B and Sun, D},
title = {Associations of Gut Microbiota Composition and Fecal Metabolomic Profiles in Patients With Acquired Premature Ejaculation: A Cross-Sectional Pilot Study.},
journal = {American journal of men's health},
volume = {20},
number = {5},
pages = {15579883261493263},
doi = {10.1177/15579883261493263},
pmid = {42813505},
issn = {1557-9891},
mesh = {Humans ; Male ; Pilot Projects ; Adult ; *Feces/microbiology/chemistry ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Premature Ejaculation/microbiology/metabolism ; Metabolomics ; Case-Control Studies ; *Metabolome ; },
abstract = {Premature ejaculation (PE) is a prevalent male sexual disorder with an incompletely understood pathogenesis and limited effective therapeutic strategies. Although the gut microbiota has been implicated in several diseases, its association with PE remains unclear. Metabolomic analyses and metagenomic sequencing were performed to compare the intestinal microbiota profiles between 20 patients with PE and 20 healthy controls, investigating the association between PE and gut microbiota. Comprehensive analysis revealed distinct microbial signatures between PE and control groups. The PE group exhibited significantly reduced relative abundances of Bifidobacteriaceae bacterium, Blautia, Coprobacillus, Ruminococcus sp. ctHOG1, Siphoviridae, and Alistipes. Metabolomic profiling identified 150 upregulated and 73 downregulated metabolites between the two groups. Kyoto encyclopedia of genes and genomes pathway enrichment analysis indicated significant enrichment of several potential signaling pathways in the PE group. This study characterized distinct gut microbiota features in patients with PE compared with healthy controls and investigated microbiota-associated pathways potentially related to PE through integrated metabolomics analysis. The findings provide preliminary insights into microbiome-associated alterations in PE.},
}

Humans
Male
Pilot Projects
Adult
*Feces/microbiology/chemistry
Cross-Sectional Studies
*Gastrointestinal Microbiome
*Premature Ejaculation/microbiology/metabolism
Metabolomics
Case-Control Studies
*Metabolome

@article {pmid42813801,
year = {2026},
author = {Xu, J and Fan, Y and Qu, G and Li, J and Peng, Y and Wang, M and Zhang, J and Feng, Y and Liu, X and Hu, Y and Kan, B and Li, Z and Zeng, M and Lu, X},
title = {Comparative gut microbiome in diarrheal and non-diarrheal children: an individually matched case-control study.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0019826},
doi = {10.1128/msystems.00198-26},
pmid = {42813801},
issn = {2379-5077},
abstract = {Diarrhea, a leading cause of under-five mortality in developing countries, drives therapeutic challenges amid global antibiotic resistance. This study aimed to compare gut microbiota, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and virulence factors (VFs) in diarrheal and non-diarrheal children, explore reasons for asymptomatic pathogen carriage, and develop a microbiome-based model to predict the potential etiology of diarrhea. This individually matched case-control study analyzed 42 paired fecal samples (selected from 716 diarrhea/non-diarrhea cases) to compare gut microbiome profiles, ARGs, MGEs, and VFs using metagenomic sequencing and pathogen-specific PCR. Diarrheal children showed reduced alpha diversity, increased Proteobacteria, and elevated VFs and MGEs. Surprisingly, ARGs were more abundant in non-diarrheal children, suggesting ARG colonization in healthy hosts. Actinomyces was enriched in non-diarrheal pathogen carriers and may be associated with asymptomatic bacterial pathogen carriage. A random forest (RF) model incorporating non-pathogenic bacteria achieved high accuracy in predicting diarrheal status and pathogen carriage. This study reveals distinct microbial ecologies between diarrheal and healthy children. The enrichment of specific bacterial taxa in asymptomatic carriers may be associated with pathogen tolerance. The unexpected ARG abundance in healthy children highlights a hidden antimicrobial resistance reservoir. These findings inform microbiome-based diagnostics and antibiotic stewardship in pediatric diarrhea.IMPORTANCEThis study is significant because it provides robust, individually matched case-control evidence linking childhood diarrhea to gut microbiome dysbiosis and the distribution of pathogenic and resistance-related genetic elements. By integrating metagenomic sequencing with pathogen-specific polymerase chain reaction (PCR), it offers a comprehensive comparison of microbial composition, virulence factors (VFs), mobile genetic elements (MHEs), and antibiotic resistance genes (ARGs) between diarrheal and non-diarrheal children. The findings demonstrate reduced microbial diversity and enrichment of Proteobacteria, virulence factors, and mobile genetic elements in diarrheal cases, highlighting microbiome instability during infection. Importantly, the unexpectedly higher abundance of antibiotic resistance genes in non-diarrheal children underscores the underestimated role of healthy populations as reservoirs of resistance. Furthermore, the establishment of predictive models for diarrhea status and pathogen carriage enhances the translational value of the study. Overall, this work advances the understanding of pediatric diarrheal disease and informs prevention, surveillance, and treatment strategies in the context of global antimicrobial resistance.},
}

@article {pmid42804011,
year = {2026},
author = {Gök, ÇC and Can, E},
title = {Systemic immune-inflammation index as a dynamic marker of therapeutic response in neonatal early-onset sepsis: implications for antibiotic stewardship.},
journal = {European journal of pediatrics},
volume = {185},
number = {10},
pages = {},
pmid = {42804011},
issn = {1432-1076},
mesh = {Humans ; *Neonatal Sepsis/drug therapy/immunology/blood/diagnosis ; Retrospective Studies ; Infant, Newborn ; *Anti-Bacterial Agents/therapeutic use ; *C-Reactive Protein/analysis/metabolism ; Biomarkers/blood ; Female ; *Antimicrobial Stewardship ; Male ; *Inflammation/blood ; ROC Curve ; Treatment Outcome ; Prognosis ; Case-Control Studies ; },
abstract = {UNLABELLED: This study investigates the systemic immune-inflammation index (SII) as a dynamic marker to track antibiotic efficacy and guide stewardship in term neonates. A retrospective cohort study evaluated 275 term neonates (85 with culture-proven early-onset sepsis [EOS] and 190 controls). Complete blood counts and C-reactive protein (CRP) were analyzed on Days 1 and 3 of therapy. At diagnosis, the calculated SII was significantly higher in the EOS group compared to controls (Median 812 [IQR: 650-1120] vs. 515 [IQR: 410-630]; p < 0.001). ROC analysis yielded an AUC of 0.87. Multivariable logistic regression confirmed the independent prognostic value of the SII after adjusting for clinical confounders. By Day 3, the SII demonstrated a faster kinetic decline than CRP in 74.1% of the sepsis cohort, functioning as an early indicator of resolving inflammation.

CONCLUSION: While diagnostic accuracy at onset is comparable to CRP, the SII demonstrates potential as a practical dynamic indicator of therapeutic response in EOS. Its clinical application provides an objective biological signal that may help identify rapid responders, potentially supporting safely shortened antibiotic courses pending prospective validation.

WHAT IS KNOWN: • CRP has a delayed kinetic rise and clearance in neonatal EOS, limiting real-time monitoring. • Prolonged empirical antibiotics in neonates alter the microbiome and increase nosocomial risks.

WHAT IS NEW: • SII is an accessible, zero-cost, and dynamic indicator of therapeutic response in neonatal EOS. • A 72-hour SII reduction identifies rapid responders early, guiding safer antibiotic cessation.},
}

Humans
*Neonatal Sepsis/drug therapy/immunology/blood/diagnosis
Retrospective Studies
Infant, Newborn
*Anti-Bacterial Agents/therapeutic use
*C-Reactive Protein/analysis/metabolism
Biomarkers/blood
Female
*Antimicrobial Stewardship
Male
*Inflammation/blood
ROC Curve
Treatment Outcome
Prognosis
Case-Control Studies

@article {pmid42804030,
year = {2026},
author = {Sun, H and Yan, R and Ma, Y and Chen, Z and Liu, L and Zhang, J and Chen, Y},
title = {Bibliometric analysis of research trends and hotspots on the microbial mediation effects.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {10},
pages = {},
pmid = {42804030},
issn = {1572-9699},
support = {24YJCZH261//Ministry of Education in China Project of Humanities and Social Sciences/ ; 252300423502//Natural Science Foundation of Henan Province/ ; 24B110003//Key Scientific Research Project of Colleges and Universities in Henan Province/ ; 231111110100//Henan Province Key Research and Development Project/ ; },
mesh = {*Bibliometrics ; Humans ; *Microbiota ; },
abstract = {The microbiome is increasingly recognized as a potential mediator linking environmental exposures and host-related factors to health outcomes. However, comprehensive bibliometric assessments of microbial mediation effects remain scarce. This study analyzed 3506 eligible articles published from 2016 to 2025, retrieved from the Web of Science Core Collection and Scopus. Using CiteSpace, VOSviewer, and the Bibliometrix R package, we examined publication trends, national and institutional contributions, co-citation networks, and keyword dynamics. According to statistics, researchers from 91 countries and 1151 institutions participated in this field, with China and the United States leading in contributions. The Chinese Academy of Sciences was the most prolific institution (49 documents, 2765 citations), while the University of California system received the highest citation count (4285). Co-citation analysis yielded 653 nodes and 771 links (Q = 0.7894 , S = 0.9304), with the largest cluster being "cancer development" (47 publications). The strongest citation burst was Belkaid and Hand (2014, Cell; burst strength = 9.54). Keyword co-occurrence analysis identified 6705 keywords, with "gut microbiota" being the most frequent; "Mendelian randomization" and "gut-brain axis" emerged as new hotspots. Overall, this study synthesizes a decade of research, demonstrating a shift from descriptive association studies to mechanistic and causal investigations of microbial mediation, in which Mendelian randomization and the microbiota-gut-brain axis have emerged as important recent research themes. These findings provide a systematic overview of the field and offer valuable insights for future research in microbiology, medicine, and ecology.},
}

*Bibliometrics
Humans
*Microbiota

@article {pmid42804474,
year = {2026},
author = {Adamu, A},
title = {Vaginal Lactic Acid and Lactobacillus-Dominated Microbiota in HIV-1 Susceptibility: Mechanistic Insights and Implications for Sub-Saharan African Women.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {96},
number = {4},
pages = {e70326},
doi = {10.1111/aji.70326},
pmid = {42804474},
issn = {1600-0897},
mesh = {Humans ; Female ; *Vagina/microbiology/immunology ; *HIV Infections/immunology/epidemiology/microbiology ; *Lactobacillus/immunology/physiology ; *Microbiota/immunology ; *HIV-1/immunology/physiology ; *Vaginosis, Bacterial/microbiology/immunology ; *Lactic Acid/metabolism ; Sub-Saharan African People ; Dysbiosis/microbiology ; Disease Susceptibility ; Africa South of the Sahara/epidemiology ; },
abstract = {Women in Sub-Saharan Africa experience disproportionately high rates of HIV-1 acquisition, a disparity not fully explained by reported sexual behavior or conventional epidemiological risk factors. Increasing evidence implicates the cervicovaginal microbiome, particularly the presence of a Lactobacillus-dominated, lactic-acid-rich environment, as an important biological determinant of susceptibility. This review synthesizes mechanistic, clinical, and epidemiological evidence linking vaginal lactic acid, Lactobacillus-dominated microbiota, bacterial vaginosis, and HIV-1 acquisition, with particular emphasis on evidence from African populations. Lactic acid produced by vaginal Lactobacillus spp. exhibits direct anti-HIV-1 activity, suppresses bacterial-vaginosis-associated organisms, and contributes to epithelial barrier homeostasis. Conversely, anaerobe-dominated dysbiosis is associated with reduced lactic acid production, epithelial disruption, heightened inflammatory signaling, and increased availability of HIV-1 target cells, with African cohorts reporting approximately two- to four-fold greater HIV-1 acquisition risk among women with dysbiotic microbiota. Emerging interventions targeting vaginal microbiota, including Lactobacillus crispatus-based live biotherapeutics, demonstrate potential to restore microbiological homeostasis and reduce bacterial vaginosis recurrence. Collectively, the evidence supports vaginal microbial restoration as a biologically plausible adjunct to HIV-1 prevention. However, regionally validated trials, durable microbiome-targeted interventions, scalable diagnostics, and integration with established prevention platforms are needed to determine clinical effectiveness and implementation feasibility in high-burden African settings.},
}

Humans
Female
*Vagina/microbiology/immunology
*HIV Infections/immunology/epidemiology/microbiology
*Lactobacillus/immunology/physiology
*Microbiota/immunology
*HIV-1/immunology/physiology
*Vaginosis, Bacterial/microbiology/immunology
*Lactic Acid/metabolism
Sub-Saharan African People
Dysbiosis/microbiology
Disease Susceptibility
Africa South of the Sahara/epidemiology

@article {pmid42804531,
year = {2026},
author = {Hirama, T and Itagaki, T and Ikushima, T and Mukai, S and Watanabe, T and Watanabe, Y and Oishi, H and Okada, Y},
title = {Microbiological Dynamics Before and After Lung Transplantation: Clinical Interpretation and Prognostic Implications.},
journal = {Clinical transplantation},
volume = {40},
number = {10},
pages = {e70702},
doi = {10.1111/ctr.70702},
pmid = {42804531},
issn = {1399-0012},
support = {23K08287//Grant-in-Aid for Scientific Research C/ ; //Japan Society for the Promotion of Science/ ; 2026-413//Kobayashi Foundation/ ; },
mesh = {Humans ; *Lung Transplantation/adverse effects ; Prognosis ; *Lung Diseases/surgery/microbiology ; },
abstract = {Respiratory cultures before and after lung transplantation are frequently obtained but often difficult to interpret. A positive culture may represent donor-derived organisms, recipient reservoir recolonization, hospital acquisition, transient colonization, invasive infection, or a marker of evolving graft vulnerability. This review summarizes how respiratory microbiology changes across the lung transplant timeline and proposes a practical framework for clinical interpretation. Conventional culture-based studies and recent airway microbiome literature are integrated to examine donor-recipient attribution, pre-transplant colonization, disease-specific reservoirs, single-lung transplantation, and pathogen-specific risk. Pre-transplant recipient colonization, particularly with multidrug-resistant gram-negative organisms, appears more consistently associated with early post-transplant pneumonia and short-term outcomes than donor culture positivity alone when targeted antimicrobial therapy is used. Disease-specific patterns are also important: cystic fibrosis and bronchiectasis favor recolonization from persistent reservoirs, whereas single-lung transplantation creates a dual-airway ecosystem in which the native lung may remain microbiologically relevant. Persistent or recurrent isolation of organisms such as Pseudomonas aeruginosa, Burkholderia cenocepacia, Staphylococcus aureus, Aspergillus species, and nontuberculous mycobacteria should be interpreted in relation to symptoms, imaging, lung function, sampling source, and timing from transplant. Contextual interpretation of respiratory cultures may improve antimicrobial planning, donor acceptance decisions, stewardship, and long-term graft surveillance.},
}

Humans
*Lung Transplantation/adverse effects
Prognosis
*Lung Diseases/surgery/microbiology

@article {pmid42804599,
year = {2026},
author = {Hensen, T and Khatib, L and Patel, L and McDonald, D and González, A and MahmoudianDehkordi, S and Blach, C and Knight, R and Kaddurah-Daouk, R and Thiele, I},
title = {Personalized whole-body modeling links gut microbiota to metabolic perturbations in Alzheimer's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2732659},
doi = {10.1080/19490976.2026.2732659},
pmid = {42804599},
issn = {1949-0984},
mesh = {Humans ; *Alzheimer Disease/microbiology/metabolism/blood ; *Gastrointestinal Microbiome ; Male ; Female ; Aged ; Bacteria/classification/isolation & purification/genetics/metabolism ; Cognitive Dysfunction/metabolism/microbiology ; Aged, 80 and over ; Metabolome ; },
abstract = {The human gut microbiome has been linked to metabolic disturbances in Alzheimer's disease (AD). However, the mechanisms by which gut microbes might influence metabolic dysfunction in AD remain poorly understood. Previously, gut microbiome-personalized whole-body models of human metabolism have been applied to predict how altered gut microbiome compositions may influence metabolites in the blood of healthy aging individuals with increased risk of AD. However, these previous results have not been validated in AD. In this study, we aimed to test these prior predictions in a cohort of AD dementia patients and individuals with mild cognitive impairment (MCI) and a probable AD diagnosis. Therefore, we created gut microbiome-personalized whole-body metabolic models for 34 AD dementia patients, 51 MCI patients, and 298 healthy controls. These in silico models were profiled to predict the metabolic influences of gut microbiomes on blood metabolites with previously reported alterations in AD. We found increased capacities of the in silico host-microbiome co-metabolism to produce S-adenosyl-L-methionine, L-arginine, creatine, taurine, and formate in the blood of AD patients. The metabolic predictions were then linked to key microbial taxa using a novel method that combines modeling-informed prediction sensitivity to alternative microbial abundances with LASSO-based taxonomic stability selection and elastic net regressions. This method found that increased relative abundances of Bacteroides uniformis and Bacteroides thetaiotamicron in AD were major factors driving the predicted metabolic changes. Furthermore, the metabolic predictions were associated with allelic variations in the APOE risk gene in healthy individuals, confirming our previous findings. In conclusion, we identified blood metabolites with known links to AD that were differentially influenced by gut microbiota in AD, and identified possible microbial drivers of these predicted shifts in host-microbiome interactions. These findings may facilitate the development of microbiome-informed treatments of AD.},
}

Humans
*Alzheimer Disease/microbiology/metabolism/blood
*Gastrointestinal Microbiome
Male
Female
Aged
Bacteria/classification/isolation & purification/genetics/metabolism
Cognitive Dysfunction/metabolism/microbiology
Aged, 80 and over
Metabolome

@article {pmid42804854,
year = {2026},
author = {Wang, C},
title = {Observation-control mismatch in host-microbiome systems: When does microbiome compression preserve intervention choice?.},
journal = {Bio Systems},
volume = {269},
number = {},
pages = {105966},
doi = {10.1016/j.biosystems.2026.105966},
pmid = {42804854},
issn = {1872-8324},
abstract = {The intestinal microbiome is a high-dimensional ecological system, but neither host physiology nor clinical measurement has access to all of that detail. Functional redundancy, ecological filtering and niche construction explain why taxonomically different communities can converge on similar functions or host phenotypes, yet they do not answer a separate decision problem: when does a predeclared microbiome representation discard distinctions that matter for intervention choice? Here I define observation-control mismatch (OCM) as a task-specific decision audit for host-microbiome systems. An action is acceptable only when its expected loss is both within a predeclared regret margin η of the best available action and below an absolute biological or clinical loss threshold τ, with any critical-harm constraints specified separately. For a finite set of experimentally constructed realizations, intervention-panel feasibility is assessed first: each tested realization must have at least one acceptable action. Conditional on that requirement, a compressed observational class is control-sufficient when the realizations share at least one acceptable action and shows OCM when each realization is individually actionable but no common acceptable action exists; a realization with no acceptable action instead indicates intervention-panel insufficiency. For population data, actionability coverage and common-action coverage are audited separately against a prespecified coverage q. All empirical conclusions are therefore conditional on the chosen X: control sufficiency means that no intervention-relevant distinction was detected beyond OE within the information represented by X, not that the underlying state S has been exhaustively resolved. This audit is complementary to heterogeneous-treatment-effect analysis and individualized treatment-rule learning: it asks whether information deliberately discarded by an existing biological or clinical representation changes what can be done, not merely whether responses differ. The intestinal boundary provides the biological motivation because microbial ecological states are projected into host-accessible consequences, whereas host physiology and interventions modify niche variables that select among microbial states. This projection-selection architecture is biological rather than a mathematical duality. OCM is not itself a universal falsifiable biological proposition; it generates task-bounded hypotheses defined by a population, representation, intervention panel, outcome, time horizon, η, τ and, for population analyses, q. Retrospective multi-intervention data can screen for mismatch, whereas prospective defined-community or gnotobiotic experiments can test finite-support intersections directly. The audit is unnecessary when a direct causal determinant or an already validated treatment rule makes within-class auditing irrelevant. Additional dynamic or host-boundary measurements are justified only when they repair a demonstrated decision blind spot.},
}

@article {pmid42805155,
year = {2026},
author = {Moutsopoulos, HM},
title = {Autoimmune diseases: distinct disorders or diverse manifestations of a common pathogenic process?.},
journal = {Current opinion in immunology},
volume = {103},
number = {},
pages = {102852},
doi = {10.1016/j.coi.2026.102852},
pmid = {42805155},
issn = {1879-0372},
abstract = {Autoimmune diseases arise from the amplification of natural autoreactive immune clones in genetically susceptible individuals under the influence of environmental triggers, epigenetic modifications, and hormonal factors. They comprise a broad and heterogeneous group of disorders characterized by immune-mediated tissue injury and dysfunction. More than 80 autoimmune diseases have been identified, affecting nearly every organ system. Although these disorders exhibit distinct clinical phenotypes and tissue specificity, many share common clinical manifestations, autoantibody profiles, genetic susceptibility loci, epigenetic alterations, and immunopathogenic mechanisms. Alterations in the composition of the microbiome (dysbiosis) have also been implicated in the development and progression of several autoimmune diseases. Furthermore, aberrant B-cell activation, impaired regulatory T-cell function, dysregulated type I interferon signaling, and chronic tissue-specific immune responses contribute to disease pathogenesis. The management of systemic autoimmune diseases, including rheumatoid arthritis, systemic lupus erythematosus, Sjögren's syndrome (autoimmune epithelitis), systemic sclerosis, Idiopathic inflammatory myopathies, mixed connective tissue disease, and systemic vasculitis, is increasingly guided by the nature and severity of clinical manifestations and the dominant immunopathological pathways rather than by traditional disease classifications alone. This review examines whether autoimmune diseases should be regarded as distinct clinical entities or as diverse manifestations of shared immunopathological processes. By analyzing common clinical features, autoantibody profiles, tissue-specific immune responses, environmental influences, genetic susceptibility, epigenetic regulation, and therapeutic approaches, we highlight both the unifying mechanisms and the distinguishing characteristics that shape autoimmune disease expression. Collectively, the available evidence supports the concept that autoimmune diseases represent a spectrum of interconnected disorders that share common pathogenic pathways while maintaining disease-specific patterns of tissue involvement.},
}

@article {pmid42805174,
year = {2026},
author = {Perl, M and Guetter, S and Shah, D and Holzinger, S and Becker, L and Tariq, M and Menauer, P and Delahais, S and Lutzny-Geier, G and Scherer, JN and Göttert, S and Herfeld, K and Heinrich, P and Kreitmeier, KG and Gebhard, C and Herr, W and Trefny, MP and Doerr, J and Sameri, S and Harrer, DC and Ziegler-Martin, K and Staudt, S and Hansmann, L and Edinger, M and Wolff, D and Weber, D and Meedt, E and Denk, A and Gessner, A and Holler, E and Wertheimer, T and Neuhaus, K and Zheng, T and Cordas Dos Santos, DM and Theurich, S and Schirmer, M and Kleigrewe, K and Schluter, J and van den Brink, M and Schmitt, M and Feuerer, M and Heuser-Loy, C and Baldwin, J and Gattinoni, L and Rehli, M and Hudecek, M and Bigenwald, C and Zitvogel, L and Subklewe, M and Blumenberg, V and Schubert, ML and Stein-Thoeringer, C and Luu, M and Kobold, S and Fante, MA and Thiele Orberg, E and Poeck, H},
title = {Opposing functions of gut immunomodulatory metabolites on CAR-T therapy.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.09.004},
pmid = {42805174},
issn = {1097-4172},
abstract = {Chimeric antigen receptor (CAR)-T cell therapy has transformed hematological cancer treatment, yet nearly half of patients still relapse or progress. Increasing evidence implicates the gut microbiome and antibiotic exposure as key modulators of clinical outcomes. In a cohort of 129 patients across three German centers, shotgun metagenomics and targeted mass spectrometry revealed that reduced short-chain fatty acids, particularly valeric acid, prior to CAR-T cell therapy correlated with increased risk of disease progression. Conversely, high levels of indole metabolites, including indole-3-carboxaldehyde and indole-3-acetic acid as well as the branched-chain fatty acid isovaleric acid, were linked to adverse outcomes. Functional validation in human and murine CAR-T cell models demonstrated that valeric acid supplementation enhanced, while indole-3-carboxaldehyde and isovaleric acid impaired, CAR-T cell efficacy. These findings reveal the opposing roles of immunomodulatory metabolites on CAR-T cell therapy, carrying significant implications for the design of metabolite-guided, microbiome-based therapeutics.},
}

@article {pmid42805210,
year = {2026},
author = {Moradi, A and Winayak, R and Pal, SK},
title = {Cancer and the microbiome: from association to intervention.},
journal = {The Lancet. Oncology},
volume = {27},
number = {10},
pages = {e519-e531},
doi = {10.1016/S1470-2045(26)00326-8},
pmid = {42805210},
issn = {1474-5488},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects/immunology ; *Neoplasms/microbiology/immunology/drug therapy/therapy ; Probiotics/therapeutic use ; Fecal Microbiota Transplantation ; *Immune Checkpoint Inhibitors/therapeutic use/adverse effects ; },
abstract = {The gut microbiome is increasingly recognised as a clinically modifiable determinant of efficacy and toxicity across systemic cancer therapies, with the most mature evidence in patients receiving immune checkpoint inhibitors (ICIs). The composition and function of intestinal microbes can influence treatment outcomes by affecting immune priming, antigen presentation, host-microbial co-metabolism, drug biotransformation, and epithelial barrier integrity. In melanoma, non-small-cell lung cancer, and renal cell carcinoma, higher microbial diversity, ecological stability, and enrichment of immunostimulatory pathways have been associated with improved ICI response and survival. By contrast, antibiotics and proton pump inhibitors are linked to inferior outcomes because they disrupt the microbiome. Microbiome-directed interventions, including faecal microbiota transplantation, dietary modifications, prebiotics, probiotics, and live biotherapeutic products, are undergoing clinical testing but remain at the investigational stage. This Review synthesises current evidence linking the intestinal microbiome to anticancer therapy outcomes, evaluates strategies and challenges for therapeutic modulation of the microbiome, and introduces emerging insights into the mycobiome.},
}

Humans
*Gastrointestinal Microbiome/drug effects/immunology
*Neoplasms/microbiology/immunology/drug therapy/therapy
Probiotics/therapeutic use
Fecal Microbiota Transplantation
*Immune Checkpoint Inhibitors/therapeutic use/adverse effects

@article {pmid42805452,
year = {2026},
author = {Fessele, K and Loftis, J and Alzahid, S and Arceneaux, B and Armah, J and Arthur, E and Chang-Swartz, M and Conley, Y and Eche-Ugwu, I and Flora, L and Gonzalez, A and Goto, T and Halpenny, B and Hammer, M and Harrison, M and Haynes-Lewis, H and Jackson, M and Jafry, K and Johnson-Beller, R and Kaler, A and Krok-Schoen, J and Lally, R and Lyon, D and Milbury, K and Mohan, A and Ponce, D and Posada, W and Saligan, L and Samami-Kojidi, E and Schmidt, R and Schumacher, M and Smith, G and Starkweather, A and Thompson, M and Tlusty, G and Uno, H and Whisenant, M and White, T and Wright, A and Brassil, K},
title = {Design of the comprehensive outcomes for after Cancer Health (COACH) trial: A randomized, wait-list control digital health coaching intervention for cancer survivors.},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {108474},
doi = {10.1016/j.cct.2026.108474},
pmid = {42805452},
issn = {1559-2030},
abstract = {BACKGROUND: There are an estimated 18.6 million cancer survivors representing approximately 5.4% of the United States (U.S.) population, projected to exceed 26 million by 2040. Due to advances in therapy, individuals with cancer are experiencing increased overall survival that is often accompanied by maintenance therapy and the management of treatment-related sequelae that can diminish overall quality-of-life (QOL) and well-being. An interprofessional team in partnership with Pack Health (now operating under Quest Diagnostics), designed a 6-month digital health coaching (DHC) intervention to improve health outcomes for cancer survivors, defined in this study as within one year of completion of primary therapy, including those with metastatic disease.

METHODS: Up to 625 survivors with diverse tumor types across eight U.S. sites are enrolling in a randomized wait-list control trial. The DHC intervention combines 1:1 calls with digital outreach delivered by certified health coaches. Primary aims are to assess feasibility and acceptability of the intervention and its effect on health self-efficacy. Secondary and exploratory aims assess associations among clinical, patient-reported, wearable, and microbiome data. Comorbidities, psychosocial status, and lifestyle behaviors are included to identify interindividual variability in survivors' experiences and needs.

CONCLUSION: The development and implementation of this multi-site DHC intervention demonstrates leveraging an academic-industry partnership to deliver continued supportive care to cancer survivors. Outcomes will evaluate the feasibility of the DHC model to extend supportive care beyond clinical settings and address survivors' QOL and well-being. The COACH intervention is a potentially scalable model designed to meet the holistic needs of survivors.},
}

@article {pmid42805516,
year = {2026},
author = {Zaeifi, D and Jamialahmadi, K and Karimi, G},
title = {The TLR4/MyD88 axis in cancer: divergent and convergent roles of NF-κB and NLRP3 inflammasome activation and therapeutic opportunities.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {109645},
doi = {10.1016/j.phrs.2026.109645},
pmid = {42805516},
issn = {1096-1186},
abstract = {The TLR4/MyD88 signaling axis serves as a central hub linking microbial- and damage-associated molecular patterns to oncogenic inflammation. Upon ligand engagement, MyD88 orchestrates two major downstream branches, including the canonical NF-κB pathway, which drives transcriptional programs for cell survival, proliferation, angiogenesis, and metastasis, and the NLRP3 inflammasome, which amplifies IL-1β/IL-18 release and pyroptosis. While these branches have been extensively studied individually, their integrated roles and crosstalk remain underexplored in cancer. Recent advances show that NF-κB provides the essential signal 1 for NLRP3 priming, yet the two pathways exert cell-type- and tumor-stage-dependent, sometimes opposing effects on tumor progression, therapy resistance, and anti-tumor immunity. We highlight cancer-type and cell-type specificity, microbiome influences, and emerging therapeutic opportunities targeting TLR4, NF-κB, and NLRP3 individually or in combination. This unified framework positions the TLR4/MyD88 axis as a high-value target for precision oncology and underscores the need for pathway-selective inhibitors to harness its divergent outputs.},
}

@article {pmid42805588,
year = {2026},
author = {Metris, A and Guan, R and Ampatzoglou, A and Murphy, B},
title = {Methods to Address Compositional Data Challenges in Clinical Studies for the Safety Assessment of Human Microbiome Perturbations.},
journal = {Journal of food protection},
volume = {},
number = {},
pages = {100933},
doi = {10.1016/j.jfp.2026.100933},
pmid = {42805588},
issn = {1944-9097},
abstract = {Advances in sequencing technologies have enabled increasingly detailed characterisation of the human microbiome in clinical studies, but interpretation of microbiome modulation which has relevance to health and disease characterisation or safety assessments remains methodologically challenging. Taxonomic profiles generated by amplicon or shotgun sequencing are inherently compositional, sparse, and limited by detection, which complicates differential abundance analysis and may lead to unstable or misleading conclusions, especially in low-biomass settings where contamination and under-detection are concerns. Here, we review strategies used to analyse and complement sequencing-derived taxonomic count data, with the aim of obtaining more quantitative information on microbial differential abundance and viability. These include transformations for relative-abundance-based analyses and bias corrections between samples based on mathematical assumptions or additional experimental measurements such as spike-ins, broad-range qPCR and flow cytometry. We find that there is no consensus on which method best addresses compositionality and that detection level and significance of low-level microbes in health and diseases are overlooked. We discuss the limitations of sequence-based methods, such as the biases induced by the experimental and analytical process, as well as viability measurements for meaningful differential abundance assessment. We illustrate the need to integrate prevalence as well as abundance and the importance of covariates in models in the case of bacterial vaginosis. Overall, meaningful assessment of microbiome perturbations requires not only statistical correctness of differential abundance analysis, but also careful study design, appropriate measurement choices, quantitative context, and explicit recognition of the biological and analytical limits of sequencing-derived data.},
}

@article {pmid42805594,
year = {2026},
author = {Fielding, A and Lam, L},
title = {Emerging Topical Therapies and Skin Care Management for Hidradenitis Suppurativa.},
journal = {Skin therapy letter},
volume = {31},
number = {5},
pages = {5-7},
pmid = {42805594},
issn = {1201-5989},
mesh = {Humans ; *Hidradenitis Suppurativa/drug therapy/therapy ; *Skin Care/methods ; *Dermatologic Agents/administration & dosage/therapeutic use ; Administration, Cutaneous ; Administration, Topical ; },
abstract = {Hidradenitis suppurativa (HS) is a painful, chronic inflammatory condition that forms recurring nodules and abscesses in skin folds, leading to severe scarring. While the exact pathogenesis is still being determined, it is thought to involve follicular occlusion and rupture, driven by multifactorial influences such as genetics, environment, hormones, microbiome, and immune dysregulation. The complex nature of this disease entails complicated management and has led to the development of various therapies targeting these different factors. While moderate-to-severe HS has seen growing therapeutic options in recent years, mild early-stage forms of the disease lack any approved treatments. This review examines the most recent developments in topical therapies specifically for mild HS, along with advancements in daily HS skin care and post de-roofing wound management. These emerging therapies offer the potential for more effective, personalized care to reduce the disease burden for patients living with HS.},
}

Humans
*Hidradenitis Suppurativa/drug therapy/therapy
*Skin Care/methods
*Dermatologic Agents/administration & dosage/therapeutic use
Administration, Cutaneous
Administration, Topical

@article {pmid42805667,
year = {2026},
author = {Hojeij, B and Tchetverikov, I and Vasileiou, E and Apostolidis, G and Dimitroulas, T and Mytilinaiou, M and Gonçalves, C and Rodrigues, AM and Coates, L and Konstantinidis, D and Dimitropoulos, K and Melanitis, N and Foolen, J and Wagenaar, W and Charisis, V and Hadjileontiadis, LJ and Luime, JJ},
title = {Psoriatic arthritis digital phenotyping and inflammation drivers (PDPID) study: protocol for an international multicentre prospective cohort.},
journal = {BMJ open},
volume = {16},
number = {9},
pages = {e115903},
doi = {10.1136/bmjopen-2025-115903},
pmid = {42805667},
issn = {2044-6055},
mesh = {Humans ; *Arthritis, Psoriatic/diagnosis ; Prospective Studies ; Digital Health ; Biomarkers/analysis ; Smartphone ; Phenotype ; Inflammation ; Research Design ; *Mobile Applications ; Machine Learning ; },
abstract = {INTRODUCTION: Changes in psoriatic arthritis (PsA) disease activity, particularly flares, are unpredictable and can impact patients' quality of life. Digital biomarkers derived from data collected via smart devices provide an opportunity for unobtrusive continuous monitoring of symptoms reflecting disease activity. Besides, our understanding of the mechanisms and triggers behind flares is limited. The primary objectives of the Psoriatic Arthritis Digital Phenotyping and Inflammation Drivers (PDPID) study are: (1) to develop digital biomarker capable of detecting PsA flare using data collected from patient's smartphone and smartwatch, and (2) to develop machine learning models for PsA flare prediction using clinical, biological, environmental and digital data.

METHODS AND ANALYSIS: The PDPID study is a 12-month multi-centre prospective cohort study conducted across four countries. Study visits are scheduled at baseline (T0), and 3, 6, 9 and 12 months follow-up visits, with additional patient-initiated visits due to flare. At inclusion, patients have a study app installed on their smartphone and receive a smartwatch. Flare information is collected using physician- and patient-reported flare questionnaires administered at each visit, and via the flare button in the app that patients can activate. The study collects clinical data (physical measurements, questionnaires), biological markers (salivary DNA, gut microbiome, hair cortisol, C-reactive protein) and environmental exposure data (weather and air pollution). The app includes in-app questionnaires, active photo and video tests and passively captures digital data from the smartphone and smartwatch sensors.

ETHICS AND DISSEMINATION: Ethical approval has been granted from each of the participating countries (Erasmus MC, the Netherlands: MEC-2023-0470; HRA and Health and Care Research Wales, UK: 332916 NOVA Medical School|Faculdade de Ciências Médicas (NMS|FCM) Ethical Committee (CEFCM), Portugal (124/2023/CEFCM); MREC Hipokrateion Hospital Thessaloniki, Greece: 5549/31.01.24). Findings of this study will be disseminated through reports to the funding body, the project website, newsletters, social media, national and international conferences and symposiums, and scientific publications.

TRIAL REGISTRATION NUMBER: NCT06347237.},
}

Humans
*Arthritis, Psoriatic/diagnosis
Prospective Studies
Digital Health
Biomarkers/analysis
Smartphone
Phenotype
Inflammation
Research Design
*Mobile Applications
Machine Learning

@article {pmid42805688,
year = {2026},
author = {Moghoofei, M and Shahbazi, R and Rezaei, M and Safarzadeh, H and Yazdanpour, Z and Panahi, P and Taki, E and Asadi, A and Pajavand, H},
title = {Possible role of bacterial infection in embryo implantation failure.},
journal = {Reproduction, fertility, and development},
volume = {38},
number = {15},
pages = {},
doi = {10.1071/RD26001},
pmid = {42805688},
issn = {1448-5990},
mesh = {Female ; Humans ; *Embryo Implantation/physiology ; *Bacterial Infections/complications/microbiology/physiopathology ; *Endometritis/microbiology/physiopathology ; *Endometrium/microbiology ; Pregnancy ; Animals ; Microbiota ; *Infertility, Female/microbiology ; },
abstract = {Embryo implantation is a critical and complex process that requires coordination between the embryo and the receptive endometrium for its success. However, a multitude of factors have the potential to contribute to implantation failure. Among these factors, bacterial infections in the uterine environment are of particular concern and are increasingly being considered as a contributing factor to implantation failure. The presence of pathogenic bacteria has been demonstrated to stimulate inflammatory responses, alter the endometrial microbiome, interfere with critical signaling pathways, and finally change the uterus microenvironments that are required for implantation. We aimed to review bacterial infection as an important potential etiology of chronic endometritis pathophysiology and its correlation with implantation failure.},
}

Female
Humans
*Embryo Implantation/physiology
*Bacterial Infections/complications/microbiology/physiopathology
*Endometritis/microbiology/physiopathology
*Endometrium/microbiology
Pregnancy
Animals
Microbiota
*Infertility, Female/microbiology

@article {pmid42805756,
year = {2026},
author = {Mueller, RS and Banovic, F and Bensignor, E and Santoro, D and Nuttall, T},
title = {Treatment of Canine Atopic Dermatitis: Updated Guidelines From the International Committee on Allergic Diseases of Animals (ICADA).},
journal = {Veterinary dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/vde.70128},
pmid = {42805756},
issn = {1365-3164},
abstract = {BACKGROUND: Canine atopic dermatitis (cAD) is a genetically, aetiologically, immunologically and clinically complex disease requiring both individualised immediate and long-term management.

OBJECTIVES: These updated guidelines from the International Committee on Allergic Diseases of Animals (ICADA) aim to substantially revise previous recommendations by organising treatment according to mechanism-of-action and by distinguishing two therapeutic phases: reactive therapy to resolve existing pruritus and skin lesions, followed by proactive therapy to maintain remission and reduce flares.

MATERIALS AND METHODS: The literature was reviewed and recommendations are based, where possible, on randomised controlled trials and systematic reviews, with evidence graded using the Strength of Recommendation Taxonomy. The guidelines review skin barrier care, antimicrobial and microbiome-modulating interventions, avoidance of nonallergenic and allergenic flare factors, allergen-specific immunotherapy, and anti-inflammatory, antipruritic and immunomodulatory treatments.

RESULTS: Rapid-acting broad-spectrum drugs, particularly glucocorticoids, are recommended for reactive treatment. Janus Kinase (JAK) inhibitors and lokivetmab may be effective depending on lesion type, severity and inflammatory complexity. Secondary infections and flare factors must be addressed. Proactive management essential to prevent repeated cycles of inflammation may include skin barrier support, infection control, allergen avoidance, allergen immunotherapy, topical glucocorticoids, ciclosporin, tacrolimus, lokivetmab or JAK inhibitors, selected according to the patient's disease pattern and response.

A number of interventions are suitable for the treatment of cAD. Interventions are neither universally required, interchangeable nor effective in all cases. Treatment selection should take into account efficacy, safety, practicality, cost, the quality-of-life of both dog and owner, and the legal regulations applicable in the country of use.},
}

@article {pmid42805786,
year = {2026},
author = {Furuya, H and Longnecker, D and Almazan, E and Hinojosa, O and Rochester, T and Carnaby, G},
title = {Oral Environment and Aspiration Pneumonia Risk in Parkinson's Disease: A Narrative Review and Conceptual Framework.},
journal = {Journal of oral rehabilitation},
volume = {},
number = {},
pages = {},
doi = {10.1111/joor.70326},
pmid = {42805786},
issn = {1365-2842},
abstract = {BACKGROUND: Aspiration pneumonia is a major clinical concern in Parkinson's disease (PD) and is associated with poor prognosis. Dysphagia is a well-recognized risk factor for aspiration pneumonia, but the oral environment may also contribute to this risk.

OBJECTIVE: This narrative review aims to synthesize knowledge on the relationship between the oral environment and dysphagia in PD and to propose a conceptual framework that incorporates oral environment management into dysphagia management.

METHODS: We searched PubMed, Scopus and Google Scholar for publications from January 2000 to December 2025. We synthesized findings on the oral environment in PD across three domains (clinical oral findings, saliva-related symptoms and the oral microbiome), with attention to disease stage where reported and examined their relationships with dysphagia.

RESULTS: The oral environment in PD was reported to be associated with disease-related motor and non-motor features and was reported to worsen with disease progression. Deterioration of the oral environment was also associated with dysphagia. Based on these findings, we proposed a stage-based conceptual framework for assessment and management of both the oral environment and swallowing function.

CONCLUSION: Assessment of both the oral environment and swallowing function across all disease stages should be considered as part of aspiration pneumonia risk management in PD. The oral environment remains a modifiable factor even in advanced stages of PD.},
}

@article {pmid42805862,
year = {2026},
author = {Alcantar, O and Dono, A and Bueno, A and Esquenazi, Y},
title = {Microbial Signals in Gliomas: Mechanisms, Clinical Implications, and Future Perspectives.},
journal = {Hematology/oncology clinics of North America},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.hoc.2026.08.002},
pmid = {42805862},
issn = {1558-1977},
abstract = {Emerging evidence suggests that the gut microbiome contributes to glioma biology through immune regulation, microbial metabolites, and modulation of the tumor microenvironment. This review summarizes current evidence linking the microbiome-gut-brain axis to glioma development, progression, and treatment response, highlighting findings from human studies, preclinical models, and recent mechanistic investigations. The review also discusses the influence of the microbiome on anticancer therapy, current limitations of the field, and future directions for microbiome-based biomarkers and therapeutic strategies. Although clinical translation remains limited, microbial signals represent a promising area of investigation in neuro-oncology.},
}

@article {pmid42805970,
year = {2026},
author = {Wu, Y and Su, Z and Zhang, B and Zhou, F and Xi, R and Peng, X and Li, Y and Yue, L and Wang, X and Chen, F and Lu, Y and Zhou, X and Ren, B and Li, J},
title = {Spatially resolved single cell atlas deciphers SAA1 inflammatory epithelial cells.},
journal = {International journal of oral science},
volume = {18},
number = {1},
pages = {},
pmid = {42805970},
issn = {2049-3169},
support = {81991501//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82170949//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32470205//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024NSFSC1584//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; 2025ZNSFSC1910//Department of Science and Technology of Sichuan Province (Sichuan Provincial Department of Science and Technology)/ ; },
mesh = {Humans ; *Epithelial Cells/metabolism ; *Serum Amyloid A Protein/metabolism ; Porphyromonas gingivalis ; *Inflammation/metabolism ; Transcription Factors/metabolism ; Cell Differentiation ; Periodontitis ; Single-Cell Analysis ; Gingiva/metabolism ; },
abstract = {Disruption of epithelial integrity is a pivotal event in inflammation, disease pathogenesis, and tissue homeostasis. To investigate these processes in chronic inflammatory disease, we performed spatial transcriptomics integrated with single-cell RNA sequencing (scRNA-seq) on human gingival tissue, coupled with metagenomic analysis of matched subgingival plaque. This approach allowed in situ characterization of epithelial heterogeneity and microbiome-epithelium-connective tissue crosstalk. We identified a distinct inflammatory epithelial subpopulation (SAA1+Epi), situated within the junctional epithelium, that becomes activated through the TLR2-PITX2 axis by Porphyromonas gingivalis lipopolysaccharide. These SAA1+Epi cells secrete TGFβ, which induces an inflammatory program in the connective tissue by driving the differentiation of inflammation-associated fibroblasts (C3+FB) via the PI3K/Akt pathway. Concurrently, SAA1+Epi cells express chemotactic factors such as CXCL6 to recruit NK cells, thereby sustaining the inflammatory niche. The transcription factor PITX2 emerged as a critical regulator of SAA1+Epi differentiation; targeting PITX2 suppressed C3+FB induction and natural killer (NK) cells recruitment, ultimately attenuating periodontitis progression. Our findings position SAA1+Epi as a frontline responder to dysbiotic bacteria at the inflammatory interface and underscore its essential role in regulating epithelial-connective tissue homeostasis during inflammation.},
}

Humans
*Epithelial Cells/metabolism
*Serum Amyloid A Protein/metabolism
Porphyromonas gingivalis
*Inflammation/metabolism
Transcription Factors/metabolism
Cell Differentiation
Periodontitis
Single-Cell Analysis
Gingiva/metabolism

@article {pmid42806067,
year = {2026},
author = {Tarracchini, C and Milani, C and Jones, CNL and Turroni, F and Burgess, G and Mahony, J and Hall, LJ and Ventura, M and van Sinderen, D},
title = {Bifidobacteria: biogeography, host adaptation and ecological functions.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42806067},
issn = {1740-1534},
abstract = {Bifidobacteria are widely recognized important symbionts of the human gut microbiome, shaping host physiology from birth to adulthood to old age. Their evolutionary success is derived from metabolic versatility, ecological adaptation and intimate host interactions. Equipped with an expansive glycan-degrading repertoire, stress-response systems and specialized cell surface structures, bifidobacteria establish stable gut colonization and influence host immune, metabolic and neuroendocrine functions. Genomics and functional studies have revealed how human-associated members of this genus shape trophic networks, tolerance and resilience within the gut ecosystem. Integration of ecological, metabolic and immunological perspectives now positions the genus Bifidobacterium as an excellent model to support human gut health and its potential use as gut microbiota-based therapeutics.},
}

@article {pmid42806137,
year = {2026},
author = {Birns, B and Murshed, S and Ni Lochlainn, M},
title = {Gut microbiome modulation can improve cognitive function in older adults: a systematic review and meta-analysis.},
journal = {Age and ageing},
volume = {55},
number = {9},
pages = {},
pmid = {42806137},
issn = {1468-2834},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; *Gastrointestinal Microbiome ; *Cognition ; Aged ; *Synbiotics/administration & dosage ; Cognitive Enhancement ; *Cognitive Aging/psychology ; *Prebiotics/administration & dosage ; Age Factors ; Treatment Outcome ; Middle Aged ; Female ; Male ; Aged, 80 and over ; },
abstract = {BACKGROUND: Age-related cognitive decline and dementia exert increasing pressure on healthcare systems. Gut microbiome modulation may offer a novel approach to improving cognitive health.

OBJECTIVE: To establish the effect of gut microbiome modulation on cognitive function in older adults.

METHODS: A systematic search was conducted of PubMed, Cochrane Library, Medline and Embase (OVID) to identify randomised controlled trials (RCTs) and observational studies assessing cognitive outcomes in adults aged ≥60. Interventions aimed at modifying the gut microbiome (prebiotics, probiotics, synbiotics) were included. Studies involving faecal transplants or comparing modifiers to one another instead of to placebo were excluded. Changes in cognitive function were measured by neuropsychological assessments and standardised cognitive tests (e.g. MMSE, MoCA).

RESULTS: Fourteen studies met inclusion criteria (13 RCTs, 1 interventional study), consisting of 10 probiotic, 2 prebiotic and 2 synbiotic trials. Participants included both healthy older adults and those with cognitive impairment. Nine studies reported statistically significant improvements in at least one cognitive domain, particularly global cognition, memory, attention and executive function. Meta-analysis of a sub-group resulted in a statistically significant (MD = 1.28; 95% CI = 0.15-2.40; P < 0.05) improvement in global cognition scores after supplementation.

CONCLUSIONS: Gut microbiome modulation through probiotic, prebiotic and synbiotic supplementation can improve cognition in older adults. Whilst heterogeneity and paucity of high-quality literature exists, the overall evidence is positive. Gut microbiome modulation therefore holds huge promise as a viable strategy to support cognitive health in older people, particularly considering the interventions are mostly already commercially available and low-risk.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
*Gastrointestinal Microbiome
*Cognition
Aged
*Synbiotics/administration & dosage
Cognitive Enhancement
*Cognitive Aging/psychology
*Prebiotics/administration & dosage
Age Factors
Treatment Outcome
Middle Aged
Female
Male
Aged, 80 and over

@article {pmid42806489,
year = {2026},
author = {Song, K and Qin, Y and Luo, J and Liu, L and Luo, C and Qiu, Y and Zhong, Y and Zhong, H and Wu, K and Ni, M and Wu, D and Dai, M and Zhu, S and Chen, H},
title = {Gut Microbial Topology and Metabolic Signatures Associated With Colorectal Neoplasia.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e77991},
doi = {10.1002/advs.77991},
pmid = {42806489},
issn = {2198-3844},
support = {2024YFA0918500//National Key Research and Development Project of China/ ; 2022-I2M-1-003//CAMS Innovation Fund for Medical Sciences/ ; 2025ZD0551704//National Science and Technology Major Program of China/ ; BRWEP2024W034010101//Beijing Research Ward Excellence Program/ ; 82273726//National Natural Science Foundation of China/ ; 82473705//National Natural Science Foundation of China/ ; XZ202501JD0021//Science and Technology Projects of Xizang Autonomous Region, China/ ; UGG06641//PUMCH Talent Development Program (Category B Project)/ ; 2025-LYZX-C-B03//National High Level Hospital Clinical Research/ ; 2025-PUMCH-C-048//National High Level Hospital Clinical Research/ ; },
abstract = {Alterations of gut microbial communities impact health. However, the structure and function of community-level topologies related to colorectal neoplasia (CRN) remain unclear. We analyzed 3807 newly sequenced stool metagenomes from participants (2725 healthy controls, 759 non-advanced adenomas, 297 advanced adenomas, and 26 colorectal cancers) in a multicenter TARGET-C screening trial and validated our findings in multiple independent cohorts. We identified a CRN-associated network (14 species, including Clostridium symbiosum) and a negatively associated network (37 species, including Roseburia and Lachnospira), forming a "seesaw-like" microbial association pattern characterized by within-group co-occurrence and between-group co-exclusion. The structures were stable across the independent datasets. A composite score derived from the microbial topology stratified CRN risk, and diagnostic models based solely on the presence/absence status of the topological species achieved moderate accuracy across the cohorts (area under the curve ranging from 0.66 to 0.87). Functionally, changes in CRN-related microbial association patterns were associated with microbe-derived metabolites. Our findings provide novel insights into the microbial topology associated with CRN and support its potential application in non-invasive risk stratification. However, the utility of these topological features in colorectal cancer remains exploratory and requires further validation in larger colorectal cancer cohorts.},
}

@article {pmid42806510,
year = {2026},
author = {Singh, S and Sharma, VK and Shrivastav, D and Kushwaha, JM and Mishra, MK and Beg, MMA},
title = {From Rhizosphere to Resistance: Microbe-Plant Interactions in Eco-Smart Biocontrol.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70398},
doi = {10.1002/mbo3.70398},
pmid = {42806510},
issn = {2045-8827},
mesh = {*Rhizosphere ; *Plant Diseases/prevention & control/microbiology ; Pest Control, Biological/methods ; Soil Microbiology ; Plant Roots/microbiology ; *Biological Control Agents ; Microbiota ; Multiomics ; Crops, Agricultural/microbiology ; Fungi ; *Plants/microbiology ; },
abstract = {The increasing limitations of chemical pesticides such as environmental pollution, pathogen resistance, and threats to human and ecosystem health have increased the demand for sustainable, biologically based crop protection methods. Eco-smart biocontrol has emerged as a game-changing paradigm that uses beneficial microorganisms associated with plants to suppress phytopathogens, boost plant immunity, and make agroecosystems more resilient over time. Moving beyond traditional single-strain biocontrol, eco-smart biocontrol integrates multi-omics discovery, artificial intelligence-assisted predictive microbiome design, and dynamic rhizosphere ecology. This review brings together ecological, molecular, and technological dimensions of eco-smart biocontrol, focusing on the rhizosphere as a dynamic hotspot for plant-microbe interactions. We investigate rhizosphere microbiome assembly and demonstrate the preferential recruitment of beneficial bacteria, fungi, actinomycetes, and mycorrhizal symbionts by plant root exudates. Moreover, the review highlights the impact of innovations in multi-omics techniques (metagenomics, transcriptomics, proteomics, and metabolomics), systems biology, and artificial intelligence on microbial biocontrol agent discovery, functional validation, and predictive design. Examples from cereal crops, legumes, and horticulture crops indicate that the application of beneficial microbial inoculants can significantly lower the burden of pests and diseases, enhance crop productivity, and fit perfectly within an integrated pest management system. Lastly, we critically analyze the main challenges preventing large-scale adoption, such as inconsistent field performance, limited microbial survival and competitiveness, and comparative regulatory frameworks across global markets. Ultimately, eco-smart microbial biocontrol combines mechanistic insights with omics-driven discovery, artificial intelligence (AI)- assisted prediction, advanced formulation strategies, and field-level validation, creating a strong, scalable, and environmentally friendly framework for resilient, low-input agricultural systems.},
}

*Rhizosphere
*Plant Diseases/prevention & control/microbiology
Pest Control, Biological/methods
Soil Microbiology
Plant Roots/microbiology
*Biological Control Agents
Microbiota
Multiomics
Crops, Agricultural/microbiology
Fungi
*Plants/microbiology

@article {pmid42806615,
year = {2026},
author = {Zhou, J and Du, C and Zhang, X and Zhao, X and Qi, G},
title = {Integrated microbiome and metabolome analysis insights into microbial roles in poplar wetwood formation and control.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71329},
pmid = {42806615},
issn = {1526-4998},
support = {2021YFD2201202//States's Key Project of Research and Development Plan/ ; },
abstract = {BACKGROUND: The globally distributed poplar wetwood disease causes huge economic losses. This study aims to elucidate the microbial communities and metabolite changes contribute to the formation of wetwood.

RESULTS: Comparative analysis reveals pathogens are enriched in wetwood. With the increase in tree age and disease index, the growth of microorganisms is inhibited and the stability of the microbial community is reduced. The key microorganisms vary with different ages and their metabolic activities affect the course of wetwood. The endophyte lignin-degrading Fusarium solani, cellulose- and hemicellulose-degrading Cladosporium, phenolic and organic acids-degrading Acinetobacter calcoaceticus, and Brenneria populi are involved in the occurrence of wetwood. Flavonoids account for the highest proportion in differential metabolites. In a pot experiment, Alternaria tenuissima, F. solani, Nigrospora and B. populi inoculated with healthy heartwood cause wetwood disease. The injection of exogenous salicylic acid promotes the occurrence of wetwood. Syringic acid, ampicillin and nystatin inhibit wetwood. Positive correlation between core microorganisms Brenneria and Desulfitobacterium with differential metabolites caffeic acid, cinnamic acid and salicylic acid indicated important role of Brenneria and Desulfitobacterium in the occurrence of wetwood disease.

CONCLUSION: The formation of poplar wetwood in Jianghan Plain involves the action of various microorganisms. © 2026 Society of Chemical Industry.},
}

@article {pmid42806690,
year = {2026},
author = {Firoozi, M and Mahdavinezhad, A and Shirzad, M and Motevaseli, E and Dalirfardouei, R and Modarressi, MH and Najafi, R},
title = {Biotechnological Approaches to Probiotics and Postbiotics through the Gut-Brain Axis Modulation.},
journal = {Iranian biomedical journal},
volume = {30},
number = {4},
pages = {193-211},
doi = {10.22034/IBJ.30.4.193},
pmid = {42806690},
issn = {2008-823X},
abstract = {The gut microbiome and gut-brain axis are central to systemic homeostasis, with dysbiosis implicated in neurodegenerative (Alzheimer's and Parkinson's) disorders and gastrointestinal conditions (inflammatory bowel disease, irritable bowel syndrome, and fibromyalgia). These conditions are marked by a reduction in beneficial taxa (e.g., Faecalibacterium prausnitzii and Bifidobacterium) and an increase in harmful ones (e.g., Escherichia coli and Clostridium scindens). Probiotic, prebiotic, postbiotic, and symbiotic interventions show therapeutic promise, but results can vary. Biotechnological advances, including CRISPR-Cas9 and genetic kill-switch systems, enable precision-engineered probiotics and postbiotics, though concerns about safety, genetic stability, gene transfer, and immune compatibility persist. Encapsulation and nanoencapsulation strategies improve microbial viability and site-specific delivery; i.e., microencapsulating Lactobacillus acidophilus and Bifidobacterium animalis in alginate-pectin matrices enhances survival during freeze-drying, storage, and gastrointestinal transit. Advancing clinical translation requires integrating multi-omics and machine learning with bioengineering approaches. This review examines the microbial-neural interface and surveys emerging biotechnological strategies for improving microbial-based therapeutics.},
}

@article {pmid42806964,
year = {2026},
author = {Li, R and Du, F and He, J and Luo, Z and Yang, R and Liu, J and Wang, Y and Zhou, C and Huang, M and He, L},
title = {Evolution, disciplinary integration, and frontiers of multi-omics and single-cell technologies in periodontology: a bibliometric analysis (2000-2025) with an early-2026 frontier update.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1875551},
pmid = {42806964},
issn = {2235-2988},
mesh = {*Multiomics ; *Bibliometrics ; *Single-Cell Analysis/methods ; Humans ; *Periodontics/trends/methods ; Systems Biology ; },
abstract = {The field of periodontology is undergoing a paradigm shift from traditional microbiology to systems biology, driven by advancements in multi-omics and single-cell technologies. Despite the rapid surge in publications, a Web of Science Core Collection (WoSCC)-based bibliometric and scientometric analysis mapping the evolutionary trajectory and emerging frontiers of these technologies in periodontal research remains needed. We performed a bibliometric and scientometric analysis of literature published from 2000 to 2025, with records from early 2026 used only as an exploratory frontier update, using the Web of Science Core Collection (WoSCC). Data visualization and network analysis were conducted using VOSviewer, CiteSpace, and the R-bibliometrix package. Additionally, Latent Dirichlet Allocation (LDA) topic modeling was employed to extract underlying research themes from unstructured text data. A total of 559 eligible publications were identified, showing a marked growth trend. China and the United States emerged as the dominant contributors. The evolutionary trajectory was delineated into three distinct phases: foundational exploration, multi-omics integration, and the single-cell resolution era. LDA modeling identified nine core topics, focusing on local host-microbiome interactions, systemic interconnections, and periodontal regeneration-related research. Keyword bursts highlighted "single-cell RNA sequencing (scRNA-seq)," "microenvironment," and "macrophage polarization" as active current frontiers. The field appears to be transitioning within the WoSCC-indexed literature from descriptive microbiome studies toward functional multi-omics and single-cell-resolution analysis, providing an exploratory knowledge-map-based reference for future precision diagnostics and regenerative research in periodontology.},
}

*Multiomics
*Bibliometrics
*Single-Cell Analysis/methods
Humans
*Periodontics/trends/methods
Systems Biology

@article {pmid42807077,
year = {2026},
author = {Wojciechowska, D and Salamon, S and Banachewicz, P and Przemieniecki, S and Kosewska, O and Błaszczyk, L and Szczapa, T and Wróblewska-Seniuk, K},
title = {Fungal DNA profiles across maternal and neonatal biological sites: findings from an exploratory pilot study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1869806},
pmid = {42807077},
issn = {1664-302X},
abstract = {BACKGROUND: The neonatal mycobiome remains an underexplored component of early-life microbial ecology. Although fungi may contribute to immune maturation and host-microbe interactions, fungal DNA profiles across maternal and neonatal body sites are poorly characterized. This exploratory pilot study aimed to characterize fungal DNA profiles across multiple maternal and neonatal biological compartments during early life.

MATERIALS AND METHODS: Ten mother-infant dyads were enrolled at ≥37 weeks' gestation. Three focal dyads (one complete and two near complete) were selected for detailed mycobiome sequencing, while additional breast milk samples expanded the dataset to 30 analyzed specimens. Maternal (vaginal, rectal, breast milk) and neonatal (skin, oral cavity, stool) samples were collected at 48-72 h after delivery and 6 weeks postpartum. Fungal DNA was analyzed using Oxford Nanopore long-read 18S rRNA sequencing. Taxonomic classification was performed with Kraken2 using the NCBI RefSeq Targeted Loci fungal 18S rRNA database. Alpha- and beta-diversity analyses were conducted in R using the phyloseq package.

RESULTS: A total of 428,555 fungal reads representing 107 genus-level operational taxonomic features were retained. Fungal DNA profiles differed across biological sites, with a greater relative abundance of Malassezia in neonatal skin and more heterogeneous profiles in gastrointestinal-associated samples. Alpha diversity did not differ significantly between sampling sites, whereas beta diversity suggested exploratory site-associated differences in community composition. Richness-based metrics were higher at 6 weeks than during early sampling, although this trend was not robust after accounting for sequencing depth, and beta-diversity analyses showed no clear temporal shift. Because negative controls were not sequenced, contamination from laboratory or reagent-derived fungal DNA cannot be excluded, and the findings should not be interpreted as evidence of viable fungi or stable colonization.

CONCLUSION: This exploratory pilot study suggests that fungal DNA profiles differ across maternal and neonatal body sites and that detectable fungal richness may increase by 6 weeks postpartum, although this finding was not robust to sequencing depth. Larger longitudinal studies incorporating ITS-based sequencing, strain-level analyses, sequenced technical controls, and functional profiling are needed to validate these observations and clarify the biological significance of early-life fungal communities.},
}

@article {pmid42807334,
year = {2026},
author = {Handa, VL and Vyas, BB and Padhi, A and Agarwal, A and Vyas, BRM},
title = {Nanomedicine against antimicrobial resistance: mechanistic insights and next-generation therapeutic potential.},
journal = {Frontiers in chemistry},
volume = {14},
number = {},
pages = {1915145},
pmid = {42807334},
issn = {2296-2646},
abstract = {Antimicrobial resistance (AMR) has emerged as one of the most critical global health threats, severely limiting the effectiveness of existing therapies against bacterial, fungal, and viral infections. The increasing prevalence of multidrug-resistant pathogens is largely driven by rapid genetic evolution, which promotes multiple resistance mechanisms such as drug degradation, target-site alteration, reduced intracellular drug accumulation, and biofilm formation, leading to persistent infections and rising mortality. These challenges highlight the urgent need for alternative therapeutic strategies beyond conventional antimicrobials. Nanomedicine has gained considerable attention due to its unique physicochemical properties, enabling improved drug stability, targeted delivery, controlled release, enhanced pathogen penetration, and multimodal antimicrobial action. This review comprehensively examines resistance mechanisms across major microbial pathogens and discusses the evolution of nanomedicine as an advanced platform for combating AMR. Particular emphasis is placed on green biogenic synthesis of nanoparticles using biological resources, offering environmentally sustainable and biocompatible antimicrobial nanomaterials. The synergistic interactions between nanomaterials and conventional antimicrobial agents that enhance therapeutic efficacy and restore susceptibility in resistant pathogens. Emerging next-generation antimicrobial nanomedicine platforms, including biomimetic nanoparticles, antimicrobial peptide delivery systems, CRISPR-enabled nanocarriers, and stimuli-responsive systems, are also highlighted for their potential in precision infection management. Finally, key challenges involving toxicity, biosafety, microbiome disruption, environmental impact, manufacturing scalability, regulatory and clinical translation. Addressing these barriers will be essential for advancing safe and effective nanomedicine-based solutions against AMR.},
}

@article {pmid42807430,
year = {2026},
author = {Kriti, M and Ojha, R and Singh, S and Sarma, DK and Verma, V and Kumawat, M and Tilwari, A and Tiwari, R and Kumar, M},
title = {Ecological associations between ambient air pollution, gut microbiome composition, and metabolic markers in urban populations of central India.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1834285},
pmid = {42807430},
issn = {2296-2565},
mesh = {India/epidemiology ; Humans ; *Air Pollution/adverse effects/analysis ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Biomarkers ; *Diabetes Mellitus, Type 2/epidemiology ; Male ; *Air Pollutants/analysis/adverse effects ; *Urban Population/statistics & numerical data ; Female ; Particulate Matter/analysis ; Middle Aged ; Environmental Monitoring ; *Environmental Exposure ; Adult ; },
abstract = {OBJECTIVE: To investigate the ecological level associations and spatial co-variation among ambient air pollutants, Type 2 diabetes (T2D) related clinical markers, and gut microbiome composition in urban populations of Bhopal, India.

METHODS: A cross-sectional ecological study was conducted involving 95 participants from three urban locations in Bhopal. Ambient air quality data, including PM2.5, PM10, NOx, and SO2, were obtained from local monitoring stations. Exposure assessment was based on location level ambient monitoring data corresponding to participants' residential localities rather than individual level personal exposure measurements. Clinical assessments were performed to measure T2D related metabolic parameters, and fecal samples were analyzed using full-length 16S rRNA sequencing to profile gut microbiome composition. Associations between pollutant levels, metabolic markers, and microbial taxa were evaluated using exploratory correlation and compositional analyses.

RESULTS: Variability was observed in both air pollutant concentrations and metabolic parameters. NOx levels were positively correlated with glycemic indices, while particulate pollutants (PM2.5 and PM10) showed inconsistent and non-directional associations with metabolic markers. Gut microbiome analyses revealed broadly similar microbial community structures with subtle differences in diversity and composition across locations. Although variations were observed in selected microbial taxa, most genus-level differences did not remain statistically significant following multiple testing correction.

CONCLUSION: Air pollution and gut microbiome composition appear to have a descriptive role in metabolic health. The findings describe ecological level co-variation between ambient air pollution indicators, metabolic parameters, and gut microbiome composition across the study populations. Because the study design was cross-sectional and exposure assessment relied on location level monitoring data, the results should be interpreted as descriptive and hypothesis-generating rather than causal. Further longitudinal studies incorporating individual level exposure assessment and functional microbiome analyses are required to better evaluate these relationships.},
}

India/epidemiology
Humans
*Air Pollution/adverse effects/analysis
Cross-Sectional Studies
*Gastrointestinal Microbiome
Biomarkers
*Diabetes Mellitus, Type 2/epidemiology
Male
*Air Pollutants/analysis/adverse effects
*Urban Population/statistics & numerical data
Female
Particulate Matter/analysis
Middle Aged
Environmental Monitoring
*Environmental Exposure
Adult

@article {pmid42807444,
year = {2026},
author = {Nderitu, MW and Khamis, FM and Ajene, IJ and Nyanjom, SG and Akutse, KS},
title = {Immunological responses and gut microbial shift of fall armyworm Spodoptera frugiperda challenged with entomopathogens.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1929843},
pmid = {42807444},
issn = {1664-302X},
abstract = {Fall armyworm (FAW), Spodoptera frugiperda is a dangerous lepidopteran pest that threatens maize production globally. Biopesticides such as entomopathogenic fungi (EPF) and Bacillus thuringiensis present safer alternatives to chemical pesticides for FAW management. This study investigated the impact of Metarhizium anisopliae and B. thuringiensis on the mortality, cellular immune response, and microbiome of FAW under different temperature regimes (15 °C, 20 °C, 25 °C, 30 °C, and 35 °C). M. anisopliae isolates ICIPE 7 and ICIPE 78 caused higher FAW larval mortality than B. thuringiensis isolates Bt43 and HD263 across all temperatures. M. anisopliae infection caused a more notable reduction in total hemocyte count (THC) in FAW, in contrast with B. thuringiensis infection, compared to control FAW groups. Plasmatocytes and granulocytes dominated the differential hemocyte counts in both challenged and control FAW larvae. Microbiome analysis of entomopathogen-infected FAW showed marginal changes in the microbiome diversity, with larvae challenged with ICIPE 7 and Bt43 having higher bacterial species richness than control samples assessed on days 0 and 10 post-exposure. Hence, we detected that infection with entomopathogens compromises the immune system of FAW and that M. anisopliae isolates ICIPE 7 and ICIPE 78 would be better candidates than B. thuringiensis isolates Bt43 and HD263 for integration into an IPM program against FAW.},
}

@article {pmid42807510,
year = {2026},
author = {Wu, Q and Meng, Y and Liu, H and Kong, Y and Chen, Y and Bu, M and Ma, Z},
title = {Moraxella salivae sp. nov., isolated from the saliva of a healthy human volunteer.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2737704},
pmid = {42807510},
issn = {2000-2297},
abstract = {BACKGROUND: Strain I5G[T] was isolated from the saliva of a healthy volunteer and polyphasic taxonomic approaches were applied for its systematic identification to clarify its taxonomic position within the genus Moraxella.

METHODS: A polyphasic taxonomic study was performed, including morphological observation, physiological and biochemical characterisation, chemotaxonomic analyses (fatty acid profile, respiratory quinone, polar lipids), 16S rRNA gene phylogeny, and whole-genome-based phylogenetic and comparative genomic analyses.

RESULTS: Strain I5G[T] is a Gram-stain-negative, aerobic, rod-shaped bacterium. Growth occurs at 25-37 °C (optimum 37 °C), pH 7.0-9.0 (optimum pH 8.0), and 0-1.0% (w/v) NaCl (optimum 0.5%). 16S rRNA gene analysis placed it in the genus Moraxella, with highest similarity (96.17%) to Moraxella oblonga IAM 14971ᵀ. Whole-genome phylogeny supported a distinct novel lineage. The maximum average nucleotide identity (ANI) (85.9%) and the highest digital DNA-DNA hybridisation (dDDH) (24.8%) values were well below species thresholds. DNA G + C content was 37.5 mol%. Major fatty acids were C₁₈:₁ ω9c, C₁₆:₀, C₁₈:₀ and Summed Feature 3 (C₁₆:₁ ω7c and/or C₁₆:₁ ω6c), major quinone was CoQ-8, major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine.

CONCLUSION: Strain I5G[T] represents a novel species within the genus Moraxella, for which the name Moraxella salivae sp. nov. is proposed. The type strain is I5G[T] (= KCTC 18404ᵀ = GDMCC 1.5953ᵀ).},
}

@article {pmid42807573,
year = {2026},
author = {Li, J and Li, M and Aboushanab, S and Ebeid, M and Hatanaka, R and Iida, M and Takase, M and Jacobs, I and Gusmanov, A and Hirata, A and Miyagawa, N and Nakaya, N and Sugiyama, D and Tilves, C and Hozawa, A and Li, X and Mueller, NT and Benos, PV and Sekikawa, A},
title = {Converting Equol Nonproducers to Producers: A Systematic Review of Randomized Clinical Trials.},
journal = {Food science & nutrition},
volume = {14},
number = {10},
pages = {e72394},
pmid = {42807573},
issn = {2048-7177},
abstract = {Soy isoflavones have been associated with benefits for menopausal symptoms, cardiovascular health, and cognitive function, yet randomized clinical trials (RCTs) in Western countries have produced inconsistent results. A key factor may be equol, a metabolite of daidzein with stronger estrogenic and antioxidant effects, produced at lower rates in Western than in East Asian populations. This systematic review evaluates RCTs aimed at converting equol nonproducers to producers (CRD420251038428). We searched PubMed, Embase, and Web of Science for RCTs published between 1991 and 2025. Twelve RCTs (n = 730, 85.5% female) met inclusion criteria. Interventions included soy isoflavones alone, soy with probiotics, fermented soy products, seaweed, and wheat bran. Studies were conducted in Japan (n = 1), Brazil (n = 1), and Western countries (n = 10), with durations ranging from a single dose to 2.5 years. Study quality was assessed using the National Heart, Lung, and Blood Institute evaluation tool. None of the interventions significantly converted equol nonproducers into producers, with methodological limitations including small sample sizes, inconsistent equol measurement, and heterogeneous populations compromising reliability. Achieving equol producer status could unlock the full nutritional potential of soy isoflavones for menopausal, cardiovascular, and cognitive health. Future studies should prioritize standardized equol measurement, microbiome-targeted interventions, and well-powered, diverse populations to develop effective dietary strategies for Western populations where soy intake and equol production remain low.},
}

@article {pmid42807681,
year = {2026},
author = {Li, Y and Wang, F and Li, T and Liu, Y},
title = {Gut microbiota-mediated chemotherapy resistance in colorectal cancer: mechanisms and precision interventions.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1966862},
pmid = {42807681},
issn = {2234-943X},
abstract = {Colorectal cancer (CRC) is a major global health burden, and chemotherapy resistance remains a major challenge to effective treatment. Increasing evidence indicates that the gut microbiota may contribute to variability in chemotherapy response in CRC through microbial metabolism, tumor-cell adaptation, immune regulation, and microbiota-derived metabolites. These processes can alter drug exposure, cellular stress responses, antitumor immunity, and metabolic conditions within the tumor-host ecosystem. In this review, we summarize current evidence on the mechanisms linking the gut microbiota to chemotherapy response in CRC, focusing on microbial drug metabolism, tumor-cell adaptation, immune and metabolic regulation, and microbial interactions with host signaling pathways. We also discuss emerging microbiome-based interventions, including probiotics, fecal microbiota transplantation, phage therapy, and targeted modulation of microbial functions, while considering the limitations of current evidence and challenges to clinical translation. Finally, we highlight future priorities, including causal validation of microbial functions, identification of robust biomarkers, and prospective evaluation of microbiome-informed patient stratification. This review provides an overview of current mechanistic evidence and the potential of microbiome-based approaches to improve chemotherapy response in CRC.},
}

@article {pmid42807691,
year = {2026},
author = {Zhang, H and Zhou, X and Ma, Y and Zong, S and Liu, X and Liu, Z and Wang, X},
title = {Gut microbiota-neuroimmune crosstalk in autoimmune encephalitis: mechanistic insights and therapeutic prospects.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1946719},
pmid = {42807691},
issn = {1664-302X},
abstract = {Autoimmune encephalitis (AE) comprises a heterogeneous group of inflammatory disorders of the central nervous system mediated by autoimmune responses, involving multiple pathological processes, including autoantibody production, aberrant immune-cell activation, and persistent neuroinflammation. In recent years, accumulating evidence has suggested that the gut microbiota may represent an important regulatory interface linking host metabolism, immunity, and the nervous system. Through microbial structural components, metabolites, and secreted signals, the gut microbiota may influence peripheral immune responses, blood-brain barrier integrity, and central nervous system inflammation. Conversely, neuroimmune dysregulation may reshape the intestinal microbial environment through neuroendocrine-immune regulatory networks, thereby establishing a dynamic bidirectional relationship between the gut microbiota and the neuroimmune system. However, the mechanisms underlying gut microbiota-neuroimmune interactions in AE, particularly their potential changes across the disease course, remain incompletely understood. This review summarizes current evidence regarding AE-associated alterations in the gut microbiota and disturbances of neuroimmune homeostasis, with particular emphasis on the potential molecular mechanisms through which the gut microbiota modulates neuroimmune responses and, reciprocally, the neuroimmune system reshapes the intestinal microbial environment. Within a proposed phase-based conceptual framework encompassing disease initiation, progression, and the chronic phase, we further discuss the potential dynamic changes in gut microbiota-neuroimmune crosstalk during AE. In addition, we summarize emerging therapeutic strategies, including dietary and nutritional interventions, probiotics, modulation of microbial metabolic functions, fecal microbiota transplantation, and precision microbiome engineering, and discuss their current evidence base and translational potential. Collectively, gut microbiota-neuroimmune crosstalk provides a useful conceptual framework for understanding disease heterogeneity in AE and exploring microbiota-targeted interventions. However, direct AE-specific evidence remains limited, and many proposed mechanisms are currently supported primarily by observational studies, experimental models, or evidence extrapolated from related neuroimmune disorders. Future studies integrating longitudinal clinical cohorts, multi-omics profiling, and functional validation are needed to define key microbial functions, host immune responses, and their dynamic relationships in AE, thereby providing a stronger mechanistic foundation for future precision diagnostic and therapeutic strategies.},
}

@article {pmid42807756,
year = {2026},
author = {Molasy, B and Rachuna, J and Wawszczak-Kasza, M and Dulębska, J and Kuszewska, K and Adamus-Białek, W},
title = {Correction: 16S rRNA sequencing and conventional culture provide complementary information in hospitalized patients with chronic lower-limb wounds.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1974019},
doi = {10.3389/fcimb.2026.1974019},
pmid = {42807756},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2026.1865385.].},
}

@article {pmid42807795,
year = {2026},
author = {Huang, S and Cheng, Y and Chen, Y and Liu, Y and Liu, X and Xu, X and Hu, P and Wu, L and Ling, Z and Xu, L},
title = {Gastric bacterial microbiota and gastric carcinogenesis: from dysbiosis to immune remodeling and therapeutic opportunities.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1953049},
pmid = {42807795},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Stomach Neoplasms/immunology/microbiology/therapy/pathology/etiology ; Animals ; *Gastrointestinal Microbiome/immunology ; *Carcinogenesis/immunology ; Tumor Microenvironment/immunology ; Helicobacter pylori ; Helicobacter Infections/immunology/microbiology ; },
abstract = {Gastric cancer remains a leading cause of cancer-related mortality worldwide. The classical Helicobacter pylori-centric paradigm of gastric carcinogenesis is being progressively expanded, as it is now recognized that the stomach harbors a complex and metabolically active microbial ecosystem whose compositional shifts fundamentally influence oncogenic progression. This review proposes a unifying dysbiosis-carcinogenesis-immune remodeling-therapeutic intervention (DCIT) framework to integrate the rapidly growing body of evidence linking gastric microbiota dysbiosis to malignancy. We survey the compositional landscape of the gastric microbiota across the Correa cascade, from healthy homeostasis through atrophic gastritis, intestinal metaplasia, and adenocarcinoma, and examine the ecological succession that releases niche constraints for oral commensals and nitrate-reducing taxa in advanced disease stages. We systematically evaluate four complementary mechanistic axes of microbial carcinogenesis: genotoxicity driven by bacterial effectors, chronic inflammation sustained by pattern recognition receptor signaling, epithelial barrier disruption facilitating bacterial translocation, and metabolic reprogramming of the gastric niche generating carcinogenic N-nitroso compounds and secondary bile acids. The review further examines how gastric microbiota remodels the tumor immune microenvironment through immune cell reprogramming, metabolite-mediated signaling, and checkpoint modulation, with direct implications for the efficacy of immune checkpoint inhibitor immunotherapy. The translational pipeline is evaluated from established H. pylori eradication regimens through probiotics, phage therapy, and fecal microbiota transplantation to emerging strategies that integrate microbiota modulation with chemotherapy and immunotherapy. Finally, we assess the methodological challenges of low-biomass gastric microbiome research, the integration of multi-omics platforms, and the critical evidence gaps that need to be addressed to realize the clinical potential of microbiota-targeted strategies for gastric cancer prevention and treatment.},
}

Humans
*Dysbiosis/immunology/microbiology
*Stomach Neoplasms/immunology/microbiology/therapy/pathology/etiology
Animals
*Gastrointestinal Microbiome/immunology
*Carcinogenesis/immunology
Tumor Microenvironment/immunology
Helicobacter pylori
Helicobacter Infections/immunology/microbiology

@article {pmid42807896,
year = {2026},
author = {Cornejo Ulloa, PE and van der Ploeg, GR and Heintz-Buschart, A and Westerhuis, JA and Smilde, AK and Zaura, E and Brandt, BW and Buijs, MJ and Bostanci, N and Silbereisen, A and Bikker, FJ and Nazmi, K and Tebbens, M and den Heijer, M and Krom, BP and van der Veen, MH},
title = {Shifting hormones, shaping health: Gender-affirming therapy & oral care.},
journal = {International journal of transgender health},
volume = {27},
number = {5},
pages = {2544-2560},
pmid = {42807896},
issn = {2689-5277},
abstract = {BACKGROUND: Gender-affirming hormone therapy (GAHT) is a critical aspect of transgender healthcare. Little is known about the effects of GAHT on oral health, which may be influenced by immune modulation, salivary composition shifts, and microbial dynamics as a result of hormone use.

AIM: To clinically, biochemically and microbiologically assess changes in oral health of transgender persons during the first year of GAHT.

METHODS: Twenty-one transmasculine and eighteen transfeminine persons took part in the study. Participants were followed for 12 months. Every 3 months, participants underwent an oral checkup, including full oral assessment and light and fluorescent photos of gums and tongue, donated saliva and filled in a questionnaire over oral health self-perception and dry mouth. Salivary samples were later analyzed for certain proteins and for microbial composition using 16S rRNA gene amplicon sequencing. N-way Partial Least Squares (NPLS) models were used to perform a supervised analysis of the variation in the data associated with GAHT.

RESULTS: GAHT induces transient disruptions in salivary composition and microbial communities during the first six months, followed by stabilization by twelve months. Differences in microbial composition were observed between transmasculine and transfeminine persons, suggesting that GAHT exerts distinct effects on oral microbiota depending on hormonal regiments, with potential implications for periodontal health.

DISCUSSION: This clinical longitudinal study investigated for the first time the oral health of transgender individuals undergoing GAHT during the first year of transition. These results underscore the importance of tailored dental care during early stages of GAHT and contribute to a more comprehensive understanding of how systemic hormonal treatments can impact oral physiology. This work supports the development of more inclusive healthcare approaches that address the unique needs of transgender populations.},
}

@article {pmid42807926,
year = {2026},
author = {Sun, J and Jing, S and Fei, Y and Zhu, J},
title = {Non-Surgical Management of Male Chronic Prostatitis/Chronic Pelvic Pain Syndrome: A UPOINT-Guided Narrative Review.},
journal = {Journal of pain research},
volume = {19},
number = {},
pages = {623240},
pmid = {42807926},
issn = {1178-7090},
abstract = {BACKGROUND: Primary prostate pain syndrome (PPPS), formerly referred to as chronic prostatitis/chronic pelvic pain syndrome (CP/CPPS) is a prevalent and heterogeneous chronic pain condition characterized by persistent pelvic pain, lower urinary tract symptoms, sexual dysfunction, and substantial psychosocial burden.

OBJECTIVE: This narrative review summarizes current evidence on the pathophysiology, phenotype-based assessment, and non-surgical management of male CP/CPPS, with emphasis on UPOINT-guided multimodal care.

METHODS: Evidence was synthesized from guidelines, systematic reviews, meta-analyses, randomized trials, observational studies, and relevant mechanistic literature addressing CP/CPPS, chronic pelvic pain, UPOINT phenotyping, pharmacological treatment, physical therapy, neuromodulation, and psychological interventions.

RESULTS: CP/CPPS is best understood as a multidimensional syndrome involving inflammation and immune dysregulation, peripheral and central sensitization, microbiome disturbance, autonomic imbalance, and psychosocial amplification. The UPOINT framework translates this heterogeneity into actionable domains and supports targeted combinations of urinary, organ-specific, infection-directed, neurologic/systemic, tenderness-focused, and psychosocial interventions.

CONCLUSION: Non-surgical management of male CP/CPPS should move toward individualized, phenotype-guided multimodal therapy. In particular, pelvic floor physical therapy (for T phenotype) and neuromodulators/central analgesics (for N phenotype) should be prioritized over empiric monotherapy or prolonged antibiotic use. Future trials should use phenotype-stratified enrollment, standardized outcome measures, and longer follow-up to define optimal combinations and durability of benefit.},
}

@article {pmid42808079,
year = {2026},
author = {Larue, M and Battipaglia, G and Poeck, H and Masetti, R and Stein-Thoeringer, C and Sanz, J and Weber, D and Ruggeri, A and Peric, Z and Duarte, R and Mohty, M and Malard, F},
title = {Healthcare professionals' knowledge and attitudes toward the microbiome and fecal microbiotherapy or microbiota transfer in hematology and oncology: an international survey.},
journal = {Clinical hematology international},
volume = {8},
number = {3},
pages = {41-47},
pmid = {42808079},
issn = {2590-0048},
abstract = {The gut microbiome has emerged as a critical factor influencing cancer progression, treatment response, and complications in hematology and oncology. Fecal microbiota transfer (FMT) is being explored as a novel biotherapeutic strategy, yet the knowledge and attitudes of healthcare professionals towards its clinical use remain poorly defined. We conducted an international survey of 152 healthcare professionals, including hematologists, oncologists, transplant specialists, and others. Most respondents were affiliated with academic centers (66.0%) and practiced primarily in hematology (48.0%) or transplantation (34.0%). Awareness of the microbiome's clinical relevance was widespread, but perceptions of microbiome profiling and FMT remained cautious. One-third of participants were in favor of routine microbiome profiling, while half considered it promising but still investigational. Direct clinical experience with FMT was limited: only 20.4% had prescribed it and 14.5% had referred patients. Nonetheless, over half indicated they would consider adopting FMT in the near future. The main reported barriers to broader use included limited regulatory approval (63.8%), logistical or supply challenges (57.9%), and physician skepticism or lack of knowledge (51.3%). Despite these challenges, more than 70% of respondents expressed strong interest in further education, standardized guidelines, and training opportunities to support safe and effective implementation. This survey highlights a strong enthusiasm regarding microbiome-based interventions in cancer and transplantation care. While current clinical use remains limited, healthcare professionals recognize the therapeutic potential of FMT and call for structured education, multidisciplinary collaboration, and clear regulatory frameworks to enable its integration into routine practice.},
}

@article {pmid42808159,
year = {2026},
author = {Kolodnitsky, AS and Lagunin, AA and Poroikov, VV},
title = {Computational approaches to predicting xenobiotic metabolism by the human gut microbiota.},
journal = {Expert opinion on drug metabolism & toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17425255.2026.2738611},
pmid = {42808159},
issn = {1744-7607},
abstract = {INTRODUCTION: The human gut microbiota significantly influences drug pharmacokinetics and pharmacodynamics, driving interindividual variability in efficacy and toxicity. As experimental characterization of microbiome-mediated metabolism remains resource-intensive, computational prediction has emerged as an auxiliary strategy for comprehensive ADMET profiling.

AREAS COVERED: Based on a structured literature search up to 2026, this review evaluates key computational resources: 10 databases, 6 predictive algorithms, 1 genome-scale metabolic reconstruction platform, and 3 microbiome-metabolome integration models. We analyze their specific strengths, limitations, and integration into drug discovery pipelines and personalized medicine scenarios.

EXPERT OPINION: While current in silico tools robustly predict qualitative metabolic potential and responsible taxa, their application in physiologically based pharmacokinetic modeling is hindered by data limitations. Training datasets exhibit a profound bias toward isolated in vitro screening, alongside a critical lack of quantitative kinetic parameters. Overcoming these bottlenecks requires generating high-quality, physiologically relevant data through collaboration among computational biologists, laboratory researchers, physicians, pharmaceutical companies, and regulatory agencies. This interdisciplinary ecosystem will enable platforms that continuously learn from real-world feedback, bridging the gap between microbiome sequencing, rational drug design, and precision medicine.},
}

@article {pmid42808406,
year = {2026},
author = {Nadeem, S and Maitra, R and Farah, - and Dutta, S and Siddiqui, K and Zulfiqar, R and Asha, MM and Termos, S},
title = {Impact of Diabetes, Hypertension, and Gut Microbial Diversity on Chemotherapy Response and Survival in Cancer Patients: A Prospective Cohort Study.},
journal = {Asian Pacific journal of cancer prevention : APJCP},
volume = {27},
number = {9},
pages = {3377-3383},
doi = {10.31557/APJCP.2026.27.9.3377},
pmid = {42808406},
issn = {2476-762X},
mesh = {Humans ; Female ; *Hypertension/complications/microbiology ; Prospective Studies ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; *Diabetes Mellitus/mortality/microbiology ; Survival Rate ; *Neoplasms/drug therapy/mortality/microbiology/pathology/complications ; Prognosis ; Follow-Up Studies ; Adult ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; },
abstract = {BACKGROUND AND AIMS: Chronic comorbidities, including diabetes mellitus and hypertension, and gut microbial factors may influence chemotherapy response and survival in cancer patients. This study quantitatively evaluated their combined impact. The main objective of this study was to evaluate the impact of diabetes, hypertension, and gut microbial diversity on chemotherapy response and survival in cancer patients.

METHODS: A prospective cohort study enrolled 250 adult cancer patients receiving chemotherapy at a tertiary care center in Bangladesh. Clinical, metabolic, and microbiome data were collected at baseline and during treatment. Chemotherapy response was assessed by RECIST 1.1 criteria, while progression-free survival (PFS) and overall survival (OS) were recorded. Gut microbial diversity was measured using 16S rRNA sequencing. Statistical analyses included chi-square tests, t-tests, Kaplan-Meier survival analysis, and multivariable Cox regression.

RESULTS: Among participants, 32.8% had diabetes and 38.4% had hypertension. Objective response rates (CR+PR) were lower in patients with diabetes (41.5%) and hypertension (45.8%) compared with non-diabetic (57.1%) and normotensive (55.8%) patients (p < 0.05). Responders exhibited significantly lower HbA1c, fasting glucose, and systolic blood pressure than non-responders (p < 0.01). Higher gut microbial alpha diversity was observed in responders (Shannon index 4.1 ± 0.6) versus non-responders (3.4 ± 0.7; p < 0.001). Median PFS and OS were shorter in patients with diabetes (8.6 and 18.4 months) and hypertension (9.1 and 20.2 months) compared with those without comorbidities (12.9 and 26.7 months; 13.4 and 27.9 months, respectively). Multivariable analysis confirmed diabetes (aHR 1.58), hypertension (aHR 1.41), low microbial diversity (aHR 1.76), and advanced tumor stage (aHR 2.34) as independent predictors of worse survival (all p < 0.05).

CONCLUSIONS: Diabetes, hypertension, and reduced gut microbial diversity are associated with poorer chemotherapy response and survival outcomes. Integrated management of metabolic and cardiovascular comorbidities, alongside microbiome-informed interventions, may enhance treatment efficacy and patient survival.},
}

Humans
Female
*Hypertension/complications/microbiology
Prospective Studies
Male
*Gastrointestinal Microbiome
Middle Aged
*Diabetes Mellitus/mortality/microbiology
Survival Rate
*Neoplasms/drug therapy/mortality/microbiology/pathology/complications
Prognosis
Follow-Up Studies
Adult
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use

@article {pmid42808427,
year = {2026},
author = {Shannon, OM and Beck, L and Castro, C and Jennings, A and Gillings, R and Lee, VY and Elsworthy, R and Gulston, M and Langerova, T and Boldurat, C and Nazeer, A and Hardeman, W and Hanson, S and Nelson, A and Siervo, M and Aldred, S and White, B and Gerasimidis, K and Griffin, J and Minihane, A and Stewart, C and Mathers, J},
title = {Impact of a Mediterranean diet and physical activity intervention on the gut microbiome and faecal metabolites: findings from the MedEx-UK randomised controlled trial.},
journal = {The British journal of nutrition},
volume = {},
number = {},
pages = {1-8},
doi = {10.1017/S0007114526108551},
pmid = {42808427},
issn = {1475-2662},
abstract = {Diet and physical activity (PA) are potential modulators of the gut microbiome, although research findings are inconsistent, and few studies have explored their combined effects. This study used data from ninety-three participants (forty-seven with pre- and post-intervention samples) from the MedEx-UK randomised controlled trial to investigate the impact of a 24-week Mediterranean diet (MedDiet) intervention, alone or with a PA intervention, on gut microbiome composition and faecal metabolites. Faecal samples were collected pre- and post-intervention from participants in each of three treatment groups: habitual lifestyle (control), MedDiet or MedDiet plus PA. Gut microbiome profiles were generated using 16S rRNA gene sequencing. Faecal SCFA, NMR-derived metabolites and bile acids were quantified. MedDiet scores were significantly increased in both intervention groups v. control (p < 0·001). PA levels did not differ significantly between groups (p = 0·17). There were no significant intervention effects on change in α diversity (Shannon index, p = 0·185), endpoint microbial community composition (p = 0·487), bacterial relative abundance (all p > 0·05), NMR metabolite profiles (p = 0·280), bile acid profiles (p = 0·677) or SCFA concentrations (all p > 0·05). Level of adherence to the MedDiet and specific MedDiet components also showed no associations with microbiome/metabolome datasets. In conclusion, we did not find any effect of a MedDiet intervention alone, or alongside a PA intervention, on the gut microbiome or faecal metabolites. This may be due to methodological factors including the heterogeneity of individual dietary changes in this personalised intervention, causing large inter-individual differences in microbiome responses relative to the overall mean effect of the interventions.},
}

@article {pmid42808722,
year = {2026},
author = {Westcott, SL and Johnson, G and Schloss, PD},
title = {Strollur: an R package for working with amplicon sequence data in R.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0083926},
doi = {10.1128/mra.00839-26},
pmid = {42808722},
issn = {2576-098X},
abstract = {Microbiologists are increasingly relying on R to analyze and visualize amplicon sequence data from microbiome studies. We present strollur, which is an open-source package that facilitates the import, export, and handling of amplicon sequence data within the R programming language.},
}

@article {pmid42808754,
year = {2026},
author = {Liao, L and Lai, T and Jiang, W and Duan, Z and Sun, P and Zhao, Y and Peng, F and Qin, Q and Ji, M and Zhang, S},
title = {Microfluidic-based high-throughput isolation enhances the recovery of novel strains and diversity from Arctic soil microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0112426},
doi = {10.1128/aem.01124-26},
pmid = {42808754},
issn = {1098-5336},
abstract = {Microbial cultivation remains essential for understanding the physiology, ecology, and biotechnological potential of environmental microbes, yet conventional plate-based methods (CPM) recover only a minute fraction of the environmental microbiome. Polar regions, particularly Arctic soils, represent unique reservoirs of "microbial dark matter" that remain challenging to cultivate, owing to oligotrophic conditions, low temperatures, and freeze-thaw cycles that impose severe physiological constraints on microbial growth. Here, we report the first systematic application of microfluidic droplet technology (MDT) to Arctic active-layer soil microbiota and benchmark its performance against CPM using identical starting cell numbers, R2A medium, and incubation at 15°C. MDT achieved 6.5- to 8.1-fold higher recovery rates than CPM and improved isolation throughput by >180-fold. Near-full-length 16S rRNA gene sequencing (PacBio) revealed that MDT recovered significantly higher taxonomic richness across all taxonomic levels, with 256 genera detected in the high-cell-input group (DropAS_H) versus 211 in the corresponding plate group (PlateAS_H). Notably, MDT yielded a more even community distribution, significantly reducing the dominance of fast-growing copiotrophs, such as Pseudomonas and Flavobacterium. Moreover, approximately 50% of the sequences from MDT were affiliated with potential novel species (<98.65% identity to type strains), and 27% with potential novel genera (<95% identity). Strain verification by Sanger sequencing confirmed 12 of 17 isolates as candidate novel species, among which one strain represented a potential novel genus within Devosiaceae. This study demonstrates that MDT is a powerful platform for accessing the uncultured majority of polar soil microbiota and establishes a pipeline for high-throughput isolation of novel cold-adapted bacteria.IMPORTANCEArctic soils harbor a vast reservoir of microbial diversity that remains largely inaccessible due to the extreme oligotrophic conditions and low temperatures characteristic of polar environments, leading to slow growth and extended lag phases in most microbes. Conventional plate-based methods (CPM) inherently favor fast-growing copiotrophs while suppressing rare or slow-growing lineages. Here, we demonstrate that microfluidic droplet technology (MDT) overcomes these fundamental constraints, representing its first systematic application to polar microbiology. By physically isolating individual cells into microliter-scale bioreactors, MDT provides independent microenvironments that allow slow-growing and oligotrophic taxa to proliferate without being outcompeted by fast-growing copiotrophs in bulk cultures. The water-in-oil emulsion format further enables extended low-temperature incubation without evaporative loss or airborne fungal contamination, issues that frequently compromise long-term plate-based cultivation of Arctic samples. Relative to CPM, MDT increased recovery rates by over 6-fold and isolation throughput by 180-fold, while markedly enhancing both taxonomic richness and evenness. Exclusively recovered by MDT, the oligotrophic genus Caulobacter and numerous cold-adapted genera underscore that MDT accesses physiologically distinct fractions of the cryospheric microbiome. Furthermore, the integration of near-full-length 16S rRNA gene sequencing with MDT cultivation assessment provided substantially improved phylogenetic resolution for species-level identification and novel taxon delineation. Collectively, these findings establish MDT as a transformative platform for cryospheric culturomics, accelerating the construction of comprehensive polar strain collections essential for understanding cold-adaptation mechanisms and exploiting the biotechnological potential of Earth's frozen microbiomes.},
}

@article {pmid42808771,
year = {2026},
author = {Price, CA and Jones, EJ and Ilker, N and Nicklin, AD and Juodeikis, R and McKee, AM and Mitchell, LJ and Stentz, R and Hall, LJ and Carding, SR and Robinson, SD},
title = {Systemically delivered Bacteroides thetaiotaomicron-derived bacterial extracellular vesicles inhibit primary and metastatic melanoma growth.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0251226},
doi = {10.1128/spectrum.02512-26},
pmid = {42808771},
issn = {2165-0497},
abstract = {UNLABELLED: The gut microbiome can contribute to anti-tumor immunity and cancer therapy responses, but translating live microbe-based interventions remains challenging due to safety, controllability, and delivery constraints. Bacterial extracellular vesicles (BEVs) are an attractive cell-free alternative, as they package bacterial cargo into a nanoscale format capable of host-cell engagement, immunological activation, and systemic distribution. Here, we investigated the anti-tumor potential of BEVs derived from the human gut commensal Bacteroides thetaiotaomicron (Bt). We show that the delivery route is a major determinant of efficacy. Intravenous, but not intraperitoneal, administration produced robust anti-tumor activity in a B16F10 melanoma mouse model. Intravenously delivered Bt BEVs suppressed primary tumor growth in a dose-dependent manner and reduced metastatic outgrowth in the lung. Bt BEVs did not reduce B16F10 metabolic viability during a 24-h in vitro exposure, but they activated NF-κB and Toll-like receptor signaling in human reporter systems, and NanoLuc-associated signal from labeled BEV preparations was detected in excised tumor tissue following systemic administration. Although the host pathways responsible for tumor control remain to be defined, these findings identify naturally produced commensal-derived Bt BEVs as a candidate cell-free microbial therapeutic modality for cancer therapy.

IMPORTANCE: Gut bacteria can influence cancer immunity, but using live microorganisms as treatments creates practical and safety challenges. Bacterial extracellular vesicles offer a cell-free way to deliver microbial molecules to the host, yet the anti-cancer potential of vesicles naturally produced by common gut bacteria remains poorly defined. Here, we show that vesicles from the human gut bacterium Bacteroides thetaiotaomicron suppress primary melanoma growth and reduce lung tumor burden in mice when delivered intravenously, whereas delivery into the abdominal cavity is much less effective. The vesicle preparations did not reduce melanoma-cell viability directly in culture, suggesting that the in vivo effect is not explained by simple toxicity to tumor cells. These findings establish that naturally produced vesicles from a common gut bacterium can exert anti-tumor activity after systemic delivery and identify the administration route as an important determinant of their activity. These findings support their further evaluation as cell-free therapeutic platforms for cancer.},
}

@article {pmid42808877,
year = {2026},
author = {Juanpere-Borras, M and Boekhorst, J and van Baarlen, P and Brugman, S and López Nadal, A},
title = {A scalable and cost-effective nanopore workflow for 16S rRNA microbiome profiling validated in a zebrafish gut model.},
journal = {Microbial genomics},
volume = {12},
number = {9},
pages = {},
doi = {10.1099/mgen.0.001828},
pmid = {42808877},
issn = {2057-5858},
mesh = {Animals ; *Zebrafish/microbiology ; *RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Workflow ; *Bacteria/classification/genetics ; *Nanopore Sequencing/methods/economics ; Sequence Analysis, DNA/methods ; Cost-Benefit Analysis ; DNA Barcoding, Taxonomic ; Nanopores ; },
abstract = {Advancements in long-read sequencing technologies, such as those developed by Oxford Nanopore Technologies (ONT), have opened new possibilities for 16S rRNA gene profiling of microbial communities by enabling full-length sequencing. In this study, we optimized and validated a cost-effective, in-house ONT workflow for zebrafish gut microbiome analysis and compared its performance to the gold-standard Illumina NovaSeq platform. Using a PCR-based barcoding strategy, we successfully sequenced both the V3-V4 and V1-V9 regions of the 16S rRNA gene, achieving high read accuracy and balanced demultiplexing across samples. Our results demonstrate that ONT short-read (V3-V4) sequencing using the latest V14 chemistry and Dorado basecaller achieves resolution comparable to that of Illumina, supporting amplicon sequence variant classification. Rarefaction analysis confirmed that the sequencing depth (~240,000 reads/sample) was sufficient to capture microbial diversity in the zebrafish gut, a complex and taxonomically rich environment. Furthermore, taxonomic classifications and diversity metrics were consistent between platforms, supporting the reliability of ONT for microbiota profiling. While full-length (V1-V9) ONT sequencing yielded higher taxonomic richness through operational taxonomic units, it did not significantly improve species-level resolution, likely due to current database and bioinformatics limitations. Our custom library preparation protocol simplified multiplexing, reduced costs and improved scalability without compromising accuracy. Although 15 samples were conservatively multiplexed per flow cell in this study, the workflow has since been applied to larger-scale datasets with up to 75 samples per run and to additional amplicon targets, demonstrating its portability and adaptability across diverse biological contexts. These findings position ONT as a viable, scalable and field-deployable alternative to Illumina for microbiome research.},
}

Animals
*Zebrafish/microbiology
*RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing/methods
Workflow
*Bacteria/classification/genetics
*Nanopore Sequencing/methods/economics
Sequence Analysis, DNA/methods
Cost-Benefit Analysis
DNA Barcoding, Taxonomic
Nanopores

@article {pmid42800207,
year = {2026},
author = {Challa, S and Kudo, N and Bashar, S and Amjad, S and Kozyrskyj, AL},
title = {Developmental Origins of Health and Disease: The role of Clostridioides difficile Colonization of Gut Microbiota During Infancy.},
journal = {Archives of medical research},
volume = {58},
number = {1},
pages = {103526},
doi = {10.1016/j.arcmed.2026.103526},
pmid = {42800207},
issn = {1873-5487},
abstract = {The DOHaD theory was originally proposed to explain the link between fetal development and risk for non-communicable disease - NCD. With advancements in human microbiome research, this theory has been extended to consider postnatal development of the infant gut microbiome and how this contributes to NCD trajectories. C. difficile transiently colonizes the gut microbiota of up to 50% of infants without causing symptoms, but has been associated with disease in the longterm. We reviewed and summarized the current literature to identify prenatal, birth and postnatal factors contributing to C. difficile colonization, and subsequent changes in host biology and NCD outcomes. Many early-life factors promote C. difficile colonization, including prenatal overweight, cesarean birth, hospitalization, antibiotic exposure, formula feeding, histamine-2 receptor antagonist treatment, household pets and smoking, and daycare attendance. Whereas, prenatal milk consumption and having siblings seem to protect against colonization. When C. difficile is present in the gut, associated changes to gut microbiota and metabolites are reported in observational studies. Clinical trial evidence suggests that preceding changes like a reduction in Bifidobacterium species, could promote C. difficile colonization. C. difficile colonization during infancy increases the risk for NCD, including obesity and many atopic diseases (asthma, eczema, food and peanut sensitization). Furthermore, its colonization and abundance was found to be a statistical mediator of these health outcomes, pointing to a potential mediating role for C. difficile in NCD onset. Evidence from the current literature supports the inclusion of C. difficile colonization during infancy as an important biomarker in the developmental origins of disease.},
}

@article {pmid42800287,
year = {2026},
author = {Delai, CV and Moura, FT and Klepa, MS and Assunção, MC and Kitagawa, HY and Ercole, TG and Ribeiro, RA and Nogueira, MA and Hungria, M},
title = {Phylogenomic analysis of Rhizobiaceae strains from the Cerrado biome, Brazil, reveals a novel genus, Brasilibacterium gen. nov., and three novel species: Brasilibacterium cachoeirinhense sp. nov., Brasilibacterium lagoinhense sp. nov., and Martinezella lalimensis sp. nov.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {6},
pages = {126772},
doi = {10.1016/j.syapm.2026.126772},
pmid = {42800287},
issn = {1618-0984},
abstract = {Rhizobiaceae is one of the most representative families, encompassing rhizobial species, valuable allies in the sustainable production of legumes such as cowpea (Vigna unguiculata). Interestingly, beyond rhizobia, studies have increasingly reported the presence of a wide diversity of non-symbiotic bacteria that compose the microbiome of cowpea nodules. In this study, we performed a systematic analysis, with an emphasis on phylogenomic aspects, of 12 strains trapped from cowpea in soils of indigenous lands in Mato Grosso do Sul, Central-Western Brazil (Cerrado biome), which had been preliminarily characterized. The results highlighted the rich and little-explored Rhizobiaceae biodiversity, revealing a novel genus, Brasilibacterium gen. nov., and three novel species: Brasilibacterium cachoeirinhense sp. nov. (CNPSo 3794[T] = BR 15710[T] = LMG 34800[T]), Brasilibacterium lagoinhense sp. nov. (CNPSo 3920[T] = BR 15708[T] = 34801[T]), and Martinezella lalimensis sp. nov. (CNPSo 3959[T] = BR 15709[T] = LMG 34802[T]). However, none of the strains belonging to these novel species was able to re-nodulate cowpea or the promiscuous legumes Phaseolus vulgaris and Macroptilium atropurpureum, suggesting either the loss of symbiotic genes or their endophytic nature. In addition to the novel species accessed, "Rhizobium atlanticum", "Martinezella aureum", "Martinezella centroccidentale", "Martinezella hainanensis", and "Martinezella dioscoreae" were also identified based on genomic sequences, with the latter two reported for the first time in Brazil.},
}

@article {pmid42800336,
year = {2026},
author = {Song, X and Teng, L and Jiang, H and Sun, X and Jiang, J and Zheng, X},
title = {Effects of biogas slurry-borne antibiotics and polypropylene microplastics on the rhizosphere microbiome and metabolome of Hybrid Pennisetum.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120843},
doi = {10.1016/j.ecoenv.2026.120843},
pmid = {42800336},
issn = {1090-2414},
abstract = {Antibiotic residues in biogas slurry and microplastic contamination are increasingly occurring in agricultural soils. However, their combined effects on rhizosphere ecological processes remain poorly understood. In this study, the individual and combined effects of polypropylene microplastics (PP-MPs, 1% w/w) and biogas slurry (BS, 0.5% w/w) on the rhizosphere soil of Hybrid Pennisetum were investigated by conducting an integrated analysis of 16S rRNA gene sequencing and untargeted metabolomics. The results revealed that PP-MPs alone significantly reduced soil bacterial α-diversity and inhibited urease, sucrase, and alkaline phosphatase activities while significantly increasing catalase and fluorescein diacetate hydrolase activities. BS amendment increased nutrient availability and microbial diversity. Notably, compared with BS alone, the coapplication of PP-MPs and BS induced significant soil acidification and increased the retention of multiple antibiotics, including tetracyclines, fluoroquinolones, and macrolides, in the rhizosphere. The combined treatment generated a unique bacterial community assemblage with increased Pseudomonadota and Bacteroidota abundances, restored microbial co-occurrence network complexity, and uniquely enriched pathways related to secondary metabolite biosynthesis and microbial metabolism in diverse environments. Procrustes analysis confirmed the tight coupling between shifts in the microbial community and metabolic reprogramming. Key hub metabolites, including prostaglandin derivatives and hydroxylated fatty acids, exhibited strong connectivity with genera frequently associated with antibiotic resistance potential, such as Pseudomonas, Bacillus, and Streptomyces. Overall, PP-MPs altered the ecological outcome of biogas slurry application by enhancing antibiotic persistence and coupling nutrient enrichment with contaminant-driven microbial and metabolic reprogramming. These results highlight the need to consider microplastic contamination when evaluating the agricultural safety of biogas slurry application in forage production systems.},
}

@article {pmid42800338,
year = {2026},
author = {Gui, Y and Yu, W and Shi, Y and Li, Y and Yang, X and Zhang, H and Yan, W and Liu, Q and Jiang, G},
title = {Microbial filtering and functional reprogramming in soil exposed to spent NCM battery black powder.},
journal = {Ecotoxicology and environmental safety},
volume = {324},
number = {},
pages = {120847},
doi = {10.1016/j.ecoenv.2026.120847},
pmid = {42800338},
issn = {1090-2414},
abstract = {Spent lithium-ion battery black powder is an emerging complex contaminant, which contains transition metals, residual electrolyte salts, and compounds derived from organic electrolytes or binders. Its ecological effects on soil microbiomes remain poorly understood. Here, we designed a soil microcosm experiment with using red soil exposed to a concentration gradient of black powder derived from nickel-cobalt-manganese (NCM) lithium-ion batteries. Samples were collected at two incubation time points and analyzed by shotgun metagenomic sequencing. Black powder exposure produced a nonlinear taxonomic response, with species-level alpha diversity increasing under intermediate exposure, while rare-taxon abundance distributions shifted markedly under medium and high exposure. The LEfSe and PLS-DA analyses identified concentration- and time-dependent indicator taxa, including enrichment of Actinomycetota-related taxa and depletion of Nitrospira and Candidatus Methylomirabilis under high exposure. Community structure diverged significantly along the concentration gradient, and PERMANOVA attributed 23.2% of taxonomic variation to treatment. Structural equation modeling showed no significant direct path from black powder concentration to functional potential; instead, the model was consistent with a possible indirect association through community restructuring. Functional alpha diversity generally declined with increasing black powder concentration. High concentration exposure was associated with reduced relative abundance of KEGG Orthology entries (KOs) related to nitrogen cycling and increased stress-response and organic-matter-decomposition signatures. Overall, these results suggest that NCM-derived black powder can alter soil microbial functional profiles by reshaping community composition.},
}