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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid42755542,
year = {2026},
author = {Eom, JH and Cho, MY and Kim, JW and Kim, Y and No, J and Hwang, J and Kim, S and Lee, D and Baek, H and Kim, BK and Kim, YY and Her, SB and Ko, DY and Hwang, I and Kim, HS},
title = {Absolute quantification by mouthwash testing screens severe periodontitis and tracks species-specific microbial response to periodontal therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1917870},
pmid = {42755542},
issn = {2235-2988},
mesh = {Humans ; *Mouthwashes ; Porphyromonas gingivalis/isolation & purification/genetics ; *Periodontitis/microbiology/therapy/diagnosis ; Retrospective Studies ; Treponema denticola/isolation & purification/genetics ; *Bacterial Load/methods ; Fusobacterium nucleatum/isolation & purification/genetics ; Cross-Sectional Studies ; Tannerella forsythia/isolation & purification/genetics ; Real-Time Polymerase Chain Reaction/methods ; Sensitivity and Specificity ; Prevotella intermedia/isolation & purification/genetics ; Prospective Studies ; *Bacteria/isolation & purification/genetics/classification ; Multiplex Polymerase Chain Reaction/methods ; Female ; },
abstract = {BACKGROUND: Non-invasive molecular tools that can both screen for severe periodontitis and quantify treatment-associated pathogen changes remain an unmet need. We evaluated a non-invasive multiplex quantitative polymerase chain reaction (qPCR) mouthwash panel providing absolute colony-forming-unit (CFU) quantification of five periodontal pathogens (Porphyromonas gingivalis, Treponema denticola, Tannerella forsythia, Prevotella intermedia, Fusobacterium nucleatum), and asked whether a single test can both screen for severe disease and track each patient's species-level treatment response.

METHODS: Treatment-response monitoring was assessed in a real-world retrospective cohort (349 patients, 703 visits; 235 paired pre/post-treatment samples) using paired Wilcoxon signed-rank tests and Jonckheere-Terpstra trend tests across baseline stage. Screening performance was independently evaluated in a prospective cross-sectional cohort (n=87; 31 healthy, 56 Stage III/IV) with leave-one-out cross-validation (LOOCV) and a pre-specified sensitivity analysis.

RESULTS: For screening, LOOCV AUC was 0.96 for P. gingivalis and 0.97 for the combined panel, preserved under inclusion of antibiotic- and treatment-exposed subjects. Beyond screening, the panel resolved each patient's species-level response to non-surgical therapy: all five species decreased significantly, with median within-patient reductions of -0.37 to -0.72 log10 CFU (paired Wilcoxon, all p<0.001) and reduction magnitude scaling with baseline severity. This response was strongly species-specific and clinically informative at the individual level: In the implant-bearing high-baseline-burden subgroup, post-treatment F. nucleatum reached or fell below the Healthy reference median in 61% of evaluable patients, whereas P. gingivalis reached it in only 5% and remained approximately 500-fold above the Healthy reference at the median final visit, identifying residual keystone-pathogen burden not captured by clinical or radiographic assessment.

CONCLUSION: In this two-cohort evaluation, a single non-invasive mouthwash qPCR test provided two linked clinical outputs: high-accuracy screening for severe periodontitis and quantitative individual-level tracking of species-specific microbial response to therapy. These findings are preliminary, derive from a single-center screening cohort and a retrospective monitoring cohort, and require external validation before clinical deployment. By placing pathogen loads on the same absolute CFU scale, the assay supports both cross-sectional disease detection and longitudinal residual-burden monitoring as an adjunct to the 2018 AAP/EFP framework. Clinical Research Information Service (CRIS) registration: KCT0011511 (https://cris.nih.go.kr).},
}

Humans
*Mouthwashes
Porphyromonas gingivalis/isolation & purification/genetics
*Periodontitis/microbiology/therapy/diagnosis
Retrospective Studies
Treponema denticola/isolation & purification/genetics
*Bacterial Load/methods
Fusobacterium nucleatum/isolation & purification/genetics
Cross-Sectional Studies
Tannerella forsythia/isolation & purification/genetics
Real-Time Polymerase Chain Reaction/methods
Sensitivity and Specificity
Prevotella intermedia/isolation & purification/genetics
Prospective Studies
*Bacteria/isolation & purification/genetics/classification
Multiplex Polymerase Chain Reaction/methods
Female

@article {pmid42755618,
year = {2026},
author = {Li, L and Luo, Y and Liu, S and Liang, C and Ruan, H and Peng, P and Huang, Z},
title = {Genome-resolved gut metagenomics identifies an Escherichia coli-Collinsella signature associated with Wagner 4 gangrenous diabetic foot ulcers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1893357},
pmid = {42755618},
issn = {1664-3224},
mesh = {Humans ; *Escherichia coli/genetics ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Gastrointestinal Microbiome/genetics ; *Actinobacteria/genetics ; Metagenome ; Male ; Female ; Feces/microbiology ; },
abstract = {Diabetic foot ulcers (DFU) are a major complication of type 2 diabetes mellitus, but whether the gut microbiome captures systemic microbial features associated with advanced ulcer severity remains unclear. We performed shotgun metagenomic sequencing of stool samples from 43 patients with type 2 diabetes mellitus and active DFU, comparing Wagner grades 1-3 (n = 30) with Wagner 4 gangrenous disease (n = 13). De novo assembly and binning recovered 440 dereplicated metagenome-assembled genomes (MAGs) meeting medium-quality or high-completeness/low-contamination thresholds. Community-level diversity and dominant-taxon composition did not separate Wagner 4 from Wagner 1-3, indicating that advanced disease was not reflected by broad ecological restructuring. Feature-level analysis instead identified a genome-resolved MAG profile. To prioritize robust candidates, we combined two complementary approaches: random forest (RF) stability selection, which identified 24 MAGs with reproducibly high classification importance across resampled folds, and covariate-adjusted MaAsLin2 differential-abundance testing. Intersecting the results of both approaches prioritized three MAGs supported by each method: one Escherichia coli MAG enriched in Wagner 4 and two Collinsella MAGs depleted in Wagner 4. This three-MAG signature (out-of-bag AUC = 0.703) retained much of the discriminatory information captured by the broader 24-MAG RF classifier, with concordant, opposing abundance directions across classifier interpretation, differential-abundance testing, and per-MAG abundance distributions. Functional annotation further separated the Wagner 4-enriched Escherichia coli from the Collinsella MAGs. The Escherichia coli MAG carried antibiotic-resistance and virulence-factor signals and encoded respiratory metabolic capacity, whereas the two Collinsella MAGs lacked detectable resistance and virulence hits and showed metabolically compact profiles. Exploratory clinical association analysis linked the E. coli-Collinsella abundance score to longer DFU duration, consistent with a gut microbial correlate of chronic or advanced disease burden. These findings support longitudinal gut metagenomic validation to determine whether this signal tracks DFU progression, treatment response, or recovery.},
}

Humans
*Escherichia coli/genetics
*Diabetic Foot/microbiology
*Metagenomics/methods
*Diabetes Mellitus, Type 2/complications/microbiology
*Gastrointestinal Microbiome/genetics
*Actinobacteria/genetics
Metagenome
Male
Female
Feces/microbiology

@article {pmid42755640,
year = {2026},
author = {Speeckaert, MM and Delanghe, JR},
title = {Editorial: Community series in gut feelings: investigating the link between microbiota and kidney disease progression, volume II.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1915260},
pmid = {42755640},
issn = {1664-3224},
}

@article {pmid42755725,
year = {2026},
author = {Sharma, I and Barman, R and Kashyap, S and Patowary, A and Parasar, BJ and Jyoti, P and Agarwala, N},
title = {Global meta-analysis of drought associated rice rhizosphere microbiome data and soil application of selected bacteria reveals potential of Pantoea dispersa for drought stress alleviation in rice plants.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1904089},
pmid = {42755725},
issn = {1664-462X},
abstract = {INTRODUCTION: Drought stress poses a significant threat to global rice productivity, jeopardizing crop yield and food security, particularly in water-limited agroecosystems. The application of plant-associated microbes to enhance drought resilience in crops has gained considerable attention in recent years. However, systematic investigation on changes in rice rhizosphere microbial diversity under drought stress remains limited. This study aimed to identify drought-responsive bacterial taxa and evaluate selected rice rhizosphere bacteria for their potential to enhance drought tolerance in rice.

METHODS: A meta-analysis of 16S rRNA amplicon sequencing datasets from rice drought-associated studies was conducted to identify drought-responsive bacterial taxa. Based on the findings of meta-analysis and previous literature, five pre-isolated rice rhizospheric bacterial strains belonging to the genera Streptomyces, Burkholderia, Pantoea, Pseudomonas, and Variovorax were selected and characterized for key plant growth-promoting traits and osmotic stress tolerance using 25% of PEG. The selected isolates were subsequently evaluated for their potential to enhance drought tolerance in two Indian rice varieties, CR Dhan 802 (drought-tolerant) and Ranjit (drought-susceptible) under pot conditions.

RESULTS: Based on meta-analysis of 16S amplicon datasets and literature review bacterial isolates possessing drought tolerance and plant growth-promoting traits, were selected for the pot experiments. Soil inoculation with selected bacterial strains showed that the treatment groups Pantoea dispersa NA-08, Burkholderia cepacia NA-07, and Consortium-I (S. jiujiangensis NA-06, B. cepacia NA-07 and P. dispersa NA-08) alleviated drought stress in both the rice varieties. Furthermore, these treatment groups showed significant enhancement in plant anti-oxidative and soil enzymatic activities. However, the treatments with Streptomyces jiujiangensis NA-06 and Variovorax guangxiensis NA-16 exhibited growth promotion in rice plants, but no significant alleviation of drought stress was observed.

CONCLUSION: The isolate P. dispersa NA-08 showed the higher potential for enhancing rice drought tolerance in pot experiments and might serve as a promising isolate for evaluation under field conditions.},
}

@article {pmid42755786,
year = {2026},
author = {Xiang, X and Zhai, X and Lei, Y and Feng, J and Wang, Q},
title = {The effectiveness of the intervention model based on cognitive behavioral therapy in reducing risky sexual behaviors among MSM.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1870879},
pmid = {42755786},
issn = {2296-2565},
mesh = {Humans ; *Cognitive Behavioral Therapy/methods ; Male ; *Homosexuality, Male/psychology ; *Risk-Taking ; Adult ; *Sexual Behavior/psychology ; *Unsafe Sex/prevention & control ; },
abstract = {METHODS: Based on CBT theory and the Internet, we established an intervention model targeting high-risk sexual behavior patterns in MSM. We then conducted a randomized controlled trial (n = 50) to assess the impact of the CBT-based intervention on high-risk sexual behaviors and gut microbiota changes in this population.

RESULTS: Prior to the implementation of the intervention, 44% of the participants engaged in high-risk behaviors despite having better cognitive levels. However, preliminary findings from post-intervention investigations indicate that intervention measures based on CBT demonstrate greater efficacy compared to traditional methods. After intervention with CBT, the incidence of unprotected anal intercourse in the intervention group was significantly reduced compared to the control group (p = 0.016). Some bacterial taxa (e.g., Bifidobacterium longum and Prevotella) showed potential associations with behavioral changes following CBT; however, these microbiome-related findings are exploratory and hypothesis-generating, not conclusive.

CONCLUSION: The high-risk sexual behaviors of MSM increase health risks. However, the method of intervention through the CBT courses can effectively correct the deviation between the cognition and practice. In this process, changes in gut microbiota were observed to be potentially associated with behavioral changes, but these associations are preliminary and warrant further investigation in confirmatory studies.},
}

Humans
*Cognitive Behavioral Therapy/methods
Male
*Homosexuality, Male/psychology
*Risk-Taking
Adult
*Sexual Behavior/psychology
*Unsafe Sex/prevention & control

@article {pmid42755803,
year = {2026},
author = {Marjanović, M and Maletin, N and Kukić, B and Nikolić, I and Petrović, N and Radić, J and Đurić, A and Knezević, M and Dejanović, B and Ćalić, V},
title = {Gut microbiome-mediated primary and acquired resistance to immune checkpoint inhibitors in MSI-H/dMMR colorectal cancer: mechanisms, biomarkers, and therapeutic implications-a narrative review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1907957},
pmid = {42755803},
issn = {2235-2988},
mesh = {Humans ; *Colorectal Neoplasms/drug therapy/genetics/immunology/microbiology ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/immunology ; *Drug Resistance, Neoplasm ; Microsatellite Instability ; Tumor Microenvironment/immunology ; DNA Mismatch Repair ; Animals ; Biomarkers, Tumor ; },
abstract = {INTRODUCTION: Immune checkpoint inhibitors (ICIs) have transformed the management of microsatellite instability-high/deficient mismatch repair (MSI-H/dMMR) colorectal cancer (CRC). However, a substantial proportion of patients exhibit primary resistance or eventually develop acquired resistance, highlighting the need for a better understanding of the biological mechanisms influencing therapeutic response. Increasing evidence suggests that the gut microbiome-immune axis is an important regulator of antitumor immunity through complex interactions among microbial communities, microbial metabolites, host immunity, and the tumor microenvironment.

MAIN BODY: This narrative review summarizes current evidence regarding the role of the gut microbiome-immune axis in mediating primary and acquired resistance to immune checkpoint inhibition in MSI-H/dMMR CRC. We discuss the physiological interactions that maintain immune homeostasis and review the functional mechanisms through which alterations in microbial metabolic pathways, including short-chain fatty acids, bile acids, tryptophan-derived metabolites, inosine, and polyamines, may influence antitumor immune responses. We further examine microbial composition and functional biomarkers associated with immune checkpoint inhibitor response, together with emerging therapeutic strategies aimed at modulating the gut microbiome-immune axis, including dietary interventions, prebiotics, probiotics, selective antimicrobial approaches, fecal microbiota transplantation, live biotherapeutic products, and next-generation precision microbiome engineering. Finally, we discuss current translational challenges and future research priorities required for successful clinical implementation.

CONCLUSION: The gut microbiome-immune axis represents a promising area of investigation for understanding resistance to immune checkpoint inhibition in MSI-H/dMMR CRC. While growing evidence supports its biological relevance, much of the current knowledge remains preclinical or is derived from early-phase clinical studies. Future progress will depend on mechanistic investigation, longitudinal multi-omic microbiome profiling, standardized methodologies, prospective biomarker validation, and the rational development of microbiome-directed therapeutic strategies to support precision immuno-oncology.},
}

Humans
*Colorectal Neoplasms/drug therapy/genetics/immunology/microbiology
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Gastrointestinal Microbiome/immunology
*Drug Resistance, Neoplasm
Microsatellite Instability
Tumor Microenvironment/immunology
DNA Mismatch Repair
Animals
Biomarkers, Tumor

@article {pmid42755879,
year = {2026},
author = {Juhász, Á and Wazzani, Y and Tavaszi-Sárosi, S and Patonay, K and Olasz, F and Posta, K},
title = {Rhizosphere bacterial and fungal community structure varies among field-grown Mentha spicata accession plots with different essential oil profiles.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1939529},
pmid = {42755879},
issn = {1664-302X},
abstract = {INTRODUCTION: Aromatic plants produce diverse secondary metabolites, yet how within-species phytochemical variation relates to rhizosphere bacterial and fungal communities remains poorly resolved. Mentha spicata displays substantial essential oil (EO) compositional variation, providing a field system to examine rhizosphere microbiome structuring among accession plots.

METHODS: Five vegetatively propagated M. spicata accessions representing three operational EO-based groups (L-carvone group, Piperitenone oxide group, and Dihydrocarvone group) were examined under open-field conditions at full flowering. Each accession was grown in a single field plot, from which three spatially separated rhizosphere soil samples were collected; managed inter-row bulk soil was included as a contextual control. Soil physicochemical properties, aerial-tissue EO composition, and bacterial 16S ribosomal RNA gene and fungal ITS amplicon profiles were characterized. Bray-Curtis ordination, permutational multivariate analysis of variance, and distance-based redundancy analysis were used to assess community differences and associations with soil properties and accession-level EO profiles.

RESULTS: Bacterial communities were dominated by Actinomycetota, Pseudomonadota, Chloroflexota, Acidobacteriota and Bacillota, whereas fungal communities were dominated by Ascomycota, followed by Mortierellomycota and Basidiomycota. Fungal taxonomic profiles varied more strongly among groups, with J14 showing the highest Ascomycota proportion and Basidiomycota being most abundant in J7 and J11. Alpha-diversity differences were limited and, for bacteria, mainly reflected lower diversity in bulk soil. After excluding bulk soil, grouping by accession plot remained significant for bacteria (R[2] = 0.6619, p = 0.0001) and fungi (R[2] = 0.5060, p = 0.0001), with bacterial communities showing more compact structuring. Soil-based constrained models were significant for both microbial groups. pH and nitrate + nitrite nitrogen were significantly associated with bacterial and fungal community composition, while humus content was additionally significant for fungi. In contrast, accession-level models based on aerial-tissue EO gradients were not significant for bacteria (p = 0.342) or fungi (p = 0.317).

DISCUSSION: Field-grown M. spicata accession plots with contrasting aerial-tissue EO profiles harbored differentiated rhizosphere bacterial and fungal communities, and community variation was significantly associated with local soil properties. A statistically supported relationship with aerial-tissue EO composition was not detected, and these profiles are best regarded as accession-level chemical descriptors rather than direct rhizosphere drivers.},
}

@article {pmid42755889,
year = {2026},
author = {Yin, S and Jing, C and Dai, C and Zhou, X and Ai, J and Sun, H},
title = {Microbiome-metabolome interaction reveals rhizosphere ecological, bioactive, and antioxidant responses of Paeonia lactiflora Pall. to intercropping and harvest timing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1934798},
pmid = {42755889},
issn = {1664-302X},
abstract = {Paeonia lactiflora Pall. (P. lactiflora) is a medicinal plant with considerable economic value. During its growth, root secondary metabolism and rhizosphere microbes interact closely; however, no systematic study has examined microbiome and metabolome dynamics under different planting systems and harvest times. To address this, we employed amplicon sequencing for microbial diversity and untargeted metabolomics for metabolite profiling. The datasets were then integrated, and correlation analysis was performed. We measured paeoniflorin by high-performance liquid chromatography (HPLC), total phenolic content by the Folin-Ciocalteu method, total flavonoid content by the NaNO2-Al(NO3)3 method, and antioxidant activity by DPPH, ABTS, hydroxyl radical scavenging, and FRAP assays. The results revealed that Proteobacteria was the most abundant phylum in the bacterial community, and among classified genera, Subgroup_2 exhibited the highest relative abundance. In the fungal community, Ascomycota dominated at the phylum level, while Coniosporium was the most abundant genus. Metabolomic analysis revealed clear separation among sample groups by principal component analysis. Four pairwise comparisons identified differential metabolites predominantly classified as lipids, phenylpropanoids, and polyketides. Functional enrichment analysis indicated that these differences were mainly associated with metabolic pathways, particularly amino acid metabolism, secondary metabolite biosynthesis, and ABC transporters. Furthermore, monoculture with late-stage harvest (CS-4) represented the optimal strategy for maximizing medicinal quality. Under intercropping, mid-stage harvest (TZ-2/TZ-3), with adjustments based on annual climatic conditions, is recommended to balance quality and ecological benefits. Collectively, these findings reveal differences in P. lactiflora across planting systems and harvest periods, providing a theoretical basis for the optimization of cultivation strategies.},
}

@article {pmid42755905,
year = {2026},
author = {Beyzaei, Z and Weiskirchen, R},
title = {Microplastics in food production systems: Sources, exposure pathways, and gastrointestinal health effects.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101557},
pmid = {42755905},
issn = {2665-9271},
abstract = {Microplastics (MPs) and nanoplastics (NPs) have become ubiquitous contaminants in food production systems, raising increasing concerns regarding their potential effects on gastrointestinal and systemic health. This review summarizes current evidence on the occurrence, sources, and biological effects of MPs/NPs within food production chains and their implications for the human gut. Experimental in vitro studies demonstrate that MPs/NPs can induce oxidative stress, inflammation, genotoxicity, metabolic dysregulation, and epithelial barrier dysfunction, while in vivo animal studies show disruption of gut homeostasis, microbiota alterations, systemic translocation, and hepatic, metabolic, and immune disturbances. Co-exposure to environmental pollutants and food-associated chemicals may further enhance toxicity through synergistic mechanisms. Although human evidence remains limited, MPs have been detected in human tissues, including the liver, indicating the possibility of systemic exposure. Emerging evidence also suggests complex interactions between MPs/NPs and the gut microbiome, although the clinical significance of these findings remains uncertain. Therefore, current knowledge is derived predominantly from experimental models, and substantial uncertainties remain regarding human exposure levels, dose-response relationships, and long-term health consequences. Further well-designed human studies and standardized exposure assessment methods are essential to clarify the health risks associated with dietary MPs/NPs.},
}

@article {pmid42755932,
year = {2026},
author = {Pascual, J and Martínez-Blanch, JF and Amaro, C and Roig, FJ},
title = {Editorial: Advances in immunity and microbiome: exploring key interactions and innovations.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1933468},
doi = {10.3389/fimmu.2026.1933468},
pmid = {42755932},
issn = {1664-3224},
}

@article {pmid42755999,
year = {2026},
author = {Feole, B and Grouzdev, D and Pales Espinosa, E and Cacot, G and Allam, B},
title = {Sampling method influences hemolymph bacterial communities in the eastern oyster, Crassostrea virginica.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1862013},
pmid = {42755999},
issn = {1664-302X},
abstract = {As the microbiome becomes increasingly recognized for its role in driving animal health and disease, accurate characterization of microbial community composition is essential. With this research comes the critical need for standardized sampling methods along with an understanding of the biases inherent to these methods. In oysters, hemolymph is a valuable system for microbiome research due to its diverse physiological functions, role as an indicator of health, and ease of collection. Unfortunately, much of the current literature regarding oyster hemolymph microbiome composition is opaque in its description of tissue collection methods. When these methods are clearly described, investigators often collect hemolymph via a needle inserted into the adductor muscle through a notch cut in the shell. However, due to the needle's movement through soft tissues and mucous membranes exposed to the surrounding seawater, this notch method carries significant risk of sample contamination. An alternative hemolymph sampling method, hereafter referred to as the hole method, minimizes this potential contamination as the needle is inserted through a hole drilled in the shell directly above the adductor muscle, circumventing other soft tissues. Here, we tested whether notch and hole hemolymph collection methods produce different 16S rRNA bacterial community profiles in C. virginica. To compare these two sampling methods and evaluate the potential method-specific biases, particularly biases that may result from tissue contamination, oysters had hemolymph collected through both a notch and hole while alternating method order. Following taxonomic classification and differential abundance analysis of the resultant 16S rRNA sequences, the presence of disproportionate Vibrio spp. enrichment in notch-associated samples was evident. Notch-collected samples yielded significantly higher 16S rRNA gene copy numbers (p = 0.037) and a 16-fold higher relative abundance of Vibrio spp. compared to hole-collected samples (52.6% vs. 3.2%, p adj = 0.006) despite no significant change in absolute counts of the dominant genus Poseidonibacter. Overall, this analysis demonstrates both the potential of the hole sampling method and the need for microbiome researchers to account for biases in bacterial community composition associated with their chosen sampling method.},
}

@article {pmid42756118,
year = {2026},
author = {Xiong, S and Yao, R},
title = {Klebsiella pneumoniae in inflammatory bowel disease and rectal cancer: from gut inflammation to a potential driver of carcinogenesis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1948813},
pmid = {42756118},
issn = {1664-302X},
abstract = {The gut microbiota is a critical modulator of intestinal inflammation and colorectal cancer (CRC), yet the specific microbial drivers that bridge inflammatory bowel disease (IBD) to rectal carcinogenesis remain poorly defined. Klebsiella pneumoniae (K. pneumoniae) has recently emerged as a compelling candidate at this nexus; however, several critical questions remain unresolved: (i) whether K. pneumoniae colonization is a cause or a consequence of rectal carcinogenesis; (ii) how strain level heterogeneity determines pathogenic versus commensal outcomes; and (iii) which rectal microenvironmental factors selectively amplify its carcinogenic potential. Moreover, the potential utility of persistent colonization with carcinogenic K. pneumoniae strains as a predictive biomarker and target for chemoprevention warrants further investigation. This review systematically addresses these questions by integrating findings from microbial ecology, virulence factor biology, host immunology, and oncogenic signaling. We dissect the dual role of K. pneumoniae along the inflammation cancer axis, focusing on its capacity to promote T helper 17 (Th17) driven inflammation, disrupt the epithelial barrier, and directly alkylate host DNA via colibactin-like genotoxins. We propose a mechanistic framework in which chronic K. pneumoniae colonization acts as a bridge between IBD activity and rectal tumorigenesis, and we critically evaluate the potential of phage therapy, virulence inhibitors, and microbiome-based biomarkers to intercept this process. Finally, we highlight key knowledge gaps and outline future directions required to establish causality and translate these insights into clinical strategies for IBD associated rectal cancer prevention.},
}

@article {pmid42756159,
year = {2026},
author = {Jiang, P and Zhou, M and Liao, Y and Du, W and Liu, M},
title = {Associations of the gut mycobiome and its cross-kingdom interactions with estrus return in post-weaning sows revealed by metagenomic analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1892244},
pmid = {42756159},
issn = {1664-302X},
abstract = {Post-weaning estrus return is a critical determinant of reproductive efficiency in the swine industry. While the gut microbiome, particularly bacteria, has been significantly associated with estrus return in sows, the role of the gut mycobiome and its cross-kingdom interactions with bacteria in this context remains largely unexplored. Here, we employed fecal metagenomics to characterize the gut mycobiome in 85 sows and investigated its association with post-weaning estrus return. A total of 22 fungal species were significantly associated with estrus return. Normal-return sows were characterized by increased abundance of Arxiozyma slooffiae (formerly Kazachstania slooffiae) and decreased abundances of Malassezia pachydermatis and Alternaria rosae. Moreover, we uncovered cross-kingdom interactions between fungi and bacteria associated with estrus return, where Arxiozyma slooffiae showed a positive correlation with Prevotella spp. enriched in normal-return sows. These interactions were predicted to involve the exchange of metabolites, including Fe[2+], thiamine, and nicotinate. Fungal biomarkers demonstrated good discriminatory power for distinguishing normal-return and non-return sows (AUC = 0.906), and the combination with bacterial biomarkers further enhanced the performance (AUC = 0.947). Integrated multi-omics analysis revealed extensive associations between gut fungi and hormones and hormone-related compounds, as well as microbial functional pathways. Notably, Arxiozyma slooffiae was positively correlated with phytoestrogens (including daidzein and genistein) and the steroid hormone biosynthesis pathway but negatively correlated with testosterone. Collectively, these findings provide comprehensive insights into the role of the gut mycobiome and its cross-kingdom interactions in sow reproductive performance.},
}

@article {pmid42756188,
year = {2026},
author = {Kang, JI and Park, CI and Seo, JH and Kang, CS and Kim, YK and Kim, SJ},
title = {Pre-treatment serum extracellular vesicle-enriched microbiome profiles and SSRI treatment response in obsessive-compulsive disorder: a prospective naturalistic cohort study.},
journal = {Frontiers in psychiatry},
volume = {17},
number = {},
pages = {1913728},
pmid = {42756188},
issn = {1664-0640},
abstract = {OBJECTIVE: The microbiome is emerging as an important component of brain-body communication and may influence treatment outcomes in psychiatric disorders. This naturalistic cohort study prospectively evaluated whether baseline microbiome abundance and composition of circulating bacterial extracellular vesicles (EVs) are associated with subsequent response to selective serotonin reuptake inhibitors (SSRIs) in patients with obsessive-compulsive disorder (OCD).

METHODS: Thirty-two drug-naïve or medication-free patients with OCD were enrolled and assessed at baseline and at 12 weeks following the initiation of SSRI pharmacotherapy. Serum EV microbiome profiling was performed at baseline, before any pharmacological treatment was commenced, ensuring that all biological measurements reflect a pharmacologically unconfounded pre-treatment state. Good responders were defined as patients with a 35% or greater reduction in the Yale-Brown Obsessive-Compulsive Scale score at 12 weeks, while poor responders were defined as those with less than a 35% reduction. Baseline microbiome abundance and composition of circulating bacterial EVs in serum were compared between these groups.

RESULTS: Of the 32 participants, 29 completed the 12-week study. Based on the treatment response at 12 weeks, the OCD group was classified into 15 good responders (5 females) and 14 poor responders (7 females). The two groups did not differ significantly in age, sex, age of onset, baseline Y-BOCS or MADRS scores, or medication type. No significant differences in alpha or beta diversity were observed between the groups. Taxonomic analysis of pre-treatment serum EV profiles revealed a nominally higher relative abundance of the genus Acinetobacter in patients who subsequently showed poor response compared to good responders. However, this association did not remain statistically significant after correction for multiple comparisons, age adjustment, or compositionally-aware reanalysis.

CONCLUSION: These results provide no statistically defensible evidence of a taxon-level microbiome difference between response groups, and the nominal Acinetobacter finding should not be regarded as a validated biomarker. Global diversity measures also did not distinguish the response groups. These findings are hypothesis-generating and support the feasibility of pre-treatment serum EV-associated bacterial profiling in OCD. Larger, adequately powered studies incorporating compositionally appropriate statistical methods and rigorous contamination-control procedures are warranted to determine whether reproducible microbiome-treatment response associations exist.},
}

@article {pmid42756190,
year = {2026},
author = {Liu, S and Feng, S and Yuan, Z and Mei, Z and Yin, J and Chen, L and Zhang, Y},
title = {The effects of maternal dietary fiber and short-chain fatty acids on the health of offspring: a mini review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1867014},
pmid = {42756190},
issn = {2296-861X},
abstract = {Maternal nutrition during pregnancy is a critical determinant of offspring long-term health. Dietary fiber has emerged as a key modifiable factor. Through gut microbial fermentation, fiber is converted into short-chain fatty acids (SCFAs), primarily acetate, propionate, and butyrate. This mini review synthesizes current evidence from molecular, animal, and human studies on the role of maternal SCFAs in programming offspring metabolic and immune health. Mechanistically, SCFAs act via two complementary pathways: activation of G protein-coupled receptors (GPCRs) and inhibition of histone deacetylases, leading to rapid signaling and long-term epigenetic regulation. Animal studies demonstrate that maternal fiber deprivation impairs offspring glucose metabolism, promotes low-grade inflammation and obesity, and compromises immune tolerance, whereas fiber or short-chain fatty acid (SCFA) supplementation confers protective effects. Human observational studies support these findings, showing associations between maternal SCFA levels and favorable neonatal metabolic profiles, neurodevelopmental outcomes, and reduced obesity risk, although randomized controlled trials remain limited. Key translational challenges include inter-species differences, individual microbiome variability, and optimal intervention timing. Despite these uncertainties, promoting adequate and diverse dietary fiber intake during pregnancy represents a safe, low-cost, and scalable public health strategy to improve intergenerational health outcomes.},
}

@article {pmid42756193,
year = {2026},
author = {Nguyen, ADD and Kern, R and Dombrovski, T and LaFramboise, T},
title = {The circulating metatranscriptome in acute myeloid leukemia patients: an RNA-seq reanalysis.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1903806},
pmid = {42756193},
issn = {2813-4338},
abstract = {The human microbiome comprises the collection of microbiota residing on or within human tissues. It is now well-established that microbial composition impacts an individual's health. In the cancer realm, the vast majority of microbiome studies have been focused either on the gut, or at the site of solid tumors. Few studies have assessed microbial content at the site of hematological malignancies - blood and bone marrow. Here we characterize the circulating metatranscriptome (i.e. the bacterial and viral RNA in circulation) of 411 patients with acute myeloid leukemia (AML). We find that the circulating metatranscriptome in AML differs substantially from that of healthy controls, and high metatranscriptome loads are associated with antibacterial host response. We observe that specific bacterial genera are associated with response to anti-cancer therapy and disease history, and are tied to host gene expression signatures of heme metabolism. Overall, our study represents an inferred landscape of circulating microbial RNA in AML and suggests potential for its use as a biomarker.},
}

@article {pmid42756390,
year = {2026},
author = {Osawa, R and Inoue, J and Fukuda, I and Shirai, Y and Kodama, Y},
title = {Function-based personalization of dietary fiber selection enhances gut microbial fermentation: a proof-of-concept crossover trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1907988},
pmid = {42756390},
issn = {2296-861X},
abstract = {UNLABELLED: Text Responses to dietary fiber supplementation vary markedly among individuals, yet no validated platform exists to prospectively identify optimal fiber types based on individual gut microbiome function. Here we present My Dietary Fiber Finder (MyDFF), an ex vivo functional screening platform that predicts optimal dietary fibers for individual gut microbiomes through direct fermentation profiling. For each participant, the dietary fiber with the highest saccharification index (SI) was designated M-PDF, and that with the lowest SI was designated L-PDF. In a crossover trial involving eight healthy Japanese adults (72 longitudinal observations, each participant serving as their own control), the pre-specified per-participant analysis (Dunnett's test) showed that M-PDF significantly increased fecal volatile fatty acid (VFA; acetate + propionate + butyrate) concentrations over baseline in two of eight participants and total short-chain fatty acid (SCFA) concentrations in one, whereas the non-personalized fiber (L-PDF) did so in none. Post hoc group-level analysis confirmed a significant increase over baseline for M-PDF (total VFA and total SCFA, both p < 0.01) but not for L-PDF, and in a within-participant comparison M-PDF exceeded L-PDF in seven of eight participants (mean difference = 32.4 μmol/g; 95% CI: 8.7-56.1; p = 0.014; Cohen's d = 1.14). However, the magnitude of the pre-intervention saccharification-index differential between the two fibers did not significantly correlate with the magnitude of the in vivo VFA response differential across participants (Pearson r = 0.082, p = 0.85), indicating that the assay did not quantitatively predict response magnitude. Exploratory 16S rRNA gene sequencing analysis showed no significant cohort-level shift in overall gut microbial community composition during either intervention phase. In four separate validation donors, individual fermentation profiles remained relatively stable over the observed 3-9-month follow-up. These proof-of-concept findings support the potential of function-based framework for personalized prebiotic design and motivate larger validation studies.

CLINICAL TRIAL REGISTRATION: https://jrct.niph.go.jp, identifier jRCTs051220163.},
}

@article {pmid42756392,
year = {2026},
author = {Chen, Z and Du, Y and Li, H and Wen, X and Chen, L and Wang, W and Wu, P},
title = {Amended engineered soil promotes coordinated soil-plant-microbiome responses during early-stage slope restoration.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1918442},
pmid = {42756392},
issn = {2296-4185},
abstract = {Amended Engineered Soil (AES), a functional substrate incorporating biomass-derived straw fiber, has been applied for the ecological restoration of degraded slopes. However, how AES affects the coordinated responses of substrate structure, root development, and rhizosphere microbiome assembly during early-stage restoration remains unclear. In this study, AES and Conventional Engineered Soil (CES) were compared during a 90-day slope restoration experiment using Lolium perenne as the target species. Compared with CES, AES substantially improved substrate moisture and nutrient conditions, with water content increasing from approximately 10.4%-16.6% and available phosphorus increasing more than fivefold. AES also promoted the formation of large water-stable aggregates, indicating improved structural stability of the reconstructed substrate. These changes were accompanied by marked improvements in vegetation establishment, including a 18.4% increase in plant height, more than 40% increase in dry biomass, and a pronounced increase in root length. Root tensile strength was also enhanced, suggesting greater belowground reinforcement. AES significantly increased bacterial richness and Shannon diversity, whereas the fungal response was mainly reflected in increased richness rather than diversity. Correlation analysis further showed close associations among substrate nutrient conditions, plant growth, root reinforcement, and microbial diversity. These findings suggest that AES promotes early-stage slope restoration through the coordinated improvement of substrate quality, vegetation establishment, root development, and rhizosphere microbial communities, while providing a sustainable pathway for biomass resource utilization.},
}

@article {pmid42756418,
year = {2026},
author = {Soufla, A and Fragoulis, GE and Iliopoulos, A},
title = {Diagnostic Pitfall: Prolonged COVID-19 Presenting as Organising Pneumonia in a Rituximab-Treated Patient with Rheumatoid Arthritis.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {3},
pages = {619-621},
pmid = {42756418},
issn = {2529-198X},
abstract = {Rituximab (RTX)-induced B-cell depletion is associated with prolonged SARS-CoV-2 infection. We describe a case of persistent COVID-19 in a patient with rheumatoid arthritis (RA) initially misdiagnosed as cryptogenic organising pneumonia (COP), highlighting the diagnostic and management challenges in RTX-treated patients. Retreatment with a second 5-day course of nirmatrelvir/ritonavir led to rapid clinical improvement and complete radiological resolution. Persistent SARS-CoV-2 infection should be considered in RTX-treated patients with non-resolving pulmonary infiltrates, particularly when corticosteroid therapy is ineffective.},
}

@article {pmid42756631,
year = {2026},
author = {Theiopoulou, DC and Vassilopoulos, D and Mavragani, CP and Bertsias, G},
title = {The Gut Microbiota in Rheumatoid Arthritis: Evaluation of Microbial Profiles, Disease Activity, Biomarkers, and Treatment Response.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {3},
pages = {469-480},
pmid = {42756631},
issn = {2529-198X},
abstract = {OBJECTIVES: Rheumatoid arthritis (RA) is a chronic autoimmune disease with complex etiopathogenesis, and variable clinical course. The human gastrointestinal (GI) tract is a dynamic ecosystem in which micro-organisms influence metabolism, immune signalling, and pathogen resistance. Understanding these interactions is key to exploring the microbiota's role in RA. This review examines how intestinal and oral microbiota differ in RA patients and influence disease activity and treatment response.

METHOD: A literature search was conducted using PubMed, from inception until January 3, 2025. Studies were selected based on the inclusion of original research involving human subjects diagnosed with RA. Exclusion criteria comprised reviews, case reports, animal studies, and studies with insufficient data. Of the 329 records identified, 72 were included in this review.

RESULTS: Most studies have implicated changes in bacterial composition involving specific phyla in RA-associated dysbiosis. The imbalance is primarily driven by alterations in the phyla Bacillota, Pseudomonadota, and Bacteroidota, with Bacillota and Pseudomonadota accounting for 70% of increased taxa, and Bacillota and Bacteroidota for 83% of decreased intestinal taxa. Other findings include reduced α-diversity in seronegative patients and associations between decreased Prevotella taxa and higher disease activity, inflammation biomarkers, and autoantibodies. Smaller studies have also reported elevated serum zonulin-a marker of intestinal permeability-in RF-positive patients.

CONCLUSION: This review highlights key bacterial phyla linked to RA and emphasises the potential of probing gut micro-biota-immune system interactions to improve diagnosis and treatment.},
}

@article {pmid42756659,
year = {2026},
author = {Abdelmaksoud, A and Igoe, A and AbdAlnaeem, MA and Toraih, EA and Roller, BA and Kaelber, KL and Kaelber, DC},
title = {Increased Risk of Gout among Patients with Trisomy 21: Insights from a Population-Based Study of over 30,000 Patients with Trisomy 21.},
journal = {Mediterranean journal of rheumatology},
volume = {37},
number = {3},
pages = {590-597},
pmid = {42756659},
issn = {2529-198X},
abstract = {BACKGROUND: Primary trisomy 21 is associated with an elevated incidence of conditions such as cardiac anomalies, hypothyroidism, type 1 diabetes mellitus, and auditory impairments. However, the potential association between trisomy 21 and gout remains insufficiently studied, with existing evidence largely limited to case reports. This study aimed to determine the prevalence of gout among individuals with trisomy 21 and compare it with those without trisomy 21 to evaluate a potential association and examine demographic factors influencing gout risk.

METHODS: This retrospective analysis utilised electronic health records from the US Collaborative Network within the TriNetX clinical research platform, representing over 100 million patients. We identified 30,171 individuals with trisomy 21 and compared them with 3,502,718 non-trisomy 21 controls using propensity score matching. Gout prevalence and relative risk (RR) with 95% confidence intervals (CI) were assessed between groups.

FINDINGS: Patients with trisomy 21 exhibited higher gout prevalence than controls (2.90% vs 1.05%, p < 0.0001). The relative risk of gout was 2.76 in individuals with trisomy 21 compared with controls (95% CI 2.43-3.14). Increased risk persisted across age, sex, and racial groups.

INTERPRETATION: These findings demonstrate an association between trisomy 21 and increased risk of gout. Further research is needed to understand the underlying mechanisms and inform targeted screening and management strategies in this population.},
}

@article {pmid42756774,
year = {2026},
author = {Huang, Z and Dai, Z and Liu, Q},
title = {Efficacy and safety of fecal microbiota transplantation for chronic constipation: a systematic review and meta-analysis integrating pre-post and single-arm evidence.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1900353},
pmid = {42756774},
issn = {1664-302X},
abstract = {BACKGROUND: Chronic constipation is a common functional gastrointestinal disorder with a global prevalence of 12%-17%. Conventional treatments have limited efficacy for refractory cases, with high recurrence and side effects. Fecal microbiota transplantation (FMT) offers a novel strategy by restoring gut microecological balance, yet its efficacy requires systematic evaluation. This meta-analysis evaluated FMT efficacy and safety through an innovative "three-in-one" framework.

METHODS: We systematically searched CENTRAL, PubMed, Embase, and CNKI for RCTs, single-arm studies, and cohort studies. The framework comprised: (1) RCT random-effects meta-analysis; (2) single-arm proportional meta-analysis with Freeman-Tukey transformation; (3) pre-post paired sensitivity analysis (r = 0.5, with sensitivity tests at r = 0.3, 0.7, 0.9). Publication bias was assessed via Egger, Harbord, trim-and-fill, and fail-safe N tests.

RESULTS: 12 RCTs (n = 1040), 16 single-arm studies (n = 403), and 4 cohort studies (n = 422) were included. After trim-and-fill adjustment for publication bias, FMT was associated with a clinical total response rate of RR = 1.21 (95% CI: 1.10-1.33). The unadjusted pooled estimate was RR = 1.36 (95% CI: 1.21-1.52, P < 0.001); however, the Harbord test indicated potential publication bias (P = 0.003), necessitating this correction. Wexner score improved (MD = -2.08, 95% CI: -3.35 to -0.81, P = 0.003). Among the 16 single-arm studies, 8 (n = 249) reported remission/improvement rates, showing a remission rate of 51.7% (95% CI: 40.3%-62.9%) and paired pre-post improvements in BSFS, Wexner, and PAC-QOL; these within-group changes cannot establish causal efficacy. During follow-up periods of up to 24 weeks, no serious adverse events were reported; long-term safety data are lacking.

CONCLUSION: Current evidence suggests FMT is a promising therapeutic option for chronic constipation, with an adjusted clinical total response rate of RR = 1.21 (95% CI: 1.10-1.33) after correction for publication bias. While FMT was associated with improvements in symptom scores, quality of life, and intestinal function, the evidence quality is limited by publication bias, high heterogeneity, and high risk of bias in all included RCTs. More high-quality, sham-controlled RCTs are needed to validate these findings.

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD420261394673, identifier: CRD420261394673.},
}

@article {pmid42756821,
year = {2026},
author = {Xie, F and He, X and Chen, W and Li, J and Lin, S and Bao, Q and Li, W and Cheng, J and Ma, Y and Wu, Z and Li, H},
title = {Integrative multi-omics analysis prioritizes compartment-specific candidate targets of gut microbiota metabolites in diabetic kidney disease.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1925910},
pmid = {42756821},
issn = {1664-3224},
mesh = {*Diabetic Nephropathies/metabolism/microbiology/genetics ; Humans ; Multiomics ; *Gastrointestinal Microbiome ; Molecular Docking Simulation ; Gene Expression Profiling ; *Metabolome ; Gene Regulatory Networks ; },
abstract = {OBJECTIVE: The gut-kidney axis has emerged as a critical area of investigation. However, the compartment-specific regulatory mechanisms of gut microbiota metabolites within the glomerular and tubulointerstitial regions of diabetic kidney disease (DKD) remain incompletely understood.

METHODS: The gutMGene, SEA, STP, GEO, Nephroseq v5, and KIT databases were interrogated. Multi-omics and experimental approaches were applied, involving differential expression analysis, Weighted Gene Co-expression Network Analysis (WGCNA), machine learning, Mendelian randomization (MR), Gene Set Enrichment Analysis (GSEA), immune infiltration, gene set variation analysis (GSVA), clinical correlation, single-cell profiling, molecular docking, molecular dynamics simulation, CCK-8 assay, and RT-qPCR. The "Microbiota-Substrate-Metabolite-Target" (M-S-M-T) network was constructed for each compartment.

RESULTS: Machine learning identified six glomerular (IGFBP6, PLA2G4A, CTSK, HTR2B, PDGFRA, MMP7) and five tubulointerstitial (CA2, HSD11B2, NQO2, MMP7, CYP24A1) core genes. Mendelian randomization, single-cell profiling, and clinical cohorts provided supportive genetic and clinical evidence linking these genes to the estimated glomerular filtration rate (eGFR) and to DKD. Immune infiltration analysis and GSVA indicated a higher estimated proportion of M2 macrophages and a shift of the estimated mast cell composition from activated to resting states in both compartments, which correlated with core gene expression. Via the "M-S-M-T" network, drug-likeness and toxicity screening, caffeic acid and naringenin chalcone were prioritized as shared candidate metabolites. Molecular docking and molecular dynamics simulations suggested favorable in silico binding to HTR2B and MMP7. Both metabolites attenuated high glucose (HG)-induced core gene dysregulation in HK-2 cells and podocytes.

CONCLUSION: This study proposed a compartment-specific "M-S-M-T" regulatory network in the DKD glomerulus and tubulointerstitium. The shared metabolites caffeic acid and naringenin chalcone, which targeted HTR2B and MMP7, produced a preliminary protective transcriptional response in vitro. These findings are hypothesis-generating and require validation in real-world microbiome, metabolomic and in vivo studies before any therapeutic inference can be drawn.},
}

*Diabetic Nephropathies/metabolism/microbiology/genetics
Humans
Multiomics
*Gastrointestinal Microbiome
Molecular Docking Simulation
Gene Expression Profiling
*Metabolome
Gene Regulatory Networks

@article {pmid42756843,
year = {2026},
author = {Baune, BT},
title = {Pharmaco-multiomics in major depressive disorder: a narrative review and proposed translational framework for difficult-to-treat and treatment-resistant depression.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1934360},
pmid = {42756843},
issn = {1663-9812},
abstract = {BACKGROUND: Antidepressant prescribing in major depressive disorder (MDD) remains dominated by sequential trial and error, particularly when illness becomes difficult to treat (DTD) or meets conventional treatment-resistant depression (TRD) criteria.

OBJECTIVE: This narrative review evaluates pharmacogenomics (PGx), therapeutic drug monitoring (TDM), metabolomics/lipidomics, immune-inflammatory markers, proteomics, transcriptomics, epigenomics, microbiomics, and multi-omics machine learning according to their capacity to improve defined pharmacological decisions.

METHODS: Evidence was identified through structured PubMed/MEDLINE searches updated to 29 July 2026, targeted searches of ClinicalTrials.gov and the WHO International Clinical Trials Registry Platform, and backward and forward citation searching. The review was restricted to adult MDD and used author-assigned categories that distinguish prognostic, predictive, pharmacokinetic, and treatment-emergent monitoring markers and differentiate discovery, independent replication, external validation, and clinical utility. The article is a narrative Review, not a PRISMA systematic review; study selection, extraction, and translational classification were performed by one author without formal study-level risk-of-bias grading.

RESULTS: Most evidence derives from general adult MDD rather than prospectively defined DTD/TRD cohorts. Drug-specific, guideline-supported PGx and indication-specific TDM are the most clinically proximal molecular tools, but their value is bounded and depends on medication history, inhibitors and inducers, adherence, organ function, assay coverage, and phenoconversion. Commercial combinatorial PGx trials show small and sometimes nonpersistent clinical effects. Metabolomic, inflammatory, proteomic, transcriptomic, epigenomic, microbiomic, and integrated machine-learning studies identify plausible mechanisms and candidate predictors, but the majority remain discovery-stage or internally validated. Positive subgroup signals, including C-reactive protein-defined differential response, are counterbalanced by null prospective trials and inconsistent thresholds.

CONCLUSION: Current clinical application should remain limited to systematic medication and interaction review, drug-specific guideline-supported PGx, and indication-specific TDM. Dynamic omics layers should be treated as investigational until locked models are externally validated and prospective biomarker-guided strategies demonstrate incremental decision value, clinical benefit, feasibility, equity, and cost-effectiveness. The review proposes a future-state architecture and staged evidence-to-implementation framework for DTD/TRD.},
}

@article {pmid42756900,
year = {2026},
author = {Cheng, Y and Zhao, H and Lin, L and Chen, Y and Lin, H},
title = {Gut microbiota-host adaptive immune interactions in type 2 diabetes mellitus: mechanisms, disease progression, and microbiota-based therapeutic strategies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1934029},
pmid = {42756900},
issn = {1664-302X},
abstract = {Type 2 diabetes mellitus (T2DM) is a prevalent metabolic disorder whose development and progression are influenced not only by genetic susceptibility, obesity, and lifestyle-related factors but also by gut microbiota dysbiosis, chronic low-grade inflammation, and disruption of immunometabolic homeostasis. The gut microbiota regulates adaptive immune responses through diverse signals, including microbial structural components, metabolites, extracellular vesicles, and other secreted molecules. These microbial-derived signals modulate antigen presentation, T-cell differentiation, B-cell function, and IgA-mediated mucosal immunity, thereby influencing adaptive immune populations such as Th1 cells, Th17 cells, CD8[+] T cells, and regulatory T cells (Tregs). Conversely, the adaptive immune system can reshape microbial composition and functional outputs by regulating intestinal barrier integrity, mucosal immune homeostasis, and ecological niche stability, forming a dynamic and bidirectional gut microbiota-adaptive immunity interaction network. This reciprocal interaction persists throughout the progression from metabolic risk accumulation and insulin resistance to T2DM onset and diabetic complications, contributing to chronic low-grade inflammation, impaired insulin signaling, and pancreatic β-cell dysfunction. Unlike previous reviews that have primarily focused on gut microbiota dysbiosis, microbial metabolites, or innate immune regulation, this review highlights the bidirectional interactions between the gut microbiota and adaptive immunity as a central framework. We systematically summarize the underlying molecular mechanisms, dynamic disease evolution, and advances in microbiota-targeted therapeutic strategies. In recent years, dietary modulation, probiotics, prebiotics, synbiotics, postbiotics, fecal microbiota transplantation, and engineered microbiome-based therapies have emerged as potential approaches targeting the microbiota-immune axis. Among these strategies, dietary interventions and certain microbiota-based supplements have obtained preliminary clinical support, whereas fecal microbiota transplantation, engineered bacteria, and phage-based therapies remain under active investigation. However, clinical translation of microbiome-targeted therapies is still challenged by interindividual microbiota heterogeneity, insufficient standardization of interventions, uncertain long-term safety, and limited causal evidence. Future efforts should integrate microbial composition, functional metabolic profiles, adaptive immune signatures, and host metabolic states to achieve precise patient stratification and facilitate the development of personalized microbiome-based interventions. This review provides a conceptual framework for understanding immunometabolic mechanisms in T2DM and offers new perspectives for precision therapeutic strategies.},
}

@article {pmid42756901,
year = {2026},
author = {Salahi, A and El-Ghany, WAA},
title = {Gut microbial signatures in poultry under low-protein diets and lysine restriction: implications for precision nutrition.},
journal = {Veterinary and animal science},
volume = {34},
number = {},
pages = {100848},
pmid = {42756901},
issn = {2451-943X},
abstract = {Three key signatures - microbial, nutritional, and epigenetic - are pivotal in nutrigenomics, mediating poultry responses to nutritional signals, such as low-protein diets (LPDs) and lysine restriction (LR). These multidimensional signatures - encompassing bacterial, archaeal, and fungal taxonomy, functional genes, and metabolomic profiles (short-chain fatty acids; SCFAs) - orchestrate host metabolism, immunity, and feed conversion ratio (FCR). This PRISMA-ScR scoping review synthesizes multi-omics evidence showing that LPDs shift cecal fermentation toward saccharolytic pathways, enriching butyrate-producing taxa (Ruminococcaceae, Lachnospiraceae) while suppressing Proteobacteria and toxic proteolytic metabolites (ammonia, branched-chain fatty acids). LR elevates Actinobacteria/Synergistetes, triggers microbial nitrogen limitation, and reconfigures SCFA profiles through cross-feeding, thereby activating host nutrient sensors (mTOR downregulation, GCN2 upregulation) to prioritize immunity and FCR gains. Methanogenic archaea (Methanobrevibacter) fine-tune hydrogen economies, although diet-induced changes require deeper exploration. Key signatures forecast performance, featuring optimized Firmicutes/Bacteroidetes ratios and ureolytic genes (gdhA/glnA) as markers of protein resilience and profiles for breed-specific responses. SCFAs drive epigenetics (HDAC suppression, histone acetylation) and immunometabolism (Treg expansion, NF-κB dampening), bridging microbiome to host benefits via gut-liver interplay. Emerging applications span next-generation probiotics (NGPs) and live biotherapeutic products (LBPs), tailored from signature consortia (L. reuteri + B. velezensis) or archaeal agents, to sustain diet-induced states in antibiotic-free regimens. Major gaps persist in causal multi-omics validation, breed-specific responses, standardized baselines, and archaeal contributions. Integrating LPD/LR with tailored NGPs/LBPs promises precision nutrition strategies that enhance nitrogen utilization, reduce emissions, and improve welfare. Gnotobiotic, FMT, and AI trials are essential for translating microbial signatures into scalable flock-level precision management.},
}

@article {pmid42756918,
year = {2026},
author = {Davies, JT and Gely, Y and Yeramilli, V and Martin, C},
title = {Maternal and perinatal risk factors for necrotizing enterocolitis.},
journal = {World journal of pediatric surgery},
volume = {9},
number = {5},
pages = {e001205},
pmid = {42756918},
issn = {2516-5410},
abstract = {Necrotizing enterocolitis (NEC) remains among the most devastating complications of prematurity, carrying significant mortality and lifelong morbidity despite decades of mechanistic and translational research. Although NEC is classically framed as an inflammatory disease of intestinal immaturity, driven by microbial dysbiosis and exaggerated immune signaling, this model does not fully explain the uneven distribution of disease burden across infants, hospitals and communities. In this review, we reframe NEC within a broader maternal-perinatal systems context grounded in the Developmental Origins of Health and Disease (DOHaD) framework. This review synthesizes evidence linking maternal psychosocial stress to activation of the hypothalamic-pituitary-adrenal axis. This alters placental signaling and disrupts fetal gut development and microbiome establishment. This is further compounded by paternal stress-related epigenetic mechanisms, suboptimal maternal nutrition, poor metabolic health and environmental pollutants that disproportionately affect socioeconomically disadvantaged neighborhoods. These prenatal influences intersect with postnatal modifiers within neonatal intensive care units and health systems. Social and structural determinants of health further affect prenatal exposures and the delivery of neonatal care. This framework does not replace traditional pathogenesis models of NEC but rather contextualizes them within broader developmental and health systems. This perspective may help identify earlier targets for prevention while supporting more equitable and multidisciplinary approaches to reducing the burden of NEC.},
}

@article {pmid42757129,
year = {2026},
author = {Fan, K and Xu, Z and Sun, K and Chu, H},
title = {Optimizing rhizosphere metabolic circular economy toward sustainable ecosystems.},
journal = {Sustainable microbiology},
volume = {3},
number = {3},
pages = {qvag037},
pmid = {42757129},
issn = {2755-1970},
abstract = {The rhizosphere metabolic circular economy (RMCE) governs the exchange, reuse, and reconfiguration of metabolites at the root-soil interface. Building on traditional binary plant-microbe models, this perspective advances an expanded RMCE framework by integrating three additional interdependent dimensions that explain how rhizosphere metabolic processes persist over time, organize across space, and recover under environmental stress. First, the live-dead plant-microbe continuum enables metabolic persistence by incorporating microbial necromass and root residues into long-term carbon sequestration and nutrient regeneration. Second, spatial organization across rhizosphere microzones optimizes microscale metabolic interactions through niche heterogeneity. Third, adaptive restoration dynamically re-establishes disrupted metabolic networks through coordinated plant-microbiome stress responses. We further outline scenario-based management strategies to translate the RMCE insights into practical solutions, which necessitates multiple approaches targeting root exudate quality, microbial necromass dynamics, rhizosphere spatial architecture, and cross-kingdom signaling. Together, these advances redefine RMCE as a dynamically regulated, spatially structured, and ecologically complex system, providing a more comprehensive basis for its optimization in sustainable ecosystems.},
}

@article {pmid42757169,
year = {2026},
author = {Guhanraj, R},
title = {Targeting cancer hallmarks with microbiome-derived bacteriocins and postbiotics: molecular mechanisms and translational opportunities in oncology.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1899156},
pmid = {42757169},
issn = {2234-943X},
abstract = {BACKGROUND: The human microbiome is an abundant reservoir of bioactive molecules with considerable therapeutic potential in oncology. Among these microbial products, bacteriocins and other postbiotic metabolites have emerged as promising anticancer agents due to their diverse biological activities and ability to modulate multiple cancer-related pathways. Growing evidence suggests that microbiome-derived compounds may provide novel opportunities for the development of safer and more targeted cancer therapeutics.

OBJECTIVES: This review aims to comprehensively evaluate the current knowledge on bacteriocins and postbiotic metabolites as anticancer agents, highlighting their sources, structural and functional properties, mechanisms of action, computational-assisted discovery approaches, nanotechnology-based delivery systems, and challenges associated with clinical translation.

METHODS: A critical analysis of the available literature was conducted to summarize the biological characteristics of bacteriocin-producing microorganisms, the classification and mechanisms of bacteriocins, and the anticancer activities of major postbiotic metabolites. Recent advances in molecular docking, molecular dynamics simulations, systems biology, artificial intelligence, and nanotechnology-based drug delivery platforms were also examined to assess their contributions to therapeutic development.

RESULTS: Bacteriocins exhibit anticancer effects through multiple mechanisms, including disruption of cancer cell membranes, induction of apoptosis, regulation of oxidative stress, inhibition of cell proliferation, suppression of angiogenesis and metastasis, epigenetic modulation, and enhancement of antitumor immune responses. In addition, postbiotic metabolites such as short-chain fatty acids, indole derivatives, reuterin, and microbial exopolysaccharides contribute to tumour suppression and modulation of host-microbe interactions. Computational approaches have accelerated the identification and optimization of bacteriocin-derived therapeutic candidates, while nanotechnology-based delivery systems have improved their stability, bioavailability, and tumour-targeting capabilities. Nevertheless, challenges including limited clinical evidence, non-standardized experimental methodologies, poor pharmacokinetic properties, manufacturing constraints, and regulatory barriers remain significant obstacles to clinical implementation.

CONCLUSION: Bacteriocins and postbiotic metabolites represent a versatile and promising class of microbiome-derived anticancer agents with substantial potential for precision oncology. The integration of microbiome science, synthetic biology, computational drug discovery, and advanced drug delivery technologies is expected to facilitate the translation of these natural compounds into clinically effective cancer therapeutics. Future research should focus on mechanistic validation, large-scale production, pharmacological optimization, and well-designed clinical studies to accelerate their development and therapeutic application.},
}

@article {pmid42757275,
year = {2026},
author = {Li, S and Wang, S and Ren, Y and Yan, J},
title = {Chemotherapy-Induced Remodeling of the Gut Microbiota-Inflammation Axis: Implications for the Course of Bipolar Disorder.},
journal = {Journal of multidisciplinary healthcare},
volume = {19},
number = {},
pages = {637471},
pmid = {42757275},
issn = {1178-2390},
abstract = {There is growing evidence that bipolar disorder, BD and cancer share several biological features, including immune dysregulation, gut microbiota alterations, and chronic inflammation. Chemotherapy remains a mainstay of cancer treatment but can substantially alter the gut microbial ecosystem, impair intestinal barrier integrity, and contribute to systemic inflammation. However, little research has been done on whether these changes brought on by chemotherapy affect how BD develops clinically. This review summarizes the mechanisms through which chemotherapy may modify the gut microbiota-inflammation axis, along with how these changes may impact BD via the microbiota-gut-brain axis. We discuss how intestinal barrier failure, microbial metabolite production, microbial composition, and inflammatory signaling pathways-such as the LPS-TLR4/NF-κB axis and NLRP3 inflammasome activation-are affected by chemotherapeutic drugs. We also investigate the role of gut-derived inflammatory responses in neuroinflammation, dysregulation of the hypothalamic-pituitary-adrenal,HPA axis, impaired neuroplasticity, neurotransmitter imbalance, and cognitive dysfunction, all of which may contribute to mood instability, treatment resistance, and neuroprogression in BD. We also evaluate developing microbiome-targeted therapies, such as probiotics, fecal microbiota transplantation, and dietary modification, and explore the possible therapeutic consequences of chemotherapy-induced microbiota remodeling for patients with concomitant cancer and BD. Taken together, the available evidence supports the possibility that chemotherapy-induced modification of the gut microbiota-inflammation axis may contribute to the clinical course of BD. This integrated mechanistic paradigm offers a potential platform for future translational research and the creation of tailored treatment approaches for patients with comorbid cancer and BD, despite the lack of direct clinical proof. This narrative review summarizes the current evidence linking chemotherapy-induced gut dysbiosis and inflammatory responses to the clinical course of bipolar disorder and discusses their potential implications for integrated therapeutic strategies.},
}

@article {pmid42757563,
year = {2026},
author = {Bravo, M and Herrera Díaz, LD and Bravo Santillana, C and Martín Terroso, R and Simón, I and Cerrato, R},
title = {Postbiotic Intervention Improves Bowel Function and Promotes Systemic Health in Institutionalized Older Adults.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {18},
pages = {e70610},
doi = {10.1002/mnfr.70610},
pmid = {42757563},
issn = {1613-4133},
mesh = {Humans ; Aged ; Male ; Double-Blind Method ; *Gastrointestinal Microbiome/drug effects ; Female ; Aged, 80 and over ; Inflammation ; *Probiotics ; Dysbiosis ; },
abstract = {Postbiotic interventions represent a promising strategy to modulate gut health, but clinical evidence in older adults is limited. This study aimed to evaluate the effects of a postbiotic supplement consisting of inactivated bacterial cells on bowel function, systemic inflammation, and gut microbiota composition in institutionalized older adults. In this randomized, double-blind intervention study, 48 older adults received either postbiotic or placebo for 8 weeks. Daily assessment of gastrointestinal manifestations, bowel movements, and laxative use were collected, alongside pre- and post-intervention hematological and clinical biochemical assessments. Postbiotic supplementation improved bowel regularity, reduced diarrheal episodes, and decreased laxative reliance, effects that paralleled reductions in systemic inflammatory markers and improvements in red blood cell parameters. These clinical and hematological changes were accompanied by a more favorable gut microbiota profile, characterized by an increase in bacterial groups associated with anti-inflammatory effects in the postbiotic group and of taxa linked to dysbiosis in the placebo group. Our findings suggest that postbiotic supplementation in institutionalized older adults promotes beneficial shifts in gut microbiota, which are associated with reduced systemic low-grade inflammation and consequent improvements in bowel function and inflammation-related anemia, indicating an integrated microbiota-mediated mechanism supporting gut and systemic health.},
}

Humans
Aged
Male
Double-Blind Method
*Gastrointestinal Microbiome/drug effects
Female
Aged, 80 and over
Inflammation
*Probiotics
Dysbiosis

@article {pmid42757589,
year = {2026},
author = {Austin, G and Ferguson, JJA and Eslick, S and Garg, ML and Martins, R},
title = {Plant-based diets, cognitive function, and Alzheimer's disease.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo01946c},
pmid = {42757589},
issn = {2042-650X},
abstract = {Background: Alzheimer's disease (AD) represents 60-70% of global dementia cases, with up to 45% attributed to modifiable risk factors. Plant-based diets (PBDs) are increasingly recognised for their potential benefits on the gut microbiome, cardiometabolic risk factors and prevention of neurodegenerative disorders. This narrative review synthesises PBDs association with cognitive decline and AD risk. Methods: This review aims to summarise evidence from observational and interventional studies examining vegan, vegetarian, pesco-vegetarian, semi-vegetarian dietary patterns, and PBD indices in relation to cognitive function, incident dementia, AD biomarkers, and neuroimaging outcomes. Results: Long-term observational studies suggest greater adherence to vegan, vegetarian and healthy PBD indexs are associated with lower risk of cognitive decline and dementia, while higher intake of red and processed meat is linked to increased risk. Pesco-vegetarian dietary patterns and higher fish intake appear to confer benefits in memory tests and reduced risk of all-cause dementia, although research is limited. Mechanistically, PBDs are rich in unsaturated fats, fibre, polyphenols and low in saturated fats, which contribute to improving lipid profiles, glycaemic control, endothelial function, and favourable gut-derived metabolites, thereby reducing cardiometabolic burden that is known to accelerate early-stage AD pathophysiology. However, nutritional considerations, including potential deficiencies in vitamin B12 and long-chain omega-3 fatty acids, require consideration when following a PBD. Conclusions: Current evidence suggests PBDs may support cognitive health and reduce the risk of dementia including AD through vascular and metabolic pathways, though long-term interventional studies incorporating biomarkers and neuroimaging are needed to clarify effects and optimise dietary recommendations for AD prevention.},
}

@article {pmid42757781,
year = {2026},
author = {Jappe, U and Risha, MA and Agache, I and Bachert, C and Bröker, B and Castagnoli, R and Gadermaier, G and Goodman, RE and Guemari, A and Hilger, C and Jacquet, A and Kespohl, S and Klimek, L and Kuehn, A and Lidholm, J and Mahler, V and Ollert, M and Platts-Mills, TA and Raulf, M and Schmid-Grendelmeier, P and Schmiedeke, F and van Hage, M and Vitte, J and Zakzuk, J and Pomés, A},
title = {IgE-Binding Bacterial Components Not Yet Documented in the Allergen Databases and Their Allergenic Mechanisms: An EAACI Position Paper.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70510},
pmid = {42757781},
issn = {1398-9995},
support = {40605//European Academy of Allergy and Clinical Immunology/ ; },
abstract = {Among bacteria that are associated with the development and/or exacerbation of allergic/atopic diseases, several have been described to produce IgE-binding components. However, only one bacterial protein, Bac s 1, is currently listed in the official database of the World Health Organization/International Union of Immunological Societies (WHO/IUIS) Allergen Nomenclature Sub-Committee. The aim of this position paper was to identify potential bacterial allergens and their reported clinical relevance in the published literature and consider candidates for the Allergen Nomenclature database. PubMed and the WHO/IUIS Allergen Nomenclature database were searched up to October 2025. Consensus was obtained during task force meetings and by a written commentary process. Sixty-six IgE-binding components in 20 different species of bacteria were found, most associated with clinical symptoms. Allergen candidates include staphylococcal superantigens, bacterial enzymes, and components from two Chlamydia species, some of which are potential marker allergens for disease severity. The results point to long-neglected evidence of "bacterial allergy" that in certain cases may be induced by unconventional mechanisms. Diseases that are currently considered non-allergic might be re-classified as allergic if these IgE-binding components are recognized as allergens and used for diagnosis in the future.},
}

@article {pmid42757843,
year = {2026},
author = {Taillandier, P and Clément, K and Le Roy, T},
title = {Complete genome sequence of Subdoligranulum sp. strain DSM 23681 isolated from the cecum of a broiler chicken.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0061926},
doi = {10.1128/mra.00619-26},
pmid = {42757843},
issn = {2576-098X},
abstract = {We report the complete genome sequence of strain ic1395 (DSM 23681), an anaerobe previously isolated from the cecum of a broiler chicken and affiliated with the Subdoligranulum genus. Its average nucleotide identity with the closest species with standing in nomenclature indicates that this strain represents a divergent and distinct lineage.},
}

@article {pmid42758012,
year = {2026},
author = {Liu, JCW and Gorbovskaya, I and Zhang, AY and Hahn, MK and De Palma, G and Müller, DJ},
title = {Investigation of the Gut Microbiome in Treatment-Resistant Schizophrenia Compared to Healthy Controls: A Cross-Sectional Pilot Study: Étude du microbiome intestinal chez les patients atteints de schizophrénie résistante au traitement par rapport aux témoins sains : étude pilote transversale.},
journal = {Canadian journal of psychiatry. Revue canadienne de psychiatrie},
volume = {},
number = {},
pages = {7067437261487782},
doi = {10.1177/07067437261487782},
pmid = {42758012},
issn = {1497-0015},
abstract = {BackgroundSchizophrenia (SCZ) is a debilitating disorder affecting approximately 1% of the Canadian population and remains a major contributor to disease burden and disability. Up to one-third of individuals with SCZ are affected by treatment-resistant SCZ (TRS). Clozapine remains the most effective treatment for TRS. However, its use is limited by serious metabolic and immune-related side effects. The gut microbiome may be a potential contributor to both SCZ pathology and antipsychotic-induced side effects, though studies examining this in the clozapine-treated TRS population remain limited.MethodsThis cross-sectional case-control study compared the gut microbiome composition of 25 TRS patients receiving long-term clozapine treatment to 25 healthy controls (HCs) matched for age, sex, body mass index, and smoking status. Participants provided fecal samples and completed assessments of psychiatric symptoms, eating behaviors, dietary intake, and metabolic measures. Fecal microbiome composition and predicted function were assessed using 16S rRNA gene sequencing (v3 region).ResultsIndividuals with TRS being treated with clozapine presented with a distinct microbiome in comparison to HC, including reduced microbial diversity. Taxonomic analyses revealed reduced relative abundance of Firmicutes, while elevated relative abundance of Eggerthella spp., Mucispirillum spp., and unclassified species within the order SHA-98 (class Clostridia). Exploratory analyses also identified nominal associations between select microbial features and clinical measures, including Positive and Negative Syndrome Scale (PANSS) scores and gastrointestinal symptoms. Predicted functional pathway analysis suggested alterations in microbial metabolic potential consistent with a metabolically stressed, pro-inflammatory microbiome.ConclusionsIndividuals with clozapine-treated TRS demonstrate differences in gut microbiome composition compared to HC and are predicted to have some functional consequences relating to metabolic potential. These findings remain exploratory but contribute to a limited but growing body of literature in this clinically relevant population and provide a basis for longitudinal studies with appropriate comparator groups to better characterize these relationships and assess their clinical relevance.},
}

@article {pmid42758297,
year = {2026},
author = {Xu, H and Zhong, T and Li, J},
title = {The link of oral microbiome diversity to stroke risk: Evidence from the National Cohort Study in the United States.},
journal = {The International journal of neuroscience},
volume = {},
number = {},
pages = {1-35},
doi = {10.1080/00207454.2026.2736054},
pmid = {42758297},
issn = {1563-5279},
abstract = {OBJECTIVE: To assess whether oral microbiome diversity and periodontal health are independently associated with stroke prevalence in a U.S. adult cohort, with implications for risk stratification in physical medicine and rehabilitation.

METHODS: We analyzed cross-sectional data from 4,438 adults in the National Health and Nutrition Examination Survey (NHANES) 2009-2012, using survey-weighted logistic regression to evaluate associations between stroke and oral microbiome β-diversity (unweighted UniFrac), α-diversity (Shannon, Simpson), and clinical periodontal measures (probing depth, clinical attachment loss, and tooth count), adjusting for age, sex, race/ethnicity, education, income, smoking, alcohol consumption, body mass index, and diabetes.

RESULTS: In crude models, each 1-mm increase in mean probing depth was associated with higher stroke odds (odds ratio [OR] = 1.89, 95% confidence interval [CI] = 1.39-2.56), as was each 1-mm increase in clinical attachment loss (OR = 1.50, 95% CI = 1.32-1.71); each additional tooth was associated with lower odds (OR = 0.91, 95% CI = 0.88-0.94). After stepwise adjustment, attachment loss (OR = 1.23, 95% CI = 1.04-1.46; P = 0.017) and tooth count (OR = 0.96, 95% CI = 0.92-0.99; P = 0.024) remained significant, whereas probing depth did not (OR = 1.30, 95% CI = 0.90-1.88; P = 0.156). A threshold effect was observed at approximately 1.46 mm for probing depth. β-Diversity clusters did not differ in stroke prevalence after adjustment (global P = 0.61), and neither α-diversity index was significant in the stepwise- or fully-adjusted models (Shannon fully-adjusted OR = 1.29, 95% CI = 0.97-1.72; P = 0.081). Periodontal associations were consistent across sex and age strata; the non-significant findings in younger participants were attributable to limited statistical power.

CONCLUSION: Clinical periodontal measures, particularly attachment loss and tooth count, were associated with stroke prevalence independently of traditional cardiovascular risk factors, whereas oral microbiome diversity indices were not. These measures may serve as readily accessible markers for refining stroke risk assessment. The cross-sectional design precludes causal inference, and findings require validation in prospective cohorts with adjudicated stroke outcomes and metagenomic profiling before clinical translation. Nevertheless, these results support integrating oral health assessment into routine stroke risk evaluation and highlight periodontal inflammation as a potentially modifiable contributor to cerebrovascular disease.},
}

@article {pmid42758428,
year = {2026},
author = {Kwiatkowska, M and Walczak, Ł and Twarowski, B and Pawłaszek, M and Rokosz-Mierzwa, J and Lejman, M},
title = {The Impact of Cancer Treatment On Oral Structures and the Facial Part of the Skull - Implications for Prosthetic Treatment and Oncological Risk.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42758428},
issn = {1534-6269},
mesh = {Humans ; Osseointegration ; *Dental Implants/adverse effects ; *Neoplasms/therapy ; *Skull/pathology/drug effects ; *Mouth/microbiology/drug effects/pathology ; },
abstract = {PURPOSE OF REVIEW: This study aims to identify complications and difficulties in oncology patients undergoing dental implant osseointegration, considering the impact of treatment on the microarchitecture of the craniofacial region, the oral cavity microbiome, and oral cavity inflammation.

RECENT FINDINGS: Surgical resection, radiotherapy, chemotherapy, and targeted therapies significantly affect the condition of bones, mucous membranes, and soft tissues, and consequently the possibilities and limitations of prosthetic rehabilitation. Chemotherapy significantly affects calcium and phosphorus metabolism. It has been observed that there is an increased risk of fractures, as well as changes in their microarchitecture, and a reduction in the resorption of biomaterials after transplantation has been observed, impairing bone repair in critical defects. These changes may also affect the processes of osteogenesis and osteoclastogenesis and lead to osteoblast cell apoptosis. The impact of therapy on the oral microbiota, as well as on increased inflammation and oxidative stress in the oral cavity, is also significant. These changes can lead to difficulties in implant osteointegration, as well as opportunistic infections, which reduce the patient's prognosis for implant acceptance. Complications after implantation in oncology patients may include inflammation of the mucosa around the implant and inflammation of the tissues around the implant, soft tissue ulceration, marginal bone loss, and partial loss of osseointegration. Due to the complexity of the processes occurring in the oral cavity of oncology patients, prosthetic treatment planning should be interdisciplinary and involve an oncologist, surgeon, prosthodontist, and conservative dentist.},
}

Humans
Osseointegration
*Dental Implants/adverse effects
*Neoplasms/therapy
*Skull/pathology/drug effects
*Mouth/microbiology/drug effects/pathology

@article {pmid42758523,
year = {2026},
author = {Lan, G and Li, X and Lu, Z and Zhang, Y and Feng, F and Liu, J and Wu, W and Liu, J and Zhou, Y and Gu, J and Ma, R and Qi, D},
title = {Gut Microbiome Functional Reprogramming Reflects Divergent Social Strategies in a Wild Primate.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70185},
pmid = {42758523},
issn = {1749-4877},
support = {2025JZG01//Foundation for Non-Invasive Research on Golden Snub-Nosed Monkeys in Baihe Nature Reserve/ ; CAZG2025C13//Chengdu Research Base of Giant Panda Breeding/ ; 32570615//National Natural Science Foundation of China/ ; },
abstract = {The gut microbiome is a critical interface between host physiology and environmental challenges, yet its role in mediating behavioral strategies in socially complex mammals remains unclear. Using metagenomic sequencing of wild golden snub-nosed monkeys (Rhinopithecus roxellana), we investigated how social status (one-male unit [OMU] leaders vs. all-male unit [AMU] individuals) and seasonal variation (winter-spring [WS] and summer-autumn [SA]) shape gut microbial structure and function. We found that seasonal shifts drive primary microbial restructuring, but social status exerts a strong influence, particularly during the SA mating season. OMU leaders maintained stable microbial communities enriched in energy conservation and cellular maintenance pathways including methane metabolism and peptidoglycan biosynthesis. In contrast, AMU individuals exhibited highly plastic microbiomes potentially suited for competition, with enhanced functions in environmental sensing (e.g., flagellar assembly and two-component systems) and nitrogen metabolism. AMU gut microbiomes also showed reduced diversity in SA, indicating specialization for competitive readiness. These results demonstrate that the gut microbiome is functionally compartmentalized by social status, providing distinct metabolic toolkits that align with divergent behavioral strategies-investment in unit fitness for OMU leaders versus risk-taking for AMU individuals. Our study reveals the gut microbiome is closely associated with social adaptation in primate societies, serving as a dynamic indicator of divergent behavioral strategies.},
}

@article {pmid42523320,
year = {2026},
author = {Morabbi, SM and Bhowmik, N and Sutherland, S and Wylie, EA and Decker, RS and Daerwish, AA and Pérez, MP and Pascual, E and Lutter, EI and Philmus, B and Stubbendieck, RM},
title = {Differential Metabolite Production Underlies Disruption of the Cystic Fibrosis Airway Microbiota by Pathogens.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42523320},
issn = {2692-8205},
abstract = {Cystic fibrosis (CF) is a multisystem disease characterized by the accumulation of mucus in the airways that promotes pathogen colonization, leading to respiratory exacerbations, lung failure, and death. Culture-independent approaches have revealed that the CF airway harbors a complex microbiota, including opportunistic pathogens and bacteria that colonize the oropharynx. Here, we reanalyzed 5,260 16S rRNA gene microbiota datasets to infer ecological associations between members of the CF microbiota. We determined that pathogens are more likely to proliferate and dominate when present, while oropharyngeal bacteria are more likely to form persistent communities. Further, we found higher diversity and increasing numbers of inferred interactions were positively associated with lung function. In contrast, pathogens were negatively associated both with each other and with oropharyngeal bacteria, suggesting that they may disrupt the microbiota. To validate these predictions, we cultured 1,597 bacterial isolates from 96 people with CF and performed 12,542 coculture assays against eight representative CF pathogenic and oropharyngeal bacteria. 23% of these interactions resulted in growth inhibition. While Pseudomonas isolates were, on average, the most inhibitory, we observed variable activity among isolates. We then confirmed that Pseudomonas aeruginosa isolates, even those from the same donor and timepoint, exhibited significant differences in their metabolome and bioactivity profiles that correlated with acquisition of mutations. Together, our results suggest that pathogens may disrupt the CF microbiota and bloom in part through differential metabolite production. Furthermore, these data highlight that characterizing multiple isolates is necessary to capture the full landscape of chemically mediated interactions within microbial communities.},
}

@article {pmid42538473,
year = {2026},
author = {Voolstra, CR and Hermann, RJ and Stibor, H and Keller, A and Becks, L},
title = {Timescale mismatch: redefining ecological opportunity for evolution in the Anthropocene.},
journal = {The EMBO journal},
volume = {45},
number = {18},
pages = {6359-6366},
pmid = {42538473},
issn = {1460-2075},
support = {9196//Gordon and Betty Moore Foundation (GBMF)/ ; CAP-2024-1692//CORDAP/ ; },
abstract = {The Anthropocene is defined by unprecedented biodiversity loss, but also by a profound mismatch of timescales: environmental change unfolds orders of magnitude faster than response times for most ecological and evolutionary processes. Rapid perturbations create transient ecological opportunities, yet these windows are often too brief for diversification to manifest. The central challenge to understanding biodiversity change in the Anthropocene is not whether ecological opportunity—the availability of novel resources or niches that relax competition—arises, but whether it persists long enough for evolution to act. Microbiome-mediated as well as behavioral and physiological plasticity can buffer organisms against short-term instability and enable swift niche shifts, but such flexibility is reversible, typically non-heritable, and fragile under sustained disturbance. Without enduring selection or sufficient genetic variation, flexibility cannot substitute for evolution. The classical framework of ecological opportunity—conceived for stable environments and gradual change—is therefore inadequate. Diversification, i.e., the rebuilding of biodiversity in the Anthropocene, demands a time-scale integrated framework that unites evolutionary, ecological, and microbiome dynamics to pinpoint when fleeting opportunities can be stabilized for lasting diversification.},
}

@article {pmid42747964,
year = {2026},
author = {Chudhary, A and Wang, X},
title = {Molecular mimicry and functional convergence of bacterial proteins in host-microbe interactions.},
journal = {Cell reports},
volume = {45},
number = {9},
pages = {117983},
doi = {10.1016/j.celrep.2026.117983},
pmid = {42747964},
issn = {2211-1247},
abstract = {Bacterial proteins modulate host immunity through diverse molecular strategies that are often broadly described as molecular mimicry. However, inconsistent terminology has obscured distinctions between genuine host-like interactions and other forms of host-directed immune modulation. We propose an operational framework that classifies bacterial proteins into four mechanistic categories: molecular mimicry, mimic-like behavior, functional convergence, and pathway interference. The framework prioritizes explicit criteria, including host-target engagement, interaction-interface similarity, functional equivalence, predominant molecular mechanism, and strength of supporting evidence, rather than immune outcome alone. Representative bacterial effectors are discussed alongside their evolutionary origins, computational prediction, experimental validation, and emerging technologies for mechanistic investigation. By separating evolutionary processes from molecular action and applying evidence-based classification criteria, this review clarifies ambiguous terminology and provides a consistent conceptual foundation for interpreting bacterial immune modulation. The framework may also guide future mechanistic studies, comparative analyses, and translational research across diverse pathogenic and commensal host-microbe interaction systems.},
}

@article {pmid42747972,
year = {2026},
author = {Sokay, A and Burke, S and Iatan, M and Byrne, S and Verdon, S and Crupper, J and Hanoudi, J and Miramontes, IM and Bout, N and Dimakos, M and Halpenny, L and White, M and McCallion, N and Curley, A and Byrne, S and O'Mahony, L and Hourihane, J},
title = {Early-life exposures in infants born during and after the COVID-19 pandemic: A comparative prospective observational study of the CORAL and FLORAL birth cohorts.},
journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology},
volume = {37},
number = {9},
pages = {e70471},
pmid = {42747972},
issn = {1399-3038},
support = {23/FFP-A/12076//Research Ireland Frontiers for the Future Programme/ ; },
mesh = {Humans ; Female ; *COVID-19/epidemiology ; Infant ; Prospective Studies ; Male ; *SARS-CoV-2 ; Infant, Newborn ; Birth Cohort ; Surveys and Questionnaires ; Pandemics ; },
abstract = {BACKGROUND: The CORAL 2020 birth cohort examined health outcomes and feeding practises in infants born during the COVID-19 pandemic, a period of reduced social mixing and altered healthcare utilization during a critical period of immune development. The 2025 FLORAL (FoLlow-on from CORAL) cohort was established to determine whether findings from the CORAL cohort were specific to the pandemic period or reflected broader evolving trends.

METHODS: FLORAL is a prospective observational birth cohort study recruiting term infants born between March and May 2025 across three Dublin maternity hospitals using almost identical methodology to the CORAL cohort. Assessments included parent-completed questionnaires and in-patient study visits. Outcomes at 6 months were compared between FLORAL and CORAL cohorts to examine differences in early-life exposures.

RESULTS: Of 574 infants whose parents provided consent, 485 completed the enrolment questionnaire. At 6 months, 442 participants completed the six-month follow-up questionnaire and 440 attended the in-person study visit. Demographic characteristics were broadly comparable between cohorts. FLORAL infants had numerically higher rates of reported infections (33.3% vs. 28%, p = .12), hospitalization (13.1% vs. 5.1%, p < .001), and antibiotic exposure (13.1% vs. 6.2%, p = .002) compared with CORAL infants. However, the introduction of allergenic foods occurred significantly more frequently in FLORAL, with peanut introduced in 44% of infants compared with 13.6% in CORAL (p < .0001).

CONCLUSION: Compared with pandemic-born infants, post-pandemic infants experienced increased infection-related healthcare utilization and increased antibiotic exposure, alongside sustained high breastfeeding rates and substantially earlier allergen introduction. These may influence microbiome development and later atopic outcomes.},
}

Humans
Female
*COVID-19/epidemiology
Infant
Prospective Studies
Male
*SARS-CoV-2
Infant, Newborn
Birth Cohort
Surveys and Questionnaires
Pandemics

@article {pmid42748030,
year = {2026},
author = {Gupta, AK and Liddy, A and Saunte, DML and Piguet, V and Jemec, G},
title = {The Skin and Gut Microbiome in Hidradenitis Suppurativa.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1},
doi = {10.1159/drm/ackag018},
pmid = {42748030},
issn = {1421-9832},
abstract = {Recent evidence indicates that both the bacterial composition of the skin and gut microbiota may contribute to the pathogenesis and progression of hidradenitis suppurativa (HS). Several studies have identified alterations in the skin bacterial microbiota, including an increased abundance of anaerobic taxa such as Prevotella spp. and Porphyromonas spp., alongside a reduction in commensal species like Cutibacterium spp., changes that may promote chronic inflammation and biofilm formation. Comparative analyses of lesional versus non-lesional skin have also revealed enrichment of bacterial pathways related to cell growth, DNA replication, and mismatch repair, suggesting enhanced microbial proliferation within HS lesions. Emerging evidence further suggests the presence of bacterial gut dysbiosis in HS, with some studies reporting reduced microbial diversity and lower abundance of protective genera Ruminococcaceae, and Lachnospiraceae families. Efforts to modulate the skin and gut microbiota in HS are underway, exploring approaches such as dietary modification, antibiotic usage, and probiotic supplementation. Moreover, comorbid conditions frequently associated with HS appear to influence disease severity and may mediate the relationship between microbial imbalance and systemic inflammation. Despite these insights, current research remains fragmented, characterized by small sample sizes, heterogeneous study designs, and a scarcity of robust interventional data.},
}

@article {pmid42748297,
year = {2026},
author = {Shcherbina, M and Potapova, L and Lipko, O and Shcherbina, L and Chekhunova, A and Mertsalova, O},
title = {The analysis of cervicovaginal microbiota and immune mediators in patients with adenomyosis.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {7},
pages = {1493-1499},
doi = {10.36740/WLek/218754},
pmid = {42748297},
issn = {0043-5147},
mesh = {Humans ; Female ; *Adenomyosis/microbiology/immunology ; *Vagina/microbiology/immunology ; Adult ; *Microbiota ; *Cervix Uteri/microbiology ; beta-Defensins ; Cytokines ; Middle Aged ; },
abstract = {OBJECTIVE: Aim: To determine and characterise changes associated with microbial, inflammatory and immune factors in patients with adenomyosis.

PATIENTS AND METHODS: Materials and Methods: 115 female patients were enrolled in the study, including 85 patients with adenomyosis and 30 healthy individuals. Vaginal cleanliness was assessed by collecting vaginal samples and plating on solid bacterial agar. Urogenital infections were determined by the PCR analysis of the cervicovaginal samples. The immunological characterisation was performed using enzyme immunoassay to analyse cervicovaginal lavage for β-defensin-2 and a defined set of cytokines. Antibody titers were quantified in patients' serum using nephelometry.

RESULTS: Results: Patients with adenomyosis displayed disrupted cervicovaginal microflora that was characterised by elevated levels of pro-inflammatory cytokines and antimicrobial peptide β-defensin-2. Serum analysis of patients with adenomyosis revealed higher concentration of IgG, IgM and IgA antibodies compared to healthy control groups.

CONCLUSION: Conclusions: Analysis of inflammatory and immunological parameters in patients with adenomyosis revealed distinct features of the pathophysiology of adenomyosis. Specifically, patients with adenomyosis had disrupted cervicovaginal microflora with higher prevalence of anaerobic species. Furthermore, patients with adenomyosis had elevated levels of pro-inflammatory cytokines and interleukins in cervicovaginal lavage, and higher levels of IgG, IgM and IgA antibody serum titres. The analysis presented in the paper represents an important step towards determining precise diagnostic parameters and effective therapies to treat adenomyosis.},
}

Humans
Female
*Adenomyosis/microbiology/immunology
*Vagina/microbiology/immunology
Adult
*Microbiota
*Cervix Uteri/microbiology
beta-Defensins
Cytokines
Middle Aged

@article {pmid42748564,
year = {2026},
author = {Zhang, F and Wang, Y and Qian, J and Li, S and Deng, X and Lu, M and Liu, Y and Yang, X and Zhang, J and Ren, Z and Yang, X},
title = {Gut microbial community assembly exhibits compartment-specific responses to selection for high body weight in female chickens.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107712},
doi = {10.1016/j.psj.2026.107712},
pmid = {42748564},
issn = {1525-3171},
abstract = {Conventional poultry breeding primarily targets host growth traits, yet breeding may also reshape the gut microbiota through host-microbe interactions. Given the spatial heterogeneity of the chicken gastrointestinal tract, whether divergent selection for body weight is associated with compartment-specific microbial assembly and differences in the digestive ecosystem remains unclear. Here, using female primitive line and a high body weight (HBW) selected line, we systematically characterized differences in host gastrointestinal traits and gut microbial ecology associated with divergent selection history. Significant differences in gut morphology and local environmental conditions were observed between the two lines, together with region-specific shifts in microbial community assembly. Specifically, crop weight was greater and microbial assembly exhibited greater stochasticity in the HBW line, potentially reflecting differences in feeding-related gastrointestinal dynamics. In contrast, the small intestine displayed improved villus morphology and altered microbial assembly patterns, accompanied by enrichment of potentially beneficial taxa associated with nutrient utilization, including Monoglobus in the duodenum and Blautia in the ileum, indicating coordinated changes in host intestinal development and microbial ecological adaptation. The cecal community showed relatively stable assembly patterns but was enriched in metabolically relevant taxa such as Lachnospiraceae and Faecalibacterium, together with differences in predicted functional potential related to nutrient metabolism. Overall, this study shows that the HBW line is associated with distinct, compartment-specific patterns of gut microbial assembly, providing a conceptual framework for considering the gut microbiota in poultry breeding strategies.},
}

@article {pmid42748616,
year = {2026},
author = {Hu, L and Mu, X and Guo, Q and Tong, J and Jiang, J and Liu, Y},
title = {Probiotic cells-encapsulated electrospun scaffolds accelerate diabetic wound healingviasynergistic anti-infection activity and skin microbiome modulation.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {269},
number = {},
pages = {116188},
doi = {10.1016/j.colsurfb.2026.116188},
pmid = {42748616},
issn = {1873-4367},
abstract = {Diabetic wound healing is often hindered by persistent pathogenic infections and associated skin microbiome dysbiosis. The efficacy of conventional antibiotic drugs is significantly compromised by increasing drug resistance and further disruption of commensal microbiota. In this study, a probiotic-loaded, dry-state electrospun scaffold, Gel@LRNF@PLA, is developed for dual-functional diabetic wound healing. By maintaining probiotic viability while enabling localized antibacterial and microbiome-regulatory effects, the dressing exhibits potent activity against both planktonic Pseudomonas aeruginosa and its biofilms. Moreover, it restores the balance of skin microbiota by suppressing opportunistic pathogens and enriching beneficial commensal bacteria, which synergistically promotes the healing of diabetic infected wounds. This approach not only offers a new structure for living cell-based wound dressings but also provides mechanistic insight into the therapeutic efficacy of living probiotics in treating diabetic wound infections.},
}

@article {pmid42748815,
year = {2026},
author = {Sala-Navarro, AC and Casado-Coy, N and Campos-Castro, A and Algora, C and Aguilar-Santana, E and Zhai, K and Alday, JG and Armas, C and Bueno, CG and Calvo, L and Carmona-Yáñez, MD and Centenaro, G and Dashevskaya, S and Humia, JD and Pereiras, AR and de Guevara, ML and Felipe-Lucia, MR and Fernández-Alonso, MJ and García-Palacios, P and Chamizo, S and de la Riva, EG and Jiménez-Prieto, B and Jiménez, JJ and Leo, M and López-Velasco, A and Lorenzo, C and Lucas-Borja, ME and Pérez-López, J and Plaza-Álvarez, PA and Prieto, I and Terrones, A and Torres, A and Martos-Maestre, AL and Melián, JAH and Ferraz, UÁ and García, MJS and Costa, J and García, E and Figueira, D and Bastida, F and Delgado-Baquerizo, M and Soliveres, S and Beltrán-Sanahuja, A and Sanz-Lazaro, C},
title = {Urban land use and management drive soil pollution across urban and nearby natural ecosystems in the Iberian Peninsula.},
journal = {Journal of hazardous materials},
volume = {517},
number = {},
pages = {143215},
doi = {10.1016/j.jhazmat.2026.143215},
pmid = {42748815},
issn = {1873-3336},
abstract = {Cities concentrate most of the world's population and human activities, generating pollution that threatens ecosystem functioning and human well-being. Yet, the relative importance of different drivers shaping urban pollution and the spatial distribution of multiple contaminants across cities remain poorly understood. Here, we conducted a standardized survey in 250 plots across 51 cities in the Iberian Peninsula to quantify heavy metals, pesticides, macrolitter and microplastics. We sampled four urban greenspace types (parks, golf courses, urban farms, roundabouts) and nearby natural areas to link contaminants with soil microbiome structure and functioning. Urban parks, roundabouts and urban farms accumulated the highest metal levels, with several sites exceeding regulatory thresholds for Zn, Pb, Ni, and As, whereas golf courses showed lower contamination levels. Pesticides were detected across both urban and natural soils, with no significant differences in concentrations among land use types. In contrast, microplastic concentrations peaked in natural areas, indicating that regional transport and deposition processes can decouple their accumulation from local urban sources. Macrolitter was most abundant in parks and roundabouts, while golf courses exhibited the lowest densities, highlighting the influence of local management and access control. The level of soil contamination, as quantified by contamination indices, was correlated with microbial richness, community composition, and key soil functions. Pesticides were negatively associated with bacterial richness and redox activity, whereas macrolitter was negatively associated with phosphatase activity. Heavy metal contamination was associated with shifts in bacterial and fungal richness and with changes in soil respiration and phosphatase activity, reflecting a potential influence of heavy metals on microbial communities. This study highlights that land use and management shape soil contamination, soil biodiversity, and ecosystem functioning, emphasizing the need for mitigation actions to support the implementation of the EU Soil Strategy in cities.},
}

@article {pmid42748875,
year = {2026},
author = {Imran, S and Junejo, Y and Ahmad, HI and Ozaslan, M and Safdar, M},
title = {From dysbiosis to resilience: Microbiome engineering for sustainable shrimp aquaculture.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {61},
number = {},
pages = {102024},
doi = {10.1016/j.cbd.2026.102024},
pmid = {42748875},
issn = {1878-0407},
abstract = {The intensification of shrimp aquaculture has increased exposure to disease, environmental perturbations, and antimicrobial pressure, making microbial stability increasingly relevant to sustainable production. Microbiome stability-encompassing resistance to disturbance and resilience of functional recovery-provides an ecological framework for understanding how shrimp and culture-environment microbial communities respond to intensive farming. This review examines the transition from microbial homeostasis to dysbiosis and evaluates how microbiome engineering could redirect disrupted communities towards resilient states. Evidence is integrated across the intestine, hepatopancreas, rearing water, sediment and biofloc to assess how host genetics, ontogeny, diet, culture conditions, antibiotics and pollutants shape microbiome assembly and destabilization. Disease-associated changes in acute hepatopancreatic necrosis disease, white faeces syndrome, Enterocytozoon hepatopenaei infection, and white spot syndrome virus infection are critically evaluated, with explicit separation of associations, pathogen-induced dysbiosis, and community-level causality. Established and emerging interventions-including probiotics, prebiotics, synbiotics, functional diets, biofloc management, phages, postbiotics, microbiota transplantation and synthetic microbial communities-are assessed according to their capacity to modify microbial function, persistence and recovery rather than taxonomic change alone. We further examine how multi-omics, microbiome-informed breeding, and environmental monitoring could support biomarker development, predictive decision support and context-specific intervention. We argue that progress requires a shift from taxonomic description to function-guided engineering, from endpoint comparisons to direct measurement of resilience, and from laboratory efficacy to reproducible farm-scale validation. Overall, microbiome management may contribute to more disease-resilient and sustainable shrimp production, provided that its effectiveness can be validated under commercial farming conditions.},
}

@article {pmid42749094,
year = {2026},
author = {Wang, J and Qi, DY and Jin, WL},
title = {Temporal Immune Surveillance in Cancer: A Circadian Framework from Mechanisms to Chronotherapeutic Integration.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105599},
doi = {10.1016/j.critrevonc.2026.105599},
pmid = {42749094},
issn = {1879-0461},
abstract = {From a traditional perspective, "immune surveillance" has long been regarded as a static process. However, recent studies have shown that the immune system's ability to detect and combat tumors is dynamically regulated by circadian rhythms; we define this concept as "temporal immune surveillance". Disruption of circadian rhythms leads to impaired immune surveillance, thereby creating an immunosuppressive microenvironment that favors the development and progression of cancer. We describe a multi-tiered regulatory network encompassing the intrinsic circadian clocks of immune cells, clock-mediated regulation of immune gene networks, and finally, systemic regulation via the neuro-immune and microbiota-immune axes. These findings pave the way for chrono-immunotherapy, a strategy built on three integrated pillars: optimizing the timing of existing therapies (e.g., immune checkpoint inhibitors), pharmacologically reprogramming disrupted circadian clocks, and pre-synchronizing host physiology through lifestyle interventions such as time-restricted eating. Developing circadian biomarkers and personalized chronotherapy regimens is crucial for advancing precision oncology.},
}

@article {pmid42749360,
year = {2026},
author = {Zhang, K and Gorelik, MG and Sullivan, JE and Radmacher, P and Escobedo, M and Warner, BB and Tarr, PI and Dantas, G},
title = {Divergent microbial preludes to necrotising enterocolitis defined by gut phages and bacterial resistomes.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338976},
pmid = {42749360},
issn = {1468-3288},
abstract = {BACKGROUND: Translating microbiome correlations into robust predictive features for complex gut disorders remains elusive, partly due to oversimplified models of pathogenesis and neglect of the virome, a key player in microbial ecosystems. Necrotising enterocolitis (NEC), a devastating disease of preterm infants with no reliable clinical predictors, exemplifies this challenge.

OBJECTIVE: To determine the predictive potential of the gut prophageome and polymicrobial aetiologies for NEC.

DESIGN: We applied integrated metagenomic and metatranscriptomic analyses and machine learning to 1825 longitudinal stool samples from 43 preterm infants who later developed NEC and 86 gestational age-matched and birthweight-matched controls across three US hospitals. We characterised gut prophageome acquisitions and their association with clinical exposures, including antibiotics, diet and pharmacotherapies. To predict NEC risk, we integrated pre-onset prophageome, antibacterial resistome and bacteriome profiles with neonatal pathology, stratifying the cohort by disease onset timing (early: ≤40 days; late: >40 days) for separate analysis.

RESULTS: NEC cases exhibited distinct viral diversity trajectories before disease onset. Early-onset NEC was best predicted by phage-bacterial interaction signatures (75% accuracy, 81% sensitivity). Metatranscriptomics revealed increased phage DNA abundance with low gene expression, suggesting a lysogenic lifestyle that may stabilise pathobionts. These phages encode metabolic genes potentially enhancing pathobiont resilience. Late-onset NEC was best predicted by antibacterial resistome profiles (83% accuracy).

CONCLUSION: The gut prophageome serves as both a source of pre-symptomatic predictive signals and an active modulator of NEC pathogenesis, with distinct microbial mechanisms driving early-onset and late-onset disease. These polymicrobial etiologies inform strategies for early detection, risk stratification and the development of microbiome-targeted preventive and therapeutic interventions.},
}

@article {pmid42749361,
year = {2026},
author = {Qian, Z and Han, J and Lyu, B and Ainiwaer, A and Zhao, Q and Wang, S and Cheng, J and Li, Y and Sun, Y and Zhang, X and Lu, Y},
title = {Longitudinal gut microbiome dynamics during immunotherapy identify microbial features of clinical benefit in advanced primary liver cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339115},
pmid = {42749361},
issn = {1468-3288},
abstract = {BACKGROUND: The gut microbiome has been linked to immune checkpoint inhibitor (ICI) outcomes, but the temporal dynamics of microbial communities during treatment remain poorly characterised.

OBJECTIVE: To characterise gut microbiome trajectories during ICI therapy and evaluate whether on-treatment microbial states improve the identification and generalisability of pretreatment biomarker signatures.

DESIGN: We performed a large prospective longitudinal shotgun metagenomic study of 315 patients with advanced primary liver cancer receiving ICI-based therapy, profiling 777 serial stool metagenomes collected at baseline and at approximately 3-month intervals on treatment. Responders (durable clinical benefit ≥6 months) contributed extended follow-up beyond 18 months. On-treatment windows were used for feature discovery; baseline-trained models were evaluated across all nine public ICI cohorts (n=1204).

RESULTS: Responders showed higher baseline alpha diversity and distinct community structure. Longitudinal profiling revealed marked ecological remodelling during therapy in both response groups, characterised by reduced network connectivity, increased modularity and strong time point specificity of discriminatory species. Using the on-treatment contrast at ~6 months (T2) as a discovery window, we identified a 16-species panel. A baseline model built from this panel outperformed models based on baseline-only feature discovery and generalised across nine public ICI studies. The resulting gut microbiome-derived immunotherapy outcome score stratified overall and progression-free survival in the discovery cohort (HRs 0.49 and 0.44) and across multiple external datasets, including stable-disease subsets.

CONCLUSION: The gut microbiome undergoes structured ecological remodelling during ICI therapy; on-treatment longitudinal windows improve pretreatment signature portability and support microbiome-guided stratification in immuno-oncology.},
}

@article {pmid42749442,
year = {2026},
author = {Moradkasani, S and Noori Goodarzi, N and Beig, M and Sholeh, M and Fereshteh, S and Khazani Asforooshani, M and Shahbazi, B and Shahbazi, S and Badmasti, F},
title = {Integrated immunoinformatics for the design of novel multi-epitope vaccine and identification of new drug targets against Stenotrophomonas maltophilia, a multidrug-resistant superbug.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {3},
pages = {100772},
doi = {10.1016/j.jgeb.2026.100772},
pmid = {42749442},
issn = {2090-5920},
abstract = {BACKGROUND: Stenotrophomonas maltophilia is a multidrug-resistant opportunistic pathogen causing severe hospital-acquired infections, especially in immunocompromised patients. The absence of an effective vaccine and rising antibiotic resistance underscore the need for novel interventions. This study employed an integrated reverse vaccinology and computational analyses to identify new immunogenic targets, design a multi-epitope vaccine (MEV), and propose potential drug targets.

METHODS: A comprehensive immunoinformatics pipeline was employed to assess antigenicity, allergenicity, human similarity, and physicochemical properties of S. maltophilia proteins. Both B- and T-cell epitopes were screened; however, only the top B-cell epitopes were selected for MEV construction, given the extracellular nature of S. maltophilia. MEV-TLR interactions were analyzed through molecular docking and dynamics simulations. In parallel, cytoplasmic proteins were screened via a subtractive genomics approach to identify essential, non-human homologous, and non-microbiome-similar proteins, which were further evaluated for druggability and interaction networks to propose novel therapeutic targets.

RESULTS: From a total of 4111 proteins, seven potential immunogenic targets were identified: GspD (WP_108270537.1), FhuE (WP_049451370.1), fimbrial protein (WP_012479122.1), TonB-dependent receptor (WP_169448402.1), TolC family protein (WP_108270106.1), autotransporter beta-barrel OMP (WP_169448945.1), and a hypothetical protein (WP_005407892.1). Subsequently, an MEV was designed using five immunogenic epitopes derived from four of these targets: WP_005407892.1 (ADQDSSNM), WP_049451370.1 (SGKAEQ and GEESKTPS), WP_108270537.1 (GVTSTQSDSERT), and WP_169448945.1 (RELGGDRNE). Molecular docking and molecular dynamics simulations demonstrated strong, stable, and feasible interactions between the MEV and TLR-2 and TLR-4 receptors. Moreover, nine novel drug targets were predicted for S. maltophilia, providing new therapeutic insights.

CONCLUSION: The designed MEV and identified immunogenic targets represent promising vaccine candidates against S. maltophilia. Further in vitro and in vivo studies are essential to confirm their safety, immunogenicity, and protective efficacy. Additionally, subtractive genomics analysis revealed nine novel, non-homologous drug targets, offering safer and more specific therapeutic avenues.},
}

@article {pmid42749475,
year = {2026},
author = {Kelleher, ST and Patangia, D and Ross, RP and James, A and Stanton, C and McMahon, CJ},
title = {Gut-brain-heart axis in congenital heart disease: emerging roles of the microbiome in cardiac physiology and neurodevelopment.},
journal = {Heart (British Cardiac Society)},
volume = {},
number = {},
pages = {},
doi = {10.1136/heartjnl-2026-328544},
pmid = {42749475},
issn = {1468-201X},
abstract = {Congenital heart disease (CHD) is increasingly recognised as a multisystem condition extending beyond structural cardiac abnormalities to include gastrointestinal, immunological and neurodevelopmental consequences. Although advances in surgical and intensive care have significantly improved survival, children with CHD remain at heightened risk for adverse neurodevelopmental outcomes, systemic inflammation and gastrointestinal morbidity. The gut microbiome plays a central role in immune regulation, metabolic homeostasis and brain development particularly during early life. Perturbations of the microbiome are common in infants with CHD due to altered gut perfusion, antibiotic exposure, feeding disruption and cardiopulmonary bypass (CPB). These changes may influence both cardiac recovery and neurodevelopment through interconnected gut-heart-brain signalling pathways. This review synthesises current evidence linking the gut microbiome to cardiac physiology and brain development in children with CHD, with particular emphasis on early-life vulnerability, perioperative factors and emerging translational insights. Understanding these interactions may inform future strategies to optimise long-term outcomes in this high-risk population.},
}

@article {pmid42749571,
year = {2026},
author = {Armstrong, R and Timmis, KN},
title = {The textile web as a probiotic interface.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.08.007},
pmid = {42749571},
issn = {1878-4380},
abstract = {Microbiome of the Built Environment research exhibits a marked 'hard-surface bias', overlooking the dynamic soft materials that dominate human-microbial exchange. We propose a theoretical reorientation: the home as a textile web of dynamic, porous microbial reactors. Grounded in immunology's Danger Theory and the principle of 'tissue-based class control', these soft interfaces function as an external tissue analog. By treating textiles as designable interfaces (ranging from airway exchange nodes to laundry bioreactors), architecture becomes a site for proactive probiotic rituals. This framework leverages competitive exclusion to support externalized mucosal 'guard duty', transitioning from prophylactic sterility to a choreography of domestic care. Notably, this reframing recognizes that hygiene encompasses more than infection prevention: domestic cleaning rituals also shape the microbial ecology that educates the immune system. Ultimately, we frame the living home as a tolerogenic exoskeleton, biologically calibrated to protect and prime the human holobiont.},
}

@article {pmid42749632,
year = {2026},
author = {Makau, RM and Chepkirui, BE and Perera, IU and Kiuno, K and Ushine, N and Shimizu, T and Hashino, M and Ishii, Y and Watanabe, K and Watarai, M},
title = {Characterization of the oral microbiota and antimicrobial resistance genes in shelter dogs in Japan.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.26-0387},
pmid = {42749632},
issn = {1347-7439},
abstract = {Companion animals can serve as reservoirs of antimicrobial resistance genes and zoonotic microorganisms, yet information on shelter dogs remains limited. This study characterized the oral microbiota and screened for antimicrobial resistance genes in shelter dogs in Japan. Oral swabs were collected from 81 dogs, microbial genomic DNA was extracted, bacterial communities were profiled by 16S rRNA gene amplicon sequencing, and antimicrobial resistance genes were screened by PCR. We detected genes conferring resistance to several antimicrobial classes, including β-lactams, tetracyclines, macrolide-lincosamide-streptogramin B, phenicols, and sulfonamides. cfxA was detected in all 81 samples, followed by sul1 (66/81), tet(M) and sul2 (65/81), floR (39/81), mecA (17/81), and erm(B) (15/81). We identified potentially pathogenic genera including Capnocytophaga, Pasteurella, Fusobacterium, Campylobacter and Corynebacterium. Microbiome analysis revealed that at the phylum level, Pseudomonadota and Bacteroidota were the most dominant, while Porphyromonas, Frederiksenia and Moraxella were the most prevalent genera. Our findings highlight that (i) the oral microbiota of shelter dogs broadly resembles that reported in companion dogs and (ii) shelter dogs represent an overlooked reservoir of clinically relevant antimicrobial resistance genes and potentially zoonotic bacteria. Therefore, it is necessary to include shelter animals in antimicrobial resistance surveillance programs to capture any potential gaps in the antimicrobial resistance prevalence in companion animals and prevent dissemination of resistant bacteria to humans following adoption of shelter dogs and cats.},
}

@article {pmid42749910,
year = {2026},
author = {Nogueira, A and Brondon, J and Haradinov, K and Gopalakrishnan, S and Huang, K and Mukherjee, D and Agarwal, S and Strickland, KC and Vidal, L and Joshi, C and Brookes, R and Prasad, R and Das, S and Mankan, AK and Munje, A and de Las Heras, B and Singh, BP and Gandia, D and Ramkissoon, S and Raza, FS and Chico, I and Prasad, SK and Perez, J and Prasad, A and Sarker, D and Taieb, J and Saini, KS},
title = {Early-Onset Colorectal Cancer: Clinical and Molecular Features with Emerging Insights from Comprehensive Genomic Profiling.},
journal = {Oncology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42749910},
issn = {2366-1089},
abstract = {Early‑onset colorectal cancer (EOCRC), defined as colorectal cancer (CRC) diagnosed before 50 years of age, is increasing globally. Colorectal cancer is currently the third most commonly diagnosed cancer and the second leading cause of cancer-related death worldwide, with GLOBOCAN 2024 estimating approximately 2.04 million new cases and 917,895 deaths in 2024. Recent studies indicate a sustained rise in EOCRC incidence across multiple regions and birth cohorts, with the greatest increases observed among younger adults. Although hereditary cancer syndromes account for 20-25% of EOCRC cases, most occur in the absence of known genetic predispositions or established risk factors. Emerging evidence implicates the gut microbiome as a potential contributor to EOCRC, with distinct microbial signatures differentiating it from late‑onset colorectal cancer (LOCRC) diagnosed after 50 years of age. This review synthesizes current evidence on clinical, molecular, and diagnostic features distinguishing EOCRC from LOCRC, including differences in anatomical distribution, histopathology, genomic and epigenetic alterations, microbiome composition, and immune landscape, and discusses their implications for personalised screening and therapeutic strategies. We performed a retrospective secondary analysis of comprehensive genomic and immune profiling data from 1737 patients with colorectal cancer tested between June 2021 and June 2023. The analysis showed that tumours arising in patients with EOCRC had lower tumour mutational burden than tumours diagnosed as LOCRC, whereas other immune-related biomarkers, including tumour immunogenicity score, did not remain significantly different after correction for multiple testing. Despite these emerging biological differences, current screening strategies remain largely dependent on an age threshold of 50 years, and EOCRC is not addressed by age‑specific treatment approaches. We therefore review the translational potential of emerging biomarkers, including microbial signatures and liquid biopsy approaches, and propose a framework for integrating molecular profiling into clinical practice. Finally, we highlight the unmet need for coordinated efforts to improve screening in younger populations, address fertility preservation considerations, and ensure adequate psychosocial support for patients with EOCRC.},
}

@article {pmid42749996,
year = {2026},
author = {Yang, H and Shi, J and Wang, J and Jin, S and Lin, Y and Zheng, Y},
title = {Differential Responses of Tree Phyllosphere and Rhizosphere Microbiomes to Mycorrhizal Types and Planting Patterns in a Young Subtropical Forest Plantation.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70425},
doi = {10.1111/1462-2920.70425},
pmid = {42749996},
issn = {1462-2920},
support = {32371595//National Natural Science Foundation of China/ ; 2022J02025//Natural Science Foundation of Fujian Province/ ; },
mesh = {*Mycorrhizae/physiology/classification ; *Rhizosphere ; *Microbiota ; *Trees/microbiology/growth & development ; Forests ; Plant Leaves/microbiology ; Soil Microbiology ; Plant Roots/microbiology ; Bacteria/classification/isolation & purification/genetics ; Fungi/classification/isolation & purification ; Symbiosis ; Seasons ; },
abstract = {Arbuscular mycorrhizal (AM) and ectomycorrhizal (EM) tree species are ubiquitous in subtropical forests and have distinctive root colonisation characteristics and leaf traits, resulting in differences in nutrient acquisition strategies and ecological functions. Here, we investigated the responses of bacteria, fungi and protists inhabiting tree phyllosphere and rhizosphere to tree mycorrhizal types (AM vs. EM) and planting patterns (single or double tree species planting with the same or different mycorrhizal type) in two seasons. Both leaf- and root-associated fungal richness and community composition were strongly structured by tree mycorrhizal type, whereas the bacterial community was primarily influenced by leaf habit. Protistan communities, however, exhibited weak host specificity and were dominated by stochastic processes, with seasonal variation acting as the main influencing factor. Overall, the phyllosphere microbiomes were jointly shaped by leaf traits and seasonal effects, but rhizosphere fungal communities were directly and indirectly regulated by tree mycorrhizal type via root nutrient and colonisation statuses. Altogether, tree phyllosphere and rhizosphere microbiomes differ from the interaction of mycorrhizal symbiosis, planting pattern and seasonality, with distinct ecological processes manipulating across bacteria, fungi and protists. This study highlights the necessity of integrating tree mycorrhizal types and above- and belowground habitats perspectives to better understand forest microbiomes.},
}

*Mycorrhizae/physiology/classification
*Rhizosphere
*Microbiota
*Trees/microbiology/growth & development
Forests
Plant Leaves/microbiology
Soil Microbiology
Plant Roots/microbiology
Bacteria/classification/isolation & purification/genetics
Fungi/classification/isolation & purification
Symbiosis
Seasons

@article {pmid42750046,
year = {2026},
author = {Sun, Y and Cheng, OJ and Ma, A and Shabnaz, S and Huang, X and Zhao, J and Tan, AC and Ma, Q},
title = {Decoding the cancer microbiome: multi-omics, AI, and translational opportunities.},
journal = {Genome biology},
volume = {27},
number = {1},
pages = {},
pmid = {42750046},
issn = {1474-760X},
support = {R01GM152585/NH/NIH HHS/United States ; },
mesh = {Humans ; Multiomics ; *Neoplasms/microbiology/genetics ; *Microbiota ; *Artificial Intelligence ; Translational Research, Biomedical ; },
abstract = {Multi-omics technologies, coupled with AI technologies, have the potential to enable the systematic investigation of complex cancer microbiome biology by uncovering informative patterns and associations across complementary datasets. Here, we review existing and emerging cancer microbiome data, discuss the development, interpretation, and validation of AI models as key considerations for their integration and analysis, and provide practical suggestions for improving the reliability and biological relevance of AI-driven discoveries. We further highlight the opportunities and challenges of translating these discoveries into clinical practice, emphasizing strategies to bridge the gap between research-oriented models and clinical implementations.},
}

Humans
Multiomics
*Neoplasms/microbiology/genetics
*Microbiota
*Artificial Intelligence
Translational Research, Biomedical

@article {pmid42750157,
year = {2026},
author = {Syukur, S and Nappi, J and Majzoub, ME and Thomas, T and Egan, S},
title = {Not All Children Are the Same: Differences in the Microbiome Assembly During Early Development of Seaweeds.},
journal = {Environmental microbiology},
volume = {28},
number = {9},
pages = {e70418},
doi = {10.1111/1462-2920.70418},
pmid = {42750157},
issn = {1462-2920},
support = {//Australian Department of Foreign Affairs and Trade/ ; },
mesh = {*Microbiota ; *Seaweed/microbiology/growth & development ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Symbiosis ; *Rhodophyta/microbiology/growth & development ; *Phaeophyceae/microbiology/growth & development ; *Ulva/microbiology/growth & development ; Chlorophyta/microbiology/growth & development ; },
abstract = {Microbial symbionts play key roles in macroalgal development, yet the processes structuring early-life microbiomes remain poorly understood. Using laboratory outgrowth experiments and 16S rRNA gene amplicon sequencing we compared microbiome acquisition and assembly during the early development of three distinct macroalgae: Ulva australis (Chlorophyta), Hormosira banksii (Phaeophyceae) and Delisea pulchra (Rhodophyta). All species established distinct bacterial communities within the first week of outgrowth, with significant shifts in community composition and structure associated with major developmental stages. Stage-enriched taxa included Phaeobacter, Roseobacter and Maribacter, which include members reported to influence algal growth or morphogenesis. Vertical inheritance contributed unevenly to the microbiome assembly across hosts. U. australis recruited low-abundance environmental bacteria, possibly via strong host filtering. H. banksii selectively retained a small, consistent subset of adult-derived bacteria, whereas D. pulchra retained fewer of its inherited bacteria. These results suggest that macroalgae can employ diverse transmission and recruitment strategies to assemble early microbiomes, combining selective inheritance with stage-specific retention and/or environmental acquisition.},
}

*Microbiota
*Seaweed/microbiology/growth & development
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Symbiosis
*Rhodophyta/microbiology/growth & development
*Phaeophyceae/microbiology/growth & development
*Ulva/microbiology/growth & development
Chlorophyta/microbiology/growth & development

@article {pmid42750261,
year = {2026},
author = {Franklin, S and Sahasrabhojane, P and Ivanov, I and Hayase, T and Hayase, E and Chang, CC and Senapati, J and Desikan, SP and Kadia, T and Lorenzi, P and Jenq, RR and Shelburne, S and Galloway-Peña, J},
title = {Inclusion of Multi-Omic Biomarkers Improves Prediction Accuracy of Response, Relapse, and Overall Survival in Acute Myeloid Leukemia Patients Receiving High-Intensity Induction Chemotherapy.},
journal = {Cancer medicine},
volume = {15},
number = {9},
pages = {e72281},
doi = {10.1002/cam4.72281},
pmid = {42750261},
issn = {2045-7634},
support = {K01AI143881//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Humans ; *Leukemia, Myeloid, Acute/drug therapy/mortality/genetics/microbiology ; Multiomics ; Female ; *Biomarkers, Tumor ; *Induction Chemotherapy/methods ; Male ; Neoplasm Recurrence, Local ; Middle Aged ; Prognosis ; Machine Learning ; Feces/microbiology ; Predictive Learning Models ; Adult ; Boosting Machine Learning Algorithms ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Recurrence ; Aged ; Risk Assessment ; },
abstract = {BACKGROUND: Despite advancements in genetic markers for acute myeloid leukemia (AML) risk stratification, outcome prediction remains challenging due to disease heterogeneity and dynamic genetic changes, highlighting the need for reliable biomarkers to improve AML treatment strategies and patient outcomes. To refine outcome predictions, we investigated the use of microbial-derived biomarkers to predict composite complete remission (CRc), relapse, and survival for patients on high- and low-intensity regimens, and to integrate those variables into the widely clinically utilized European Leukemia Network (ELN-2022) genetic risk classification model for high-intensity-treated patients.

METHODS: We first developed machine learning models that integrate baseline fecal metabolomics, 16S rRNA-based stool microbiome features, and clinical metadata (sex, antibiotic administration, AML somatic mutations, and cytogenetics) from two cohorts of AML patients (n = 83) undergoing remission induction chemotherapy. Univariate tests and sparse canonical correlation analysis were employed for variable selection and to explore fecal metabolite-microbe relationships. A robust machine learning approach using XGBoost was employed, with 100 stratified data splits (80% training, 20% testing) and coarse-to-fine hyperparameter optimization. Variable importance was aggregated across all models to select key predictors.

RESULTS: For high-intensity-treated patients, XGBoost models achieved aggregated AUROC scores of 0.719, 0.729, and 0.65 for CRc, relapse, and overall survival, respectively. For low-intensity-treated patients, these models achieved aggregate AUROC scores of 0.945, 0.724, and 0.768 for these same outcomes, respectively. Integrating the biomarkers identified in the high-intensity machine-learning models with the current ELN-2022 AML risk stratification system effectively stratified patients into risk categories, which obtained higher concordance indices and likelihood ratios, demonstrating improved prognostic accuracy for each outcome compared to ELN-2022 alone.

CONCLUSIONS: The inclusion of microbial-derived biomarkers serves as a robust prognostic tool to improve outcome prediction in AML patients, highlighting the potential of its integration into AML risk assessment and paving the way for personalized treatment strategies and improved patient outcomes.},
}

Humans
*Leukemia, Myeloid, Acute/drug therapy/mortality/genetics/microbiology
Multiomics
Female
*Biomarkers, Tumor
*Induction Chemotherapy/methods
Male
Neoplasm Recurrence, Local
Middle Aged
Prognosis
Machine Learning
Feces/microbiology
Predictive Learning Models
Adult
Boosting Machine Learning Algorithms
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Recurrence
Aged
Risk Assessment

@article {pmid42750336,
year = {2026},
author = {Chittimalli, K and Rozario, HE and Martinez, V and McAdams, ZL and Adkins, SA and Ericsson, AC and Jarajapu, YPR},
title = {Alamandine/MrgD pathway modulates gut-bone marrow axis in ageing.},
journal = {British journal of pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bph.70656},
pmid = {42750336},
issn = {1476-5381},
support = {AG056881/NH/NIH HHS/United States ; P20GM103442/NH/NIH HHS/United States ; U42 OD010918/NH/NIH HHS/United States ; },
abstract = {BACKGROUND AND PURPOSE: Ageing is associated with colon epithelial barrier disruption and up-regulation of myelopoiesis in the bone marrow (BM). Alamandine (Ala) and MrgD are novel members of the renin angiotensin system (RAS). This study tested the hypothesis that Ala restores the colon epithelial barrier integrity in ageing via modulating gut-BM axis.

EXPERIMENTAL APPROACH: Mice, 2-3 (Young) or 22-24 months (Old), were treated with saline or Ala by using Osmotic pumps. The intestinal permeability was evaluated using FITC-dextran. Lgr5[+]Olfm4[+] intestinal stem cells (ISCs), Wnt3a and β-catenin were evaluated by immunohistochemistry or western blotting. Faecal microbiome was analysed by 16S rRNA sequencing. Monocyte-macrophages were characterized by flow cytometry. Caecal or serum bacterial metabolites were analysed and the caecal supernatants (CS) were tested for myelopoietic potential.

KEY RESULTS: MrgD was expressed in ISCs, which was decreased in the Old. Increased intestinal permeability in ageing was reversed by Ala. In the colon organoids, Ala increased Wnt3a levels and this was antagonized by NF449, SQ22536 or 666-15. Ala restored phospho-CREB and active β-catenin levels that were decreased in the Old colon-organoids. Ala increased the richness and β-diversity of the microbiota with decreased Bacillota/Bacteroidota in ageing. Ala decreased the CD80[+] and increased CX3CR[+] macrophages in the Old colons. Old-CS induced myelopoiesis in BM cells with higher number of pro-inflammatory macrophages, which was prevented by Ala treatment.

CONCLUSIONS AND IMPLICATIONS: Targeting Ala/MrgD pathway is a promising approach for ameliorating the inflammatory stress in ageing by restoring homeostasis in the gut-BM inter-organ communication.},
}

@article {pmid42750414,
year = {2026},
author = {Tóth, A and Furka, S and Vengríni, J and Neogrády, P and Bandura, A and Dueñas Casas, S and Petrovič, R and Tomka, M and Slopovský, J and Furka, D},
title = {Artificial Intelligence-Driven Multidimensional Phenotyping of Gut Metabolic States for Personalized Prebiotic, Probiotic, and Postbiotic Strategies.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {18},
pages = {e70607},
pmid = {42750414},
issn = {1613-4133},
mesh = {Humans ; Feces/microbiology/chemistry ; Phenotype ; *Probiotics ; *Prebiotics ; *Artificial Intelligence ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Machine Learning ; Dysbiosis ; },
abstract = {This study presents multidimensional physicochemical phenotyping of human gut metabolic states using integrated multimodal profiling and machine learning. A total of 680 stool samples were analyzed using time-resolved optical, electrochemical, acoustic, magnetic, and spectral measurements implemented in a compact 3D-printed screening platform. Multivariate analysis explained 78.4% of structured variance, and cluster optimization identified seven primary clusters and 26 structurally retained subclusters representing proteolytic, saccharolytic, bile/lipid-rich, oxidative, diarrheal, pigment-linked, and normobiotic-like profiles. Clinical categories were linked to 21 subclusters after descriptor-based structure definition. A separate supervised layer assessed out-of-fold reproduction of fixed primary CL1-CL7 assignments, achieving 81.7% accuracy and a 0.799 macro F1-score in repeated cross-validation. Separately, cohort-internal diagonal category-to-subcluster distribution reached 84.1% (572/680 diagonal assignments, Wilson 95% CI: 81.2%-86.7%). 16S rRNA/laboratory-marker profiling supported the physicochemical structure, showing high diversity and low dysbiosis in the normobiotic-like phenotype, acidic high-diversity behavior in the saccharolytic phenotype, alkaline proteolytic behavior with elevated phenols and ammonia, bile-associated functional enrichment, and high dysbiosis with reduced diversity in the pigment-rich phenotype. SHAP and LIME attributed CL1-CL7 assignment to coordinated multimodal contributions. The method represents standardized extractable stool matrix profiling associated with microbiome-supported functional states, not a stand-alone diagnostic test.},
}

Humans
Feces/microbiology/chemistry
Phenotype
*Probiotics
*Prebiotics
*Artificial Intelligence
*Gastrointestinal Microbiome/physiology
RNA, Ribosomal, 16S/genetics
Machine Learning
Dysbiosis

@article {pmid42750456,
year = {2026},
author = {Park, S and Lee, B and Sun, H and Shin, W and Mok, JY and Seo, J and Choi, HJ and Choi, GH and Son, JY and Yoo, B},
title = {Effects of Wilac D001 (Weissella confusa WIKIM51) Supplementation on Metabolic Parameters and Central Adiposity in Overweight Adults: A 12-Week Randomized, Double-Blind, Placebo-Controlled Trial.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2606054},
doi = {10.4014/jmb.2606.06054},
pmid = {42750456},
issn = {1738-8872},
mesh = {Animals ; Male ; Mice, Inbred C57BL ; Glucagon-Like Peptide 1/metabolism ; Mice ; Humans ; Adult ; *Probiotics/administration & dosage ; Double-Blind Method ; Middle Aged ; *Weissella ; *Overweight/metabolism/therapy ; Diet, High-Fat ; Dietary Supplements ; *Adiposity/drug effects ; Young Adult ; Glucose Tolerance Test ; Blood Glucose ; Gastrointestinal Microbiome ; },
abstract = {Recent research has emphasized the importance of gut microbiota in regulating energy and lipid metabolism as well as gut hormone secretion, indicating that probiotics could contribute to improving metabolic parameters associated with excess adiposity. This study evaluated the metabolic effects of Weissella confusa WIKIM51 (Wilac D001) and explored the potential involvement of glucagon-like peptide-1 (GLP-1)-related mechanisms. First, GLP-1 secretory activity following Wilac D001 treatment was evaluated in vitro using STC-1 enteroendocrine cells. Male C57BL/6 mice were fed a high-fat diet to induce obesity-associated metabolic dysregulation, and Wilac D001 was orally administered for 10 weeks. Glucose tolerance was subsequently examined using an oral glucose tolerance test (OGTT). Finally, in a 12-week randomized, double-blind, placebo-controlled clinical trial, overweight adults aged 19-64 years received either Wilac D001 (1.0 × 10[10] colony-forming units/day) or a placebo. Blood lipid parameters, glycated hemoglobin, abdominal fat distribution, body composition, body weight, regional anthropometric measures, and lifestyle factors were evaluated. Wilac D001 significantly increased GLP-1 secretion in STC-1 cells versus the control (p < 0.01). High-fat diet-fed mice administered Wilac D001 exhibited lower fasting blood glucose levels and more rapid glucose recovery during the OGTT (p < 0.01). In the clinical trial, Wilac D001 supplementation led to reductions in several markers, including a significant reduction in triglyceride levels, alongside improvements in total abdominal fat area, visceral fat area, and subcutaneous fat area. No serious adverse events were reported. These findings support the potential of Wilac D001 as a functional probiotic for promoting microbiome-based metabolic health management.},
}

Animals
Male
Mice, Inbred C57BL
Glucagon-Like Peptide 1/metabolism
Mice
Humans
Adult
*Probiotics/administration & dosage
Double-Blind Method
Middle Aged
*Weissella
*Overweight/metabolism/therapy
Diet, High-Fat
Dietary Supplements
*Adiposity/drug effects
Young Adult
Glucose Tolerance Test
Blood Glucose
Gastrointestinal Microbiome

@article {pmid42750461,
year = {2026},
author = {Yang, F and Qin, W and Zhang, G and Li, X and Yang, X and Zhou, L and Xing, Y},
title = {Probiotics in Cardiometabolic Diseases: Current Evidence, Postbiotic Perspectives, and Future Directions.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2605001},
doi = {10.4014/jmb.2605.05001},
pmid = {42750461},
issn = {1738-8872},
mesh = {*Probiotics/therapeutic use ; Humans ; *Cardiovascular Diseases/therapy/microbiology ; Gastrointestinal Microbiome/drug effects ; Animals ; *Metabolic Syndrome/therapy ; Precision Medicine ; *Metabolic Diseases/therapy ; },
abstract = {The rise in urbanization and sedentary lifestyles, along with the aging of the global population, is contributing to an increasing burden of life-threatening diseases. The cardiometabolic disease (CMD) spectrum, which includes heart failure, hypertension, coronary heart disease, and diabetes, is closely associated with metabolic syndrome components such as obesity and elevated hepatic lipid accumulation. The gut microbiome mediates these disorders through multiple signaling axes. Imbalance of the intestinal microbiota is closely linked to the pathogenesis of atherosclerosis and hypertensive vascular remodeling. Supplementation with probiotics - and, more recently, their derived postbiotic products - can alter the composition and functional metabolic outputs of the gut ecosystem, offering a mechanistically informed approach for CMD management. This review delineates the mechanisms of action of six well-studied probiotics (Akkermansia muciniphila, Bifidobacterium, Lactobacillus, Bacillus, Enterococcus, and Lactococcus lactis), with selected discussion of their postbiotic derivatives where evidence is available. We further examine how antimicrobial and metabolic interventions integrated through the gut-heart-liver axis may improve clinical outcomes and attenuate disease progression. The advancement of precision cardiometabolic medicine through the combined effects of these therapies may facilitate the development of personalized treatment strategies.},
}

*Probiotics/therapeutic use
Humans
*Cardiovascular Diseases/therapy/microbiology
Gastrointestinal Microbiome/drug effects
Animals
*Metabolic Syndrome/therapy
Precision Medicine
*Metabolic Diseases/therapy

@article {pmid42750565,
year = {2026},
author = {Pothikamjorn, TL and Gonzales, JA},
title = {Molecular biomarker profiling in noninfectious uveitis: a chronological review of discovery.},
journal = {Current opinion in ophthalmology},
volume = {},
number = {},
pages = {},
pmid = {42750565},
issn = {1531-7021},
abstract = {PURPOSE OR REVIEW: Noninfectious uveitis (NIU) encompasses a heterogeneous group of immune-mediated intraocular inflammatory diseases whose complexity has driven systematic molecular biomarker discovery. This review presents NIU molecular biomarkers organized by biological category; autoantigens, human leukocyte antigens (HLA) and genetic markers, cellular immune subsets, cytokines, chemokines, and multiomics platforms including proteomics, microbiome metagenomics, metabolomics, and single-cell transcriptomics with each category presented in strict chronological order of landmark discovery.

RECENT FINDINGS: We present a review organized along two nested timelines. Categories are presented in the order they historically emerged in the field, and within each category, landmark discoveries appear in chronological sequence. This allows the reader to trace how each biomarker category evolved: from foundational autoantigen identification in experimental uveitis models, through the genomic revolution of HLA association studies, into cellular immunophenotyping, cytokine profiling of aqueous humor, chemokine mapping of intraocular trafficking, and finally the emerging omics platforms that may potentially anchor precision medicine in NIU. Each biomarker is paired in line with its linked targeted therapeutic.

SUMMARY: Biomarker research has transformed the understanding of NIU from a clinically defined syndrome into a group of molecularly distinct immune disorders. Advances spanning autoantigens, genetics, immune-cell profiling, cytokines, chemokines, and multiomics have revealed novel pathogenic mechanisms and therapeutic targets. Integration of these biomarkers with targeted therapies may accelerate the transition toward precision medicine in uveitis care.},
}

@article {pmid42750798,
year = {2026},
author = {Bhandari, P and Sideeg, A and Elfeki, M and Xie, C and Singal, AK},
title = {Therapeutic modulation of the gut-brain axis in alcohol use disorder: A systematic review.},
journal = {Metabolism open},
volume = {32},
number = {},
pages = {100495},
pmid = {42750798},
issn = {2589-9368},
abstract = {BACKGROUND: Alcohol Use Disorder (AUD) involves gut-brain axis dysfunction. Modulating microbiota offers a promising therapeutic strategy.

METHODS: Clinical trials on fecal microbiota transplant (FMT), prebiotics (inulin), probiotics, and neurohormonal agents like glucagon-like peptide-1 (GLP-1) and ghrelin receptor antagonists) were identified through PubMed, Google Scholar, Scopus, and ClinicalTrials.gov (until 07/31/2026). Of the eleven included studies, five identified gut dysbiosis as a common feature in individuals with AUD.

RESULTS: Gut dysbiosis-directed interventions were associated with benefits on behavioral (alcohol craving, consumption, relapse), psychological (anxiety, sociability), and physiological (MELD score, AST/ALT ratio, systemic inflammation) outcomes. However, the magnitude and consistency of these effects varied among studies. Three studies specifically involved AUD patients with alcohol-associated liver disease (ALD), while the others focused on AUD. In another study, Ghrelin, which was investigated as a neurohormonal target, emerged as a potential anti-inflammatory agent. However, ghrelin receptor antagonism in the presence of alcohol did not alter systemic inflammation. Of five trials using GLP-1 receptor agonists, three showed a reduction in alcohol use, but the other two, although directionally consistent, did not reach statistically significant effects. The current evidence supports the gut-brain axis as a dual therapeutic target, offering potential benefits for both AUD and ALD. Microbial therapies (FMT, probiotics, prebiotics) show some benefits in AUD, albeit studies are small. Hormonal targets such as ghrelin and GLP-1 receptors are mechanistically relevant. Data on ghrelin are limited. Data on GLP-1 receptor agonists are directionally consistent but not statistically robust. Large-scale, controlled trials are needed to validate and optimize the integration of this approach into AUD treatment strategies.},
}

@article {pmid42750861,
year = {2026},
author = {Chai, Y and Lan, J and Li, K and Mei, X and Chen, Y and Zhou, N and Liu, X and Gong, W and Lei, H},
title = {Gut microbiota dysbiosis and the gut-lung axis in COPD: mechanisms, clinical relevance, and microbiota-targeted interventions.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1915007},
pmid = {42750861},
issn = {2296-634X},
abstract = {Chronic obstructive pulmonary disease (COPD), which is characterised by persistent inflammation and airflow limitation, has increasingly been linked to the gut-lung axis. Patients with COPD commonly exhibit reduced diversity of gut microbiota, decreased levels of bacteria that produce short-chain fatty acids (SCFAs), increased levels of opportunistic pathogens, and compromised intestinal barrier function. These alterations are driven by factors such as smoking, hypoxia, oxidative stress, medication use and ageing, and promote bacterial translocation and systemic inflammation, thereby exacerbating lung injury. Gut microbiota metabolites, including SCFAs, bile acids, tryptophan metabolites and trimetlylamine N-oxide (TMAO), further modulate immune responses and metabolic pathways, thereby influencing disease progression. Intervention strategies targeting the microbiome, including dietary fibre, probiotics, prebiotics, faecal microbiota transplantation (FMT) and phage therapy, have demonstrated potential therapeutic value, though clinical evidence remains limited. Elucidating the mechanisms linking gut dysbiosis and COPD will provide novel targets for precision interventions and disease management.},
}

@article {pmid42750901,
year = {2026},
author = {Musleh, L and Montilli, M and Ammendolia, MG and Sciarra, A and Riccioli, A and Maurizi, L and Longhi, C},
title = {More than an infection: the ecological puzzle of recurrent urinary tract infections.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1927507},
pmid = {42750901},
issn = {2235-2988},
mesh = {Humans ; *Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology ; Recurrence ; Microbiota ; Reinfection/microbiology ; Host Microbial Interactions ; Dysbiosis ; Urinary Tract/microbiology ; },
abstract = {Recurrent urinary tract infections (rUTIs) represent one of the most common infectious conditions worldwide, yet their pathophysiology extends far beyond repeated episodes of acute bacterial cystitis. Increasing evidence indicates that recurrence may arise through overlapping mechanisms including reinfection from intestinal or periurethral reservoirs, intracellular bacterial persistence, microbial dysbiosis, impaired mucosal immunity and chronic inflammatory remodelling of the bladder microenvironment. Current diagnostic frameworks remain largely based on symptom-based definitions and standard urine culture, approaches that incompletely capture the biological complexity of recurrent disease. This limitation is evident even at the definitional level, where clinically pragmatic categories often fail to reflect the heterogeneous mechanisms underlying recurrence. Advances in expanded urine culture techniques, metagenomics and metabolomics have reshaped the understanding of the urinary tract as a dynamic ecological system interconnected with vaginal, intestinal and prostatic microbial compartments. These approaches have identified diverse microbial communities, virulence-associated functional profiles and host-microbe interactions linked to recurrence-prone phenotypes. Significant challenges continue to persist in elucidating the biological mechanisms driving recurrence. Addressing these gaps is essential to improve disease characterization and support the development of more effective diagnostic and therapeutic approaches.},
}

Humans
*Urinary Tract Infections/microbiology/diagnosis/drug therapy/immunology
Recurrence
Microbiota
Reinfection/microbiology
Host Microbial Interactions
Dysbiosis
Urinary Tract/microbiology

@article {pmid42751010,
year = {2026},
author = {Wan, M and Kong, Z and Gao, Y and Yin, Y and Li, F and Duan, Y},
title = {Maternal methionine supplementation in low-protein diets during late gestation and lactation increases performance and alters fecal microbiota of sows and their offspring.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {27},
number = {},
pages = {206-217},
pmid = {42751010},
issn = {2405-6383},
abstract = {Methionine (Met) is known to enhance antioxidant defense and reproductive efficiency in sows, but its role under low-protein feeding conditions is unclear. This study evaluated the effects of Met supplementation on lactation performance, antioxidant status, and gut microbiota of sows and their offspring. Sixty-six multiparous sows with two parity and similar body weight (244.1 ± 1.73 kg) were assigned to a normal protein diet (18% crude protein [CP]) or low-protein diets (15% CP) containing graded standardized ileal digestible (SID) Met levels (0.23%, 0.30%, 0.37%, 0.44%, and 0.51%, respectively) from d 107 of gestation to d 21 of lactation, with 11 replicates in each group and one sow per replicate. The results showed that sows fed low-protein diets supplemented with 0.30% Met achieved milk yields and piglet growth comparable to those of the normal protein group (P > 0.05). In addition, 0.30% Met supplementation reduced serum urea nitrogen content, enhanced the concentrations of milk immunoglobulin M, glutathione, and taurine, and increased the activities of serum total superoxide dismutase in sows and glutathione peroxidase in piglets when compared with the normal protein diet (P < 0.05). Microbiome analysis indicated higher relative abundance of Christensenellaceae _R-7_group in piglets from the 0.30% Met group, and this relative abundance was positively correlated with growth traits. These findings suggest that supplementation with 0.30% Met within the 15% CP diet supports sow performance and piglet development comparable to normal protein feeding, via enhanced antioxidant capacity and favorable modulation of gut microbiota.},
}

@article {pmid42751019,
year = {2026},
author = {Muñoz Puebla, D and Mindiola-Reyes, K and Nieto-Wigby, J and Cevallos-Cevallos, JM},
title = {Mangrove microbiomes: diversity, ecological functions, and applications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1908615},
pmid = {42751019},
issn = {1664-302X},
abstract = {Mangrove ecosystems are dynamic coastal environments that offer essential ecological services, socioeconomic benefits, and resilience against climate change. Central to their functionality there are complex microbial communities-primarily bacteria and fungi-that drive key biogeochemical processes such as organic matter decomposition, nitrogen fixation, carbon sequestration, and sulfur cycling. This review aims to synthesize current knowledge on mangrove microbiomes, focusing on microbial taxonomic diversity, ecological roles, and environmental responsiveness. The effect of abiotic factors such as salinity, tidal regimes, vegetation type, and anthropogenic pressures on microbial community structure and function is also assessed. Key findings highlight the presence of both conserved microbial taxa across biogeographic regions and functional adaptations to local conditions, underscoring the global ecological significance of these microbial assemblages. Particular attention is given to microbe-mediated nutrient cycling, symbiotic plant-microbe interactions, and microbial contributions to pollutant degradation, including microplastics and heavy metals. Additionally, recent advances in omics-based approaches have expanded our understanding of microbial functionality and unveiled promising avenues for biotechnological applications, such as enzyme production and bioactive compound discovery. The review also identifies critical knowledge gaps, including the need for long-term monitoring, methodological standardization, and integrated multi-omics frameworks. Overall, recognizing microbial communities as foundational components of mangrove health is essential for effective conservation, ecosystem restoration, and sustainable resource management in the face of accelerating global environmental change.},
}

@article {pmid42751182,
year = {2026},
author = {Liang, X and Chen, D and Hu, J and Guo, L and Yang, H and Guo, Q and Zhang, R},
title = {Childhood asthma and the microbiome: from gut-lung axis mechanisms to precision prevention strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1902053},
pmid = {42751182},
issn = {1664-3224},
mesh = {Humans ; *Asthma/prevention & control/microbiology/immunology/etiology ; *Gastrointestinal Microbiome/immunology ; Child ; *Lung/immunology/microbiology ; Animals ; Precision Medicine ; *Microbiota ; Biomarkers ; Probiotics/therapeutic use ; Environmental Exposure/adverse effects ; Disease Susceptibility ; },
abstract = {Childhood asthma is a highly heterogeneous chronic respiratory disease, and its onset and progression are intricately linked to genetic susceptibility, environmental exposure, immune development, and the establishment of the early-life microbiome. In recent years, studies on the gut and respiratory microbiomes have suggested that the composition, metabolic functions, and interactions of microbial communities with the host immune system may be involved in the formation of asthma susceptibility, shaping of inflammatory phenotypes, and disease progression in children. The gut-lung axis, as an important pathway connecting gut microbiome, respiratory immunity, and systemic inflammatory responses, provides a new perspective for understanding the early mechanisms of childhood asthma. This article reviews the characteristics of the respiratory and gut microbiomes associated with childhood asthma, with a focus on the roles of the gut-lung axis, microbial metabolites, mucosal immune regulation, and environmental exposure. It also evaluates the research progress of probiotics, prebiotics, nutritional interventions, and novel microecological therapies. Additionally, the potential of microbial maturity, microbial metabolites, and immunophenotypes as biomarkers for risk prediction, phenotype stratification, and treatment response is analyzed. Furthermore, the role of multi-omics integration in supporting the identification of responsive populations, matching of intervention strategies, and dynamic monitoring of efficacy is discussed. Current evidence suggests that the microbiome offers promising targets for risk assessment and precision prevention of childhood asthma. However, relevant research still faces challenges such as ambiguous causality, high cohort heterogeneity, limited reproducibility of candidate biomarkers, inconsistent intervention outcomes, and insufficient evidence of long-term safety. At present, most biomarkers and multi-omics models remain in the stage of association discovery, lacking unified thresholds, cross-cohort validation, and biomarker-guided randomized controlled trials in children. Therefore, they cannot be routinely used for patient stratification or intervention selection. Future efforts should rely on standardized longitudinal birth cohorts, multi-omics integration, external validation, and high-quality clinical trials to clarify the incremental value of microbiome biomarkers over traditional clinical indicators and their clinical utility in the individualized management of childhood asthma.},
}

Humans
*Asthma/prevention & control/microbiology/immunology/etiology
*Gastrointestinal Microbiome/immunology
Child
*Lung/immunology/microbiology
Animals
Precision Medicine
*Microbiota
Biomarkers
Probiotics/therapeutic use
Environmental Exposure/adverse effects
Disease Susceptibility

@article {pmid42751268,
year = {2026},
author = {Doolin, ML and Woodhams, DC},
title = {Advancing the study of microbial symbionts of amphibians and reptiles.},
journal = {Frontiers in amphibian and reptile science},
volume = {4},
number = {},
pages = {},
pmid = {42751268},
issn = {2813-6780},
abstract = {Amphibian and reptile microbiomes are important contributors to host health and ecosystem dynamics but understudied compared to microbiomes of other vertebrates. Through study of amphibian and reptile microbiomes, investigators can advance theory and practice in animal health, ecosystem function, conservation, and more. This special issue of Frontiers of Amphibian and Reptile Science features six publications in the field of amphibian and reptile microbiome research, and here, we highlight the contributions of these and other recent publications to four main areas of recent advancement in the field: 1) expanding "microbiome" beyond bacteria, 2) expanding study of host life-history stages and anatomical microbial habitats, 3) characterizing whole microbial communities, particularly in disease ecology studies, and 4) developing and implementing databases and bioinformatics tools. We also discuss several avenues for future research that would bring amphibians and reptiles to the forefront of microbiome research. With the continued implementation of classic culture-based and sequencing approaches paired with cutting-edge tools in vivo, in vitro, and in silico, herpetofauna microbiome research is poised for exciting growth in the near future.},
}