@article {pmid42326066,
year = {2026},
author = {Jeon, K and Kim, U and Ji, CH and Kamaraj, M and Laird, NZ and Wang, Z and Yu, H and Ermis, M and Sullan, RMA and Shen, X and Falcone, N},
title = {Modeling cancer with bacteria-integrated tumor microenvironments using biomaterials: Emerging concepts and opportunities.},
journal = {Materials today. Bio},
volume = {39},
number = {},
pages = {103330},
pmid = {42326066},
issn = {2590-0064},
abstract = {The tumor microenvironment (TME) is a dynamic and heterogeneous ecosystem in which cancer, stromal, immune, and physicochemical components collectively regulate disease progression and therapeutic response. Recent evidence further indicates that intratumoral bacteria are active contributors to tumor metabolism, immune modulation, and treatment outcomes, revealing a previously underexplored multi-kingdom dimension of solid tumors. However, mechanistic understanding of tumor-microbe interactions remain limited by the absence of experimental platforms that integrate microbial components into physiologically relevant and controllable tumor models. Here, we propose bacteria-integrated tumor microenvironments as an emerging bioengineering framework for modeling cancer as a multi-kingdom system with biomaterials. We first lay out the existence of bacteria in our body and outline key design principles for these systems, including control of microbial localization, nutrient and oxygen gradients, and interkingdom signaling within engineered matrices. We further discuss applications in studying microbial contributions to therapeutic resistance, evaluating engineered bacterial therapies, and developing patient-specific tumor-microbiome models for precision oncology. Finally, we highlight challenges in standardizing multi-kingdom tumor platforms and integrating them with advanced imaging, sequencing, and computational tools. Collectively, bacteria-integrated TME establish a new paradigm for engineering cancer as a multi-kingdom system with translational potential in oncology.},
}

@article {pmid42326130,
year = {2026},
author = {Roshan Arbaaz, B and Maheswaran, T and Adalarasan, S and Kavin, T and Sivaguru, K and Jisha, G},
title = {Oral Manifestations of Prediabetes: A Narrative Review of an Early Diagnostic Window for Dental Practice.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e109375},
pmid = {42326130},
issn = {2168-8184},
abstract = {Prediabetes is a common metabolic condition affecting a substantial proportion of adults worldwide; however, most individuals remain undiagnosed owing to the prolonged asymptomatic phase of this condition. The oral cavity generates a constellation of clinically detectable changes during this intermediate glycemic stage, including periodontal attachment loss, salivary dysfunction, and oral microbiome dysbiosis, all of which can be examined by dental professionals. Periodontal clinical attachment loss and elevated glycated hemoglobin (HbA1c) levels show a dose-dependent relationship in nondiabetic populations, and active matrix metalloproteinase-8 (aMMP-8) in oral fluids correlates independently with prediabetes, even in its early stages. Salivary oxidative stress markers, adipokines, cariogenic bacterial loads, and physicochemical parameters are measurably altered before overt hyperglycemia is established. Oral microbial communities show reduced species richness, altered IgA immune responses, and shifts in keystone taxa in prediabetic individuals compared to those in healthy individuals. Chairside HbA1c measurement, aMMP-8 point-of-care testing, and structured interprofessional referral models have demonstrated high diagnostic yields in real-world dental settings. This narrative review explores the current literature and proposes dental practice as a first-line venue for opportunistic prediabetes detection, with an emphasis on actionable clinical strategies for practicing dentists.},
}

@article {pmid42326394,
year = {2026},
author = {Butler, JM},
title = {INTERPOL Review of Forensic Biology and DNA, 2023-2025.},
journal = {Forensic science international. Synergy},
volume = {13},
number = {},
pages = {100705},
pmid = {42326394},
issn = {2589-871X},
abstract = {As a part of the 21st INTERPOL International Forensic Science Managers Symposium, this work explores the latest scientific developments, methodologies, and trends in forensic biology and forensic DNA analysis of biological evidence during the years 2023 to 2025 and builds upon previous INTERPOL DNA reviews. Almost 2000 references covering the three-year time range of this review were located via various online searches including use of Scopus, Web of Science, and PubMed. The scientific articles, which originated from more than 300 different journals, were curated in a Zotero reference manager database (see Supplemental File 1) and sorted into 15 topics and 116 sub-topics (see Supplemental File 2) under sections focused on advances in current practices (Section 3) and emerging technologies and research studies (Section 4). This triennial review describes 24 books or major reports, 20 special issues of journals on aspects of forensic DNA, 292 articles from 2 International Society for Forensic Genetics (ISFG) conference proceedings, and 70 guidance documents from 17 different organizations to assist in quality DNA testing. Publications were evaluated and sorted into 10 topics around advances in current practices and 5 topics related to emerging technologies and research studies. These topics, which are further sub-divided in a compiled list (see Supplemental File 2) included rapid DNA analysis; law enforcement DNA databases and ethics; forensic investigative genetic genealogy (FIGG); forensic biology and body fluid identification; DNA processing; DNA typing with short tandem repeat (STR) markers; DNA interpretation at the source or sub-source level of the hierarchy of propositions along with mixture interpretation using probabilistic genotyping software (PGS); DNA interpretation at the activity level along with aspects of DNA transfer, persistence, prevalence, and recovery (TPPR); statistics and population genetic data; human identification and kinship analysis; next-generation sequencing (NGS) and technology developments; forensic DNA phenotyping (FDP) and methylation; lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome analyses); new markers and approaches (microhaplotypes, insertion/deletion markers, proteomics, microbiome, single-cell analysis, using environmental DNA, and biomarkers for diagnosis of sudden death, molecular autopsy, or post-mortem interval); and non-human DNA testing and wildlife forensics. Artificial intelligence (AI) tools for summarizing references were explored and utilized in performing this review of over 1900 publications.},
}

@article {pmid42326397,
year = {2026},
author = {Cherdthong, A and Foiklang, S and Altermann, E},
title = {Editorial: Assessing the environmental impact of ruminants: mitigation strategies and climate change implications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1883961},
pmid = {42326397},
issn = {1664-302X},
}

@article {pmid42326398,
year = {2026},
author = {Zhao, S and Peng, S and Li, H and Yang, G and Gao, X and Xu, K and Shi, L and Yu, H and Qiao, S},
title = {An approach for diagnosis of diarrhea in neonatal piglets based on the core gut microbiota and machine learning.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1852304},
pmid = {42326398},
issn = {1664-302X},
abstract = {Diarrheal diseases, such as yellow dysentery and white dysentery caused by pathogens or viruses, in newborn piglets lead to substantial economic losses in the swine industry worldwide. Gut microbiota dysbiosis is frequently observed in diarrheic piglets and is thought to play a role in disease pathogenesis, although causal relationships remain to be established. However, developing reliable microbiome-based diagnostic tools still poses a significant challenge. This study aimed to develop a diagnostic model for piglet diarrhea by integrating core microbiota analysis with machine learning. Fecal samples from diarrheic and healthy piglets were subjected to metagenomic sequencing to characterize archaeal, bacterial, and fungal communities. We identified diarrhea-associated bacterial biomarkers via LEfSe, DESeq2, and microbial cooccurrence network analysis. These microbial features were used to construct and compare multiple machine learning classifiers. Our results revealed significant disparities in the structure and diversity of the gut microbiota between diarrheic and healthy piglets, with the bacterial community showing the most notable changes. Among the models developed, the decision tree classifier based on bacterial genus-level features achieved the highest prediction accuracy of 91.18%. Furthermore, a simplified model utilizing a panel of 18 core bacterial genera also demonstrated high efficacy, with a support vector machine model achieving 88.24% accuracy. In independent validation using our internal dataset, the random forest model exhibited the best generalizability and stability. This study establishes a robust, microbiota-based diagnostic model for diarrhea in neonatal piglets, highlighting the potential of machine learning in leveraging microbiome data for disease classification and health management in livestock production.},
}

@article {pmid42326399,
year = {2026},
author = {Joseph, S and Stanley Abraham, L and Rajendran, T and Gopal, D and Inbakandan, D and Manikandan, S and Thangavel, B and Jones, S and Setyaningrum, R and Cho, H and Mani, RR and Chang, SW and Ravindran, B},
title = {Extremophilic bacteriorhodopsin from hypersaline salt pan: characterization and photoelectrochemical assessment for potential biosensor applications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1805566},
pmid = {42326399},
issn = {1664-302X},
abstract = {INTRODUCTION: Salt pans host a diverse microbiome, including specialized extremophilic haloarchaea capable of producing industrially valuable biomolecules, yet remains underexplored extreme environment. Photosensitive bacteriorhodopsin (BR) is a naturally occurring seven helix trans-membrane protein with emerging relevance due to its light driven proton pumping activity, photochemical stability and efficient light to electrical energy conversion.

METHODS: In this study, BR was extracted from haloarchaeal strains isolated from the Tuticorin salt pan using the Bead mix method and confirmed by SDS-PAGE. The extracted BR was further characterized using thin-layer chromatography (TLC), reverse-phase high performance liquid chromatography (R-HPLC), and Raman spectroscopy. The Purified BR was evaluated for its photovoltage response and a prototype biosensor was successfully developed.

RESULTS: Haloarchaeal isolate Halostagnicola larsenii (TP6) demonstrated a remarkable production yield of 360 mg/L of BR under native minimal saline medium conditions, the notably highest recorded for this native strain to date. This isolate was used for further optimization of BR production involving different carbon and nitrogen sources. Two different protein extraction methods were evaluated, of which the bead mix method proved to be effective, yielding around 48.4 mg/L of BR with 72.7% yield. We examined the morphological and physiological traits of these isolates and confirmed the presence of a 26 kDa protein using SDS-PAGE.

DISCUSSION: The isolated extremophilic haloarchaea have the potential to produce large amount of BR, and the characteristics were similar to those previously reported BR from native strains. The observed photoresponsive ability highlights the potential of BR as a bio-based functional component for food bio-sensing, optical devices, and photoelectrochemical biosensors. Overall, this highlights the feasibility of naturally occurring BR from haloarchaea as a sustainable source of photoactive biomolecules for emerging food biotechnology and sustainable biosensor development.},
}

@article {pmid42326403,
year = {2026},
author = {Ryazanov, V and Vershinina, I and Inchagova, K and Bukareva, E and Kolpakov, V and Ruchay, A and Kosyan, D and Marinchev, M and Zdorov, A},
title = {Fecal microbiota and microbial community transplantation: a review of current research.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1814047},
pmid = {42326403},
issn = {1664-302X},
abstract = {Homeostasis across diverse ecosystems, ranging from human hosts to environmental matrices, is profoundly governed by microbial communities. Dysbiosis, the disruption of this microbial equilibrium, leads to significant adverse outcomes in medicine, agriculture, aquaculture, and environmental health. This review synthesizes current knowledge on microbial transfusions, defined as the deliberate transfer of microbial communities or their components to restore, reconstitute, or enhance functional capacities across these systems. We explore the historical context and cutting-edge applications, including Fecal Microbiota Transplantation (FMT) for Clostridioides difficile infection, metabolic and neurological disorders, alongside advancements in vaginal microbiota transplantation. In agriculture, we summarize the engineering of soil microbiomes for enhanced plant health, stress adaptation, and bioremediation, as well as transplantation practices in livestock and wild species. Furthermore, we discuss the role of microbiota transplantation in aquaculture for improving fish health and disease resistance, highlighting both natural and synthetic consortia. The application of microbial communities in bioremediation and ecological restoration is explored, addressing challenges such as stability, cost, and ecological impacts. Ultimately, this review integrates these diverse applications within a "One Health" framework, emphasizing the systemic links among human, animal, and environmental microbiomes. We underscore the potential of microbiota transplantation as a sustainable strategy for restoring ecological balance while identifying critical research gaps and future directions regarding standardized methodologies and the long-term functionality of transplanted microbiomes.},
}

@article {pmid42326407,
year = {2026},
author = {Dai, MK and Kuang, X and Wang, YF and Liu, XX and Jin, YF and Li, YY and Tai, WL},
title = {From probiotic depletion to inflammatory cascade: multi-omics reveals the temporal progression of sleep deprivation-induced gut-liver axis disruption in mice.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1846136},
pmid = {42326407},
issn = {1664-302X},
abstract = {INTRODUCTION: Sleep deprivation (SD) is increasingly recognized as a risk factor for metabolic and hepatic disorders, yet the temporal dynamics linking gut dysbiosis to liver injury remain poorly characterized.

METHODS: In this study, we established a platform-based SD model in a total of 24 C57BL/6J mice (n = 4 per group per weekly time point) over 3 weeks and systematically investigated the weekly progression of gut microbiome alterations, hepatic metabolite profiles, and liver injury markers using Accu16S[®] absolute quantification sequencing and untargeted LC-MS/MS metabolomics.

RESULTS: Our results revealed a temporally ordered three-stage cascade of gut-liver axis disruption. In week 1, core probiotics including Bifidobacterium and Dubosiella declined concurrently with protective metabolites such as tryptamine and glycocholic acid, alongside perturbation of primary bile acid biosynthesis. In week 2, concurrent enrichment of a compensatory Lactobacillaceae member (Ligilactobacillus) and an opportunistic pathogen (Streptococcus) was accompanied by reduced microbiota-metabolite correlation density, coinciding with peak serum ALT/AST levels and metabolic pathway remodeling involving nucleotide sugar and tryptophan metabolism. By week 3, synchronous decline of Lactobacillus, Bifidobacterium, and Dubosiella coincided with full-scale activation of arachidonic acid metabolism and inflammatory immune pathways, accompanied by elevated serum LPS levels suggestive of intestinal barrier perturbation. Correlation analyses revealed that the progressive depletion of beneficial bacteria was associated with the sequential loss of protective metabolites, reorganization of the metabolic network, and inflammatory mediator accumulation, although these relationships remain correlational and require causal validation.

DISCUSSION: These findings describe a "protective loss-homeostatic decoupling-inflammatory signature" descriptive model. Because these findings are based on correlation analyses in a mouse model without causal validation, further mechanistic and interventional studies are required before any clinical implications can be drawn.},
}

@article {pmid42326408,
year = {2026},
author = {Cha, J and Yang, J and Zhang, Z and Qian, L and Yang, F and Li, S and Li, J and Jian, Z and Cheng, W},
title = {Comparative metagenomic analysis of gut microbiomes in Yunnan ponies and Dutch warmblood horses.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1807081},
pmid = {42326408},
issn = {1664-302X},
abstract = {INTRODUCTION: The Yunnan pony is an officially protected pony breed in China. However, its gut microbiome characteristics remain largely unexplored. This study aimed to compare the gut microbiome and antibiotic resistance genes (ARGs) profiles between Yunnan ponies and Dutch warmblood horses.

METHODOLOGY: A total of 14 fresh fecal samples were collected from Yunnan ponies and Dutch warmblood horses. Metagenomic sequencing was employed to comprehensively analyze and compare the gut microbial composition, function, and ARGs profiles between the two breeds.

RESULTS: The results showed no significant differences between the two breeds in core phylum composition or overall microbial diversity. A total of 146 bacterial genera were identified with significant differences at the genus level. Functional analysis revealed that the gut microbiota of Yunnan ponies was significantly enriched in pathways related to carbohydrate metabolism and pectin degradation, which are involved in basic energy acquisition. In contrast, Dutch warmblood horses were more enriched in host immune interaction pathways such as Toll-like receptor signaling. Analysis of ARGs indicated that while there was no difference in the overall diversity of ARGs between the two groups. Their association networks with specific bacterial hosts were markedly distinct, and the dominant ARG subtypes differed.

DISCUSSION: This study provides a descriptive characterization of the gut microbiome of Yunnan ponies, offering baseline data for future research on the conservation of this genetic resource and its health management in breeding.},
}

@article {pmid42326410,
year = {2026},
author = {Ma, G and Peng, L and Qin, L and Cai, R and Tan, X and Gao, R},
title = {Human milk microbiota: origins, determinants, and roles in maternal-infant microbial transmission and infant microbiome assembly.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1790225},
pmid = {42326410},
issn = {1664-302X},
abstract = {Human milk is a complex and dynamic biological fluid that provides essential nutrients and harbors a diverse, functional microbiota, playing a critical role in infant microbial colonization and early life development. The milk microbiota is derived from multiple maternal and environmental sources, including the maternal gut via the entero-mammary pathway, the mammary and skin microbiota, infant oral microbes through retrograde flow, and environmental exposures. Its composition is influenced by a range of factors, such as maternal metabolic and health status, diet, and antibiotic use, as well as delivery mode, lactation stage, infant characteristics, and geographic context. Human milk contributes to the establishment of oral, airway, and gut microbial communities by transferring key taxa such as Bifidobacterium and Lactobacillus, which are commonly detected in milk; however, direct evidence of specific strains establishing in the infant gut remains limited. Breastfeeding may partially compensate for microbiome deficits in cesarean-delivered, preterm, and antibiotic-exposed infants, supporting protection against infections, allergies, asthma, obesity, and other health outcomes. Translational strategies may help modulate the milk microbiota. These include maternal probiotic or prebiotic supplementation, dietary optimization, and approaches targeting microbiota or bioactive milk components. Such strategies offer feasible and cost-effective means to support healthy infant microbiome development. However, methodological constraints including low-biomass contamination, sequencing biases, and limited strain-level resolution remain significant challenges in accurately characterizing the human milk microbiota. Despite substantial advances, the relative contributions of distinct transmission routes, the persistence of maternal strains, and the efficacy of targeted maternal interventions remain incompletely understood. Addressing these gaps will be essential for refining strategies to promote healthy microbiome maturation and improve lifelong health outcomes.},
}

@article {pmid42326411,
year = {2026},
author = {Xu, J and Chang, Y and Ma, J and Wang, H and Li, X and Chen, X and Niu, S and An, Y and Zhao, Y},
title = {Oral microbiome signatures of post-stroke cognitive impairment.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1722999},
pmid = {42326411},
issn = {1664-302X},
abstract = {INTRODUCTION: To investigate the characteristics of oral microbiota in patients with post-stroke cognitive impairment (PSCI) and to evaluate its potential as a noninvasive candidate microbial signature associated with PSCI.

METHODS: This cross-sectional study enrolled 108 participants, including 40 PSCI patients, 40 post-stroke patients with normal cognition (PSNC), and 28 healthy controls (HC). Saliva samples were collected for 16S rRNA sequencing. Diversity analyses, differential taxa identification, and correlation analyses were performed. Candidate microbial signatures were screened using the least absolute shrinkage and selection operator (LASSO) regression and Random Forest (RF), followed by the construction of multiple machine learning models.

RESULTS: Compared with PSNC and HC, patients with PSCI exhibited significantly reduced richness and diversity of the oral microbiota, and beta-diversity analyses suggested group-level differences in community composition. The relative abundances of gram-negative taxa, such as Proteobacteria, Campylobacterota, Gammaproteobacteria, Pseudomonadales, and Alloprevotella were increased in PSCI samples. In contrast, commensal taxa Leptotrichia, and Veillonella were markedly decreased. Significant associations were observed between differential taxa and cognitive scores (MMSE and MoCA). Three key microbial features were ultimately identified. Models based on these features showed favorable exploratory internal discriminatory performance between PSCI and PSNC within this dataset. In the test set, the RF model achieved an AUC of 0.979 and an Average Precision of 0.983. However, these findings should be interpreted cautiously and require validation in larger independent cohorts.

CONCLUSION: Patients with PSCI present with notable oral microbiota dysbiosis, characterized by depletion of commensal taxa and enrichment of Gram-negative bacteria. Oral microbiota-based models showed favorable exploratory internal discriminatory performance within this dataset, but these findings remain hypothesis-generating and require external validation in larger independent cohorts.},
}

@article {pmid42326413,
year = {2026},
author = {Peng, C and Delle Grazie, G and Ghanbari, M and May, A and Abeel, T},
title = {Antibiotic growth promoter and phytogenic feed additive consistently alter microbial community structure in chicken cecum.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1702973},
pmid = {42326413},
issn = {1664-302X},
abstract = {BACKGROUND: Efforts to replace antibiotic growth promoters (AGPs) in livestock are often hindered by a limited mechanistic understanding of how sub-therapeutic antibiotic doses enhance animal growth. Since AGP concentrations are typically too low to directly suppress pathogens, their effects on the gut microbiome, particularly its ecological dynamics, warrant closer investigation. A critical but underexplored dimension is how these additives influence the structure and stability of microbial communities as interconnected ecosystems.

METHODS: We conducted a comparative network-based analysis to examine the effects of zinc-bactracin, a commonly used AGP, and Digestarom[®], an alternative phytogenic feed additive (PFA) on cecal microbiome dynamics in broiler chickens. Using metagenomic data from a repeated cross-sectional randomized controlled trial of 96 broiler chickens assigned to three dietary groups: Basal (Control), AGP and PFA, we constructed microbial co-occurrence networks using Spearman's correlation for birds raised on basal, AGP-, or PFA-supplemented diets at key developmental stages (Day 3, 14, 21, and 35). We assessed changes in network topology, modular organization and node centrality. We evaluated whether the network-prioritized keystone taxa could discriminate among diets using a Random Forest classifier.

RESULTS: Compared to the Control group, both AGP and PFA treatments induced consistent shifts in network topology, including reduced connectivity, increased modularity, increased percentage of positive interactions, enhanced mucosa connectivity, and improved structural robustness over experiment time. Overall, these treatment-induced changes were more pronounced under AGP than under PFA. Despite these changes, we identified conserved subgraphs with stable interconnections across diets and time points during the experiment. The node centrality analysis revealed condition-specific keystone taxa, but Linear Discriminant Analysis (LDA) and Random Forest (RF) struggled to accurately differentiate between diets using their abundance, particularly between PFA and the two other groups.

CONCLUSION: Our findings reveal that feed additives can reshape gut microbial dynamics without producing marked compositional shifts. The consistent network-level changes observed for both AGP and PFA highlight the value of ecological network analysis in uncovering microbial community responses. These insights improve our understanding of cecal microbiome responses in chickens, highlight potential modes of action of AGPs, and offer a comparative framework for assessing the microbial impacts of alternative feed additives.},
}

@article {pmid42326416,
year = {2026},
author = {Alva-Murillo, N and Khaiboullina, S and Tarashi, S},
title = {Editorial: Women in infectious agents and disease: 2025.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1884772},
pmid = {42326416},
issn = {1664-302X},
}

@article {pmid42326424,
year = {2026},
author = {Liang, L and Min, L and Liu, J and Liu, Y and Cheng, W},
title = {Gut microbiota dysbiosis in endometriosis: mechanistic insights and gut microbiota-targeted therapeutic strategies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1776574},
pmid = {42326424},
issn = {1664-302X},
abstract = {Endometriosis (EMs) is a prevalent, estrogen-dependent gynecological disorder characterized by the ectopic implantation and proliferation of endometrial-like tissue outside the uterine cavity, affecting approximately 10% of reproductive-aged women globally. Despite its high incidence, the exact pathogenesis of EMs remains incompletely elucidated, and current clinical treatments are often limited by suboptimal efficacy and adverse effects. Accumulating evidence over the past decade has revealed a strong observational association between gut microbiota dysbiosis and EMs development, suggesting that the gut microbiota may serve as a novel potential target for understanding and managing this disease. This review systematically summarizes the potential mechanistic links underlying the interplay between gut microbiota dysbiosis and EMs progression, focusing on three core pathways: intestinal barrier dysfunction and microbial translocation, immune dysregulation and ectopic lesion immune escape, and estrogen metabolism disorder mediated by microbial enzymes and metabolites. In addition, this review stratifies gut microbiome profiles by EMs clinical subtypes (peritoneal, ovarian, deep infiltrating), clarifies anatomical correlations of the gut-lesion axis, and discusses confounding factors and causal inference methodologies. Beyond mechanistic insights, this review also discusses emerging gut microbiota-targeted therapeutic strategies for EMs, including probiotic supplementation, prebiotic intervention, fecal microbiota transplantation (FMT), and dietary modulation, with supplementary ethical considerations for FMT. Collectively, this review provides a comprehensive overview of the gut microbiota-EMs axis, highlighting current evidence levels and offering perspectives for the development of innovative, effective, and safe therapeutic approaches for EMs patients.},
}

@article {pmid42326431,
year = {2026},
author = {Mei, X and Wu, W and Fang, N and Guo, Y and Dai, X},
title = {Sludge compost: a double-edged sword for depleted soil restoration revealed by integrated multi-omics analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1731456},
pmid = {42326431},
issn = {1664-302X},
abstract = {The prospective use of sludge compost for restoring depleted soils requires balancing its agronomic benefits against potential ecological risks. This study employed an integrated metagenomic and metabolomic approach to evaluate the dose-dependent effects of sludge compost on soil properties, maize growth, and rhizosphere microbial communities. Results showed that moderate compost application (≤15% w/w) enhanced soil nutrient availability, promoted root development, and enriched beneficial microbial taxa (Streptomyces, Mesorhizobium, Flavisolibacter), while upregulating plant stress-response metabolites (terpenoids, flavonoids). Conversely, excessive application (>20%) induced salinity stress, impaired root growth, and altered the microbial community, favoring thermophilic and xenobiotic-metabolizing taxa. Critically, high application rates led to the accumulation of residual pharmaceuticals (anti-neoplastic and anti-epileptic agents) and pesticides (insecticides and rodenticides), which correlated with the enrichment of microbial pathways associated with human diseases, highlighting a significant ecological risk. In addition, root integrity was the primary determinant of a sustainable plant-microbe feedback loop. These findings underscore the necessity for tailored application strategies to harness the soil-restorative potential of sludge compost while mitigating contaminant-driven risks, providing a framework for its safe use in sustainable agriculture.},
}

@article {pmid42326495,
year = {2026},
author = {Walters, D and Alam, MBE and Harris, T and Lo, D and Diaz, JSG and Napravnik, TC and Lynn, EJ and Boatright, LD and Figueroa, DN and Judge, A and Bhaskar, CCJ and Fontillas, A and Ehsan, SF and Wang, R and Aref, SNJ and Ajami, NJ and Sastry, J and Sims, TT and Romaguera, J and Dorta-Estremera, S and Klopp, A and Godoy-Vitorino, F and Colbert, LE},
title = {The Cervical Microbiome in Hispanic Populations in Texas and Puerto Rico with and without Cervical Dysplasia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8002153/v1},
pmid = {42326495},
issn = {2693-5015},
abstract = {Within the United States, Hispanic women, especially those in Puerto Rico, face an increased risk of cervical cancer development. The objective of this study was to explore the cervical microbiota of Hispanic women at high risk of developing HPV-induced cervical dysplasia or with cervical dysplasia treated in Texas and Puerto Rico. Cervical swab samples were collected from 296 participants (N = 80 Texan Non-Hispanic White, N = 98 Texan Hispanic, and N = 118 Puerto Rican Hispanic) during each patient's initial visit and subjected to 16S V4 rRNA gene sequencing for microbiome profiling. HPV types were grouped as HPV 16, other high-risk HPV types, and other using HPV genotyping. Among participants, 71% (N = 211) were classified as high-risk normal, and 29% (N = 85) had cervical dysplasia. HPV 16 was detected in 15% (N = 45), other high-risk HPV types in 33% (N = 98), while 52% (N = 152) of patients were classified as "other". Comparative analysis of microbial community structures across locations revealed distinct compositions, with Texan Hispanic women showing higher alpha diversity for two alpha diversity metrics (Pielou evenness and Shannon Diversity Index). The prevalence of CSTs varied across locations and disease states, with CSTs III and IV-B being among the most common in the study cohorts. Overall, this descriptive study provides a better understanding of cervical microbiome in Hispanic women across multiple geographic locations, in order to guide future interventions.},
}

@article {pmid42326511,
year = {2026},
author = {Chiyaka, TL and Moodley, S and Simon, D and Shaw, JA and Malherbe, ST and Li, Y and Warren, RM and Clemente, JC and Segal, LN and Chegou, NN and Theron, G and Marsh, CC},
title = {Bacterial topography of the respiratory tract, including pulmonary site-of-disease, in people with active tuberculosis: a case-control study.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9956587/v1},
pmid = {42326511},
issn = {2693-5015},
abstract = {BACKGROUND: No comprehensive characterization of the respiratory tract (RT) microbiota has been done in people with tuberculosis (TB), a leading global cause of death.

METHODS: 16S rRNA gene sequencing was done on upper RT (URT; oral-washes, naso- and oro-pharyngeal swabs, supraglottic fluid), sputum and lower RT [LRT; bronchoalveolar lavage fluid (BALF) and protected specimen brushings] specimens from HIV-negative people with Xpert MTB/RIF-confirmed TB (cases; n=17) and healthy controls (n=11). In addition to their diseased lobe, cases had their non-diseased lobe sampled.

RESULTS: The LRT had the lowest α-diversity and β-diversity differed compared to other respiratory compartments. In cases, Mycobacterium relative abundance was highest in the diseased lobe 1.537% (CI 0-3.114), followed by the nasopharynx 0.059% (0.012-0.105), non-diseased lobe 0.054% (0-1.620), oropharynx 0.003% (0-0.010) and sputum 0.002% (0-0.004). Compared to the URT and sputum, cases' LRTs were Mycobacterium- and Moraxella -enriched (Erythromicrobium -enriched versus sputum only). In paired comparisons of diseased versus non-diseased lobes in cases, the only differential taxon was Mycobacterium . Amongst non-diseased lobes, those of cases versus controls had reduced α-diversity with Mycoplasma -enrichment and Moraxella- and Klebsiella- depletion.

CONCLUSION: Compared to healthy people, those with TB have a less diverse LRT microbiota, characterized by Mycobacterium -enrichment (within the diseased lobe and surprisingly least so in sputum) and depletion of taxa associated with healthy people. In people with TB, most microbial DNA is not mycobacterial within the diseased lobe and even the non-diseased lobes of cases are microbially distinct from controls. These findings provide a foundation for understanding respiratory tract host-microbiome interactions in TB.},
}

@article {pmid42326513,
year = {2026},
author = {Knight, R and Khatib, L and Patel, L and MahmoudianDehkordi, S and Labus, J and Agongo, J and Borkowski, K and Ambre, M and Brydges, C and Schimmel, L and Blach, C and Consortium, AGMP and Karu, N and Taylor, M and Diaz, E and Brosch, J and Bendlin, B and Swerdlow, R and Henderson, V and Chen, D and Saykin, A and Craft, S and Brewer, J and Wisniewski, T and Roberson, E and Dorrestein, PC and Kaddurah-Daouk, R},
title = {Interconnected influences of diet, gut microbiome, and metabolome on cognition across three metabolomics platforms.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9917711/v1},
pmid = {42326513},
issn = {2693-5015},
abstract = {Cognitive impairment is increasing with global aging, yet mechanisms linking diet, the gut microbiome, and metabolism to cognitive function remain unclear. To investigate a diet-microbiome-metabolome axis associated with cognition, we integrated fecal metagenomics, diet, and multi-platform plasma metabolomics in 505 older adults from four ADRCs. Several microbes broadly associated with circulating metabolites were also linked to multiple measures of cognitive performance. These taxa exhibited coordinated metabolic signatures, with cognition-positive microbes associated with antioxidant, lipid, and microbial-host co-metabolites, and microbes negatively associated with cognition were linked to inflammatory and aromatic amino acid-derived metabolites. Dietary patterns, particularly the Healthy Eating Index Greens and Beans component, were associated with microbial composition and metabolomic structure. Mediation analyses supported a diet-microbe-metabolite-cognition pathway, while metabolites remained associated with cognition after accounting for microbial features. These findings highlight the metabolome as a central integrator of diet, microbial activity, and cognitive function.},
}

@article {pmid42326540,
year = {2026},
author = {Yang, J and Nie, D and Zhang, Y and Li, C},
title = {Exploratory Pilot Multi-Omics Profiling of Gut Microbiota and Metabolic Features in Patients with Prolactinoma.},
journal = {Cancer management and research},
volume = {18},
number = {},
pages = {608026},
pmid = {42326540},
issn = {1179-1322},
abstract = {BACKGROUND: Growing evidence suggests a potential role of the gut microbiota in pituitary neuroendocrine tumors (PitNETs). This exploratory study focused on prolactinoma, the most prevalent PitNET subtype, to preliminarily characterize gut microbial and metabolic features associated with the disease.

MATERIALS AND METHODS: Fecal samples were collected from five patients with hyperprolactinemic prolactinoma and five patients with nonfunctioning (NF) PitNETs. Exploratory metagenomic and metabolomic analyses were performed to profile gut microbiota composition and metabolic alterations.

RESULTS: Compared with NF PitNET controls, prolactinoma patients showed distinct trends in gut microbial composition, including increased abundances of Bacteroides and Eubacterium and decreased abundances of Blautia and Clostridium. Metabolomic profiling identified differential metabolic features, including elevated fatty acid esters of hydroxy fatty acids (FAHFAs) and palmitoleic acid, which were mainly associated with glucose and lipid metabolism pathways.

CONCLUSION: This pilot multi-omics analysis provides preliminary evidence of altered gut microbiome-metabolite profiles in prolactinoma. These findings are hypothesis-generating and may support further investigation of gut-pituitary axis interactions in larger, well-powered cohorts.},
}

@article {pmid42326568,
year = {2026},
author = {Stacul, A and Valido, E and Nyfeler, N and Bertolo, A and Zeh, RM and Fontana, AO and Pannek, J and Krebs, J and Leichtle, A and Glisic, M and Stoyanov, J},
title = {Precision Rehabilitation in Spinal Cord Injury: A Systematic Review of Omics Applications for Intervention Monitoring in Spinal Cord Injury.},
journal = {Archives of rehabilitation research and clinical translation},
volume = {8},
number = {2},
pages = {100598},
pmid = {42326568},
issn = {2590-1095},
abstract = {OBJECTIVE: To systematically evaluate the application and utility of omics technologies, high-throughput methods measuring the complete or targeted set of molecules inside a biological system at a certain timepoint, in monitoring and optimizing rehabilitation interventions in traumatic spinal cord injury.

DATA SOURCES: Embase, Medline/Ovid, and Web of Science were searched from inception to November 27, 2024.

STUDY SELECTION: Eligible studies included adults (≥18 years) with spinal cord injury undergoing rehabilitation interventions assessed using omics technologies (genomics, epigenomics, transcriptomics, proteomics, metabolomics, or metagenomics).

DATA EXTRACTION: Following PRISMA guidelines, independent screening, data extraction, and risk of bias (RoB) assessment (National Institutes of Health Quality Assessment Tools) were performed by 2 investigators. Based on RoB assessment, studies were classified from level 1 (most reliable) to level 4 (least reliable).

DATA SYNTHESIS: Twenty-three trials were included: 8 randomized controlled trials, 5 non-randomized controlled trials, and 10 pre-post trials. Twenty-two studies (96%) exhibit a moderate RoB due to small sample size and heterogeneity. Omics technologies were primarily applied to exercise and electrical muscle stimulation interventions (65%), followed by hormonal and cellular therapies (22%), and diet (13%). Transcriptomic analyses revealed consistent molecular adaptations, including increased mitochondrial biogenesis (proliferator-activated receptor gamma coactivator 1-alpha) and reduced muscle atrophy gene expression (myostatin), correlating with enhanced insulin sensitivity and improved aerobic capacity. Metagenomics consistently identified microbiome shifts, such as decreased inflammatory taxa and increased beneficial taxa, associated with improved metabolic profiles and bowel function. Proteomics and metabolomics highlighted systemic changes related to neurorecovery, immune modulation, and sperm motility, linking molecular signatures directly to clinical outcomes.

CONCLUSIONS: Omics technologies enable early identification of molecular alterations. However, given small sample sizes and heterogeneity of the current studies, these findings should be interpreted with caution. Gradual integration of omics, particularly epigenomics which may capture long-term, injury-related changes holds promise for developing personalized rehabilitation protocols and monitoring clinical progression in spinal cord injury.},
}

@article {pmid42326627,
year = {2026},
author = {Camini, AM and Cogo, LR and Delawi, ME and Anton, DB and Koakovski Acosta, J and de Lima, JC and Saraiva Macedo Timmers, LF},
title = {Beyond Urease: New Potential Enzymatic Targets in Helicobacter pylori.},
journal = {ACS omega},
volume = {11},
number = {23},
pages = {33320-33332},
pmid = {42326627},
issn = {2470-1343},
abstract = {H. pylori infection remains one of the most widespread bacterial diseases globally and a leading risk factor for peptic ulcer disease and gastric cancer. Despite decades of research, the treatment of H. pylori still depends on multidrug antibiotic regimens, whose efficacy is waning due to the rise in antimicrobial resistance. Although significant progress has been made in understanding H. pylori pathogenesis, most studies targeting bacterial enzymes have focused almost exclusively on urease, a well-characterized virulence factor, while other metabolic and structural pathways remain comparatively underexplored. Targeting essential enzymes involved in bacterial metabolism and structural integrity may disrupt vital processes, potentially reducing off-target effects on the host microbiota and overcoming resistance mechanisms. To address this gap, this systematic review, conducted according to PRISMA 2020 guidelines, synthesized experimental studies published between 2014 and 2024 that investigated enzyme-targeted compounds against H. pylori, excluding those focused on urease. Literature searches in PubMed and the Web of Science identified 49 eligible studies exploring enzymes across multiple metabolic pathways. The main pathways identified included purine metabolism, the shikimate and futalosine pathways, and nitrogen metabolism, along with several other enzymatic systems, such as thioredoxin, thymidylate, and peptidoglycan biosynthesis, all of which represent promising targets for selective inhibition in H. pylori. The reported inhibitors exhibited micromolar to submicromolar activity and, in some cases, demonstrated potent antibacterial effects with minimal cytotoxicity. However, most studies remained limited to in vitro assays, and only three included animal tests. These findings highlight enzymatic inhibition as a promising approach for the rational design of narrow-spectrum microbiome-sparing agents. Advancing these discoveries through in vivo validation and druggability assessment will be essential to translating enzyme-based inhibition into effective therapeutic options against H. pylori.},
}

@article {pmid42326740,
year = {2026},
author = {Avina-Bravo, EG and García-Lorenzo, I and Alfaro-Ponce, M and Breton-Deval, L},
title = {Machine learning-based classification of COVID-19 severity using respiratory microbiome profiles from shotgun metagenomic sequencing.},
journal = {Frontiers in bioinformatics},
volume = {6},
number = {},
pages = {1801685},
pmid = {42326740},
issn = {2673-7647},
abstract = {Accurate clinical triage is critical for optimizing decision-making and resource allocation during infectious disease outbreaks such as COVID-19. In this study, we present an AI-driven decision-support tool for the triage of COVID-19 patients based on respiratory microbiome profiles derived from shotgun metagenomic sequencing. We analyzed 477 shotgun respiratory metagenomes from three independent public cohorts and generated genus-level taxonomic profiles, which were integrated with minimal clinical metadata (age, sex, and antibiotic exposure) to train supervised machine-learning models, including Random Forest, Support Vector Machine, and XGBoost. Model performance was evaluated using standard classification metrics, cross-validation, and particle swarm optimization for hyperparameter tuning. Across cohorts, we observed a consistent transition from microbiomes dominated by commensal taxa to dysbiotic states enriched in opportunistic and clinically relevant genera, particularly Acinetobacter and Staphylococcus, in severe and deceased patients. Among the evaluated models, XGBoost consistently achieved the best performance, reaching up to 96.1% accuracy, 97.6% F1-score, and 98.2% ROC-AUC in individual cohorts. When trained on the integrated dataset, XGBoost maintained robust performance (95.1% accuracy, 97.2% F1-score, 94.3% ROC-AUC) and demonstrated greater stability and lower variance compared to alternative models. Feature-importance analyses identified a compact and interpretable set of recurrent microbial predictors, and reduced-feature models retained substantial discriminative power when augmented with key clinical variables. These results support the respiratory microbiome as a valuable source of information for outcome-oriented clinical triage and position microbiome-informed machine learning as a scalable and interpretable decision-support approach for managing COVID-19 and future infectious disease scenarios.},
}

@article {pmid42326836,
year = {2026},
author = {Yi Jia, AT and Peacock, CS and Dye, DE and Christophersen, CT},
title = {Ig-microbiota binding patterns in mothers and infants: a scoping review.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e12},
pmid = {42326836},
issn = {2632-2897},
abstract = {Studies characterising the immunoglobulin (Ig)-bound microbiota apply varying methodologies, making comparisons difficult. This scoping review synthesised evidence on Ig-microbiota binding patterns in maternal and infant contexts, identified recurrent Ig-bound and -unbound bacteria across studies, and highlighted knowledge gaps for further study. Nine articles investigating Ig-microbiota binding patterns in stool or breastmilk samples in mothers or infants were included. Ig-microbiota associations were influenced by sample type, Ig-subclass, genetics, and diet. The most important antibody was IgA, with partial functional redundancy with IgM, while IgG appeared more selective for pathobionts. Ig-bound taxa in early life included important commensals and pathobionts, with high levels of individuality. Ig-microbiota associations shifted with microbiome maturation, environmental and host factors, resembling adults at around 2 years of age. Transfer of Ig-bound Bifidobacterium through breastmilk may contribute to vertical transmission from mother to infant. Ig-microbiota associations also differed between health and disease states, beyond the overall microbiota. Results were limited by study numbers and a lack of methodological consistency. We propose the standardised term "Ig-Seq" in referring to the technique to study Ig-microbiota binding patterns, and suggest standardisation of laboratory protocols, bioinformatic pipelines, and statistical analyses to improve consistency in Ig-Seq.},
}

@article {pmid42326837,
year = {2026},
author = {Virwani, PD and Qian, G and Cheung, CN and Pijarnvanit, TKKTS and Hsu, MSS and Chow, YH and Tang, LK and Tse, YH and Xian, JW and Lam, SS and Lee, CPI and Lo, CCW and Liu, RKC and Ho, TL and Chow, BY and Leung, KS and Lo, EKK and Yuen, MF and Leung, SY and Hung, IF and Louie, JCY and Teo, KC and El-Nezami, H and Ho, JWK and Lau, KK},
title = {Associations between gut microbiome and 24-hour blood pressure variability: a cross-sectional study highlighting sex differences and potential therapeutic targets.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e9},
pmid = {42326837},
issn = {2632-2897},
abstract = {Blood pressure (BP) variability is an independent risk factor for cardiovascular disease. Gut microbiome (GM) regulates BP, but its association with BP variability remains unclear. We examined the association of GM, determined by stool shotgun metagenomic sequencing, with 24-hour BP average real variability (ARV) assessed by ambulatory BP monitoring in 235 community-dwelling adults from Hong Kong (111 men and 124 women, mean age 54 ± 6 years) using covariate-adjusted statistical models. The GM alpha diversity was negatively associated with systolic BP (SBP) ARV in the full cohort, driven by women. In men, beta diversity of both GM species and function was associated with SBP ARV, while Bacteroides nordii and the steroid hormone biosynthesis pathway had a positive association with SBP ARV. Bacteroides nordii emerged as the key species driving the significant positive association of steroid hormone biosynthesis and other pro-pathogenic pathways with SBP ARV, including lipopolysaccharide biosynthesis, phenylalanine, and sulfur metabolism in men, warranting further investigation for its causal role. We demonstrated distinct signatures of GM dysbiosis, composition, and function with minimal overlap between men and women with increased 24-hour SBP variability. Our work suggests that sex differences should be an important consideration in mechanistic and therapeutic investigations of GM-mediated BP variability.},
}

@article {pmid42326879,
year = {2026},
author = {Edwards, WJ and Salman Al-Adilee, YM and Denoyelle, C and Mackins, H and Griffiths, RA and Tsaousis, AD},
title = {Rewilding reshapes gut microbiomes and parasite exposure in European bison: a 17‑month release from Wilder Blean.},
journal = {Journal for nature conservation},
volume = {92},
number = {},
pages = {None},
pmid = {42326879},
issn = {1617-1381},
abstract = {Reintroductions can restore lost ecological processes, but managers require practical health indicators to track the acclimation of released animals. We longitudinally profiled the gut microbiomes of European bison (European bison bonasus) released to the Wilder Blean area (Kent, UK), sampling three adult females before and after release, and a post‑release male and calf. Using V3-V4 16S rRNA gene sequencing, we quantified alpha‑ and beta‑diversity, identified differentially abundant taxa, and screened faeces for Cryptosporidium, Enterocytozoon bieneusi and Blastocystis. Post‑release, adult microbiomes shifted significantly (PERMANOVA P = 0.001) and consistently across all examined animals. Calf microbiome profiles transitioned from early‑life communities to an adult‑like state concurrent with weaning. Parasite screening via separate PCR and qPCR showed that Cryptosporidium positivity declined in females from 36% pre‑release to 13% post‑release, whereas E. bieneusi emerged only after release (∼10% of samples), with multiple genotypes detected. These patterns are consistent with dietary and environmental turnover following release, and they highlight opportunities for using microbiome and parasite metrics as complementary, non‑invasive indicators of rewilding progress. We recommend reporting simple, management‑relevant indicators, archiving sequence data, and documenting soft‑release design and supplementary feeding info to aid interpretation. Integrating routine faecal microbiome and parasite monitoring into rewilding programmes can support adaptive management, inform supplementary feeding decisions, and strengthen biosecurity risk assessments.},
}

@article {pmid42327082,
year = {2026},
author = {Loya, O and Villarreal, ES and Carneiro, A and Agarwal, S and Fraidenburg, D and Sun, J and de Jesus Perez, V and Lahm, T and Oliveira, SD},
title = {Sex-linked Lung Estrobolome May Contribute to Pulmonary Hypertension Penetrance of Bmpr2 R899X Mutation via an ET-1 [high] Endoregulatory Macrophage Phenotype.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.08.729693},
pmid = {42327082},
issn = {2692-8205},
abstract = {Mutations in the bone morphogenetic protein receptor 2 (BMPR2) are a major genetic driver of pulmonary arterial hypertension (PAH), yet their penetrance is strikingly sex-biased: females are disproportionately affected, while males experience poorer outcomes. While hormonal and chromosomal factors have been implicated, the biological basis for this disparity remains not fully understood. Here, we investigated the role of the lung microbiome in sex-linked PAH pathogenesis. We hypothesized that increased BMPR2 mutation penetrance in females is partly driven by the accumulation of potent vasoactive molecules, such as endothelin-1 (ET-1), in response to lung microbiome dysbiosis. Using humanized Bmpr2 [+/R899X] mice, we integrate lung metagenomics with basic functional immune profiling to show that females develop a distinct microbiome profile, characterized by increased microbial-derived lipopolysaccharide (LPS), potentially fueling the pathogenic effects of the estrogen metabolite 16α-hydroxyestrone (16α-OHE). These signals converge on macrophages, where co-exposure led to a hyperactivated state characterized by enhanced phagocytosis and ET-1 secretion. Tissue-level analyses confirmed immune cell infiltration and spatial association with elevated ET-1, providing evidence that these factors may contribute to the onset of sex-linked PAH. Taken together, these findings identify a previously unrecognized microbiome-estrogen-immune axis that amplifies BMPR2 dysfunction and provides a mechanistic basis for female-biased disease penetrance.},
}

@article {pmid42327170,
year = {2026},
author = {Russell, BJ and Hasenoehrl, E and Marando, VM and Lu, J and Chen, JM and James, MJ and Goyal, M and Walker, S and Rakoff-Nahoum, S and Jost, M},
title = {Identification of the complete pathway for conversion of bilirubin to urobilinogen by human gut bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.10.731317},
pmid = {42327170},
issn = {2692-8205},
abstract = {Bilirubin, the predominant product of heme catabolism in mammals, enters the intestine via the hepatobiliary system and subsequently is metabolized by the gut microbiome. This process consumes bilirubin and generates multiple downstream derivatives, such as urobilinogen and stercobilinogen. Levels of bilirubin and its derivatives are associated with susceptibility to inflammatory and metabolic disorders, but the microbial species and enzymes that metabolize bilirubin have remained largely unknown. Here, demonstrate that metabolism of bilirubin to urobilinogen requires two separate reactions that can occur in either order and identify novel enzymes and pathway intermediates required for conversion. We find that bilirubin reductase (BilR), an enzyme that was recently discovered and proposed to convert bilirubin to urobilinogen, is specific for reducing the methine bridges of bilinoids, converting bilirubin to the novel intermediate divinylurobilinogen and mesobilirubin to urobilinogen. Using transcriptomic profiling, we identify the bilinoid vinyl reductase (BilV) responsible for reducing the vinyl groups of bilirubin and divinylurobilinogen. BilV is a flavin-dependent oxidoreductase of the Old Yellow Enzyme (OYE) superfamily with a broad distribution across human gut bacteria that overlaps with but does not completely mirror the distribution of BilR. These findings establish the complete pathway for bacterial conversion of bilirubin to urobilinogen, enabling defined studies to interrogate how this metabolism contributes to human health and disease.},
}

@article {pmid42327301,
year = {2026},
author = {Chakraverti-Wuerthwein, MS and Domenig, A and Kuehn, S},
title = {Phylogenetic coherence in microbiome composition across environmental gradients.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.06.07.730742},
pmid = {42327301},
issn = {2692-8205},
abstract = {Global surveys of microbial communities across biomes have shown that environmental variables such as depth and pH are strong determinants of community composition. However, we do not understand how the traits of individual taxa, and their evolutionary conservation, conspire to give rise to these patterns. Exploiting large-scale surveys of top soil and marine microbiomes, we use canonical correlation analysis (CCA) to concurrently infer directions of environmental variation and the associated compositional changes. We find that the primary canonical direction, capturing the dominant environmental gradient, exhibits a strong phylogenetic signal: individual species' responses to environmental shifts along this direction are similar among taxa with shared evolutionary history. In contrast, secondary canonical directions show weak or no phylogenetic structure. Together, these results suggest a two-scale view of microbial community assembly. Deeply evolutionarily conserved traits govern community reorganization along the main environmental driver of community composition. Additional environmentally driven changes in community composition then reflect traits that are more evolutionarily labile.},
}

@article {pmid42327471,
year = {2026},
author = {Li, YM and He, FF and Donge-Liu, and Bin-Xu, and Shuyi-Li, },
title = {Multi-Omic Profiling of Gut Microbiota and Fecal Metabolites in Patients With Polycystic Ovary Syndrome: A Cross-Sectional Study.},
journal = {Health science reports},
volume = {9},
number = {6},
pages = {e72593},
pmid = {42327471},
issn = {2398-8835},
abstract = {BACKGROUND AND AIM: Intestinal flora composition in polycystic ovary syndrome (PCOS) varies, and the relationship between intestinal flora, fecal metabolites, clinical characteristics, and PCOS pathogenesis remains unclear. This study aimed to elucidate the gut microbiota characteristics of patients with PCOS, focusing on changes in normal-weight individuals, to provide new insights into its pathogenesis.

METHODS: We combined 16S rRNA gene sequencing re-analysis with metagenomics and metabolomics to investigate gut microbiota and fecal metabolome alterations in PCOS. We re-analyzed our previous data on normal-weight women with PCOS (PCOS, n = 24; healthy controls [HC], n = 12) and the public databases (PCOS, n = 98; HC, n = 71) to further investigate the structure and function of the PCOS intestinal flora. Subsequently, from our previous study samples, we selected 10 patients residing in the Kaifu district, and their fecal samples (normal-weight PCOS group, n = 6; HC group, n = 4) were analyzed using metagenomic sequencing and non-targeted fecal metabolomics. Finally, the correlations among intestinal flora, fecal metabolites, and clinical indicators were evaluated.

RESULTS: Based on the 16S rRNA data reanalysis, there were no significant differences in beta and alpha diversity between PCOS and normal controls. However, the PCOS group displayed a significantly higher relative abundance of Ruminococcus, Lachnospiraceae, and Escherichia-Shigella (p < 0.05) but a significantly lower relative abundance of Prevotella (p < 0.05) compared with the HC group. Subsequent metagenomics and metabolomics analyses revealed functional alterations, particularly in pathways related to secondary bile acid and lipid metabolism. Furthermore, Ruminococcus and Roseburia were positively correlated with Homeostasis Model Assessment of Insulin Resistance (HOMA-IR) and negatively correlated with high-density lipoprotein (HDL) in patients with normal-weight PCOS.

CONCLUSIONS: This study highlights gut microbial dysbiosis as a key feature of PCOS. Reanalysis of 16S rRNA data revealed specific taxonomic shifts without altering overall diversity, notably an enrichment of Ruminococcus and a depletion of Prevotella. Furthermore, our metagenomics study identified functional reprogramming in pathways related to secondary bile acid and lipid metabolism. Crucially, even in normal-weight PCOS patients, these microbial alterations significantly correlated with adverse metabolic profiles (heightened insulin resistance and lower HDL levels), highlighting the microbiome as a potential therapeutic target.

ETHICAL REVIEW NO: CHiECRT1900028223.},
}

@article {pmid42327630,
year = {2026},
author = {Katarzyna, BS and Danuta, CL and Wiktoria, K and Małgorzata, T and Natalia, K and Dominika, MM and Karina, R and Joanna, P and Karina, K and Barbara, G and Danuta, LK and Helena, G and Wiśniewska, M and Karolina, SŻ and Stachowska, E},
title = {The impact of freeze-dried food on gut microbiota composition: a preliminary study.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101470},
pmid = {42327630},
issn = {2665-9271},
abstract = {Freeze-dried food is widely used during space expeditions or flights. However, evidence on how this affects the gut microbiota is limited. This study aimed to assess changes in the composition of gut microbiota in volunteers subjected to a 14-day stay in a controlled space-analogue habitat. Five adults provided stool samples at baseline and after two weeks. Meals were freeze-dried and standardized for portion size and composition. Meals were served according to a daily schedule with no additional snacks allowed. Coffee and tea were permitted. Compliance was monitored by returning and verifying the packaging. Bacterial community profiles were assessed using shallow shotgun metagenomics and analyzed using paired statistical methods, including alpha diversity indices and beta diversity ordination with permutation-based testing. Differential abundance analyses were performed to identify taxa showing trends toward change during the intervention. Overall gut bacterial diversity and community structure were essentially stable over 14 days among all participants. No statistically significant changes in alpha diversity were observed, and global beta diversity patterns did not indicate a consistent separation of the entire community between baseline and day 14. Exploratory analyses suggested small changes within individuals in the relative abundance of selected taxa; however, inter-individual variability prevailed, and the small sample size limited statistical power. It appears that a diet consisting entirely of freeze-dried foods, consumed for 14 days, did not significantly affect the overall diversity of the gut microbiota or the structure of its communities. However, these studies are preliminary in nature and provide hypotheses for use in larger, controlled studies aimed at elucidating the microbiome's response to dietary regimens based on freeze-dried products.},
}

@article {pmid42327664,
year = {2026},
author = {Antoine, MW},
title = {Microbiome Hype Meets Epilepsy: Signal, Noise, and Mechanism.},
journal = {Epilepsy currents},
volume = {},
number = {},
pages = {15357597261459806},
pmid = {42327664},
issn = {1535-7597},
}

@article {pmid42327708,
year = {2026},
author = {Gomes, M and Li, Z and Olaitan, A and Gentry-Maharaj, A},
title = {Predictive modeling for cervical cancer: existing AI approaches and the emerging role of vaginal microbiome.},
journal = {Frontiers in network physiology},
volume = {6},
number = {},
pages = {1799486},
pmid = {42327708},
issn = {2674-0109},
abstract = {Cervical cancer remains a major global health burden, yet current screening tools lack precision in identifying which women with high-risk human papillomavirus (HPV) infection will progress to high-grade lesions or cancer. Within a network-physiology framework, cervical carcinogenesis is viewed as emerging from dynamic interactions between viral dynamics, host immunity, vaginal ecology, vaccination status and behaviour rather than from isolated risk factors. This perspective review examines artificial intelligence (AI) approaches for cervical cancer prediction and evaluates the emerging role of the vaginal microbiome as a complementary biomarker within these interconnected physiological networks. The review synthesises evidence linking non-Lactobacillus-dominated or Lactobacillus iners-rich vaginal communities with increased HPV persistence and cervical intraepithelial neoplasia, contrasted with protective Lactobacillus crispatus-dominant communities, and outlines how these ecological signatures could be combined with HPV genotype and clinical factors in multi-modal models. A structured narrative synthesis of published AI tools demonstrates that current prognostic, diagnostic and screening algorithms rely mainly on demographic, clinical or imaging variables, with no validated models yet integrating vaginal microbiome profiles into cervical cancer risk calculators. The manuscript proposes a technical framework for microbiome-enabled modelling, covering feature engineering from community state types, algorithm selection, handling of high-dimensional omics data, and staged validation in NHS-relevant populations. Finally, it outlines a translational pathway for embedding microbiome-informed risk models into cervical screening using self-collected tampon sampling, AI-driven triage and digital decision support, and identifies key unmet needs, including longitudinal multi-omic cohorts, international consortia and robust bias auditing.},
}

@article {pmid42327718,
year = {2026},
author = {Zhang, X and Chen, F and Yang, J and Ma, J and Li, X and Wang, H and Li, Q and Zhao, Y and Xu, J},
title = {Oral and gut microbiota dysbiosis with strengthened oral-gut connectivity in post-stroke cognitive impairment.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1851811},
pmid = {42327718},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology ; Female ; *Stroke/complications/microbiology ; Male ; *Cognitive Dysfunction/microbiology/etiology ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Aged ; *Mouth/microbiology ; Feces/microbiology ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Microbiome studies in post-stroke cognitive impairment (PSCI) have focused on the gut, while upstream oral dysbiosis and oral-gut axis signatures remain undercharacterized. We profiled paired oral and gut microbiota in PSCI to assess coordinated alterations and cross-site associations.

METHODS: This single-center cross-sectional study enrolled 133 post-stroke participants (64 PSCI). Paired tongue-coating and fecal samples underwent 16S rRNA gene sequencing. We compared α/β diversity, taxonomic composition, and predicted functional pathways at both sites, quantified within-individual oral-gut dissimilarity and the gut fraction of oral-gut shared microbiota, and adapted an oral enrichment score (OES) to index gut "oralization". Differential microbiota, predicted pathways, and MMSE/MoCA scores were integrated into a multi-layer association framework. Machine-learning models were built using oral features, gut features, and combined oral-gut features, with SHAP for interpretability.

RESULTS: PSCI showed reduced oral richness (ACE/Chao1) and reduced gut diversity/evenness (Shannon/Simpson), with significant β-diversity differences at both sites. Oral commensals (Leptotrichia, Neisseria) were depleted, whereas opportunistic taxa (Pseudomonas, Alloprevotella, Streptococcus) were enriched. In the gut, SCFA-associated microbiota (Coprococcus, Faecalibacterium, Ruminococcus) decreased, while Gram-negative potential pathogens (Enterobacter, Pseudomonas, Klebsiella) increased. Tax4Fun2-based inference suggested predicted gut functional alterations involving lipopolysaccharide biosynthesis potential and tryptophan metabolism-related pathways. Oral-gut metrics supported stronger oral-gut association in PSCI, including lower paired dissimilarity, a higher shared-genera fraction, and elevated OES (median 0.0368 vs 0.0142), mainly driven by oral-dominant microbiota (Streptococcus, Fusobacterium, Veillonella and Haemophilus). Combined oral-gut features showed the most favorable exploratory test-set performance (XGBoost AUC 0.945; average precision 0.943).

CONCLUSIONS: PSCI was associated with coordinated oral and gut dysbiosis, characterized by loss of commensals, enrichment of opportunistic or Gram-negative taxa, and a stronger gut oralization signal reflected by reduced oral-gut dissimilarity and elevated OES. Tax4Fun2 suggested predicted functional potential related to lipopolysaccharide biosynthesis and tryptophan metabolism, while combined oral-gut features showed favorable exploratory internal discrimination of PSCI. These findings require validation in larger longitudinal multi-omics cohorts.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology
Female
*Stroke/complications/microbiology
Male
*Cognitive Dysfunction/microbiology/etiology
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
Aged
*Mouth/microbiology
Feces/microbiology
Bacteria/classification/genetics

@article {pmid42327728,
year = {2026},
author = {Maiese, K},
title = {Agitation, Alzheimer's disease, and autophagy: mechanistic insights into aging pathways, gut microbiome, and artificial intelligence.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1846280},
pmid = {42327728},
issn = {1664-3224},
mesh = {Humans ; *Alzheimer Disease/metabolism/therapy/psychology/etiology ; *Aging ; *Autophagy ; *Gastrointestinal Microbiome ; Animals ; *Artificial Intelligence ; },
abstract = {The presentation of mood disorders that involve agitation and anxiety in patients with cognitive loss represent significant challenges for the care of patients with Alzheimer's disease (AD). Additional concerns rest with the rising lifespan and aging of the global population with expectations that over the next two decades more than 50 percent of the elderly population will suffer from mental health disease and at least 30 million of these individuals will also succumb to cognitive loss with AD. Although current treatments for mood disorders and cognitive loss can have a multi-modal approach with behavioral therapy, cognitive training sessions, physical exercise, nutritional care, environmental changes, and disease modifying agents, these therapies are primarily symptomatic in nature that do not halt disease progression and possess risks for further nervous system insults. Given these consideration, novel work that addresses the shared underlying pathways for mood disorders and cognitive loss with autophagy and related mechanisms of programmed cell death, aging and cellular senescence, perivascular system dysfunction, inflammatory microglial cell dynamics, oxidative stress, metabolic pathways that involve diabetes mellitus and apolipoprotein E, the gut microbiota, glucagon-like peptide-1 receptor agonism, innovative diagnostic strategies, artificial intelligence, and machine learning can offer rewarding avenues for the innovative development of therapeutic strategies that address disease onset and progression of these disorders. These pathways that oversee mood disorders and cognitive are both critical and complex in their intimate relationships and warrant in-depth knowledge of the mechanisms that can influence biological outcome for clinical translation.},
}

Humans
*Alzheimer Disease/metabolism/therapy/psychology/etiology
*Aging
*Autophagy
*Gastrointestinal Microbiome
Animals
*Artificial Intelligence

@article {pmid42327767,
year = {2026},
author = {Hunter, JGL and Roach, A and Nieves, L and Islas, A and Islas, A and DiPalma, M},
title = {The intratumoral microbiome: a review of the tumor microenvironment's fourth axis shaping anti-tumor immunity, cancer prognosis, and therapeutic response.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1820477},
pmid = {42327767},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Microbiota/immunology ; Prognosis ; *Neoplasms/immunology/therapy/microbiology ; Animals ; },
abstract = {The tumor microenvironment (TME) is a well-documented, complex, and dynamic ecosystem traditionally considered among three major axes: 1) malignant cells, 2) stromal cells, and 3) infiltrating immune cells; all whose interactions have been assumed to shape tumor growth, progression, and therapeutic response. Specific TME profiles are strongly associated with cancer prognosis, especially those characterized by distinct immune cell populations. Within the TME, less-studied populations of various microorganisms constitute the intratumoral microbiome. While the systemic microbiome is well-established as a regulator of overall health, disease progression, and cancer prognosis, the role of microorganisms residing directly within tumors remains largely underexplored and often overlooked. As evidence on the intratumoral microbiome continues to emerge, it is increasingly apparent that, in addition to the previously characterized components of the TME, these tumor-resident microbes may significantly impact the TME through complex interactions, effectively constituting a fourth component that must be considered alongside malignant, immune, and stromal cells. We therefore propose a framework in which the TME is defined across four axes: malignant cells, stromal cells, infiltrating immune cells, and intratumoral microbes. Herein, we review the effects of intratumoral microbes on various immune cell types commonly studied within the TME, their effects on specific cancers, and subsequent therapeutic insights that arise from understanding the intratumoral microbiome.},
}

Humans
*Tumor Microenvironment/immunology
*Microbiota/immunology
Prognosis
*Neoplasms/immunology/therapy/microbiology
Animals

@article {pmid42327780,
year = {2026},
author = {Zeng, Y and Feng, Y},
title = {The association between atopic dermatitis and rosacea: a comprehensive review from comorbidities to pathogenic mechanisms.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1837198},
pmid = {42327780},
issn = {1664-3224},
mesh = {Humans ; *Rosacea/immunology/epidemiology ; *Dermatitis, Atopic/immunology/epidemiology ; Immunity, Innate ; Comorbidity ; Animals ; Skin/immunology ; Skin Microbiome ; Adaptive Immunity ; },
abstract = {OBJECTIVE: Atopic dermatitis (AD) and rosacea have traditionally been regarded as two distinct inflammatory skin disorders with divergent pathophysiology. However, emerging evidence has progressively revealed unexpected convergences between these conditions in clinical manifestations, comorbidity profiles and pathogenic mechanisms-raising the question of whether the apparent mechanistic overlaps represent true pathophysiological convergence-sharing common upstream drivers-or merely parallel, non- specific innate immune responses triggered by entirely distinct microbial and genetic factors? This distinction carries profound implications for the design of shared versus disease-specific therapeutic strategies. this review aims not simply to enumerate similarities but to critically evaluate whether the observed convergences represent true mechanistic overlap, or parallel but independent responses.

METHODS: Literature search strategy: A comprehensive literature search was conducted in PubMed, Embase and Scopus, the Cochrane Library between April, 2016 and April, 2026. The search strategy combined controlled vocabulary and free-text terms, including " rosacea", " atopic dermatitis", " mast cells", " comorbidity", " microbiome", " innate immunity", " adaptive immunity", and " neurovascular". Reference lists of relevant articles were also manually screened to identify additional eligible studies.

Studies were included if they: (1) focused on atopic dermatitis and/or rosacea; (2) investigated relevant immunological mechanisms, comorbidities, or pathophysiological pathways; and (3) provided sufficient data to support qualitative synthesis. Both original research articles and high- quality reviews or meta-analyses were considered. Studies were excluded if they: (1) were duplicate publications; (2) lacked sufficient methodological detail or extractable data; or (3) were not directly relevant to the objectives of this review.

Study selection and data extraction were performed independently by two reviewers. Titles and abstracts were initially screened, followed by full-text assessment for eligibility. Any discrepancies were resolved through discussion, and when necessary, a third reviewer was consulted to reach consensus.

STUDY SELECTION PROCESS: A total of 5381records were identified through database searching, with an additional 83 records identified through manual reference screening. After removal of duplicates, 3185records remained for title and abstract screening, of which 2864 were excluded due to irrelevance. A total of 321 full-text articles were assessed for eligibility, and 216 were further excluded for the following reasons: lack of relevance (n =117), insufficient data (n =53), or low methodological quality/non-original articles (n = 46). Ultimately, 105 studies were included in the qualitative synthesis. The study selection process is summarized in a PRISMA-style flow diagram (Graphical Abstract, below). Given the narrative nature of this review, no formal risk-of-bias assessment was performed.

RESULTS: Critical appraisal of the evidence reveals that both diseases share an upstream innate immune activation platform' encompassing TLR2/TLR4 signaling, NLRP3 inflammasome activation, mast cell degranulation and neurovascular dysregulation via the CGRP/SP/VEGF/TRP axis. However, they diverge at the level of adaptive immune polarization: AD is dominated by Th2/ILC2 skewing with IgE sensitization and deficient antimicrobial peptide responses, while rosacea is characterized by Th 1/Th17 involvement with autonomous LL-37 overproduction as its primary amplification loop. Intriguingly, dupilumab-induced rosacea-like dermatitis suggests that these polarization states may not merely differ but actively compete, raising questions about the nature and limits of mechanistic overlap between the two conditions. This duality may challenge simplistic models of mechanistic overlap and has direct implications for differential clinical management. Future research should employ multi-omics approaches and prospective comorbidity cohorts to clarify causal pathways and translate mechanistic insights into optimized therapeutic strategies.},
}

Humans
*Rosacea/immunology/epidemiology
*Dermatitis, Atopic/immunology/epidemiology
Immunity, Innate
Comorbidity
Animals
Skin/immunology
Skin Microbiome
Adaptive Immunity

@article {pmid42327783,
year = {2026},
author = {Hong, S and Um, GS and Kang, BS and Kim, O and Lee, SU and Ko, HS and Nam, S and Lee, S and Park, IY and Shin, S},
title = {Vaginal dysbiosis and inflammatory signatures in preterm labor: an integrated model for predicting preterm birth.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1809046},
pmid = {42327783},
issn = {1664-3224},
mesh = {Humans ; Female ; *Dysbiosis/microbiology/immunology ; Pregnancy ; *Obstetric Labor, Premature/microbiology/immunology/metabolism ; *Vagina/microbiology/immunology ; *Premature Birth/microbiology/immunology/diagnosis/etiology ; Adult ; Cytokines/metabolism ; Microbiota ; Prospective Studies ; Biomarkers ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Preterm birth (PTB) is a major cause of neonatal morbidity and mortality, with vaginal microbiome dysbiosis and local immune responses implicated in its pathogenesis. However, the role of vaginal immune and extracellular matrix (ECM) remodeling factors in the progression from preterm labor (PTL) to PTB remains unclear. This study examines the associations between microbiome composition and immune and ECM-related protein composition in PTL patients to identify key factors and predictive models associated with the risk of PTB.

METHODS: This prospective study included 136 pregnant women classified into three groups: Control (Term Birth, TB), PTL-TB (Preterm Labor with Term Birth), and PTL-PTB (Preterm Labor with Preterm Birth). Vaginal microbiome composition was analyzed using 16S rRNA sequencing and categorized by dysbiosis status and community state types (CST). Cytokines (IL-1β, IFN-γ, IL-2, IL-4, IL-6, IL-8, IL-10, IL-12p70) and ECM remodeling enzymes (MMP-1, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-12, MMP-13, IGFBP-1) were quantified in vaginal secretions using the Luminex[®] Assay multiplex kit. A multivariable logistic regression model was constructed to predict preterm birth, using significant microbiome, cytokine, and MMP variables, with performance evaluated by ROC analysis.

RESULTS: Dysbiosis and CST IV were more prevalent in the PTL-PTB group. IL-1β was highest in CST III, while MMP-9 and other MMPs were elevated in CST IV. CVF MMP-9 was consistently increased across PTL-PTB cases, dysbiosis, and CST IV. However, IGFBP-1, MMP-8, and MMP-13 were significantly different by clinical outcome but not correlated with microbiome composition. A logistic regression model incorporating non-Lactobacillus fraction, IGFBP-1, MMP-9, MMP-13, and TNF-α demonstrated excellent predictive performance (AUC = 0.910) for PTB.

CONCLUSIONS: Distinct microbial and immune profiles are associated with the progression from PTL to PTB. MMP-9 may serve as a key effector linking dysbiosis to extracellular matrix remodeling and PTB. Integrative biomarker models may support early risk stratification in women with PTL.},
}

Humans
Female
*Dysbiosis/microbiology/immunology
Pregnancy
*Obstetric Labor, Premature/microbiology/immunology/metabolism
*Vagina/microbiology/immunology
*Premature Birth/microbiology/immunology/diagnosis/etiology
Adult
Cytokines/metabolism
Microbiota
Prospective Studies
Biomarkers
RNA, Ribosomal, 16S/genetics

@article {pmid42327791,
year = {2026},
author = {Pospich, R and Abdurrahman, G and Honstein, T and Nordengrün, M and Traidl, S and Begemann, G and Kienlin, P and Werfel, T and Bröker, BM and Roesner, LM},
title = {Staphylococcus aureus serine protease-like protein B elicits a type 1/type 2 immune response in atopic dermatitis patients.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1798583},
pmid = {42327791},
issn = {1664-3224},
mesh = {Humans ; *Dermatitis, Atopic/immunology/microbiology ; *Staphylococcus aureus/immunology/enzymology ; Male ; Female ; Immunoglobulin E/blood/immunology ; *Bacterial Proteins/immunology ; *Serine Proteases/immunology ; Cytokines/metabolism ; Adult ; *Th2 Cells/immunology ; Lymphocyte Activation/immunology ; *Th1 Cells/immunology ; Skin/immunology ; Young Adult ; Middle Aged ; Adaptive Immunity ; },
abstract = {INTRODUCTION: Atopic dermatitis (AD), a common chronic inflammatory skin disease, is characterized by type-2-mediated inflammation, along with the detection of type-1 and type-3 cytokines in lesional skin. The skin microbiome of lesional skin is dominated by the pathogen Staphylococcus aureus, which can aggravate the disease via pathogenicity factors. To elucidate the impact of the adaptive immune response on inflammation in AD, this study focused on staphylococcal serine-like proteases (Spl) of S. aureus, a family of secreted pathogenicity factors with the potential to induce type-2 responses.

METHODS: Specific serum IgE against Spl family members was quantified, and SplB-specific CD4[+] T cells were identified by surface expression of CD154 after in vitro stimulation with recombinant SplB. Immunodominant epitopes within the SplB primary structure were predicted to generate MHC multimers for staining, sorting, and cytokine analysis of SplB-specific T cells. TCRB sequencing was applied to identify SplB-specific T cells in AD skin lesions.

RESULTS: We observed significantly elevated levels of IgE antibodies specific for Spl family proteins in patients with AD compared to healthy controls. In vitro, recombinant SplB was sufficient to induce T cell activation and cytokine secretion in PBMCs from patients with AD and healthy controls. SplB-specific T helper cells, which were cell-sorted from patients' blood by MHC-II multimers, showed the capacity to produce IFN-γ and IL-13 ex vivo. Clonal propagation of specific T cells was confirmed by TCR sequencing, and SplB-specific TCR sequences were re-identified in autologous lesional skin biopsy material.

DISCUSSION: The presence of clonally propagated SplB-specific T cells in the skin of patients with AD strongly suggests an impact on inflammation. This type of cellular immune response, which is not exclusively polarized towards type 2, reflects the AD phenotype. This suggests that the adaptive immune response to S. aureus contributes to this phenotype.},
}

Humans
*Dermatitis, Atopic/immunology/microbiology
*Staphylococcus aureus/immunology/enzymology
Male
Female
Immunoglobulin E/blood/immunology
*Bacterial Proteins/immunology
*Serine Proteases/immunology
Cytokines/metabolism
Adult
*Th2 Cells/immunology
Lymphocyte Activation/immunology
*Th1 Cells/immunology
Skin/immunology
Young Adult
Middle Aged
Adaptive Immunity

@article {pmid42327796,
year = {2026},
author = {Peng, J and Li, Z and Wu, W and Sun, N and Yang, X and Liu, Q and Li, H},
title = {Non-invasive detection of pediatric atopic dermatitis based on fecal microbiota and metabolite profiles: a diagnostic approach.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1836716},
pmid = {42327796},
issn = {1664-3224},
mesh = {Humans ; *Dermatitis, Atopic/diagnosis/microbiology/metabolism ; Female ; *Feces/microbiology ; Male ; *Metabolome ; Child ; Case-Control Studies ; Biomarkers ; *Gastrointestinal Microbiome ; Child, Preschool ; Metabolomics/methods ; Bacteria/classification/genetics ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is a common chronic skin inflammation, which affects 15-20% of children worldwide. Gut microbiota and its metabolites are crucial modulators of the "gut-skin axis" in atopic dermatogenesis. However, systematic investigations integrating microbiome and metabolome profiling in mild-to-moderate pediatric AD remain limited.

OBJECTIVES: To characterize gut microbiota and metabolic profiles in children with mild-to-moderate AD versus healthy controls, and to identify potential biomarkers and mechanistic pathways involved in disease pathogenesis.

METHODS: This single-center case-control study investigated 53 children diagnosed with AD and 16 healthy participants, and collected their fecal samples for microbial and metabonomic analysis.

RESULTS: Mild-moderate pediatric AD patients exhibited significantly increased gut microbial richness and distinct β-diversity compared to controls (PERMANOVA, R²=0.025, P = 0.017). Bacteroidota was enriched while Actinomycetota was depleted in AD patients (P < 0.05). At genus level, Parabacteroides and Klebsiella increased, whereas Bifidobacterium decreased in AD. Species-level analysis revealed enrichment of bacteroides_plebeius, bacteroides_thetaiotaomicron, bacteroides_xylanisolvens, and parabacteroides_merdae in AD. A combined biomarker panel (Bacteroidota, Parabacteroides, and four key species) demonstrated promising exploratory diagnostic potential (AUC = 0.941, accuracy 84.6%), although these results require external validation in larger independent cohorts. Spearman analysis showed correlations between gut microbiome and clinical severity indicators. Thermodesulfobacteriota, Actinomycetota, Bifidobacterium, and specific ruminococcus strains positively correlated with the severity of AD. Metabolomics identified 68 differentially accumulated metabolites, primarily involved in lipid metabolism and nucleotide metabolism. Bacteroides species showed significant positive correlations with isovaleric acid levels in microbiota-metabolite analyses.

CONCLUSION: Mild-to-moderate pediatric AD is characterized by distinct gut microbiota dysbiosis and metabolic alterations involving lipid metabolism. Cross-sectionally identified microbial features show exploratory associations with AD status, but causal inference is not possible. These hypothesis-generating findings support further investigation of the gut-skin axis in AD development and provide a rationale for future interventional studies targeting the microbiome and metabolome.},
}

Humans
*Dermatitis, Atopic/diagnosis/microbiology/metabolism
Female
*Feces/microbiology
Male
*Metabolome
Child
Case-Control Studies
Biomarkers
*Gastrointestinal Microbiome
Child, Preschool
Metabolomics/methods
Bacteria/classification/genetics

@article {pmid42239166,
year = {2026},
author = {Ghadermazi, P and Emerson, JB and Olm, MR},
title = {ZipStrain Enables Rapid and Precise Strain-Resolved Metagenomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42239166},
issn = {2692-8205},
abstract = {Strain-resolved metagenomics characterizes microbial communities at nucleotide-level resolution, enabling researchers to differentiate identical from closely related organisms and characterize population structure and gene content variation. Here we introduce ZipStrain, a program that performs highly accurate strain-resolved metagenomics over 500× faster than available methods while offering superior RAM management. Applied to a dataset of 2,754 samples spanning human populations, we identify a strain-sharing gradient across social relationships, reveal striking variation in clonal structure across bacteria and bacteriophage, and pinpoint genes whose nucleotide identity deviates from genome-wide expectations. ZipStrain is distributed as an open-source Python package and accompanying Nextflow pipeline at https://github.com/OlmLab/ZipStrain.},
}

@article {pmid42316154,
year = {2026},
author = {Seo, E and Kim, SH and Kwak, MJ and Hwang, JK and Mustafa, G and Chang, YS and Hoh, JK and Jeon, BH and Park, HK and Kim, Y},
title = {Gut dysbiosis associated with neonatal respiratory distress syndrome and biological plausibility of disease-specific probiotic intervention: a translational study.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08462-x},
pmid = {42316154},
issn = {1479-5876},
support = {202400000002957//College of Medicine, Hanyang University/ ; RS-2023-00255939//Korea Institute of Energy Technology Evaluation and Planning/ ; NSIT; RS-2025-16068814//National Research Foundation of Korea/ ; },
abstract = {BACKGROUND: Neonatal respiratory distress syndrome (RDS) is among the most prevalent morbidities in late preterm and term infants. Although the gut-lung axis has been implicated in neonatal respiratory disease, the relationship between RDS and early gut microbiome composition remains poorly characterized. This study aimed to characterize gut microbiome alterations associated with RDS and surfactant replacement therapy (SRT), and to evaluate the biological plausibility of a disease-specific probiotic intervention.

METHODS: Two complementary cohorts were prospectively enrolled. In the clinical observational cohort (n = 45), fecal samples collected within 48 h of birth were analyzed by Nanopore 16S rRNA sequencing across three groups: infants without RDS (control group, n = 25), infants with RDS who did not receive SRT (RDS(S-) group, n = 7), and infants with RDS who received SRT (RDS(S+) group, n = 13). In the probiotic discovery cohort (n = 40), gut microbiota of infants without RDS (CON group, n = 17) and infants with RDS (RDS group, n = 23) were characterized by metagenomic sequencing and culturomics. Candidate probiotic strains were evaluated in a fermenter for intestinal microbiota model (FIMM) and a fecal microbiota transplantation (FMT) mouse model.

RESULTS: The RDS(S-) group exhibited depletion of beneficial taxa including Bifidobacterium and Lacticaseibacillus and enrichment of opportunistic pathogens including Enterococcus and Staphylococcus. Following SRT, gut microbial profiles partially shifted toward those of the control group. Limosilactobacillus fermentum SLAM_LAF05 and Bifidobacterium longum SLAM_BIL02 were identified as CON-enriched candidate probiotic strains through direct microbiome comparison and selected based on superior acid and bile tolerance and adhesion capacity. In the FIMM model, probiotic supplementation increased microbial diversity and suppressed opportunistic pathogens. In the FMT mouse model, probiotic supplementation was associated with upregulation of ZO-1, MUC2, and Reg3g, reduction of fecal calprotectin, and restoration of serum IgG levels.

CONCLUSIONS: This study provides an early translational characterization of RDS-associated gut dysbiosis and its partial resolution following SRT, and establishes proof-of-concept for a disease-specific probiotic approach. These findings offer a new perspective on the interplay between gut microbial dynamics and the early postnatal respiratory course, and provide a basis for future investigations into microbiota-targeted strategies in neonates with RDS.},
}

@article {pmid42316315,
year = {2026},
author = {Zebardast, A and Javadi, K},
title = {Human microbiome alterations in Epstein-Barr Virus infection: a systematic review.},
journal = {Gut pathogens},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13099-026-00854-0},
pmid = {42316315},
issn = {1757-4749},
support = {724137379//Babol University of Medical Sciences/ ; },
abstract = {Epstein-Barr virus (EBV) is associated with several malignancies and immune-mediated conditions, but its relationship with human microbial communities remains incompletely understood. We systematically searched PubMed, Embase, and Scopus for human studies evaluating EBV-associated alterations in the microbiome. Because of substantial clinical and methodological heterogeneity, findings were synthesized narratively, and study quality was assessed using the ROBINS-I tool. Nine observational studies published between 2017 and 2025 were included, covering the oral cavity, nasopharynx, gut, gastric tissue, and subgingival plaque. EBV positivity or EBV-related clinical status was associated with niche-specific microbial shifts, including altered gut bacterial profiles, distinct microbial patterns in EBV-associated gastric cancer tissue, and enrichment of oral-associated pathobionts in nasopharyngeal carcinoma compartments. Alpha- and beta-diversity findings were inconsistent across studies. Overall, the evidence suggests context-dependent alterations in the microbiome in EBV-positive or EBV-related disease settings. However, these findings should be interpreted as EBV-associated rather than EBV-specific, particularly when EBV status overlaps with malignancy. The small observational evidence base, heterogeneous EBV-status definitions, methodological variability, and residual confounding limit causal inference. Larger longitudinal and standardized multi-omic studies are needed to clarify directionality, mechanisms, and clinical relevance.},
}

@article {pmid42316350,
year = {2026},
author = {Zhao, J and Su, Q and Wang, S and Li, Q and Chen, L and Kang, X and Xu, Q and Liu, C and Zhao, H},
title = {Differentiating hemorrhagic shock and organophosphate poisoning through integrated skin microbiome-metabolome signatures.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05276-1},
pmid = {42316350},
issn = {1471-2180},
support = {2024B04J0022//Guangzhou Science and technology planning project/ ; 82371901//National Natural Science Foundation of China/ ; 2023JC36//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; },
abstract = {Accurate determination of cause of death and estimation of postmortem interval (PMI) are critical yet challenging tasks in forensic science, particularly in cases with rapid demise and absence of obvious morphological abnormalities. We employed an integrative multi-omics approach to characterize postmortem microbial succession and metabolic alterations on facial skin in mouse models of hemorrhagic shock (HS) and organophosphorus poisoning (OP) across three decomposition stages: bloating (2 days), active decay (8 days), and advanced decay (16 days). Metagenomic profiling revealed significantly reduced α-diversity in HS compared with OP throughout all stages (p < 0.001), accompanied by stage-dependent compositional shifts, including early enrichment of Firmicutes in HS and Proteobacteria in OP. A total of 237 differential taxa were identified, with Providencia and Morganella predominating in OP, whereas Staphylococcus and Corynebacterium dominated bloating stage of HS. Untargeted metabolomics uncovered distinct cause-of-death-linked metabolites, notably elevated 2'-deoxycytidine-5'-diphosphate in early OP and persistent cholic acid/cholate accumulation in HS at later PMI. Functional analysis highlighted histidine and phosphate/phosphonate metabolism as key discriminatory pathways, exhibiting stage-specific oscillations and strong correlations with characteristic taxa. These findings demonstrate that skin-based metagenomic-metabolomic integration provides robust, mechanistically informed biomarkers for both PMI estimation and cause-of-death differentiation, offering a minimally invasive and temporally dynamic tool for forensic investigations.},
}

@article {pmid42316485,
year = {2026},
author = {Juma, NS and Shuaibu, A},
title = {Bioactive carbohydrates: a mini-review.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70835},
pmid = {42316485},
issn = {1097-0010},
abstract = {Bioactive carbohydrates, including dietary fibers, prebiotics and resistant starches, play emerging roles in gut health, metabolic regulation, as well as chronic disease prevention. This mini review systematically classifies these compounds, summarizes their mechanisms of action, and evaluates their current and potential applications in functional food development. It also identifies several critical gaps, for example: how structural properties (type, source, molecular characteristics) and non-short-chain fatty acid fermentation metabolites influence physiological outcomes, the challenge of maintaining stability and functionality during processing (heat and pH optimization), the need to investigate nano-carbohydrate systems and prebiotic delivery matrices for microbiota modulation, metabolite release, and bioavailability, and the optimization of resistant starch extraction and application to balance functional benefits with sensory quality and in vivo validation. Translational evidence gaps, regulatory frameworks, personalized nutrition, and microbiome-based therapeutics are also discussed as future priorities. Generally, this mini-review provides a brief overview of the role of bioactive carbohydrates in food and nutrition. © 2026 Society of Chemical Industry.},
}

@article {pmid42316492,
year = {2026},
author = {Epelde, F},
title = {The Microbiota-Gut-Brain Axis: A New Frontier in Precision Neuropsychopharmacology.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X438648260611062058},
pmid = {42316492},
issn = {1875-6190},
abstract = {INTRODUCTION: The gut microbiota has emerged as a relevant modulator of brain function, behavior, and treatment response through the microbiota-gut-brain axis. This bidirectional system may influence the pharmacokinetics and pharmacodynamics of psychotropic drugs, offering new perspectives for neuropsychopharmacology and precision psychiatry. The aim of this review was to synthesize current evidence on the mechanisms by which gut microbiota affects the absorption, metabolism, efficacy, and safety of neuroactive drugs, and to explore its clinical implications in psychiatric practice.

METHODS: A narrative review was conducted using preclinical and clinical studies published in recent years. Evidence was gathered from peer-reviewed articles indexed in PubMed, Scopus, and Web of Science, integrating findings from microbiology, neuroscience, pharmacology, and psychiatry. Particular attention was given to microbiota-drug interactions involving antidepressants, antipsychotics, mood stabilizers, and anxiolytics.

RESULTS: Gut microorganisms may modulate psychotropic drug effects through enzymatic biotrans-formation, alterations in host metabolic pathways, regulation of neurotransmitter systems, and modulation of immune and endocrine signaling. Differences in microbiota composition have been associated with variability in therapeutic response, tolerability, and adverse-effect profiles. Emerging evidence also suggests that microbiota-targeted strategies, including probiotics, prebiotics, and dietary interventions, may act as adjuvant approaches to improve efficacy and reduce side effects.

DISCUSSION: Although the microbiota-gut-brain axis represents a biologically plausible and clinically relevant determinant of psychotropic outcomes, current evidence remains heterogeneous and largely associative. Methodological variability, small sample sizes, and limited longitudinal data restrict translation into routine clinical practice. Microbiota-informed prescribing appears promising, but requires standardized multi-omics profiling, harmonized sampling procedures, and robust prospective validation.

CONCLUSION: Gut microbiota may play an important role in psychotropic drug outcomes and could support more personalized, effective, and safer psychiatric care. Further mechanistic studies and standardized clinical trials are needed before microbiota-informed prescribing can be reliably implemented.},
}

@article {pmid42316512,
year = {2026},
author = {Maeno, S and Kataoka, N and Matsutani, M and Yakushi, T},
title = {Discordance Between 16S rRNA Similarity and Genome-Based Species Boundaries in Gluconobacter.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70335},
pmid = {42316512},
issn = {2045-8827},
mesh = {*RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; Phylogeny ; *Gluconobacter/genetics/classification ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; },
abstract = {The 16S rRNA gene is widely used for bacterial identification, but its resolving power is limited in several taxa. In the genus Gluconobacter, species boundaries remain unclear despite reliance on 16S-based classification. To examine these limitations, we analyzed all publicly available complete genomes (n = 12) together with curated 16S rRNA sequences and compared 16S rRNA sequences similarity with genome-based relatedness. Within the sampled complete genomes, 16S rRNA sequences were highly conserved and showed substantial overlap between intra- and interspecific similarities. In contrast, average nucleotide identity (ANI)-based divergence was pronounced: ANI values ranged from 79.7% to 100%, and G. oxydans included more than one genomic lineage. Notably, two strains (H24 and 1.637) showed higher ANI values (97.2%-97.4%) to G. thailandicus than to other G. oxydans strains. Even the hypervariable V4, V6, and V8 regions lacked clade-specific signatures, indicating limited species-level resolution within this group. Furthermore, type-strain 16S rRNA sequences of G. oxydans, G. frateurii, and G. japonicus show ≥ 99% similarity and are grouped within the same non-redundant representative in the SILVA NR99 database, indicating limited species-level resolution. These results demonstrate a clear mismatch between 16S rRNA sequences similarity and genomic structure in Gluconobacter. Genome-based criteria, supported by refined reference databases and validated gene markers, are essential for accurate taxonomy and microbiome-based analyses.},
}

*RNA, Ribosomal, 16S/genetics
*Genome, Bacterial
Phylogeny
*Gluconobacter/genetics/classification
DNA, Bacterial/genetics
Sequence Analysis, DNA

@article {pmid42316541,
year = {2026},
author = {Upadhyay, SK},
title = {Holobiont Plasticity Under Abiotic Stress: A Systems Biology Perspective on Plant-Bacteria-Fungi Interactions.},
journal = {Physiologia plantarum},
volume = {178},
number = {3},
pages = {e70971},
doi = {10.1111/ppl.70971},
pmid = {42316541},
issn = {1399-3054},
mesh = {*Stress, Physiological/physiology ; *Systems Biology ; *Plants/microbiology ; *Bacteria/metabolism ; *Fungi/physiology ; Plant Growth Regulators/metabolism ; Plant Roots/microbiology ; Rhizosphere ; Microbiota/physiology ; },
abstract = {Abiotic stress frequency and intensity are increasing, severely impacting plants' health, hence leading to significant crop yield losses (~20%-40% globally). In addition to modifying their genetic and physiological traits to increase stress tolerance, growing research revealed that plant-microbiome interaction plays a remarkable role in determining stress resilience. This review integrates physiological, ecological, and multi-omics data suggesting holobiont plasticity is an unifying paradigm for mechanistic understanding of stress-induced plant-microbe system reorganization. Abiotic stress causes rapid changes in plants' root metabolism and root exudate composition, which alter the release of organic acids, phenolics, osmolytes, and signaling compounds, which selectively change the microbial community's structure in the rhizosphere and endosphere. Microbial taxonomic diversity usually declines under stress conditions. Meanwhile, functional redundancy within the microbial communities is generally maintained or can increase. However, network connectivity may often remain stable or become stronger under stress, and the centrality of keystone taxa usually increases. These keystone microbes play a critical role in sustaining microbial community structure and function. Microbial regulation of phytohormones (such as auxin, ethylene, and abscisic acid), along with control of redox balance, osmotic adjustment, and nutrient cycling, improves plant water use, nutrient uptake, and root development. This often makes them more tolerant to stress by 15%-60% without increasing their biomass. Holobiont plasticity emerges as a quantifiable and potentially predictive characteristic of plant stress responses by integrating microbial network structure, functional gene profiles, metabolomic responsiveness, and host regulatory mechanisms. These responses function on ecological timescales (days to weeks), preceding the more gradual process of host genetic adaptation. This halobiont plasticity-based framework shows promising potential but requires validation under field conditions to prove its robustness and applicability. This opens new avenues for microbiome-assisted plant growth and development of a climate-resilient agricultural system.},
}

*Stress, Physiological/physiology
*Systems Biology
*Plants/microbiology
*Bacteria/metabolism
*Fungi/physiology
Plant Growth Regulators/metabolism
Plant Roots/microbiology
Rhizosphere
Microbiota/physiology

@article {pmid42316543,
year = {2026},
author = {Jia, L and Wang, H},
title = {Crohn's Disease Enteritis: Pathophysiological Mechanisms and Therapeutic Approaches.},
journal = {Scandinavian journal of immunology},
volume = {103},
number = {6},
pages = {e70129},
doi = {10.1111/sji.70129},
pmid = {42316543},
issn = {1365-3083},
mesh = {Humans ; *Crohn Disease/therapy/immunology/etiology ; Animals ; Intestinal Mucosa/immunology/pathology ; Gastrointestinal Microbiome/immunology ; Cytokines/metabolism ; Genetic Predisposition to Disease ; Intestinal Barrier Function ; *Enteritis/therapy/immunology ; Signal Transduction ; },
abstract = {Crohn's disease (CD) is a chronic, relapsing-remitting inflammatory condition of the gastrointestinal tract. This review provides a comprehensive analysis of the underlying pathophysiological mechanisms, highlighting the interplay between intestinal epithelial cells, dysregulated immune responses, gut microbiota and environmental triggers in CD. Key genetic susceptibilities (e.g., NOD2, ATG16L1, IL23R) and dysregulated T-cell signalling, particularly involving T-helper 1 (Th1) and T-helper 17 (Th17) pathways, are central to CD pathogenesis. The progression of the disease is driven by complex cytokine and chemokine networks (e.g., TNF-α, IL-6, IL-17), epithelial barrier dysfunction and microbial dysbiosis, all of which contribute to chronic inflammation and mucosal damage. Advanced models, including organoids and patient-derived xenografts, have elucidated these mechanisms, aiding in biomarker discovery and drug development. Diagnostic advancements such as capsule endoscopy, magnetic resonance enterography, faecal calprotectin and molecular assays enable precise characterization of CD phenotypes and activity. Therapeutic strategies now encompass targeted biologics that neutralize key cytokines, small-molecule Janus kinase (JAK) inhibitors that interrupt intracellular inflammatory signalling and emerging modalities targeting epithelial repair and microbiome restoration. Despite significant progress, challenges persist in managing refractory CD, including loss of response to biologics and fibrostenotic or fistulizing complications. Personalized approaches based on immunological profiling, microbiota composition and molecular diagnostics hold promise for more effective interventions. This review underscores the complexity of intestinal inflammation in CD and advocates for integrated, personalized strategies to improve patient outcomes.},
}

Humans
*Crohn Disease/therapy/immunology/etiology
Animals
Intestinal Mucosa/immunology/pathology
Gastrointestinal Microbiome/immunology
Cytokines/metabolism
Genetic Predisposition to Disease
Intestinal Barrier Function
*Enteritis/therapy/immunology
Signal Transduction

@article {pmid42316765,
year = {2026},
author = {Liang, L and Chen, S and Zhu, B and Huang, Y and Lu, X and Wang, S and Wang, W and Han, R and Zhou, J and Xiong, D and Li, H and Li, X and Ning, Y and Wu, F and Wu, K},
title = {Continuous Alterations in the Gut Microbial Landscape Associated With Suicidal Ideation in First-Episode Drug-naïve Major Depressive Disorder.},
journal = {CNS neuroscience & therapeutics},
volume = {32},
number = {6},
pages = {e70892},
pmid = {42316765},
issn = {1755-5949},
support = {2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; //Clinical Medical Research Institute/ ; GCAAL2022001//Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; },
mesh = {Humans ; *Major Depressive Disorder/psychology/microbiology ; *Gastrointestinal Microbiome/physiology ; *Suicidal Ideation ; Female ; Male ; Adult ; Dysbiosis/psychology ; Cohort Studies ; },
abstract = {BACKGROUND: Major depressive disorder (MDD) has been closely associated with gut microbiota dysbiosis; however, the role of the gut microbiota in the progression from depression to suicidal ideation (SI) remains unclear.

METHODS: We enrolled a well-characterized clinical cohort of first-episode, drug-naïve MDD patients, explicitly classified into those without SI (MDDNSI) and those with SI (MDDSI), and matched with healthy controls (HC) on demographic variables. A severity-ordered HC-MDDNSI-MDDSI framework was established to capture progressive microbial and functional shifts, and correlation analyses were used to evaluate their relationships with clinical symptoms and cognitive function.

RESULTS: We identified a group of taxa showing clear severity-related trends, with the potential pathogenic species Bacteroides stercoris and Bacteroides eggerthii increasing across the clinical spectrum, while seven species, including Faecalibacillus intestinalis and Dialister massiliensis, showed a steady decrease. Functional annotation indicated that several major metabolic pathways, such as the bacterial secretion system, weakened progressively with disease severity and formed stable microbe-pathway modules together with pathways involved in energy metabolism and signal transduction. These differential taxa and pathways showed strong associations with clinical features, with Bacteroides stercoris positively correlated with SI, whereas Bifidobacterium pseudocatenulatum displayed a negative association. In addition, mediation analysis further showed that Bacteroides stercoris indirectly influenced SI through the bacterial secretion system pathway, suggesting a meaningful mediating role in SI.

CONCLUSION: These results revealed progressive alterations in gut microbial composition and metabolic function associated with SI, indicating that gut dysbiosis serves as a potential biological marker for suicide risk in MDD.},
}

Humans
*Major Depressive Disorder/psychology/microbiology
*Gastrointestinal Microbiome/physiology
*Suicidal Ideation
Female
Male
Adult
Dysbiosis/psychology
Cohort Studies

@article {pmid42316807,
year = {2026},
author = {Chowdhury, MAH and Reem, CSA and Ashrafudoulla, M and Yoon, HJ and Ha, SD},
title = {Biofilm Formation and Spore-Mediated Persistence of Clostridium perfringens in Meat and Poultry Processing Environments and Their Implications for Control Strategies.},
journal = {Journal of food science},
volume = {91},
number = {6},
pages = {e71193},
pmid = {42316807},
issn = {1750-3841},
support = {//Chung-Ang University Young Scientist Scholarship in 2024/ ; //Chung-Ang University research grant in 2025/ ; },
mesh = {*Biofilms/growth & development ; *Clostridium perfringens/physiology/drug effects ; Animals ; *Spores, Bacterial/physiology ; *Meat/microbiology ; Poultry/microbiology ; *Food Handling ; Food Microbiology ; Food Contamination/prevention & control ; Food, Processed ; Anti-Bacterial Agents/pharmacology ; Quorum Sensing ; },
abstract = {Clostridium perfringens (C. perfringens) biofilms pose a persistent challenge in meat and poultry processing environments due to their structural resilience, spore-mediated survival and toxin-associated virulence. These biofilms readily develop on food-contact surfaces under typical processing conditions including organic residue accumulation, temperature fluctuations, and localized anaerobic niches, leading to increased tolerance to sanitation and thermal treatments. Mechanistically, biofilm resilience in C. perfringens is governed by the integration of sporulation processes, quorum sensing-regulated gene expression and extracellular polymeric substance (EPS) matrix formation, which collectively enhance stress tolerance, limit antimicrobial penetration, and facilitate persistence under fluctuating environmental conditions. The interaction between spore formation and EPS architecture further promotes survival during thermal processing and enables rapid re-establishment of biofilms following sanitation. This review synthesizes current knowledge on the formation and persistence of C. perfringens biofilms, key environmental drivers in meat and poultry processing systems and the mechanistic basis of their stress resistance and survival strategies. It also critically examines how these mechanisms influence the efficacy of existing intervention strategies. It further evaluates the limitations of conventional control strategies and highlights emerging approaches for biofilm prevention and control, including food-grade antimicrobials, surface engineering, enzymatic disruption, and microbiome-based interventions, with emphasis on their modes of action and applicability in industrial settings. Overall, this review provides a mechanistic and systems-level perspective to support the development of more effective biofilm control strategies in meat processing environments.},
}

*Biofilms/growth & development
*Clostridium perfringens/physiology/drug effects
Animals
*Spores, Bacterial/physiology
*Meat/microbiology
Poultry/microbiology
*Food Handling
Food Microbiology
Food Contamination/prevention & control
Food, Processed
Anti-Bacterial Agents/pharmacology
Quorum Sensing

@article {pmid42316904,
year = {2026},
author = {Saheb Sharif-Askari, N and Eladham, MW and Mdkhana, B and Sekar, P and Hafezi, S and Shakartalla, SB and Hachim, I and Saheb Sharif-Askari, F and Halwani, R},
title = {The Role of Fecal Microbiome Transplantation in Steroid Hyporesponsive Asthma.},
journal = {Comprehensive Physiology},
volume = {16},
number = {3},
pages = {e70196},
doi = {10.1002/cph4.70196},
pmid = {42316904},
issn = {2040-4603},
support = {24010902170//University of Sharjah/ ; 25011103119//University of Sharjah/ ; 2401110399//University of Sharjah/ ; 24010903159//University of Sharjah/ ; ORF-RC-2026-0509//King Saud University/ ; },
mesh = {*Asthma/therapy/microbiology ; *Fecal Microbiota Transplantation ; Animals ; *Gastrointestinal Microbiome ; Humans ; Dysbiosis/therapy ; *Adrenal Cortex Hormones/therapeutic use ; },
abstract = {Asthma is a chronic inflammatory airway disease characterized by airflow obstruction, airway hyperresponsiveness, and structural remodeling. Corticosteroids remain the mainstay of asthma therapy; however, a substantial proportion of patients with severe disease develop steroid hyporesponsiveness, limiting therapeutic efficacy and increasing disease burden. Emerging evidence implicates the gut microbiome as a key regulator of systemic immune responses, with growing relevance to asthma pathogenesis and treatment responsiveness. In this study, we investigated whether gut microbiota dysbiosis contributes to steroid hyporesponsive lung inflammation and whether fecal microbiota transplantation (FMT) can restore steroid responsiveness. Using a steroid-hyporesponsive asthma model, we demonstrate that the disease is associated with significant gut microbial dysregulation, characterized by reduced microbial diversity and depletion of immunoregulatory taxa. FMT partially restored gut microbial diversity, normalized community structure, and selectively replenished beneficial commensal bacteria, including Akkermansia muciniphila and Faecalibacterium prausnitzii, while suppressing pathogenic taxa. Importantly, restoration of gut microbial balance was associated with attenuation of lung inflammation and improved steroid responsiveness. These findings support a functional gut-lung axis in steroid hyporesponsive asthma and identify modulation of gut microbiota as a potential therapeutic strategy. Incorporating microbiota-directed interventions such as FMT may represent a novel adjunct approach for the management of refractory steroid-hyporesponsive asthma.},
}

*Asthma/therapy/microbiology
*Fecal Microbiota Transplantation
Animals
*Gastrointestinal Microbiome
Humans
Dysbiosis/therapy
*Adrenal Cortex Hormones/therapeutic use

@article {pmid42317058,
year = {2026},
author = {Yue, R and Wen, Y and Zhao, S and Liu, X and Luo, L and Liu, Y and Zeng, L},
title = {Tea and digestive system health: integrating gut microbiota-involved ADME and personalized nutrition for gastrointestinal disorders intervention.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-34},
doi = {10.1080/10408398.2026.2684712},
pmid = {42317058},
issn = {1549-7852},
abstract = {The global burden of digestive diseases is escalating, marked by rising incidence and severity. Tea, a widely consumed beverage rich in polyphenols, offers a promising dietary intervention due to its demonstrated capacity to modulate gut microbiota, suppress inflammation, and enhance gastrointestinal barrier function. This review provides a systematic integration of the ADME characteristics of key tea compounds with their complex interplay with the gut microbiome, underscoring the central role of microbial biotransformation in mediating the health benefits of tea. We critically examine the specific protective mechanisms of tea against prevalent gastrointestinal disorders, including gastritis, gastric ulcers, inflammatory bowel disease, irritable bowel syndrome, constipation, and diarrhea. A major focus is placed on the pivotal impact of interindividual variability, shaped by host factors and distinct gut microbial metabolic phenotypes, on the outcomes of tea-based interventions. This synthesis thus advances a novel "component-microbiota-metabolite-host" axis as a unifying framework for understanding tea's pleiotropic mechanisms in gastrointestinal health. Beyond mechanistic insight, the review lays a conceptual foundation and proposes a translational roadmap for developing evidence‑based, personalized tea interventions aligned with precision nutrition.},
}

@article {pmid42317296,
year = {2026},
author = {Ahmad, R and Zobel, G and Hannaford, R and Maclean, P and Olson, T and Hurst, C and Bracegirdle, J and Young, W and Rettedal, E and Anderson, RC and Dalziel, JE},
title = {Social isolation during adolescence alters novel object recognition memory, brain and gut gene expression, and microbiota composition in a sex-specific manner.},
journal = {Brain, behavior, & immunity - health},
volume = {55},
number = {},
pages = {101284},
pmid = {42317296},
issn = {2666-3546},
abstract = {Adolescent social isolation is a known risk factor for anxiety and depression related disorders, yet its effects on brain-gut communication and potential sex differences remain unclear. We hypothesised that isolation would heighten anxiety- and depression-related behaviors and consequently impair memory in both sexes. To investigate this we exposed male (M) and female (F) rats to four weeks of social isolation beginning at 3 weeks of age and assessed behavior, brain and gut gene expression and microbiota, in single- (S) or pair-housed (P) animals. Contrary to our hypothesis, the results showed higher novel object recognition memory in socially-isolated females (FS vs FP). No isolation-induced changes in anxiety-related behaviours were detected in either sex. Social isolation in females (FS vs FP) increased expression of hippocampal Grik5 (glutamate receptor/memory/learning), and decreased expression of prefrontal cortex genes: Mbp, Mobp, Plp1 (neuroplasticity), Cnp (neuroprotection) and Tph2 (serotonin synthesis). There was a trend toward lower microbial diversity in socially-isolated females (FS vs FP). Although no behaviour change was detected in isolated males, amygdala c-Fos (neuronal activity) and prefrontal cortex Gabbr1 (inhibitory) expression were decreased. Il6r, Tgfb1, Tlr9 (immune-related) were increased in the colon (MS vs MP). In both sexes, social isolation increased Tph1 expression in the colon (FS vs FP; MS vs MP). These findings indicate sex-specific responses to adolescent social isolation, with females showing enhanced novel object recognition memory performance alongside changes in genes linked to neuroplasticity and memory, while males showed altered brain and gut gene expression linked to brain neuro-activity and gut-immune function.},
}

@article {pmid42317353,
year = {2026},
author = {Lohani, SC and Zhang, C and Mandal, S and Zhao, M and Cheng, Y and Ramer-Tait, AE and Li, Q},
title = {Fecal microbiota transplantation reduces inflammation and modulates gene expression in HIV-infected double humanized-BLT (dHu-BLT) mice on antiretroviral therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1773716},
pmid = {42317353},
issn = {1664-3224},
mesh = {Animals ; *Fecal Microbiota Transplantation ; *HIV Infections/therapy/immunology/microbiology/genetics/drug therapy ; Mice ; Humans ; *Inflammation/therapy/immunology ; Gastrointestinal Microbiome ; Disease Models, Animal ; *Anti-Retroviral Agents/therapeutic use ; Gene Expression Regulation ; },
abstract = {INTRODUCTION: Persistent immune activation and inflammation remain significant barriers to managing comorbidities in people living with HIV (PLWH) on suppressive antiretroviral therapy (ART). While ART substantially reduces plasma viral loads to an undetectable level, it fails to fully restore gut microbial homeostasis and prevent microbial translocation, a critical pathogenic contributor to systemic persistent immune activation and inflammation. To evaluate the potential of human fecal microbiota transplantation (FMT) as an adjunctive therapy to restore gut health and attenuate inflammation and immune activation in PLWH on ART, we utilized a double humanized-BLT (dHu-BLT) mouse model, featuring a functional human immune system and a human-like microbiome.

METHODS: Two groups of HIV-infected dHu-BLT mice were used in the study. One group received FMT in addition to ART, while the control group received ART alone. Using both a multi-omics approach (16S rRNA sequencing and RNA-seq) and an immune-based assay, we compared alterations in gut microbial composition, profiled transcriptomic changes in the intestinal tissue, and quantified markers of systemic immune activation and inflammation between the groups.

RESULT: FMT supplementation in ART-treated mice increased the relative abundance of beneficial bacteria and modulated the transcriptomic profile of both human- and murine-related genes. Notably, genes associated with cellular structure and tissue maintenance, including Mcpt4, were upregulated, along with the extracellular matrix organization pathway predicted as the most strongly activated pathway in the FMT-supplemented group compared to ART alone. In contrast, genes and signaling pathways associated with inflammation were downregulated. Importantly, the FMT-supplemented group exhibited a significant reduction of plasma inflammatory markers, including CD62E, sCD14, sCD163, and FABP2, relative to the ART alone group.

CONCLUSION: These results suggest that FMT may serve as a promising adjunctive strategy for mitigating systemic inflammation by improving gut health, thereby contributing to the reduction of comorbidities in PLWH on ART.},
}

Animals
*Fecal Microbiota Transplantation
*HIV Infections/therapy/immunology/microbiology/genetics/drug therapy
Mice
Humans
*Inflammation/therapy/immunology
Gastrointestinal Microbiome
Disease Models, Animal
*Anti-Retroviral Agents/therapeutic use
Gene Expression Regulation

@article {pmid42317363,
year = {2026},
author = {Blake, S and Mortara, L and Spada, S},
title = {Editorial: Microbiota-immune interactions: a new frontier in cancer treatment optimization.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1882251},
pmid = {42317363},
issn = {1664-3224},
}

@article {pmid42317531,
year = {2026},
author = {Thoenen, L and Giroud, C and Probst, C and Rouyer, L and Schandry, N and Schlaeppi, K},
title = {Customizable High-Throughput Chemical Phenotyping of Root Bacteria.},
journal = {Bio-protocol},
volume = {16},
number = {11},
pages = {e5710},
pmid = {42317531},
issn = {2331-8325},
abstract = {Chemical phenotyping is a fundamental technique to study the metabolic properties or chemical sensitivities of bacteria. Traditional methods such as dilution methods, discs, or gradient diffusion assays are labor-intensive, often have high material requirements, and are limited in scalability. High-throughput cultivation approaches based on 96-well plates scale efficiently to large numbers of samples. A stacker, when coupled with a plate reader system (often already available in most laboratories), greatly enhances assay scalability and robustness. Here, we describe a customized high-throughput, flexible, scalable, robust, and affordable method for the chemical phenotyping of bacteria. This liquid culture-based growth system allows screening many bacteria in parallel and in a replicated manner for their tolerance to various chemicals, including specialized metabolites of plants, antibiotics, or pesticides. Compared to commercial solutions, our approach offers high flexibility in experimental conditions while keeping costs for consumables low. Key features • Approach to determine tolerance of bacteria against diverse chemicals, including specialized plant metabolites. • Experimental platform where parameters like strains, media, chemicals, concentrations, or exposure time can be flexibly varied for bacterial phenotyping. • Coupling a stacker to a plate reader permits highly replicated and efficient screenings of large bacterial collections and numerous different compounds.},
}

@article {pmid42317759,
year = {2026},
author = {Jiya, N and Sha, SP and Khudai, W and Yadav, S and Sasane, R and Sah, SP and Ghatani, K and Sharma, A},
title = {Distinct bacterial and fungal communities linked to functional potential in fermented fish and vegetables.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1850075},
pmid = {42317759},
issn = {1664-302X},
abstract = {INTRODUCTION: Traditional fermented foods constitute a vital component of ethnic community diets; consequently, characterizing their specific food microbiome is essential for elucidating their nutritional, functional and health related attributes.

METHODS: In this study, targeted metagenomics was employed to investigate the bacterial and fungal compositions of fermented fish and vegetables from North Bengal, India. The functional predictions of the fermented food microbiomes was performed using PICRUSt2.

RESULTS AND DISCUSSION: High throughput sequencing of 16S rRNA and ITS genes revealed substantial differences in the diversity indices amongst the fermented fishes and vegetables. Fish samples were dominated by Pseudomonadota (23.05%), whereas vegetables were enriched in Bacillota (32.17%), with Psychrobacter and Aliivibrio prevalent in fishes and lactic acid bacteria including Levilactobacillus, Paucilactobacillus and Pediococcus dominant in vegetables. The fungal genera Bisifusarium belonging to Ascomycota and Cystobasidium affiliated to Basidiomycota, were abundant in the fermented fishes and vegetables, respectively. Functional predictions of bacterial and fungal communities revealed enhanced carbohydrate metabolism, biosynthesis pathways related to vitamins, short-chain fatty acids, organic acids, proteolytic enzymes and compounds contributing to organoleptic attributes in these fermented foods. The assessment of microbial communities associated with the traditionally fermented foods of North Bengal revealed the key microbial taxa involved in the fermentation process and their nutritional properties.},
}

@article {pmid42317762,
year = {2026},
author = {Joshi, G and Rani, S and Bharti, D and Panda, N and Chavan, P and Mathpal, S and Ramaiah, S and Anbarasu, A},
title = {The role of the gut microbiome in antibiotic-driven antimicrobial resistance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1856738},
pmid = {42317762},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) is one of the most pressing threats to global health system. The human gut harbors a complex microbial ecosystem coordinated through mechanisms of metabolic interdependence. The gut microbiota plays a vital role in normal growth and physiological processes of the human body. It serves both as a target of antibiotic-mediated disruption and as a reservoir for the propagation of antimicrobial resistance genes. Although antibiotics remain indispensable for the treatment of bacterial infections, their broad ecological impact on the gut microbiota can undermine the microbial balance that protects the host against pathogen invasion and metabolic dysfunction. The gut microbiome also functions as a reservoir of antimicrobial resistance genes collectively termed the "resistome," which can be mobilised and transferred between commensal and pathogenic bacteria via horizontal gene transfer mechanisms such as conjugation, transformation, and transduction. This review examines the composition and functions of the human gut microbiota, the mechanism of antibiotic-induced gut dysbiosis, and the role of host factors like age, genetics, diet and immune status, on microbiome dynamics and AMR development. We further evaluate emerging methods for resistome characterisation, which include PCR, next-generation sequencing, functional metagenomics and artificial intelligence-driven tools. Finally, we discuss microbiome-targeted therapeutic strategies such as faecal microbiota transplantation (FMT), phage therapy, CRISPR-based therapies, and antimicrobial peptides for combating AMR and restoring gut microbial homeostasis. Overall, this review highlights that maintaining and re-establishing the integrity of the gut microbiome should be considered a fundamental component of antimicrobial stewardship strategies aimed at controlling AMR worldwide.},
}

@article {pmid42317866,
year = {2026},
author = {Alotaibi, W},
title = {Chrononutrition and cardiometabolic health: circadian timing as a dimension of precision nutrition.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1779033},
pmid = {42317866},
issn = {2296-861X},
abstract = {Cardiometabolic diseases, including obesity, type 2 diabetes mellitus (T2DM), hypertension, and cardiovascular disease (CVD), remain major global health challenges despite widespread adoption of evidence-based dietary guidelines. Traditional nutrition recommendations have largely focused on dietary composition and energy intake, with limited consideration of the timing of food consumption. Growing evidence indicates that metabolic processes are strongly regulated by circadian rhythms, suggesting that when food is consumed may be a critical but underappreciated determinant of cardiometabolic health. Chrononutrition, which examines the interaction between meal timing and the circadian system, has therefore emerged as an important area of research. This narrative review synthesizes human evidence linking chrononutrition to cardiometabolic outcomes, with a focus on obesity, insulin resistance and T2DM, lipid metabolism, and cardiovascular risk. Findings from observational studies, randomized clinical trials, and mechanistic investigations consistently demonstrate that eating later in the biological day or night is associated with impaired postprandial glucose regulation, reduced insulin sensitivity, altered lipid handling, and adverse cardiometabolic profiles, independent of dietary composition and total energy intake. In contrast, eating patterns aligned with endogenous circadian rhythms characterized by earlier energy intake and avoidance of late-night eating appear metabolically favorable. This review further situates chrononutrition within the framework of precision nutrition. While precision nutrition aims to explain interindividual variability in metabolic responses using genetic, metabolic, and microbiome-based approaches, circadian timing is rarely considered. Because metabolic capacity varies across the day-night cycle, failure to account for meal timing, chronotype, and circadian alignment may contribute to unexplained variability in dietary responses. Integrating chrononutrition into precision nutrition frameworks may therefore improve interpretation of metabolic phenotypes and enhance the personalization of dietary strategies. Finally, key research gaps are identified, highlighting the need for long-term, diverse human studies and time-resolved metabolic phenotyping to clarify the role of chrononutrition in cardiometabolic disease prevention.},
}

@article {pmid42317870,
year = {2026},
author = {Perillo, F and Mascaretti, F and Maragno, P and Amoroso, C and Oriani, E and Baeri, A and Pinco, P and Pozzi, L and Baldari, L and Caprioli, F and Ghidini, M and Strati, F and Facciotti, F},
title = {Preoperative malnutrition is associated with suppressed intratumoral T cell function and distinct tumor-associated microbiota in colorectal cancer: a prospective pilot study.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1802354},
pmid = {42317870},
issn = {2296-861X},
abstract = {INTRODUCTION: Cancer-related malnutrition significantly reduces therapeutic effectiveness, lowers chemotherapy tolerance, and impairs immunotherapy efficacy. Monitoring nutritional status using tools such as the Malnutrition Universal Screening Tool (MUST) may improve clinical outcomes. Malnutrition also profoundly affects immune system functions and gut microbiota composition. However, the relationship between pre-surgery nutritional status, anti-tumor immunity, and tumor-associated microbiota remains poorly understood.

METHODS: We prospectively enrolled 43 colorectal cancer (CRC) patients who underwent resection surgery between July 2017 and August 2021 at IRCCS Ca' Granda Ospedale Maggiore Policlinico in Milan. Patients were evaluated for biochemical, anthropometric, and nutritional profiles, as well as intratumoral immune phenotypes and tumor-associated microbiota. Tumor-associated microbiota analysis was performed in a subset of 8 patients (5 malnourished and 3 non-malnourished) for whom mucosal samples were available.

RESULTS: Malnutrition was associated with increased tissue-infiltrating neutrophils and altered T cell phenotypes, including reduced expression of effector-associated cytokines in conventional T-helper and iNKT cells. Gut microbiota analysis revealed significant associations between neutrophil lymphocyte ratio (NLR) and the bacterial genera Bacteroides, Prevotella, and Parabacteroides, suggesting a potential role for these microbes in shaping immune responses in malnourished individuals.

DISCUSSION: These findings suggest a link between malnutrition, gut microbiota composition, and suppressed anti-tumor immunity in CRC patients.},
}

@article {pmid42317872,
year = {2026},
author = {Singh, G and Singh, G and Shreya, and Kumari, A and Aran, KR},
title = {Nutrients and bioactive compounds as modifiers of neurodegenerative trajectories: molecular mechanisms, translational barriers, and precision nutrition.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1819432},
pmid = {42317872},
issn = {2296-861X},
abstract = {The Neurodegenerative diseases (NDs) such as Alzheimer's disease (AD), Parkinson's disease (PD), Multiple sclerosis (MS), and Amyotrophic lateral sclerosis (ALS) are a growing health burden across the world with minimal disease-modifying treatment and therapy. It is emerging that neurodegeneration is not only a progressive loss of neurons, but also a nutrient-sensitive systems-level dysfunction that takes the form of redox imbalance, chronic neuroinflammation, mitochondrial dysfunction, impaired proteostasis, and synaptic loss. The aging brain are more prone to metabolic vulnerability, and subclinical deficiencies in essential nutrients and bioactive dietary compounds may exacerbate cellular stress responses that contribute to disease progression. It summarizes the existing data on the effects of nutrients like vitamins, minerals, polyunsaturated fatty acids, and various phytochemicals in modulating neuronal homeostasis by regulating oxidative signaling, inflammatory cascades, mitochondrial resilience, autophagy, and synaptic plasticity. These nutrient-mediated effects collectively influence neuronal survival, synaptic integrity, and cognitive function by affecting disease susceptibility and progression. Additionally newer metabolites of the marine and microbiome act as new neuroactive agents. The evidence from in-vitro and preclinical models, translation to clinical benefit remains inconsistent due to heterogeneity in study design, bioavailability, blood- brain barrier penetration, dosing strategies and disease stage. This review highlights emerging potential of precision nutrition frameworks that integrate nutrigenomics, metabolomics, and microbiome interactions, and individualized metabolic profiling to enable context-dependent and stage-specific interventions. Moreover, conceptualizing neurodegeneration as a nutrient-sensitive, systems level disorder, propose a mechanistically informed and integrative approach that combine targeted nutritional strategies with pharmacological and lifestyle therapies to more effectively modify neurodegenerative trajectories.},
}

@article {pmid42317952,
year = {2026},
author = {Andafa, TW and Imoh, EC and Adekanmbi, SA},
title = {Artificial Intelligence Applied to the Brain-Gut Axis in Irritable Bowel Syndrome: Advancing Toward Clinical Translation.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e109142},
pmid = {42317952},
issn = {2168-8184},
abstract = {Irritable bowel syndrome (IBS) is one of the most common functional gut disorders affecting the global population, characterized by chronic abdominal pain and altered bowel habits in the absence of structural disease. The brain-gut-microbiota axis, a bidirectional network integrating central nervous system processing, enteric and autonomic function, immune signaling, and gut microbial ecology, provides a mechanistic framework that helps explain the substantial symptom heterogeneity and variable treatment response observed across patients. Artificial intelligence (AI) and machine learning (ML) approaches offer the ability to model complex, nonlinear relationships across high-dimensional biological datasets generated from this axis, including microbiome composition profiles, resting-state functional MRI connectivity matrices, multiomics data layers, and psychological and clinical feature sets. This narrative review evaluated primary human studies applying AI and ML to brain-gut axis data in IBS, identified through structured searches of PubMed/MEDLINE and Scopus supplemented by citation chaining, with literature included up to April 2026. Across microbiome profiling, neuroimaging, multiomics integration, and psychological feature modeling, ML approaches have demonstrated proof-of-concept performance for IBS classification and, in a smaller number of studies, for prediction of clinically meaningful outcomes, including cognitive behavioral therapy (CBT) response. A notable early signal is the integration of baseline microbiome and brain features to predict CBT response, with high reported discrimination, although these results are derived from small, single-center cohorts with only internal validation and should be regarded as hypothesis-generating. The current evidence base is limited by small single-center cohorts, reliance on internal validation, healthy-control comparators, limited external replication, and substantial overfitting and data-leakage risk in high-dimensional small-sample settings. AI and ML applications in IBS are promising but remain exploratory and are not yet suitable for routine clinical use. Clinical translation will require larger multicenter datasets, harmonized preprocessing pipelines, external validation, calibration reporting, and evaluation against clinically realistic comparators and decision points.},
}

@article {pmid42318010,
year = {2026},
author = {Yang, H and Wu, G and Liang, S and Zan, R and Chen, Y and Yuan, W and Chen, H and Huang, G},
title = {Millettia speciosa reprograms the lung proteome and suppresses CCL24-driven eosinophilic inflammation in allergic asthma.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1726706},
pmid = {42318010},
issn = {2673-6101},
abstract = {BACKGROUND: Asthma is a Th2-skewed inflammatory disorder characterized by eosinophilic infiltration, cytokine dysregulation, and airway remodeling. Emerging evidence highlights the role of immunometabolic pathways and the gut-lung axis in asthma pathogenesis.

METHODS: We investigate the therapeutic effects of Niudali (Millettia speciosa), a traditional Chinese medicinal herb, in an ovalbumin-induced mouse model of allergic asthma using high-resolution data-independent acquisition (DIA) lung proteomics integrated with cytokine profiling.

RESULTS: Niudali treatment significantly alleviated airway inflammation and eosinophilic infiltration. Proteomic analysis revealed 179 differentially expressed proteins (DEPs), with a notable finding that CCL24, a key eosinophil-recruiting chemokine, was completely suppressed in Niudali-treated mice but highly expressed in the asthma model. This highlights the central role of CCL24 inhibition in the mechanism through which Niudali mitigates eosinophil-mediated inflammation.Functional enrichment analyses revealed that Niudali modulates pathways involved in complement and coagulation cascades, lipid transport, antioxidant defense, and PPAR signaling, reflecting a shift toward immune resolution and metabolic homeostasis. Network analysis identified key hub proteins, including Alb, Apoe, Apoa1, Proc, and Serpina7, which orchestrate lipid metabolism, antioxidant functions, and immune regulation. The modulation of serpins, apolipoproteins, and extracellular space-related proteins suggests a broad immunometabolic reprogramming effect. Notably, this molecular signature aligns with the gut-lung axis paradigm, potentially reflecting microbiota-mediated modulation via short-chain fatty acids (SCFAs). Consistent with proteomic findings, bronchoalveolar lavage fluid (BALF) analyses showed significant reductions in IgE, IL-4, IL-5, and IL-6, further confirming suppression of Th2-mediated inflammation.

CONCLUSION: study provides proteomic evidence that Niudali treats asthma by disrupting the CCL24-eosinophil axis and rebalancing immunometabolic networks. These findings support Niudali as a promising candidate for gut-lung axis-targeted interventions in asthma and provide a systems-level framework for future microbiome metabolome integrated studies. While our findings suggest a potential link between these molecular changes and the gut-lung axis, this mechanism was not directly investigated in the present study and should therefore be considered hypothetical. Future studies incorporating microbiome and metabolomic analyses will be essential to clarify the role of gut-derived metabolites, including SCFAs, in mediating these effects.},
}

@article {pmid42318064,
year = {2026},
author = {Li, XT and Zhang, X and Liang, ZL and Jiang, Z and Huang, Y and Han, YQ and Tan, ZB and Ying-Liu, and Liu, ZH and Yin, HQ and Liu, SJ and Jiang, CY},
title = {A culturomics biobank decodes extremophile evolution and metabolism in acid mine drainage.},
journal = {Environmental science and ecotechnology},
volume = {32},
number = {},
pages = {100722},
pmid = {42318064},
issn = {2666-4984},
abstract = {Extreme environments such as acid mine drainage (AMD) host highly specialized microbial communities that drive profound biogeochemical cycles. Within these ecosystems, iron- and sulfur-metabolizing taxa catalyze mineral weathering, generating intense acidity and mobilizing heavy metals. However, more than 97% of these microorganisms remain uncultured "microbial dark matter," heavily restricting our understanding of extremophile metabolism and adaptation. Here we present the Microbial Biobank of AMD (mbAMD), a culturomics-derived collection of 652 isolates spanning 42 species-including 21 novel taxa-that achieves 86.7% coverage of the global AMD core microbiome. Functional validation demonstrates that 36 of these taxa possess active iron or sulfur metabolic capacities, including the discovery of the first pure cultures of acid-tolerant sulfate reducers. Comparative genomic analyses across these isolates reveal that extreme environmental adaptation is predominantly driven by pervasive horizontal gene transfer. Specifically, extremophiles preferentially acquire adaptive genes governing acid tolerance and metal resistance from phylogenetically proximal relatives rather than distant donors. These findings elucidate the modular evolutionary strategies of extremophiles and provide critical functional resources for advancing biohydrometallurgy and environmental bioremediation. This mbAMD resource will accelerate biohydrometallurgical process optimization and environmental bioremediation strategies while advancing evolutionary microbial ecology research.},
}

@article {pmid42318276,
year = {2026},
author = {Krithika, C and Sridhar, C and Santhanakrishnan, S and Mahendra, J and Sankari, L and Sivakumar, T},
title = {Salivary Biomarkers for Diagnosis and Monitoring of Thyroid Diseases: A Systematic Review of Current Evidence.},
journal = {Biomarker insights},
volume = {21},
number = {},
pages = {11772719261452222},
pmid = {42318276},
issn = {1177-2719},
abstract = {BACKGROUND: Thyroid hormones have a crucial impact on all physiological systems. Diagnosis of thyroid diseases using salivary biomarkers is an emerging discipline and requires consolidation of existing information.

AIMS: This systematic review is aimed at identifying and analyzing salivary biomarkers that are associated with thyroid diseases and evaluate their potential as diagnostic applicability as non-invasive indicators of thyroid dysfunction.

METHODOLOGY: Literature search was conducted in PubMed, Cochrane, EBSCO, ProQuest, and Google Scholar from date of inception to May 2025. Human observational studies, clinical trials, and diagnostic accuracy studies published in the English language, that related biomarkers in saliva to thyroid diseases were collected and analyzed for relevant information. The search resulted in 35 records, followed by PRISMA 2020 compliant screening which resulted in 9 records included for data synthesis. Data extraction, tabulation and Risk of Bias assessment was carried out by 2 independent reviewers.

RESULTS: Included studies suggest that FT3, amino acids, salivary metabolic profiling, glycan profiles, microbiome, and thyroid antibodies present in saliva could be putative and noninvasive biomarkers of diagnostic and prognostic importance.

CONCLUSION: Heterogeneity in study design and analytical techniques has limited definitive conclusions about said markers, necessitating future well-designed clinical studies for validation of these biomarkers for noninvasive thyroid screeing and diagnosis.},
}

@article {pmid42318277,
year = {2026},
author = {Wilding, MC and Shaffer, AD and Rapsinski, GJ and Johnson, M and Hilliam, Y and Williams, JV and Bomberger, JM and Stapleton, AL},
title = {Viral Detection and Clinical Disease Features in Pediatric Chronic Rhinosinusitis.},
journal = {Laryngoscope investigative otolaryngology},
volume = {11},
number = {3},
pages = {e70465},
pmid = {42318277},
issn = {2378-8038},
abstract = {OBJECTIVES: Chronic rhinosinusitis (CRS) results from complex host-environment interactions with microbiome dysbiosis and viral infections postulated to drive inflammation and anatomic remodeling. This study investigates the impact of viral presence on pediatric sinonasal disease and clinical outcomes.

METHODS: A prospective, case-control study with retrospective data collection was conducted at a single-institution tertiary children's hospital. Pediatric patients undergoing sinus surgery for CRS (cystic fibrosis [CF] and non-CF CRS groups) and a control group undergoing structural septoplasty were enrolled from 2018-2022. Sinus swabs were collected intraoperatively and during up to 3 years of follow-up. A 14-virus panel was run. 16S and custom amplicon sequencing and quantitative PCR assessed microbial profiles. Clinical and endoscopic data were recorded.

RESULTS: Sinonasal swabs were collected from 15 CF-CRS, 21 non-CF CRS, and 32 control patients during initial sinus surgery. At least one virus was detected in 30.9% of samples (n = 21/68): 18.8% (n = 6/32) in controls, 33.3% (n = 7/21) in non-CF, and 53.3% (n = 8/15) in CF. Human rhinovirus (HRV) was most common, comprising 45.8% (n = 11/24) of viral detections. Across study duration, viral-positive CRS individuals were 3.49 times more likely to report nasal drainage (95% CI: 1.59-9.25, p = 0.005) and 4.23 times more likely to exhibit discharge on endoscopy (95% CI: 1.40-12.81, p = 0.011) than viral-negative individuals. HRV-positive samples had decreased Corynebacterium prevalence (p = 0.025), increased Haemophilus prevalence (p = 0.052), and increased Pseudomonas relative abundance (p = 0.076) versus viral-negative samples.

CONCLUSION: Viral infections can exacerbate pediatric CRS by increasing nasal drainage and endoscopic discharge while promoting chronic inflammation and persistent disease.

LEVEL OF EVIDENCE: 4.},
}

@article {pmid42318308,
year = {2026},
author = {Yu, C and Dong, L and Zhang, R and Li, H and Shi, X and Wu, H and Zhou, W and Li, Y and Wei, WB},
title = {Causal Effects of Gut Microbiota and Associated Metabolites on Retinal Diseases and Visual Impairment: A Mendelian Randomization Study.},
journal = {Journal of ophthalmology},
volume = {2026},
number = {},
pages = {4233490},
pmid = {42318308},
issn = {2090-004X},
abstract = {BACKGROUND: Previous observational study findings have indicated a vital association between gut microbiota features and retinal diseases based on the "gut-retina" axis. However, whether their relationships underlie causal effects remains to be established.

METHODS: Instrumental variables of 211 gut microbiota taxa were obtained from a genome-wide association study (GWAS), and 28 gut-associated metabolites and pathways were included as exposures. A two-sample Mendelian randomization (MR) study was carried out to estimate gut microbiota effects on diabetic retinopathy (DR), early age-related macular degeneration (eAMD), retinal detachments and breaks (RDs/RBs), retinal vascular occlusion (RVO), disorders of the choroid and retina (D-C/R), and visual impairment. MR methods, including inverse variance weighted (IVW), MR‒Egger, weighted median, simple mode, and weighted mode methods, were used to investigate the causal relationship between gut microbiota features and various outcomes. Heterogeneity, pleiotropy, and stability tests of MR results were performed, and Bonferroni's correction was used to test the strength of the causal relationships between exposures and outcomes, as well as reverse and multivariable MR analyses.

RESULTS: Through MR analysis of 211 microbes and six clinical phenotypes, a total of 35 gut microbiome and 3 associated metabolites were found to be associated with various outcomes. Cochrane's Q test revealed that there was no significant heterogeneity between various single-nucleotide polymorphisms. In addition, no significant level of pleiotropy was found according to the MR‒Egger and MR-PRESSO global tests. After the Bonferroni-corrected test, Genus id.2041 (OR = 0.874, 95% CI: 0.816-0.936, p = 1.10e - 04, IVW) showed robust causality with D-C/R, which had a nominal association with multiple other retinal diseases as well. Seven exposure-outcome effects markedly remained valid when BMI or alcohol intake frequency was separately included in multivariable MR analyses. According to the results of reverse MR analysis, no significant causal effect of outcomes was found on gut microbiota. No significant heterogeneity of instrumental variables or horizontal pleiotropy was found.

CONCLUSION: We confirmed a potential causal relationship between some gut microbiota features and retinal diseases, thus providing new insights into the gut microbiota-mediated mechanism of retinopathy and indicating vital biomarkers for potential diagnostic, therapeutic, and prevention strategies.},
}

@article {pmid42318566,
year = {2026},
author = {Shetty, J and Hegde, NN and Hegde, MN},
title = {Mineral encapsulation of microorganisms in calcified oral biofilms: implications for immune dysregulation and vascular calcification.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1849108},
pmid = {42318566},
issn = {2673-4915},
abstract = {Oral biofilms represent highly organized microbial ecosystems embedded within extracellular matrices enriched with calcium and phosphate ions that promote the nucleation of calcium phosphate minerals, including hydroxyapatite. During plaque mineralization, microorganisms may become incorporated within calcium phosphate-protein matrices, forming mineralized microenvironments that facilitate microbial persistence while partially shielding pathogens from host immune surveillance. Hydroxyapatite crystals can also directly influence innate immune responses. Macrophages exposed to these particles exhibit altered polarization, impaired antigen presentation, and sustained low-grade inflammatory signaling accompanied by dysregulated tissue repair mechanisms. In biological fluids, calcium phosphate nanoparticles rapidly acquire a protein corona that modulates cellular uptake, biodistribution, and systemic interactions. These particles may disrupt intracellular calcium homeostasis, promote endothelial dysfunction, influence coagulation pathways, and contribute to vascular remodeling. We propose that calcium phosphate mineralization within oral biofilms encapsulates microbial cells within mineral-protein matrices that behave as protected reservoirs capable of systemic dissemination, immune modulation, and promotion of vascular calcification. This mineral encapsulation model provides a mechanistic framework linking opportunistic oral microorganisms with chronic inflammation and cardiovascular disease and suggests potential targets for therapeutic intervention.},
}

@article {pmid42318592,
year = {2026},
author = {Sun, Q and Ling, X and Zhang, Y and Yim, CC and Peng, Y and Yang, Y and Chan, HN and Zhang, X and Kam, KW and Chu, WK and Ip, P and Young, AL and Tsui, SK and Tham, CC and Pang, CP and Chen, LJ and Yam, JC},
title = {Association between secondhand smoke exposure and ocular microbiome changes in children.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100630},
pmid = {42318592},
issn = {2666-5174},
abstract = {PURPOSE: To investigate whether secondhand smoke (SHS) exposure alters the ocular surface microbiome (OSM) in children and to explore potential functional consequences.

METHODS: 432 children aged 3-18 years were enrolled, including 111 SHS-exposed and 321 unexposed controls. Conjunctival swabs were collected and analyzed by 16S rRNA gene sequencing targeting the V3-V4 region. Sequencing data were processed with Qiime2 and DADA2, and taxonomic classification was based on the SILVA 138 database. Alpha diversity and beta diversity were compared using t-tests and PERMANOVA. Differentially abundant taxa were identified using LEfSe, and predicted functional pathways were analyzed using PICRUSt2 with MetaCyc and KEGG annotation.

RESULTS: SHS-exposed children showed significantly altered alpha diversity (Chao1, Shannon, Simpson) and distinct beta diversity compared with controls. LEfSe analysis revealed enrichment of several phyla and genera, including Lactobacillus and Rubellimicrobium in controls, with no taxa enriched in SHS-exposed children. Functional prediction showed enrichment of metabolism pathways such as L-methionine salvage, biphenyl, heparin, and toluene degradation and immune-related pathways, including complement activation, T and B cell receptor signaling, MAPK, and TGF-beta pathways.

CONCLUSION: SHS exposure in children is associated with significant alterations in ocular surface microbial diversity, community structure, and predicted functional pathways related to environmental stress and immune signaling. These findings highlight the sensitivity of the pediatric OSM to SHS exposure and underscore the importance of minimizing environmental tobacco smoke to protect children's ocular health.},
}

@article {pmid42318955,
year = {2026},
author = {Oh, SY and Lee, J and Han, K and Ku, GY and Yoo, N},
title = {Risk of Metabolic Disease After Right- vs Left-Sided Colectomy for Colon Cancer: A Nationwide Cohort Study.},
journal = {Diseases of the colon and rectum},
volume = {},
number = {},
pages = {},
doi = {10.1097/DCR.0000000000004350},
pmid = {42318955},
issn = {1530-0358},
abstract = {BACKGROUND: The metabolic consequences of colon cancer surgery may vary by anatomic resection site, but direct comparisons of right- versus left-sided colectomy are limited.

OBJECTIVE: To compare the incidence of new-onset diabetes mellitus, hypertension, and dyslipidemia after right- versus left-sided colectomy for colon cancer.

DESIGN: Retrospective population-based cohort study.

SETTINGS: Nationwide data from the Korean Clinical Data Utilization for Research Excellence project, linking cancer registry, insurance claims, and health screening databases.

PATIENTS: Adults aged 30 years or older with histologically confirmed colon cancer who underwent colectomy between January 1, 2013, and December 31, 2019.

MAIN OUTCOME MEASURES: New-onset diabetes mellitus, hypertension, and dyslipidemia occurring after colectomy. Hazard ratios were estimated with Cox models adjusted for demographics, lifestyle factors, body mass index, waist circumference, Surveillance, Epidemiology, and End Results summary stage, and treatment; Fine-Gray subdistribution models accounted for the competing risk of death. Inverse probability of treatment weighting (IPTW) was used to address residual confounding.

RESULTS: Among 8,228 patients (mean [standard deviation] age, 58.8 [11.4] years; 4,633 [56.3%] male), 3,253 underwent right-sided and 4,975 underwent left-sided colectomy. During a median follow-up of 4.0 years (interquartile range, 2.5-5.8), 358 patients (4.4%) developed diabetes mellitus, 1,050 (12.8%) developed hypertension, and 1,167 (14.2%) developed dyslipidemia. Right-sided colectomy was associated with a 20% lower risk of incident dyslipidemia compared with left-sided colectomy (adjusted hazard ratio, 0.80; 95% confidence interval, 0.71-0.91; p = 0.005), with no significant differences for diabetes or hypertension.

LIMITATIONS: Observational design using administrative data limits causal inference; direct measurements of bile acids, microbiome composition, or inflammatory markers were unavailable; results from a Korean population may not be generalizable to other ethnic groups.

CONCLUSIONS: The anatomic laterality of colectomy was differentially associated with metabolic outcomes; right-sided resection was associated with a lower risk of incident dyslipidemia. These findings suggest that surgical laterality may inform postoperative metabolic risk stratification and support incorporating routine lipid monitoring into post-colectomy survivorship care. See Video Abstract.},
}

@article {pmid42319135,
year = {2026},
author = {Udayakumar, S and Pollock, J and Irungu, E and Muthoga, P and Adhiambo, W and Huibner, S and Kungu'u, M and Kabuti, R and Babu, H and , and Ngurukiri, P and Weiss, HA and Seeley, J and Abramsky, T and Beattie, TS and Kimani, J and Kaul, R},
title = {Genital Immune Correlates of Seroprevalent and Seroincident Herpes Simplex Type 2 Infection Among Women Who Sell Sex in Nairobi, Kenya.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {95},
number = {6},
pages = {e70273},
pmid = {42319135},
issn = {1600-0897},
support = {MR/R023182/1/MRC_/Medical Research Council/United Kingdom ; MR/R010161/1//European Union grant/ ; #PJT-180629//Canadian Institute of Health Research (CIHR)/ ; #PJT-156123//Canadian Institute of Health Research (CIHR)/ ; },
mesh = {Humans ; Female ; Kenya/epidemiology ; Adult ; *Herpesvirus 2, Human/immunology ; *Herpes Genitalis/immunology/epidemiology ; Cadherins/metabolism ; *HIV Infections/epidemiology/immunology ; Young Adult ; *Vagina/immunology/virology ; Antibodies, Viral/blood ; Prevalence ; Sex Workers ; Seroepidemiologic Studies ; Incidence ; },
abstract = {PROBLEM: Most Herpes simplex virus type 2 (HSV-2) infection is asymptomatic but increases the risk of HIV acquisition, possibly due to alterations in genital immunology. We examine associations of HSV-2 prevalence and incidence with epithelial barrier disruption.

METHOD OF STUDY: The study was nested within the longitudinal Maisha Fiti cohort of women who sell sex in Nairobi, Kenya. HSV-2 serostatus was assessed by Kalon HSV-2 IgG assay. Socio-behavioural characteristics were assessed by questionnaire and analysed by logistic regression. Immune factors (including soluble E-cadherin (sE-cad)) were assayed in cervicovaginal secretions by multiplex immunoassay, log-transformed and analysed through linear regression.

RESULTS: Among 731 HIV-negative participants, 414 (57%) were HSV-2 seropositive. These women were older (median age 35 vs 28 years; p < 0.001) and reported increased intravaginal washing (64 vs 56%; p = 0.027) than those who were HSV-2 seronegative. Genital sE-cad levels were similar, and IL-6 levels were lower in seropositive participants (1.15 vs 1.28 pg/mL, p < 0.01). Seroincidence was 10.7/100 person (95% CI: 7.3, 15.2) years among the 317 initially seronegative participants. Incident infection was associated with older age (31 vs 28 years, p = 0.001), increased number of clients (6 vs 4 clients/week, p = 0.005), and bacterial vaginosis (BV) (32 vs 15%, p = 0.009). Although women who acquired HSV-2 had higher sE-cad and lower MIP-3α levels, there was no association after controlling for Nugent score.

CONCLUSIONS: Subclinical epithelial barrier disruption is unlikely to be underpinning HIV acquisition in asymptomatic HSV-2 infection. There was no evidence of genital immune predictors of HSV-2 acquisition, whereas the vaginal microbiome is important.},
}

Humans
Female
Kenya/epidemiology
Adult
*Herpesvirus 2, Human/immunology
*Herpes Genitalis/immunology/epidemiology
Cadherins/metabolism
*HIV Infections/epidemiology/immunology
Young Adult
*Vagina/immunology/virology
Antibodies, Viral/blood
Prevalence
Sex Workers
Seroepidemiologic Studies
Incidence

@article {pmid42319242,
year = {2026},
author = {Papadopoulou, A and Tournas, G and Antsaklis, P and Daskalakis, G and Domali, E},
title = {Do Not Treat a Sequencing Report: Therapeutic Stewardship in Endometrial Microbiome Testing.},
journal = {American journal of therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1097/MJT.0000000000002175},
pmid = {42319242},
issn = {1536-3686},
}

@article {pmid42319359,
year = {2026},
author = {Ursu, Ș and Ciocan, RA and Ursu, CP and Moldovan, RC and Zaharie, F and Spârchez, Z and Moisoiu, T and Bărăian, AI and Pop, RS and Bodea, CI and Iuga, CA and Gherman, CD and Hajjar, NA},
title = {Metabolomic Profiling of Plasma Bile Acids in Resectable Gastric Cancer.},
journal = {Chirurgia (Bucharest, Romania : 1990)},
volume = {121},
number = {Ahead of print},
pages = {aop},
doi = {10.21614/chirurgia.3314},
pmid = {42319359},
issn = {1221-9118},
mesh = {Humans ; *Stomach Neoplasms/blood/surgery/pathology/diagnosis/metabolism ; *Bile Acids and Salts/blood ; Female ; Male ; Case-Control Studies ; Middle Aged ; *Biomarkers, Tumor/blood ; *Metabolomics/methods ; Aged ; Prognosis ; Neoplasm Staging ; Predictive Value of Tests ; Tandem Mass Spectrometry ; Liquid Chromatography-Mass Spectrometry ; Biomarkers/blood ; Chromatography, Liquid ; },
abstract = {Background: Gastric cancer (GC) is characterized by late-stage diagnosis and a lack of reliable non-invasive biomarkers. This study aims to investigate the plasma bile acid (BA) profile to enhance the understanding of GC metabolism and identify potential diagnostic and prognostic tools. Methods: In a case-control design, 62 GC patients (stages I III) and 70 matched controls were recruited. Using liquid chromatography-tandem mass spectrometry (LC-MS/MS), the concentrations of 48 metabolites in plasma were measured. Statistical analysis included univariate tests, principal component analysis, and linear discriminant analysis (LDA). Results: GC patients showed a significantly lower CA/CDCA ratio and alterations in secondary and conjugated bile acids, including TLCA, GLCA, TDCA, GDCA, and GUDCA, suggesting involvement of the gut liver microbiome axis. The ability to distinguish between groups was moderate (AUC = 0.731). Furthermore, BA levels were negatively correlated with tumor stage, tumor size, and systemic inflammatory markers (CRP, mGPS), while they were positively correlated with nutritional and hematological markers such as albumin and hemoglobin. Conclusions: Gastric cancer is associated with a distinct circulating BA profile that reflects not only tumor-related metabolic remodeling, but also systemic inflammation, nutritional status, and disease burden. The reduced CA/CDCA ratio and alterations in secondary and conjugated bile acids support the involvement of the gut-liver-microbiome axis in GC biology. Although BA profiling alone showed moderate diagnostic performance, its integration with conventional tumor markers, inflammatory indices, and clinico-pathological parameters may improve multimodal biomarker panels for noninvasive patient stratification, disease assessment, and future prognostic evaluation.},
}

Humans
*Stomach Neoplasms/blood/surgery/pathology/diagnosis/metabolism
*Bile Acids and Salts/blood
Female
Male
Case-Control Studies
Middle Aged
*Biomarkers, Tumor/blood
*Metabolomics/methods
Aged
Prognosis
Neoplasm Staging
Predictive Value of Tests
Tandem Mass Spectrometry
Liquid Chromatography-Mass Spectrometry
Biomarkers/blood
Chromatography, Liquid

@article {pmid42319373,
year = {2026},
author = {Shi, S and Liang, Y},
title = {Nutrition as a regulator of hematopoietic stem cell biology and transplantation.},
journal = {Current opinion in hematology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MOH.0000000000000940},
pmid = {42319373},
issn = {1531-7048},
abstract = {PURPOSE OF REVIEW: Nutrition is increasingly recognized as a biologically active regulator of hematopoietic stem cell (HSC) function and transplant recovery. This review summarizes recent advances linking nutrient availability, metabolic signaling, and the gut-marrow axis to HSC maintenance and hematopoietic stem cell transplantation (HSCT) outcomes.

RECENT FINDINGS: Recent work supports a model in which nutrient sensing, glucose, amino acid and lipid metabolism, mitochondrial redox control, and microbiome-derived metabolites collectively shape HSC quiescence, regenerative capacity, immune recovery, and susceptibility to transplant-related complications. Dietary states such as caloric restriction, fasting, obesity, and high-fat diet exposure alter HSC behavior through metabolic, inflammatory, and niche-mediated pathways. In HSCT, nutritional status before and after transplantation appears to interact with mucosal injury, microbial disruption, graft-versus-host disease (GVHD), infection, and overall outcomes, although causal evidence remains limited.

SUMMARY: Nutrition should be viewed as more than a background component of supportive care in hematology. A better mechanistic understanding of how diet and metabolism influence HSC biology may help define biomarker-informed and clinically actionable nutritional strategies to improve transplant recovery.},
}

@article {pmid42319454,
year = {2026},
author = {Xie, M and Jie, Y},
title = {From Health to Disease: A Comprehensive Review of Ocular Surface Microbiota and Detection Methods in Dry Eye.},
journal = {Current microbiology},
volume = {83},
number = {8},
pages = {},
pmid = {42319454},
issn = {1432-0991},
support = {82371022//the National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Microbiota ; *Dry Eye Syndromes/microbiology/diagnosis ; Bacteria/genetics/classification/isolation & purification ; *Eye/microbiology ; Fungi/isolation & purification/genetics/classification ; Tears/microbiology ; },
abstract = {Dry eye disease (DED) is a prevalent and multifactorial condition that significantly impacts the ocular surface, characterized by symptoms of discomfort, visual disturbance, and tear film instability. Recent research has increasingly focused on the ocular surface microbiome (OSM) and its potential role in the pathogenesis and progression of DED. The OSM consists of a diverse community of microorganisms, including bacteria, fungi, and viruses, that interact with the host to maintain ocular surface health. Dysbiosis, or the imbalance of these microbial communities, has been linked to various ocular surface disorders, including DED. This review comprehensively summarizes the current understanding of the differences in OSM between healthy individuals and patients with different types of DED, such as aqueous-deficient dry eye, evaporative dry eye, and DED associated with autoimmune conditions. Additionally, it explores the detection methods used to study the OSM, highlighting the strengths and limitations of culture-based approaches, 16 S rRNA sequencing, metagenomic shotgun sequencing, and emerging technologies like 2bRAD-M. The review also outlines future research directions, emphasizing the need for advanced multi-omics approaches, personalized microbiome-based therapies, and longitudinal studies to further elucidate the role of the OSM in DED. By enhancing our understanding of the OSM composition and function, these insights may lead to innovative diagnostic and therapeutic strategies for managing DED.},
}

Humans
*Microbiota
*Dry Eye Syndromes/microbiology/diagnosis
Bacteria/genetics/classification/isolation & purification
*Eye/microbiology
Fungi/isolation & purification/genetics/classification
Tears/microbiology

@article {pmid42319657,
year = {2026},
author = {Shon, WJ and Kim, KA and Kim, JS and Kim, BG and Im, JP and Lee, HJ and Kim, SH and Kim, JW and Kang, HW and Kim, KW and Choi, JW and Cheon, DH and Kim, D and Choi, J and Kim, ES and Koh, SJ},
title = {Habitual Ultra-processed Food Intake Is Associated with Gut Dysbiosis and Pro-inflammatory Metabolite Profiles in Korean Patients with IBD.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42319657},
issn = {1573-2568},
abstract = {BACKGROUND AND AIMS: Ultra-processed food (UPF) is increasingly consumed worldwide and may influence gut microbial ecology relevant to inflammatory bowel disease (IBD). However, patient-level multi-omics data remains scarce. We investigated whether habitual UPF intake is associated with specific microbiota and metabolite profiles in Korean patients with IBD.

METHODS: Dietary intake was assessed using a validated food frequency questionnaire, and food was categorized by the NOVA system. UPF intake was expressed as percent of energy, and 313 patients were stratified into UPF low (Q1-Q2) and UPF high (Q3-Q4). Fecal samples of 174 patients underwent 16S rRNA sequencing and untargeted metabolomics. Microbiome differences were tested using PERMANOVA for beta-diversity and Mann-Whitney U tests for taxa. Differential metabolites were defined by p < 0.05 and |fold change|≥ 1.5, followed by Reactome enrichment with FDR correction. Correlations among microbiota, metabolites, and UPF subgroups were examined using Spearman tests with Benjamini-Hochberg adjustment. Associations between UPF intake and clinical characteristics were analyzed using Spearman tests, η[2] from ANOVA and point-biserial correlation.

RESULTS: Microbial beta-diversity differed significantly between UPF low and UPF high participants. UPF high participants showed expansion of pro-inflammatory pathobionts (Escherichia-Shigella, Proteus, Parasutterella, Enterococcus, Fusobacterium, and Clostridium innocuum group) and depletion of anti-inflammatory commensals (Faecalibacterium, Butyricicoccus, Lachnospiraceae ND3007 group, and Bifidobacterium). Metabolomic profiling revealed enrichment of inflammatory pathways (phospholipid metabolism, eNOS/NO signaling, mitochondrial β-oxidation, FMO3-mediated TMA to TMAO, tryptophan catabolism) and reduction of anti-inflammatory metabolites (AHR ligands, BAAT-conjugated bile acids). Integrated analyses demonstrated significant correlations between dysbiotic taxa and inflammatory metabolites. Among NOVA-defined UPF subgroups, sugar-sweetened beverages, ready-to-eat dishes, and packaged snacks and confectioneries showed the strongest associations with these adverse signatures. Analysis of clinical characteristics showed trends between total UPF intake and inflammatory markers (WBC, CRP, fecal calprotectin), and association with upper gastrointestinal tract involvement in patients with CD. Subgroup analysis showed that sugar-sweetened beverage intake was significantly associated with CRP elevation and upper gastrointestinal involvement in patients with CD.

CONCLUSIONS: In IBD, higher UPF intake, particularly from specific NOVA-defined subgroups, is associated with gut dysbiosis and a pro-inflammatory metabolome, which in turn correlates with unfavorable clinical characteristics. These findings provide patient-based multi-omics evidence and underscore clinically relevant dietary targets for IBD management.},
}

@article {pmid42320152,
year = {2026},
author = {Bell, A and Ergas, SJ and Main, K and Rhody, N and Guttman, L},
title = {Performance of moving bed biofilm, periphyton, and halophyte biofilters in marine multi-trophic aquaculture systems.},
journal = {The Science of the total environment},
volume = {1045},
number = {},
pages = {181943},
doi = {10.1016/j.scitotenv.2026.181943},
pmid = {42320152},
issn = {1879-1026},
abstract = {Combining multi-trophic recirculating aquaculture system (MT-RAS) biofilter types leverages the strengths of different ecological biomes, benefits water treatment, resource recovery, economics, and environmental sustainability. The overall goal of this study was to determine the effects of different aquaculture biofilter combinations on MT-RAS. Three duplicate biofilter combinations were tested in a pilot scale MT-RAS with red drum (Sciaenops ocellatus): 1) periphyton with halophytes (P + H), 2) periphyton with moving bed biofilm reactors (P + M), and 3) periphyton only (P[2]). Experiments were performed in two trials (spring and summer) with four replicates. Water quality tests validated that NH3/NH4[+], NO2[-], NO3[-], and CO2 were below fish toxic limits for all biofilter combinations. Fish mortalities were low, with food conversion ratios between 1.1 and 2.0. In all trials, periphyton added dissolved oxygen (DO) to the water (at an average of +3.95 ± 6.52 mg/(L*d)), thus reducing energy costs. Periphyton was also found to include valuable lipid content (4.55 ± 2.24% of dry weight) with the detection of Ω-3 fatty acids. The P[2] trials maintained a stable alkalinity and pH balance. The M + P trials removed NH3/NH4[+] at a high rate; however, they also required more energy for DO. Edible sea purslane growth rates (1.0431 ± 0.3361 g/day/plant) were efficient in all P + H trials. The microbiome revealed abundance of Ignavibacterium bacteria, Navicula and Chlorella algae, Nitrospira, Nitrospirae, Nitrosospharota, and Nitrosoarchaeum nitrogen cyclers. Overall, periphyton biofilter combinations nitrify, denitrify, stabilize pH, photosynthesize, and produce oxygen and a value-added product.},
}

@article {pmid42320497,
year = {2026},
author = {Miller, SJ and Rogers, GB},
title = {What constitutes a healthy vaginal microbiome? Implications for intervention strategies.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101474},
doi = {10.1016/j.lanmic.2026.101474},
pmid = {42320497},
issn = {2666-5247},
}

@article {pmid42320590,
year = {2026},
author = {Zhang, JS and Lu, W and Zhu, H and Liang, Z and Chu, CH and Jakubovics, NS and Chen, Z and Yu, OY},
title = {Staging-Dependent Dysbiosis of Plaque Microbiota in Early Childhood Caries.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106846},
doi = {10.1016/j.jdent.2026.106846},
pmid = {42320590},
issn = {1879-176X},
abstract = {OBJECTIVES: The stage-specific ecological and functional microbial features of ECC remains poorly defined. This study aimed to characterize the lesion-associated microbiome and evaluate stage-specific microbial signatures of ECC.

METHODS: Paired supragingival plaque samples were collected from an active cavitated lesion (caries) and a spatially-matched intact surface (control) of 84 ECC-affected children aged 3 - 4 years. Lesions were classified by depth as enamel caries and dentine caries. Microbial profiles were generated by 16S rRNA sequencing and analysed for community diversity, structure, and differentially abundant taxa. PICRUSt2 was used for functional prediction.

RESULTS: Alpha diversity did not differ between caries and controls, but beta diversity revealed significant compositional separation. PERMANOVA identified disease status as the main driver of community variation, with disease staging as an additional significant factor. Caries lesions were enriched with classical and emerging cariogenic taxa, including Streptococcus mutans, Prevotella histicola, Prevotella salivae, Selenomonas sputigena, Scardovia wiggsiae, and Veillonella dispar. A 13-species panel distinguished caries from controls with an AUC of 0.85. Stratification by caries staging revealed pronounced dysbiosis confined to the dentine caries subgroup. Functional prediction suggested that dentine caries had a distinct inferred profile, with predicted enrichment of carbohydrate metabolism pathways, the phosphotransferase system, and the pentose phosphate pathway.

CONCLUSIONS: In ECC-affected children, plaque microbiome in carious lesions showed distinct compositional, ecological and functional alterations versus unaffected surfaces, with further dysbiosis driven by caries progression. Dentine caries featured a stage-specific consortium of cariogenic taxa and a predicted functional shift toward intensified carbohydrate uptake and fermentation, informing potential microbiome-targeted strategies for ECC management.

CLINICAL SIGNIFICANCE: The identified ecological progression of ECC offers key microbial biomarkers to inform microbiome-targeted preventive and therapeutic strategies, ultimately improving clinical outcomes in pediatric dentistry.},
}

@article {pmid42320750,
year = {2026},
author = {Siddiqui, S and Kahkasha, K},
title = {Gut-pancreas-metabolism axis: emerging anti-diabetic roles of gut-derived bioactive molecules.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113383},
doi = {10.1016/j.diabres.2026.113383},
pmid = {42320750},
issn = {1872-8227},
abstract = {The rising global burden of diabetes mellitus necessitates exploration of mechanisms beyond classical pancreatic dysfunction. The gut-pancreas-metabolism axis has emerged as a central regulatory network linking gut microbiota, enteroendocrine signaling, immune modulation, and pancreatic function in glucose homeostasis. Gut-derived bioactive metabolites, including short-chain fatty acids, bile acid derivatives, indole compounds, lipopolysaccharide fragments, and microbial peptides, significantly influence insulin secretion, insulin sensitivity, inflammation, and energy metabolism. These metabolites regulate key pathways such as AMP-activated protein kinase, PI3K/Akt signaling, G-protein-coupled receptor activation, and inflammatory cascades, thereby contributing to β-cell preservation and metabolic balance. Dysbiosis-associated shifts in microbial metabolite profiles are strongly associated with insulin resistance, impaired incretin responses, and chronic low-grade inflammation in type 2 diabetes. This review summarizes recent mechanistic advances in the gut-pancreas-metabolism axis and highlights the therapeutic potential of microbiota-derived bioactive compounds. Furthermore, it discusses emerging translational strategies, including probiotics, prebiotics, postbiotics, and dietary modulation of the gut microbiome, as adjunctive approaches for diabetes management. Targeting this axis provides promising opportunities for precision-based metabolic therapy in diabetes care.},
}

@article {pmid42320811,
year = {2026},
author = {Wang, Y and Wu, X and Deng, H and Yan, G and Xu, Z and Zhu, L},
title = {A high-molecular-weight polysaccharide from Polygonatum sibiricum inhibits distant tumor growth associated with gut microbiota remodeling and synergizes with αPD-1 therapy.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153116},
doi = {10.1016/j.ijbiomac.2026.153116},
pmid = {42320811},
issn = {1879-0003},
abstract = {BACKGROUND: Defined polysaccharide fractions can reshape the gut microbiome and influence systemic antitumor immunity. We investigated whether an operationally defined high-molecular-weight Polygonatum sibiricum polysaccharide fraction (PSP-H) enriched by 100 kDa ultrafiltration suppresses growth of subcutaneous MC38 tumors via microbiota-dependent mechanisms and potentiates anti-PD-1 therapy.

MATERIALS AND METHODS: PSP-H was isolated by cascade ultrafiltration and compared with a total polysaccharide extract (PSP-T) and lower-MW fractions. We profiled fecal metagenomes, serum metabolites, tumor molecular readouts (immunoblotting; HDAC activity), and immunity. Fecal microbiota transplantation (FMT) tested the microbiota dependence and sufficiency of PSP-H-remodeled communities to transfer the immunometabolic phenotype. Combination with anti-PD-1 (RMP1-14) was evaluated.

RESULTS: PSP-H showed minimal direct cytotoxicity while suppressing tumor growth, selectively enriching butyrate-producing taxa (e.g., Lachnospiraceae) and elevating serum butyrate and inosine, with TNF-α reduced. In vitro, butyrate enhanced T-cell IFN-γ/IL-2/granzyme-B, inhibited tumor HDAC activity, and counteracted IFN-γ-induced PD-L1; in vivo, PSP-H created a T-cell-activating milieu with adaptive STAT1/PD-L1 up-regulation. FMT recapitulated the key metabolite/cytokine signature. PSP-H + anti-PD-1 synergistically increased intratumoral CD8[+] T cells and yielded superior tumor control versus monotherapy.

CONCLUSION: PSP-H is a defined microbiota-modulating adjuvant that engages a microbiome-butyrate-immune axis to restrain subcutaneous tumors and sensitizes them to PD-1 blockade by converting systemic immunity while inducing targetable adaptive resistance.},
}

@article {pmid42320851,
year = {2026},
author = {Shen, S and Zhang, J and Qi, X},
title = {The role of short-chain fatty acids as key mediators of gut microbiota - host crosstalk in thyroid diseases.},
journal = {Autoimmunity reviews},
volume = {25},
number = {9},
pages = {104123},
doi = {10.1016/j.autrev.2026.104123},
pmid = {42320851},
issn = {1873-0183},
abstract = {The gut-thyroid axis has emerged as a pivotal area of research in endocrinology. Growing evidence suggests that gut microbiota (GM) dysbiosis is implicated in the pathogenesis of thyroid diseases. Short-chain fatty acids (SCFAs), key microbial metabolites, are proposed as critical mediators in this interplay, but a comprehensive synthesis of their roles is needed. This review provides an overview of the mechanisms and therapeutic potential of SCFAs in thyroid diseases. Patients with thyroid diseases commonly exhibit gut microbiota dysbiosis, characterized by reduced SCFA-producing bacteria and decreased systemic SCFA levels. Mechanistically, SCFAs regulate immune and metabolic homeostasis through G protein-coupled receptor signaling, histone deacetylase inhibition, mitochondrial metabolism, mTOR-S6K signaling, and intestinal barrier protection. Their deficiency may disrupt immune tolerance, promoting autoimmunity and tumor progression. However, current research remains largely correlative, with insufficient mechanistic evidence. SCFAs are central to gut-thyroid crosstalk. Targeting SCFA pathways through probiotics, prebiotics, or microbiota transplantation represents a promising therapeutic frontier. Future research must prioritize establishing causality using advanced models and validating these approaches in rigorous clinical trials to pave the way for personalized microbiome-based therapies for thyroid diseases.},
}

@article {pmid42321165,
year = {2026},
author = {Zhang, L and Lv, C and Guo, W and Fu, Q and Li, Y and Liu, X},
title = {Multi-omics insights into isovaleric acid effects on broiler performance, physiological health, and meat quality.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01053-0},
pmid = {42321165},
issn = {2055-5008},
support = {2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; 2662023DKPY002//Fundamental Research Funds for the Central Universities/ ; },
abstract = {Isovaleric acid (IVA) has been shown to benefit gut health, but its effects on broiler meat quality remain unclear. A total of 864 broilers were assigned to control or 0.05%, 0.1%, or 0.2% IVA groups to evaluate the effects of IVA supplementation on performance, blood biochemistry, immunity, gut microbiota, metabolome, and meat quality. IVA increased average daily gain and, at some doses, feed intake and villus height, while reducing feed conversion ratio. It also lowered serum blood urea nitrogen at 21 and 42 days and modulated inflammatory and immune indices. IVA improved meat quality by increasing breast and leg muscle protein content at 42 days, reducing drip loss and shear force, and improving color parameters. Microbiome analysis showed that IVA reduced Ace index and altered bacterial and fungal β-diversity at 21 days, whereas at 42 days it increased bacterial Shannon index and shifted community composition, while fungal α-diversity remained largely unchanged. Metabolomics revealed marked changes in lipid and amino acid metabolism. Integrative analysis identified Collinsella, norank_f__Ruminococcaceae, and unclassified_f__Oxalobacteraceae as key taxa associated with beneficial muscle metabolites. These findings highlight a gut microbiota-metabolome-muscle axis contributing to improved broiler meat quality and inform nutritional interventions in poultry production.},
}

@article {pmid42321256,
year = {2026},
author = {Zhao, Y and Wang, Y and Bai, S and Tan, J and Niu, H and Zhang, A and Guo, G and Fang, L and Jiang, L},
title = {Reprogramming hydrogen metabolism for methane mitigation in dairy cows: mechanistic insights from polyphenols using meta-omics approaches.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01068-7},
pmid = {42321256},
issn = {2055-5008},
support = {JR25027//Beijing High-Level Innovation and Entrepreneurship Talent Program-Basic Research Talent Project/ ; 2023YFD1301801//National Key R&D Program of China/ ; BAIC05-2025//Beijing Livestock Industry Innovation Team/ ; },
abstract = {Enteric methane emissions from ruminants contribute significantly to agricultural greenhouse gases. Plant-derived phytochemicals such as grape seed proanthocyanidins (GSP) are promising natural antimethanogenic feed additives, yet their modes of action remain incompletely understood. This study aimed to comprehensively elucidate the microbiological and functional mechanisms underlying phytochemical-induced methane mitigation using integrative meta-omics. Both in vivo and in vitro experiments demonstrated that GSP supplementation significantly reduced methane emissions; in lactating dairy cows, GSP decreased methane emission intensity by 16.5% (g/kg energy-corrected milk). Metagenomic and metatranscriptomic analyses revealed a reprogramming of microbial communities, with decreased abundance and transcriptional activity of methanogenic archaea (e.g., Methanobrevibacter) and enhanced activity of alternative hydrogenotrophic bacteria (Selenomonas, Veillonella, Sharpea). Functionally, GSP elevated expression of genes involved in reductive acetogenesis (e.g., acsB), nitrate ammonification (narG, nrfA), and sulfate reduction (dsrA), thereby redirecting hydrogen flux away from methanogenesis. These shifts were accompanied by increased microbial carbohydrate metabolism and antioxidative responses. Our findings provide the first meta-omics-based mechanistic framework for understanding methanogenesis suppression by phytochemicals in ruminants. GSP modulates microbial composition and function to reroute reductant flows and suppress archaeal methanogenesis through enhanced bacterial electron sinks. This work highlights the potential of polyphenols to modulate the rumen microbiome for sustainable methane mitigation, supporting the development of next-generation feed additives.},
}

@article {pmid42321259,
year = {2026},
author = {Lu, CR and Hu, WP and Hsu, CH and Wang, CC and Chang, SS and Lin, YN and Lin, YK and Chung, WH and Chang, KC and Wang, JM and Cho, DY and Hsu, YY and Tsai, HH and Lai, ZL and Wang, YJ and Hsueh, PR and Lai, HY},
title = {Gut microbiome signatures discriminate deep vein thrombosis through machine learning and metabolic analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-55650-2},
pmid = {42321259},
issn = {2045-2322},
support = {DMR-113-007//China Medical University Hospital/ ; CMU113-N-11//China Medical University, Taiwan/ ; NSTC114-2314-B-039-053-MY2//National Science and Technology Council/ ; },
abstract = {Deep vein thrombosis (DVT) remains difficult to distinguish because of its often silent presentation and the limited specificity of current diagnostic tools. We aimed to evaluate whether integrating gut microbiome profiles with routine clinical data could enhance the classification performance for identifying DVT in a case-control cohort. Stool samples were collected from individuals with DVT (n = 58), coronary artery disease (CAD, n = 56), and healthy controls (HC, n = 500). Full-length 16S rRNA gene sequencing was used to characterize the gut microbiota at species-level resolution. A random forest classifier was trained using a nested cross-validation framework, with permutation importance and SHAP (Shapley additive explanations) analyses applied to assess model interpretability. Decision curve analysis (DCA) was employed to evaluate the discriminative value of the models in an independent test set. Following linear discriminant analysis (LDA) effect size (LEfSe) screening, 95 candidate microbial features were entered into a random forest framework. Features were reduced using mutual information filtering and embedded selection to retain the final 10 for DVT vs. non-DVT classification. The integrated microbial-clinical model demonstrated substantially improved discrimination compared with the clinical-only model, achieving higher ROC-AUC [0.947 (95% CI 0.870-0.991) vs. 0.874 (95% CI 0.794-0.941)] and PR-AUC [0.793 (95% CI 0.602-0.931) vs. 0.497 (95% CI 0.274-0.724)]. Importantly, the microbiome-derived signals were robustly associated with DVT risk after adjustment for clinical covariates. Functional prediction analysis indicated enrichment of vitamin K2 and lipopolysaccharide (LPS) biosynthesis pathways in DVT, suggesting potential microbial links to coagulation and inflammation, whereas healthy controls were predominantly enriched in NAD and tetrahydrofolate (THF) biosynthesis pathways. Together, these results demonstrate that microbiome-based classification provides complementary biological insights that distinguish DVT cases from controls.},
}

@article {pmid42321264,
year = {2026},
author = {Mtshali, A and Togo, AH and Kama, A and Letsoalo, M and Mzobe, G and Sivro, A and Garrett, N and Zondo, N and Mahomed, S and Archary, D and Ngcapu, S},
title = {Cervicovaginal microbiome diversity was not associated with mucosal pharmacokinetics of systemically delivered HIV broadly neutralizing antibodies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57511-4},
pmid = {42321264},
issn = {2045-2322},
support = {REF: TTK240315209308//National Research Foundation/ ; EDCTP Grant number: RIA2017S//European and Developing Countries Clinical Trials Partnership/ ; },
abstract = {Broadly neutralizing antibodies (bNAbs) are a promising HIV prevention strategy due to their potent antiviral activity and potential for long-acting protection. While the vaginal microbiome can influence mucosal immunity and the efficacy of topical interventions, its effect on the pharmacokinetics of systemically administered bNAbs remains unclear. Forty-two women were included in a retrospective analysis of the CAPRISA 012B clinical trial evaluating passive immunization for HIV prevention. Vaginal microbiota were profiled using 16 S rRNA gene sequencing and classified into three community state types (CSTs): CST I (Lactobacillus crispatus-dominated), CST III (Lactobacillus iners-dominated), and CST IV (diverse, non-Lactobacillus-dominated). Mucosal concentrations of CAP256V2LS were measured from Soft-cup[®] cervicovaginal fluid using the Meso Scale Discovery (MSD) platform with electrochemiluminescence (ECL) detection. Longitudinal analyses assessed CST stability, transitions, and associations with mucosal antibody pharmacokinetics. Lactobacillus-dominated CSTs were most frequent (CST I, 5.3%; CST III, 57.9%), whereas BV-associated CST IV subtypes were less common (CST IV-A, 2.6%; CST IV-B, 34.2%). Lactobacillus-dominated communities were generally stable, while high-diversity CST IV communities were more dynamic, with transitions toward Lactobacillus-dominated states observed over time. Despite these microbial shifts, mucosal bNAb kinetic patterns appeared broadly similar across CSTs. Within the limits of this exploratory analysis, we did not observe clear evidence of an association between CST composition and the timing or magnitude of mucosal bNAb accumulation. These observations were descriptive and not derived from inferential statistical or pharmacokinetic modelling analyses. In this exploratory sub-analysis, cervicovaginal microbiome composition was not clearly associated with differences in mucosal concentrations of systemically administered bNAbs. These findings suggest that systemic bNAb delivery may achieve measurable genital tract exposure across diverse vaginal microbial communities; however, larger studies incorporating inferential pharmacokinetic and immunological analyses are needed to confirm these observations and exclude subtle microbiome-associated effects.},
}

@article {pmid42321538,
year = {2026},
author = {Holmberg, SM and Schroeder, BO},
title = {Fatty diets disrupt mucus-microbiome-metabolite interactions to increase intestinal lipid uptake.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42321538},
issn = {2058-5276},
support = {2025-02844//Vetenskapsrådet (Swedish Research Council)/ ; 2021-06602//Vetenskapsrådet (Swedish Research Council)/ ; 2024-0100//Familjen Erling-Perssons Stiftelse (Erling-Persson Family Foundation)/ ; },
}

@article {pmid42321605,
year = {2026},
author = {Sun, Y and Tang, J and Ma, S and Maimaiti, A and Liu, J and Qiu, J and Ge, J},
title = {Stage-specific rhizosphere microbial succession is associated with nutrient cycling in the desert plant Leymus racemosus (Lam.) tzvelev.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09294-z},
pmid = {42321605},
issn = {1471-2229},
support = {XKLEAEEEO-03//Xinjiang Key Laboratory for Ecological Adaptation and Evolution of Extreme Environment Organisms, College of Life Sciences, Xinjiang Agricultural University/ ; 23XJTRZW20//the Special Fund of the Xinjiang Key Laboratory of Soil and Plant Ecological Processes/ ; },
abstract = {BACKGROUND AND AIMS: Plants regulate nutrient uptake and growth by recruiting rhizosphere microorganisms via root exudates. However, a systematic understanding of how the rhizosphere core and functional microbiota jointly regulate the dynamics of carbon, nitrogen, phosphorus, and potassium across the entire plant life cycle in desert ecosystems remains limited. In this study, we asked: how does the succession of rhizosphere bacterial communities align with stage-specific nutrient demands in the desert plant Leymus racemosus?

METHODS: We used 16 S rRNA high-throughput sequencing to analyze the rhizosphere bacterial communities and nutrient contents of the desert plant Leymus racemosus at three growth stages (seedling, flowering, maturity) in the Kalamaili Nature Reserve, Xinjiang, China. For each stage, ten 5 × 5 m quadrats (20 m apart) were established; 6-10 healthy plants were sampled per quadrat, and rhizosphere soil from each quadrat was pooled into one composite sample (n = 10 per stage).

RESULTS: Arthrobacter, identified as a core taxon, was associated with the stability of hydrolyzable nitrogen across all growth stages. Bacillus became the dominant genus during the flowering stage, based on correlation and functional prediction, it may contribute to nutrient supply, reflecting a potential "investment" strategy. At maturity, enhanced microbial cooperation (inferred from co-occurrence and correlation analyses) combined with reduced plant demand was associated with the accumulation of rhizosphere nutrients, possibly facilitating energy storage for subsequent growth. These findings provide a potential answer to our question, suggesting that the plant recruits distinct microbial alliances at different phenological phases-a persistent Arthrobacter-based system for nitrogen buffering, a transient Bacillus-enriched community for rapid nutrient mobilization at flowering, and a synergistic network at maturity for delayed nutrient accumulation.

CONCLUSIONS: This study reveals the developmental dynamics of rhizosphere bacterial community assembly and nutrient regulation in L. racemosus and provides a theoretical basis for further elucidating plant-microbe interactions in desert ecosystems. However, the proposed functional roles of specific taxa are primarily derived from correlation and predictive analyses; experimental validation (e.g., strain isolation, inoculation tests, and metabolomics) is needed to establish causality.},
}

@article {pmid42321612,
year = {2026},
author = {Nikparast, A and Sepehrinia, M and Zamanian, N and Razaz, JM and Tabatabaeyan, A and Hadi, S and Homayounfar, R},
title = {Adherence to the dietary index for gut microbiota and the 5-year incidence of metabolic dysfunction-associated steatotic liver disease in Iranian adults: a prospective cohort study.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-026-05036-5},
pmid = {42321612},
issn = {1471-230X},
abstract = {BACKGROUND: Diet is a key modulator of gut microbiota and may influence the development of metabolic dysfunction-associated steatotic liver disease (MASLD). The Dietary Index for Gut Microbiota (DI-GM) has been proposed to capture the overall capacity of diet to promote a favorable gut microbial profile. Prospective evidence linking DI-GM to MASLD risk remains limited.

METHODS: This prospective analysis included 5,058 adults without MASLD at baseline from the Monitoring of Metabolic Diseases Risk Factors in Tehran (MMRT) study. Dietary intake was assessed using a validated 125-item food frequency questionnaire. The five-year incidence of MASLD was evaluated using multivariable logistic regression models, and associations were expressed as odds ratios (ORs) with 95% confidence intervals (CIs). Subgroup analyses were conducted to assess potential effect modification. Sensitivity analyses examined the robustness of results after excluding participants with substantial weight gain and after additional adjustment for metabolic and dietary factors. Mediation analyses were performed to explore potential pathways underlying the observed associations.

RESULTS: Over five years of follow-up, 562 participants developed MASLD. Higher DI-GM scores were associated with a lower likelihood of incident MASLD. In the fully adjusted model, individuals in the highest quartile of DI-GM had 42% lower odds of MASLD compared with those in the lowest quartile (OR:0.58; 95%CI:0.42-0.80; P-trend < 0.01). Each one-standard-deviation increment in DI-GM score was associated with reduced odds of MASLD (OR:0.72; 95%CI:0.65-0.81;P-value < 0.001). The inverse association was more pronounced among women and participants aged ≥ 45 years (P-interaction < 0.01). Mediation analyses suggested that CAP, HOMA-IR, and serum vitamin D partially explained the association.

CONCLUSIONS: Greater adherence to a diet supportive of gut microbiota, as reflected by higher DI-GM scores, was associated with a lower five-year risk of MASLD. These findings highlight the potential role of microbiota-related dietary patterns in MASLD prevention.},
}

@article {pmid42321771,
year = {2026},
author = {Nielsen, DP and Holding, ML and Del Carlo, RE and Everson, KM and Ochsenrider, K and Simison, WB and Henderson, J and Dearing, MD and Hayes, JP and Frese, SA and Richards, LA and Ferguson, BS and Forbey, JS and Matocq, MD},
title = {Diet change reveals asymmetric response in gene expression and microbial composition across the digestive tract of two closely related herbivores.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02658-9},
pmid = {42321771},
issn = {1741-7007},
abstract = {BACKGROUND: Understanding what shapes variation in organisms' capacity to utilize novel resources is essential to predicting how species will respond to environmental change. For herbivores, exposure to toxic phytochemicals in novel plants may limit persistence in new habitats. We investigated the behavioral, physiological, genetic, and microbial consequences of diet switching in two closely related species of rodent herbivores that each consume differentially toxic plants in their native habitat, and that maintain different dietary strategies (i.e., relative dietary specialist versus relative generalist).

RESULTS: In reciprocal laboratory feeding trials, we exposed wild-caught woodrats (genus Neotoma) to toxins characteristic of either familiar or novel plant secondary compounds. We measured changes in food and water intake, locomotor activity, gut microbial composition, and gene expression across the digestive tract following feeding trials. The dietary generalist responded minimally, but the specialist responded strongly when exposed to the novel diet. This response included behavioral and genetic components including increased water intake, reduction in locomotor activity, increased differential expression of detoxification genes, and a greater shift in gut microbial composition.

CONCLUSIONS: The dietary specialist exhibited a strong response to diet switching that corresponded with ecologically relevant shifts in behavior and physiology that would have negative fitness consequences. Although the dietary specialist had a strong genetic and microbial response to novel plant secondary compounds, this response would likely be insufficient to overcome the immediate challenge of exposure to novel dietary toxins in the wild. Our results underscore the link between feeding strategy and the capacity to shift to novel dietary resources in response to environmental change.},
}

@article {pmid42321864,
year = {2026},
author = {Wang, W and Huang, X and Wu, F and Liu, X},
title = {Identification of keystone taxa shaping biocrust formation and biodeterioration of limestone monuments in the Xiaoling Tomb of the Ming Dynasty.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42321864},
issn = {2524-6372},
support = {BK20250086//Basic Research Program of Jiangsu Province/ ; 32570139 and 32370105//National Natural Science Foundation of China/ ; },
abstract = {The limestone monuments of the Rectangular Tower in the Xiaoling Tomb of the Ming Dynasty, created in the mid-fourteenth century, are biodeteriorating from environmental exposure, resulting in the formation of black biocrusts. However, the microbiomes that shape biocrust formation and the biodeterioration processes involved remain unclear, significantly challenging the conservation of stone monuments at this archaeological site. Here, we systematically investigated the physicochemical properties and microbial communities of biocrusts to identify keystone taxa that shape their formation and biodeterioration. Physicochemical analysis indicated that biological crusts are associated with calcium mobilization and redistribution of the limestone monuments. Microscopy and spectroscopy indicated that microbial interactions with limestone promote the formation of biological crusts. Importantly, we observed the significant predominance of Cyanobacteria and/or Chloroflexi in biocrusts, suggesting that photosynthesis may be a crucial process in biocrust formation. Fungal communities in biocrusts were dominated by Ascomycota, Basidiomycota, and Chytridiomycota, while archaeal communities were dominated solely by Nitrososphaerota. Microbial co-occurrence network and correlation analyses identified 12 keystone taxa across 11 genera that shape biocrust formation. Importantly, Scytonema spp. could provide organic carbon and nitrogen for Spirosomaceae spp., and members of the classes Cyanobacteriia and Agaricomycetes, as well as the genera Setophaeosphaeria and Plectosphaerella, are likely the keystone taxa responsible for both biocrust formation and the associated biodeterioration. Additionally, two predominant ammonia-oxidizing archaeal families (i.e., Nitrososphaeraceae and Candidatus Nitrocosmicus) could support chemolithoautotrophic growth in the microbiome by oxidizing ammonia and fixing carbon dioxide. Together, these findings underscore the need for targeted conservation strategies to mitigate microbial biodeterioration of stone monuments during biocrust formation.},
}

@article {pmid42321912,
year = {2026},
author = {Zhou, M and Deng, Y and Huang, Y and Yu, C and Chen, X and Yang, Q and Liao, Y and Wang, S and Zhang, P and Chen, A and Ling, W and Chen, X and Li, J and Xue, H},
title = {Dietary index for gut microbiota, plasma metabolome, and risks of metabolic dysfunction-associated steatotic liver disease and other chronic liver diseases.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-026-01145-w},
pmid = {42321912},
issn = {1743-7075},
support = {82304130//National Natural Science Foundation of China/ ; SL2023A04J01145//Basic research project of Guangzhou Science and Technology Bureau/ ; },
abstract = {BACKGROUND: The dietary index for gut microbiota (DI-GM) is a newly proposed metric for assessing diet quality linked to gut microbiota. However, prospective evidence is scarce on the associations between DI-GM and adverse liver outcomes.

METHODS: The DI-GM was calculated by averaging the intakes of 12 foods and nutrients. Elastic net regression was performed to identify metabolites associated with DI-GM and metabolic signature reflecting higher adherence to DI-GM was constructed. Cox proportional hazards regression and mediation analyses were employed to explore the potential associations and mechanisms.

RESULTS: This prospective cohort study included 168,456 participants from the UK Biobank. Compared to participants with DI-GM scores of 0-3, those scoring ≥ 6 presented 22% lower risk of MASLD (HR = 0.78, 95% CI = 0.68-0.90). Metabolic signature for DI-GM and dietary index beneficial to gut microbiota (BDI-GM) were also inversely correlated with MASLD. Similar inverse correlations between DI-GM and BDI-GM and the risks of other chronic liver diseases were identified. Furthermore, phenotypic age, body mass index, metabolic score, inflammatory score, and metabolic signature significantly mediated the relationship between DI-GM and MASLD. No significant interactions were observed between DI-GM and polygenic risk score of hepatic steatosis, and the associations between DI-GM and adverse liver outcomes persisted regardless of genetic risk.

CONCLUSIONS: Higher adherence to DI-GM significantly correlates with reduced risks of MASLD and other chronic liver diseases, independent of genetic susceptibility. And the apparent mediating effects of five indices highlight the role of aging, obesity, metabolic disorders, inflammation, and metabolomic alterations in the association between DI-GM and MASLD. Further research is warranted to evaluate the utility of metabolic signatures in metabolic profile monitoring and risk stratification.

IMPACT AND IMPLICATIONS: This large-scale cohort study first demonstrates that higher adherence to a gut microbiota-beneficial diet (DI-GM) is associated with a lower risk of MASLD and other chronic liver diseases, independent of genetic susceptibility. The estimated population attributable fractions, while derived from observational data and requiring cautious interpretation, suggest that a substantial portion of liver disease cases in the study population might be linked to suboptimal DI-GM adherence. These findings underscore the importance of integrating gut microbiome health into public health strategies for liver disease prevention, offering a practical approach to reduce disease burden at both individual and population levels. The DI-GM-associated metabolic signature represents a candidate objective biomarker meriting evaluation in future studies for its potential in early risk assessment. Mediation analyses further reveal that a diet promoting healthy gut microbiota may reduce MASLD risk by maintaining gut microbiota homeostasis, decelerating biological aging, ameliorating obesity, attenuating metabolic disorders, alleviating inflammation, and altering metabolome. Collectively, this study generates important hypotheses and provides a rationale for future interventional research to determine whether promoting DI-GM-aligned diets can effectively reduce liver disease risk at the population level.},
}

@article {pmid42322129,
year = {2026},
author = {Usui, T and Yu, J and Frederickson, ME},
title = {For colonization success, should hosts and microbes travel alone, together, or swap partners along the way?.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71372},
pmid = {42322129},
issn = {1469-8137},
support = {//Natural Sciences and Engineering Research Council of Canada/ ; GBM10635//Gordon and Betty Moore Foundation/ ; GBMF9536//Gordon and Betty Moore Foundation/ ; //University of Toronto/ ; },
abstract = {Microbiomes that enhance the performance of host plants are likely to be co-introduced with their host during colonization because of their intimate association. Yet, it is unclear how co-introduced microbes will impact host colonization, as both the microbiome and its effects could vary upon introduction into a new habitat. Using the duckweed Lemna japonica - a cosmopolitan, freshwater angiosperm - and its microbiome, we tracked the colonization of both plants and microbes during an experimental co-introduction in the wild. We tested how plant performance varied during colonization when plants were co-introduced with microbes from their home habitat or with microbes local to the introduced habitat. We found that plant performance was substantially reduced when plants were co-introduced with microbes from their home habitat (i.e. with microbes that are non-local to the introduced habitat), relative to hosts with a local microbiome. Moreover, negative impacts from the initial, non-local microbiome persisted for multiple host generations despite a rapid turnover in microbiome composition. Our results suggest that the initial microbiome plants are co-introduced and can leave lasting impacts on plant performance during colonization. Considering the identity of the co-introduced microbiome will therefore be critical to predicting plant colonization dynamics in an era of global change.},
}

@article {pmid42322204,
year = {2026},
author = {Moran, GP and McQuillan, A and Ho, GT and Whelan, RJ and Navas-López, VM and Lawrence, S and Rolandsdotter, H and Olen, O and Martín-de-Carpi, J and Sigall Boneh, R and Wine, E and Hussey, S},
title = {Modified Crohn's Disease Exclusion Diet and exclusive enteral nutrition (EEN) resolve oral dysbiosis in pediatric Crohn's disease: a prospective cohort study.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag107},
pmid = {42322204},
issn = {1536-4844},
support = {c/18/2//Children's Health Foundation/ ; },
abstract = {BACKGROUND AND AIMS: Changes to the oral microbiome have been reported in patients with Crohn's disease (CD). The aim of this study was to determine the characteristics and dynamics of the oral microbiome in children randomized to 1 of 2 nutritional treatments for CD.

METHODS: Participants (n = 54) in this randomized controlled trial (NCT02843100) received the Crohn's Disease Exclusion Diet (CDED) with either partial enteral nutrition (PEN; n = 28) or exclusive enteral nutrition (EEN; n = 26). The oral microbiome was assessed via swabs from the dorsum of the tongue and the buccal gingiva by 16S rRNA sequencing at 0, 2, 8, 14, 24, and 52 weeks.

RESULTS: There were no significant differences in primary or clinical outcomes between the 2 groups. Due to the COVID-19 pandemic, sampling by 24 weeks was limited to 34 participants. At week 0, moderate-severe disease activity (Pediatric Crohn's Disease Activity Index [PCDAI] > 30) was associated with decreased Porphyromonas, Haemophilus, Alloprevotella, Neisseria, and Bergeyella species and increased Actinomyces. As patients entered remission (PCDAI < 10), we observed a restoration in the abundance of these taxa. A modified oral dysbiosis index (MODI) was generated, capable of distinguishing mild from moderate-severe disease activity based on microbiome profiles. Dysbiosis decreased as treatment continued and patients entered remission. Patients on CDED exhibited more significant dysbiosis index changes at weeks 8-24, compared with the EEN group. Application of the index across published oral microbiome data sets validated its ability to discriminate health from CD.

CONCLUSION: Oral microbiome changes in pediatric CD reflect disease activity and parallel therapeutic response to CDED and EEN over time. Additional validation of the proposed dysbiosis index should be undertaken in adequately powered future studies.},
}

@article {pmid42322208,
year = {2026},
author = {Thi Dang, ND and Nguyen, MT and Nguyen, DS and Nguyen, QV},
title = {Wild guava (Psidium guajava L.) leaf extract: multifaceted effects on gut microbiota, gene expression, and metabolic regulation in a zebrafish model of type 2 diabetes.},
journal = {Natural product research},
volume = {},
number = {},
pages = {1-10},
doi = {10.1080/14786419.2026.2689480},
pmid = {42322208},
issn = {1478-6427},
abstract = {Wild guava (Psidium guajava L.) leaf extract shows promise for type 2 diabetes mellitus (T2DM) management through its effects on the gut microbiota, gene expression, and metabolism. This study examined the extract's effects on probiotic growth, gut microbiota, and diabetes-related gene expression in a zebrafish T2DM model. The extract enhanced probiotic growth of Lactobacillus casei, L. plantarum, and YC-381 by up to 33.11% in hyperglycaemic conditions. In diabetic zebrafish, it restored gut microbiota diversity, reduced pathogenic genera, and increased beneficial taxa like Leuconostoc and Bacillus. Functional analysis showed improved microbial polyphenol and lipid metabolism. The extract downregulated ACC1, normalised insulin receptor expression, reduced SGLT1, and moderately increased GLP1. Transcriptomic analysis revealed the homeostatic effects of the extract on metabolic pathways, in contrast to the pharmacological modulation of metformin. These results demonstrate the potential of wild guava leaf extract as a T2DM intervention through its effects on the microbiome-transcriptome-phenotype axis.},
}

@article {pmid42322288,
year = {2026},
author = {Silva, E and Santana Aguiar, MC and Vilhena Araújo, E and França, P and Berlinck, RGS and Ballester, AR and González-Candelas, L and Fill, T},
title = {Green Mold of Citrus: Recent Insights into Penicillium digitatum Pathogenicity and Biological Control Strategies.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c02943},
pmid = {42322288},
issn = {1520-5118},
abstract = {P. digitatum, the causal agent of citrus green mold, remains the most destructive postharvest pathogen of citrus worldwide. Recent advances have greatly expanded our understanding of the molecular dialogue between P. digitatum and citrus hosts, revealing coordinated virulence strategies involving cell wall-degrading enzymes, major facilitator superfamily transporters, transcription factors, and secondary metabolism, alongside host defenses mediated by phytohormones and specialized metabolites. This review integrates genomic, transcriptomic, metabolomic, and functional genetic discoveries, including CRISPR/Cas9 and Agrobacterium tumefaciens-mediated transformation, which have accelerated the characterization of fungal pathogenicity and host resistance. We further assess biological control as a sustainable alternative to chemical fungicides, emphasizing complementary mechanisms such as niche competition, antibiosis, volatile organic compound (VOC) production, biofilm formation, iron sequestration, lipopeptide synthesis, and induction of host defenses. In addition, we highlight microbiome-informed strategies and the design of synthetic microbial communities (SynComs) as promising next-generation approaches to enhance efficacy, stability, and ecological resilience in citrus postharvest disease management.},
}

@article {pmid42322355,
year = {2026},
author = {de Souza Menezes, JD and da Silva, MQ and Dos Santos, ER and de Carvalho, SRPVT and Faria, MAG and de Cássia Helú Mendonça Ribeiro, R and André, JC},
title = {Clinical potential of the gut microbiome in oncology: a scoping review of treatment response, toxicity and biomarker development.},
journal = {Supportive care in cancer : official journal of the Multinational Association of Supportive Care in Cancer},
volume = {34},
number = {7},
pages = {},
pmid = {42322355},
issn = {1433-7339},
mesh = {Humans ; *Neoplasms/microbiology/therapy/drug therapy ; *Gastrointestinal Microbiome ; *Antineoplastic Agents/adverse effects/therapeutic use/administration & dosage ; Precision Medicine/methods ; Immunotherapy/methods/adverse effects ; Biomarkers, Tumor ; Biomarkers ; Treatment Outcome ; },
abstract = {PURPOSE: This scoping review aimed to systematically map and critically describe the current evidence on the role of the gut microbiome as a biomarker in oncology, including microbiome-based predictive models and microbial signatures associated with treatment response, toxicity and disease course, and to identify methodological gaps and challenges for clinical translation in precision medicine.

METHODS: This scoping review was conducted following the Joanna Briggs Institute (JBI) guidelines for scoping reviews and reported according to the PRISMA Extension for Scoping Reviews (PRISMA-ScR). The search was performed in five electronic databases (PubMed/MEDLINE, Web of Science, Scopus, SciELO, and LILACS) using a structured PICO strategy. Studies involving adult cancer patients undergoing systemic oncological therapies (including chemotherapy, immunotherapy and combined regimens), with gut microbiome analysis and the investigation, development or validation of microbiome-based biomarkers or predictive models, were included.

RESULTS: The literature demonstrates that specific microbial taxa significantly influence the efficacy of immunotherapies (e.g., AUCs up to 0.88 for ICI response prediction) and chemotherapies, and modulate toxicity (e.g., mucositis reduction from 47.1% to 25% with probiotics). Microbiome-based predictive models often outperform clinical markers (e.g., AUC of 0.88 vs. 0.50 in urothelial carcinoma), and variations in microbiota composition can predict disease progression. The literature mapping of the 20 included studies demonstrates that specific microbial taxa significantly influence the efficacy of immunotherapies (e.g., AUCs up to 0.88 for ICI response prediction) and chemotherapies. Regarding toxicity, while the review focuses on baseline biomarkers, exploratory intervention-based data were addressed, showing that a probiotic cocktail reduced Grade 3-4 oral mucositis from 47.1% to 25%. Furthermore, microbiome-based predictive models demonstrated enhanced discriminatory accuracy in predicting patient outcomes compared to standard clinical classification markers alone (e.g., achieving an Area Under the Curve [AUC] of 0.88 vs. 0.50 for clinical factors in urothelial carcinoma), though these models remain in early exploratory stages.

CONCLUSION: Overall, the evidence suggests a growing interest and potential for microbiome-based predictive models in oncology; however, their clinical translation remains limited by methodological heterogeneity, insufficient external validation, and incomplete mechanistic understanding.},
}

Humans
*Neoplasms/microbiology/therapy/drug therapy
*Gastrointestinal Microbiome
*Antineoplastic Agents/adverse effects/therapeutic use/administration & dosage
Precision Medicine/methods
Immunotherapy/methods/adverse effects
Biomarkers, Tumor
Biomarkers
Treatment Outcome

@article {pmid42322360,
year = {2026},
author = {Anderson, KL and Shipley, LA and Staudenmaier, AR and Galla, SJ and Forbey, JS},
title = {Influence of Plant Secondary Metabolites on intake, Detoxification Costs, and Microbial Communities in Deer.},
journal = {Journal of chemical ecology},
volume = {52},
number = {4},
pages = {},
pmid = {42322360},
issn = {1573-1561},
support = {1018967//USDA National Institute of Food and Agriculture, McIntire-Stennis Project/ ; 2437743//U.S. National Science Foundation/ ; OIA-1826801//U.S. National Science Foundation/ ; },
mesh = {Animals ; *Deer/microbiology/physiology/metabolism ; Herbivory ; *Plants/metabolism/chemistry ; Feces/microbiology ; Secondary Metabolism ; Glucuronic Acid/urine ; *Gastrointestinal Microbiome ; Bacteria/classification/metabolism/isolation & purification ; Inactivation, Metabolic ; },
abstract = {Plants available to wild herbivores, especially browsers, often contain plant secondary metabolites (PSMs). Herbivores have evolved behavioral, physiological, and microbial mechanisms for avoiding and detoxifying PSMs. The detoxification limitation hypothesis suggests that herbivores can reduce toxicity by consuming a mixture of PSMs to avoid overloading a particular detoxification pathway. Although this hypothesis has been examined for smaller mammalian hindgut-fermenters, less is known about responses to PSM mixtures in wild ruminants. To assess the role of host and microbial responses to PSM composition, we used controlled feeding trials to measure voluntary dry matter and PSM intake, urinary excretion of glucuronic acid (GA, a byproduct of PSM detoxification through conjugation), and the diversity and relative abundance of gastrointestinal bacterial families in the feces of two species of captive-raised deer (Odocoileus hemionus, O. virginianus). Deer were fed five mixtures of four purified PSMs that included two same-chemical class mixtures, two different-class mixtures, and one 4-way mixture of all chemicals. Overall, we found that PSM composition had minimal effect on intake, that GA was a consistent physiological biomarker of PSM intake regardless of PSM composition, and that dietary phenolics may influence microbial communities more than monoterpenes. Our results partially conformed to the detoxification limitation hypothesis, where deer consumed less of one same-class mixture (monoterpenes) than different-class mixtures. Our results point to the complexity of the interplay between different behavioral, physiological, and microbial mechanisms that can mediate the consequences of PSMs.},
}

Animals
*Deer/microbiology/physiology/metabolism
Herbivory
*Plants/metabolism/chemistry
Feces/microbiology
Secondary Metabolism
Glucuronic Acid/urine
*Gastrointestinal Microbiome
Bacteria/classification/metabolism/isolation & purification
Inactivation, Metabolic

@article {pmid42322403,
year = {2026},
author = {Tadros, M and Lemmon, B and Bhide, A and Digesu, A and Fernando, R and Khullar, V},
title = {Changes in Uropathogen Distribution in Relation to the COVID-19 Pandemic Timeline.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {42322403},
issn = {1433-3023},
abstract = {INTRODUCTION AND HYPOTHESIS: Recent research has shown that the COVID-19 virus changes the gastrointestinal microbiome as it is a bacteriophage [1], leading to immune dysregulation and bowel dysbiosis [2]. This creates an environment where opportunistic pathogens thrive while beneficial bowel flora diminish [3]. There is an association among the bowel, vaginal and bladder microbiomes where the bacteria from the bowel are found in the bladder [4]. Urinary tract infections (UTIs) are among the most common bacterial infections, typically caused by Escherichia coli (E. coli), Enterococcus faecalis (E. faecalis), Klebsiella spp, and Proteus mirabilis (P. mirabilis) in women [5]. Changes in the bowel microbiome lead to changes in the bladder microbiome [6]. We aimed to evaluate whether the composition of observed uropathogens differed across the different phases of the COVID-19 pandemic.

METHODS: This retrospective study analysed positive urine cultures from women before, during and after the COVID-19 pandemic. The leading three causative uropathogens with a count over 10[3] cfu/mL were reported.

RESULTS: There were 5543 positive cultures with pre-COVID-19 from 1 January 2019 to 30 January 2020, n = 204, during from 1 February 2020 to 4 May 2023, n = 2518, and after from 5 May 2023 to 1 February 2025, n = 2821. In total, 10,456 bacteria were identified. After May 2023, E. coli prevalence dropped from 27 to 21%, and Pseudomonas spp decreased from 6 to 2% (p value < 0.001). In contrast, Klebsiella spp incidence rose from 8 to 12%. Corynebacterium spp (p < 0.05) and Acinetobacter spp (p < 0.001) were increasingly isolated in symptomatic UTIs after May 2023.

CONCLUSIONS: The bacterial organisms found in urinary tract infections detected before and subsequent to the onset of COVID-19 have changed. This may reflect an interaction between changes in the bowel microbiome and pathological urinary tract infections.},
}

@article {pmid42322405,
year = {2026},
author = {Reasoner, SA and Francis, J and Gidney, M and Amponsah, A and Frainey, B and Schrepf, A and Kelly, AG and Ryden, AM and Crofford, LJ and Dmochowski, RR and Hadjifrangiskou, M and McKernan, LC},
title = {Urobiome Analysis in Interstitial Cystitis/Bladder Pain Syndrome Reveals Nuanced Differences Associated with Localized Pain.},
journal = {International urogynecology journal},
volume = {},
number = {},
pages = {},
pmid = {42322405},
issn = {1433-3023},
support = {K23DK118118/DK/NIDDK NIH HHS/United States ; P20DK123967/DK/NIDDK NIH HHS/United States ; F30AI169748//National Institute of Allergy and Infectious Diseases/ ; UL1TR002243/TR/NCATS NIH HHS/United States ; },
abstract = {INTRODUCTION AND HYPOTHESIS: Interstitial cystitis/bladder pain syndrome (IC/BPS) is a prevalent chronic pain syndrome associated with functional urinary disorders. IC/BPS symptoms can be localized to the pelvic-region or have co-occurring widespread pain. Importantly, response to treatment depends on pain localization phenotype. The etiology of IC/BPS remains elusive, and whether bacteria contribute to IC/BPS pathophysiology remains uncertain. We hypothesized that the urobiome does not differentiate phenotypic presentations of IC/BPS.

METHODS: We used urine samples collected from a longitudinal randomized controlled trial of psychotherapy for individuals with IC/BPS to study the association of the urobiome and IC/BPS symptoms over time. Individuals provided urine samples at baseline, posttreatment, and at 5 months. We performed a secondary analysis on urine samples applying 16S rRNA sequencing and assigned bacterial taxonomy to amplicon sequence variants (ASVs) to characterize the urobiome. We compared urobiome diversity and stability over time, their associations with IC/BPS symptoms, and relationships with pain localization.

RESULTS: As validation of this dataset, we noted a strong influence of menopausal status and recent urinary tract infection on the composition of the urobiome. We did not detect widespread differences in the urobiome that correlated with an individuals' pain localization or severity. Instead, we observed specific bacterial sequences that were altered in abundance in relation to symptomatology, such as reduced abundance of a Dialister ASV in persons with localized pelvic pain.

CONCLUSIONS: Together, this dataset advances our understanding of the urobiome in IC/BPS and sets the stage for future studies on the urobiome and IC/BPS symptoms.},
}