@article {pmid42398311,
year = {2026},
author = {Guleria, A and Bagal, D and Mishra, S and Mehrotra, S and Srivastava, V},
title = {Phytomicrobiome-based approaches for sustainable crop performance and environmental resilience.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128605},
doi = {10.1016/j.micres.2026.128605},
pmid = {42398311},
issn = {1618-0623},
abstract = {The plant microbiome refers to the dynamic microbial communities including bacteria, fungi, protists, viruses, and nematodes that colonize diverse plant tissues and coevolve intimately with their host. The primary objective of microbiome engineering is to improve plant performance by enhancing tolerance to biotic and abiotic stresses, increasing plant fitness, and boosting crop productivity. By discovering the modern approaches and plant-microbe interactions, many experts can design artificial microbial consortia and other biotechnological tools suited to specific crops and environmental conditions. Therefore, in current work special attention is given to the goals, applications, and advanced tools-such as genome editing, synthetic biology, metagenomics, and AI-driven modelling used to optimize plant-microbe interactions for sustainable agriculture and ecosystem restoration. Further, recent advances in ecological, biochemical, and molecular approaches have also introduced a new paradigm for addressing microbiome-based challenges in agricultural management. In this context, microbiome engineering has emerged as a promising biotechnological strategy aimed at the targeted addition, removal, or modification of microbial community traits to achieve greater specificity and efficacy.},
}

@article {pmid42398461,
year = {2026},
author = {Sleytr, UB and Schuster, B},
title = {S-layers as natural building blocks for nanobiotechnology and synthetic biology.},
journal = {Current opinion in microbiology},
volume = {92},
number = {},
pages = {102787},
doi = {10.1016/j.mib.2026.102787},
pmid = {42398461},
issn = {1879-0364},
abstract = {Crystalline bacterial cell surface layers (S-layers) are self-assembling protein lattices that constitute the outermost envelope structure of many Bacteria and most Archaea. Beyond their classical role as cell surface components, S-layers are increasingly recognized as programmable, two-dimensional biological materials that combine nanometer-scale precision, defined porosity, and exceptional physicochemical properties. In this review, we synthesize current understanding of S-layer architecture, assembly, and functionalization to position them as a unifying platform for nanobiotechnology and synthetic biology. We highlight how their intrinsic self-assembly and genetic engineerability enable the design of ordered biomolecular interfaces with applications ranging from molecular sieving, biosensors, biomineralization, and nanoscale patterning. Engineered S-layer fusion proteins allow the modular and spatially controlled display of functional domains, bridging bottom-up materials design with biological complexity. Beyond their technological relevance, S-layers play underappreciated roles in host-microbe interactions, where their structural regularity and surface accessibility shape immunogenicity and cellular recognition, with implications for vaccine development, targeted delivery, and microbiome engineering. We argue that overcoming current limitations in scalable production, stability, and system integration will be key to unlocking the full potential of S-layers as genetically programmable, bio-inspired interfaces, enabling a new class of adaptive nanomaterials and advancing the design principles of synthetic biological systems.},
}

@article {pmid42398519,
year = {2026},
author = {Sridhar, A and Minna, JD},
title = {Co-medications and gut microbiome in NSCLC immunotherapy.},
journal = {The Lancet. Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1470-2045(26)00289-5},
pmid = {42398519},
issn = {1474-5488},
}

@article {pmid42398520,
year = {2026},
author = {Brunetti, L and Santo, V and Pinato, DJ and Citarella, F and Orlando, S and Acker, F and Colella, V and Ricciuti, B and Naidoo, J and Nassar, A and Wakelee, HA and Takada, K and Naqash, AR and Garassino, MC and Greco, C and Ramella, S and Pantano, F and Tonini, G and Vincenzi, B and Arlunno, B and Remon, J and Parisi, C and Planchard, D and Besse, B and Desilets, A and Routy, B and Elkrief, A and Barlesi, F and Derosa, L and Cortellini, A},
title = {Differential impact of proton pump inhibitors and antibiotics on immunotherapy efficacy after chemoradiotherapy in locally advanced non-small-cell lung cancer: a post-hoc analysis of the PACIFIC trial.},
journal = {The Lancet. Oncology},
volume = {},
number = {},
pages = {},
doi = {10.1016/S1470-2045(26)00191-9},
pmid = {42398520},
issn = {1474-5488},
abstract = {BACKGROUND: Baseline exposure to antibiotics and proton pump inhibitors has been associated with reduced efficacy of immune checkpoint inhibitors in patients with advanced tumours, possibly through gut microbiome disruption. Whether this outcome extends to those with earlier-stage disease remains unclear. We aimed to assess the association of baseline antibiotics and proton pump inhibitors with progression-free survival and overall survival in patients with unresectable stage III non-small cell lung cancer (NSCLC).

METHODS: PACIFIC was a randomised, double-blind, placebo-controlled phase 3 trial done in patients aged 18 years or older with unresectable stage III squamous or non-squamous NSCLC, WHO performance status 0-1, and no progression after two or more cycles of concurrent chemoradiotherapy. Patients were randomly assigned (2:1) to durvalumab 10 mg/kg intravenously every 2 weeks for up to 12 months or placebo, starting 1-42 days after chemoradiotherapy; patients were stratified by age, sex, and smoking history. This post-hoc analysis was based on the final 5-year data cutoff date of the completed trial and included the treated population with consent for exploratory analyses. Co-primary endpoints were progression-free survival and overall survival, assessed according to baseline exposure to proton pump inhibitors and systemic antibiotics. This trial is registered on ClinicalTrials.gov (NCT02125461).

FINDINGS: Between May 9, 2014, and April 22, 2016, 713 patients were randomly assigned; 660 were included in this post-hoc analysis, of whom 449 received durvalumab and 211 received placebo; 203 (30·8%) were female and 453 (68·6%) were male. Race was reported as Asian in 153 (23·1%) patients, Black or African American in five (0·7%), White in 424 (64·2%), and unknown in 78 (11·8%). Baseline proton pump inhibitor exposure was recorded in 263 (40%) of 660 patients and antibiotic exposure was recorded in 69 (10%). Median follow-up in the pooled population was 62·4 (IQR 61·9-63·2) months. In the durvalumab group baseline exposure to proton pump inhibitors was associated with shorter progression-free survival (9·4 months [95% CI 7·6-13·7] vs 17·2 months [15·4-23·2]; hazard ratio [HR] 1·57 [95% CI 1·28-1·93]; p<0·0001) and overall survival (33·0 months [95% CI 21·9-46·7] vs 57·9 months [48·7-not computable (NC)]; HR 1·66 [95% CI 1·30-2·13]; p<0·0001) compared to no exposure to proton pump inhibitors, while baseline exposure to antibiotics was associated with shorter progression-free survival (9·2 months [95% CI 4·9-18·1] vs 15·6 months [13·6-17·6]; HR 1·50 [95% CI 1·08-2·10]; p=0·016) compared to no exposure to antibiotics, but there was no significant change in overall survival (37·7 months [95% CI 18·8-NC; 28 events] vs 49·2 months [39·7-57·3]; HR 1·33 [95% CI 0·90-1·97]; p=0·16). In the placebo group, neither proton pump inhibitor exposure nor antibiotic exposure was associated with changes in progression-free survival and overall survival. Interactions between treatment and proton pump inhibitors for progression-free survival (p=0·023) and overall survival (p<0·0001) were significant, but not for antibiotics.

INTERPRETATION: Baseline exposure to proton pump inhibitors and antibiotics was associated with inferior outcomes with durvalumab, but not with placebo, consistent with potential attenuation of the benefit of durvalumab with proton pump inhibitors and antibiotics in patients with unresectable stage III NSCLC.

FUNDING: None.},
}

@article {pmid42398560,
year = {2026},
author = {Khalil, W and Song, H and Li, Z and He, Y and Xu, C and Ye, Q},
title = {Role of oral microbiome in cancer immunotherapy.},
journal = {Seminars in cancer biology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.semcancer.2026.06.006},
pmid = {42398560},
issn = {1096-3650},
abstract = {The oral microbiome is comparable to the gut microbiome in ecological complexity and is now recognized as a contributor to anticancer immune responses. Although the relationship between the gut microbiome and anticancer immunity is well established, the connection between the oral microbiome and anticancer immunity has received increasing attention, with accumulating evidence pointing to the direct effects of the oral microbiome on immune cell populations. The relationship between cancer and the oral microbiome is bidirectional: each influences the behavior of the other. The tumor microenvironment (TME) and oncological therapies such as chemotherapy and radiation can cause oral microbiome dysbiosis. Once dysbiosis is established, it creates conditions that favor tumor initiation and recurrence through chronic inflammation and impaired immune surveillance. Furthermore, the oral microbiome indirectly affects distant cancers and contributes to systemic inflammation and microbial dissemination through gastrointestinal, respiratory, hematogenous, neurological, and lymphatic pathways. Prebiotics, probiotics, postbiotics, and microbiota transplantation represent promising therapies targeting this microbial community to enhance the efficacy of cancer immunotherapy.},
}

@article {pmid42398615,
year = {2026},
author = {Majeed, A and Javaid, MH and Mahreen, N and Hussain, M and Kang, Y and Hussain, K and Su, J},
title = {Nucleic acid and multi-omics approaches for understanding plant-microbiome interactions in grassland ecosystems.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {153356},
doi = {10.1016/j.ijbiomac.2026.153356},
pmid = {42398615},
issn = {1879-0003},
abstract = {Grasslands are among the largest terrestrial biomes and play essential roles in livestock production, carbon sequestration and global food security. The productivity and resilience of these ecosystems are driven by complex molecular interactions between plants and their associated microbiomes. Although recent advances in nucleic acid research and multi-omics approaches have provided new insights into these interactions, the molecular mechanisms underpinning plant-microbiome interactions in these ecosystems remain insufficiently explored. This review synthesizes the latest progress in nucleic-acid and multi-omics approaches to better understand plant-microbiome interactions. It integrates nucleic acid-based technologies with multi-omics frameworks to explain plant-microbiome interactions across molecular, ecological, and management scales. By linking microbial community structure, functional genes, gene expression, metabolite profiles, ecosystem multifunctionality and sustainable grassland management, this review provides a broader framework for translating molecular insights into practical strategies for grassland resilience, productivity, and food security. Advances in amplicon sequencing, shotgun and long-read metagenomics, environmental DNA (eDNA) monitoring, plant and microbiome genome-wide association studies (GWAS) and transcriptomics have provided valuable insights into plant-microbiome interaction. This review highlights how these techniques enable functional and mechanistic understanding by linking microbial diversity with gene expression, nutrient cycling and plant performance. Additionally, long-read sequencing technologies provide genome-resolved analysis, improving the detection of structural and epigenetic variations, which are essential for understanding these interactions. These approaches reveal the role of beneficial microbes in enhancing grassland fertility, ultimately improving grassland productivity. Integrating these findings with metabolomics and phenomics offers a novel approach for predictive modeling in sustainable grassland management. The review concludes by emphasizing the need for standardized protocols, longitudinal field studies and experimental validation through synthetic communities and genome editing to harness plant-microbiome interactions for enhanced productivity and food security.},
}

@article {pmid42398703,
year = {2026},
author = {Becetti, I and Lamont, H and Dysart, L and Asanza, E and Tolley, C and Holman, K and Mitchell, C and Dekel, S and Hadjikhani, N and Lee, H and Ravichandran, CT and Carter, CS and Kingsbury, MA and Erdman, SE and Plessow, F and Lawson, EA},
title = {Rationale, design, and statistical analysis plan for a randomized, double-blind, placebo-controlled trial of Limosilactobacillus reuteri to support mother-infant bonding and maternal socioemotional functioning in postpartum women at increased risk for postpartum depression.},
journal = {Contemporary clinical trials},
volume = {},
number = {},
pages = {108399},
doi = {10.1016/j.cct.2026.108399},
pmid = {42398703},
issn = {1559-2030},
abstract = {BACKGROUND: Postpartum depression (PPD) is common and can impair early mother-infant bonding. Oxytocin (OXT) supports socioemotional adaptation, yet intranasal OXT yields supraphysiological exposure and mixed results. The probiotic Limosilactobacillus reuteri (L. reuteri) increases endogenous oxytocin levels in rodents, suggesting that it may enhance OXT signaling via gut-brain pathways in humans. We designed a proof-of-concept trial to test whether postpartum L. reuteri improves early mother-infant bonding and maternal mental health, impulse control, and emotion recognition.

METHODS: In this randomized, double-blind, placebo-controlled trial, mothers aged ≥18 years at elevated PPD risk (history of depression, prior PPD, and/or increased prenatal depressive symptoms) received 6 weeks of once-daily L. reuteri or placebo, stratified by delivery mode (vaginal/Cesarean section). The primary endpoint is mother-infant bonding quality at Week 6; secondary endpoints include maternal mental health, impulse control, and emotion recognition at Week 6. Salivary OXT at Week 2 serves as a mechanistic endpoint.

RESULTS: Forty-six participants (mean age ± SD: 34.3 ± 4.5 years) were enrolled and randomized; 38 (82.6%) completed the Week-6 visit. Baseline characteristics are reported.

CONCLUSION: This trial evaluates whether a lactation-compatible L. reuteri intervention targeting endogenous OXT improves early mother-infant bonding and maternal well-being. Findings will inform feasibility, safety, and effect size estimates, clarify OXT's mechanistic role in PPD pathophysiology, and guide development of microbiome-based therapeutics for perinatal mental health.

TRIAL REGISTRATION NUMBER: ClinicalTrials.gov: NCT04472065.},
}

@article {pmid42398706,
year = {2026},
author = {He, J and Xue, Y and Ji, C and Wang, J and Ji, R},
title = {Integrated Microbiome and Metabolomics Analysis Reveals Dynamic Changes in Raw Camel Milk During Refrigeration Storage.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28502},
pmid = {42398706},
issn = {1525-3198},
abstract = {This study investigated microbial and metabolite dynamics in raw camel milk stored at 4°C. Physicochemical and microbial monitoring identified d 3 as a critical transition point, with samples from d 0, 1, 3, and 6 subjected to 16S rRNA sequencing and metabolomic analysis. The dominant genera shifted from Lactococcus to Pseudomonas. Metabolomic analysis showed that non-volatile metabolites were primarily composed of esters, lipids, and organic acids, with 9 of these metabolites exhibiting a continuous increasing trend. Similarly, the levels of volatile metabolites, including ketones, esters, and alcohols also increased gradually throughout refrigeration. Correlation analysis linked Lactococcus to organic acid production, while Pseudomonas was associated with esters and lipids. These findings highlight microbial succession and metabolite shifts as key determinants of refrigerated camel milk quality, providing theoretical support for improved quality control and product development.},
}

@article {pmid42399225,
year = {2026},
author = {Gao, S and Yin, N and Wei, R and Li, X and Cheng, Q and Zhula, A and Zhou, W and Zhang, Y and Li, S and Zhou, W and Wang, X and Zhang, R and Wang, Q and Fan, H and Peng, S and Zhang, H and Li, K and Hu, Y and Gao, Y and Shi, W and Qi, H and Wang, J},
title = {Oral microbiome modulation mitigates hyperglycemia exacerbation in gestational diabetes mellitus.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74917-w},
pmid = {42399225},
issn = {2041-1723},
support = {T2341010//National Natural Science Foundation of China (National Science Foundation of China)/ ; U21A20346//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Dysglycaemia and periodontal inflammation frequently co-occur during pregnancy, but the microbial mechanisms linking these conditions and their potential for intervention remain incompletely understood. Here, we establish prospective pregnancy cohorts including more than 2500 volunteers and longitudinally profile oral microbiome dynamics in 534 pregnant women. We show that gestational diabetes mellitus (GDM) is associated with a progressive shift from Streptococcus-dominated oral microbiota to Prevotella/Porphyromonas-enriched dysbiosis. In mouse and cellular models, this dysbiotic oral microbiota induces periodontal inflammation, systemic IL-17 and IL-1β responses, suppression of glucagon-like peptide-1 and insulin, and exacerbation of hyperglycemia. Conversely, oral microbiota remodeling through transplantation of Streptococcus-dominated bacteria attenuates periodontal inflammation, restores glucagon-like peptide-1 and insulin levels, and improves glycaemic status in mice. Salivary metabolomics identifies docosahexaenoic acid (DHA) depletion in GDM, and in vitro assays show selective suppression of dysbiosis-associated oral pathogens by DHA. We therefore test topical gingival DHA in a double-blind randomized controlled trial of 40 pregnant women with GDM (ChiCTR2400080741), with probing depth and fasting blood glucose as primary endpoints and gingival index, attachment loss and plaque index as secondary endpoints. Daily gingival DHA application for six weeks improves probing depth and attenuates fasting glucose increase compared with placebo, with median fasting glucose changes from baseline of 0.10 versus 0.27 mmol/L. Together, these findings identify oral dysbiosis as a microbial driver of periodontal and glycaemic deterioration during pregnancy and support oral microbiome modulation as a potential adjunctive strategy for pregnancy care, although the clinical findings remain preliminary and require validation in larger trials with broader glycaemic endpoints.},
}

@article {pmid42399252,
year = {2026},
author = {Dai, D and Wang, P and Zhang, H and Qi, G and Wang, J},
title = {Temporal landscapes of the gut microbiota-host axis reveal mechanisms of age-related eggshell quality decline in laying hens.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01079-4},
pmid = {42399252},
issn = {2055-5008},
support = {32402797//National Natural Science Foundation of China/ ; 32322078//National Natural Science Foundation of China/ ; CARS-40//China Agriculture Research System/ ; ASTIP//Agricultural Science and Technology Innovation Program/ ; },
abstract = {Age-related shifts in the gut microbiota of laying hens significantly affect eggshell quality. However, the temporal interactions of the gut microbiota during the eggshell mineralization cycle remain unclear. Existing research often overlooks the rhythmic synchronization required for mineralization, as well as the specific cellular landscape of the aging intestine that impairs effective host-microbe crosstalk. We integrated 16S rRNA sequencing, metagenomics, untargeted metabolomics, and single-cell RNA sequencing to compare young and aged hens during the initial (7 h post-oviposition) and rapid growth (17 h post-oviposition) phases of eggshell mineralization. Aged hens exhibited significantly lower eggshell strength, thickness, and Ca/P concentrations (P < 0.05), which were associated with mitochondrial cristae disruption and necrocytosis in ileal tissues. 16S and metagenomic analyses revealed that young hens maintain stochastic microbial assembly, whereas aged hens shift toward deterministic processes driven by environmental stress. Rhythmic shifts in Lactobacillus and Ligilactobacillus were observed in young hens, supporting energy metabolism and mineral absorption pathways. In contrast, the aged hen microbiome remained focused on basal survival and oxidative stress responses. scRNA-seq identified nine cell populations, highlighting T cell exhaustion and HIF-1-driven metabolic reprogramming in epithelial cells of aged hens. Mediation analysis identified Ligilactobacillus salivarius as a keystone species that enhances eggshell breaking strength and thickness by increasing rhamnose and tyrosol levels and modulating host CALB1 and BLB2 expression. These findings indicate that aging disrupts proactive host-microbe synergy required for eggshell formation and identify L. salivarius-derived metabolites as promising candidates for restoring mineralization function in aged hens.},
}

@article {pmid42399304,
year = {2026},
author = {Sun, Y and Cheng, X and Zhou, J and Li, R and Wei, Y and Li, H and Qin, Y and Bao, J and Ren, X and Qu, S and Liu, W},
title = {Bio-stimulants improve tomato growth by regulating the rhizosphere microbiome involved in phosphorus and nitrogen cycling.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59808-w},
pmid = {42399304},
issn = {2045-2322},
support = {2024CXPT056//the Key R&D Plan of Shandong Province (Competitive Innovation Platform) Project: Green, Ecological and Efficient Modern Agricultural Biological Product Development/ ; },
abstract = {Bio-stimulants are promising environment friendly alternatives to support sustainable agricultural development, capable of boosting crop growth and yield while cutting down excessive dependence on chemical synthetic fertilizers. Nevertheless, the explicit regulatory mechanisms by which bio-stimulants exert the role of growth-promoting functions still remain largely unclear and require further systematic clarification. In this study, we explored the influences of bio-stimulants (rich in humic acid) on tomato growth performance and rhizosphere microbial community assembly via greenhouse trials, and comparatively analyzed the functional differences between foliar spraying and root irrigation application modes. The results demonstrated that bio-stimulants treatment markedly improved tomato aboveground biomass, plant nitrogen and phosphorus accumulation by 17.1%, 27.4% and 22.7%, respectively. Meanwhile, bio-stimulants application effectively raised soil available nitrogen and soil organic matter levels, and further facilitated phosphorus assimilation in tomato plants. Metagenomic sequencing confirmed that bio-stimulants substantially reshaped the overall structure and composition of tomato rhizosphere microbiome. Specifically, they dramatically enriched the relative abundance of core microbial taxa responsible for soil nitrogen fixation and phosphorus solubilization. Collectively, these results clearly elaborate the underlying action mechanism: bio-stimulants optimize rhizosphere micro-ecological environment, enrich functional nutrient-solubilizing microorganisms, improve soil nutrient availability, and ultimately promote nutrient absorption and vegetative growth of tomato plants. This study confirms that bio-stimulants can serve as efficient and reliable regulators to advance green and sustainable crop production.},
}

@article {pmid42399316,
year = {2026},
author = {Basting, CM and Schroeder, TA and Ferbas, KG and Shields-Cutler, RR and Tobin, NH and Chakrawarti, A and Velez, A and Swanson, E and Broedlow, CA and Langat, R and Cromarty, R and Schifanella, L and Bramante, CT and Aldrovandi, GM and Rimoin, A and Yang, OO and Fulcher, JA and Klatt, NR},
title = {Gut barrier integrity biomarkers are associated with increased inflammation and predict disease status in hospitalized COVID-19 patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59934-5},
pmid = {42399316},
issn = {2045-2322},
abstract = {The COVID-19 global pandemic persists as an endemic disease with case spikes and a significant continued burden on public health. One hallmark of severe COVID-19 is a dysregulated immune response that leads to systemic inflammation and contributes to disease severity but is not explained by viral replication alone. Severe COVID-19 has been shown to disrupt the gut microbiome and increase intestinal permeability which may contribute to immune dysregulation and systemic inflammation. Here, we investigated the differences in plasma biomarkers for intestinal permeability as well as circulating cytokines between healthy volunteers and patients hospitalized with COVID-19. Correlation analyses were used to characterize differences in biomarker relationships between groups, and a random forest model was used to assess their discriminative accuracy. Our results demonstrated that hospitalized COVID-19 patients have elevated concentrations of pro-inflammatory cytokines and microbial translocation markers, and the relationships between these biomarkers were significantly altered compared to healthy volunteers, especially those related to mucosa-associated homeostatic cytokines IL-17A and IL-23. Further, IL-6 and LBP were the top biomarkers for prediction accuracy in the random forest model. This work highlights the importance of managing microbial translocation in COVID-19 and its potential utility as a biomarker for disease severity.},
}

@article {pmid42399329,
year = {2026},
author = {Davis, ET and Afshin, EE and Stratigakis, N and Bard, JE and Sharpe, J and Zhang, Q and Tierney, BT and Mason, CE and Yergeau, D and Hallaj, S and Barron Arrambide, AO and Weinreb, RN and Zangwill, LM and Hyman, L and Danias, J},
title = {Microbial characterization of oral microbiome in patients with open-angle glaucoma.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59687-1},
pmid = {42399329},
issn = {2045-2322},
support = {R01EY11008/EY/NEI NIH HHS/United States ; R01EY14267/EY/NEI NIH HHS/United States ; P30EY022589/EY/NEI NIH HHS/United States ; },
abstract = {Glaucoma is a progressive optic nerve degenerative disease that often leads to blindness. Local inflammatory responses in the retina and optic nerve are implicated in the pathology of glaucoma. In addition, microbial populations in other parts of the body have been linked to glaucoma. To explore the relationship between oral health and glaucoma we queried the FinnGen database (Risteys 10.0) to assess whether poor oral health carries an increased risk of subsequently developing primary open angle glaucoma (POAG). In a separate study, we also collected mouthwash samples and administered a questionnaire relating to oral health status to a cohort of participants enrolled in Diagnostic Innovations in Glaucoma Study (DIGS) that included 107 participants with glaucoma and 19 healthy non-glaucomatous controls. 16S sequencing was performed to characterize the number of bacteria species and total bacteria count of the samples. A significant association between having dental conditions affecting the teeth, gingiva, or periodontium and developing glaucoma after 1 year, 1-5 years, 5-15 years and cumulatively was detected in the FinnGen data, a population of 429,209 with at least 153,661 having a dental condition and 10,687 having POAG. Among the cohort of the DIGS ancillary study, the total bacterial count of the glaucoma group was significantly higher compared to that of controls (Mean ± SD: 1.7 ± 1.4 and 0.9 ± 0.6, respectively, p < 0.03, two-sample t-test), while the species richness was significantly lower in glaucoma subjects compared to controls (p < 0.0005, Wilcoxon rank sum test). While the top taxa ordered by total abundance were similar between the two groups, mostly organisms associated with the commensal oral microbiome, there were some taxa linked with periodontal disease that were associated with glaucoma cases. However, the study was underpowered for the differences in top taxa between the glaucoma and non-glaucomatous control groups to achieve statistical significance (< 0.05) after adjusting for multiple comparison testing. A different bacterial abundance profile was detected between cases and controls by stepwise linear discriminant analysis. Inclusion of sleep apnea and the presence of cardiovascular disease as covariates in the analysis models did not significantly affect the results. Answers to the questionnaire about oral health and oral/dental history did not show a statistically significant difference between the two groups. The above findings suggest a potential link between oral health and glaucoma that may warrant further investigation.},
}

@article {pmid42399573,
year = {2026},
author = {Parthiban, R and Bhavya, E and Shireen, SM and Solomon, JAJ},
title = {Neonatal predictors of neurodevelopment: the interplay between APGAR score and neonatal microbiome.},
journal = {Irish journal of medical science},
volume = {},
number = {},
pages = {},
pmid = {42399573},
issn = {1863-4362},
abstract = {BACKGROUND: Neonatology has made significant advances in identifying factors that influence long-term neurodevelopmental outcomes in newborns. Among these, APGAR scores and the neonatal microbiome have emerged as important determinants of neurological development.

OBJECTIVE: To review the current evidence regarding the relationship between APGAR scores, neonatal microbiome composition, and neurodevelopmental outcomes and to explore their combined influence on neurodevelopmental pathways.

RESULTS: The APGAR score remains an important clinical tool for assessing neonatal health immediately after birth, with low scores often indicating potential central nervous system compromise. However, its ability to predict long-term neurodevelopmental outcomes remains variable. Emerging evidence highlights the critical role of the gut-brain axis and neonatal microbiome in shaping neurodevelopment. Alterations in microbial colonization may contribute to inflammatory processes and increase the risk of neurodevelopmental disorders, including cerebral palsy and autism spectrum disorder. Current findings suggest that APGAR scores and microbiome composition may act synergistically in influencing neurodevelopmental trajectories.

CONCLUSION: Understanding the interplay between APGAR scoring, neonatal microbiome composition, and central nervous system development may enhance early risk assessment and facilitate the development of personalized microbiome-targeted interventions. Further research is warranted to clarify these relationships and improve strategies for preventing long-term neurological complications.},
}

@article {pmid42399628,
year = {2026},
author = {Yuan, J and Zhang, XY and Yang, S and Luo, CL and Wang, ZH and Wang, QQ and Hao, YY and He, Y and Wang, S and Kong, FL and Zhao, M and Cao, ZJ and Li, SL and Wang, W},
title = {Peripartum hypophosphatemia is associated with a hindgut-centered microbiota-metabolite-host axis in transition dairy cows.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01078-5},
pmid = {42399628},
issn = {2055-5008},
support = {32202713//National Natural Science Foundation of China/ ; },
abstract = {The transition period in dairy cows is accompanied by profound shifts in mineral homeostasis and gut microbial ecology. While endocrine regulation of hypocalcemia has been extensively characterized, adaptive responses to hypophosphatemia-and the potential involvement of the gut microbiota-have received far less attention. Twenty-four Holstein dairy cows were randomly assigned to control or low-phosphorus groups. Hypophosphatemia was induced by dietary supplementation with 300 g/d synthetic zeolite from 21 days prepartum to 3 days postpartum. Blood and feces samples were collected at -21, -7, 0, 1, and 3 d relative to calving for longitudinal analysis of physiology, hindgut microbiome and plasma metabolomics to investigate host-microbiome adaptation to peripartum hypophosphatemia in dairy cows. Cows with hypophosphatemia exhibited pronounced compositional remodeling of their hindgut microbiota and extensive, persistent alterations in their plasma metabolome, with glycerophospholipid metabolism being a consistently affected pathway. Integrated correlation and mediation analyses revealed close associations between hindgut microbial variation, host metabolic reprogramming, and circulating phosphorus dynamics. In addition, a plasma feature putatively annotated as α-methyl-m-tyrosine (AMT) was identified as a candidate statistical mediator associated with the observed relationships between Lachnospiraceae_NK3A20_group abundance with systematic phosphorus concentrations. Collectively, these findings indicate that peripartum hypophosphatemia in dairy cows is accompanied by coordinated host metabolic and hindgut microbial remodeling, supporting a hindgut-centered host-metabolite-microbiome framework for understanding phosphorus adaptation during early lactation.},
}

@article {pmid42399737,
year = {2026},
author = {Steele, S and Mazengenya, P and Chambuso, R},
title = {Pathology-derived clinical micro-architectural diagnostics of tumour-microbiome interactions in colorectal cancer.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08426-1},
pmid = {42399737},
issn = {1479-5876},
abstract = {BACKGROUND: Classical tumour pathology reports contain a largely untapped layer of information that may indicate tumour-microbial interactions. However, routine colorectal cancer pathology staging does not take into account microbiome-associated tumour micro-architecture signatures, thus limiting insights into intratumoral microbial ecology, prognostic stratification and treatment-relevant microbial information. In this study, we analysed scanned USA pathology reports to quantify likely intratumoral microbiome-associated micro-architectural signatures.

METHODS: We studied 1,978 TCGA colorectal cancer pathology reports from 1,249 colon adenocarcinomas, 559 rectal adenocarcinomas and 170 reports without a definitive anatomic site using rule-based natural language processing to extract microbiome-linked micro-architectural features. Barrier-disruption and invasion-access signatures were identified from the reports as microbiome-associated pathology micro-architecture signatures that occur with microbial-related necrosis, hypoxia, toxins, colonisation, persistence, metabolic activity and/or tumour interaction. We developed a z-scored composite index called Report-based Microbial Ecology Likelihood Score (RMELS) and used Kaplan-Meier log-rank analyses, multivariable Cox regression, Kruskal-Wallis tests and receiver operation characteristic curves with bootstrap confidence intervals. Proportional hazards assumptions were tested for statistical significance at two-sided p < 0.05.

RESULTS: Microbiome-associated pathology micro-architectural signatures were highly prevalent in the pathology reports. Barrier-disruption features, including ulceration (41.1%) and mucin alteration (16.7%), were common and increased with tumour stage (Kruskal-Wallis p < 0.0001). Prominent invasion-access features included infiltrative growth (59.4%, 95% CI 57.2-61.5), lymphovascular invasion (18.6%, 95% CI 17.0-20.4) and perineural invasion (22.9%, 95% CI 21.1-24.8). All showed heterogeneous, non-monotonic distributions across pathologic stages, indicating activation of microbial injury and invasion programmes. Integration of these features into our signature score, ordered tumours along a continuous microbiome-permissiveness gradient independent of pathological stage. With limited information, our signature score discriminated early (T1) from advanced (T4) disease more effectively than barrier or invasion features alone (AUC = 0.66, 95% CI 0.58-0.74, p < 0.0001). Right-sided colonic tumours exhibited significantly higher scores than left-sided colonic and rectal tumours (FDR q < 0.001), aligning with known microbial biogeography. In multivariable Cox models adjusted for pathological stage, our signature score RMELS showed modest but directionally consistent association with overall and progression-free survival, capturing microbiology-relevant risk not resolved by pathological staging.

CONCLUSIONS: Routine classical colorectal cancer pathology reports contain intratumoral microbiome-associated pathology micro-architectural signatures. Quantifying these exploratory tumour-microbial signatures using digital pathology will enable scalable, microbiology-informed risk stratification and prognostic modelling to complement the current pathological staging.},
}

@article {pmid42399784,
year = {2026},
author = {Putpim, A and Noonin, C and Chawanpaiboon, P and Pawano, O and Phuangkham, S and Peerapen, P and Thongboonkerd, V},
title = {Lactobacillus acidophilus abolishes oxalate-mediated renal epithelial barrier disruption and calcium oxalate monohydrate crystal adhesion to renal epithelial cells.},
journal = {Cellular & molecular biology letters},
volume = {},
number = {},
pages = {},
doi = {10.1186/s11658-026-00985-x},
pmid = {42399784},
issn = {1689-1392},
abstract = {BACKGROUND: It is generally known that kidney stone disease (KSD) is associated with alterations in urinary microbiome, but the roles of the urinary microbiome in KSD pathogenesis remain unclear.

METHODS: This study addressed the impact of Lactobacillus acidophilus (a commensal bacterium found in normal urine) on renal epithelial integrity, calcium oxalate monohydrate (COM) crystal-cell adhesion, expression of membrane receptors of COM crystals, and oxalate degradation under oxalate-induced stress (a known inducer of KSD). Inner medullary collecting duct cells (mIMCD-3) were cultured for 24 h under control or oxalate-induced (by 0.6 mM sodium oxalate; NaOx) conditions without or with L. acidophilus (at 1 × 10[3] colony-forming unit (CFU)/ml) co-incubation.

RESULTS: NaOx reduced transepithelial resistance (TER) of the mIMCD-3 monolayer and downregulated ZO-1, a tight junction (TJ) protein. Additionally, NaOx enhanced the COM crystal-binding capability of mIMCD-3 cells by upregulating a COM crystal receptor, annexin A2, on cell membranes. Such harmful effects of NaOx were abolished when mIMCD-3 cells were co-cultured with L. acidophilus. Moreover, culturing L. acidophilus in artificial urine (AU) supplemented with NaOx for 24 h revealed that the oxalate level in AU decreased, suggesting the oxalate-degrading activity of the bacterium in an AU environment.

CONCLUSIONS: L. acidophilus prevented oxalate-mediated renal epithelial barrier disruption and COM crystal adhesion to renal epithelial cells by preserving ZO-1 and annexin A2 expression at their basal levels, at least in part, via its oxalate-degrading property.

CLINICAL TRIAL NUMBER: Not applicable (This is not a clinical trial).},
}

@article {pmid42399931,
year = {2026},
author = {Ismail, H and Al-Daoud, F and Mushtaq, G},
title = {Association between dental plaque index and COVID-19 severity: a cross-sectional study in a conflict-affected humanitarian setting.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-09169-7},
pmid = {42399931},
issn = {1472-6831},
abstract = {BACKGROUND: COVID-19 shows marked variation in clinical severity. Identifying demographic and clinical factors associated with severity is particularly important in conflict-affected, resource-limited settings. This study assessed the relationship between COVID-19 symptom severity and selected variables, including sex, age, marital status, and dental plaque index, among patients in northwest Syria.

METHODS: This cross-sectional analytical study was conducted from 12 October to 23 November 2021 in three COVID-19 isolation centers in northwest Syria. Sixty adult patients with confirmed SARS-CoV-2 infection were enrolled through consecutive screening with purposive quota balancing by clinical severity category, resulting in 20 patients in each of the mild, moderate, and severe groups. Demographic data were recorded, and oral examination was performed by one trained examiner to assess plaque index using the modified Greene-Vermillion index. Associations were analyzed using Spearman's rank correlation, Pearson correlation, Kruskal-Wallis H test, and chi-squared test, with statistical significance set at p ≤ 0.05.

RESULTS: The sample included 38 females (63.3%) and 22 males (36.7%), aged 18-82 years. COVID-19 severity was significantly associated with sex, with greater severity among males (Spearman's ρ = - 0.428, p = 0.001). Age showed a weak but significant positive correlation with severity (Pearson's r = 0.287, p = 0.026). Marital status was also associated with severity (Spearman's ρ = 0.329, p = 0.010), although this relationship appeared to be strongly confounded by age. Dental plaque index showed a moderate positive association with COVID-19 severity (Spearman's ρ = 0.533, 95% CI: 0.307-0.702; p < 0.001), indicating that higher plaque accumulation was associated with more severe symptoms.

CONCLUSION: In this conflict-affected humanitarian setting, male sex, older age, and higher dental plaque index were significantly associated with increased COVID-19 symptom severity. These findings are preliminary and should be interpreted cautiously because of the cross-sectional design, small sample size, and limited data on potential confounders. Nevertheless, the study contributes evidence from an underrepresented crisis-affected population and suggests that oral health assessment may have value as part of broader COVID-19 risk evaluation in resource-constrained settings.},
}

@article {pmid42399940,
year = {2026},
author = {He, N and Tian, J and Wu, J and Tan, L and Wang, Y and Dai, H and Chen, Y and Lu, J and Zhang, G and Jiang, S},
title = {Optimal dietary nano-VD3 enhances growth performance and bone development in broilers through remodeling the gut microbiome and metabolites.},
journal = {BMC veterinary research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12917-026-05558-w},
pmid = {42399940},
issn = {1746-6148},
support = {xbmuyjrc202513//Talent Introduction Project of Northwest Minzu University, China/ ; 2025-QN-058//Youth Science and Technology Talent Innovation Project of Lanzhou Science and Technology Bureau, China/ ; 2026B-040//Innovation Fund for University Faculty of Gansu Provincial Department of Education, China/ ; },
abstract = {BACKGROUND: Skeletal maldevelopment is a significant challenge in broiler production, causing substantial economic losses. Vitamin D3 (VD3) plays a critical role in poultry skeletal health, but its optimal dietary inclusion level for medium-growth broilers remains to be determined due to bioavailability differences among forms. This study investigated the effects of dietary VD3 levels (conventional vs. nano-formulated) on growth performance, bone development, and gut microbiota composition and metabolite profile in broilers. A total of 420 one-day-old male Luhua broilers were randomly assigned to four groups in an 84-day experiment: a control group fed a basal diet, and three treatment groups supplemented with 3,750 IU/kg conventional VD3 (CVD), 2,500 IU/kg low-dose nano-VD3 (LNVD), or 3,750 IU/kg high-dose nano-VD3 (HNVD).

RESULTS: Both CVD and LNVD significantly enhanced average daily gain (ADG) and bone development by improving bone mineral content (BMC) and bone mineral density (BMD), mechanical properties (yield strength, stiffness, Elastic modulus), increasing calcium and ash content, and upregulating osteogenic gene expression (ALP, OC, OPG, BMP1) in the femur and tibia. Compared to CVD, LNVD led to significantly higher ADG from days 1-84 and greater bone indices at days 28, 56 and 84, including fresh bone weight (FBW), fat-free dry weight (FFDW), yield strength, elastic modulus, and calcium and ash content in the femur and tibia. In contrast, HNVD significantly decreased ADG and bone indices. Furthermore, cecal microbiome and metabolomics analysis showed that LNVD increased the relative abundance of beneficial bacteria (e.g., Ligilactobacillus, Muribaculaceae, NK4A214_group) and key metabolites (e.g., butyric acid, kynurenic acid, glutathione), while reducing harmful taxa (e.g., Desulfovibrio, Campylobacter_jejuni) and detrimental metabolites (e.g., leukotriene E3, 4-hydroxy-2-nonenal-Cys-Gly conjugate). These shifts significantly correlated with improved growth and bone traits.

CONCLUSIONS: In summary, 2,500 IU/kg nano-VD₃ is recommended as the optimal supplementation level for Luhua broilers under the conditions of this study, offering a strategy to enhance VD₃ nutrition and skeletal health.},
}

@article {pmid42399985,
year = {2026},
author = {Ma, K and Zhang, Q and Jin, Z and Hao, R and Sun, X and Zhou, L and Li, M},
title = {Gut microbiota-derived extracellular vesicles: bridging microbial-host crosstalk in metabolic disorders.},
journal = {Cell communication and signaling : CCS},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12964-026-03034-4},
pmid = {42399985},
issn = {1478-811X},
support = {ZYZB-2022-798//National Administration of Traditional Chinese Medicine/ ; },
abstract = {Gut microbiota-derived extracellular vesicles have emerged as crucial mediators in microbe-host communication, not only facilitating intracellular communication, quorum sensing, and horizontal gene transfer among bacteria but also playing a central role in cross-kingdom dialogue. In recent years, bacterial extracellular vesicles (BEVs) have attracted widespread attention due to their ability to carry a diverse array of bioactive molecules-such as proteins, lipids, and nucleic acids-and deliver them to host cells, thereby precisely regulating host metabolic and immune homeostasis. This review systematically elaborates the entire biological process of BEVs, from their biogenesis to functional interactions with host cells, with a specific emphasis on revealing their roles in the pathogenesis of various metabolic diseases-including obesity, type 2 diabetes (T2DM), metabolic dysfunction-associated steatotic liver disease (MASLD), atherosclerosis, and hypertension-at both molecular and cellular levels. Furthermore, leveraging their inherent stability, biocompatibility, and targeting capabilities, we discuss the translational potential and challenges of BEVs in the diagnosis and treatment of metabolic disorders. Beyond summarizing the latest research advances on BEVs in metabolic disorders, this review provides a critical analysis of current mechanistic insights and clinical translation pathways, aiming to establish a theoretical framework for developing novel microbiome-based metabolic interventions. Deciphering the BEV-mediated microbiota-host interaction network holds promise for pioneering new strategies for the precision prevention and treatment of metabolic disease.},
}

@article {pmid42305046,
year = {2026},
author = {Lee, D and Jeong, H and Gwon, H and Lee, K and Kim, JY and Shim, JJ and Lee, JH},
title = {Lactiplantibacillus plantarum HY7715 Attenuates Oxidative Stress-Induced Neurobiological Aging-Related Changes by Modulating Senescence-Associated Markers and Gut Microbiota.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2604063},
pmid = {42305046},
issn = {1738-8872},
mesh = {Animals ; *Oxidative Stress/drug effects ; *Aging/drug effects ; *Lactiplantibacillus plantarum/physiology ; Mice ; Reactive Oxygen Species/metabolism ; *Gastrointestinal Microbiome/drug effects ; Hippocampus/metabolism/cytology ; Cellular Senescence ; Glutathione Peroxidase GPX1 ; Hydrogen Peroxide ; Cell Line ; Male ; 8-Hydroxy-2'-Deoxyguanosine ; Mice, Inbred C57BL ; Glutathione Peroxidase/metabolism/genetics ; Tumor Suppressor Protein p53/metabolism ; Superoxide Dismutase-1/metabolism/genetics ; Brain ; Biomarkers ; *Probiotics/pharmacology ; beta-Galactosidase/metabolism ; Deoxyguanosine/analogs & derivatives/metabolism ; Antioxidants/metabolism ; },
abstract = {External stressors can accelerate biological aging-related processes by promoting oxidative stress and senescence-associated molecular alterations in the brain. This study investigated the potential of Lactiplantibacillus plantarum HY7715 to attenuate oxidative stress-induced neurobiological aging-related changes using H2O2-induced HT22 hippocampal cells and a restraint-stressed mouse model. In HT22 cells, HY7715 reduced reactive oxygen species accumulation, decreased 8-hydroxy-2'-deoxyguanosine (8-OHdG) levels, and lowered the proportion of senescence-associated β-galactosidase-positive cells. These effects were accompanied by suppression of p53/p21 signaling and restoration of Tert expression. In restraint-stressed mice, HY7715 reduced the number of p21-positive cells in the hippocampus, significantly lowered p53 expression, restored Tert expression, reduced Il-6 expression, and improved antioxidant-related gene expression, including Gpx1 and Sod1. Microbiome analysis showed that HY7715 reshaped the stress-altered gut microbiota toward a Lactobacillus-enriched profile and reduced the abundance of Lachnospiraceae, Acetatifactor, Desulfovibrio, and Oscillibacter. Collectively, these findings suggest that HY7715 may attenuate oxidative stress-induced neurobiological aging-related changes by modulating senescence-associated molecular markers and stress-altered gut microbiota, highlighting its potential as a candidate for supporting healthy brain aging.},
}

Animals
*Oxidative Stress/drug effects
*Aging/drug effects
*Lactiplantibacillus plantarum/physiology
Mice
Reactive Oxygen Species/metabolism
*Gastrointestinal Microbiome/drug effects
Hippocampus/metabolism/cytology
Cellular Senescence
Glutathione Peroxidase GPX1
Hydrogen Peroxide
Cell Line
Male
8-Hydroxy-2'-Deoxyguanosine
Mice, Inbred C57BL
Glutathione Peroxidase/metabolism/genetics
Tumor Suppressor Protein p53/metabolism
Superoxide Dismutase-1/metabolism/genetics
Brain
Biomarkers
*Probiotics/pharmacology
beta-Galactosidase/metabolism
Deoxyguanosine/analogs & derivatives/metabolism
Antioxidants/metabolism

@article {pmid42305125,
year = {2026},
author = {Jakubczyk, D and Pyclik, M and Kozakiewicz, D and Macała, J and Zabłocka, A and Górska, S},
title = {Comprehensive Protocol for Handling Human Small Airway Epithelial Cells (HSAECs) to Establish Air-Liquid Interface (ALI) Cultures With TEER-Based Barrier Integrity Assessment.},
journal = {Bio-protocol},
volume = {16},
number = {11},
pages = {e5699},
pmid = {42305125},
issn = {2331-8325},
abstract = {Understanding epithelial barrier function is essential for studying both its normal physiology and its role in disease, yet choosing an appropriate experimental model remains challenging. Animal models are commonly used but often suffer from interspecies differences that limit translational relevance. Human-derived cell lines offer a more suitable alternative, although establishing them often requires immortalisation strategies that involve overexpression of oncogenes, which can introduce phenotypic and functional changes. In contrast, primary cells, such as human small airway epithelial cells (HSAECs), provide a more physiologically accurate model. A critical aspect of replicating the native respiratory environment is maintaining continuous air exposure, which can be achieved through air-liquid interface (ALI) culture. This protocol provides a unified, step-by-step workflow for cultivating primary HSAECs under ALI conditions, covering the entire process from initial recovery after cryopreservation to the formation of a barrier-like layer. The protocol incorporates non-invasive methods such as transepithelial electrical resistance (TEER) measurements to monitor its integrity. While individual elements of this workflow have been described separately in different studies, a consolidated version encompassing the full workflow has not been widely available. This resource is intended for researchers with limited experience in airway epithelial culture and offers practical, clear guidance through each step of the process. Key features • Using primary HSAECs enables modelling the human respiratory barrier while avoiding limitations of immortalised or animal-derived cell lines. • ALI culture technique allows continuous air exposure, closely resembling in vivo conditions for airway epithelial cells. • TEER measurement offers a non-invasive, rapid method to assess epithelial barrier integrity without damaging the cultured cell layer. • Protocol supports barrier function studies, including but not limited to respiratory infections, allergic responses, toxicology screening, microbiome interactions, and drug delivery investigation.},
}

@article {pmid42305229,
year = {2026},
author = {Park, JW and Choi, SA and Kim, JW and Ji, JH and Kim, KM and Park, JK and Han, GH and Im, S},
title = {Anti-inflammatory effect of Canis familiaris (dog) gingival derived microorganisms on Porphyromonas gingivalis derived lipopolysaccharide treated RAW 264.7 macrophage.},
journal = {Journal of animal science and technology},
volume = {68},
number = {3},
pages = {875-888},
pmid = {42305229},
issn = {2055-0391},
abstract = {Porphyromonas gingivalis is recognized for its significant association with periodontal diseases, encompassing conditions like gingivitis and periodontitis. P. gingivalis infiltrates periodontal tissues, liberating diverse outer membrane vesicles, notably lipopolysaccharide (LPS). These vesicles serve as triggers for innate immune responses, fostering inflammation. For this reason, LPS is commonly studied in research as a key tool for exploring microbiome infection and colonization dynamics. In the present study, we discovered a Canis familiaris Canine derived novel microbiome associated with the reduction of PG-LPS. We identified C. familiaris Canine derived microbiome, and we cultured candidate effective microbiome. Subsequently, in order to investigate the PG-LPS reducing effects of the microbiome, we conducted RAW 264.7 macrophage culture. We validated the expression patterns of inflammation marker genes on microbiome treatment in PG-LPS induced RAW 264.7. As a result, concentration of Nitric oxide, which were used for inflammation markers were decreased by candidate microbiome treatment. In addition, inflammation marker genes (interleukin 1 beta [IL1B], interleukin 6 [IL6], and tumor necrosis factor alpha [TNF-a]) were down regulated in microbiome and LPS co-treatment while it was up-regulated in RAW 264.7 cell induced with LPS as control group, which suggested that the candidate microbiome may have reduced the inflammation, but the mechanism in which this would have been done is yet known. Further studies should focus on elucidating the mechanism associated with candidate microbiomes and Inflammation reduction.},
}

@article {pmid42305230,
year = {2026},
author = {Ku, JY and Lee, MJ and Jung, Y and Park, KM and Baek, J and Kim, Y and Yoon, JS and Choi, KS and Choi, HJ and Park, J},
title = {Differences in gut microbiome of Hanwoo (Korean indigenous cattle) calves as driven by bovine rotavirus and bovine coronavirus infection.},
journal = {Journal of animal science and technology},
volume = {68},
number = {3},
pages = {904-916},
pmid = {42305230},
issn = {2055-0391},
abstract = {The gut microbiome of cattle suppresses pathogens and aids host immunity. However, the gut microbiome of newborn calves is still developing; therefore, diarrhea caused by pathogen infection is common. Rapid changes in the gut microbiome due to diarrhea have a significant impact on the health and growth of calves. Until recently, there have been few studies on the changes in the gut microbiome following infection with major digestive pathogens that cause diarrhea in Hanwoo (Korean indigenous cattle) calves. Therefore, this study was conducted to identify viral digestive pathogens that cause severe diarrhea in Hanwoo calves. Seven normal calves without diarrhea and eight calves with diarrhea were selected, and their feces were collected to analyze pathogens and the gut microbiome. Bovine rotavirus (BRV) and bovine coronavirus (BCoV) were detected in the feces of the calves with diarrhea. There was no significant difference in the alpha diversity of the microbiome between normal calves and calves infected with viruses; however, a significant decrease in NPShannon and Shannon indices and a significant increase in Simpson index were observed in calves infected with BRV compared to calves infected with BCoV. In addition, beta diversity of the microbiome differed distinctly between normal calves and calves infected with BRV or BCoV. At the class level, BRV infection increased Gammaproteobacteria and Actinobacteria, whereas BCoV infection increased Clostridia and decreased Bacilli. In addition, the abundance of Lactobacillus was significantly reduced upon infection with BRV and BCoV. In this study, we confirmed the differences in the gut microbiome based on viral pathogens causing diarrhea in Hanwoo calves. The results of pathogen-targeting research are expected to be helpful in preventing common pathogens in calves.},
}

@article {pmid42305251,
year = {2026},
author = {Zicos, MH and Barnes, I and Frantz, L and Brace, S},
title = {Megaherbivore coprolite DNA: yields and comparison of three ancient DNA extraction protocols on coprolites of giant ground sloth Mylodon darwinii.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21009},
pmid = {42305251},
issn = {2167-8359},
mesh = {Animals ; *DNA, Ancient/isolation & purification/analysis ; *Sloths/genetics ; },
abstract = {Coprolites offer rich potential for palaeodietary studies as snapshots of past dietary behaviour and environment. They require adapted laboratory methods to retrieve the DNA of the depositor, its microbiome, diet and environmental taxa. Here we compare the performance of three common ancient DNA (aDNA) extraction methods to recover metagenomes from coprolites of Darwin's ground sloth Mylodon darwinii from Cueva del Milodón (Chile). The Qiagen PowerSoil Kit outperformed the other two methods in terms of DNA recovery and library complexity, but the communities inferred from the DNA extracted by the three methods were similar. We were able to recover signatures of local Patagonian flora, as well as sloth mitochondrial genomes, confirming the taxonomic identity of the coprolite depositors.},
}

Animals
*DNA, Ancient/isolation & purification/analysis
*Sloths/genetics

@article {pmid42305538,
year = {2026},
author = {He, Y and Wang, X and Hu, Q and Huang, L and Zhang, S and Zhang, S and Zhong, Z},
title = {Human umbilical cord mesenchymal stem cell-derived exosomes are associated with changes in renal injury markers, gut microbiota composition, and inflammatory signaling in IgA nephropathy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1854005},
pmid = {42305538},
issn = {1664-3224},
mesh = {*Glomerulonephritis, IGA/metabolism/immunology/pathology/microbiology ; *Exosomes/metabolism/immunology/transplantation ; Humans ; Animals ; Mice ; *Mesenchymal Stem Cells/metabolism ; *Gastrointestinal Microbiome/immunology ; Signal Transduction ; *Umbilical Cord/cytology ; Inflammasomes/metabolism ; Disease Models, Animal ; Podocytes/metabolism/immunology ; Biomarkers ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Male ; },
abstract = {BACKGROUND: IgA nephropathy (IgAN) is the most common primary glomerulonephritis worldwide and a leading cause of end-stage kidney disease, yet disease-specific therapeutic options remain limited. Emerging evidence implicates gut microbiota dysbiosis and innate immune activation, particularly NLRP3 (NOD-, LRR- and pyrin domain-containing protein 3) inflammasome-related signaling, in IgAN pathogenesis. However, whether human umbilical cord mesenchymal stem cell-derived exosomes (hUCMSC-Exos) are associated with changes in renal injury and gut-immune-related parameters in IgAN remains unclear.

METHODS: hUCMSC-Exos were isolated and administered to an IgAN-like mouse model. Renal function, histopathological changes, and systemic inflammatory markers were assessed. Gut microbiota composition was analyzed using 16S rRNA sequencing, and exploratory microbial co-occurrence networks were constructed. In vitro, podocytes stimulated with galactose-deficient IgA1 (Gd-IgA1) were used to evaluate inflammasome-related markers following exosome exposure. Transcriptomic data from human IgAN glomeruli (GSE93798) were analyzed to explore inflammatory and immune-related gene signatures.

RESULTS: hUCMSC-Exos were associated with changes in renal injury markers in IgAN-like mice, along with alterations in gut microbial composition. Microbiome analysis showed a shift toward a microbial profile closer to controls, with enrichment of bacterial taxa previously reported in association with gut metabolic homeostasis in other cohorts, including Anaerostipes, Dorea, and Ruminococcus. These taxa showed correlations with renal dysfunction indicators and inflammatory markers and were identified as hub taxa in an exploratory co-occurrence network. Transcriptomic analysis of human IgAN glomeruli revealed altered expression of NLRP3 inflammasome-related genes and aryl hydrocarbon receptor (AhR)-related signaling components, suggesting context-dependent inflammatory activity requiring further validation. In vitro, hUCMSC-Exos were associated with reduced levels of NLRP3, IL-1β, and IL-18 in Gd-IgA1-stimulated podocytes.

CONCLUSIONS: hUCMSC-Exos were associated with changes in renal injury markers in an IgAN-like model, accompanied by alterations in gut microbiota composition and inflammasome-related inflammatory markers. These findings are consistent with a potential association between gut microbiota, innate immune-related signaling, and renal injury in IgAN. hUCMSC-Exos may represent a cell-free candidate for further investigation in IgAN. However, these observations are descriptive and associative in nature, and causal mechanisms cannot be inferred from the present study.},
}

*Glomerulonephritis, IGA/metabolism/immunology/pathology/microbiology
*Exosomes/metabolism/immunology/transplantation
Humans
Animals
Mice
*Mesenchymal Stem Cells/metabolism
*Gastrointestinal Microbiome/immunology
Signal Transduction
*Umbilical Cord/cytology
Inflammasomes/metabolism
Disease Models, Animal
Podocytes/metabolism/immunology
Biomarkers
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
Male

@article {pmid42305556,
year = {2026},
author = {Wu, Y and Li, H and Peng, Y and Fan, W},
title = {Sustained complete response to TMEp-CI-M platform in refractory small-cell lung cancer with brainstem metastasis: a case report with over 20 months of disease-free survival.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1807865},
pmid = {42305556},
issn = {1664-3224},
mesh = {Humans ; Male ; Middle Aged ; *Lung Neoplasms/pathology/therapy ; *Small Cell Lung Carcinoma/therapy/pathology/immunology ; *Tumor Microenvironment/immunology ; *Brain Stem Neoplasms/secondary/therapy/immunology ; *Immune Checkpoint Inhibitors/therapeutic use ; Disease-Free Survival ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Pathologic Complete Response ; Etoposide/administration & dosage ; },
abstract = {BACKGROUND: Brainstem metastasis from small-cell lung cancer (SCLC) is exceedingly rare and is associated with a dismal prognosis. This study presents a case of brainstem metastasis from SCLC treated with the TMEp-CI-M platform, achieving no evidence of disease (NED) for more than 20 months. The TMEp-CI-M platform is designed to overcome resistance in immunologically "cold" tumors through sequential tumor microenvironment priming (TMEp), checkpoint inhibition (CI), and microbiome modulation. We have previously reported its efficacy in pancreatic neuroendocrine carcinoma, hepatocellular carcinoma, pancreatic ductal adenocarcinoma, non-small cell lung cancer (NSCLC), and colorectal cancer.

CASE INTRODUCTION: A 60-year-old male with programmed death ligand 1 (PD-L1)-negative extensive-stage small-cell lung cancer (ES-SCLC) and brainstem metastasis received the TMEp-CI-M regimen. The TMEp phase integrated stereotactic body radiotherapy (SBRT), low-dose etoposide, and anlotinib, followed by CI with the programmed death 1 (PD-1)/cytotoxic T lymphocyte antigen 4 (CTLA-4) bispecific antibody cadonilimab and concurrent probiotic supplementation. The patient's pro-gastrin-releasing peptide (ProGRP) level normalized after the first cycle (from 1803 pg/mL to 23.71 pg/mL) during a total of 6 treatment cycles. At the time of this report (20 months after treatment initiation), the patient remains NED, with only Grade 1 hypothyroidism as an adverse event.

CONCLUSION: The TMEp-CI-M platform may enhance the efficacy of immunotherapy in ES-SCLC, enabling durable responses even in patients with brainstem metastases. Although this platform has demonstrated promise across multiple tumor types, further prospective and mechanistic studies are warranted to confirm its clinical utility.},
}

Humans
Male
Middle Aged
*Lung Neoplasms/pathology/therapy
*Small Cell Lung Carcinoma/therapy/pathology/immunology
*Tumor Microenvironment/immunology
*Brain Stem Neoplasms/secondary/therapy/immunology
*Immune Checkpoint Inhibitors/therapeutic use
Disease-Free Survival
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use
Pathologic Complete Response
Etoposide/administration & dosage

@article {pmid42305661,
year = {2026},
author = {Yang, Y and Zhang, H and Shuang, Q and Xia, YN},
title = {Bacterial microbiome and flavor metabolome shifts in traditional Hinggan league sauerkraut fermentation.},
journal = {Food chemistry. Molecular sciences},
volume = {13},
number = {},
pages = {100430},
pmid = {42305661},
issn = {2666-5662},
abstract = {Microbial diversity is crucial for the flavor and quality of fermented vegetables. The unique geography and fermentation techniques of Hinggan League, Inner Mongolia, endow local sauerkraut with distinctive characteristics; however, the association between its microbiota and metabolites, as well as the underlying flavor formation mechanism, remains unclear, representing a gap in current research. Therefore, this study systematically investigated the interactions between microbial communities and metabolites during traditional sauerkraut fermentation in Hinggan League, Inner Mongolia, before and after fermentation. Using MiSeq sequencing technology, the core microbiota was identified, mainly including Lactobacillus, Halomonas, and Psychrobacter, with specific strains Azospirillum and Aureimonas observed exclusively in pre-fermentation (VC) samples. Metabolomics analysis detected a total of 335 abundant metabolites, among which 146 upregulated metabolites such as organic acids, amino acids, and fatty acid derivatives significantly accumulated during the late fermentation stage. Notably, 3-phenyllactic acid and 5-aminovaleric acid were the most representative characteristic metabolites. Metabolites pathway enrichment analysis revealed that arginine and proline metabolism, alanine/aspartate/glutamate metabolism, and cyanoamino acid metabolism were the major pathways significantly activated during fermentation, closely associated with energy metabolism, acid-base homeostasis regulation, and flavor generation. Correlation analysis showed a strong association between Lactococcus and 31 flavor compounds, including palmitic acid, L-phenylalanine, and heptadecanoic acid. Functional annotation indicated that Lactococcus-driven protein degradation, amino acid conversion, and lipolytic activities generate key precursors for sour and umami flavor development. Collectively, this study elucidates the microbial community succession characteristics, inter-microbial interaction patterns, and the associated metabolic regulation mechanisms of flavor formation during sauerkraut fermentation, providing a theoretical basis for the targeted modulation of characteristic flavor compound synthesis and the optimization of traditional fermentation processes.},
}

@article {pmid42305675,
year = {2026},
author = {Wu, Y and Lu, Z and Ma, S and Zhang, H and Zhang, W and Ma, X and Yuan, K and Wang, J},
title = {The variation profile of associated microbiota in juvenile whelk Hemifusus tuba (Gmelin, 1791) in dietary transition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1843060},
pmid = {42305675},
issn = {1664-302X},
abstract = {Hemifusus tuba (Gmelin, 1791) is a commercial marine gastropod that undergoes an ontogenetic dietary transition from egg-capsule nutrition (lecithotrophy) to herbivory and finally to lifelong carnivory. How associated microbiota respond to this feeding habit transition remained largely unexplored. Here, we characterized taxonomic composition, diversity and functional prediction of associated microbiota in H. tuba across three dietary stages (CK, egg-capsule nutrition or lecithotrophic; He, herbivory; Ca, carnivory) using 16S rRNA amplicon sequencing. A total of 457,412 high-quality reads from 14 libraries were clustered into 12,091 OTUs, identifying 811 genera within 38 phyla. And five dominant phyla (Proteobacteria, Bacteroidota, Firmicutes, Actinobacteriota, and Planctomycetota) accounted for 99% of total abundance and formed the core microbiota. Alpha diversity increased from CK to He and peaked in Ca, whereas beta diversity analyses consistently separated Ca from CK and He, indicating microbiota restructuring following the transition to carnivory. During the feeding habit transition, Proteobacteria and Planctomycetota increased, while Bacteroidota, Firmicutes, and Actinobacteriota declined. LEfSe identified Hyphomicrobiales/Bradyrhizobiaceae, Burkholderiales/Betaproteobacteria, and Rhodobacterales/Roseobacteraceae as biomarkers for CK, He, and Ca, respectively. PICRUSt2 functional predictions indicated that CK enriched for tryptophan and butyrate metabolism and fatty acid degradation, whereas Ca appeared to be enriched for methane and pyruvate metabolism and the TCA cycle. These diet-associated microbiome shifts might facilitate nutrient utilization and energy metabolism during feeding habit transition, and provided microbial candidates for feed optimization in H. tuba domestication.},
}

@article {pmid42305953,
year = {2026},
author = {Carbone, RG and Russell, AM},
title = {Editorial: Deciphering the microbiome's role in the progression of interstitial lung diseases.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1879251},
pmid = {42305953},
issn = {2296-858X},
}

@article {pmid42305965,
year = {2026},
author = {Mei, L and Zhang, P and Xiang, T and Sun, C},
title = {Pyroptosis-immunity-microbiome axis in acute upper gastrointestinal bleeding: mechanisms, risk prediction, and individualized strategies.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1780566},
pmid = {42305965},
issn = {2296-858X},
abstract = {Acute upper gastrointestinal bleeding (UGIB) is a critical emergency commonly encountered in gastroenterology. Its pathogenesis is complex and involves diverse etiologies. Emerging evidence indicates that pyroptosis, dysregulated immune-inflammatory responses, and gut microbiome imbalance are pivotal mechanisms driving gastric mucosal injury and hemorrhage. This review systematically synthesizes the risk factors, pathophysiological mechanisms, risk prediction models, and therapeutic strategies for UGIB, with particular emphasis on the intricate interplay among pyroptosis, immunity, and the microbiome and on their value as potential therapeutic targets. We first summarize the common etiologies and risk factors of UGIB, including pharmacological agents, infections, advanced age, comorbidities, and genetic predispositions. We then delineate the pathogenic role of pyroptosis in gastric mucosal injury, with particular focus on activation of the GKN2-NLRP3 axis. Next, we discuss the utility of systemic inflammatory markers such as the neutrophil-to-lymphocyte ratio (NLR) and C-reactive protein (CRP) in UGIB risk stratification, together with the mechanisms by which gut microbiome dysbiosis compromises mucosal barrier integrity and amplifies inflammatory responses through microbial metabolites and pathogen translocation. The core section provides an in-depth analysis of the reciprocal, self-amplifying network linking pyroptosis, immune activation, and microbiome perturbation, thereby elucidating the basis for the frequent co-occurrence of systemic inflammation and microbial dysbiosis in UGIB. Finally, we critically evaluate established risk-scoring systems (Glasgow-Blatchford Score, Rockall score, and AIMS65) and emerging biomarkers. Overall, this review assesses emerging therapeutic strategies, including pyroptosis inhibitors and microbiome-modulating interventions, and provides a theoretical framework for personalized management of UGIB.},
}

@article {pmid42306033,
year = {2026},
author = {Birigwa, C and Tong, Q and Qu, B and Zuo, T and Yuan, W and Xiong, J and Luo, J},
title = {Gut microbiota-epigenetic interactions in systemic aging: mechanistic drivers for endocrine and reproductive network remodeling and therapeutic modulation.},
journal = {Frontiers in aging},
volume = {7},
number = {},
pages = {1826382},
pmid = {42306033},
issn = {2673-6217},
abstract = {Researchers now see aging as a process shaped by the interactions among metabolism, epigenetics, and hormones. Recent studies suggest that gut microbes play an important role in this system by making metabolites that can affect gene expression and chromatin structure. Still, it is not fully clear how gut microbes and the body influence each other as we age, since both are constantly changing. This review brings together current research on how metabolites from gut microbes-such as short-chain fatty acids, bile acids, tryptophan derivatives, and polyamines-affect the body's epigenetic machinery through processes such as DNA methylation, histone modifications, and chromatin remodeling. We examine evidence from cell studies, animal experiments, and human research to assess the strength of the links and distinguish direct effects on chromatin from indirect metabolic or gene-expression changes. We focus especially on endocrine and reproductive organs, such as the hypothalamus, pancreas, liver, fat tissue, and cells that support the gonads, where signals from gut microbes overlap with hormonal control and metabolism. In these tissues, microbial metabolites influence key pathways related to inflammation, mitochondria, and nutrient sensing, but there is still little direct evidence in humans. The review also points out differences between lab models and what is observed in patients, highlighting the need for further work to apply these findings in real-world settings. Interactions between gut microbes and epigenetics form a two-way link between metabolism, immunity, and aging of the endocrine system. While more evidence shows that microbial metabolites can shape gene activity and epigenetic patterns, most of what we know comes from animal studies rather than direct tests in people. Moving forward, researchers will need to use broad, long-term studies that combine different types of data to figure out cause and effect and which tissues are involved. Understanding this system better could help create new biomarkers and treatments to influence aging by targeting the microbiome and its effects on epigenetics.},
}

@article {pmid42306090,
year = {2026},
author = {Bandi, DP and Krishnaswamy, B and Victor, DJ},
title = {Differential prevalence of periodontal pathogens in pregnant women with gestational diabetes mellitus and periodontitis: A cross-sectional microbiological study.},
journal = {Journal of oral biology and craniofacial research},
volume = {16},
number = {4},
pages = {101479},
pmid = {42306090},
issn = {2212-4268},
abstract = {BACKGROUND: Gestational diabetes mellitus (GDM), characterized by pregnancy-induced insulin resistance, and periodontal disease, a chronic inflammatory condition of the periodontium, are intricately linked and may collectively amplify the risk of adverse maternal and fetal outcomes. This study aimed to evaluate periodontal microbial associations in periodontitis in relation to GDM.

METHODS: An observational cross-sectional study was conducted among 80 pregnant women with periodontitis, stratified into GDM (Group A; n = 40) and non-GDM (Group B; n = 40) groups. Clinical parameters, including Plaque Index, Oral Hygiene Index-Simplified, Modified Sulcular Bleeding Index, and Probing Pocket Depth (PPD), along with glycemic parameters (OGTT), were recorded. Subgingival plaque samples were analyzed using real-time Polymerase Chain Reaction for key periodontal pathogens (Fusobacterium nucleatum, Porphyromonas gingivalis, Prevotella intermedia, Prevotella nigrescens, Selenomonas sputigena, Treponema denticola, and Tannerella forsythia). Pearson correlation analysis assessed associations between clinical and glycemic parameters and pathogens, followed by multiple linear regression to determine the independent effects of predictors on the outcomes (p < 0.05).

RESULTS: Group A demonstrated significantly lower Ct values (higher bacterial load) for P. gingivalis, S. sputigena, P. nigrescens, T. denticola, and F. nucleatum (p ≤ 0.005). Strong positive correlations in the overall population were observed between P. gingivalis and probing pocket depth (r = 0.79, p = 0.001) and clinical attachment loss (r = 0.73, p = 0.010), followed by S. sputigena (r = 0.64, p = 0.01). Multiple regression analysis identified MSBI, PPD, and CAL as significant predictors of P. intermedia and P. gingivalis in both groups (p < 0.05), with OGTT-1h emerging as an additional predictor of P. gingivalis. In contrast, F. nucleatum and S. sputigena demonstrated significant inverse associations with these parameters (p < 0.05).

CONCLUSION: The results of the present study demonstrate that GDM is associated with an increased periodontal pathogenic burden, with clinical and glycemic parameters emerging as significant independent determinants, highlighting the intricate interplay between metabolic dysregulation and periodontal disease.},
}

@article {pmid42306420,
year = {2026},
author = {Zhang, J and Liu, Q and Chen, J and Zhou, Y and Zhang, B and Yuan, Z and Li, P and Pang, Z},
title = {Moderate organic-inorganic fertilization optimizes soybean productivity by reshaping rhizosphere microbiome-metabolite networks.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1823609},
pmid = {42306420},
issn = {1664-462X},
abstract = {Soybean, a key oilseed and fodder crop, is pivotal for national food security in China. And sustainable soybean production requires fertilization strategies that enhance yield while restoring rhizosphere ecological function. Balancing chemical and organic fertilization is crucial for sustainable soybean production, yet the underlying rhizosphere mechanisms driving crop performance remain underexplored. We conducted a nutrient-equalized gradient substitution experiment comparing chemical fertilizer (CF) with 30%, 70%, and 100% organic fertilizer replacement (OF30, OF70, OF100), investigating the effects on soybean growth, rhizosphere soil properties, bacterial and fungal microbiomes, and metabolomes, while maintaining equivalent nutrient inputs. Moderate organic-inorganic fertilization (30/70% organic substitution, designated as OF30 and OF70) significantly enhanced plant height, root length, biomass, nodulation, nitrogenase activity, photosynthetic capacity, and yield compared to full chemical fertilization (CF, 0% organic) and full organic fertilization (OF100%, 100% organic), the application of 30% organic and 70% inorganic fertilization in combination identified as the optimal strategy. These gains suggest that rhizosphere soil exhibited improved pH, organic carbon, and nutrient availability (K and P), alongside balanced nitrogen. Bacterial communities showed conserved core structure but increased α-diversity and turnover toward metabolically versatile genera (e.g., Flavobacterium, Geobacter, Luteibacter) under organic-inorganic fertilization. Fungal assemblages preserved a stable core while enriching saprotrophic and beneficial guilds (e.g., Serendipita, Chaetomium, Arthrobotrys). Metabolomics revealed conserved profiles with targeted enrichment of carbon-related classes (e.g., glycerophospholipids, flavonoids like delphinidin), supporting microbial activity and plant-microbe signaling. Integrated analyzes indicated that moderate organic substitution (30/70%) reshapes the rhizosphere toward balanced nutrient cycling, enhanced microbiome diversity, and functional metabolite pools, fostering symbiotic interactions and improving nutrient availability. These findings highlight moderate organic-inorganic blending as an optimal strategy for improving soybean productivity and soil health, with implications for sustainable cropping systems.},
}

@article {pmid42306745,
year = {2026},
author = {Hang, M and Liu, Y and Shen, X and Zhao, Y and Xu, Y and Gong, X and Xu, L and Li, N and Dong, L},
title = {The clinical and translational perspectives on the lung microbiome in interstitial lung diseases: a bibliometric review.},
journal = {Journal of thoracic disease},
volume = {18},
number = {5},
pages = {478},
pmid = {42306745},
issn = {2072-1439},
abstract = {BACKGROUND: Increasing evidence suggests that microbiota plays important roles in the pathogenesis and progression of interstitial lung diseases (ILDs). However, the global research landscape and emerging trends in this field remain insufficiently characterized. This study aimed to systematically characterize the research landscape, evolving hotspots, and future trends in the field of host microbiota and ILDs using bibliometric and visualization approaches, and to further explore the progress of related clinical studies.

METHODS: Publications up to November 8, 2025 were retrieved from the Web of Science Core Collection. Concurrently, clinical trials within the same timeframe were extracted from PubMed to assess advancements in the field. Bibliometric and visual analyses were conducted using VOSviewer, CiteSpace, SCImago Graphica, and Microsoft Excel.

RESULTS: A total of 295 publications were included, showing a marked increase in research output since 2012. China and the United States were the leading contributors, with the United States demonstrating higher academic impact and stronger international collaboration. Core institutions and authors were mainly concentrated in North America and Europe. Keyword analysis revealed a clear evolution of research focus, shifting from early exposure-related studies and hypersensitivity pneumonitis to lung microbiome dysbiosis, the gut-lung axis, and metagenomic approaches. Recent hotspots emphasize microbiome-based clinical applications, with increasing attention to host-microbiome interactions and immune regulatory mechanisms.

CONCLUSIONS: Research on microbiota and ILDs has expanded rapidly and shows increasing interdisciplinary integration. Future studies should enhance international collaboration, clarify underlying mechanisms, and promote clinical translation of microbiome-based biomarkers and personalized therapeutic strategies.},
}

@article {pmid42306833,
year = {2026},
author = {B, J and Adeyeye, SAO},
title = {Application of artificial intelligence in synbiotic and functional food development for precision nutrition.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d6fo00295a},
pmid = {42306833},
issn = {2042-650X},
abstract = {Synbiotic and functional food formulations modulate gut microbiota, SCFA production, immune signalling and metabolic pathways, yet current development pipelines remain largely empirical and constrained by nonlinear trade-offs among probiotic viability, prebiotic functionality and sensory acceptance. Artificial Intelligence (AI) and machine learning (ML) approaches offer data-driven strategies to support formulation, multi-objective optimization and functional assessment. This review systematically identified and critically synthesized literature published between 2020 and 2025 across five thematic domains: (i) formulation and ingredient selection; (ii) viability and shelf-life modelling; (iii) functional and antioxidant bioactivity assessment; (iv) sensory and consumer prediction; and (v) personalization and precision nutrition. Studies were identified through database searches and screened for relevance to synbiotics, functional foods, microbiome modulation and nutrition outcomes, following PRISMA 2020 guidelines. Current evidence indicates that AI can assist ingredient pairing, viability forecasting, sensory modelling and functional property prediction, often complementing conventional statistical tools such as Response Surface Methodology in multivariate design spaces. However, most implementations remain computational or pilot-scale, with minimal integration of microbiome-informed personalization, clinical endpoints or adherence outcomes. Major translational gaps include data heterogeneity, model interpretability, regulatory substantiation and scarcity of longitudinal evidence. AI should therefore be considered a complementary decision-support tool that can accelerate hypothesis generation and formulation refinement rather than substitute mechanistic validation or human trials. Bridging computational modelling with microbiome science and nutritional evidence may enable precision synbiotic strategies and next-generation functional food innovation.},
}

@article {pmid42306846,
year = {2026},
author = {Dubey, AA and Ermolaeva, M},
title = {Microbiome-host proteostasis crosstalk-An emerging perspective on mechanisms and interventions toward healthy longevity.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70386},
pmid = {42306846},
issn = {1873-3468},
support = {//Deutsche Forschungsgemeinschaft/ ; //HORIZON-WIDERA international consortium TWIN4EarLiStAge (European Commission)/ ; ERC CoG2022 LifeLongFit (European Commission)/ERC_/European Research Council/International ; //Carl-Zeiss-Stiftung/ ; },
abstract = {Proteostasis and the gut microbiota are two major determinants of host health and longevity. Proteostasis ensures proper protein folding and degradation thereby preventing the accumulation of unwanted proteins. Similarly, microbiota contribute to host metabolism, immunity, and protection from pathogens. However, as aging progresses, the proteostasis network declines, and the composition and functionality of gut microbiota are altered, often resulting in dysbiosis. While the impact of the microbiota on various aspects of host physiology is extensively studied, its specific influence on host protein quality control remains relatively underexplored. In this review, we provide an integrated overview of the relationship between microbiota and host proteostasis. Accumulating findings, particularly from C. elegans models, provide substantial support for the concept that microbiota-derived factors (vitamins and RNA) can shape host proteostasis and influence aging-related phenotypes. We discuss emerging evidence showing that microbial communities and their metabolites can either support or impair cellular proteostasis, highlighting their potential as prebiotics or dietary intervention candidates for promoting healthy aging. Understanding the intricate interplay between microbiota and proteostasis opens new avenues for designing microbiota-based strategies for healthy aging.},
}

@article {pmid42307077,
year = {2026},
author = {Zhang, F and Zhang, W and Ren, X and Liu, B and Zhou, X},
title = {Butyrate-Producing Bacteria in Intestinal Disease Therapy: Potential and Challenges.},
journal = {Biotechnology journal},
volume = {21},
number = {6},
pages = {e70260},
doi = {10.1002/biot.70260},
pmid = {42307077},
issn = {1860-7314},
support = {2025A-259//2025 Gansu Provincial University Teacher Innovation Fund Project: Omics-Based Study on the Molecular Regulatory Mechanism Between Gut Microbiota and β-Hydroxybutyrate Energy Supply in Heart Failure Mice/ ; GS-2023FZZ03//Director Responsibility System Project of Gansu Medical College: Isolation, Identification of Butyrate-Producing Bacteria in Animal Intestine and Their Molecular Mechanism in Alleviating Colitis in Mice/ ; },
mesh = {Humans ; *Butyrates/metabolism ; *Intestinal Diseases/therapy/microbiology ; *Gastrointestinal Microbiome ; Animals ; *Bacteria/metabolism ; Inflammatory Bowel Diseases/therapy/microbiology ; },
abstract = {Butyrate-producing bacteria have emerged as keystone species whose metabolic activity orchestrates host-microbial homeostasis in the human gut. This review synthesizes current understanding of how these anaerobic Firmicutes, including Faecalibacterium prausnitzii, Roseburia spp., and Eubacterium rectale, function as key contributors to intestinal health through convergent mechanisms: serving as the primary energy source for colonocytes, enforcing mucosal hypoxia that excludes facultative pathogens, and modulating immunity via histone deacetylase inhibition and G-protein-coupled receptor signaling. We critically examine the translational trajectory of butyrogenic therapies across inflammatory bowel disease, colorectal cancer, and emerging applications in radiation injury, infection, and graft-versus-host disease. Despite compelling mechanistic rationale and consistent clinical associations linking butyrate-producer depletion with disease activity, therapeutic translation faces formidable bottlenecks: extreme oxygen sensitivity complicates manufacturing; cross-feeding networks necessitate ecological rather than monostrain approaches; and host context determines whether butyrate exerts protective or permissive effects. We evaluate cutting-edge strategies to overcome these barriers, including rationally designed consortia, precision prebiotics, phage-mediated niche engineering, synthetic biology approaches, and AI-guided personalization. By integrating mechanistic insight with translational pragmatism, this review outlines a path toward evidence-based butyrogenic therapies that may complement existing strategies for intestinal disease.},
}

Humans
*Butyrates/metabolism
*Intestinal Diseases/therapy/microbiology
*Gastrointestinal Microbiome
Animals
*Bacteria/metabolism
Inflammatory Bowel Diseases/therapy/microbiology

@article {pmid42307225,
year = {2026},
author = {Hoffbeck, C and Taylor, MW},
title = {The microbiome in reptile health, disease, and ecology.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0012825},
doi = {10.1128/mmbr.00128-25},
pmid = {42307225},
issn = {1098-5557},
abstract = {SUMMARYReptiles are a diverse and speciose class of animals that are broadly threatened by habitat loss, climate change, and other factors. From a microbiological perspective, reptiles have historically been examined as a source of disease, particularly salmonellosis, with most studies being culture-based investigations into causative agents of disease and potential for zoonoses. More recent work has sought to characterize the oral, skin, and gut microbiomes of reptiles more broadly to understand their contribution to reptile health and digestion. Non-avian reptiles are particularly interesting as ectothermic tetrapods, which usually lay eggs and have limited interaction with their young, as their digestion and life history strategies diverge substantially from the more well-studied mammals. Here, we review the reptile skin, oral, gut, eggshell, and nest microbiomes, along with the relationship between the microbiome and temperature stress. We present findings that distinguish the reptile microbiome from those of other studied vertebrate taxa, and place them in the context of their phylogenetic and ecological similarities to other animals. We discuss major disease-causing agents in reptiles, which was historically the main lens through which to view reptile microbiology, along with potential zoonoses. Finally, we examine how temperature and thermoregulation interact with the microbiome in reptiles, and how the microbiome may play a role in reptile conservation.},
}

@article {pmid42307249,
year = {2026},
author = {Liao, Y and Yu, Q and Chen, T and You, R and Zhang, Q and Li, X},
title = {Interaction between rhizobacterial community and host root metabolism influences poplar salt tolerance.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0063526},
doi = {10.1128/msystems.00635-26},
pmid = {42307249},
issn = {2379-5077},
abstract = {Soil salinization worldwide affects agroforestry, restraining output and functions of farmland and forest ecosystems. Soil microbiota play vital roles in plant growth and resistance to stress, but how plants interact with root microbiomes to fight adverse environments remains elusive. Here, we employed high-throughput sequencing to investigate the rhizobacterial community composition of three poplar varieties that were Populus davidiana × P. bolleana Loucne (SXY), P. deltoides × P. euramericana "Nanlin 895" (NL895), and P. alba × P. glandulosa "84K" (84K) under salt stress. Our results showed that no differences in growth parameters and damage indices were observed across varieties before treatments. Furthermore, SXY exhibited the highest salt tolerance, characterized by the highest growth parameters and lowest damage indices under salt stress, while NL895 was the most sensitive genotype. The 16S rRNA gene sequencing unveiled the lowest diversity and distinct composition in the rhizobacterial community of SXY compared to other varieties. SXY accumulated a higher abundance of Pseudomonas, Pseudoxanthomonas, and Rhizobiaceae in the rhizosphere, which showed positive correlations with host salt tolerance. Moreover, metabolomic analysis revealed higher levels of certain secondary metabolites in SXY roots than in the roots of the other varieties. Four metabolites, including D-threitol, maslinic acid, 4',5-dihydroxy-7-methoxyflavanone, and trans-3-coumaric acid, were identified as key regulators that potentially mediate the enrichment of salt tolerance-associated rhizobacterial taxa. Our findings indicate an interaction between root metabolism and rhizosphere microbiome in poplar adaptation to salt stress, providing a theoretical basis for directional modulation of plant resistance under global change.IMPORTANCEAgroforestry frequently encounters soil salinization that limits crop yields and ecosystem services. Soil microbiota plays an important role in plant adaptation to stress, but their interaction mechanisms with host roots remain unclear. Through combining high-throughput sequencing and root metabolome analysis, we unraveled the interactions between rhizobacterial communities and host root metabolism, as well as their role in plant adaptation to salt stress, providing new strategies for microbial application under global change.},
}

@article {pmid42307633,
year = {2026},
author = {Carasso, S and Kasher-Dvora, M and Gefen, T and Geva-Zatorsky, N},
title = {Phase variation-mediated bacterial functional plasticity as a lens for understanding microbe‒host interactions.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2687913},
doi = {10.1080/19490976.2026.2687913},
pmid = {42307633},
issn = {1949-0984},
mesh = {Humans ; *Host Microbial Interactions ; *Bacteria/genetics/classification ; *Gastrointestinal Microbiome/physiology ; *Bacterial Physiological Phenomena ; Animals ; },
abstract = {The human gut microbiome represents a dynamic microbial ecosystem profoundly influencing host physiology, immune development, and disease susceptibility. While metagenomic approaches have advanced our understanding of microbial composition and functional potential, they remain insufficient to capture the real-time molecular events governing host‒microbe interactions. Taxonomic abundance and genomic content alone do not reflect active gene expression or phenotypic output, and functional roles cannot be reliably inferred from phylogenetic identity, given the substantial heterogeneity observed even within species. Central to bridging this gap is the concept of bacterial functional plasticity, with a focus on phase-mediated functional plasticity, the intrinsic capacity of microbes to rapidly remodel their activity and phenotype in response to environmental and host-derived cues. This review highlights phase variation as a prominent and evolutionarily conserved mechanism underlying plasticity, encompassing DNA inversions, short-sequence repeat modifications, and broader structural genomic variation. Emerging evidence demonstrates not only the prevalence of phase-variable mechanisms across diverse gut taxa but also their significant regulatory, ecological, and immunological consequences. These findings reframe the microbiome from a static consortium of species to a functionally dynamic system capable of rapid rewiring in response to environmental pressures. By integrating genomic, ecological, and host-response data, this review lays the groundwork for mechanistic frameworks that could explain how flexible microbial strategies influence bacterial behavior and host outcomes. Moving beyond cataloging microbial composition toward deciphering the logic of functional adaptation will be essential for translating microbiome research into predictive, diagnostic, and therapeutic applications.},
}

Humans
*Host Microbial Interactions
*Bacteria/genetics/classification
*Gastrointestinal Microbiome/physiology
*Bacterial Physiological Phenomena
Animals

@article {pmid42307649,
year = {2026},
author = {Dogra, KA and Sharma, M and Ghosh, N and Kaur, G and Singh, J and Sinha, P},
title = {Gut microbiota and immune modulation: role in neurodegenerative disorders and cancer.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42307649},
issn = {1573-4978},
mesh = {Humans ; *Neurodegenerative Diseases/immunology/microbiology ; Animals ; *Neoplasms/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Probiotics ; Prebiotics ; *Immunomodulation ; },
abstract = {The gut microbiota plays a crucial role in maintaining host metabolic balance and immune homeostasis, with increasing evidence linking its dysregulation to neurodegenerative diseases and cancer. This review aims to provide a comprehensive and integrative analysis of gut microbiota-mediated immune modulation in Parkinson's disease, Alzheimer's disease, and cancer. A structured literature-based approach was employed to examine recent studies focusing on microbial composition, metabolite production, and host microbe immune interactions. We summarize the role of key microbial metabolites, particularly short-chain fatty acids, in regulating immune responses, maintaining gut barrier integrity, and modulating systemic inflammation. In addition, the bidirectional communication along the gut-brain axis is discussed, highlighting its differential involvement in neurodegenerative disorders, while microbiota driven immune mechanisms contributing to tumorigenesis are also evaluated. Importantly, this review emphasizes the translational relevance of microbiome-targeted interventions, including prebiotics, probiotics, synbiotics, and emerging postbiotic strategies, in modulating disease progression and therapeutic outcomes. Although limitations lies in correlating the human gut microbiota to the results obtained from the animal studies which may not fully reflect the physiological conditions of the human gut as it is affected by several factors, this work provides a unified framework linking gut microbiota, immune regulation, and disease pathogenesis, and outlines future directions for the development of targeted and personalized microbiome-based therapies which may be achieved through well designed longitudinal and large scale clinical studies further.},
}

Humans
*Neurodegenerative Diseases/immunology/microbiology
Animals
*Neoplasms/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Probiotics
Prebiotics
*Immunomodulation

@article {pmid42307995,
year = {2026},
author = {Laiton, L and Acevedo, FE},
title = {Gut microbiome of the grape berry moth, Paralobesia viteana (Lepidoptera: Tortricidae) larvae through the grape ripening process revealed by high-throughput 16S and 18S rRNA sequencing.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
pmid = {42307995},
issn = {2057-5858},
mesh = {Animals ; *Vitis/parasitology/growth & development/microbiology ; RNA, Ribosomal, 16S/genetics ; Larva/microbiology ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; *Moths/microbiology ; Bacteria/classification/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Fungi/classification/genetics/isolation & purification ; },
abstract = {The grape berry moth (GBM) Paralobesia viteana (Lepidoptera: Tortricidae) is an important pest of grapes in eastern North America. The larvae damage grape clusters by direct feeding and by increasing susceptibility to fungal and bacterial pathogens. In this study, we sequenced the V3-V4 region of the 16S rRNA gene and the V4 region of the 18S rRNA gene to characterize the composition and diversity of GBM larval gut bacterial and fungal communities when fed on immature and mature 'Concord' grapes. The data were analysed with QIIME 2, and downstream analyses included taxonomic composition, differential abundance, phylogenetic, functional and alpha/beta diversity analyses. While overall bacterial community diversity did not differ significantly between treatments, differential abundance analysis identified specific bacterial taxa enriched in each larval group. Ninety-three per cent of the bacterial communities belonged to the phylum Proteobacteria, and some may play roles in amino acid and carbohydrate metabolism in the insect gut. Analyses of the 18S rRNA region showed significant taxon-level compositional differences in fungal communities between larvae grown on grapes at different ripening stages. Ascomycota was the dominant phylum (98%) present in the guts of larvae fed on mature grapes, while larvae fed on immature grapes mainly contained fungi within the Cryptomycota (51%). Larvae fed on ripe grapes had a 10-fold higher fungal abundance and were enriched in Saccharomycetales yeasts. Several of the identified microbial taxa in larval guts are commonly found in grapes, which suggests they might be transient insect residents that are ingested with the diet. In conclusion, diet strongly shaped GBM gut-associated fungal communities; specific bacterial taxa also differed between larval groups despite similar overall bacterial diversity. These results contribute to basic knowledge of gut-associated microbes in fruit-feeding insects.},
}

Animals
*Vitis/parasitology/growth & development/microbiology
RNA, Ribosomal, 16S/genetics
Larva/microbiology
RNA, Ribosomal, 18S/genetics
Phylogeny
*Gastrointestinal Microbiome/genetics
*Moths/microbiology
Bacteria/classification/genetics/isolation & purification
High-Throughput Nucleotide Sequencing
Fungi/classification/genetics/isolation & purification

@article {pmid42308020,
year = {2026},
author = {Sirigu, S and Roret, T and Mocaër, PY and Larocque, R and Jouanneau, D and Legrand, P and Baudoux, AC and Czjzek, M},
title = {Biochemical and structural characterization of a tail-spike protein with depolymerase activity identified in a marine podovirus.},
journal = {Acta crystallographica. Section D, Structural biology},
volume = {82},
number = {Pt 7},
pages = {785-799},
doi = {10.1107/S2059798326005425},
pmid = {42308020},
issn = {2059-7983},
support = {ANR-15-CE01-0009//Agence Nationale de la Recherche/ ; },
mesh = {*Podoviridae/chemistry/enzymology ; Crystallography, X-Ray ; Models, Molecular ; *Viral Tail Proteins/chemistry/metabolism ; Amino Acid Sequence ; Protein Conformation ; },
abstract = {Marine phages are, through the infection of their bacterial hosts, key regulators of microbiome and carbon fluxes in the ocean. Despite their important role, the specific molecular mechanisms that underlie infection are so far understudied. Previously, the podovirus Cobetia marina virus 1 (Carin-1), which infects the marine γ-proteobacterium C. marina, was shown to display exopolysaccharide depolymerase activity. This activity is likely to mediate degradation of the host capsule to facilitate access to the bacterial membrane receptor, but no corresponding gene could be annotated in the genome of Carin-1 by comparative genomics. Biochemical characterization enabled assignment of this activity to Dpo31, a protein sharing less than 10% sequence identity with any characterized protein. Here, we report the structural domain organization and biochemical characterization of Dpo31, revealing an overall structure that is analogous to podovirus tail-spike proteins, allowing us to locate the depolymerase activity to the D3 domain and to identify original structural features that explain the absence of detectable similarity at the primary-sequence level.},
}

*Podoviridae/chemistry/enzymology
Crystallography, X-Ray
Models, Molecular
*Viral Tail Proteins/chemistry/metabolism
Amino Acid Sequence
Protein Conformation

@article {pmid42308050,
year = {2026},
author = {Bottacin, G and Raach, B and Fröhlich, L and Künnecke, J and Kaczmarczyk, A and Tejada-Arranz, A and Ugolini, GS and Stocker, R and Jenal, U and Bumann, D and Dittrich, PS and Schubert, OT and van Vliet, S},
title = {Opposing range-dependent interactions create complex spatial patterns of antibiotic tolerance in multispecies biofilms.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {25},
pages = {e2604163123},
pmid = {42308050},
issn = {1091-6490},
support = {202186//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 225148//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 180541//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 225154//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 310030_208107//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 205321_207488//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; },
mesh = {*Biofilms/drug effects/growth & development ; *Pseudomonas aeruginosa/drug effects/physiology/metabolism ; *Anti-Bacterial Agents/pharmacology ; *Staphylococcus aureus/drug effects/physiology ; Glycolipids/metabolism/pharmacology ; *Drug Resistance, Bacterial ; },
abstract = {Many microbial communities form multispecies biofilms where cells interact through diffusible molecules. In these biofilms, multiple interactions, often with opposing effects, occur simultaneously, yet we lack quantitative frameworks to predict how they combine to shape community functions. Here, we hypothesized that complex spatial patterns can emerge when opposing interactions have distinct spatial ranges. To test this, we studied how two Pseudomonas aeruginosa exoproducts, HQNO and rhamnolipids, jointly modulate Staphylococcus aureus antibiotic tolerance by respectively increasing and decreasing it. Using microfluidics-based imaging, we quantified spatial-tolerance patterns at single-cell resolution and found that tolerance indeed shows a complex spatial pattern: S. aureus cells survived treatment only at intermediate distances from P. aeruginosa, while cells closer or farther away did not. Combining experiments and modeling, we showed that this remarkable pattern emerges because rhamnolipids have a stronger but short-ranged effect, while HQNO has a weaker but longer-ranged effect. We found that spatial arrangement affects overall tolerance by shifting the balance between the two opposing interactions. Finally, using bioprinting, we confirmed that HQNO and rhamnolipids modulate tolerance in highly mixed biofilms. In more segregated biofilms, spatial arrangement still strongly modulated tolerance, but independently of these compounds, suggesting additional interactions. Together, our results show that spatial-tolerance patterns emerge from the combined effect of opposing range-dependent interactions and cannot be predicted from either alone. By predicting how opposing interactions jointly determine community properties, our framework provides a foundation for understanding and ultimately engineering microbiome functions.},
}

*Biofilms/drug effects/growth & development
*Pseudomonas aeruginosa/drug effects/physiology/metabolism
*Anti-Bacterial Agents/pharmacology
*Staphylococcus aureus/drug effects/physiology
Glycolipids/metabolism/pharmacology
*Drug Resistance, Bacterial

@article {pmid42308119,
year = {2026},
author = {Holman, DB and Gzyl, KE and Kommadath, A and Määttänen, P},
title = {Multi-omic characterization of the sow colostrum and milk microbiome and proteome.},
journal = {Microbial genomics},
volume = {12},
number = {6},
pages = {},
pmid = {42308119},
issn = {2057-5858},
mesh = {Animals ; *Colostrum/microbiology ; *Milk/microbiology ; Female ; *Proteome/genetics ; Multiomics ; *Microbiota/genetics ; Swine ; *Bacteria/classification/isolation & purification/genetics ; Metagenomics/methods ; Proteomics ; },
abstract = {Sow colostrum and milk provide essential nutrients, immune protection and one of the earliest microbial exposures for piglets. However, the microbial composition, functional potential and host interactions of these mammary secretions remain poorly characterized. Here, we combined culturomics, metagenomics and proteomics to comprehensively characterize the microbiome and proteome of sow colostrum and milk collected at farrowing and at 7 and 21 days postpartum. We recovered 132 bacterial isolates representing at least 42 species, including 15 putatively novel taxa. These isolates included both potentially pathogenic species, such as Sarcina perfringens and Streptococcus suis, and potentially beneficial bacterial species like Lactobacillus amylovorus and Lactiplantibacillus plantarum. The microbial composition and functional potential shifted significantly as the milk matured, with L. amylovorus, Limosilactobacillus reuteri and Rothia spp. among the most relatively abundant taxa. Several antimicrobial resistance genes, including erm(C), tet(K), tet(M), lnu(A), poxtA and fexB, were identified on contigs encoding plasmid replicons in the isolates, indicating potential for horizontal gene transfer. Functional annotation of isolate genomes indicated broad carbohydrate-active enzyme (CAZyme) repertoires, including β-galactosidase-associated families and other CAZyme families consistent with potential milk oligosaccharide utilization. The colostrum and milk proteome also shifted during lactation, reflecting declining immune-related proteins and increasing metabolic and structural proteins. Correlations between specific microbial taxa and host proteins, including Rothia spp. and immune proteins or glycoproteins, suggested potential host-microbe interactions during lactation. Together, these findings provide a multi-omic perspective on how mammary microbiome dynamics and host responses during lactation may influence neonatal microbial colonization and health.},
}

Animals
*Colostrum/microbiology
*Milk/microbiology
Female
*Proteome/genetics
Multiomics
*Microbiota/genetics
Swine
*Bacteria/classification/isolation & purification/genetics
Metagenomics/methods
Proteomics

@article {pmid42308500,
year = {2026},
author = {He, M and Ferrini, A and Chisari, E and Kolhoff, F and Sehgal, P and Parvizi, J},
title = {Heading Toward a Different Future: The Microbiome, Dysbiosis, Microbial Translocation, and Beyond.},
journal = {The Journal of bone and joint surgery. American volume},
volume = {},
number = {},
pages = {},
doi = {10.2106/JBJS.25.01100},
pmid = {42308500},
issn = {1535-1386},
abstract = {➢ The relationship between the gastrointestinal tract and joint diseases has garnered increased attention over recent decades, leading to the introduction of the gut-joint axis concept.➢ Infections at sites such as joints and the spine may originate endogenously from the gut microbiome.➢ The idea of microbial translocation through a compromised epithelial barrier, resulting in the circulation of pathogens or their byproducts, and the idea of immune cell-mediated transport of pathogens to various sites are gaining further attention.➢ By understanding the interaction between the immune system and gut microbiota, potential therapeutic strategies, such as the use of organoids, can be developed to restore the gut barrier integrity, to replenish gut microbiota, and to provide biodiversity.➢ To better understand the mechanisms linking gut health and joint diseases, future basic-science research and well-designed clinical trials, exploiting advanced next-generation sequencing techniques, are needed.},
}

@article {pmid42308545,
year = {2026},
author = {Yuan, Y and Yin, X and Liu, J and Jing, J and Shi, Y and Tao, S and Guo, L and Wang, D and Jiang, W and Liong, MT and Chen, D and Zhang, J},
title = {Bifidobacterium lactis XLTG11 Reduces Eczema and Infections in Infants: A Randomized Trial.},
journal = {QJM : monthly journal of the Association of Physicians},
volume = {},
number = {},
pages = {},
doi = {10.1093/qjmed/hcag148},
pmid = {42308545},
issn = {1460-2393},
abstract = {BACKGROUND: Early-life gut microbiota profoundly influences immune system maturation and disease susceptibility. Perturbations in microbial development have been linked to rising rates of allergic and infectious diseases in children. Probiotic interventions offer a promising strategy to restore microbial-immune homeostasis; however, evidence from rigorously designed, strain-specific randomized trials integrating clinical and microbiome outcomes remains limited.

OBJECTIVE: To evaluate the efficacy of Bifidobacterium animalis subsp. lactis XLTG11 in reducing the incidence of eczema and respiratory infections during early childhood, and to explore its associations with gut microbial ecology and immune function.

METHODS: In this randomized, double-blind, placebo-controlled trial, 352 healthy infants and young children (aged <3 years) were randomly allocated to receive XLTG11 (1 × 1010 CFU/day) or placebo for 180 days. Primary outcome was eczema incidence; secondary outcomes included respiratory and gastrointestinal symptoms, growth parameters, gut microbiota composition (16S rRNA gene sequencing), and gut immune biomarkers.

RESULTS: Children receiving XLTG11 showed significantly lower incidence of eczema (p = 0.017) and erythema (p = 0.028), and a lower incidence of physician-confirmed pneumonia (RR = 0.40, 95% CI 0.17-0.94; p = 0.030) compared with placebo. Probiotic supplementation improved stool consistency (p = 0.018) without affecting growth. 16S rRNA gene sequencing revealed enrichment of Faecalibacterium, Akkermansia, and other short-chain fatty acid-producing taxa, alongside suppression of Helicobacter and Citrobacter. Predictive functional profiling suggested enrichment of pathways related to energy metabolism, vitamin biosynthesis, and antimicrobial peptide (DEFB2, LL-37) production, alongside preservation of secretory IgA.

CONCLUSIONS: Daily B. lactis XLTG11 supplementation safely reduces eczema and respiratory infection risk in early childhood by remodeling the gut microbiome and reinforcing mucosal immunity. These findings support its use as a preventive strategy for allergy and infection via gut-immune modulation.

TRIAL REGISTRATION: ClinicalTrials.gov (NCT07490587).

ETHICS APPROVAL: Shanghai Sixth People's Hospital Human Ethics Committee (No. 2023-142).},
}

@article {pmid42308735,
year = {2026},
author = {Choi, Y and Park, J and Kang, A and Seo, E and Lee, DJ and Son, SH and Jang, KB and Kim, WK and Kang, D and Kim, Y},
title = {Synergistic effects of two bacteriophages with distinct infection patterns and broad host specificity against multidrug-resistant Salmonella Typhimurium and their potential applications in the poultry industry.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107289},
pmid = {42308735},
issn = {1525-3171},
abstract = {Controlling Salmonella Typhimurium in poultry requires effective alternatives to conventional antimicrobials. This study evaluated the efficacy of a two-phage cocktail composed of S. Typhimurium-infecting phages SLAM_phiST45 and SLAM_phiST56 and investigated its mechanistic basis. Host-range profiling of 61 phages against 10 S. Typhimurium strains revealed two major host-associated clusters (swine-human vs. poultry). Notably, the cocktail exhibited broad host ranges that crossed these clusters. The cocktail showed clear synergy, supported by complementary receptor usage and reduced emergence of phage-resistant mutants. In egg-based food application assays, the cocktail achieved rapid bacterial suppression even at an MOI of 1 and fully eliminated S. Typhimurium under refrigerated conditions. In a chick infection model, the cocktail improved growth performance, reduced intestinal and systemic bacterial loads, alleviated intestinal lesions, and restored inflammatory and barrier-related gene expression. While the overall gut microbiota structure remained stable, subtle alterations in low-abundance taxa indicated that phage treatment may cause minor off-target shifts. Overall, this study demonstrates that the phage cocktail is a potent and practical biocontrol tool capable of reducing Salmonella in both food matrices and live birds. These findings support its application in poultry production and highlight the importance of monitoring microbiome-level impacts in future phage-based interventions.},
}

@article {pmid42308739,
year = {2026},
author = {Tabish, RW and Lin, Y and Rochell, SJ and Pacheco, WJ and Bailey, MA and Dozier, WA and Hoerr, FJ and Robinson, K and Hauck, R},
title = {Jejunal histopathology, metagenome, and mucosal transcriptome of broilers after an enteric challenge and fed diets with different fiber types and concentrations.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107215},
pmid = {42308739},
issn = {1525-3171},
abstract = {This study investigated the efficacy of various dietary fiber sources and combinations in mitigating subclinical enteric infection in broilers. Using a randomized complete block design, 2,160 d-old YP x Ross 708 male broilers were assigned to eight treatments. These included an unchallenged control and a challenged control, followed by six dietary treatments applied to challenged broilers. The dietary treatments consisted of fiber supplementation with oat hulls (OH) or soy hulls (SH), either alone or in combination with wheat middlings (WM) or sugar beet pulp (SBP). Birds were challenged with Eimeria spp. followed by Clostridium perfringens, and a multi-omics approach was employed to analyze jejunal histopathology, microbiome, and host mucosal transcriptome. While the enteric challenge induced significant histopathological changes, fiber combinations including OH-WM and OH-SBP significantly (P < 0.05) reduced cumulative pathology scores. The challenge caused a shift toward Lactobacillus crispatus dominance in the microbiome. Each fiber source altered the microbiome distinctively: OH increased Romboutsia sp., OH-SBP enriched beneficial Limosilactobacillus spp., and SH combinations enhanced butyrate-producing Dysosmobacter welbionis. Transcriptome analysis revealed that fiber supplementation suppressed inflammatory pathways while upregulating cell cycle progression and DNA repair pathways. Integration of bacteriome with host gene expression data revealed coordinated associations, including a link between Glutamicibacter protophormiae, Spirosoma, Eggerthella, and Blautia through host genes APOB, DSEL, and ENPP7, indicating a correlation of fiber-degrading bacteria with host lipid metabolism and extracellular matrix remodeling. These findings suggest that combining insoluble and soluble fibers may create a more resilient gut environment against enteric challenges through complementary mechanisms, with OH based combinations notably exhibiting reduced pathology, stronger anti-inflammatory response and suppression of opportunistic species.},
}

@article {pmid42308743,
year = {2026},
author = {Lyte, JM and Seyoum, MM and Ayala, D and Kers, JG and Caputi, V and Johnson, T and Zhang, L and Rehberger, J and Zhang, G and Dridi, S and Hale, B and De Oliveira, JE and Grum, D and Smith, AH and Robinson, K and Kogut, M and Olson, EG and Ricke, SC and Ballou, A and Potter, B and Proszkowiec-Weglarz, M},
title = {Best practices framework for using 16S rRNA gene sequencing in poultry microbiota research.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107275},
pmid = {42308743},
issn = {1525-3171},
abstract = {Microbiome research has shown significant potential in enhancing poultry health and productivity. Despite the increasing volume of data linking the microbiota with various host traits, challenges persist regarding the consistency and reproducibility of findings. A major underlying issue is the variability in methodologies employed across studies. As such, a need exists to establish a set of standardized guidelines that help guide experimental design, DNA extraction, sequencing, data analysis, and reporting in poultry microbiota research. Rather than advocating for a single standardized protocol, we propose a best practices framework designed to enhance methodological rigor while accommodating distinct research contexts. Such a framework emphasizes the use of appropriate positive and negative controls and improved data reporting to facilitate cross-study comparisons and reproducibility. As a companion to our previous review of the 16S rRNA gene sequencing landscape in poultry microbiota research, this manuscript represents a collaborative effort among experts from academia, industry, and government. It aims to offer a practical set of guidelines that serve as a checklist for designing, conducting, analyzing, and reporting poultry microbiota studies. These guidelines seek to improve consistency, reproducibility, and robustness of poultry microbiota research.},
}

@article {pmid42308768,
year = {2026},
author = {Wang, J and Ryou, K and Shim, H and Lee, HJ and Shin, M},
title = {Advancing in vitro gut fermentation: the convergence of gut-on-a-chip and digital twins.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103541},
doi = {10.1016/j.copbio.2026.103541},
pmid = {42308768},
issn = {1879-0429},
abstract = {The gut has gained increasing recognition as a key organ affecting systemic physiological regulation, and the gut microbiota is strongly associated with various human diseases. In vitro gut fermentation systems provide a robust alternative to in vivo clinical experiments for functional food development and for studies of nutrition and drug metabolism. Despite their cost-effectiveness, ethical compliance, and precise control of experimental variables, critical challenges remain, most notably the lack of physiological host interactions and profound interindividual variability. Emerging technologies, specifically gut-on-a-chip platforms and digital twin systems, can be integrated with in vitro gut fermentation to overcome these fundamental limitations and markedly advance its translational applicability. Here, we review the current landscape of in vitro gastrointestinal-simulating methodologies and explore their convergence with these cutting-edge technologies to model the complex host-microbiome ecosystem.},
}

@article {pmid42308920,
year = {2026},
author = {Xu, Z and Zhu, W and Xia, Q and Huang, W and Chi, Y and Qi, H and Chan, OYP and Ching, JY and Chan, FK and Chan, NN and Ng, SC},
title = {Synbiotics and antioxidants synergistically attenuate disease progression in metabolic dysfunction-associated steatotic liver disease.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {201},
number = {},
pages = {119656},
doi = {10.1016/j.biopha.2026.119656},
pmid = {42308920},
issn = {1950-6007},
abstract = {BACKGROUND & AIMS: Metabolic dysfunction-associated steatotic liver disease (MASLD) is linked to gut dysbiosis, highlighting gut microbiome modulation as a promising therapeutic strategy. This study investigated the synergistic effects of synbiotics and antioxidants in MASLD.

METHODS: We evaluated the effects of synbiotics, antioxidants, and their combination (SLD07) on metabolic and histopathological parameters and energy balance (Promethion system) in high-fat diet-fed mice. Plasma metabolome and faecal microbiome were analysed. In a 3-month pilot study of patients with MASLD (n = 27), we examined the safety and efficacy of SLD07 (20 billion CFU/day), with microbiome alterations assessed by metagenomic sequencing.

RESULTS: In mice, SLD07 significantly attenuated metabolic and hepatic parameters, including body weight gain, white adipose tissue, serum triglycerides, low-density lipoprotein, liver histology (p < 0.05), and increased the respiratory exchange ratio (p < 0.001). Synbiotics enhanced glucose tolerance and insulin sensitivity (p < 0.05), while antioxidants primarily reduced adipose tissue (p < 0.05). Liver tissue MDA levels were reduced only in the combination group, whereas GSSG levels were reduced in the combination and antioxidants alone groups (p < 0.05). Liver transcriptomics revealed that all treatments reversed HFD-upregulated inflammation and oxidative pathways, with the combination showing the broadest effect. Gut microbiota was mainly modulated by synbiotics, while systemic metabolome changes were driven by antioxidants. In the clinical pilot study, treatment reduced liver fat and stiffness (p < 0.01), increased Bifidobacterium, and upregulated the L-glutamine pathway, with no serious adverse events.

CONCLUSION: This integrated translational investigation demonstrates that the synbiotic-antioxidant combination alleviates MASLD through dual modulation of gut microbiota and systemic oxidative stress.},
}

@article {pmid42309017,
year = {2026},
author = {Yang, X and Liu, W and Mao, Y and Wang, H},
title = {Correlation analysis of lead stress-induced alterations in root metabolome and rhizosphere microbiome of Cuminum cyminum L.},
journal = {Ecotoxicology and environmental safety},
volume = {320},
number = {},
pages = {120390},
doi = {10.1016/j.ecoenv.2026.120390},
pmid = {42309017},
issn = {1090-2414},
mesh = {*Rhizosphere ; *Microbiota/drug effects ; *Metabolome/drug effects ; *Plant Roots/drug effects/metabolism/microbiology ; *Soil Pollutants/toxicity ; *Cuminum/drug effects/metabolism/microbiology ; *Lead/toxicity ; Soil Microbiology ; Stress, Physiological ; Soil/chemistry ; },
abstract = {Lead (Pb) contamination in agricultural soils poses serious threats to crop production and food safety. Cuminum cyminum L. is an important spice crop widely cultivated in arid regions, but its rhizosphere responses to Pb stress remain poorly understood. Here we conducted a field plot experiment with four Pb treatment levels (0, 400, 800, and 1200 mg/kg) and employed an integrated approach combining soil physicochemical and enzymatic analyses, metagenomics, and root metabolomics to characterize the rhizosphere of C. cyminum after 40 days of Pb exposure. Pb significantly decreased soil pH, organic matter, nitrogen availability, and available phosphorus and potassium, while altering soil enzyme activities by suppressing urease and acid phosphatase and enhancing catalase activity. Pb stress reshaped rhizosphere microbial communities by increasing microbial richness at low and moderate Pb levels but reducing community evenness under high Pb stress. Metal-tolerant taxa, including Sphingomonas, Arenimonas, and Gemmatimonas, were selectively enriched. Functional analyses revealed a broad enhancement of microbial metabolic potential, particularly in amino acid, carbohydrate, and energy metabolism pathways. Concurrently, Pb exposure correlated with extensive root metabolic reprogramming, characterized by accumulation of amino acids, organic acids, and flavonoids. The random forest results indicated that soil physicochemical properties had a stronger correlation with plant growth than root metabolites or rhizosphere microorganisms under Pb stress conditions. Overall, this study reveals a coordinated rhizosphere strategy of C. cyminum to Pb stress, providing new insights into heavy metal adaptation mechanisms in spice crops and informing sustainable cultivation in Pb-contaminated soils.},
}

*Rhizosphere
*Microbiota/drug effects
*Metabolome/drug effects
*Plant Roots/drug effects/metabolism/microbiology
*Soil Pollutants/toxicity
*Cuminum/drug effects/metabolism/microbiology
*Lead/toxicity
Soil Microbiology
Stress, Physiological
Soil/chemistry

@article {pmid42309163,
year = {2026},
author = {Sutthiboonyapan, P and Jungpraditphol, I and Krasaesin, A and Khamwachirapitak, C and Choi, Y and Porntaveetus, T and Wiriyakijja, P},
title = {Supragingival Plaque Microbiome Composition Associated with Oral Lichen Planus Activity and Desquamative Gingivitis Severity: An Exploratory, Cross-Sectional, Shotgun Metagenomic Study.},
journal = {European journal of dentistry},
volume = {},
number = {},
pages = {},
doi = {10.1055/s-0046-1824444},
pmid = {42309163},
issn = {1305-7456},
abstract = {OBJECTIVES: The microbial contribution to desquamative gingivitis (DG), a frequent and debilitating form of immune-mediated oral lichen planus (OLP), remains undefined. This study employed shotgun metagenomic sequencing to investigate the role of the oral microbiome in DG site involvement and severity, as well as OLP disease activity.

MATERIALS AND METHODS: In this exploratory, cross-sectional study, supragingival plaque samples were collected from nine OLP patients at desquamative gingivitis-affected sites (DG sites), sites not affected by desquamative gingivitis (non-DG sites), and pooled full-mouth samples. Shotgun metagenomic sequencing was performed to reveal oral microbial profiles and their functional pathways. Disease severity was assessed using the Oral Lichen Planus Disease Activity Scale (OLP-DAS) and the Desquamative Gingivitis Clinical Score (DGCS).

STATISTICAL ANALYSIS: Associations between microbial profiles and disease severity were assessed using Spearman's correlation. Microbial and functional pathway profiles were compared between DG and non-DG sites using the paired Wilcoxon signed-rank test. A p-value <0.05 was considered statistically significant.

RESULTS: Significant differences in microbial composition between DG and non-DG sites were identified, including 6 genera and 17 species (p < 0.05). Several taxa showed notable correlations with disease severity (r ≥ 0.7), according to DGCS, with 10 genera and 16 species positively associated with DGCS, and 5 genera and 8 species associated with OLP-DAS. Notably, the fructan biosynthesis pathway showed a significant inverse correlation with DG severity (r = - 0.70, p < 0.05) and was linked to Actinomyces sp. oral taxon 448, which was enriched in DG sites. This suggested that increasing disease severity may be associated with reduced microbial polysaccharide-production potential.

CONCLUSIONS: The DG microbiome shows distinct functional and taxonomic changes. Fructan biosynthesis was more abundant in DG sites than in non-DG sites, but showed an inverse correlation with DG severity, highlighting candidate biomarkers and potential therapeutic targets.},
}

@article {pmid42309238,
year = {2026},
author = {R, K and Chandra, A and Pal, S and Tiwari, H and Shekhar, A and Agarwal, R},
title = {Microbial dysbiosis in oral potentially malignant disorders: A systematic review.},
journal = {Journal of stomatology, oral and maxillofacial surgery},
volume = {127},
number = {6},
pages = {102876},
doi = {10.1016/j.jormas.2026.102876},
pmid = {42309238},
issn = {2468-7855},
abstract = {BACKGROUND: Oral potentially malignant disorders (OPMDs) including oral leukoplakia (OLK), proliferative verrucous leukoplakia (PVL), and oral verrucous hyperplasia (OVH) pose variable malignant transformation risk to oral squamous cell carcinoma (OSCC), yet the role of microbial dysbiosis in their progression remains ambiguous.

OBJECTIVES: To elucidate microbial shifts in OPMDs, their association with dysplasia progression and malignant transformation, highlighting prospects for early detection and risk stratification.

MATERIAL AND METHODS: A comprehensive literature search was conducted across scientific databases up to May 2025. Studies investigating microbial dysbiosis in OLK, PVL, or OVH using 16S rRNA sequencing, metagenomic, or transcriptomic analyses were included. Risk of bias was assessed using the modified Newcastle-Ottawa scale.

RESULTS: OPMDs showed inconsistent alpha diversity and distinct beta diversity compared to controls. Microbial composition differed by lesion type: OLK was enriched with Fusobacterium periodonticum, Porphyromonas pasteri, Streptococcus, and Haemophilus; PVL with Campylobacter concisus, Leptotrichia, and Haemophilus parainfluenzae; and OVH with Porphyromonas gingivalis, Tannerella forsythia, and Saccharibacteria TM7. High-risk OLK showed reduced diversity and enrichment of Fusobacterium nucleatum, Parvimonas, and Streptococcus infantis. Malignant transformation revealed lesion-specific shifts, including increased Fusobacterium, Capnocytophaga and Porphyromonas in OLK-OSCC, while Neisseria was specifically enriched in progressive OLK lesions, Treponema and Campylobacter in PVL-OSCC, and Capnocytophaga sputigena and Prevotella oris in OVHOSCC.

CONCLUSION: This review highlights the pivotal role of microbial dysbiosis in the evolution of OPMDs to malignancy. Distinct microbial signatures across OLK, PVL, and OVH may serve as biomarkers for disease stratification and early detection of high-risk lesions.},
}

@article {pmid42309422,
year = {2026},
author = {Curcio, R and Di Serio, A and Sica, A and Cangemi, S and Spaccini, R and Agrelli, D and Iannece, P and Ronga, D and Mazzei, P},
title = {Sustainable valorization of waste horticultural biomasses to develop a novel hydrochar to improve soil health and modulate the lettuce metabolism.},
journal = {Environmental research},
volume = {305},
number = {Pt 2},
pages = {125034},
doi = {10.1016/j.envres.2026.125034},
pmid = {42309422},
issn = {1096-0953},
abstract = {Hydrothermal carbonization (HTC) represents an innovative and sustainable chemical approach based on sub-critical water and useful to valorize waste biomass to develop a novel solid material with a huge potential for soil microbiota and plant productivity. Two hydrochar types were produced, under mild (180 °C, 10 Bar) and severe (215 °C, 20 Bar) HTC conditions (HC180 and HC215, respectively), by processing spinach, red chicory, and escarole wastes resulting from industrial horticultural production. These hydrochars were characterized for elemental composition and molecular composition via advanced techniques ([13]C CPMAS NMR and ATR-FT-IR) and compared with the values detected for initial biomass types. HTC progressively converted labile into carbon-dense, aromatic materials, with greater severity reducing nutrient availability. Solid hydrochars retained up to 2.82 g of water per g of material, thus representing a tool to make soil more resilient against the drought. Greenhouse pot experiments on baby-leaf lettuce revealed that HC180 strongly promoted plant shoot and root growth, matching conventional mineral fertilization, while HC215 showing only limited effects. [1]H NMR metabolomics indicated that HC180 stimulated primary metabolism, increasing the level of sugars and amino acids, linked to energy production and stress responses, highlighting a biostimulant effect mediated by enhanced nutrient availability and soil-microbiome interactions. These findings demonstrate that mild HTC conditions produce safe hydrochars with plant biostimulant activity, characterized by a balanced composition of labile carbon and nitrogen as well as a spectrum of plant-available nutrients. This offers a tunable strategy for sustainable horticultural residue management to produce a product enhancing soil fertility and vitality.},
}

@article {pmid42309429,
year = {2026},
author = {Plotkin, L and Aharoni-Frutkoff, Y and Pollak, D and Azulay, A and Shavit, Z and Focht, G and Livovsky, J and Lev-Tzion, R and Koslowsky, B and Boneh, RS and Weiss, B and Slae, M and Dotan, I and Godny, L and Kierkuś, J and Garwolińska, M and Broide, E and Moshe, G and Griffiths, AM and Tersigni, C and Naftali, T and Abramas, L and D'arcangelo, G and Yerushalmy-Feler, A and Schwerd, T and Crowley, E and Wine, E and Yassour, M and Reifen, R and Turner, D},
title = {Tasty&Healthy exclusive whole food diet in asymptomatic children and young adults with biologically active Crohn's disease: the TASTI-E randomized controlled trial.},
journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cgh.2026.05.029},
pmid = {42309429},
issn = {1542-7714},
abstract = {BACKGROUND: Tasty&Healthy is an exclusive whole food diet designed to reduce inflammation in Crohn's disease (CD) without the need for formula. This TASTI-E randomized-controlled trial compared the effect of Tasty&Healthy versus habitual diet on subclinical inflammation in CD (NCT#04239248).

METHODS: Clinically quiescent patients with CD, 6-40 years of age, with Mucosal Inflammation Non-invasive (MINI) index >8 reflecting bowel inflammation, were randomized to an 8-week Tasty&Healthy intervention or to continue their regular diet. Thereafter, the habitual group was offered an 8-week open-label Tasty&Healthy intervention. The primary outcome was >50% decline in calprotectin. The study was terminated early due to COVID-19-related challenges.

RESULTS: Of the 46 randomized patients (mean age, 18.2±7.6 years; median disease duration, 9.01 months [IQR 2.9-17.1]), 19 were allocated to Tasty&Healthy and 27 to habitual diet. Calprotectin response was greater in the Tasty&Healthy (53%) versus habitual arm (7%, relative risk=3.23 [95%CI 1.15-9.01], p=0.028). Among 15 patients who crossed-over to Tasty&Healthy, the rates of calprotectin<250 μg/g (53% vs. 7%, respectively, p=0.045) and MINI <8 (93% versus 20%, p=0.002) were higher at week 16 versus week 8. Adherence to Tasty&Healthy was 77% based on self-reported questionnaires and 71% by fecal gluten. Micronutrient and macronutrient consumption was similar between the groups, except for higher fiber intake with Tasty&Healthy. The Tasty&Healthy intervention resulted in a unique serum metabolic signature.

CONCLUSIONS: The Tasty&Healthy diet may reduce calprotectin levels in patients with CD with subclinical inflammation. Its flexible structure, free of formula, likely explains the high adherence among asymptomatic individuals.},
}

@article {pmid42309504,
year = {2026},
author = {Barros, DC and de Freitas, LHK and Gomes, MP},
title = {Microbiome-Informed Pathways Linking Nature-Based Treatment Systems to Antimicrobial Resistance Outcomes.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70358},
doi = {10.1111/1462-2920.70358},
pmid = {42309504},
issn = {1462-2920},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 302226/2022-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; BRD2024011000004//Fundação Araucária/ ; },
mesh = {*Microbiota ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Wetlands ; *Bacteria/drug effects/genetics ; Rhizosphere ; *Drug Resistance, Microbial ; },
abstract = {Antimicrobial resistance (AMR) is a One Health challenge driven by clinical antibiotic use and environmental processes that shape microbial selection and genetic exchanges. Nature-based solutions (NbS), particularly constructed wetlands, are increasingly used to remove complex contaminant mixtures from aquatic systems. Although these systems often achieve considerable efficiencies, their effects on AMR dynamics remain unclear. This review synthesizes evidence on how aquatic rhizospheres function as microbiome-associated ecological reactors, in which contaminant mixtures, redox gradients and microbial interactions jointly influence resistance. We show that wetlands can function along a continuum between antimicrobial resistance attenuation, persistence, and dissemination, depending on the design, operation, and ecological context. Importantly, the removal of bioactive compounds does not necessarily translate to a reduced resistance risk, as selective pressures may persist within biofilms, sediments, and plant-associated compartments. We propose a microbiome-informed conceptual framework for interpreting AMR in nature-based systems. This perspective identifies potentially modifiable leverage points for understanding, interpreting, and potentially mitigating resistance-related risks and underscores the need for monitoring and risk assessment strategies that extend beyond conventional chemical metrics and incorporate the One Health exposure pathways. Together, these insights reposition wetlands as conditional solutions, whose sustainability depends on explicitly addressing antimicrobial resistance, alongside contaminant removal.},
}

*Microbiota
*Drug Resistance, Bacterial
*Anti-Bacterial Agents/pharmacology
Wetlands
*Bacteria/drug effects/genetics
Rhizosphere
*Drug Resistance, Microbial

@article {pmid42309599,
year = {2026},
author = {Kumar, H and Kumar, P and Prajapati, MR and Bharti, MK and Prakash, S and Dixit, R and Khilari, K and Pathak, A and Singh, J and Gangwar, LK and Gaurav, SS and Verma, H and Kapoor, N},
title = {Profiling of bacterial community associated with sugarcane rhizosphere.},
journal = {Journal, genetic engineering & biotechnology},
volume = {24},
number = {2},
pages = {100694},
pmid = {42309599},
issn = {2090-5920},
abstract = {Sugarcane (Saccharum officinarum L.) is an important cash crop in India, and its cultivation contributes significantly to the country's economy by producing sugar, bioethanol, and other valuable by-products. The rhizosphere microbiome plays a vital role in nutrient cycling, plant health, and soil functioning. Hence, the soil microbiome associated with sugarcane cultivation plays a crucial role in nutrient cycling, plant health, and overall ecosystem functioning. However, information on the composition and diversity of bacterial communities in sugarcane rhizosphere soils of Uttar Pradesh remains limited. In different places, the outcomes of different cropping systems on the microbiome differ, affecting crop health and productivity. In the present study, bacterial diversity was characterized using 16S rRNA amplicon sequencing across different locations. The results revealed distinct variations in microbial community composition among sites, as supported by beta diversity analysis. Dominant bacterial phyla included Pseudomonadota, Bacillota, Bacteroidota, Actinomycetota, and Acidobacteriota, indicating their potential roles in rhizosphere functioning. These findings provide insights into the structure of sugarcane-associated microbial communities and highlight their importance in sustainable crop production.},
}

@article {pmid42309987,
year = {2026},
author = {Veitch, DP and Miller, MJ and Kanoria, S and Aisen, PS and Beckett, LA and Green, RC and Harvey, DJ and Jack, CR and Jagust, W and Lee, EB and Nho, K and Nosheny, R and Okonkwo, OC and Perrin, RJ and Petersen, RC and Mindt, MR and Saykin, AJ and Shaw, LM and Toga, AW and Tosun, D and Landau, SM and Weiner, MW and , },
title = {Contributions of the Alzheimer's Disease Neuroimaging Initiative to advancing AD research: a targeted review of recent publications.},
journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association},
volume = {22},
number = {6},
pages = {e71566},
pmid = {42309987},
issn = {1552-5279},
support = {/NH/NIH HHS/United States ; /AG/NIA NIH HHS/United States ; },
mesh = {*Alzheimer Disease/diagnostic imaging/pathology ; Humans ; *Neuroimaging/methods ; Disease Progression ; Amyloid beta-Peptides/metabolism ; Brain/diagnostic imaging/pathology ; Biomarkers ; },
abstract = {The Alzheimer's Disease Neuroimaging Initiative (ADNI) recently celebrated its 20th anniversary, reflecting two decades of major contributions to Alzheimer's research through open data sharing and longitudinal multimodal assessments. This review synthesizes 122 high-impact studies using ADNI data or biospecimens from 2023 to mid-2025 to clarify mechanisms of Alzheimer's disease (AD) progression. Studies describe impairment of glymphatic clearance and the impact of cerebral small vessel disease, trajectories of amyloid beta and tau deposition, inflammation, metabolic disturbances, synaptic dysfunction, and neurodegeneration, leading to cognitive impairment and neuropsychiatric symptoms. Multifactorial contributions from genetic and epigenetic influences, co-pathologies and comorbidities, and mechanisms of resilience modulate disease progression. Finally, heterogeneity of clinical presentation and disease course is described in the context of multiple contributing factors, highlighting the complexity of AD. By integrating imaging, fluid biomarkers, genetics, and clinical measures, ADNI provides a comprehensive research dataset for unraveling mechanisms underlying AD progression.},
}

*Alzheimer Disease/diagnostic imaging/pathology
Humans
*Neuroimaging/methods
Disease Progression
Amyloid beta-Peptides/metabolism
Brain/diagnostic imaging/pathology
Biomarkers

@article {pmid42310475,
year = {2026},
author = {Askari, P and Dashtbin, S and Navidifar, T and Dadgar-Zankbar, L and Asadi, A and Ghamari, M and Najafi, P and Alamdary, SZ and Afifirad, R and Ghanavati, R and Darbandi, A},
title = {Fecal Microbiome Alterations in Colorectal Cancer: A Systematic Review of Compositional Changes and Microbial Biomarkers.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70326},
pmid = {42310475},
issn = {2045-8827},
support = {401087//Behbahan Faculty of Medical Sciences/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology/diagnosis ; *Feces/microbiology ; *Gastrointestinal Microbiome ; *Biomarkers, Tumor ; *Bacteria/classification/isolation & purification/genetics ; },
abstract = {Colorectal cancer (CRC) is one of the most common types of cancer worldwide, and the gut microbiome plays a crucial role in its development. In the study, we examine the variation in gut microbial community composition among individuals diagnosed with CRC based on human fecal samples. A systematic search of online databases, including MEDLINE (PubMed), Web of Science, Embase, and Scopus up to March 2026, following the requirements outlined in the PRISMA guideline. The search strategy was based on a combination of keywords, including "colorectal cancer," "gut microbiome", and "feces." The study analyzed 43 research articles on colorectal cancer microbiome. Most investigations utilized culture-independent techniques, revealing variations in microbial profiles between colorectal cancer cases and healthy controls. Fusobacterium and Porphyromonas emerged as potential colorectal cancer biomarkers, while multi-bacteria predictive models showed promise in enhancing colorectal cancer detection sensitivity and specificity. In this review, we will explore how advanced sequencing techniques have the potential to complement current non-invasive methods for early diagnosis and prevention of colorectal cancer. This includes conducting studies with robust statistical power and consistent, replicable methodologies, taking into consideration host factors, and performing external validation of predictive models.},
}

Humans
*Colorectal Neoplasms/microbiology/diagnosis
*Feces/microbiology
*Gastrointestinal Microbiome
*Biomarkers, Tumor
*Bacteria/classification/isolation & purification/genetics

@article {pmid42310522,
year = {2026},
author = {Rutkowska, N and Sekuła, B and Marchut-Mikołajczyk, O},
title = {Mining the Galium aparine L. microbiome: genome-guided discovery and experimental validation of metallophore-producing endophytic bacteria.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13037-7},
pmid = {42310522},
issn = {1471-2164},
support = {W5/FU2N/02/2024//Lodz University of Technology/ ; },
abstract = {BACKGROUND: Environmental pollution resulting from heavy metals constitutes a critical global issue. Remediation technologies offer potential solutions, particularly through the innovative use of endophytic microbes, either independently or in conjunction with plants. This solution is based on the ability of certain endophytic bacteria to produce metallophores, which are low-molecular-weight compounds capable of chelating various heavy metals.

METHODS: This study investigates ten bacterial endophytes isolated from the medicinal plant Galium aparine L. belonging to the Bacillus, Priestia, and Peribacillus genera. We tested different media to efficiently induce their production and assessed their ability to chelate various heavy metals, including highly toxic Pb[2+], Cd[2+] and Hg[2+]. Moreover, we examined in detail of their metallophore gene clusters, their organization, diversity and prevalence, by broad homology search.

RESULTS: All strains exhibited moderate to high metallophore production ability, with few strains capable of chelating more metals than iron. Among them, Priestia sp. GS2 was identified as promising producer, reaching up to 60% SU, with binding activity also towards Co[2+], Mn[2+], Zn[2+], Ni[2+] or Cu[2+]. Also, Peribacillus frigoritolerans GR2 exhibits a remarkable ability to chelate Pb[2+], Hg[2+] and Cd[2+]. An in-depth analysis of the biosynthetic gene clusters and enzymes involved in metallophore biosynthesis revealed homologous clusters within previously deposited genomes, highlighting their distribution and potential evolutionary conservation.

CONCLUSIONS: The strains demonstrated capacity for metallophore production and heavy metal chelation, which makes them promising candidates for the development of advanced microbial solutions. A genome-guided selection approach can guide the selection of strains for agricultural applications, where they enhance plant nutrient uptake, suppress soil pathogens, and support sustainable fertilization strategies beyond sequestering crucial metals. Apart from agriculture, purified metallophores can aid bioremediation and mobilization of heavy metals from various environments and matrices.},
}

@article {pmid42310653,
year = {2026},
author = {Farhat, ES and Abd El Halim, AM and Elessawy, AF and Elhefny, RA and Ahmed, MI and Ahmed, AM and Fouad, SA},
title = {The bacteriology of bronchiectasis patients and relation to disease severity.},
journal = {BMC pulmonary medicine},
volume = {26},
number = {1},
pages = {},
pmid = {42310653},
issn = {1471-2466},
mesh = {Humans ; *Bronchiectasis/microbiology/physiopathology ; Severity of Illness Index ; Female ; Male ; Pseudomonas aeruginosa/isolation & purification ; Aged ; Middle Aged ; Pseudomonas Infections ; Klebsiella/isolation & purification ; *Bronchoalveolar Lavage Fluid/microbiology ; Staphylococcus aureus/isolation & purification ; Haemophilus influenzae/isolation & purification ; Spirometry ; Dyspnea ; Forced Expiratory Volume ; Cough ; },
abstract = {BACKGROUND: Bronchiectasis is a progressive pulmonary disease with repeated cough, expectoration and frequent respiratory infections. Every patient should have sample collected for routine bacteriological culture. Determining the disease's severity can help with therapy and follow-up choices.

AIM OF THE STUDY: To detect the bacteriology of bronchiectasis patients and relation to disease severity.

RESULTS: 60 patients with bronchiectasis exacerbation were investigated at chest department of Fayoum University Hospital. Broncho alveolar lavage for culture and sensitivity was done. Disease severity was assessed by cough score, mMRC dyspnea score, oxygen saturation, no of lobes affected in CT chest and modified rieff score, Spirometry and classification of severity by FEV1, and finally FACED and BSI scores were calculated. Isolation of H.Influenza represents 40%, Pseudomonas represents 26.7%, Klebsiella represents 20%, Staph aureus represents 10% and Pseudomonas& Klebsiella represent 3.3%. There was a statistically significant lower mean of oxygen saturation in cases infected with both pseudomonas and Klebsiella. There was a statistically significant high percentage of mild Modified Reiff score among cases infected with H. influenza, moderate degree among cases infected with Klebsiella, but severe degree among cases infected with pseudomonas.

CONCLUSION: H. influenzae consider as a major pathogen isolated by BAL culture in patients with bronchiectasis exacerbation, followed by P. aeruginosa, then klebsiella then S. aureus. Cases infected with P. aeruginosa and klebsiella have the worst oxygen saturation. The highest modified Rieff score was in P. aeruginosa than other isolated organisms.},
}

Humans
*Bronchiectasis/microbiology/physiopathology
Severity of Illness Index
Female
Male
Pseudomonas aeruginosa/isolation & purification
Aged
Middle Aged
Pseudomonas Infections
Klebsiella/isolation & purification
*Bronchoalveolar Lavage Fluid/microbiology
Staphylococcus aureus/isolation & purification
Haemophilus influenzae/isolation & purification
Spirometry
Dyspnea
Forced Expiratory Volume
Cough

@article {pmid42310720,
year = {2026},
author = {Nabeshima, K and Onuma, M},
title = {Winter migratory birds may carry diverse antimicrobial resistance genes into Japan.},
journal = {One health outlook},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42522-026-00223-6},
pmid = {42310720},
issn = {2524-4655},
abstract = {BACKGROUND: Environmental surveillance of antimicrobial resistance (AMR) in wildlife remains limited, despite increasing recognition that resistance determinants can circulate across human, livestock, and natural ecosystems. Migratory waterbirds move long distances and aggregate at shared stopover and wintering sites, potentially facilitating the acquisition and redistribution of antimicrobial resistance genes (ARGs) across regions. However, nationwide evidence describing the breadth of ARGs carried by winter migratory birds in Japan is scarce. We assessed the diversity and distribution of ARGs in pooled fecal samples from winter migratory birds across Japan.

METHODS: We analyzed pooled fecal DNA collected at migratory bird habitats across 12 local governments during the 2021-2022 and 2022-2023 winter seasons (24 pools). Avian host origin was inferred by DNA metabarcoding, and ARGs were profiled by probe-based target enrichment with read-based detection (ARG detected at ≥ 10 reads).

RESULTS: Ducks (Anas spp. and Mareca spp.) were the predominant inferred hosts. ARGs were detected in all areas and included genes associated with resistance to multiple antibiotic classes used in livestock production. Across the two seasons, genes associated with resistance to gentamicin, cephalosporins, macrolides, tetracyclines, fosfomycin, clindamycin, penicillins, streptogramins, sulfonamides/trimethoprim, colistin, erythromycin, chloramphenicol, rifampicin, and isoniazid were detected in all 12 areas in at least one season. Genes associated with resistance to agents restricted for use in Japanese livestock production, including colistin, erythromycin, chloramphenicol, and rifampicin, were also detected in all 24 pools. Isoniazid-, gentamicin-, meropenem-, and tigecycline-associated genes were detected in 23/24, 20/24, 11/24, and 9/24 pools, respectively.

CONCLUSIONS: These data indicate widespread environmental occurrence of diverse ARGs and support the possibility that migratory birds could contribute to long-distance dispersal of ARGs. Culture-based isolation, phenotypic testing, and quantitative analyses will be needed to identify host bacteria and assess clinical relevance.},
}

@article {pmid42310809,
year = {2026},
author = {Zhu, F and Ying, H and Siadat, SD and Fateh, A},
title = {Retraction Note: The gut-lung axis and microbiome dysbiosis in non-tuberculous mycobacterial infections: immune mechanisms, clinical implications, and therapeutic frontiers.},
journal = {Gut pathogens},
volume = {18},
number = {1},
pages = {},
doi = {10.1186/s13099-026-00856-y},
pmid = {42310809},
issn = {1757-4749},
}

@article {pmid42311204,
year = {2026},
author = {Harden, M and Koos, DS and Arzuyan, K and Kovalev, M and Lansford, R and Alberto, F and Nuzhdin, S},
title = {Heat stress induces organelle alterations in Macrocystis pyrifera gametophytes.},
journal = {Journal of phycology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpy.70196},
pmid = {42311204},
issn = {1529-8817},
support = {GR1022773//Advanced Research Project Agency - Energy/ ; GR1063448//The Builders Initiative, Research and restoration of Giant kelp at Catalina/ ; },
abstract = {Kelp, brown macroalgae in the order Laminariales, provide ecosystem services vital to ocean biodiversity. However, kelp forests worldwide are declining due to abiotic stressors such as ocean warming. In this study, we present results from high-resolution confocal microscopy and in vivo imaging system imaging using protocols developed to visualize kelp gametophyte cells exposed to heat-stress treatments. Imaging revealed chloroplast mislocalization, fragmentation, and subsequent loss of chloroplasts in heat-stressed gametophyte cells. Additionally, nuclei exhibited fragmentation and a progressive loss of fluorescent signal, and the associated microbiome proliferated under various heat-stress treatments. Notably, because brown algae possess a continuous outer membrane that connects the nuclear envelope and the chloroplast envelope, these observations suggest a cellular vulnerability underlying thermal sensitivity in brown macroalgae. Finally, by comparing heat-stress tolerant and heat-stress sensitive genotypes, we found that genotypes with higher heat tolerance exhibited substantially fewer abnormalities compared to sensitive ones.},
}

@article {pmid42311375,
year = {2026},
author = {Gehlot, P and Yadav, J and Jain, T},
title = {Qualitative and quantitative evaluation of phosphate-solubilizing ability of Lysinibacillus macroides: a climate-resilient biofertilizer candidate for sustainable crop nutrition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1849362},
pmid = {42311375},
issn = {1664-302X},
abstract = {Phosphorus (P) is a critical macronutrient governing plant productivity, however its bioavailability in agricultural soils remains severely constrained due to fixation in insoluble mineral complexes, particularly calcium-bound phosphates in alkaline systems. The low use efficiency of chemical fertilizers, coupled with escalating environmental concerns, necessitates biologically driven strategies for sustainable phosphorus management. In this study, rhizospheric bacteria associated with chili (Capsicum annuum L.) were systematically investigated to elucidate the phosphate-solubilizing potential of Lysinibacillus macroides, an underexplored spore-forming plant growth-promoting rhizobacterium (PGPR). A total of 23 isolates were characterized using integrated qualitative and quantitative assays. All isolates exhibited halo formation on Pikovskaya's agar (1.26-4.70 mm), while NBRIP broth analysis revealed substantial tricalcium phosphate solubilization, reaching up to 30.03 μg mL[-1]. This activity was consistently associated with pronounced acidification, with pH declining from 7.0 to 3.2-4.1, indicating an acidification-driven solubilization mechanism. A strong inverse correlation between soluble phosphate and pH (r = -0.91, p < 0.01), supported by multivariate analysis, suggests that phosphate mobilization is governed by metabolically regulated acidification dynamics, likely mediated through organic acid production and proton extrusion. Among the isolates, 2.B (L. macroides) and 4.1 (L. fusiformis) exhibited superior solubilization efficiency and were distinctly separated through clustering analysis. Functional validation through seed biopriming demonstrated significant enhancement in germination (96.66%) and Seedling Vigor Index (766.88), establishing a direct linkage between microbial phosphorus mobilization and early plant development. Lysinibacillus macroides maintained significant growth across a broad range of pH (4-10), temperature (15-45°C), and salinity (0.01-0.1% NaCl), demonstrating its inherent tolerance to multiple abiotic stresses and confirming its potential as a climate-resilient plant growth-promoting bacterium. This study provides a quantitative and multivariate demonstration of acidification-coupled phosphate solubilization in Lysinibacillus macroides, integrating biochemical, statistical, and plant-based validation to elucidate a consistent mechanism of phosphorus mobilization. Collectively, the findings establish L. macroides as a resilient biofertilizer candidate for enhancing phosphorus-use efficiency and sustainable nutrient management in chili and other crops.},
}

@article {pmid42311376,
year = {2026},
author = {Bachir, A and Altaie, AM and Bendardaf, R and Talaat, IM and Hamoudi, R},
title = {Microbial dysbiosis drives colorectal carcinogenesis via integrated inflammatory, metabolic, and biofilm pathways.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1795882},
pmid = {42311376},
issn = {1664-302X},
abstract = {Colorectal cancer (CRC) arises from a multifaceted interplay among the intestinal microbiota, chronic inflammation, and host genomic instability, with microbial dysbiosis serving as an active driver rather than a by-product of malignant transformation. Genotoxic Escherichia coli (colibactin-positive), enterotoxigenic Bacteroides fragilis, and Fusobacterium nucleatum contribute to distinct stages of CRC progression by engaging the DNA-damage response and activating β-catenin-dependent Wnt signaling and NF-κB/STAT3 transcriptional programs controlling pro-inflammatory (IL-6, IL-8), pro-survival (BCL-2, BCL-XL), and proliferative (MYC, CCND1) gene expression.. Here, we propose a tri-axial pathogenic framework in which (i) cyclic dinucleotide-mediated activation of the cGAS-STING pathway engages TBK1-IRF3 and NF-κB signaling, driving type I interferons (IFN-β) and pro-inflammatory cytokines (IL-6, TNF-α) that couple microbial genotoxic stress to innate inflammation; (ii) altered microbial metabolites, including indoles and bile acids, reprogram AhR and FXR/TGR5 signaling; and (iii) crypt-anchored biofilms spatially amplify IL-6 leading to activation of STAT3, epigenetic silencing of tumor suppressors, and immune evasion. This review critically synthesizes current evidence supporting these axes and maps them onto CRC molecular subsets and tumor location. Recognition of these integrated microbial-host circuits identifies mechanistically grounded candidates for biomarker development, microbiome-based diagnostics, and targeted interventions to restore microbial and immune equilibrium, thereby providing a refined framework for the molecular classification and precision management of CRC.},
}

@article {pmid42311381,
year = {2026},
author = {Amso, D and Fahur Bottino, G and Forest, TT and Bonham, KS and Zieff, MR and Patel, F and Miles, M and Herr, D and , and Espinoza-Heredia, C and D'Amato, CL and Ren, J and Gladstone, M and Mbale, E and Alexander, DC and Jones, DK and Williams, SCR and Fifer, WP and Gabard-Durnam, LJ and Donald, KA and Klepac-Ceraj, V},
title = {Microbiome-behavior coupling shapes infant adaptation to early maternal unpredictability.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1830339},
pmid = {42311381},
issn = {1664-302X},
abstract = {How do some human infants adapt to environmental challenges while others do not? We examined whether infant behavioral responses to maternal unpredictability predict early inhibitory control and are linked to gut microbial community composition and neuroactive metabolic potential. Maternal unpredictability, quantified as the entropy of sensory signal transitions during mother-infant interaction (N = 255; 2-6 months), predicted poorer infant inhibitory control at 19-28 months. However, infants who exhibited high visual orienting behavior (VOB) under high unpredictability showed later inhibitory control comparable to infants exposed to low unpredictability, suggesting an adaptive behavioral buffering strategy. In a subset of infants (n = 87), we tested whether infant age, sex, delivery mode, feeding, maternal education, and maternal unpredictability explained variation in gut microbial community diversity. Only feeding status and VOB were significantly associated with both taxonomic and functional microbial profiles. VOB was associated with taxonomic and functional variation along a Bifidobacterium breve and Bifidobacterium longum axis and enrichment of microbial tryptophan and glutamate synthesis genes. Although feeding groups differed in alpha diversity, VOB was not associated with feeding status, suggesting that feeding is not the primary driver of the observed VOB-microbiome signatures. Interaction models of neuroactive gene functions revealed that microbial signatures vary across combinations of VOB and maternal unpredictability, suggesting that the microbial support for deploying visual attentional strategies differs under distinct levels of environmental unpredictability. Together, these findings support a framework in which infant behavioral strategy is associated with variation in gut microbial composition and metabolic gene potential.},
}

@article {pmid42311385,
year = {2026},
author = {Sun, M and Li, D and Wang, L and He, Y and Hu, Y and Yang, M and Luo, Z and Miao, X and Yu, S and Hua, M and Niu, H and Wang, J},
title = {The selenium-enriched Rhodotorula mucilaginosa JAASRY1 improved oxidative stress during the aging process via the gut-liver-brain axis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1809542},
pmid = {42311385},
issn = {1664-302X},
abstract = {BACKGROUND: Oxidative stress, induced by the aging process, has been demonstrated to engender a variety of deleterious effects on the organism. The effectiveness of selenium-enriched Rhodotorula mucilaginosa remains unproven.

METHODS: In this study, selenium-enriched Rhodotorula mucilaginosa JAASRY1 (Se-RMSRY) was comprehensively characterized. Scanning electron microscopy coupled with energy-dispersive X-ray spectroscopy was employed to analyze its morphology and the elemental distribution of selenium. Furthermore, the specific chemical forms of biogenic selenium in Se-RMSRY were identified and quantified using high-performance liquid chromatography-inductively coupled plasma mass spectrometry. The potential of Se-RMSRY to exert antioxidant mechanisms for anti-aging effects was then systematically elucidated. Animal behavioral tests demonstrated behavioral differences induced by Se-RMSRY, thereby evaluating the improvement in aging phenotypes. Histopathological analysis of the hippocampus, liver, and intestine was performed to examine structural integrity and pathological changes. Intracellular reactive oxygen species (ROS) levels were detected using fluorescence-based assays to confirm oxidative stress mitigation. Western blotting was employed to validate the expression of aging-related proteins. Additionally, gut microbiome analysis via 16S rRNA sequencing was carried out to explore the composition and diversity of gut microbiota, thereby uncovering potential links between antioxidant activity and gut health in the anti-aging process.

RESULTS: The results showed that selenomethionine (SeMet) was the predominant bioselenium composition of Se-RMSRY, with a concentration of 1213.16 mg/kg. Furthermore, Se-RMSRY significantly enhanced intestinal homeostasis by enriching beneficial Lactobacillus sp. populations and reprogramming microbial metabolism toward carbohydrate utilization while suppressing amino acid metabolism in aging mice (p < 0.05). Systemic antioxidant capacity was augmented via coordinated activation of the Nrf2/NQO1/HO-1 signaling pathway and glutathione metabolism, with concomitant reductions in hepatic and intestinal oxidative stress markers (p < 0.05). The intervention attenuated apoptosis through Bcl-2/Bax pathway modulation and improved gut barrier integrity (p < 0.05), while hippocampal CA1 neuronal preservation correlated with reduced anxiety-like behaviors and enhanced cognitive performance (p < 0.05).

CONCLUSION: These findings establish Se-RMSRY as a promising dietary intervention against age-related pathologies through gut-microbiota-organ axis regulation, thereby addressing the previously unproven efficacy of Se-RMSRY in counteracting aging-related oxidative stress.},
}

@article {pmid42311552,
year = {2026},
author = {Velasco, AJ and Dalmacio, LM},
title = {COVID-19 Infection and Gut Microbial Dysbiosis Among Filipinos with Type 2 Diabetes Mellitus.},
journal = {Journal of the ASEAN Federation of Endocrine Societies},
volume = {41},
number = {1},
pages = {72-81},
pmid = {42311552},
issn = {2308-118X},
mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology/microbiology/complications ; *Dysbiosis/epidemiology/microbiology ; *COVID-19/epidemiology/complications ; *Gastrointestinal Microbiome ; Male ; Female ; Middle Aged ; Adult ; SARS-CoV-2 ; RNA, Ribosomal, 16S ; Feces/microbiology ; },
abstract = {BACKGROUND: Both type 2 diabetes mellitus (T2DM) and COVID-19 are associated with gut microbial alterations. It remains unclear whether COVID-19 causes further gut dysbiosis among individuals with T2DM.

OBJECTIVE: This study aimed to characterize the gut microbiome of Filipinos with T2DM who had COVID-19.

METHODOLOGY: 101 Filipinos, aged 30-59, residing in the Greater Manila Area, were recruited into one of four groups: non-COVID/non-T2DM (A), COVID-recovered/non-T2DM (B), non-COVID/T2DM (C), and COVID-recovered/T2DM (D). Gut microbial composition was characterized through 16S rRNA gene profiling of stool samples using Illumina MiSeq-nextgeneration Sequencing. These sequences were subjected to mothur and PICRUSt2 for taxonomic and functional analyses.

RESULTS: Gut microbial analysis revealed potential disease biomarkers, as Roseburia is more abundant among participants with COVID-19 history, while Parabacteroides is more abundant among participants with T2DM. Principal coordinate analysis (PCOA) revealed that participants with T2DM clustered together, while participants without T2DM displayed significantly different clustering.

CONCLUSION: These findings suggest that COVID-19 does not cause further gut dysbiosis among individuals with T2DM and that T2DM exerts a stronger influence on the gut microbiome compared to COVID-19. These findings are useful for clinicians to better understand the COVID-19 risk to T2DM.},
}

Humans
*Diabetes Mellitus, Type 2/epidemiology/microbiology/complications
*Dysbiosis/epidemiology/microbiology
*COVID-19/epidemiology/complications
*Gastrointestinal Microbiome
Male
Female
Middle Aged
Adult
SARS-CoV-2
RNA, Ribosomal, 16S
Feces/microbiology

@article {pmid42311643,
year = {2026},
author = {Li, Y},
title = {Multimodal biomarker panel for early prediction of anastomotic leak after colorectal surgery: from inflammation to ischemia.},
journal = {Frontiers in surgery},
volume = {13},
number = {},
pages = {1809885},
pmid = {42311643},
issn = {2296-875X},
abstract = {Anastomotic leakage is one of the most serious complications following colorectal surgery, with an incidence ranging from 2% to 19%, and is closely associated with increased perioperative mortality, prolonged hospital stay, and poor oncological outcomes. Traditional clinical diagnosis relies on signs, symptoms, and imaging studies, which exhibit significant time delays. In recent years, researchers have explored early warning biomarkers from multiple perspectives including inflammatory response, tissue ischemia, microbial changes, and extracellular matrix remodeling, accumulating abundant research data. This article systematically reviews the current application status of serum inflammatory markers, peritoneal drain fluid cytokines, ischemic metabolites, microbiome markers, and tissue repair-related molecules in predicting anastomotic leakage, with emphasis on analyzing the diagnostic performance, optimal detection time windows, and clinical operability of various biomarker categories. Based on this foundation, we propose a multimodal prediction framework integrating four dimensions of "inflammation-ischemia-microbiome-tissue repair" and discuss the challenges in translating this framework into clinical decision-making tools. Machine learning algorithms demonstrate application potential in integrating multi-source heterogeneous data, but insufficient external validation remains the primary bottleneck constraining clinical implementation. Future research directions should focus on large-scale multicenter prospective cohort validation, establishment of standardized detection protocols, and development of implantable real-time monitoring technologies.},
}

@article {pmid42312024,
year = {2026},
author = {Liu, Z and Mao, Y and Zhang, L and Wang, B and Tian, J and Li, Y and Li, S and He, Y and Zeng, M and Meng, P and Song, H},
title = {Association between oral microbiome alpha and beta diversity and MASLD risk: a large-scale, population-based retrospective study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1784034},
pmid = {42312024},
issn = {2235-2988},
mesh = {Humans ; Female ; RNA, Ribosomal, 16S/genetics ; Retrospective Studies ; *Microbiota ; Male ; Adult ; Middle Aged ; *Mouth/microbiology ; *Fatty Liver/epidemiology/microbiology ; Phylogeny ; Nutrition Surveys ; Bacteria/classification/genetics ; Biodiversity ; Risk Factors ; Young Adult ; United States/epidemiology ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the most common chronic liver disease globally, yet its pathogenesis remains incompletely understood. The "oral-gut-liver axis" hypothesis suggests that oral microbiota may influence liver metabolism through direct or indirect pathways; however, large-scale population-based evidence is still limited.

METHODS: Data from the 2009 to 2012 National Health and Nutrition Examination Survey (NHANES) included 2,759 U.S. adults aged ≥ 20 years. MASLD was defined using a U.S. Fatty Liver Index score ≥ 30. Oral rinse samples were sequenced targeting the 16S rRNA V4 region to evaluate alpha diversity (Observed OTUs, Faith's Phylogenetic Diversity, Shannon-Wiener Index, and Inverse Simpson Index) and beta diversity (Bray-Curtis dissimilarity and UniFrac distance). Survey-weighted multivariable logistic regression models with sequential adjustment for demographic, lifestyle, and clinical metabolic covariates evaluated the association between oral microbial diversity and MASLD. Analyses were stratified by body mass index and smoking status.

RESULTS: The final analysis included 2,759 adults, of whom 183 individuals had MASLD. Oral microbial richness and diversity were significantly lower in individuals with MASLD. Multivariable analyses demonstrated a strong inverse association between oral microbial diversity and MASLD risk: Each increase in diversity was associated with a substantially reduced likelihood of MASLD. A clear dose-response relationship was observed, with individuals in the highest bacterial diversity group having a 65% lower risk than those in the lowest group. This association remained significant after adjusting for age, body weight, and diabetes. Stratified analysis revealed that the association was consistent across different body weight groups but was modified by smoking status. Finally, we identified that the overall makeup of the bacterial communities in the mouth was distinctly different between individuals with and without MASLD.

CONCLUSION: This study demonstrates the association between oral bacteria and liver disorders. We found that lower diversity of oral microbes is independently correlated with a higher risk of disease, even after accounting for factors such as weight and blood sugar. The protective role of a diverse oral microbiome can be reduced by smoking and increased body weight. These findings establish the oral microbiome as a new and independent factor in liver health.},
}

Humans
Female
RNA, Ribosomal, 16S/genetics
Retrospective Studies
*Microbiota
Male
Adult
Middle Aged
*Mouth/microbiology
*Fatty Liver/epidemiology/microbiology
Phylogeny
Nutrition Surveys
Bacteria/classification/genetics
Biodiversity
Risk Factors
Young Adult
United States/epidemiology

@article {pmid42312035,
year = {2026},
author = {Radzieta, M and Malone, M and Schwarzer, S and Bergamin, E and Whitely, G and Jensen, S},
title = {Anaerobe-associated microbial shifts at infection onset in diabetes-related foot ulcers revealed by longitudinal metagenomics.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1812721},
pmid = {42312035},
issn = {2235-2988},
mesh = {Humans ; *Diabetic Foot/microbiology ; *Metagenomics/methods ; *Bacteria, Anaerobic/classification/genetics/isolation & purification ; *Microbiota ; Longitudinal Studies ; Male ; Female ; Aged ; Middle Aged ; Metagenome ; },
abstract = {INTRODUCTION: Diabetes-related foot infections (DRFIs) are a major cause of hospitalisation and carry a significantly increased risk of lower extremity amputation. To date there is a lack of longitudinal studies examining within-patient microbiome dynamics during the transition from non-infected to infected diabetes-related foot ulcers (DRFUs).

METHODS: We used shotgun metagenomic sequencing to longitudinally profile the wound microbiome of 6 patients with DRFUs who developed clinical infections, utilising taxonomic profiling, metagenome assembly and binning and strain level analysis to characterise within-patient microbial shifts.

RESULTS: DRFUs with no signs of clinical infection were colonised by virulent pathogens including Staphylococcus aureus, Streptococcus agalactiae, Enterococcus faecalis, Enterobacter hormaechei and Pseudomonas aeruginosa. In most patients, infection onset was associated with a decrease in pathogen abundance and a significant increase in obligate anaerobes including Prevotella spp, Peptoniphilus spp, Porphyromonas spp and Anaerococcus spp.

CONCLUSION: These findings highlight the potential importance of anaerobes and hypoxia in DRFIs and may support monitoring of tissue oxygen saturation as a predictor of infection onset.},
}

Humans
*Diabetic Foot/microbiology
*Metagenomics/methods
*Bacteria, Anaerobic/classification/genetics/isolation & purification
*Microbiota
Longitudinal Studies
Male
Female
Aged
Middle Aged
Metagenome

@article {pmid42312182,
year = {2026},
author = {Wang, Z and Zhu, Y and Liu, X and Li, Z and Bai, J and Zou, M and Zhang, C and Liu, Y and Li, F and He, K},
title = {iSymBase: an integrative functional-genomic platform for ecological exploration of insect symbionts.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag128},
pmid = {42312182},
issn = {2730-6151},
abstract = {Insect symbionts play essential roles in host biology, influencing nutrition, immunity, reproduction, and environmental adaptation, ultimately shaping insect physiology, ecology, and evolution. With the rapid growth of functional and genomic datasets on insect symbionts, there remains a critical need for a dedicated platform to systematically compile, organize, and analyze these datasets from an integrative ecological perspective. Here, we developed an insect Symbiont database, named as iSymBase, by manually curating functional records and genomic datasets of insect symbionts from published academic literature. Currently, iSymBase contains over 2657 insect symbiont functional records spanning 795 host species, along with 1494 metagenomes, 14 992 amplicon datasets, and standardized genome and gene catalogs, providing a comprehensive resource for ecological and comparative insect symbiont researches. iSymBase offers standardized query functionalities, such as data browsing, keyword associative search, sequence alignment, data download, and submission. Beyond conventional database functionalities, iSymBase provides several innovative tools: insect-symbiont interaction network for host-symbiont ecological relationships, a batch annotation tool for detecting ecologically functional symbionts from microbiome profiles, and an artificial intelligence (AI)-powered chatbot iSymSeek designed to assist researchers with related knowledge queries. Taken together, iSymBase will serve as an open-access and continually updated platform for storing, querying, and analyzing insect symbiont data, supporting ecological exploration of host-symbiont interactions, symbiont functional diversity, and microbiome-driven adaptation. Database URL: http://symbiont.insect-genome.com/.},
}

@article {pmid42312183,
year = {2026},
author = {Zheng, YL and Guo, YS and Ren, XY and Wang, YF and Cui, HL and Zhang, LM and Ding, LJ and Zhu, YG},
title = {Unveiling the role of soil microorganisms in indicating paddy soil health via metagenomics combined with machine learning.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag133},
pmid = {42312183},
issn = {2730-6151},
abstract = {The soil microbiome performs various ecological functions, making it a potentially vital component of soil health assessment; however, the indicator taxa of soil health remain unidentified. This study explored these taxa in paddy soils of the black soil region in Northeast China. First, the soil health index (SHI) was evaluated using representative physicochemical and biological parameters, revealing that approximately one-third of the soils had a low health level. A Random Forest model was then developed based on microbial species' relative abundance to predict the SHI, achieving an R [2] value greater than 0.6. Based on the SHapley Additive exPlanations values of this model, 40 microbial species were identified as potential indicator taxa of soil health, with 39 of these taxa occurring in more than 50% of the samples. Specifically, paddy soils with more abundant carbon (C)- and nitrogen (N)-fixing bacteria exhibited higher soil organic matter and total N contents, along with higher health levels. Conversely, soils rich in denitrifying bacteria exhibited lower SHI values because of increased N loss. Furthermore, C-fixing, N-fixing, and denitrifying genes showed functional relationships with the corresponding soil properties and SHI. In addition, halophilic, halotolerant, and eutrophic bacteria indicated soil health by reflecting salinity and nutrient status. The potential of these indicator taxa was validated at multidecadal and regional spatial scales. These results highlight the practical value of such indicator taxa, which elucidate the ecological processes associated with soil health and respond predictably to changes in soil health, thereby serving as rapid diagnostic tools for assessing soil health.},
}

@article {pmid42312184,
year = {2026},
author = {Millar, ME and Abele, M and Harris, HC and Koev, TT and Telatin, A and Kiu, R and Van Sinderen, D and Khimyak, YZ and Ludwig, C and Hall, LJ and Warren, FJ},
title = {Bifidobacterial genes upregulated by resistant starch investigated using multi-omics have orthologs in infant gut isolates.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag136},
pmid = {42312184},
issn = {2730-6151},
abstract = {Bifidobacterium species and strains are key members of the human gut microbiota, appearing soon after birth and persisting into adulthood. Resistant starch is an important dietary substrate for adult-associated bifidobacteria, where its fermentation supports host health. However, less is known about how different starch structures interact with bifidobacteria. Here we show that growth kinetics and gene expression differ depending on starch structure. Using detailed growth assays, genomics, and metabolomic analyses, bifidobacterial starch hydrolysis capabilities were closely associated with their CAZyme profiles. In one isolate of Bifidobacterium globosum, we identified a gene cluster encoding three multi-functional amylase enzymes complemented by several starch-binding modules, the genes and proteins of which were significantly upregulated in response to starch. Homologs of genes in the cluster were found in the genomes of bifidobacterial isolates from weaning infants providing insights into their role in the maturation process of the microbiota. Uncovering mechanisms of metabolic interaction between starch structures and bifidobacteria underscores the importance of this ecological function and potential health implications.},
}

@article {pmid42312244,
year = {2026},
author = {Heidrich, V and Fackelmann, G and Ricci, L and Spadazzi, R and Baldanzi, G and Punčochář, M and Catassi, G and Marchi, P and Modesto, M and Piccinno, G and Porcari, S and Rondinella, D and Asnicar, F and Valles-Colomer, M and Mattarelli, P and Ianiro, G and Segata, N},
title = {Strain transmission links human microbiomes along the oral-gut axis and across cohabiting individuals.},
journal = {Cell press blue},
volume = {1},
number = {3},
pages = {None},
pmid = {42312244},
issn = {3051-3839},
abstract = {Interpersonal strain transmission shapes the human microbiome, yet a comparative understanding of the transmission dynamics across body sites is lacking. We analyzed 1,644 paired oral and fecal metagenomes to investigate microbiome transmission among healthy cohabitants and intra-individual oral-gut overlap. Cohabitants shared significantly more oral and gut strains than non-cohabitants. Romantic partners exhibited the highest oral strain-sharing rates, exceeding their gut strain sharing. Higher oral transmissibility was associated with increased longitudinal strain replacement, while the most transmissible gut species were linked to poorer cardiometabolic health. Within individuals, 74.5% of cases of species detected in both sites involved the same strains, primarily related to abundant oral species such as Streptococcus salivarius, suggesting saliva-mediated transmission. Conversely, Bifidobacterium longum strains never overlapped between sites, with the recently proposed B. longum subsp. nexti uniquely colonizing the oral cavity. These findings extend our understanding of microbiome spread and its potential consequences for human health.},
}

@article {pmid42312840,
year = {2026},
author = {Peterson, LF and Wang, J and Gow, NAR and LeibundGut-Landmann, S and Brewer, MG},
title = {Influence of fungi on epithelial homeostasis and role in inflammatory diseases.},
journal = {Clinical microbiology reviews},
volume = {},
number = {},
pages = {e0031925},
doi = {10.1128/cmr.00319-25},
pmid = {42312840},
issn = {1098-6618},
abstract = {SUMMARYThe skin harbors a diverse fungal community that contributes to both epidermal homeostasis and inflammatory disease. Historically, studies of cutaneous fungi focused primarily on opportunistic infections in immunocompromised hosts. Advances in sequencing technologies and metagenomic analyses have revealed that commensal yeasts of the skin microbiome likely influence host physiology and cutaneous disease severity. In this review, we summarize the current knowledge of host-fungal interactions at the skin epithelium, with particular emphasis on the yeast genera Malassezia and Candida. We discuss how fungal colonization shapes epidermal biology through direct interactions with keratinocytes and immune cells, highlighting fungal virulence factors such as secreted proteases and candidalysin, as well as host-sensing pathways. We further examine how these interactions contribute to inflammatory skin diseases, particularly atopic dermatitis and psoriasis, and how fungi participate in polymicrobial networks with bacteria and viruses to alter susceptibility to infection. Finally, we discuss how emerging therapeutic strategies change the fungal composition on skin. These advances suggest the importance of fungi as active regulators of skin immunity and emphasize key knowledge gaps that need to be addressed in future studies to better understand how they contribute to cutaneous diseases.},
}

@article {pmid42312855,
year = {2026},
author = {Lim, SJ and Thompson, LR and Goodwin, K},
title = {Metagenomic analysis of water column samples collected from Green Canyon 233 prior to the Deepwater Horizon incident.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0079926},
doi = {10.1128/aem.00799-26},
pmid = {42312855},
issn = {1098-5336},
abstract = {UNLABELLED: The Gulf of Mexico/Gulf of America provides ecosystem services derived from marine biodiversity and oil and gas resources. Threats posed by unintended releases of oil and gas can be attenuated by microbial processes, necessitating the documentation of baseline microbial diversity to better understand spill dynamics and to inform bioremediation strategies. Here, we analyze metagenomic sequencing of 10 water column samples collected from the Green Canyon 233 (GC233) lease block near the mussel-fringed brine lake, Brine Pool NR-1. Bioinformatics processing produced 60 bacterial metagenome-assembled genomes (MAGs), 11 archaeal MAGs, 149 microbial taxa predicted from assembled full-length small subunit (SSU) rRNA genes, and 389 microbial genera predicted from single-copy marker genes. Abundant taxa classified from these analyses included archaeal Nitrosopumilaceae, Nitrosopelagicus, and Thalassarchaeaceae and the bacterial taxa Pelagibacteraceae and SAR324. The MAGs revealed genes that degrade gaseous and non-gaseous hydrocarbons, including methane, other alkanes, and aromatic compounds. These samples were collected in 2009, fortuitously prior to the 2010 Deepwater Horizon (DWH) oil spill. Therefore, we searched for members of the rare biosphere that dominated the DWH plume during the early phase of microbial succession. Sequences related to Bermanella spp. were not detected initially. The search was expanded by mapping reads from ours and an additional 55 metagenomic libraries to two Bermanella MAGs. Read recruitment to Bermanella sp913054445 enriched in DWH plume samples was low (<1%) for our samples, those collected after the spill, and most experimental samples compared to samples collected outside (3%) and inside the DWH plume (19%-23%) during the spill.

IMPORTANCE: Microbes execute oil spill biodegradation through complex interactions involving whole microbiome communities by harnessing genes distributed across multiple taxa. Therefore, metagenomic data sets provide taxonomic and functional annotations to aid in understanding spill dynamics. Although the Deepwater Horizon oil spill provided opportunities to observe ecosystem recovery, data about the microbiome prior to the spill are scarce and limited to amplicon sequencing. Our metagenomic libraries, although not derived from the same lease block as the blowout, contribute linkages between microbial taxonomy and function in an area of active oil and gas production. This analysis can aid microbial indicator development, machine learning, and modeling efforts to bioremediate hydrocarbon influxes in marine environments.},
}

@article {pmid42312862,
year = {2026},
author = {Gracia, L and Hughes, ER and Middleton, DR and Mueller, KD and Portillo, JA and Sharma, A and Davey, L and Panzetta, ME and Chanin, RB and Bhatt, AS and Valdivia, RH},
title = {A phase-variable capsule facilitates Akkermansia muciniphila colonization of the intestinal mucus layer.},
journal = {mBio},
volume = {},
number = {},
pages = {e0104826},
doi = {10.1128/mbio.01048-26},
pmid = {42312862},
issn = {2150-7511},
abstract = {UNLABELLED: Akkermansia muciniphila is a mucophilic commensal bacterium that significantly impacts metabolic and immune homeostasis. However, the bacterial factors involved in colonization of the gastrointestinal tract are not well understood. Here, we clarify the role of capsular polysaccharides (CPS) in Akkermansia (Akk) colonization. We show that Akkermansia species have multiple cps loci, with cps1 being the most conserved across species. We find that cps1 is regulated by phase variation via invertible genetic elements, leading to population diversity during growth in culture media, mice, and humans. An A. muciniphila mutant that cannot produce capsular polysaccharides successfully colonized the intestines of mice but showed a reduced ability to interact with the mucus layer. Additionally, this mutant tended to form biofilms and increased aggregation on abiotic surfaces and within the gastrointestinal lumen. Our findings suggest that the A. muciniphila capsule acts as a phase-variable regulator of colonization by balancing planktonic mucus-associated states and biofilm formation.

IMPORTANCE: Akkermansia muciniphila, a member of the human gut microbiota, is associated with improved metabolic and immune health. However, the bacterial factors that allow this organism to thrive in the intestine and interact with the host are not fully understood. We identify capsular polysaccharides as key regulators of A. muciniphila association with mucin-rich layers in the gastrointestinal tract and its proximity to the intestinal lining. Furthermore, capsule synthesis in Akkermansia is controlled by epigenetic switches; hence, a small but significant fraction of bacteria lack a capsule. These capsule-free bacteria cluster and are prone to forming biofilms. Therefore, capsular phase variation enables A. muciniphila to switch between different colonization states, underscoring the role of A. muciniphila glycans in adapting to the gut environment.},
}

@article {pmid42312893,
year = {2026},
author = {Zhang, X and Lu, B and Jin, LN and Yang, S and Ji, Y and Cao, K and Fan, C and Li, D and Chen, J},
title = {Crowded Public Spaces as Hotspots of Airborne Microbial Risk: A Population-Weighted Risk Assessment in Urban Environments.},
journal = {Environmental science & technology},
volume = {60},
number = {25},
pages = {17996-18010},
doi = {10.1021/acs.est.6c04000},
pmid = {42312893},
issn = {1520-5851},
mesh = {*Air Microbiology ; Risk Assessment ; Humans ; Cities ; Environmental Monitoring ; },
abstract = {Airborne pathogens and antimicrobial resistance (AMR) pose growing health risks in cities, where enclosed spaces, inadequate ventilation, and high population density enhance their persistence and dissemination. However, the microbial burden and risk associated with high-occupancy public spaces remain poorly quantified. Here, we compared bioaerosol characteristics across university cafeterias and a subway station, dry- and mixed-waste collection facilities (WCFs), and an urban air monitoring site by using culture-based, molecular, source-tracking, and risk-assessment approaches. The results showed that Crowded Public Spaces (CPSs) harbored culturable bacterial and AMR burdens comparable to those in WCFs, both far exceeding levels at the urban air monitoring site. Human-associated sources contributed to ∼50% of airborne bacteria, and multidrug-resistant isolates (∼60%), high-risk β-lactam ARGs, and clinically relevant pathogens were further enriched in CPSs. We further applied a population-weighted infection burden (PWIB) metric that integrates infection risk with pedestrian volume and dwell time. Although contamination levels in CPSs were similar to those in conventional microbial hotspots, CPSs contributed more to the city-scale infection burden once population exposure was taken into account. These findings reveal that urban airborne microbial risk is shaped not only by contamination intensity but also by human occupancy and exposure patterns. This study highlights the value of incorporating human activity into microbial risk assessment in high-density urban environments.},
}

*Air Microbiology
Risk Assessment
Humans
Cities
Environmental Monitoring

@article {pmid42313058,
year = {2026},
author = {Merkesvik, J and Lindstad, LJ and Umu, ÖCO and Sandholm, RM and La Rosa, SL and Hvidsten, TR and Pope, PB and Westereng, B},
title = {In vitro model reveals structural and metabolic insights into the porcine cecal microbiota in response to β-mannan exposure.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0014026},
doi = {10.1128/aem.00140-26},
pmid = {42313058},
issn = {1098-5336},
abstract = {UNLABELLED: The gastrointestinal microbiota plays a pivotal role in shaping host physiology and health. By selectively promoting bacteria associated with improved host health, microbiota-directed fibers offer a strategy to enhance the beneficial functions of the microbiota. In this work, we developed a pH-controlled in vitro fermentation system (InVitSim) as a model to evaluate the effects of such a fiber-acetylated galactoglucomannan from Norway spruce-on the composition and functionality of porcine cecal microbial communities. We validated the experimental outcomes by comparing the response of the in vitro model to a previous in vivo feeding trial utilizing the same β-mannan fibers. Long-read sequencing with Oxford Nanopore, metatranscriptomics, and short-chain fatty acid measurements were undertaken to survey microbial community dynamics and functionality. Microbial communities in pigs and InVitSim responded similarly to β-mannan supplementation, with taxa like Prevotella, Catenibacterium, and Faecalibacterium increasing in abundance. Intriguingly, some taxa were observed to be more affected by β-mannan supplementation in InVitSim than in vivo. These taxa included several bacterial species that were not previously known to utilize β-mannan, yet exhibited upregulated genes encoding carbohydrate-active enzymes involved in the degradation of this substrate.

IMPORTANCE: In this study, we establish a fermenter system able to preserve more than 70% of over 300 distinct microbial taxa identified in the porcine cecal gut. The in vitro model and the functional omic data generated from it enabled us to identify relevant microbial populations that responded to the presence of AcGGM by upregulating β-mannan-specific polysaccharide utilization loci. Our results highlight the value of in vitro approaches as a complementary tool to in vivo trials for learning about the gastrointestinal microbiome's response to dietary interventions on the host level.},
}

@article {pmid42313156,
year = {2026},
author = {Quintanilla, E and Salazar, J and van de Water, J and Madurell, T},
title = {Bacterial Microbiota Signatures Suggest Acclimation of the Gorgonian Leptogorgia sarmentosa to Highly Impacted Environments in the Mediterranean Sea.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02809-z},
pmid = {42313156},
issn = {1432-184X},
abstract = {Anthropogenic disturbances increasingly compromise marine environments, with severe consequences for vulnerable coral ecosystems. While global stressor impacts on stony corals are well-documented, the mechanisms by which local perturbations influence gorgonians remain poorly characterized. This limits our ability to predict the tolerance of temperate octocorals in human-dominated coastal landscapes. The Mediterranean gorgonian Leptogorgia sarmentosa is remarkably resilient, thriving in both marine protected areas (MPAs) and highly impacted urban habitats. To investigate the microbiota's role in this adaptability, we characterized the bacterial communities of L. sarmentosa from a protected site (Western Mediterranean) and an impacted seaport (Barcelona). For broader regional context, results were compared in parallel with a re-analysis of datasets from similarly contrasting Mediterranean sites (Cassis and La Spezia). Our results reveal distinct site-specific microbial signatures, but no differences in alpha diversity or dispersion between seaport and the MPA. However, significant compositional shifts occurred in the impacted Barcelona seaport, characterized by a reconfiguration of the dominant symbiont genus Endozoicomonas and an enrichment of Spongiibacteraceae_clade BD1-7. Similarly, Endozoicomonas strain abundances differed between Cassis and the high-runoff environment of La Spezia, which exhibited increased Mycoplasma abundance. Collectively, these findings suggest a high degree of microbiome flexibility. This microbiota plasticity, alongside predicted functional pathways, suggests a contribution to preserving and acquiring key holobiont functions, highlighting the capacity of L. sarmentosa to persist in disturbed habitats through strategic microbial reconfiguration. This study provides crucial insights into the mechanisms underlying coral acclimation; essential for developing conservation strategies and predicting the long-term viability of Mediterranean marine biodiversity.},
}

@article {pmid42313858,
year = {2026},
author = {Meijer, S and Hugerth, LW and Nouri, M and Erlandsson, L and Lavasani, S and Hansson, SR},
title = {Comparative analysis of gut microbiome alterations in early- and late-onset preeclampsia: A case control study.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0348943},
pmid = {42313858},
issn = {1932-6203},
mesh = {Humans ; Female ; Pregnancy ; *Pre-Eclampsia/microbiology ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Dysbiosis/microbiology ; Metagenomics ; Bacteria/classification/genetics ; },
abstract = {Preeclampsia (PE) is a complication during pregnancy characterized by hypertension, organ damage, and systemic inflammation. Increasing evidence suggests that the gut microbiome may play a role in the pathophysiology of PE. However, previous studies on the gut microbiome have generally overlooked the distinction between subgroups of PE, although clinical manifestations may differ. Also, most studies have not used deep sequencing techniques. Therefore, this study aimed to explore further potential differences in gut dysbiosis in different PE subgroups compared to controls using shotgun metagenomics. We studied the bacterial gut microbiome using shotgun metagenomic sequencing in 37 pregnant patients in the third trimester from a Swedish cohort, separating patients according to subtype (healthy controls N = 21, late-onset PE N = 8, early-onset PE N = 8). Differential relative abundances and alpha diversity were evaluated using Wilcoxon rank sum test, and beta diversity was evaluated using PERMANOVA. Multiple linear regression was used to study associations between gut microbiome composition differences and clinical parameters. Late-onset PE and early-onset PE were both associated with significantly different beta diversity compared to controls. Differences remained significant after adjusting for age, and were not affected by gestational age, BMI or parity. Alpha diversity was lower in late-onset PE compared to controls. While no significant differences in taxonomic abundances were seen after correcting for multiple testing, several interesting leads were identified, including a higher abundance of genus Blautia in late-onset PE, and lower abundance of Coprococcus catus and unclassified Lachnospiraceae in early-onset PE. Functional analysis did not reveal any significant differences after false discovery rate (FDR) correction. In conclusion, our results showed subgroup-specific gut microbiome differences in PE with more pronounced associations in late-onset PE, despite limited power due to the observational design and small cohort. Accordingly, our results highlight the importance of subgroup analysis when studying PE.},
}

Humans
Female
Pregnancy
*Pre-Eclampsia/microbiology
Case-Control Studies
*Gastrointestinal Microbiome
Adult
Dysbiosis/microbiology
Metagenomics
Bacteria/classification/genetics

@article {pmid42314194,
year = {2026},
author = {Lee, M and SoRelle, JA and Everest-Dass, A and Gerber, DE and von Itzstein, MS},
title = {Predictive Biomarkers for Immune Checkpoint Inhibitor Efficacy: Challenges, Innovations, and a Pathway to Precision Medicine in the Era of Cancer Immunotherapy.},
journal = {Clinical chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/clinchem/hvag062},
pmid = {42314194},
issn = {1530-8561},
support = {//University of Texas Southwestern Medical Center/ ; 1U01AI156189-01/NH/NIH HHS/United States ; 1R01AI192499-01/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) have transformed oncology practice. However, treatment response remains heterogeneous, rendering predictive biomarkers critical for optimal patient care. The 3 established biomarkers, programmed death-ligand 1, tumor mutational burden (TMB), and microsatellite instability-high/deficient mismatch repair, are approved and clinically validated but are modest predictors of benefit. As a result, multiple novel predictive biomarkers remain under investigation.

CONTENT: This review highlights established and investigational predictive ICI efficacy biomarkers. For established biomarkers, we describe biology, assay modalities, approved companion diagnostics, landmark studies, and notable limitations. Due to the multisystem nature of antitumor immune effects, investigational biomarkers span multiple domains, including tumor genomic biomarkers (e.g., mutational signatures, TMB, neoantigen clonality), tumor microenvironment (e.g., tumor-infiltrating lymphocytes [TILs], tertiary lymphoid structures), systemic immune biomarkers (e.g., cytokines, autoantibodies, glycoproteins, peripheral blood mononuclear cells), and the microbiome (e.g., gastrointestinal microbial diversity, responder-enriched taxa).

SUMMARY: The established biomarkers PD-L1, TMB, and microsatellite instability-high/deficient mismatch repair inform ICI use in clinical practice but have important limitations. Multiple investigational biomarkers show promise in refining patient selection and optimizing therapy. Moving forward, increased assay harmonization, prospective validation, and standardized parameters may improve performance. Composite models integrating complementary signals across domains may further individualize treatment and lead to an era of personalized cancer immunotherapy.},
}

@article {pmid42314287,
year = {2026},
author = {Roshid, MHO and Hill, E and Moraskie, M and O'Connor, G and Dikici, E and Zingg, JM and Deo, S and Bachas, LG and Daunert, S},
title = {A two-component relay-switch biosensor enables precise and quantitative detection of the B. subtilis quorum peptide PhrF: Implications in probing the microbiome.},
journal = {Biosensors & bioelectronics},
volume = {311},
number = {},
pages = {118919},
doi = {10.1016/j.bios.2026.118919},
pmid = {42314287},
issn = {1873-4235},
abstract = {We engineered a biosensor for detection of the Bacillus subtilis quorum sensing peptide (QSP), PhrF, which is integral to the bacterial Rap-Phr system regulating competence, sporulation, biofilm formation, and antimicrobial peptide production. Quorum sensing is pivotal in host-microbiome interactions, modulating physiological processes such as immune function and metabolism, and influencing health maintenance or the onset of disease. Despite extensive mechanistic understanding of B. subtilis quorum sensing and prior ComA dependent reporter strains, quantitative, analytically validated whole-cell biosensor for measuring bioavailable PhrF in complex matrices remains limited. To address this gap, we designed a biosensor for PhrF using the native relay-switch architecture that couples the ComQXPA two-component system (TCS) with the Rap-Phr regulatory system. Unlike conventional engineering biosensor designs, the analyte does not directly control reporter expression; instead, PhrF binds RapF, releasing phosphorylated ComA to activate the luxCDABE operon under the surfactin promoter (PsrfAA), producing a dose-dependent bioluminescent output. This TCS design decouples sensing from reporting, enabling precise signal transduction in multicomponent networks. The biosensor demonstrated high selectivity and sensitivity, with a detection limit of 0.40 nmol/L and a dynamic range of 4 × 10[-10] to 1 × 10[-4] mol/L. Validation using ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) confirmed accuracy across bacterial cultures, soil, and human stool samples. PhrF was detected at concentrations ranging from 0.24 to 6.91 μmol/kg in stool and up to 84 nmol/kg in soil, indicating its presence across diverse environments. This cost-effective biosensor offers a robust approach for quantitative measurement of PhrF levels, thereby facilitating research into probing the functional role of B. subtilis in regulating host-microbiome interactions and homeostasis within the environment, human health, and industrial effluents.},
}

@article {pmid42314290,
year = {2026},
author = {Li, Y and Cui, J and Shang, Y and Paraskevas, V and Lee, Y and Zhang, G},
title = {Inulin enhances systemic health and egg quality by regulating gut microbiota and metabolomic profiles in laying hens.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107265},
pmid = {42314290},
issn = {1525-3171},
abstract = {This study investigated the effects of dietary inulin supplementation on systemic health and egg quality in laying hens through changes in the gut microbiota and metabolome. A total of 288 healthy 15-week-old laying hens were randomly assigned to a basal diet (CON) or the same diet supplemented with 1.5 g/kg inulin (INU). At the peak laying age of 35 weeks, egg yolk fatty acid composition was determined, cecal microbial composition was analyzed by 16S rRNA gene amplicon sequencing, and cecal metabolites were assessed using untargeted metabolomics. Compared with the CON group, the INU group showed significantly improved laying performance, systemic health-related indicators, egg quality, serum and yolk antioxidant capacity, and yolk fatty acid composition (P < 0.05), along with a significantly lower yolk malondialdehyde concentration (P < 0.05). In addition, compared with the CON group, the INU group had a higher relative abundance of potentially beneficial microbiota, particularly Bacteroides and Faecalibacterium, and higher concentrations of acetic acid, butyric acid, and isobutyric acid (P < 0.01). Cecal metabolomic analysis further showed that, compared with the CON group, the INU group had significantly altered metabolic pathways mainly related to histidine metabolism, biotin metabolism, glycerophospholipid metabolism, and tryptophan metabolism. These results indicate that dietary inulin supplementation improved laying performance, systemic health, yolk antioxidant capacity, and egg quality in laying hens, and these beneficial effects were associated with cecal microbiota shifts, increased microbial fermentation products, altered metabolic pathways, and improved antioxidant status.},
}

@article {pmid42314296,
year = {2026},
author = {Beckerman, E and Patel, S and Bennett, DC and Pokharel, S and Ismail, MA and Laummert, A and Kim, WK and Kang, I},
title = {Effects of dietary spirulina (Arthrospores platensis) on the growth performance and meat quality of broiler chickens.},
journal = {Poultry science},
volume = {105},
number = {9},
pages = {107282},
pmid = {42314296},
issn = {1525-3171},
abstract = {This study evaluated the effects of spirulina supplementation in broiler diets on growth performance of live birds and meat quality of carcasses. A total of 270 one-day-old Ross 708 broiler chicks were obtained from a local hatchery, weighed, and assigned to 18 floor pens (4' × 4' each, 15 birds/pen). Birds were fed corn and soybean meal (SBM) based diets supplemented with spirulina at inclusion levels of 0% (control), 2.5%, and 5% during the starter (0-2 weeks), grower (2-4 weeks), and finisher (4-6 weeks) phases. Body weight and feed intake were measured weekly to calculate body weight gain and feed conversion ratio (FCR). On 6th week, eighteen broilers (one bird per pen) were processed and evaluated for color, meat quality, and sensory attributes. No significant difference was observed among the dietary treatments for feed intake, FCR, or body weight throughout the study period. Spirulina supplementation had no significant effect on villi height (VH), crypt depth (CD), and VH/CD ratio (P > 0.05). However, spirulina supplementation positively influenced gut microbiome composition by promoting the abundance of fiber-fermenting and probiotic-associated bacteria while maintaining microbial balance. No significant effects were observed on chilling yield, pH, or shear force across the treatment groups (P > 0.05). A notable increase in yellowness (b*) was observed in carcass skin and skinless fillets (P < 0.05). Sensory analysis revealed that 2.5% spirulina enhanced appearance scores (P < 0.05), whereas 5% spirulina reduced juiciness (p < 0.05), with no change for flavor, tenderness, aftertaste, and overall. Based on these results, spirulina served as an alternative feed resource up to 5.0% inclusion with favorable effects on gut health and carcass yellowness.},
}

@article {pmid42314470,
year = {2026},
author = {Ji, J and Huang, J and Zhang, Z and Ye, S and Li, X and Zhang, Y and Lian, H and Xiao, Z and Feng, M and Wei, G and Wei, Y and Mao, H and Chen, B and Zheng, Y and Hu, X},
title = {Multi-omics insights into the physiological mechanisms of bile acid accumulation in the gallbladder in brumation-like snakes.},
journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics},
volume = {60},
number = {},
pages = {101910},
doi = {10.1016/j.cbd.2026.101910},
pmid = {42314470},
issn = {1878-0407},
abstract = {Hibernation/brumation represents an important physiological adaptation for animals to cope with seasonal environmental changes. Field observations suggested increased gallbladder weight in the Five-pacer viper (Deinagkistrodon acutus) during brumation, and our quantitative measurements confirmed this increase together with bile acid accumulation. By integrating a multi-omic approach, this study elucidates the regulatory mechanisms of bile acid accumulation in the gallbladder during brumation. Results showed that taurocholic acid (TCA) and taurodeoxycholic acid (TDCA) were the major components in the gallbladder of the brumation-like group, with significantly elevated concentrations of bile acids, whereas bile acid concentrations in serum and intestinal contents were markedly reduced, indicating suppression of the enterohepatic circulation and consequent accumulation of bile acids in the gallbladder. Hepatic transcriptomic analysis revealed significant downregulation of bile acid synthesis and regulatory genes in brumation-like snakes. In contrast, the alternative synthesis pathway gene sterol 27-hydroxylase (CYP27A1) and some transporter genes were slightly upregulated. Further, some modification genes and regulatory genes showed no significant differences between active and brumation-like states. Gut microbiota analysis demonstrated Akkermansia muciniphila, Bacteroides fragilis, and Citrobacter freundii were more enriched in the active group, which were common microbes related to bile acid metabolism, and the correlation analysis confirmed this relationship. Taken together, these findings indicate that the "physiological bile acid accumulation" observed in snakes during brumation-like state is jointly driven by suppressed hepatic synthesis, reduced enterohepatic circulation, and remodeled microbial community structure. The study provides novel comparative physiological insights into extreme metabolic homeostasis in animals.},
}

@article {pmid42314879,
year = {2026},
author = {Mostofi, K and Caragliano, G},
title = {Surgical Site Infections in Spine Surgery: A Retrospective Study of 1,578 Procedures with Identification of Tattooed Skin as a Novel Risk Factor Associated with Surgical Site Infection.},
journal = {The Journal of hospital infection},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jhin.2026.06.006},
pmid = {42314879},
issn = {1532-2939},
abstract = {BACKGROUND: Surgical site infections (SSIs) are a major complication of spinal surgery. The influence of tattoos overlying the operative incision has not been previously evaluated as a risk factor in this context.

METHODS: Retrospective cohort study of 1,578 consecutive spinal procedures performed by a single senior surgeon (November 2015-December 2025). Presence of a tattoo overlying or crossing the planned incision, ASA score, and standard demographics were prospectively recorded. SSI diagnosis applied CDC/NHSN criteria.

RESULTS: Sixty-four SSIs were recorded (overall rate: 4.06%; 95% CI [3.1-5.0%]). Among 98 tattooed patients (6.2%), 10 (10.2%) developed an SSI versus 54/1,480 (3.65%) non-tattooed patients (OR = 3.00 [95% CI: 1.48-6.09]; p = 0.005). Infected tattooed patients had a mean ASA score of 1.8 (80% were ASA 1-2), suggesting that poor general health status is unlikely to be a major confounding driver in this subgroup, although residual confounding cannot be fully excluded. The median tattoo-to-surgery delay was 3.0 years (range: 2-7), ruling out any acute tattooing effect. Advancing age was also significant (66.0 vs. 61.3 years; p = 0.010). Staphylococcus aureus was the predominant pathogen (55.4%). No significant association was found for sex, diabetes, BMI, or smoking.

CONCLUSION: Tattooed skin at the operative site was significantly associated with an increased risk of SSI in spine surgery, with a nearly 3-fold increased risk. These findings support consideration of systematic preoperative documentation and individualized perioperative protocols.},
}

@article {pmid42314883,
year = {2026},
author = {Šínová, R and Turková, K and Šimek, M and Berka, V and Foglová, T and Šindelář, M and Schwarzer, M and Nešporová, K and Kubala, L},
title = {Hyaluronan exerts unique microbiome and metabolic effects compared with pectin: a multi-omics study of dietary polysaccharides.},
journal = {International journal of biological macromolecules},
volume = {372},
number = {},
pages = {153043},
doi = {10.1016/j.ijbiomac.2026.153043},
pmid = {42314883},
issn = {1879-0003},
abstract = {Dietary polysaccharides are increasingly recognized as modulators of host metabolism through intestinal interactions, yet not all exert comparable systemic effects. In this context, dietary hyaluronan (HA) is distinguished by its clinical efficacy on connective tissues. We investigated whether oral HA modulates the small-intestinal microbiome, systemic metabolome, and lipid metabolism, and compared its effects with pectin. Using a healthy murine model, we combined 16S rRNA sequencing, metabolomics, lipidomics, and correlation analyses. Oral HA triggered profound and previously undescribed shifts in the small-intestinal microbiome, while pectin's effects were markedly weaker. Both supplements increased microbial diversity, with HA specifically enriching taxa such as Turicibacter, Clostridium, and Lachnoclostridium. HA was also associated with elevated systemic metabolites, enhancing redox status. Hydroxybutyrate and related metabolites increased, consistent with enhanced lipolysis. HA was linked to reduced glycogen degradation without effects on synthesis, whereas pectin was related to lowered glycogen synthesis without alterations in degradation. Notably, HA was associated with modulated plasma and hepatic lipid metabolism. Specifically, lipid mediators playing roles in organismal homeostasis, inflammation, and pain modulation were altered. Collectively, these findings indicate that oral HA exerts a unique effect on the intestinal microbiome, systemic metabolome, and lipidome compared to pectin.},
}

@article {pmid42315001,
year = {2026},
author = {Weltz, TK and Peng, S and Larsen, A and Bak, EEF and Tran, JVQ and Gudjonsdottir, LR and Hemmingsen, MN and Ørholt, M and Mielke, LV and Trillingsgaard, J and Elberg, JJ and Hölmich, LR and Jensen, LT and Vester-Glowinski, P and Bjarnsholt, T and Trivedi, U and Clemens, MW and Li, X and Sørensen, SJ and Herly, M},
title = {Breast implant surface texture is associated with distinct implant microbiome profiles in humans.},
journal = {Acta biomaterialia},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.actbio.2026.06.038},
pmid = {42315001},
issn = {1878-7568},
abstract = {Surface topography of silicone breast implants modulates foreign body responses, but its connection to implant-associated microbial communities remains unclear. We analyzed the microbiome of 391 explanted breast implants from 221 patients with different surface textures using 16S rRNA gene sequencing. We found that the surface texture is associated with distinct microbial communities depending on a surface roughness gradient. Rougher surfaces had lower microbial diversity, driven by lower evenness and a higher relative abundance of Staphylococcus than smoother surfaces. Compositional differences across surface groups followed this gradient. In a subset of samples, absolute bacterial quantification using digital PCR showed increasing total bacterial burden with increasing surface roughness. Smooth and minimally textured implants displayed similar microbiome profiles despite large differences in implantation time. Together, these findings suggest that surface roughness is associated with the local microbial microenvironment, linking material design with microbial burden and the foreign body response. STATEMENT OF SIGNIFICANCE: Breast implant surface topography may influence implant-associated microbial communities, but human evidence across commonly used textures is limited. Using 16S rRNA gene sequencing of 391 explanted implants from multiple manufacturers, we found that microbial diversity and composition varied systematically with a surface roughness gradient. Rougher textures showed lower diversity driven by reduced evenness and a higher relative abundance of Staphylococcus, while compositional differences across surface groups followed the same gradient. Quantitative digital PCR further suggested a higher total bacterial burden on rougher surfaces. In contrast, smooth and minimally textured implants displayed similar microbiome profiles despite large differences in implantation time. These findings link implant surface design to microbial ecology and may help explain texture-associated differences in foreign body responses.},
}

@article {pmid42315010,
year = {2026},
author = {Barznji, HN},
title = {A causal inference framework to bridge association and mechanism in the gut-brain axis.},
journal = {Progress in neuro-psychopharmacology & biological psychiatry},
volume = {148},
number = {},
pages = {111797},
doi = {10.1016/j.pnpbp.2026.111797},
pmid = {42315010},
issn = {1878-4216},
abstract = {The gut-brain axis represents a major paradigm shift in how we evaluate diseases in neuroscience, with microbial dysbiosis affecting many neurological and psychiatric disorders. However, the clinical translation of these findings into effective therapies is currently stalled at a methodological impasse. This Causality Conundrum arises due to the fact that current models fail to resolve the bidirectional noise and cyclic feedback loops inherent in the gut-brain axis. These insufficiencies have made the field rely on cross-sectional cohorts and functionally blind 16S rRNA sequencing, creating a Resolution-Causality Gap, trapping the field in a cycle of correlation. Therefore, this perspective study argues for a new framework "Causality Funnel" for establishing causality in microbiome research. The framework introduces a multi-staged resource-prioritization protocol rooted in the epidemiological principle of triangulation. It prioritizes human-centric discovery using powerful causal inference methods like Mendelian Randomization, followed by multi-omics for molecular mechanism identification, and concluding with definitive validation in reductionist gnotobiotic models. By strategically using resource intensive research only on high-confidence hypotheses the field can move from human data to validating mechanisms through resource-efficient discovery. Furthermore, by anchoring this protocol in disease exemplars such as pediatric epilepsy and neurodevelopmental trajectories the field can navigate in a much more effective way, providing a road map that moves beyond just finding associations and accelerating the development of a new generation of targeted, evidence-based neurotherapeutics.},
}

@article {pmid42315132,
year = {2026},
author = {Franz, A and Constantinou, A and Wilborn, D and Krokowski, I and Blume-Peytavi, U},
title = {The follicular microbiome in hair-follicle-associated inflammatory diseases: A systematic review.},
journal = {Clinical and experimental dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/ced/llag251},
pmid = {42315132},
issn = {1365-2230},
abstract = {BACKGROUND: Hair follicles represent distinct cutaneous microenvironments that host microbial communities. Dysbiosis has been increasingly associated with inflammatory skin and hair disorders, but available studies were limited in scope and sample size, limiting confidence in the conclusions that can be drawn.

OBJECTIVES: To assess the bacterial microbiome of hair follicles across inflammatory hair-follicle-associated skin and hair diseases and identify recurrent alterations.

METHODS: We searched six databases, including MEDLINE and Embase, for studies published from 2007 to August 2024. Studies using culture-independent methods to characterize the bacterial microbiome in inflammatory hair-follicle-related conditions were included. Owing to expected heterogeneity, a qualitative synthesis was conducted based on the JBI Manual for Evidence Synthesis and reported in line with PRISMA.

RESULTS: Fifty-five studies involving 1,811 patients from 19 countries were included. Methods varied substantially across sampling, storage, DNA extraction, sequencing, and analysis. Cutibacterium and Staphylococcus most frequently showed altered relative abundance. Across diseases, Staphylococcus showed increased relative abundance, particularly in scarring alopecias, seborrheic dermatitis/dandruff, and acne. Reduced Cutibacterium abundance was reported in seborrheic dermatitis/dandruff, whereas Cutibacterium acnes appeared more prevalent in androgenetic alopecia. Findings regarding Cutibacterium were inconsistent in scarring alopecias and acne. Results in alopecia areata and rosacea were inconclusive, whereas hidradenitis suppurativa suggested enrichment of anaerobic opportunists such as Porphyromonas and Prevotella.

CONCLUSIONS: Despite substantial methodological heterogeneity, recurrent genus-level shifts involving Cutibacterium and Staphylococcus were observed across several diseases. Their causal significance remains unclear. Larger, standardized studies with functional analyses are needed to clarify biological relevance and therapeutic potential.},
}

@article {pmid42315161,
year = {2026},
author = {Jung, P and Werner, L and Brand, R and Briegel-Williams, L and Baumann, K and Letendu, G and Lakatos, M},
title = {Fog, Symbiosis, and Survival: The Ecological Architecture of the Grit Crust From the Atacama Desert Represents a Lichen Holobiome Rather Than a Soil Microbiome.},
journal = {Environmental microbiology},
volume = {28},
number = {6},
pages = {e70350},
pmid = {42315161},
issn = {1462-2920},
support = {JU 3228/1-1//Deutsche Forschungsgemeinschaft/ ; 03WIR4502A//Bundesministerium für Bildung und Forschung/ ; W2V-Strategy2Value//Bundesministerium für Bildung und Forschung/ ; 03WIR4516A//Bundesministerium für Bildung und Forschung/ ; 03WIR4505B//Bundesministerium für Bildung und Forschung/ ; 724-0079#2024/0004-1501 15404//Ministry of Science and Health Rhineland-Palatinate/ ; 182531//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Lichens/physiology/classification/microbiology/genetics ; Desert Climate ; *Soil Microbiology ; Chile ; *Symbiosis ; *Microbiota ; Bacteria/classification/genetics/isolation & purification ; Fungi/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Ascomycota/genetics ; },
abstract = {Biological soil crusts (biocrusts) fulfil key ecological functions in arid ecosystems, yet their microbiome composition remains insufficiently resolved. Here, we characterise the microbial communities of the fog-dependent grit crust in the Pan de Azúcar National Park (Atacama Desert, Chile) using multi-marker metabarcoding (16S rRNA, 18S rRNA, ITS2) across 11 coastal-inland sites. Chlorophylla+b concentrations reached up to 900 mg m[-2], ranking among the highest reported for arid biocrusts and reflecting exceptional fog-sustained productivity. Bacterial assemblages were dominated by Proteobacteria and Actinobacteria, fungal communities by lichenized Ascomycota (Caliciaceae), and eukaryotic diversity by the green algal photobiont genus Trebouxia. Black-pigmented crusts with dense colonisation exhibited higher biomass but lower taxonomic richness, consistent with later-successional, lichen-dominated stages, whereas lighter, less colonised crusts were taxonomically richer yet functionally less integrated, indicative of earlier succession. The prevalence of Trebouxia, lichenized fungi, and lichen-associated bacterial taxa demonstrates that the grit crust microbiome is structured around symbiotic photobiont-mycobiont interactions rather than typical edaphic microbial assemblages. These findings redefine biocrust paradigms by documenting a fog-driven, chlorolichen-based system that bridges the ecological spectrum between lithic lichen communities and conventional soil crusts, establishing a critical baseline for assessing dryland microbial resilience under climate change.},
}

*Lichens/physiology/classification/microbiology/genetics
Desert Climate
*Soil Microbiology
Chile
*Symbiosis
*Microbiota
Bacteria/classification/genetics/isolation & purification
Fungi/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Ecosystem
Ascomycota/genetics

@article {pmid42315187,
year = {2026},
author = {Benga, L and Rehm, A and Gougoula, C and Bischoff, S and Janssen, S},
title = {Is the Microbial Status an Extrinsic, Intrinsic, or Intermediate Influence on Experimental Animals?.},
journal = {Journal of the American Association for Laboratory Animal Science : JAALAS},
volume = {},
number = {},
pages = {1-4},
doi = {10.30802/AALAS-JAALAS-26-036},
pmid = {42315187},
issn = {2769-6677},
abstract = {Living entities, inlcuding laboratory animals, are composed of the host and its associated microbial communities and defined as holobionts. The host genotype and its microbiome drive together as a metagenome, the holobiont phenotype, with the microbiome itself as a well-recognized source of phenotypic variation. Multiple environmental (diet, light/dark cycles, etc.) as well as host-related factors (genotype, maternal effect, etc.) not only influence the animal experimental phenotype but also contribute to the shaping of the microbiome, raising the question of whether the microbiome of experimental animals represents an extrinsic, intrinsic, or intermediate influence. Currently, there is sufficient evidence that microbial communities at different body sites are shaped by distinct endogenous and exogenous factors, indicating that the host does not leave its microbial status to chance but instead actively modulates it through host-specific mechanisms, despite extrinsic influences. This leads to a microbiome that reflects a 'fingerprint' of its own endogenous and exogenous influences. This suggests that the microbiome of experimental animals is an intermediate factor with both intrinsic and extrinsic components and underscores the importance of refining the selection of the appropriate metagenome for each specific rodent experiment.},
}

@article {pmid42315257,
year = {2026},
author = {Cramer, C and Marshall, IPG and Abramson, MJ and Jõgi, NO and Khomich, M and Peddada, SD and Skottvoll, BS and Schlünssen, V and Bertelsen, RJ},
title = {Role of oral bacteria composition and functional gene profiles in respiratory diseases.},
journal = {BMJ open respiratory research},
volume = {13},
number = {1},
pages = {},
pmid = {42315257},
issn = {2052-4439},
mesh = {Humans ; Female ; Male ; *Microbiota/genetics ; Cross-Sectional Studies ; *Asthma/microbiology ; *Mouth/microbiology ; Adult ; Middle Aged ; *Rhinosinusitis/microbiology ; Norway/epidemiology ; Australia/epidemiology ; Estonia/epidemiology ; Nitric Oxide ; Fractional Exhaled Nitric Oxide Testing ; *Bacteria/isolation & purification/genetics ; Chronic Disease ; Spirometry ; },
abstract = {INTRODUCTION: The oral microbiome has been shown to be associated with respiratory health, primarily in adult case studies or among children. This relationship has been scarcely investigated in adult population-based cohorts.

OBJECTIVES: To investigate the association between oral microbiome and respiratory health, more specifically asthma, chronic rhinosinusitis (CRS), lung function and fractional exhaled nitric oxide (FeNO) in a population-based cross-continental multicentre study among adults.

METHODS: Subgingival samples from 355 adult European Community Respiratory Health Survey participants from Norway, Australia and Estonia underwent metagenomic sequencing. Respiratory disease was defined from questionnaires and sensitisation from specific immunoglobulin E (IgE)/skin prick tests. Spirometry and FeNO were measured. The associations between alpha diversity and disease status were evaluated in cross-sectional analyses using logistic regression adjusting for sex, smoking and study centre. Differential abundance analyses were performed using analysis of compositions of microbiomes with bias correction.

RESULTS: Alpha diversity differed by study centre and sensitisation status and was associated with non-allergic CRS (richness: 1.12, 95% CI 1.03 to 1.22). A similar though not statistically significant pattern was seen for forced vital capacity (FVC) below the lower limit of normal (LLN). Lachnospiraceae and Xanthomonas were more abundant in the oral microbiome of non-asthmatics and individuals without CRS, respectively, as compared with asthmatics and CRS patients. Several functional genes (1477-3391) and genera (54-98) were only present in the non-case groups, whereas individuals with affected respiratory health had 0-74 unique functional genes, but no unique genera present only in their respective groups.

CONCLUSION: Increased alpha diversity was associated with non-allergic CRS and a similar trend was seen for FVC below LLN. Bacterial composition and functional profiles of the oral microbiome differed by respiratory health status. This study is novel in exploring functional gene profiling in relation to asthma and FeNO.},
}

Humans
Female
Male
*Microbiota/genetics
Cross-Sectional Studies
*Asthma/microbiology
*Mouth/microbiology
Adult
Middle Aged
*Rhinosinusitis/microbiology
Norway/epidemiology
Australia/epidemiology
Estonia/epidemiology
Nitric Oxide
Fractional Exhaled Nitric Oxide Testing
*Bacteria/isolation & purification/genetics
Chronic Disease
Spirometry

@article {pmid42315484,
year = {2026},
author = {Fujii, T and Ohno, E and Nakano, N and Nakaoka, K and Takahashi, H and Funasaka, K and Doi, Y and Hirooka, Y and Tochio, T},
title = {Disease-specific gut microbial signatures generate model-derived cancer probability scores through targeted fecal qPCR profiling.},
journal = {Bioscience, biotechnology, and biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1093/bbb/zbag090},
pmid = {42315484},
issn = {1347-6947},
abstract = {The gut microbiome is a potential source of non-invasive cancer biomarkers. We evaluated six fecal microbial markers and developed targeted qPCR-based logistic models for colorectal cancer (CRC) and pancreatic cancer (PC). Using LASSO with the 1-standard-error rule, four markers were selected for CRC (afb, nan, fsr, and 5ar) and three for PC (but, fsr, and saa). In post-selection leave-one-out cross-validation of fixed model structures, the CRC and PC models yielded AUCs of 0.824 and 0.780, respectively. Fixed-model application yielded AUCs of 0.716 for colorectal adenoma and 0.540 for the pancreatic high-risk group. In an exploratory Early PC versus high-risk comparison, the fecal qPCR score showed a higher AUC point estimate than CA19-9, while the difference was not statistically significant. Overall, the disease-specific model performance and fixed-model behavior across clinically related groups support further evaluation of model-derived cancer probability scores as exploratory cancer-assessment tools.},
}