@article {pmid42395429,
year = {2026},
author = {Stoner, SN and Larson, ED and Fulte, S and Shaw, SC and Fish, ER and Janoff, EN and Mack, M and Clark, SE},
title = {Myeloid cell reprogramming drives enhanced defense against Streptococcus pneumoniae lung infection following exposure to commensal Prevotella.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
pmid = {42395429},
issn = {2692-8205},
abstract = {Clinical data link the prevalent respiratory tract anaerobe Prevotella with reduced pneumonia mortality, but the mechanisms directing Prevotella regulation of lung immune homeostasis are unclear. Here, single-cell RNA sequencing was employed to define the transcriptional immune signatures underlying improved clearance of Streptococcus pneumoniae following lung exposure to Prevotella melaninogenica. Overall, we observed a substantial shift in myeloid cell transcriptional programming from interferon-dominant to a more antibacterial profile in S. pneumoniae-infected mice after pre-exposure to P. melaninogenica, correlating with increased macrophage and neutrophil phagocytosis of S. pneumoniae and improved pathogen clearance. In neutrophils, TNF signaling through TNFR2 was essential for increased antimicrobial function. Moreover, improved defense required CCR2-dependent monocyte-derived macrophages, with selective enrichment of more a mature Cxcl3+ population which was distinct from the hallmark S. pneumoniae-associated C1qa+ population enriched in the absence of effective clearance. Together, these findings inform the myeloid cell transcriptional changes associated with natural infection resistance mediated by pulmonary microbial exposures.},
}

@article {pmid42437837,
year = {2026},
author = {Devi, U and Ramadass, B and Pullattayil, AK and Vishnu Bhat, B},
title = {Gut Microbiome in Neonatal Necrotizing Enterocolitis - A Comprehensive Review of Evidence.},
journal = {Indian journal of pediatrics},
volume = {},
number = {},
pages = {},
pmid = {42437837},
issn = {0973-7693},
abstract = {Necrotizing enterocolitis (NEC) is one of the most catastrophic gastrointestinal emergency occurring predominantly in preterm neonates. It contributes to substantial neonatal morbidity and mortality. Disturbances in the intestinal microbiome are crucial to disease pathogenesis. In preterm infants, an immature intestinal barrier, dysregulated immune responses, and environmental exposures altogether predispose to alteration in microbial colonization and intestinal inflammation. This review was done to present the current evidence on gut microbiome alterations associated with NEC in preterm infants. A systematic search of the MEDLINE and EMBASE databases was performed using search strategy related to prematurity, intestinal microbiota, and necrotizing enterocolitis. A total of 42 studies assessing microbial composition, microbial progression, or microbial functional patterns in relation to NEC were included. Across the included studies, NEC was commonly preceded by reduced microbial diversity, delayed maturation of anerobic communities, and expansion of Proteobacteria, particularly Enterobacteriaceae family such as Klebsiella and Escherichia. Longitudinal studies further showed that these microbial changes may become evident days to weeks before clinical disease, suggesting a potential window for early risk identification. Functional analyses also showed alterations in microbial metabolic pathways, including short-chain fatty acids, tricarboxylic acid intermediates, volatile compounds, and viral signatures that may lead to epithelial injury and inflammatory signaling. Clinical and environmental factors including antibiotic exposure, mode of delivery, feeding practices, and NICU microbial ecosystem are important determinants of neonatal gut microbiome development. Thus, the current evidence supports a reproducible pattern of intestinal dysbiosis preceding NEC. Better understanding of microbiome dynamics may aid early risk stratification and support microbiome-targeted preventive strategies in vulnerable preterm populations.},
}

@article {pmid42437873,
year = {2026},
author = {Piper, FI and Oporto, C and Reyes-Bahamonde, C and Moreno-Meynard, P and Nespolo, RF and Saona, L and Cubillos, FA and Fajardo, A},
title = {Bark-associated yeasts and their potential role as tree carbon sink at the treeline of the southern Andes.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70251},
pmid = {42437873},
issn = {1438-8677},
support = {NCN2024_040//Agencia Nacional de Investigación y Desarrollo/ ; 1220026//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 1231026//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; 3240649//Fondo Nacional de Desarrollo Científico y Tecnológico/ ; FB210006//Instituto de Ecología y Biodiversidad/ ; },
abstract = {The upper elevation of the tree life form (treeline) is explained by temperature limitations in the carbon (C) investment in biomass (the growth limitation hypothesis, GLH). The GLH predicts that tissue concentrations of non-structural carbohydrates (NSC) increase with elevation. This prediction has received mixed support in deciduous species. In addition, other potentially relevant C sources (e.g., inner bark) and sinks (e.g., bark microbiome) have not been considered. We assessed the year-round NSC concentrations in the inner bark, roots and branches of Nothofagus pumilio at the treeline and 200 m below it in the southern Andes of Chile. We furthermore quantified the abundance of bark-associated yeasts and evaluated the relative importance of inner bark's starch and soluble sugars (SS), tree size and seasonality as predictors of the yeast abundance. NSC, starch and SS concentrations decreased in springtime in both elevations. In late spring, NSC, starch and SS concentrations were significantly lower at the treeline than below the treeline for all organs and most so for the inner bark. Bark's starch and SS concentrations were the best predictors of yeast abundance. At the treeline, yeast abundance was highly predicted by the month, peaking in spring. We found support for C limitation in the treeline formation of N. pumilio in late spring, when C reserves were at their minimum concentrations and yeasts' abundance was at their maximum. Given that yeast abundance was mostly predicted by starch and SS concentrations, our results suggest that yeasts act as a C sink, particularly at the treeline.},
}

@article {pmid42437920,
year = {2026},
author = {Diaz-Canestro, C and Cheung, K and Roche, E and Sarabia, JM and Tse, MA and Xu, A},
title = {Multi-omics signatures of circulating factors associated with cardiorespiratory fitness adaptations in individuals with prediabetes.},
journal = {Cardiovascular diabetology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12933-026-03286-x},
pmid = {42437920},
issn = {1475-2840},
abstract = {BACKGROUND: Patients with insulin resistance exhibit reduced cardiorespiratory fitness (CRF), assessed by peak oxygen consumption (VO2peak), compared with healthy age-matched individuals. Although high-intensity interval training (HIIT) can substantially improve VO2peak, there is considerable interindividual variability in this response. Therefore, further research is needed to elucidate the molecular mechanisms underlying the heterogeneous response of VO2peak to HIIT in individuals with prediabetes.

METHODS: Proteomic analyses of serum samples, along with fecal metagenomic and targeted metabolomic profiling, were conducted in medication-naïve, overweight and obese Chinese men with prediabetes (n = 35; aged 24-62 years). All participants underwent a 12-week HIIT intervention, and biological samples were collected both before and after the intervention to evaluate exercise-induced alterations in circulating proteins, gut microbial composition, and metabolite profiles.

RESULTS: After 12 weeks of HIIT, mean VO₂peak increased by 0.47 L/min with individual responses ranging from 0 to 1.7 L/min. Baseline levels of short-chain fatty acid (SCFA)-producing genera, including Prevotella (β = 105.65, P = < 0.001, FDR = 0.034), Coprococcus (β = 50.22, P = 0.01, FDR = 0.39), and Hungatella (β = 40.72, P = 0.025, FDR = 0.50), were positively associated with ΔVO₂ peak. In contrast, baseline levels of the erythropoiesis-stimulating hormone erythropoietin (EPO) (β = -279.03, P = 0.024, FDR = 0.99) were negatively associated with ΔVO₂ peak. Exercise-induced changes in growth hormone 1 (β = 63.97, P = 0.04, FDR = 0.99) were positively associated with ΔVO₂ peak, whereas exercise-induced changes in BTB and CNC Homology 1 (β = -250.82, P = 0.01, FDR = 0.99), a repressor of heme oxygenase-1, were negatively associated with ΔVO₂ peak. In multiple linear regression analysis including clinical variables, percentage lean mass (β = 64.17, P = 0.0005) was the strongest variable associated with ΔVO₂peak. The clinical model explained 27% of the variance which increased to 37% (P = 0.002) upon inclusion of exercise-associated circulating factors such as EPO.

CONCLUSIONS: Our findings reveal that baseline proteomic and metagenomic signatures are associated with VO₂peak adaptations. These multi-omics signatures may support the clinical implementation of personalized exercise interventions to improve CRF in individuals with prediabetes.},
}

@article {pmid42437941,
year = {2026},
author = {Herbinger, J and Ramakrishnan, DK and Reißfelder, J and Babor, M and Höhne, M and Abdelfattah, A},
title = {Predicting the seed microbiome using phylogeny-driven machine learning.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-026-00936-1},
pmid = {42437941},
issn = {2524-6372},
abstract = {BACKGROUND: The composition of the seed-associated bacterial microbiome can reflect host evolutionary relationships, a pattern consistent with phylosymbiosis. While machine learning offers new opportunities to predict microbial community composition, existing models often require prior microbial profiles or environmental variables, limiting their application to unsampled hosts. Here, we tested whether plant nuclear internal transcribed spacer (ITS) sequences, used as a marker of host relatedness, can predict species-level seed-associated bacterial communities using 16S rRNA data from 61 plant species.

RESULTS: We introduced customized machine learning models that use sequence-based Hamming distances to capture plant host relatedness. Among the tested models, the Hamming Distance-based k-Nearest Neighbor model (HD-KNN) achieved the highest overall predictive accuracy, yielding an average Jensen-Shannon divergence (JSD) of 0.276 between observed and predicted microbiome profiles. HD-KNN performed particularly well within densely sampled host groups, including Brassicaceae and Poaceae, where closely related reference species were available. In contrast, Hamming Distance-based Gaussian Process Regression (HD-GPR) showed slightly better performance for phylogenetically isolated species, suggesting that model performance depends on host representation within the training dataset.

CONCLUSIONS: Our framework demonstrates that plant nuclear ITS-derived host relatedness carries a partial predictive signal for seed-associated bacterial microbiome composition. These results provide a foundation for low-input predictive modelling of seed-associated bacteria and may help prioritise microbiome predictions for unsampled plant species when closely related reference species are available. However, our conclusions are strictly limited to seed-associated bacterial communities and should not be directly generalized to fungal communities or other plant compartments, such as the rhizosphere or phyllosphere, which may be shaped by different environmental filtering mechanisms.},
}

@article {pmid42438014,
year = {2026},
author = {Matsumoto, M},
title = {Oral microbiome research toward the prevention of oral frailty.},
journal = {Journal of prosthodontic research},
volume = {70},
number = {3},
pages = {viii-ix},
doi = {10.2186/jpr.JPR_D_26_00228},
pmid = {42438014},
issn = {2212-4632},
}

@article {pmid42438061,
year = {2026},
author = {Hiseni, P and Furu, K and Wang Pedersen, V and Øverland, L and Kirubakaran, GT and Casén, C},
title = {Towards standardized gut microbiota diagnostics: normobiosis beyond geographical borders.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2701485},
doi = {10.1080/19490976.2026.2701485},
pmid = {42438061},
issn = {1949-0984},
mesh = {Humans ; *Dysbiosis/diagnosis/microbiology ; *Gastrointestinal Microbiome ; Feces/microbiology ; Female ; Inflammatory Bowel Diseases/microbiology/diagnosis ; Adult ; Retrospective Studies ; Male ; *Bacteria/classification/isolation & purification/genetics ; Irritable Bowel Syndrome/microbiology/diagnosis ; Middle Aged ; },
abstract = {Defining clinically meaningful reference states of the human gut microbiota remains a major barrier to the clinical translation of microbiome testing, largely due to variability across populations. We aimed at evaluating whether dysbiosis can be identified in a standardized, geography-independent manner, using a composite, system-level microbiome diagnostic framework. We performed a retrospective observational analysis of 831 adult stool samples collected from healthy individuals and patients with inflammatory bowel disease, irritable bowel syndrome, or other chronic inflammatory conditions across seven countries. In addition, U.S. National Institute of Standards Technology (NIST) human fecal reference materials were analyzed. Dysbiosis was assessed using a fixed microbial marker panel and composite distance metrics anchored to a clinically validated healthy Scandinavian reference population, using GA-map® Dysbiosis Test as an exemplar of this diagnostic framework. The diagnostic framework reproducibly identified normobiosis and dysbiosis across geographically distinct populations (USA, Canada, Germany, Italy, and the UK). Severe dysbiosis was detected with high specificity (93.6%) and positive predictive value (90.2%), independent of subjects' country of origin. Healthy individuals showed highly comparable dysbiosis index distributions across regions. These findings demonstrate that clinically useful dysbiosis diagnostics do not require geographically tailored reference populations and support the feasibility of standardized, geography-independent microbiome diagnostics for clinical application.},
}

Humans
*Dysbiosis/diagnosis/microbiology
*Gastrointestinal Microbiome
Feces/microbiology
Female
Inflammatory Bowel Diseases/microbiology/diagnosis
Adult
Retrospective Studies
Male
*Bacteria/classification/isolation & purification/genetics
Irritable Bowel Syndrome/microbiology/diagnosis
Middle Aged

@article {pmid42438224,
year = {2026},
author = {Langgeng, A and Sigaud, M and Prameswari, W and Priambada, NP and Rianti, P and Moore, R and Sanchez, KL and Lee, W and MacIntosh, AJJ and Matsuda, I},
title = {Oral and Gut Microbiomes Reveal Potential Physiological Constraints on Release Readiness in Rehabilitating Javan slow lorises.},
journal = {American journal of primatology},
volume = {88},
number = {7},
pages = {e70184},
doi = {10.1002/ajp.70184},
pmid = {42438224},
issn = {1098-2345},
support = {//Ministry of Education, Culture, Sports, Science and Technology/ ; //Nagao Environmental Foundation Commerative Grant Fund for Capacity Building of Young Scientist/ ; //Japan-ASEAN Science, Technology, and Innovation Platform/ ; JPJSCCB20250006//Core-to-Core Program, Asia-Africa Science Platforms/ ; },
mesh = {Animals ; Feces/microbiology ; *Mouth/microbiology ; *Lorisidae/microbiology/physiology ; *Gastrointestinal Microbiome ; Female ; *Microbiota ; Wildlife Trade ; RNA, Ribosomal, 16S/analysis ; Male ; Saliva/microbiology ; Bacteria/classification ; },
abstract = {Illegal wildlife trade and habitat degradation displace thousands of animals annually in Southeast Asia, with many confiscated primates housed in rehabilitation centers that increasingly function as long-term holding environments. In slow lorises, dental clipping associated with the pet trade may generate persistent disruption along the oral-gut axis, potentially undermining physiological readiness for release in ways not captured by conventional screening. Here, we evaluated whether microbiome structure provides an integrative marker of release readiness in rehabilitating Javan slow lorises (Nycticebus javanicus). From June to October 2024, we collected fecal (n = 26) and saliva (n = 18) samples from 19 adults housed at YIARI, including 10 release candidates and 9 non-candidates classified primarily based on tooth loss, medical history, and release suitability. Bacterial communities were characterized using 16S rRNA (V3-V4) amplicon sequencing, with alpha and beta diversity, taxonomic enrichment (LEfSe), and predicted functional profiles (PICRUSt2) assessed. Microbiome composition was strongly compartmentalized by body site, with higher alpha diversity in the gut. Release candidacy was associated with modest gut compositional differences, whereas oral microbiomes showed pronounced divergence between candidates and non-candidates. Non-candidates were enriched in dysbiosis-associated taxa and degradation-oriented functional pathways, while candidates showed enrichment of biosynthetic and central energy metabolism pathways. Gut microbiome structure was stable across pre-release and soft-release phases. These findings indicate that oral and gut microbiomes represent distinct physiological niches and that persistent oral microbiome restructuring may retain signatures of cumulative rehabilitation history. Microbiome-informed approaches may provide complementary insights into physiological variation relevant to rehabilitation and release decisions.},
}

Animals
Feces/microbiology
*Mouth/microbiology
*Lorisidae/microbiology/physiology
*Gastrointestinal Microbiome
Female
*Microbiota
Wildlife Trade
RNA, Ribosomal, 16S/analysis
Male
Saliva/microbiology
Bacteria/classification

@article {pmid42438277,
year = {2026},
author = {Mu, P and Haider, FU and Li, S and Zhang, P and Jiang, M and Yang, A and Li, X},
title = {Multi-Generational High Nitrogen Application Inhibits Seed Germination in Wheat: Insights Into Metabolic Dynamics and Microbial Interactions.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70734},
pmid = {42438277},
issn = {1365-3040},
support = {2023HTDGZ-KF-06//National Key Laboratory for Black Soil Protection and Utilization/ ; 32372228//National Natural Science Fund/ ; 20240101010JJ//Science and Technology Development Program of Jilin Province/ ; 0217-00084B//Danmarks Frie Forskningsfond/ ; },
abstract = {Excessive nitrogen (N) application can affect soil health and crop performance, yet the multi-generational effects of prolonged high-N exposure on wheat seed germination remain unclear. We profiled seed metabolomes and endophytic bacterial communities across seven consecutive wheat generations (F1-F7) under normal-N and high-N regimes, and assessed germination of F7 seeds. Spatial metabolomics, spatial transcriptomics and 16S rRNA sequencing were used to resolve embryo- and endosperm-specific responses. Seven generations of high-N treatment delayed progeny seed germination and decreased the germination index by 12.3%, whereas the vigor index was not significantly affected. Spatial omics revealed strong embryo-endosperm heterogeneity and a high-N-associated shift in endosperm metabolism, including a 73.9% decrease in endosperm L-aspartic acid. Compartment-resolved microbiome analysis showed enrichment of Bacillus under high-N exposure. Functional assays showed that L-aspartic acid promoted germination/early outgrowth, whereas Bacillus grew with L-aspartic acid as the sole C/N source and reduced germination under L-aspartic acid-supplemented conditions. These results support a model in which multi-generational high N reduces wheat seed germination through endosperm amino-acid depletion and altered endophytic bacterial assembly.},
}

@article {pmid42438369,
year = {2026},
author = {Kubicki, M and McHill, AW and Melanson, EL and Reisdorph, N and Wright, KP and Depner, CM},
title = {Internal Circadian Misalignment of the Human Metabolome Links Night Shiftwork to Metabolic Impairment.},
journal = {Journal of biological rhythms},
volume = {},
number = {},
pages = {7487304261459478},
doi = {10.1177/07487304261459478},
pmid = {42438369},
issn = {1552-4531},
abstract = {Circadian misalignment, as experienced during shiftwork, impairs glucose metabolism and body weight regulation, yet the underlying biochemical mechanisms remain incompletely understood. Characterizing how circadian misalignment alters circulating metabolites provides a promising avenue to help identify these mechanisms. Although data from metabolomics studies have identified circulating metabolites with daily rhythms, it is not comprehensively known which rhythms shift during circadian misalignment and whether such shifts relate to metabolic impairment. We conducted 24-hour (h) metabolomic profiling every 4 h in 14 healthy adults (8 women) aged 26.4 ± 1.2 years (mean ± SD), undergoing a 6-day simulated night-shiftwork protocol. 24-h modeling analyses identified metabolite rhythms influenced by circadian versus behavioral cycles (sleep, food intake) and quantified internal circadian misalignment using acrophase shifts. Metabolic outcomes included glucose homeostasis (test meals) and energy expenditure (EE; whole-room calorimetry). Night-shiftwork produced widespread alterations in metabolite rhythms, with significant internal misalignment in multiple metabolites across pathways including pyrimidine metabolism, bile acid-microbiome signaling, and lipid metabolism. During misalignment, glucose and insulin area under the curve increased (p < 0.05) and EE decreased (p < 0.05). Internal misalignment of uridine and glycoursodeoxycholic acid was associated (p < 0.05) with impaired glucose tolerance, while their circulating concentrations were associated with decreased EE. Misalignment of uridine and glycoursodeoxycholic acid suggests dysregulated pyrimidine and bile acid-microbiome pathways as potential mechanisms linking circadian misalignment to cardiometabolic disease risk.},
}

@article {pmid42438428,
year = {2026},
author = {Haller, R and Feldbacher, N and Fürst, S and Woltsche, J and Gulden, L and Schwarzl, J and Traub, J and Madl, T and Habisch, H and Horvath, A and Stadlbauer, V},
title = {Clinical and Mechanistic Association Between Intestinal Permeability and the Gut Microbiome in Cirrhosis: Role of Phascolarctobacterium.},
journal = {United European gastroenterology journal},
volume = {14},
number = {6},
pages = {e70262},
doi = {10.1002/ueg2.70262},
pmid = {42438428},
issn = {2050-6414},
support = {KLIF-741 B34//Austrian Science Fund/ ; KLI 741//Austrian Science Fund/ ; 10.55776/COE14//Austrian Science Fund/ ; 10.55776/P28854//Austrian Science Fund/ ; 10.55776/I3792//Austrian Science Fund/ ; 10.55776/DOC130//Austrian Science Fund/ ; 10.55776/W1226//Austrian Science Fund/ ; //Österreichische Forschungsförderungsgesellschaft/ ; //Integrative Metabolism Research Center Graz/ ; //Austrian Infrastructure Program 2016/2017/ ; //Styrian Government; Zukunftsfonds; doc.fund program/ ; //City of Graz/ ; //BioTechMed-Graz/ ; //Doctoral program MOLMED/ ; },
mesh = {Humans ; *Liver Cirrhosis/microbiology/physiopathology/metabolism ; Haptoglobins ; Feces/chemistry/microbiology ; Intestinal Barrier Function ; Male ; Protein Precursors/analysis ; *Gastrointestinal Microbiome/physiology ; Female ; Middle Aged ; Permeability ; Cholera Toxin/metabolism/analysis ; Biomarkers/analysis/metabolism ; *Intestinal Mucosa/metabolism/microbiology ; Aged ; Magnetic Resonance Spectroscopy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: In patients with liver cirrhosis, intestinal permeability and the composition of the gut microbiome are altered. Thus, the microbiome might be a therapeutic target for the treatment of both liver diseases and intestinal permeability. We aimed to investigate the relationship between the intestinal barrier and microbiome composition in cirrhosis and elucidate potential mechanisms for how bacteria influence permeability.

METHODS: We analyzed the fecal permeability biomarker zonulin by ELISA and microbiome composition by 16s rDNA sequencing in a discovery (n = 78) and a validation cohort (n = 90) of patients with liver cirrhosis. In the validation cohort, we analyzed the composition of the fecal metabolome by NMR spectroscopy. For mechanistic exploration, an intestinal barrier cell culture model using T84 cells was used.

RESULTS: In the discovery cohort (n = 78, 77% Child-Pugh Grade A, 21% Child-Pugh Grade B, 3% Child-Pugh Grade C), decreasing zonulin levels in stool over 6 months were associated with higher Phascolarctobacterium abundance in the microbiome. Phascolarctobacterium was associated with better liver function (lower bilirubin, p = 0.04, INR p = 0.04, MELD Score, p = 0.02). Lower Phascolarctobacterium levels were observed in decompensated cirrhosis and were associated with 36-month mortality in two cohorts. Metabolomics analysis showed an association between Phascolarctobacterium and lower succinate levels. Succinate increased gut permeability in vitro, and Phascolarctobacterium succinatutens strains improved the intestinal permeability, potentially by alleviating the effect of succinate.

CONCLUSION: Phascolarctobacterium may represent a candidate biomarker of adverse outcomes in cirrhosis and a promising target for further investigation as a next-generation probiotic involved in gut barrier function and succinate homeostasis.

TRIAL REGISTRATION: NCT01607528, NCT03080129.},
}

Humans
*Liver Cirrhosis/microbiology/physiopathology/metabolism
Haptoglobins
Feces/chemistry/microbiology
Intestinal Barrier Function
Male
Protein Precursors/analysis
*Gastrointestinal Microbiome/physiology
Female
Middle Aged
Permeability
Cholera Toxin/metabolism/analysis
Biomarkers/analysis/metabolism
*Intestinal Mucosa/metabolism/microbiology
Aged
Magnetic Resonance Spectroscopy
RNA, Ribosomal, 16S/genetics

@article {pmid42438639,
year = {2026},
author = {Alkhaldi, M and Vicente, AF and Fansey, V and Salins, RM and Mahmoo, A and Alamgir, M and Dominic, AM and Siddig, MIS and Suk, C and Haider, QA and Wensel, JN and Rai, M},
title = {The Gastro-Circadian Metabolic Axis: A Comprehensive Framework for Chronotherapy in Gastroenterology.},
journal = {Cureus},
volume = {18},
number = {6},
pages = {e110724},
pmid = {42438639},
issn = {2168-8184},
abstract = {Circadian rhythms exert fundamental control over gastrointestinal and metabolic physiology, governing 24-hour patterns of motility, secretion, nutrient absorption, microbial activity, immune regulation, and hepatic metabolism. Accumulating evidence indicates that the gastrointestinal tract is not an isolated system but is tightly integrated with systemic metabolic and neuroendocrine networks, forming a coordinated gastro-circadian metabolic axis (GCMA). This axis links molecular clocks in the gut, liver, adipose tissue, and skeletal muscle with rhythmic inputs from the gut microbiome, feeding-fasting cycles, autonomic signaling, and enteroendocrine mediators. Disruption of circadian alignment, through shift work, sleep deprivation, irregular meal timing, or nocturnal light exposure, leads to desynchronization between central and peripheral clocks, promoting inflammation, impaired epithelial barrier function, dysbiosis, altered bile acid signaling, insulin resistance, and disturbed energy homeostasis. These mechanisms contribute to a wide spectrum of gastrointestinal disorders, including gastroesophageal reflux disease, functional dyspepsia, irritable bowel syndrome, metabolic dysfunction-associated steatotic liver disease, inflammatory bowel disease, and potentially gastrointestinal malignancies. This review synthesizes molecular, translational, and clinical evidence to position the GCMA as a unifying framework for understanding circadian influences on digestive and metabolic disease. Importantly, it highlights emerging therapeutic opportunities in chronotherapy, including time-optimized pharmacotherapy, chrononutrition, and microbiota-targeted interventions. While current translation is limited by interindividual chronotype variability and heterogeneous clinical evidence, advances in wearable circadian monitoring, multi-omics profiling, and computational modeling offer promising avenues for precision implementation. Integrating GCMA principles into clinical practice may improve disease outcomes and establish circadian alignment as a cornerstone of preventive and therapeutic gastroenterology.},
}

@article {pmid42438663,
year = {2026},
author = {Ahmed, I and Chadha, K and Paudel, KR},
title = {Irritable Bowel Syndrome: Contemporary Management Approaches, Limitations, and Future Directions.},
journal = {Cureus},
volume = {18},
number = {6},
pages = {e110741},
pmid = {42438663},
issn = {2168-8184},
abstract = {Irritable bowel syndrome (IBS) is a common disorder of gut-brain interaction characterized by recurrent abdominal pain associated with altered bowel habits in the absence of structural disease. Despite its high prevalence and substantial impact on quality of life, healthcare utilization, and long-term symptom burden, IBS management remains challenging because of its heterogeneous pathophysiology and variable treatment response. Current evidence supports a multifactorial model involving altered motility, visceral hypersensitivity, dysregulated brain-gut signaling, mucosal immune activation, microbiome changes, and intestinal barrier dysfunction, all of which contribute to the complexity of care. This narrative review summarizes contemporary management approaches for IBS, including dietary interventions, psychological therapies, pharmacologic treatments, biomarker-guided strategies, digital health technologies, and integrated care models. Particular attention is given to the low fermentable oligosaccharide, disaccharide, monosaccharide, and polyol (FODMAP) diet, soluble fiber, cognitive behavioral therapy (CBT), gut-directed hypnotherapy, subtype-specific pharmacologic agents, and emerging digital therapeutics that improve access to behavioral and self-management support. Although the literature demonstrates meaningful benefit across several treatment domains, important limitations remain, including short follow-up duration, lack of mechanistic stratification, inconsistent biomarker validation, and uncertainty regarding long-term treatment sequencing and personalization. Future progress in IBS care will likely depend on precision-oriented approaches that integrate clinical phenotyping, biologic markers, and multimodal treatment pathways tailored to individual patients. Continued emphasis on pragmatic trials, real-world implementation, and mechanism-based care models will be essential to improve outcomes and reduce the overall burden of IBS.},
}

@article {pmid42438737,
year = {2026},
author = {Faleiros, CA and Gonçalves, OS and Nunes, AT and Pires, CS and Poleti, MD and Fukumasu, H},
title = {Host breed and geography shape the antiviral defense landscape of the bovine rumen microbiome.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag162},
pmid = {42438737},
issn = {2730-6151},
abstract = {The rumen microbiome represents a complex, phage-rich ecosystem where microbial survival depends on both metabolic cooperation and antiviral defense. However, global and breed-associated variations in rumen prokaryotic immune systems remain poorly understood. Here, we performed the most comprehensive profile to date of antiviral defense systems (DS) in the rumen, analyzing 6530 microbial genomes and metagenome-assembled genomes (MAGs) from diverse cattle breeds and geographic regions. In this global dataset, we identified >90 000 DS, the most abundant of which were restriction-modification, PDC-S01, deoxyribonucleic acid modification systems (DMS_other), AbiE and SoFic, with variations influenced by both host the lineage and geographic region. A more in-depth analysis was performed using two complementary antiviral annotation frameworks for Nellore cattle (Bos indicus) from Brazil. Data exhibited a remarkably enriched antiviral defense repertoire, with over 15 632 DS encoded across 547 high-quality MAGs. These systems were densely clustered in dominant rumen lineages, such as Prevotella, and positively correlated with prophage abundance, consistent with virus-host coevolution. Notably, we also detected viral contigs encoding both antiviral defense and anti-defense genes, underscoring the arms race between the phages and their microbial hosts. Metatranscriptomic data from North America and Oceania revealed high expression levels of toxin-antitoxin modules, clustered regularly interspaced short palindromic repeats components, and restriction enzymes, suggesting a basal level of antiviral activity. These findings reveal the rumen as an antiviral innovation hotspot, highlighting microbiome resilience with implications for ecology, adaptation, and phage-based interventions.},
}

@article {pmid42438783,
year = {2026},
author = {Cao, W and Fan, Y and Chen, H and Sun, J and Jin, X},
title = {Etiology-Driven Mouse Models of Hepatocellular Carcinoma: Paving the Way for Precision Oncology.},
journal = {Journal of hepatocellular carcinoma},
volume = {13},
number = {},
pages = {621043},
pmid = {42438783},
issn = {2253-5969},
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) is biologically heterogeneous, and its genomic alterations, inflammatory context, and tumor immune microenvironment are strongly shaped by the underlying etiology, including chronic hepatitis B virus (HBV) infection, metabolic dysfunction-associated steatotic liver disease (MASLD), and alcohol exposure. This etiological diversity complicates the selection and interpretation of preclinical models. Genetically engineered mouse models (GEMMs), particularly when combined with dietary, chemical, viral, or alcohol-related insults, provide useful systems for dissecting how defined genetic drivers interact with disease-specific liver environments in an immunocompetent host.

MAIN BODY: This review summarizes etiology-aligned GEMMs and related mouse models for HCC. In HBV-related models, we discuss how viral antigen exposure, HBV-associated genomic instability, Tert activation, and Trp53 loss support a multi-driver framework rather than a single-lesion model of carcinogenesis. In MASLD-associated HCC, we examine models involving Wnt/β-catenin activation, Acvr2a loss, Pten deficiency, and MUP-uPA driven steatohepatitis, emphasizing their value for studying immune exclusion, lactate-rich immunosuppression, IgA+ plasma-cell accumulation, and altered responses to immune checkpoint blockade. In alcohol-associated HCC, we review models centered on Aldh2 deficiency, ER stress-lysosomal lipid remodeling through the ATF4/LPLA2 axis, NF-κB-related inflammatory regulation, and neutrophil-driven tumor promotion. Across these etiologies, we compare model strengths and limitations, including tumor latency, penetrance, reproducibility, lack of cirrhotic remodeling, sex-dependent variability, microbiome-related environmental effects, and incomplete modeling of tumor-stroma co-evolution.

SHORT CONCLUSION: Etiology-aligned GEMMs can help match biological questions to appropriate preclinical platforms and generate testable hypotheses about therapy response. However, etiology alone should not be treated as a substitute for molecular profiling or clinical validation. Future models should integrate precise genetic engineering with fibrotic or cirrhotic backgrounds, microbiome-aware environmental modulation, and complementary human-relevant systems to better capture the complex evolution of human HCC.},
}

@article {pmid42438837,
year = {2026},
author = {Byars, SG and Stearns, SC and Boomsma, JJ},
title = {Childhood appendectomy is linked with higher digestive, respiratory, and genitourinary disease risk but lower inflammatory bowel disease risk.},
journal = {Evolution, medicine, and public health},
volume = {14},
number = {1},
pages = {1-12},
pmid = {42438837},
issn = {2050-6201},
abstract = {BACKGROUND AND OBJECTIVES: Appendectomy is a common pediatric procedure generally considered safe beyond perioperative risks. However, the appendix may support gut biofilm maintenance and immune function, raising questions about potential long-term health consequences of its removal during childhood.

METHODOLOGY: We examined associations between appendectomy before age 12 and subsequent risk of 25 disease outcomes between ages 12 and 30, using a population-based cohort of up to 1 071 086 children born in Denmark between 1979 and 1999 and followed through linked national registers until 2009. Stratified Cox regression models compared surgically treated individuals with matched controls without significant pre-surgical health differences. Analyses adjusted for pregnancy complications, parental disease history, birth weight, Apgar score, sex, and socioeconomic factors.

RESULTS: Childhood appendectomy was associated with increased risk of several disease categories, particularly digestive [relative risk (RR) 1.45-1.64], respiratory (RR 1.20-1.73), and genitourinary disorders (RR 1.30-1.72). In contrast, inflammatory bowel disease (IBD) risk was reduced (RR 0.58). Absolute risk increases were most notable for digestive (up to 2.81%) and respiratory diseases (up to 4.89%), suggesting measurable population-level associations.

CONCLUSIONS AND IMPLICATIONS: Childhood appendectomy is associated with altered long-term disease risk. These findings support evidence that the appendix contributes to digestive and immune function. Although the reduced risk of IBD may represent a beneficial association, our results suggest that the appendix is not functionally redundant, particularly during immune development in childhood.},
}

@article {pmid42439052,
year = {2026},
author = {Scott, RK and Marzinke, MA and Prodger, JL and Powell, AM and Attalla, AE and Ghosh, M},
title = {Special Issue: New Horizons in HIV and Reproductive Health Research: HIV Acquisition and Reproductive Health in Key Populations.},
journal = {American journal of reproductive immunology (New York, N.Y. : 1989)},
volume = {96},
number = {1},
pages = {e70280},
doi = {10.1111/aji.70280},
pmid = {42439052},
issn = {1600-0897},
mesh = {Humans ; *HIV Infections/epidemiology/immunology ; Female ; Pregnancy ; *Reproductive Health ; Male ; Sex Workers ; Transgender Persons ; },
abstract = {Despite tremendous scientific breakthroughs in the prevention of HIV in the past decade, considerable gaps in knowledge persist regarding biologic vulnerabilities among the key populations who bear the greatest burden of the global HIV pandemic. Key conditions and subgroups with increased susceptibility to HIV include transgender and gender diverse persons and cisgender women-specifically during pregnancy, those who are survivors of sexual violence and female sex workers. Across groups, increased vulnerability to HIV is related to both increased physiologic susceptibility as well as synergistic social vulnerabilities, such as social marginalization and shifts or discordance in power dynamics in sexual and interpersonal relationships-which can both increase exposure to HIV and decrease access to and utilization of HIV prevention modalities (e.g., HIV pre-exposure prophylaxis, post-exposure prophylaxis, and barrier protection). In this review we examine epidemiology, immune system and hormonal regulation, microbiome, and known gaps in science associated with HIV acquisition among these key populations/conditions.},
}

Humans
*HIV Infections/epidemiology/immunology
Female
Pregnancy
*Reproductive Health
Male
Sex Workers
Transgender Persons

@article {pmid42439334,
year = {2026},
author = {Peng, J and Sun, L and Chen, Z and Wan, L and Wang, C and Peng, L and Chen, D and Long, Z and Gong, Y and Tan, Y and Wu, Q and Qiu, R and Tang, B and Jiang, H},
title = {Alterations in Skin Microbiota in Patients with Spinocerebellar Ataxia Type 3: A Pilot Study.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X460646260630071933},
pmid = {42439334},
issn = {1875-6190},
abstract = {BACKGROUND: Spinocerebellar ataxia type 3 (SCA3) exhibits marked variability in age of onset and disease progression that cannot be fully explained by CAG repeat length, indicating the presence of additional modifiers. The skin, as a neuro-immune interface, has been linked to neurological diseases but remains understudied in SCA3. The study aimed to characterize the skin microbiota in SCA3 and assess its relationship with disease severity.

METHODS: The study characterized the neck and armpit skin microbiota in 30 genetically confirmed SCA3 patients and 30 age and sex-matched healthy controls using 16S rRNA sequencing, and assessed site-specific microbial differences and their associations with clinical and genetic measures.

RESULTS: The neck exhibited higher alpha diversity and a distinct microbial composition compared with the armpit (P = 0.001). Microbial differences between patients and healthy controls were observed at both sites (armpit, P = 0.009; neck, P = 0.023). Relative abundances of 7 taxa were associated with motor severity, disease duration, and/or CAG repeat length, with functional predictions indicating alterations in metabolic and stress-related pathways. Site-specific microbial signatures from the neck or armpit showed diagnostic potential, achieving an AUC of 0.84 (95% CI, 0.64-1.00).

DISCUSSION: These findings suggest that the skin microbiome may represent a disease-associated signal in SCA3, warranting larger longitudinal and mechanistic studies to clarify its clinical relevance and biological significance.

CONCLUSIONS: SCA3 is associated with alterations in the skin microbiota. These changes are associated with disease severity and show potential for distinguishing patients from controls, supporting their possible utility as biomarkers.},
}

@article {pmid42439335,
year = {2026},
author = {Singh, S and Singh, S and Khandelwal, V and Bharti, U and Singh, PK},
title = {Gut Microbiota in Neuroinflammation, Neurodegenerative Disorders, and Neuropsychiatric Disorders: A Comprehensive Narrative Review.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273455874260702045636},
pmid = {42439335},
issn = {1996-3181},
abstract = {Neurodegenerative and neuropsychiatric illnesses are characterized by neuroinflammation, which is driven by microglial activation, cytokine production, and breakdown of the blood-brain barrier (BBB). It is currently known that the gut microbiota plays an important role in modulating neuroimmune signaling, which in turn may trigger anxiety-like behaviors and depressive phenotypes through the microbiota-gut-brain axis. This review aims to integrate the most recent mechanistic knowledge on treatment strategies targeting the gut microbiota to modulate neuroinflammation. This review article discusses preclinical and clinical studies that investigated microbial composition, metabolite profiles, and host-microbe interactions involved in neuroinflammatory processes. However, special attention was given to signaling via the vagus nerves and bile acids, as well as to tryptophankynurenine metabolism and short-chain fatty acids (SCFAs). To examine the potential connection between the two, researchers used animal models such as germ-free animals and antibiotic-injected mice for fecal microbiota transplantation (FMT). This article defines dysbiosis as amplifying neuroinflammatory responses by altering microglial phenotypes, disrupting the blood-brain barrier, and triggering the production of pro-inflammatory cytokines. In contrast, microbiome diversity rehabilitation through the use of probiotics, prebiotics, synbiotics, and dietary modifications reduces neuroinflammatory markers and enhances cognitive and behavioral status. Clinical trials have shown considerable promise in diseases such as Alzheimer's disease (AD), Parkinson's disease (PD), autism spectrum disorder (ASD), and depression. However, variability in treatment protocols, treatment resistance, and host-specific factors continue to pose significant challenges. This narrative review integrates mechanistic insights into microglial activation, cytokine signaling, blood-brain barrier regulation, vagal pathways, tryptophan metabolism, and short-chain fatty acids with emerging clinical evidence and therapeutic strategies, including probiotics, prebiotics, dietary modulation, and personalized microbiome-based interventions. Despite promising therapeutic potential, microbiome engineering faces important challenges, including safety concerns, lack of standardized intervention protocols, and substantial inter-individual variability in host-microbiome responses, which currently limit clinical translation. This review focuses on both neurodegenerative and neuropsychiatric disorders, examining shared neuroinflammatory mechanisms mediated by the gut-brain axis and evaluating microbiotatargeted therapeutic strategies across these disease categories. The review discusses both preventive strategies, including dietary modulation, prebiotics, and lifestyle-based microbiome interventions, as well as therapeutic approaches such as microbiota-targeted treatments aimed at mitigating neuroinflammation and disease progression.},
}

@article {pmid42439467,
year = {2026},
author = {Luo, Y and Kang, FL and Li, QM and Yang, WC},
title = {Metagenomic Association Uncovers Host Genotype-Structured Rhizobacterial Networks and Novel Taxa That Enhance Soybean Salt Tolerance.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76373},
doi = {10.1002/advs.76373},
pmid = {42439467},
issn = {2198-3844},
support = {YSBR-011//CAS project for Young Scientists in Basic Research/ ; 2023YFD1200600//National Key Research and Development Program of China/ ; XDA24010205//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA26030105//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2016QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; },
abstract = {Salinity is an escalating agricultural challenge, yet plant microbiomes offer a promising avenue for improving salt tolerance. Nevertheless, most naturally occurring microbes remain unevaluated for plant growth-promoting function, and systematic approaches to uncover salt-tolerance-enhancing plant growth-promoting rhizobacteria (PGPR) are limited. Here, using soybean as a model, we implement a quantitative framework to characterize rhizosphere microbial networks and nominate novel taxa functionally associated with plant salt tolerance. We introduced a salt tolerance index (STI) to quantify plant salt tolerance and normalize performance across heterogeneous natural soil salinity. Metagenomic sequencing and co-occurrence analysis revealed distinct rhizosphere microbiota structures between tolerant and susceptible soybeans. In tolerant soybeans, Pseudomonas dominated as the hub of a highly interconnected network, whereas susceptible accessions showed a fragmented network dominated by Acinetobacter. Correlation analyses identified bacterial taxa positively associated with STI, including documented salt-tolerant PGPR and novel candidates. Greenhouse experiments showed that one candidate, Thalassospira xiamenensis, enhances soybean salt tolerance and reshapes host ion-transport and oxidative-stress gene expression under salinity, validating our screening strategy. Our culture-independent metagenomic association approach reveals host genotype-structured rhizosphere microbial networks underlying salt tolerance and provides an efficient, labor-saving means for high-throughput identification of salt-tolerant PGPR.},
}

@article {pmid42439519,
year = {2026},
author = {Iyer, MS and Hagström, E and Näslund, K and Andersson, SGE},
title = {Harnessing endogenous CRISPR-Cas9 for inducible genetic engineering of Apilactobacillus kunkeei.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0072826},
doi = {10.1128/aem.00728-26},
pmid = {42439519},
issn = {1098-5336},
abstract = {UNLABELLED: Despite substantial advances in bacterial genome engineering, functional genetic analysis remains challenging in many non-model bacterial species, particularly among host-associated gram-positive bacteria. The fructophilic species Apilactobacillus kunkeei has been investigated for more than two decades and is a dominant member of the honeybee microbiome, where it contributes to pathogen resistance and colony fitness. Nevertheless, the mechanistic investigation of this ecologically important species has remained limited despite its growing probiotic relevance. To enable functional genomics in this organism, we developed an inducible genome-engineering platform that leverages its endogenous Type II-A CRISPR-Cas9 system. The system uses a sakacin-responsive dual-plasmid initiator-effector design in which phage-derived recombineering genes and a single-guide RNA are coordinately expressed, while DNA cleavage is mediated by natively expressed Cas9. Using this approach, we achieved scarless deletion of individual genes, including targets as large as ~25 kb, gene replacement with a fluorescent reporter, C-terminal epitope tagging, and precise nucleotide substitutions, with editing efficiencies approaching 100%. Both plasmids can be readily cured following modification, allowing recovery of clean mutant genotypes. We further demonstrate that endogenous Cas9 can be repurposed for CRISPR interference using a single, self-contained plasmid to enable targeted transcriptional repression. Together, this work establishes a robust strategy for genetic manipulation of A. kunkeei and expands the toolkit available for harnessing endogenous CRISPR-Cas systems in genetically recalcitrant, non-model gram-positive bacteria.

IMPORTANCE: Many ecologically and industrially important bacteria remain genetically recalcitrant, limiting functional genomic studies. As research increasingly extends beyond traditional model organisms, these limitations are especially apparent in non-model gram-positive bacteria from host-associated or environmental niches. Here, we establish an inducible genome-editing framework exploiting the endogenous Cas9 system of Apilactobacillus kunkeei, a key member of the honeybee microbiota. This approach enables reliable scarless gene deletions, precise nucleotide changes, large-scale genome modifications, and programmable transcriptional repression. By enabling genetic manipulation in A. kunkeei, this work facilitates experimental studies of its roles in honeybee health, microbial interactions, and host-associated adaptation, and highlights the potential of endogenous CRISPR-Cas systems for expanding genetic access in non-model bacteria.},
}

@article {pmid42439521,
year = {2026},
author = {Chanson, A and Gould, IJ and Almås, ÅR and Paz, AM and Castanheira, NL and Antunes, JF and Barker, A and Goddard, MR},
title = {Supporting crop yields under climate change by engineering innate soil microbiomes.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0043726},
doi = {10.1128/aem.00437-26},
pmid = {42439521},
issn = {1098-5336},
abstract = {We test the idea that innate agricultural soil microbiomes can be engineered to help support crops under climate change conditions. Salinization is one of the key drivers of agricultural soil degradation globally, and rising sea levels combined with decreasing rainfall are exacerbating this threat to food production. Changes in soil microbial community structures measured from DNA and functions and fitness measured from RNA and labeled amino acid uptakes support the hypothesis that the deliberate use of part-saline irrigation adapts soil microbiomes to increased salinities. While saline irrigation suppressed crop establishment in some cases, this microbiome response combined with inferences of increased microbial nutrient cycling and energy management correlates with final crop yield data and supports the hypothesis that engineered soil communities have helped protect yields under increased salinity conditions. This work provides evidence of the efficacy of a novel pragmatic, cost-effective innate soil microbiome engineering intervention for optimizing and securing food systems for future climate change conditions.IMPORTANCEThe consequences of climate change comprise significant and increasing threats to sustainable global food security. The salinization of agricultural soils is one of the main threats to agricultural production globally: this currently affects around 30% and is predicted to affect 50% of agricultural land by 2050. We show innate agricultural soil microbial communities can be engineered by low levels of saline irrigation. The engineered soil communities are better able to tolerate saline conditions and are inferred to have better nutrient turnover, and this correlates with protecting crop yields of established plants under saline conditions. This shows that it is possible for growers and farmers to "teach" or "prepare" soil microbiomes to become more tolerant of elevated soil and irrigation salinities predicted due to climate change in a way that will also meet sustainable food security requirements.},
}

@article {pmid42439572,
year = {2026},
author = {Walenkiewicz, B and Alvarez, L and Cava, F},
title = {LD-transpeptidation in bacterial cell walls: biochemical principles and functional diversity.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0009024},
doi = {10.1128/mmbr.00090-24},
pmid = {42439572},
issn = {1098-5557},
abstract = {SUMMARYPeptidoglycan (PG) is a dynamic, load-bearing polymer whose crosslinking chemistry governs envelope mechanics, growth modes, and stress tolerance. For decades, PG crosslinking was viewed primarily through the lens of penicillin-binding proteins (PBPs). However, accumulating evidence over the past 2 decades has established LD-transpeptidases (LDTs) as important contributors to PG remodeling. Here, we organize the expanding LDT field into macro-domains bridging biochemistry, evolution, and ecology. We initially describe the reaction mechanisms, structural diversification, and convergent solutions and then explore the evolution across species. We highlight non-canonical LD-crosslinking chemistries, including L-Ala-meso-DAP (1-3) linkages, that broaden the design space of the sacculus. We then map functional repertoires across lineages-from reinforcement during envelope stress to outer membrane tethering, predation, specialized secretion, dormancy, and biofilms. In pathogens where LD-crosslinking is dominant or essential, carbapenems and penems remain particularly effective inhibitors of LDTs, yet family-wide diversity calls for structure-guided selectivity and ecological awareness. We also chart underexplored connections to microbiome ecology and propose LDT-derived biomarkers that report growth modes and dormancy. We integrate dispersed evidence into a complete landscape in which two-component systems and environmental cues coordinate LD pathways. Building on these threads, we propose a unifying model of LDTs as adaptive architects of PG whose acyl-enzyme intermediate and modular substrate gating endow reversibility, partner choice, and context-dependent outcomes-reinforcement, remodeling, anchoring, or controlled self-breach. Finally, we outline methods that enabled the discovery of LDTs and explore future directions. Together, these perspectives reframe LDTs from auxiliary enzymes to central designers of envelope architecture and bacterial fitness.},
}

@article {pmid42439778,
year = {2026},
author = {Brychcy, M and Mildenberger, M and Fricke, WF and Schmidt, NS and Sina, C and Schmidt, H},
title = {Complete genomes of 12 Streptococcus salivarius strains and one Streptococcus raffinosi strain isolated from the human oral cavity and gastric lavage.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0022826},
doi = {10.1128/mra.00228-26},
pmid = {42439778},
issn = {2576-098X},
abstract = {In this study, 11 Streptococcus salivarius strains, one Streptococcus raffinosi strain isolated from the human oral cavity and a gastric lavage sample, as well as one S. salivarius reference strain, were whole-genome sequenced to investigate their genomic heterogeneity. Bioinformatic analysis indicated two major clades.},
}

@article {pmid42439788,
year = {2026},
author = {Sluydts, V and Bouilloud, M and Galan, M and Alburkat, H and Bordes, A and Bourret, V and Colombo, V and DeBruyn, L and Dutra, L and Eccard, J and Firozpoor, J and Gallet, R and Grzybek, M and Henttonen, H and Jacob, J and McManus, A and Sironen, T and Stuart, P and Tatard, C and Roche, B and Leirs, H and Charbonnel, N},
title = {Drivers of Host-Pathogen Community Assemblages in European Forests and Urban Green Spaces.},
journal = {Integrative zoology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1749-4877.70149},
pmid = {42439788},
issn = {1749-4877},
abstract = {Despite advances in understanding infectious diseases, the persistence and re-emergence of wildlife pathogens continue to raise public and veterinary health concerns. This study investigates the relationship between biodiversity and rodent-borne diseases in Europe, focusing on habitat alterations and their impact on rodent diversity. We present host-pathogen data from 21 temperate forest sites and eight urban green spaces throughout five European countries, environments where rodents are abundant and human/domestic animals-wildlife interactions are likely to occur. From 2020 to 2022, 3766 specimens comprising 15 different small mammal species were analyzed. Samples were screened for bacteria via 16S rRNA sequencing or PCR, and for viral antibodies using immunofluorescent assays. Pathogens from several genera, including Bartonella, Borrelia, Mycoplasma, Anaplasma, Neoehrlichia, Leptospira, Orthohantavirus, and Orthopoxvirus, were detected at non-negligible prevalence in 11 host species. Host community composition differed between habitats, with more urban adapters in parks than in forests. Pathogen richness increased with an increase in host species diversity, supporting the "host-diversity begets parasite-diversity" hypothesis, though not with anthropization. The absence of some vector-transmitted parasites in urban areas suggests a shift in pathogen community driven by human impact. Host species and intrinsic factors were dominant explanatory variables for Mycoplasma species and Sarcocystidae, while extrinsic environmental and climatic factors influenced variations in several vector-transmitted pathogens. Apodemus sylvaticus and Clethrionomys glareolus served as important connector hosts in urban spaces and temperate forests, respectively. These results improve our understanding of the complex local host-pathogen system, aiding future management decisions and supporting the public health sector.},
}

@article {pmid42439808,
year = {2026},
author = {Dotson, C and Kurowski, C and Grillo, M},
title = {Effect of selenium hyperaccumulation on the root endophytic and rhizosphere microbiome of two Astragalus species.},
journal = {Plant biology (Stuttgart, Germany)},
volume = {},
number = {},
pages = {},
doi = {10.1111/plb.70263},
pmid = {42439808},
issn = {1438-8677},
abstract = {Metal hyperaccumulation is prevalent throughout plant evolution, particularly in the legume family (Fabaceae), and acts as a presumed chemical defence against herbivory. However, metal hyperaccumulation can have non-target impacts on other biological interactors, including plant-microbe interactions. This information is important given the interest in utilizing hyperaccumulating plants for phytoremediation of anthropogenically contaminated soils. Here we employ a greenhouse experiment manipulating selenium level along with 16S rRNA gene amplicon sequencing methods to explore the effect of selenium on the prokaryotic microbiome of the selenium hyperaccumulator Astragalus crotalariae and non-accumulator A. lentiginosus var. borreganus. Regardless of hyperaccumulator status, both plant species accumulated high levels of selenium in leaf tissue when grown on soils with high selenium levels. The effect of selenium on the prokaryotic communities was slightly more pronounced in A. lentiginosus than in A. crotalariae, explaining ~5% more of the observed variation. This effect of selenium addition is seen most prevalently in A. lentiginosus root endosphere communities, in which selenate treatment impacted alpha diversity and whole community composition. Many individual microbes were affected by selenium addition; notably, an ASV identified as Allomesorhizobium, the nodulation-inducing genera of Astragalus spp., appeared in significantly less abundance in roots of A. lentiginosus plants grown on highly seleniferous soils. This project highlights the potential significance of ecological partners in metal accumulating plants and the necessity of their consideration when using these plants for phytoremediation.},
}

@article {pmid42439913,
year = {2026},
author = {Reyes, EIM and Veloso, TGR and da Luz, JMR and Aziz, MA and González, MAB and da Silva, MCS},
title = {Comparison of physical preservation strategies for accurate characterization of the coffee fruit microbiome.},
journal = {Archives of microbiology},
volume = {208},
number = {10},
pages = {},
pmid = {42439913},
issn = {1432-072X},
mesh = {*Microbiota ; *Coffea/microbiology ; Fungi/genetics/classification/isolation & purification ; *Fruit/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Cryopreservation/methods ; Freeze Drying ; *Preservation, Biological/methods ; Refrigeration ; *Coffee/microbiology ; DNA, Bacterial/genetics ; },
abstract = {The method used to preserve samples prior to DNA extraction is crucial for the accurate characterization of microbial diversity. This study evaluated the effects of different storage conditions on microbial DNA preservation in Coffea arabica fruit samples. Coffee cherries were harvested directly from plants, placed in plastic tubes, and stored at 4 °C before being subjected to four treatments: lyophilization, cryopreservation at - 80 °C, and refrigeration at 4 °C. Samples were stored for 3 and 13 days. Microbial communities were characterized by next-generation sequencing. Lyophilization retained more than 80% of the ASVs shared between days 3 and 13 of storage, whereas refrigeration at 4 °C retained less than 50%. These findings demonstrate that preservation method significantly affects the integrity of bacterial and fungal microbiomes in C. arabica beans. The absence of a time-zero control, chemical preservative comparisons, and the study's limited scope (single variety, location, and short storage period) warrant cautious interpretation of the findings. Although lyophilization was the best-performing physical preservation strategy evaluated here, broader validation across coffee cultivars, environments, and storage durations is still required before it can be considered a standard preservation protocol for preserving microbial materials derived from coffee samples.},
}

*Microbiota
*Coffea/microbiology
Fungi/genetics/classification/isolation & purification
*Fruit/microbiology
*Bacteria/genetics/classification/isolation & purification
Cryopreservation/methods
Freeze Drying
*Preservation, Biological/methods
Refrigeration
*Coffee/microbiology
DNA, Bacterial/genetics

@article {pmid42440071,
year = {2026},
author = {Jin, M and Jin, C and Shang, S and Gu, Y and Jin, P and Yu, H and Li, D},
title = {Synergistic T cell and microbiome dysregulation in FOXP3-mediated immune enteritis: insights from multimodal omics.},
journal = {Science China. Life sciences},
volume = {},
number = {},
pages = {},
pmid = {42440071},
issn = {1869-1889},
}

@article {pmid42440156,
year = {2026},
author = {Almutawif, YA and Eid, HMA},
title = {Microbiome-metabolite signaling networks in gastrointestinal disease: systems biology, network rewiring, and precision therapeutics.},
journal = {Archives of microbiology},
volume = {208},
number = {10},
pages = {},
pmid = {42440156},
issn = {1432-072X},
mesh = {Humans ; Systems Biology ; *Signal Transduction ; *Gastrointestinal Diseases/microbiology/metabolism/therapy ; *Gastrointestinal Microbiome/physiology ; Animals ; Inflammatory Bowel Diseases/microbiology/metabolism ; Gastrointestinal Tract/microbiology/metabolism ; },
abstract = {The gastrointestinal tract operates as a highly integrated, multi-layer signaling ecosystem in which microbial communities, metabolite flux, epithelial receptors, immune circuits, and neuroendocrine pathways form a coordinated regulatory network rather than isolated biological compartments. The Microbiome-Metabolite Signaling Network (MMSN) framework conceptualizes gastrointestinal homeostasis and disease as emergent properties of dynamic cross-layer interactions. This review explores the framework principally on inflammatory bowel disease and irritable bowel syndrome as representative gastrointestinal disorders, drawing on other conditions only for illustrative contrast. Within this architecture, microbiota-derived metabolites including short-chain fatty acids, bile acid derivatives, and tryptophan catabolites serve as biochemical intermediaries that relay ecological signals to host receptor systems such as GPR41/43, FXR, TGR5, the aryl hydrocarbon receptor, and innate immune sensors. These receptor-mediated inputs converge on intracellular signaling hubs, including NF-κB, STAT3, inflammasomes, and neuroimmune mediators, which act as high-centrality nodes governing epithelial integrity, cytokine gradients, metabolic coordination, and visceral sensitivity. Signaling hubs are mechanistic convergence nodes that integrate diverse upstream perturbations into coordinated inflammatory or regulatory outputs. In contrast, network fragility denotes the loss of redundancy, modularity, and buffering capacity, predisposing the system to nonlinear amplification and pathological attractor states. Gastrointestinal disorders are therefore more accurately interpreted as manifestations of network rewiring characterized by hub centralization, metabolite imbalance, and strengthened inter-module coupling rather than simple microbial compositional shifts. This review explains the clinical heterogeneity, fluctuating disease trajectories, and variable therapeutic responsiveness. A network-based translational strategy emphasizes hub stabilization, metabolite recalibration, and restoration of distributed connectivity, shifting precision therapeutics toward topology-informed intervention. Integration of microbiology, immunology, neuroscience, systems biology, and computational medicine establishes a pathway toward predictive, mechanistically grounded gastrointestinal network care.},
}

Humans
Systems Biology
*Signal Transduction
*Gastrointestinal Diseases/microbiology/metabolism/therapy
*Gastrointestinal Microbiome/physiology
Animals
Inflammatory Bowel Diseases/microbiology/metabolism
Gastrointestinal Tract/microbiology/metabolism

@article {pmid42440204,
year = {2026},
author = {Roy, MK and Bhattacharjee, A and Borah, B and Singh, AK},
title = {Soil to host environmental determinants fueling horizontal gene transfer and global AMR dissemination.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {42440204},
issn = {1874-9356},
support = {OLP-2403 and OLP-2503A//Council of Scientific and Industrial Research, India/ ; GPP-0423//Anusandhan National Research Foundation/ ; },
abstract = {Antimicrobial resistance poses a critical and escalating threat to global health, with horizontal gene transfer serving as a primary driver of resistance dissemination among microbial communities across diverse ecological niches. The three classical horizontal gene transfer mechanisms, including transformation, transduction, and conjugation, are complemented by supplementary routes involving outer membrane vesicles, gene transfer agents, and nanotubes. Both internal and external drivers synergistically influence horizontal gene transfer. Factors influencing the within-host microbiome include gut metabolites, antibiotic exposure, temperature fluctuations, and microplastic ingestion, while external environmental drivers such as antibiotic residues, heavy metals, agrochemicals, and micro/nano-plastics similarly enhance the mobility of antimicrobial resistance genes. The main mechanisms contributing to increased antimicrobial resistance gene transfer include elevated oxidative stress markers, altered membrane permeability, and stimulation of conjugation-related gene expression. The synergistic effects of these biotic and abiotic pressures have accelerated the co-selection of antimicrobial resistance genes and mobile genetic elements, intensifying the proliferation of antimicrobial resistance in both clinical and environmental reservoirs. Novel mitigation strategies such as conjugation inhibitors, bacteriophage-based interventions, and biochar amendments show promise in curbing horizontal gene transfer-mediated antimicrobial resistance; however, these approaches still lack insight into the intricate molecular mechanisms underlying horizontal gene transfer and often act non-specifically against different pathogens. Moreover, strategies utilizing biochar remain time-consuming and require further optimization. Overall, understanding the mechanistic interplay between environmental stressors and genetic exchange pathways is essential for developing sustainable interventions to counteract antimicrobial resistance. This review highlights the pressing need for integrated surveillance and ecological risk assessment to effectively manage the environmental aspects of antimicrobial resistance.},
}

@article {pmid42440278,
year = {2026},
author = {Couch, CE and Divilov, K and Herron, CL and Wang, B and Hakanson, OM and Scanlan, MM and Whitman, LD and Davis, MJ and Schreck, CB and Peterson, JT},
title = {Effects of a low-lipid diet on the gut microbiome and head kidney transcriptome of juvenile Chinook Salmon.},
journal = {Journal of aquatic animal health},
volume = {},
number = {},
pages = {},
doi = {10.1093/jahafs/vsag004},
pmid = {42440278},
issn = {1548-8667},
support = {//Oregon State University Agricultural Research Foundation/ ; //Oregon Hatchery Research Center/ ; },
abstract = {OBJECTIVE: Pacific salmon Oncorhynchus spp. reared in production hatcheries are typically fed high-lipid, energy-dense diets to achieve large size and high body condition prior to release. In contrast, juveniles in natural environments tend to consume low-lipid, high-protein diets, and fish reared for research or conservation purposes are sometimes fed diets that are formulated to mimic natural diets and promote wild-like phenotypes. Understanding how these alternative diets affect fish health beyond growth and body condition could ultimately contribute to improving hatchery fish fitness.

METHODS: In this work, we evaluated changes in the fecal microbiome and gene expression of juvenile Chinook Salmon O. tshawytscha on a standard high-lipid hatchery diet versus a low-lipid diet formulated to mimic the nutrition profile of natural-origin fish. To evaluate the time scale at which diet alters the fecal microbiome, we collected longitudinal samples over a 12-week period and switched the diets of a subset of fish twice during the experiment. We used 16S ribosomal RNA gene amplicon sequencing to characterize fecal microbiome differences between fish on the two diets as well as hatchery-reared fish at a production hatchery, hatchery fish that had been captured after release into a stream, and natural-origin, stream-reared fish of similar ages. Additionally, we conducted RNA sequencing on head kidney samples from laboratory-reared fish to evaluate changes in gene expression in this important immune organ.

RESULTS: We found that the low-lipid diet and the hatchery diet resulted in microbiomes that differed from the microbiome of natural-origin fish and from each other and that diet-driven changes to the microbiome could occur in under 14 d. The low-lipid diet did not result in a microbiome that resembled the microbiome of naturally produced fish. Instead, the low-lipid diet resulted in a microbiome community that was distinct from those of fish reared on the hatchery diet and fish sampled from the wild. The RNA sequencing results indicated differential enrichment of pathways related to immunity, metabolism, and hormone synthesis between fish that were fed the two experimental diets.

CONCLUSIONS: The results suggest that additional environmental factors influence the microbiome more strongly than diet formulation or that the low-lipid diet has a smaller effect on the microbiome than a natural, -invertebrate-based diet. Given that the gut microbiome and systemic immune function contribute significantly to disease resistance, our findings highlight the importance of understanding how diets fed to fish in captivity may affect fish health beyond growth and body condition metrics.},
}

@article {pmid42440521,
year = {2026},
author = {Lv, M and Xu, W and Wang, T and Mou, K and Ni, Z and Tu, Q and Zhang, J and Wu, X and Song, S and Cheng, G},
title = {Host-microbiome-immune disequilibrium in oral disease: mechanisms, dysbiosis, and precision therapeutics.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1854213},
doi = {10.3389/fimmu.2026.1854213},
pmid = {42440521},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology ; *Microbiota/immunology ; Animals ; Immunity, Mucosal ; *Mouth Diseases/immunology/microbiology/therapy ; Precision Medicine ; *Host Microbial Interactions/immunology ; Mouth/microbiology/immunology ; },
abstract = {BACKGROUND: The oral cavity harbors a dynamic microbial ecosystem that interacts with epithelial barriers, host immunity, and local tissue environments. Disruption of this balance is increasingly recognized as a key driver of major oral diseases, including periodontitis, dental caries, and oral squamous cell carcinoma (OSCC). However, the biological links between microbial ecology, immune regulation, and disease progression are insufficiently integrated, limiting mechanistic understanding and translational progress.

METHODS: This structured narrative review searched PubMed/MEDLINE, Web of Science, Embase, and Scopus for relevant studies on oral microbiome ecology, mucosal immunity, dysbiosis, oral diseases, and emerging therapies. Evidence was narratively synthesized across microbiome ecology, mucosal immunology, disease pathogenesis, and translational research, with consideration of study type, mechanistic relevance, and translational significance.

RESULTS: Current evidence supports that oral homeostasis relies on coordinated interactions among commensal microbial communities (CMC), epithelial and salivary barriers, and immune surveillance. Dysbiosis disrupts this equilibrium by promoting the expansion of pathobionts, amplifying inflammatory responses, and contributing to tissue injury. This systems-level perspective helps explain the persistence and heterogeneity of oral diseases beyond pathogen-centered models. Emerging technologies are reshaping this field. These include microbiome-modulating therapies, host-directed interventions, multi-omics approaches, and artificial intelligence (AI). These approaches are advancing disease stratification, biomarker discovery, and precision therapeutic development.

CONCLUSION: Oral diseases should be understood as disorders of host-microbiome-immune disequilibrium rather than as isolated infections. This perspective highlights the need for integrated strategies that consider microbial ecology, immune regulation, epithelial barrier function, and clinical context to improve prevention, diagnosis, and treatment in precision oral medicine.},
}

Humans
*Dysbiosis/immunology
*Microbiota/immunology
Animals
Immunity, Mucosal
*Mouth Diseases/immunology/microbiology/therapy
Precision Medicine
*Host Microbial Interactions/immunology
Mouth/microbiology/immunology

@article {pmid42440607,
year = {2026},
author = {Liu, Y and Gong, J and Zhang, Y and Wang, H and Feng, H},
title = {The oral-gut-joint axis in osteoarthritis: a multiomics case-control study.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1833218},
doi = {10.3389/fcimb.2026.1833218},
pmid = {42440607},
issn = {2235-2988},
mesh = {Humans ; *Osteoarthritis/microbiology/pathology ; Multiomics ; Case-Control Studies ; Female ; Cross-Sectional Studies ; Male ; RNA, Ribosomal, 16S/genetics ; Aged ; Middle Aged ; *Mouth/microbiology ; *Gastrointestinal Microbiome ; Proteomics ; Feces/microbiology ; Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Microbiota ; Gene Expression Profiling ; *Joints/microbiology ; },
abstract = {BACKGROUND: Osteoarthritis (OA) is a globally prevalent degenerative joint disorder that imposes significant socioeconomic burdens. While traditionally viewed as a localized "wear-and-tear" disease, emerging evidence supports a systemic pathogenesis involving the gut-joint axis. The oral-gut-joint pathway remains underexplored in OA pathophysiology.

OBJECTIVE: This study aimed to characterize oral and gut microbiota signatures in OA patients and elucidate their functional connections to cartilage degeneration through multiomics integration.

METHODS: We conducted a cross-sectional observational study involving 25 OA patients and 20 healthy controls. 16S rDNA gene amplicon sequencing was performed on fecal and oropharyngeal swab samples. Cartilage tissues were subjected to transcriptomic and proteomic analyses.

RESULTS: We identified distinct dysbiosis patterns in both the gut and oral microbiomes of OA patients. The α-diversity of the gut microbiota significantly increased (P<0.05) with enrichment of Ruminococcaceae and Subdoligranulum. Concurrently, the oral microbiota showed increased α-diversity and activation of the lipopolysaccharide biosynthesis pathway. We constructed two significant cross-omics correlation modules: one linking gut microbes (Lachnospiraceae and Muribaculaceae) to cartilage inflammatory genes (MAPK11, ITGB3, CD55 and ANGPT2) and extracellular matrix remodelling proteins and another connecting gut microbes (Helicobacter, Pseudomonas, and Phocea) with CXCL14 and GNGT2.

CONCLUSION: Our study revealed the dysbiotic characteristics of the oral-gut microbiome and its complex associations with pathological changes in cartilage. These findings offer novel mechanistic insights and potential therapeutic targets for microbiota-based precision interventions in OA.},
}

Humans
*Osteoarthritis/microbiology/pathology
Multiomics
Case-Control Studies
Female
Cross-Sectional Studies
Male
RNA, Ribosomal, 16S/genetics
Aged
Middle Aged
*Mouth/microbiology
*Gastrointestinal Microbiome
Proteomics
Feces/microbiology
Dysbiosis/microbiology
Bacteria/classification/genetics/isolation & purification
Microbiota
Gene Expression Profiling
*Joints/microbiology

@article {pmid42440727,
year = {2026},
author = {Abuhasanein, S},
title = {Oncobiotics in urinary bladder cancer. A narrative review of living cancer therapeutics.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1845015},
doi = {10.3389/fonc.2026.1845015},
pmid = {42440727},
issn = {2234-943X},
abstract = {Urinary bladder cancer (UBC) remains a major global health burden, with high recurrence rates and limited therapeutic options for patients who fail standard intravesical and systemic treatments. In recent years, Living Cancer Therapeutics (LCTs)-including bacteria-, virus-, and microbiome-based oncobiotics-emerged as innovative biological strategies capable of overcoming key limitations of conventional cancer therapies. This article is a narrative review aimed at mapping the mechanistic landscape, historical development, and translational progress of LCTs in UBC. Five interrelated mechanisms were identified through which oncobiotics exert therapeutic effects: (i) direct tumor destruction via bacterial colonization, cytolysis, and metabolic deprivation; (ii) immune system modulation through innate and adaptive immune activation; (iii) engineered drug delivery and synthetic biology enabling programmable, tumor-restricted payload release; (iv) oncolytic virotherapy combining selective tumor lysis with immune priming; and (v) microbiome-driven immune modulation influencing treatment responsiveness. Although conceptually distinct, these mechanisms frequently overlap in practice, reflecting the multifunctional nature of living therapeutics. Clinical translation has progressed furthest for immune-mediated approaches such as Bacillus Calmette-Guérin (BCG) and selected oncolytic viral platforms, particularly in BCG-unresponsive UBC, although current evidence remains limited by small studies, heterogeneous endpoints, and insufficient long-term follow-up. Advances in genetic engineering and synthetic biology have enabled the development of increasingly sophisticated investigational platforms, including engineered oncolytic viruses, programmable bacterial vectors, and microbiome-based therapeutic strategies; however, most remain at an early preclinical or translational stage. UBC may represent a favorable setting for LCT development due to the accessibility of the bladder and the established use of intravesical therapies, although delivery efficiency and therapeutic durability remain important challenges. Despite encouraging early findings, significant limitations persist, including biological delivery barriers, host immune neutralization, interpatient heterogeneity, biosafety concerns, regulatory complexity, and the scarcity of late-phase randomized clinical data. Further translational research, biomarker development, and long-term clinical evaluation will therefore be required to determine the future role of LCTs in UBC management.},
}

@article {pmid42440795,
year = {2026},
author = {Shi, C and Gao, Y and Zhang, L and Chen, C and Su, L and Ren, K and Liu, Z and Liu, J},
title = {Gut-heart axis at high altitude: a dynamic mediator from hypoxic dysbiosis to adaptive cardioprotection.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1861538},
doi = {10.3389/fmicb.2026.1861538},
pmid = {42440795},
issn = {1664-302X},
abstract = {High-altitude hypoxia severely disrupts physiological homeostasis and markedly increases cardiovascular disease (CVD) risk through mechanisms that remain incompletely understood. Emerging evidence regards the gut microbiota as a crucial dynamic regulator within the gut-heart axis, constructing a bridge between the environmental hypoxic stress and the cardiovascular outcomes. This review has summarized the dynamic changes of the gut microbiota in high-altitude environments, from acute dysregulation to adaptive remodeling. We systematically delineate the pathogenic mechanisms whereby acute microbial imbalance drives CVD: at the metabolic level, there is a reduction in the production of short-chain fatty acids (SCFAs), accumulation of trimethylamine N-oxide (TMAO), buildup of hypoxia-induced energy metabolism intermediates (lactic acid and succinic acid), and dysregulation of secondary bile acid metabolism. At the immune inflammatory level, impaired intestinal barrier leads to lipopolysaccharide (LPS) translocation, combined with hypoxia-inducible factor-1α (HIF-1α) overexpression, collectively promoting the development of atherosclerosis, hypertension, and heart failure. The adaptive remodeling reduces vascular injury by enhancing myocardial energy metabolism mediated by SCFA, strengthening the intestinal barrier, regulating anti-inflammatory immunity, stabilizing blood pressure, and also reprogramming uric acid metabolism, thereby playing a role in cardiac protection. Finally, we propose microbiome-targeted intervention strategies, including high-fiber dietary modulation, probiotic/prebiotic/synbiotic supplementation, fecal microbiota transplantation, and metabolite-directed therapies, which provides new theoretical basis and precise therapeutic targets for the prevention of cardiovascular diseases in high-altitude environments.},
}

@article {pmid42440964,
year = {2026},
author = {Zhu, H and Wei, S and Liu, H and Yang, H and Liu, T and Jiang, W and Lu, W and Lan, T},
title = {Integrated analysis of fecal microbiome and serum metabolome reveals the profiling of gut microbiota-related metabolites in rats and mice subjected to prolonged exposure to a high-humidity environment.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1782615},
doi = {10.3389/fcimb.2026.1782615},
pmid = {42440964},
issn = {2235-2988},
mesh = {Animals ; *Metabolome ; *Feces/microbiology ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Humidity ; Rats, Sprague-Dawley ; Mice ; RNA, Ribosomal, 16S/genetics ; *Serum/chemistry ; Male ; Rats ; Metabolomics ; Multiomics ; Chromatography, Liquid ; },
abstract = {BACKGROUND: High humidity, as a key climate risk factor, has become one of the significant threats to public health. However, less is known about the mechanism by which the high-humidity environment affects the health of the population. The present study was designed to reveal the profile of gut microbiota-related metabolites in rats and mice subjected to prolonged exposure to a high-humidity environment.

METHODS: Sprague-Dawley rats and C57BL/6 mice were housed under standard conditions (relative humidity of 60% ± 5%) or prolonged exposure to a high-humidity environment (relative humidity of 90% ± 5%) for 7, 14, and 28 days, respectively. Integrated analysis of fecal microbial diversity and serum metabolome was performed using 16S rRNA sequencing and non-targeted metabolomics with LC-MS/MS.

RESULTS: High-humidity exposure led to significant changes in the composition of the gut microbiota and serum metabolic profiles in both rat and mouse models. Our results revealed that disorders in glycerophospholipid metabolism, ABC transporters, and phenylalanine metabolism are key metabolic characteristics of hyperhumidity exposure. In addition, multi-omics correlation analysis identified the key gut microbiota-related metabolites, including phosphocholine, choline, LPC(16:0), taurine, L-valine, L-proline, 2-hydroxycinnamic acid, phenylacetaldehyde, P-salicylic acid, and PC(16:0/20:4(5Z,8Z,11Z,14Z)), which contributed to the pathogenic effect of high humidity.

CONCLUSIONS: The present study revealed that high-humidity exposure disrupts the host's metabolic homeostasis by altering the gut microbiota-related metabolites in rat and mouse models, showing commonalities and specificities. Our findings may provide new ideas and insights for further study on the pathogenic mechanism of hyperhumidity and intervention strategies targeting the microbiota.},
}

Animals
*Metabolome
*Feces/microbiology
*Gastrointestinal Microbiome
Mice, Inbred C57BL
*Humidity
Rats, Sprague-Dawley
Mice
RNA, Ribosomal, 16S/genetics
*Serum/chemistry
Male
Rats
Metabolomics
Multiomics
Chromatography, Liquid

@article {pmid42440971,
year = {2026},
author = {Gahlot, KD},
title = {Dietary modulation of the gut resistome: ecological and metabolic pathways driving antimicrobial resistance.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1868638},
doi = {10.3389/fnut.2026.1868638},
pmid = {42440971},
issn = {2296-861X},
abstract = {Antimicrobial resistance (AMR) is traditionally viewed as a consequence of antibiotic exposure and genetic adaptation; however, resistance also emerges from the ecological and metabolic context of microbial communities. The human gut microbiome represents a major reservoir of antibiotic resistance genes (ARGs), and diet is increasingly recognised as a dominant regulator of its structure and function. Here, I synthesise current evidence and propose a conceptual framework in which diet shapes resistome dynamics through three interrelated pathways: ecological selection, metabolic regulation, and physicochemical modulation of horizontal gene transfer. Dietary components influence microbial composition, metabolic activity, and the spatial organisation of fermentation along the colon. Diverse fibre types differentially regulate short-chain fatty acid production and microbial competition, whereas high-fat, low-diversity diets destabilise communities and favour opportunistic taxa. Beyond macronutrients, food additives and the physical structure of food alter gut barrier function, microbial stress responses, and spatial ecology, thereby influencing resistome stability. Diet-induced metabolic states further determine antibiotic susceptibility, including transitions between tolerance and resistance. Taken together, this integrated ecological perspective positions diet as a modifiable driver of AMR and highlights nutritional strategies as complementary approaches to mitigating resistome expansion.},
}

@article {pmid42441094,
year = {2026},
author = {Dal, GE and Çelik, B and Sabuncu, A and Yılmaz, M and Kekeç, AI and Dümen, E and İkiz, S and Diker, KS},
title = {Metagenomic analysis of the vaginal microbiota in cows with ovarian cysts.},
journal = {Journal of veterinary research},
volume = {70},
number = {2},
pages = {215-225},
doi = {10.2478/jvetres-2026-0028},
pmid = {42441094},
issn = {2450-7393},
abstract = {INTRODUCTION: This study compared the vaginal microbiota composition of dairy cows with follicular and luteal ovarian cysts using metagenomic analysis.

MATERIAL AND METHODS: Ovarian cysts, which impair reproductive performance through endocrine disruption, were diagnosed by ultrasonography and serum hormone evaluation in Holstein cows 30-60 d postpartum. Forty-five cows were initially included and divided into follicular cyst, luteal cyst and control groups. Vaginal lavage samples were analysed using third-generation sequencing, and taxonomic classification was performed through 16S rRNA gene analysis.

RESULTS: A total of 258 operational taxonomic units (OTUs) were identified, with the highest diversity observed in the control group (mean of 56.8 OTUs) and the lowest in the luteal cyst group (mean of 49.0 OTUs). Proteobacteria was the dominant phylum across all groups (93.4%), followed by Tenericutes (5.9%). Firmicutes, Bacteroidetes and Fusobacteria accounted for less than 1%. At the family level, Burkholderiaceae (62.7%) and Pasteurellaceae (24.0%) were predominant, while of the genera, Ralstonia was the most abundant (62.2%). The luteal group had the highest relative abundance of Burkholderiaceae, whereas Pasteurellaceae was most abundant in the control group.

CONCLUSION: These results indicate that cystic cows exhibit reduced microbial diversity and altered bacterial composition in comparison with healthy animals. The predominance of Proteobacteria and Ralstonia suggests a potential link between endocrine imbalance and changes in the vaginal microenvironment. Hormonal analyses supported the classification of cyst types, with follicular cyst cows showing low progesterone (0.31 ± 0.05 ng/mL) and high oestradiol-17β concentrations (55.57 ± 7.91 pg/mL), whereas luteal cyst cows exhibited higher progesterone (2.89 ± 0.74 ng/mL) and lower oestradiol-17β concentrations (6.19 ± 0.56 pg/mL) (P < 0.001). These results may support future studies evaluating vaginal microbial profiles as complementary indicators of ovarian status in dairy cows.},
}

@article {pmid42441206,
year = {2026},
author = {Shah, D and Karam, J and Hao, A and Shufelt, C and Kinnucan, J},
title = {Impact of Menopause and Clinical Considerations in Patients With Inflammatory Bowel Disease.},
journal = {Gastroenterology & hepatology},
volume = {22},
number = {4},
pages = {196-204},
pmid = {42441206},
issn = {1554-7914},
abstract = {Menopause is marked by a natural decline in estrogen and progesterone that alters gut barrier integrity, immune regulation, and systemic inflammation. In women with inflammatory bowel disease (IBD), this interplay may result in increased symptoms and worse clinical outcomes. Women with IBD face diagnostic delays, distinct disease phenotypes, higher rates of extraintestinal manifestations, and greater treatment burden. In menopausal women with IBD, specific guidance remains scarce. Beyond gut-specific effects, menopausal women are at an increased risk of osteoporosis, cardiovascular disease, and mood disorders. Lacking is a framework that promotes individualized, multidisciplinary care for menopausal women with IBD, focusing on the alterations in the immune system, gut microbiome, clinical presentations, multisystem risks, and therapeutic considerations. This article aims to synthesize the current evidence and research gaps around the impact of menopause in IBD, evaluate the safety and effectiveness of menopausal hormone therapy in this context, and propose a practical, patient-centered management framework for clinicians.},
}

@article {pmid42441335,
year = {2026},
author = {Zhang, L and Chakraborty, S and Székely, T and Komdeur, J},
title = {Parental Social Environment Has no Effect on Offspring Development in the Dung Beetle: A Test of Adult Sex Ratio Effects.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e73833},
doi = {10.1002/ece3.73833},
pmid = {42441335},
issn = {2045-7758},
abstract = {The adult sex ratio (ASR) is a key demographic parameter that shapes sexual selection and social interactions. While ASR variation drives profound behavioral plasticity within a generation, it remains unclear whether parental experience of skewed ASRs influences offspring development via transgenerational plasticity (TGP), and if so, which of the two core nongenetic pathways: pre-zygotic germline-mediated information transfer and post-zygotic parental investment, predominates. To disentangle these mechanistically distinct pathways, we conducted a controlled egg-transplantation experiment in the dung beetle Onthophagus taurus. We exposed parental beetles to female-biased, unbiased, and male-biased social environments, first confirming that our ASR manipulations generated the predicted gradients of social stress by quantifying contest and courtship behaviors. We then transplanted eggs from naturally produced brood balls across different ASR treatments into standardized artificial brood balls to strictly isolate germline-mediated TGP effects, while weighing original dried brood ball mass to independently assess parental investment. Our results revealed a striking dissociation between parental behavioral responses and intergenerational outcomes. ASR strongly modulated adult social interactions: male-biased treatments exhibited the highest contest intensity, whereas female-biased treatments displayed significantly higher courtship frequency than both unbiased and male-biased groups. Despite these pronounced parental adjustments, parental ASR experience had no significant effect on any measured offspring developmental trait, including developmental speed, emergence weight, and stage-specific developmental duration. Concurrently, parental investment (dried brood ball mass) did not differ across ASR treatments. These findings demonstrate that ASR-induced social pressures do not propagate to offspring metamorphic development via either core TGP pathway within a single generation, suggesting that offspring development is strongly canalized against parental social fluctuations. Future research should disentangle cryptic non-nutritional transmission pathways (e.g., microbiome inoculation) and employ gametic epigenetic assays to determine if social experiences leave molecular traces under alternative ecological contexts or longer evolutionary timescales.},
}

@article {pmid42441496,
year = {2026},
author = {Xie, L and Chen, K and Pan, X and Zhong, X and Li, X},
title = {Gut Microbiota and Metabolomic Changes In Type 2 Diabetes Mellitus: Insights From 16S rDNA Sequencing and Bioinformatics.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {232},
pages = {},
doi = {10.3791/70219},
pmid = {42441496},
issn = {1940-087X},
mesh = {*Diabetes Mellitus, Type 2/microbiology/metabolism ; Humans ; *RNA, Ribosomal, 16S/genetics ; *Computational Biology/methods ; *Gastrointestinal Microbiome/physiology/genetics ; DNA, Ribosomal/genetics ; Feces/microbiology ; Sequence Analysis, DNA/methods ; Metabolomics/methods ; },
abstract = {The global rise in type 2 diabetes mellitus (T2DM) underscores the need to better understand its underlying biological mechanisms, particularly those involving host-microbiome interactions. This study aimed to characterize gut microbial diversity, taxonomic composition, and predicted metabolic pathways in newly diagnosed T2DM patients compared with the non-diabetic matched (NM) group. Fresh stool samples were analyzed using 16S rDNA sequencing. Alpha diversity (Chao, ACE, Shannon, and Simpson indices) and beta diversity were calculated to assess microbial community structure. Taxonomic differences were evaluated using Wilcoxon rank-sum tests and linear discriminant analysis effect size (LEfSe). Functional pathway prediction was performed using phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt2) based on KEGG and MetaCyc annotations. Mendelian randomization (MR) analysis, including inverse-variance weighting, MR-Egger, and weighted median methods, was applied to assess genetically predicted associations between microbial taxa and T2DM. Results showed reduced microbial richness, as reflected by lower Chao and ACE indices, and altered diversity structure, as reflected by lower Shannon and higher Simpson indices, in T2DM patients, accompanied by significant compositional shifts. Increased relative abundance of Proteobacteria and decreased abundance of beneficial taxa such as Lachnospiraceae and Blautia were observed. Functional prediction indicated reduced abundance of pathways related to the non-oxidative pentose phosphate pathway, isobutanol biosynthesis, and L-isoleucine biosynthesis. MR analysis provided complementary evidence supporting associations between specific microbial taxa and T2DM susceptibility. In conclusion, T2DM is associated with reduced microbial richness, altered diversity structure, and distinct taxonomic and functional changes. These findings highlight the relevance of gut microbiota in T2DM and support the potential utility of microbiome-based biomarkers and therapeutic strategies. Further studies are required to validate these findings and clarify underlying mechanisms.},
}

*Diabetes Mellitus, Type 2/microbiology/metabolism
Humans
*RNA, Ribosomal, 16S/genetics
*Computational Biology/methods
*Gastrointestinal Microbiome/physiology/genetics
DNA, Ribosomal/genetics
Feces/microbiology
Sequence Analysis, DNA/methods
Metabolomics/methods

@article {pmid42441559,
year = {2026},
author = {Al-Tameemi, NK and Grove, JI and Hoad, CL and Wai, JWS and Olaru, A and Mandal, S and Rollins, KE and Bradley, CR and Francis, ST and Gowland, PA and Valdes, AM and Aithal, GP},
title = {The impact of pectin supplementation on systemic inflammation pathways, gut microbiome, and metabolic health in patients with Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD): A study protocol for a randomised controlled trial.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0352397},
doi = {10.1371/journal.pone.0352397},
pmid = {42441559},
issn = {1932-6203},
mesh = {Humans ; *Pectins/administration & dosage/pharmacology/therapeutic use ; *Dietary Supplements ; Adult ; *Gastrointestinal Microbiome/drug effects ; Female ; *Inflammation/metabolism ; Male ; Double-Blind Method ; Middle Aged ; *Fatty Liver/metabolism ; *Non-alcoholic Fatty Liver Disease/metabolism ; Liver ; },
abstract = {BACKGROUND: Metabolic dysfunction-associated steatotic liver disease (MASLD) is the leading cause of chronic liver disease, affecting over 30% of adults worldwide. Emerging evidence suggests that dietary fibre, particularly pectin, may improve metabolic health by modulating inflammation, gut microbiota composition, and intestinal permeability. However, controlled human studies in MASLD are limited. This study aims to evaluate the effect of pectin supplementation on systemic inflammation, gut microbiome, and metabolic health in patients with MASLD.

METHODS: This single-centre, double-blind, randomised, placebo-controlled dietary intervention will be conducted at Nottingham University Hospitals NHS Trust in partnership with the University of Nottingham. Thirty adults with MASLD will be randomised (1:1) to receive either 15g/day Low-methoxyl (LM) pectin or a matched placebo for six weeks. Each participant will attend baseline and post-intervention visits during which anthropometric data, fasting blood samples, and stool samples will be collected. FibroScan® assessments will be performed for all participants at both visits to quantify liver stiffness and steatosis. Twenty-two participants will take part in a magnetic resonance imaging (MRI) sub-study to evaluate hepatic and intestinal characteristics at baseline and post-intervention. Laboratory analyses will include liver function, lipid, glycemic, and inflammatory markers, alongside profiling of gut microbiota composition and short-chain fatty acids.

DISCUSSION: This is the first randomised controlled study to evaluate the mechanistic effects of pectin supplementation on inflammation, gut microbiome composition, and metabolic outcomes in MASLD. The results may generate novel evidence on the role of soluble fibre in modulating the gut-liver axis and support the development of scalable, nutrition-based interventions to improve metabolic and hepatic health in this population.

CLINICAL TRIAL REGISTRATION: The trial was registered on ClinicalTrials.gov (Identifier: NCT07093346).},
}

Humans
*Pectins/administration & dosage/pharmacology/therapeutic use
*Dietary Supplements
Adult
*Gastrointestinal Microbiome/drug effects
Female
*Inflammation/metabolism
Male
Double-Blind Method
Middle Aged
*Fatty Liver/metabolism
*Non-alcoholic Fatty Liver Disease/metabolism
Liver

@article {pmid42441583,
year = {2026},
author = {Luo, H and Zhang, H and Xu, L and Hong, L and Tang, H and Wang, C},
title = {Application of Acupuncture in the Management of Skin Diseases: A Review from the Perspective of the Microbiome.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {232},
pages = {},
doi = {10.3791/71199},
pmid = {42441583},
issn = {1940-087X},
mesh = {Humans ; *Acupuncture Therapy/methods ; *Microbiota ; *Skin Diseases/therapy/microbiology/immunology ; Skin Microbiome ; },
abstract = {Inflammatory skin diseases (e.g., atopic dermatitis, psoriasis, acne vulgaris, and chronic urticaria) are increasingly recognized as systems-level disorders arising from the interplay among immune dysregulation, barrier impairment, neuroendocrine imbalance, and microbial dysbiosis. High-resolution microbiome studies have moved the field beyond species-level associations to strain-level and functional insights, highlighting pathogenic Staphylococcus aureus lineages in atopic dermatitis (AD), disease-relevant Cutibacterium acnes phylotypes in acne, and gut microbial signatures that may prime type 17 helper T cell/regulatory T cell (Th17/Treg) imbalance and systemic inflammation across multiple dermatoses. Acupuncture is widely applied in dermatology to alleviate pruritus and reduce disease burden, with emerging sham-controlled trials and high-quality randomized evidence in chronic spontaneous urticaria (CSU) suggesting clinically meaningful symptomatic improvement. Mechanistically, acupuncture can engage neuro-immune circuits (including vagal anti-inflammatory pathways), modulate cytokine networks, and improve epithelial barrier integrity-host processes that strongly shape microbial ecology and metabolite production. Meanwhile, accumulating microbiome-focused studies in non-dermatologic conditions indicate that acupuncture can alter gut microbiota composition and diversity, as well as microbial metabolites (e.g., short-chain fatty acids), providing a plausible biological bridge to the gut-skin axis. In this narrative review, we synthesize evidence linking (i) skin/gut microbiome dysbiosis with inflammatory skin pathogenesis, (ii) acupuncture-mediated neuro-endocrine-immune modulation, and (iii) microbiome remodeling as a potential mediator of systemic and cutaneous immune modulation. We propose an integrative mechanistic framework and discuss methodological pitfalls (heterogeneous acupuncture protocols, challenges with sham designs, limited dermatology-specific microbiome endpoints, and gaps in causal inference), providing actionable directions for multi-omics longitudinal trials and mechanistic validation.},
}

Humans
*Acupuncture Therapy/methods
*Microbiota
*Skin Diseases/therapy/microbiology/immunology
Skin Microbiome

@article {pmid42441839,
year = {2026},
author = {Deng, S and Yang, Y and Guo, X and Yuan, MM and Zhang, Y and Wu, L and Shi, W and Zhou, X and Cornell, CR and Bates, CT and Liu, XA and Zhang, Q and Tian, R and Jian, S and Liu, S and Liang, Z and Lei, J and Gao, Q and Shi, Z and Wu, L and Liu, X and Luo, Y and Ning, D and Tiedje, JM and Zhou, J},
title = {Experimental drought drives divergent succession of soil microbiota.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {29},
pages = {e2537753123},
doi = {10.1073/pnas.2537753123},
pmid = {42441839},
issn = {1091-6490},
support = {32161123002//MOST | National Natural Science Foundation of China (NSFC)/ ; DE-SC0004601//U.S. Department of Energy (DOE)/ ; DE-SC0010715//U.S. Department of Energy (DOE)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; },
abstract = {As droughts become increasingly severe and prolonged worldwide, understanding how belowground biodiversity changes over time under water limitation is critical for assessing ecosystem resilience. However, long-term and continuous observations of soil microbial responses to drought remain rare. Here, using a 6-y experimental drought in a tallgrass prairie ecosystem, we showed that experimental drought reshaped the community compositions of soil bacteria, fungi, and protists, accompanied by progressive declines in microbial diversity and biomass. Analyses of time-decay relationships and paired community differences between drought and ambient conditions revealed increasingly divergent successional trajectories of soil microbiota under drought. Although stochastic processes dominated community assembly overall, their relative importance declined over time, particularly for bacteria in drought-treated soils, suggesting increasingly strong deterministic environmental filtering imposed by drought. In addition, drought reduced microbial network size but increased the complexity and stability of bacterial networks by favoring drought-tolerant taxa. Furthermore, drought-driven shifts in microbial community compositions significantly altered functional genes and associated ecosystem functioning. These findings suggest that microbial communities may become less variable but more vulnerable, and the detrimental effects of biodiversity loss on ecosystems could be more severe in an increasingly drought-prone world.},
}

@article {pmid42442203,
year = {2026},
author = {Zhang, XK and Long, XN and Tang, SS and Zheng, TX and Chen, D and Wei, FG and Wang, YL and Wu, Y and Dai, K and Cao, GH and He, S},
title = {Arbuscular mycorrhizal symbiosis decouples arsenic risk from saponin biosynthesis in Panax notoginseng (Araliaceae) by reprogramming rhizosphere and root processes.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142971},
doi = {10.1016/j.jhazmat.2026.142971},
pmid = {42442203},
issn = {1873-3336},
abstract = {Arsenic (As) contamination poses a serious threat to the safety and medicinal quality of Panax notoginseng, a high-value medicinal herb rich in triterpenoid saponins. Arbuscular mycorrhizal fungi (AMF) can improve plant tolerance to metal(loid) stress, but how AMF coordinate rhizosphere processes with host metabolic regulation to reduce As accumulation while maintaining medicinal quality remains poorly understood. Here, we integrated physiological assays, As partitioning and subcellular fractionation, rhizosphere microbiome profiling, root exudate metabolomics, phytohormone quantification, transcriptomics, proteomics, and partial least squares path modelling (PLS-PM) to investigate the effects of Entrophospora etunicatum inoculation on P. notoginseng under As stress. AMF colonization alleviated As-induced toxicity by improving plant growth, photosynthetic performance, and antioxidant capacity. Notably, AMF reduced As accumulation in medicinal taproot, while promoting As retention in fibrous roots and immobilization in cell wall-associated fractions. AMF also reshaped the rhizosphere bacterial community, enhanced glomalin-related soil protein (GRSP) accumulation and soil enzyme activities, and altered root exudate and endogenous hormone profiles. Transcriptomic and proteomic analyses indicated coordinated regulation of detoxification, transport, carbon metabolism, phenylpropanoid biosynthesis, and secondary metabolism. In parallel, AMF promoted the accumulation of major notoginseng saponins, suggesting that As detoxification was coupled with preservation of medicinal quality rather than a growth-defense trade-off. PLS-PM supported linkages among AMF colonization, rhizosphere reassembly, As sequestration, host metabolic reprogramming, and saponin accumulation. Overall, our results reveal a multiscale mechanism by which AMF reduce As risk in medicinal tissues while sustaining bioactive compound biosynthesis, providing promising biological strategy for safe production of medicinal plants in As-contaminated soils.},
}

@article {pmid42442277,
year = {2026},
author = {Zhang, X and Han, S and Zhao, A and Wei, B and Chang, X and Song, S and Zhao, Y and Zhao, Z and Zhang, X and Chen, J},
title = {Dietary cypermethrin exposure reshapes the rumen microbiota and enriches antibiotic resistance genes: Metagenomic evidence of co-selection.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120488},
doi = {10.1016/j.ecoenv.2026.120488},
pmid = {42442277},
issn = {1090-2414},
abstract = {Pesticide residues in crop-derived feedstocks represent a pervasive environmental stressor in agro-ecosystems, yet their role in driving the non-antibiotic co-selection of antimicrobial resistance (AMR) within the ruminant gut reservoir remains poorly understood. This study investigated the physiological trade-offs and indirect mechanisms of resistome expansion in a ruminant model exposed to environmentally relevant levels of cypermethrin. Integrated metagenomic and phenotypic assays revealed that cypermethrin exposure did not impair growth performance, but significantly increased daily feed intake and shifted fermentation profiles toward acetate. This metabolic compensation was supported by a reshaped core microbiome, characterized by increased abundance of fibrolytic consortia (e.g., Fibrobacter, Ruminococcus), enrichment of carbohydrate-active enzymes (GH3, GH5, GH13, and GH43), and upregulation of glycolysis and acetate-producing pathways. However, this metabolic adaptation came at a severe physiological cost, evidenced by systemic oxidative injury and hepatic dysfunction in the host. Crucially, cypermethrin acted as a potent non-antibiotic selective agent that expanded the ruminal resistome and mobilome, specifically, enriching efflux pumps (e.g., oqxA, MexB) confirmed target alteration genes (e.g., vanE). Consequently, dietary cypermethrin exposure forces microbial metabolic compensation at the expense of host hepatic health, while turning the ruminant gut into an overlooked repository for AMR. These findings highlight the critical ecological risks of pesticide-induced resistance co-selection, threatenting the One Health framework. Future research should incorporate multi-dose gradients, evaluate long-term exposure effects using sequential temporal sampling, and utilize non-invasive baseline monitoring across diverse ruminant species to fully elucidate these ecological risks.},
}

@article {pmid42442303,
year = {2026},
author = {Moshref-Javadi, M and Ahmadbeigi, G and Ataollahi, H and Boroomand, S and Kia, SK and Soleimani, N and Zia-Jahromi, N and Hedayati, M},
title = {Bidirectional microbiota-cancer crosstalk: Emerging platforms for advanced diagnostics and precision therapeutics in oncology.},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {201},
number = {},
pages = {119745},
doi = {10.1016/j.biopha.2026.119745},
pmid = {42442303},
issn = {1950-6007},
abstract = {Cancer is among the major causes of morbidity and mortality worldwide, and current treatment methods are limited by various drawbacks such as drug resistance, non-specificity, and differences among patients. With recent developments in this field, the human microbiota has emerged as one of the most important determinants for the onset, progression, and treatment of cancer. The bidirectional interactions of host microbiota and malignancies were investigated comprehensively in this review. Firstly, the origins, composition, and functional dynamics of the intra-tumoral microbiome were discussed, and then examined how microbial dysbiosis drives cancer development through DNA damage, chronic inflammation, epithelial-mesenchymal transition, and pharmacological inactivation. Moreover, some of the microbiome-based therapies, including phage-based therapy, bacterial extracellular vesicles, engineered probiotics, CRISPR/microbiome interactions, and microbiome regulation of immune checkpoint inhibitors and CAR T-cell therapy, were considered. In addition, the relevance of metabolites produced by the microbiome and taxonomy-based signatures as non-invasive biomarkers for detecting cancer at its early stages and predicting treatment outcomes is highlighted. The use of pharmacomicrobiomics and multi-omics profiling, along with artificial intelligence/machine learning, will accelerate the process of translating microbiome research into clinical applications and personalized cancer therapy. This review presents practical approaches that will help in leveraging the interaction between the microbiome and host in order to optimize the efficacy of immunotherapy while minimizing the risk of toxicity. Finally, we highlight a refined understanding of the microbiota-cancer axis, which has strong potential to redefine clinical paradigms in oncology and pave the way for more precise, effective, and individualized cancer management.},
}

@article {pmid42442320,
year = {2026},
author = {Sabater, C and Calvete-Torre, I and Vázquez, X and Cobo-Díaz, JF and Álvarez-Ordoñez, A and Ruas-Madiedo, P and Ruiz, L and Margolles, A},
title = {Metagenomics to assess authenticity and traceability of Asturian Gamonéu PDO cheese: A multi-omic study.},
journal = {International journal of food microbiology},
volume = {460},
number = {},
pages = {111939},
doi = {10.1016/j.ijfoodmicro.2026.111939},
pmid = {42442320},
issn = {1879-3460},
abstract = {Cheese is one of the most widely consumed fermented foods in Europe. The Principality of Asturias (northern Spain) has a broad tradition in cheese making including four cheeses under Protected Designation of Origin (PDO) status (Cabrales, Gamonéu, Casín and Afuega'l Pitu). The added value of PDO food products increases the risk of fraudulently copied cheeses reaching the market. The aim of this work was to develop a novel microbiome-based method contributing to the assessment of the authenticity of Gamonéu PDO cheese. For this purpose, cheese metagenomes and volatile organic compounds (VOCs) profiles were integrated using machine learning (ML) algorithms. Computational models accurately discriminated between samples from 9 Gamonéu PDO cheese producers, as well as between cheeses ripened in different natural caves. Furthermore, they allowed distinguishing PDO and non-PDO Gamonéu-like cheeses produced in the same area. Potential microbial markers of the geographical origin of Gamonéu PDO cheese included Debaryomyces hansenii, Lacticaseibacillus paracasei and Penicillium roqueforti (more abundant in non-PDO cheeses), and Brachybacterium faecium (more abundant in PDO cheeses). Computational models presented in this work may contribute to improving existing traceability methods in the field of fermented foods and may be applied to a wide range of cheese varieties.},
}

@article {pmid42442424,
year = {2026},
author = {Luo, Z and Zhang, K and Wang, L and Zhang, J and Huang, Y and Lu, X and Zhao, F and Cao, S and Li, J},
title = {Astragalus polysaccharides reshape gut resistome of postpartum dairy cows.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {135399},
doi = {10.1016/j.biortech.2026.135399},
pmid = {42442424},
issn = {1873-2976},
abstract = {Antibiotic resistance genes (ARGs) in livestock feces represent an important environmental reservoir of antimicrobial resistance. Natural product intervention is a potential strategy for regulating the gut microbiome of livestock; however, its effects on the gut resistome of postpartum dairy cows remain poorly understood. In this study, we investigated the effects of Astragalus polysaccharides (APS) supplementation on the fecal microbiome, ARGs, mobile genetic elements (MGEs), virulence factors (VFs), and ARG-carrying metagenome-assembled genomes (MAGs) in dairy cows during postpartum period. Alpha and beta diversity analyses showed that APS supplementation did not significantly alter the global resistome, mobilome, or virulome structure. The content of several ARGs and VFs, including AAC(6')-Iw, qacEdelta1, ast, PM_RS00425, and sdrF, significantly decreased in the APS group, and several plasmid-associated MGEs genes showed group-specific changes. Co-occurrence network analysis revealed complex associations between ARGs, VFs, and core bacterial taxa, with Paludibacter and Parabacteroides identified as potential microbial reservoirs of resistance- and virulence-associated genes. Furthermore, 101 metagenome-assembled genomes (MAGs) were recovered, 42 of which carried multiple ARGs. Bin.1, assigned to Scatovivens, had the highest ARG count. APS supplementation reduced the overall ARG load, particularly the ARG contribution in bin.1. However, APS utilization potential was not significantly correlated with ARG density or ARG load across MAGs. Thus, this study provides new insights into APS supplementation and nutritional strategies that can mitigate the fecal ARG burden in dairy production.},
}

@article {pmid42442519,
year = {2026},
author = {Li, Y and Deng, W and Li, Q and Zhou, C and Sun, N and Liu, W and Zhao, X and Xie, M and Zhu, M and Wang, X and Zhang, F and Li, L and Zhang, Q and Jiang, F and Zhu, X and Ge, Y and Guan, W and Li, J},
title = {Engineered novel protease-stable multifunctional peptides attenuate metabolic dysfunction-associated steatotic liver disease via disrupting bile acid micelle and activating PPAR pathway.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108341},
doi = {10.1016/j.phrs.2026.108341},
pmid = {42442519},
issn = {1096-1186},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) poses a global health challenge, yet effective therapies are hindered by limited efficacy of synthetic medications and poor druggability of natural bioactive compounds. Here, we report an engineered therapeutic strategy for MASLD that overcomes the gastrointestinal (GI) instability of a soy-derived peptide, soystatin (SP), through structural optimization and live probiotic delivery. Firstly, we developed two protease-resistant peptide analogs of SP, SP2 and SP9, which maintain potent bile acids micellar-disruptive capacities in the degradative environment of the GI tract. These peptides significantly reduced serum and hepatic lipids while resolving hepatic steatosis, which is superior to that of cholestyramine at the same dose and equivalent weight, the first-line cholesterol-lowering and traditional sequestrant. Additionally, pharmacokinetic analysis documented that these peptides exhibited gut-localized with negligible systemic exposure. Further investigations revealed that SP2 and SP9 work via a "dual-hit" lipid-lowering mechanism. Physically, like cholestyramine, they block intestinal cholesterol absorption by impairing micelle formation. Biologically, they reprogram hepatic lipid metabolism by activating the peroxisome proliferator-activated receptor signaling pathway and fatty acid β-oxidation, while modulating the bile acid pool linked to altered gut microbiome. These peptides may also mitigate the oxidative hepatocellular damage via the downregulation of oxidative phosphorylation. Finally, we engineered a gut-colonizing Lactobacillus plantarum WCSF1 strain to continuously secrete SP2 and SP9-repeats in situ, significantly attenuating MASLD activity scores and improving lipid profiles. Our results demonstrate that coupling optimized bioactive peptides with engineered probiotic chassis provides a promising strategy for the long-term management of chronic metabolic liver diseases.},
}

@article {pmid42442593,
year = {2026},
author = {Qi, T and Liu, Q and Li, M and Li, H and Liang, G and Tu, W},
title = {Integrating lung microbiome, amino acid metabolism, and host immune response in elderly patients for severe lower respiratory Infections diagnosis: a multi-omics study.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121232},
doi = {10.1016/j.cca.2026.121232},
pmid = {42442593},
issn = {1873-3492},
abstract = {BACKGROUND: Lower respiratory infections (LRIs) cause significant morbidity and mortality in elderly individuals, but the mechanisms driving severe deterioration remain unclear.

METHODS: This prospective study enrolled 105 patients aged ≥60 with suspected LRIs between October 2024 and April 2025. Bronchoalveolar lavage fluid (BALF) was analyzed using 16S rRNA sequencing, metagenomics, untargeted metabolomics, and cytokine profiling. Multi-omics data were integrated into a tripartite network, and severity-associated signatures were identified via PLS-DA, logistic regression, and ROC analysis.

RESULTS: The cohort included 40 severe (sLRIs) and 65 mild (mLRIs) cases. sLRIs exhibited reduced microbial diversity, shifting from commensal genera to opportunistic pathogens (Klebsiella, Corynebacterium, Elizabethkingia), with Klebsiella pneumoniae as a major bacterial hub. Metabolomics revealed 180 differential metabolites. Phenylalanine and beta-Alanine metabolism emerged as key severity-associated pathways. sLRIs showed accumulation of pro-inflammatory metabolites L-phenylalanine and phenylpyruvic acid. L-3-phenyllactic acid (PLA) served as the central metabolic hub. Cytokine profiling revealed local hyperinflammation (elevated IL-1β, IL-6, IL-8, TNF-α, IFN-γ), with IL-6 as central hubs. Multivariate analysis identified PLA and IL-8 as independently associated with severe status. Combined metabolic-immune signatures achieved high diagnostic accuracy (AUC: 0.858-0.882).

CONCLUSIONS: sLRIs in elderly patients are characterized by microbial dysbiosis, opportunistic pathogen enrichment, and remodeled Phenylalanine and beta-Alanine metabolism that correlates with hyperinflammation. BALF PLA and IL-8 represent promising metabolic-immune biomarkers for severity stratification.},
}

@article {pmid42442631,
year = {2026},
author = {Nam, J and Kwon, D and Moon, Y},
title = {Microbiota-Circadian Desynchrony as a Mechanistic Interface for Xenobiotic-Induced Systemic Metabolic Fatigue.},
journal = {Chemico-biological interactions},
volume = {},
number = {},
pages = {112256},
doi = {10.1016/j.cbi.2026.112256},
pmid = {42442631},
issn = {1872-7786},
abstract = {Fatigue is increasingly recognized as a systemic manifestation of disrupted metabolic and neuroendocrine homeostasis under conditions of xenobiotic and iatrogenic stress, yet its underlying toxicological mechanisms remain poorly defined. Emerging evidence indicates that environmental toxicants and antibiotics perturb host physiology not only through direct cellular toxicity but also by destabilizing microbiota-dependent circadian regulation. In this review, we synthesize current experimental and clinical evidence to delineate a microbiota-circadian axis as a mechanistic interface linking xenobiotic exposure to systemic metabolic dysfunction and fatigue-related phenotypes. Mechanistically, toxicant- and antibiotic-induced dysbiosis disrupts the production of key microbial metabolites, including short-chain fatty acids, secondary bile acids, and tryptophan-derived compounds. These metabolites function as critical regulators of peripheral circadian clocks, mitochondrial bioenergetics, and neuroendocrine signaling. Their depletion leads to circadian misalignment, impaired metabolic efficiency, and activation of neuroinflammatory pathways, notably through a shift in tryptophan metabolism toward the kynurenine pathway and altered mesolimbic dopaminergic signaling. We further re-evaluate legacy clinical evidence on antibiotic-associated fatigue, proposing that inconsistent findings may reflect limitations in study design, including inadequate assessment of circadian disruption and delayed microbiome recovery. Importantly, circadian disruption itself emerges as a key modifier of host susceptibility, amplifying the biological impact of xenobiotic and microbial perturbations. Finally, we discuss translational implications, highlighting chronotherapeutic and microbiome-targeted strategies aimed at restoring temporal and metabolic homeostasis. By positioning fatigue as a downstream consequence of xenobiotic-driven microbiota-circadian disruption, this review provides a mechanistic framework for understanding environmentally induced systemic dysfunction and identifies potential avenues for targeted intervention.},
}

@article {pmid42442659,
year = {2026},
author = {Yannakoulia, Μ and Kontogianni, ΜD and Antonopoulou, S and Fragopoulou, E and Kyriacou, A and Gutierrez de Piñeres, V and Panagiotakos, D and Mantzoros, CS},
title = {Mediterranean diet: definitions, health effects and metabolic pathways - evidence and future directions.},
journal = {Metabolism: clinical and experimental},
volume = {},
number = {},
pages = {156690},
doi = {10.1016/j.metabol.2026.156690},
pmid = {42442659},
issn = {1532-8600},
abstract = {The Mediterranean diet (MedDiet) is one of the most extensively studied dietary patterns in relation to chronic disease prevention and management. MedDiet reflects a plant-forward dietary model characterized by high intake of fruits, vegetables, legumes, whole grains, nuts, and olive oil, moderate consumption of fish and dairy, low intake of red and processed meats, and optional moderate wine intake with meals. This review summarizes current evidence linking adherence to the MedDiet with major health outcomes, including cardiovascular disease, type 2 diabetes mellitus, metabolic dysfunction-associated steatotic liver disease, chronic kidney disease, neurodegenerative disorders, and cancer. Evidence from prospective cohort studies, randomized controlled trials, and meta-analyses consistently supports protective associations, particularly for cardiovascular and metabolic endpoints. Biological pathways underlying these effects include modulation of inflammation, oxidative stress, endothelial function, thrombosis, gut microbiome composition and/or function, and metabolomic profiles. Advances in metabolomics and microbiome research provide emerging insight into potential intermediary mechanisms linking dietary exposure to disease risk. Methodological challenges in assessing adherence and heterogeneity in scoring systems are also discussed as well as future research priorities.},
}

@article {pmid42443246,
year = {2026},
author = {Park, YY and Lee, J and Lee, KY and Oh, ST},
title = {Fecal microbiome profiles in uncomplicated right colonic diverticulitis: An exploratory prospective case-control study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61278-z},
pmid = {42443246},
issn = {2045-2322},
abstract = {Right colonic diverticulitis is common in East Asian populations, but its microbiome features remain poorly characterized. This exploratory prospective case-control study compared fecal microbiome profiles between patients with uncomplicated right colonic diverticulitis (URCD) and healthy controls (HC) and explored clinical-course-related patterns. Twenty patients with CT-confirmed acute URCD and ten HC participants underwent stool sampling and 16S rRNA gene sequencing using the EzBioCloud Microbiome Taxonomic Profiling workflow. Alpha and beta diversity did not differ significantly between the overall URCD and HC groups, and no taxon remained significant after false discovery rate correction. In patients sampled before symptom relief, those requiring antibiotics (n = 2) showed nominal enrichment of Proteobacteria compared with those recovering without antibiotics (n = 8) (9.917% [interquartile range, 9.656-10.178] vs. 1.626% [0.650-2.423], p = 0.044; q = 0.467), although these findings were not significant after multiple-testing correction. Among patients who recovered without antibiotics and had documented sampling timing, the Firmicutes-to-Bacteroidetes ratio was higher in the after-symptom relief subgroup (n = 6) than in before-symptom relief subgroup (n = 8) (0.98 [0.710-2.150] vs. 0.22 [0.130-0.340], p = 0.008), and beta-diversity profiles differed between these subgroups (PERMANOVA, p = 0.003). These exploratory findings suggest that fecal microbiome differences in URCD are not clearly detectable in overall case-control comparisons but may show clinical-course-related patterns in selected subgroups. Larger longitudinal studies with serial sampling are needed.},
}

@article {pmid42443264,
year = {2026},
author = {Kunihiro, BP and Yamamoto, BY and Juarez, R and Maunakea, AK},
title = {Gut microbiome signatures associate with DNA methylation-based biological aging.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42443264},
issn = {2045-2322},
support = {R56MD014630/MD/NIMHD NIH HHS/United States ; R01MD016593/MD/NIMHD NIH HHS/United States ; P20GM139753/GM/NIGMS NIH HHS/United States ; },
abstract = {Recent advances in machine learning have applied novel tools to aging research, yet the relationship between the gut microbiome and epigenetic aging remains underexplored. This proof-of-concept study investigates whether gut microbial composition is associated with biological aging pace independent of chronological age. Using paired 16S rRNA gene sequencing and DNA methylation data from 123 monocyte-enriched samples in a cohort including Native Hawaiian and Pacific Islander participants, we developed "EpiBiome" models to predict epigenetic age acceleration residuals and DunedinPACE, a DNA methylation biomarker that estimates the instantaneous pace of biological aging. Models predicting residuals of traditional clocks (Horvath, Levine, GrimAge2) showed no predictive signal at either taxonomic rank. By contrast, the EpiBiome-Accel model for DunedinPACE reached statistical significance at both the species level (R[2] = 0.152, Spearman ρ = 0.408, p = 0.012; permutation p < 0.001) and the genus level (R[2] = 0.099, permutation p = 0.036). Adding chronological age as a feature did not improve performance (ΔR[2] = - 0.046 at species level), indicating age-independence. SHAP analysis of the species-level ElasticNet model identified Bifidobacterium adolescentis as the dominant contributor and the strongest predictor of decelerated aging, with Succinivibrio dextrinosolvens showing the strongest association with accelerated aging. These findings reveal specific gut taxa as hypothesis-generating candidates for mechanistic follow-up, rather than as individual-level diagnostic markers.},
}

@article {pmid42443349,
year = {2026},
author = {Yang, Q and Fu, L and Chen, H and Huang, W and Guo, Y and Liu, L and Fu, Q and Liu, T and Chen, F},
title = {An investigation of the abnormalities in the microbiome‑gut‑brain axis in betel quid chewers.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60616-5},
pmid = {42443349},
issn = {2045-2322},
support = {Qhyb2023-183//the Hainan Provincial Graduate Innovation Research Project/ ; ZDYF2024SHFZ058, ZDYF2023SHFZ096//the Key Science and Technology Project of Hainan Province/ ; 82271977, 82160327//the National Nature Science Foundation of China/ ; YSPTZX202514//the Innovation Platform for Academicians of Hainan Province and Hainan Academician Innovation Platform Scientific Research Project/ ; },
abstract = {Betel quid (BQ) chewing, a prevalent practice affecting over 600 million people globally, is associated with systemic toxicity and neurological alterations. While dysbiosis of the gut microbiota is implicated in neuropsychiatric disorders via the gut-brain axis (GBA), its role in BQ chewers remains unexplored. This exploratory study aimed to investigate whether chronic BQ chewing is associated with gut dysbiosis and alterations in spontaneous brain activity. Fecal samples (n = 30 BQ chewers, n = 19 healthy controls) were subjected to whole metagenome shotgun sequencing (WMGS) to assess microbial composition and function. Amplitude of low-frequency fluctuations (ALFF) values, a resting-state functional magnetic resonance imaging metric reflecting regional spontaneous neural activity, were assessed in a subset of 29 BQ chewers and 21 healthy controls. Group differences in microbiota and ALFF were analyzed using the Wilcoxon rank-sum test and two-sample t-test (adjusted for age, sex, education, smoking and alchohol). Partial Spearman's correlation analysis was performed to link microbial taxa with ALFF alterations. Motivated by the presence of complex polysaccharides and polyphenols in BQ, carbohydrate-active enzyme (CAZyme) profiles were also assessed. Chronic BQ chewers exhibited significant gut microbiome alterations, characterized by reduced microbial diversity, enrichment of pro-inflammatory genera, and depletion of beneficial taxa. Analysis of carbohydrate-active enzymes further revealed altered metabolic potential in BQ chewers. Furthermore, reduced ALFF was observed in the limbic lobe of BQ chewers. At a nominal significance level, Streptococcus abundance correlated positively with limbic ALFF (partial ρ = 0.35, 95% CI [0.07, 0.58], raw p = 0.04), whereas Dorea formicigenerans exhibited a negative correlation (partial ρ = -0.36, 95% CI [- 0.55, - 0.08], raw p = 0.04). Chronic BQ chewing is associated with gut microbial dysbiosis and functional metabolic shifts. Exploratory analyses suggest that these microbial features may correlate with spontaneous neural activity in the limbic lobe, providing preliminary evidence for a potential involvement of the GBA in BQ‑associated neurological sequelae. These findings highlight the need for further investigation into microbiota‑targeted strategies in BQ chewers.},
}

@article {pmid42443351,
year = {2026},
author = {Gancz, NN and Savoca, PW and Callaghan, BL},
title = {The oral microbiome is associated with stress, adversity, and mental health in young adults.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-60803-4},
pmid = {42443351},
issn = {2045-2322},
support = {1F31MH139356-01A1./MH/NIMH NIH HHS/United States ; R00MH113821/MH/NIMH NIH HHS/United States ; },
abstract = {Acute stress responsivity and early-life adversity are both associated with oral microbiome differences that lead to increased mental and physical health risk. However, the joint association of stress responsivity and early adversity with the oral microbiome is not yet understood. Additionally, while the link between the oral microbiome and cortisol has been investigated, another major component of stress responsivity - the parasympathetic response - has been relatively neglected. Therefore, we examined parasympathetic functioning during an acute stressor, retrospective early adversity, oral microbiome (using the bacterial 16S gene), and anxiety and depression symptoms in 76 undergraduates. Early adversity was associated with lower microbiome diversity. Independently of adversity, parasympathetic withdrawal during the stressor was positively associated with Alysiella, a genus previously linked to latent viral infections. Early adversity and parasympathetic function did not significantly interact. Additionally, depressive symptoms were negatively associated with Butyrivibrio, which produces neuroprotective metabolites. Our findings suggest that childhood adversity and parasympathetic stress response are independently associated with oral microbiome differences, and that the oral microbiome is associated with mental health. By characterizing the associations of the oral microbiome with stress, adversity, and mental health, this study lays important groundwork for future research on psychophysiological causes and outcomes of oral microbiome differences.},
}

@article {pmid42436262,
year = {2026},
author = {Kelley, M and Rathore, S and Chandrasegaran, K and Herbert, C and Sabile, CEG and Wood, T and Joves, J and Palacios, A and Hamal, B and Tompkin, J and Susanto, E and Uhran, M and Ledezma-Ramírez, A and Chen, SC and Singh, K and Rust, R and Solorio, MM and Khalid, MS and Mitra, AT and Vinauger, C and Buschbeck, EK and Limbach, PA and Benoit, JB},
title = {Microbiome-derived queuine vitamers underlie tyrosine metabolism and predator avoidance in mosquito larvae.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10537-w},
pmid = {42436262},
issn = {2399-3642},
support = {R01AI148551//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R21AI176098//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01AI155785//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; VA-1017860//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; VA-160212//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; IOS-1856241//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; DEB-1654417//NSF | BIO | Division of Environmental Biology (DEB)/ ; },
abstract = {The gut microbiome is a rich source of nutrients that are critical to the development and biology of eukaryotes. Transfer RNAs (tRNAs) are essential components of protein synthesis, and certain chemical modifications of tRNAs depend on the availability of microbiome-derived nutrients. In eukaryotes, the nucleobase queuine (q) or nucleoside queuosine (Q) is salvaged from the microbiome or diet and incorporated into tRNA, where it influences the speed and efficiency of protein synthesis. Here, we examine the role of microbiome-derived Q in mosquito larval development and behavior. When mosquito larvae are grown with a microbiome incapable of synthesizing Q, there is a significant impact on tyrosine levels and downstream processes, which correlate with defects in behavior and cuticle formation. Likely due to effects on movement and behavior, Q-deficient larvae exhibit impaired predator evasion, resulting in increased capture by predaceous beetle larvae. The broad effects of Q-deficiency in mosquito larvae highlight the importance of previously unexplored microbiome-derived nutrients for mosquito physiology and behavior.},
}

@article {pmid42436290,
year = {2026},
author = {Vimonsuntirungsri, T and Samuthpongtorn, C and Tangkijvanich, P and Tharavej, C and Chobarporn, T and Mesiri, D and Pittayanon, R},
title = {Gastric mucosal brushing enhances gastric microbiome profiling compared with conventional biopsy in gastric cancer.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-61440-7},
pmid = {42436290},
issn = {2045-2322},
support = {RA67/034//Ratchadapiseksompotch Fund Chulalongkorn University/ ; RA67/034//Ratchadapiseksompotch Fund Chulalongkorn University/ ; RA67/034//Ratchadapiseksompotch Fund Chulalongkorn University/ ; RA67/034//Ratchadapiseksompotch Fund Chulalongkorn University/ ; RA67/034//Ratchadapiseksompotch Fund Chulalongkorn University/ ; RA67/034//Ratchadapiseksompotch Fund Chulalongkorn University/ ; RA67/034//Ratchadapiseksompotch Fund Chulalongkorn University/ ; },
abstract = {Gastric microbiota dysbiosis has been implicated in gastric carcinogenesis; however, the specific sampling method for assessing non-Helicobacter pylori microbiota associated with gastric cancer (GC) remains unestablished. This study compared gastric mucosal brushing with conventional biopsy for microbiota profiling in patients with GC and controls. We enrolled treatment-naïve GC patients and controls and analysed paired brushing and biopsy specimens using 16 S rRNA sequencing. Microbial analyses were compared between sampling methods and between the GC and control groups, and taxa-GC associations were assessed using age- and sex-adjusted mixed models. Overall brushing samples exhibited higher α-diversity than biopsy, including genus richness 60 ± 46.5 vs. 25.5 ± 19.5, Shannon 3.45 ± 0.71 vs. 2.80 ± 0.79, and Simpson 0.95 ± 0.03 vs. 0.92 ± 0.06 (all p < 0.0001), with different β-diversity (R[2] = 0.05, p < 0.001). In brushing samples, GC showed reduced α-diversity compared with controls (richness 39.5 ± 35 vs. 82 ± 51.8, p = 0.01; Shannon 3.20 ± 0.53 vs. 3.78 ± 0.52, p < 0.0001; Simpson 0.94 ± 0.05 vs. 0.96 ± 0.02, p = 0.002) and altered β-diversity (R[2] = 0.05, p = 0.01), whereas biopsy showed no α- and β-diversity differences. Our study demonstrates that brushing yielded higher bacterial diversity and different gastric microbiota profile compared with conventional biopsy sampling. Brushing also revealed depleted microbial diversity and altered microbial profile in gastric cancer. These findings suggest that brushing may improve the detection of certain gastric cancer-associated microbiota alterations.},
}

@article {pmid42436378,
year = {2026},
author = {Zhang, H and Yao, H and Zhang, K and Zhang, C},
title = {Short-term temporal variation in the early-life gut microbiota links maternal clinical phenotypes to neonatal jaundice.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05383-z},
pmid = {42436378},
issn = {1471-2180},
abstract = {BACKGROUND: Maternal clinical phenotypes shape the neonatal gut microbiome and influence infant health outcomes, yet the microbial mechanisms linking maternal conditions to neonatal jaundice remain largely unknown. To investigate this, we characterized bacterial community profiling in prenatal maternal feces, meconium, and postnatal Day 3 neonatal feces from a mother-infant cohort, and integrated microbiota-phenotype association analyses and mediation models.

RESULTS: We found that meconium microbiota showed slightly lower divergence from maternal fecal microbiota than neonatal fecal microbiota did. Canonical correspondence analysis (CCA) showed that maternal HbA1c consistently contributed to early-life gut microbial community structure, explaining 7% of the variation in meconium microbiota and 11% of the variation in neonatal fecal microbiota. Neonatal transcutaneous bilirubin levels on Day 3 were also associated with early-life microbial variation, with a stronger association observed in neonatal fecal microbiota than in meconium. In addition, maternal HbA1c significantly correlated with maternal urinary bacterial counts. The abundance distribution patterns of meconium ASVs related to maternal diabetes status and urinary bacterial detection status were also observed in the corresponding taxa of neonatal gut microbiota and were associated with subsequent neonatal jaundice. Notably, specific differentially abundant ASVs affiliated with Bifidobacterium, Clostridium_T, and Rothia mediated the interconnected rather than independent effects of maternal HbA1c and urinary bacterial counts on neonatal jaundice.

CONCLUSIONS: The results suggest that meconium microbiota features associated with maternal diabetes-related phenotypes influence early neonatal gut microbial community structure and may contribute to neonatal jaundice. This study highlights the potential role of early-life gut microbiota shifts in mediating the effects of maternal physiological variation on neonatal health outcomes.},
}

@article {pmid42436575,
year = {2026},
author = {Mou, HL and Wang, ZX and Zhang, MD and Liu, YL and Ren, T and Ruan, PC and Han, YG and Zeng, Y and Zhang, HY and Lu, JG and Zhang, Y and Liu, CL and Huang, YF and Zhao, YJ and Zhao, ZQ and Pan, X and Zhou, LP and Ceccobelli, S and E, GX},
title = {Host genetic architecture and gut microbiota cooperatively regulate early growth in goats.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00597-y},
pmid = {42436575},
issn = {2524-4671},
support = {32272834//Innovative Research Group Project of the National Natural Science Foundation of China/ ; },
abstract = {Early postnatal growth is a critical determinant of meat production efficiency and long-term genetic improvement in goats; however, the molecular mechanisms underlying individual variation in growth performance remain poorly understood. In this study, a total of 123 Hechuan white goats were included. First, a genome-wide association study (GWAS) for average daily gain (ADG) was performed using all 123 individuals. Subsequently, based on the coefficient of variation of ADG (CV = 65.6%), an extreme phenotype sampling (EPS) strategy was applied to select 39 individuals with extreme growth phenotypes for subsequent metabolomic, microbiome, and integrated mGWAS analyses.The results showed that ADG approximately followed a normal distribution across the 123 goats. GWAS identified 22 loci significantly associated with ADG, mapping to genes including DLK1, NCAPG2, LCORL, CNTNAP2, and SLC8A1, which are involved in pathways related to skeletal muscle development, cell cycle regulation, ion transport, and immune function. Metabolomic profiling detected 1,589 putative metabolites, revealing differential enrichment of lipid, amino acid, and bile acid metabolic pathways between fast- and slow-growing goats. Gut microbiome analysis demonstrated that Christensenellaceae_R-7_group and Monoglobus were significantly enriched in fast-growing individuals, whereas Desulfovibrio was more abundant in slow-growing goats.Integrated mGWAS analysis further revealed extensive effects of host genetic variation on gut microbiota and fecal metabolites. Specifically, 11 bacterial genera were significantly associated with host genomic variants, among which Desulfovibrio exhibited the highest number of associated loci. Integration of multiple variant types consistently linked Desulfovibrio, Eubacterium_hallii_group, and Candidatus_Saccharimonas with genes such as ARHGAP24 and IGF2BP2. In addition, 14 metabolites were significantly associated with host genetic variants, with Lysopc(14:1(9Z)/0:0) and glycocholic acid showing the strongest associations. Notably, the peak signal for Lysopc was located within HMGA2.Collectively, these findings define a coordinated host genome-gut microbiota-metabolite network underlying early growth variation in goats and provide a mechanistic foundation for precision breeding and targeted nutritional strategies in goat production systems.},
}

@article {pmid42436588,
year = {2026},
author = {Yang, Y and Nettifee, J and Azcarate-Peril, MA and Muñana, KR and Callahan, B},
title = {Gut microbiome alterations in canine idiopathic epilepsy: a pairwise case-control study.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00594-1},
pmid = {42436588},
issn = {2524-4671},
abstract = {BACKGROUND: Idiopathic epilepsy (IE) is the most common chronic nervous system disorder of dogs, and its cause is poorly understood. Emerging evidence suggests that microbiome alterations can occur with IE via the microbiota-gut-brain axis. Therefore, we analyzed the fecal microbiomes of 98 dogs (49 IE, 49 control) in a pairwise case-control observational study using 16S rRNA gene sequencing.

RESULTS: Although the microbial community was mostly similar between groups, IE was associated with a modest but significant shift in weighted UniFrac distance (p = 0.042). We used six differential abundance (DA) methods to identify differentially abundant amplicon sequencing variants (ASVs) between IE and control groups. Notably, one Collinsella ASV was found to be significantly more abundant in IE dogs by all six methods. The gut microbial compositions varied drastically across households (accounting for about 69% of the total variation), but did not have significant differences between sex, age, or breed. Phenobarbital administration in IE dogs had a significant effect on seizure control, and was not associated with changes in the microbiome.

CONCLUSION: Our findings suggest a relationship between gut microbiomes and IE. However, the specific mechanism needs to be further investigated.},
}

@article {pmid42436613,
year = {2026},
author = {Vourlaki, IT and Furman, O and Tapio, I and Guan, LL and Waters, SM and Kenny, D and Smith, P and Kirwan, SF and Kelly, D and Evans, R and Quintanilla, R and Piles, M and Reverter, A and Alexandre, PA and Li, F and Garnsworthy, PC and Bani, P and Pope, PB and Morgavi, DP and Mizrahi, I and Ramayo-Caldas, Y},
title = {Ruminosignatures associated with methane emissions and feed efficiency across geographies and cattle breeds.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag185},
pmid = {42436613},
issn = {1751-7370},
abstract = {The cattle rumen microbiota represents a complex and dynamic ecosystem whose organization and relationship to host phenotypes are important for food security and environmental sustainability. We analyzed rumen microbiota profiles from 2,496 cattle representing five breeds and production systems across five countries, identifying microbial co-abundance groups termed Ruminosignatures. We detected fourteen distinct Ruminosignatures, including two consistently observed across all populations dominated by Prevotella and UBA2810. Additional Ruminosignatures showed breed- and diet-specific patterns and collectively explained 96-99% of variance in rumen microbial composition. Integrative cross-country analysis confirmed 10 out of 14 Ruminosignatures identified in cohort-specific analyses. Several Ruminosignatures were associated with methane emissions and feed efficiency traits and were partially under host genetic control, with heritability estimates ranging from 0.09 to 0.58. Structural equation modelling revealed consistent negative genetic and phenotypic correlations between the UBA2810-dominated Ruminosignature (RS_UBA2) and methane emissions across cohorts (rg = -0.40 to -0.65), with structural coefficients concordant in sign across all populations, supporting the expected direction of phenotypic response to selection on RS_UBA2. Meta-analysis confirmed positive associations of RS_UBA2 with average daily gain and negative associations with methane-related traits and feed conversion ratio. Functional genome-based predictions suggested RS_UBA2 may reduce methanogenesis through alternative hydrogen utilization pathways competing with methanogenic archaea. Production system type influenced both Ruminosignature occurrence and relationships with host phenotypes, emphasizing the relevance of context-specific strategies for microbiome modulation. Our findings highlight the potential of the Ruminosignatures framework for microbiome-informed breeding programs aimed at improving feed efficiency while reducing the environmental impact of cattle production.},
}

@article {pmid42436618,
year = {2026},
author = {Parappalliyalil, H and Padmakumar, A and Ghosal, D and Reynolds, EC},
title = {Architectural Intelligence: Toward a Spatial Framework for Interpreting Microbiome-Associated Human Disease.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag180},
pmid = {42436618},
issn = {1751-7370},
}

@article {pmid42436619,
year = {2026},
author = {Zheng, C and Song, J and Shan, M and Zhang, H and Qiu, M and Zhang, L and Yu, Y and Wang, X and Fang, H},
title = {Bridging ecological processes to elevated antibiotic resistance risk in tomato microbiome under fungicide stress.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag182},
pmid = {42436619},
issn = {1751-7370},
abstract = {From a "One Health" perspective, antibiotic resistance genes (ARGs) harbored by the plant microbiome pose a significant threat to public health, yet their ecological mechanisms under fungicide stress remain largely unexplored. Here, a comprehensive framework integrating selection, dispersal, antagonistic interactions, and horizontal gene transfer (HGT) is established to elucidate the ecological risks and assembly mechanisms of the tomato resistome under fungicide stress, using multi-omics and several validation experiments. The indirect/direct ecological risks of ARGs in aboveground tomato tissues increase by 1.69-93.81-fold and 1.29-123.49-fold under fungicide exposure, respectively, compared to the control. Dispersal and selection emerge as the dominant ecological processes shaping the resistome under fungicide stress, driven by antibiotic-resistant bacteria (ARB) with streamlined and multifunctional metabolic traits, respectively. A fluorescently labeled ARB migration model and an indigenous ARB-based conjugation model demonstrate that fungicides promote the upward dispersal of native ESKAPE pathogens and intensify HGT among them, facilitating the emergence of multidrug-resistant bacteria. Validation experiments confirm that fungicides induce metabolic reprogramming of flavonoid biosynthesis in roots, which enhances HGT by modulating various physiological phenotypes. These findings underscore the ecological risks posed by fungicides in promoting ARG dissemination within the plant microbiome through multiple ecological mechanisms.},
}

@article {pmid42436804,
year = {2026},
author = {Yi, M and Luo, J and Abdo, E and Lu, Z and Pan, X and Han, X and Sun, X and Xia, Y and Dai, J and Shi, K and Chen, Z},
title = {Orally administered biomimetic nanovesicles engineered with FGF2 orchestrate mucosal healing and microbiome remodeling in inflammatory bowel disease.},
journal = {Materials today. Bio},
volume = {39},
number = {},
pages = {103430},
pmid = {42436804},
issn = {2590-0064},
abstract = {Inflammatory bowel disease (IBD) is characterized by chronic intestinal inflammation and profound microbial dysbiosis, presenting significant therapeutic challenges. While fibroblast growth factor 2 (FGF2) possesses potent regenerative capabilities, its oral administration is severely hindered by rapid gastrointestinal degradation. To overcome these delivery barriers, this study investigates a novel, targeted therapeutic strategy utilizing nanoscale outer membrane vesicles (OMV/FGF2) naturally secreted during the normal growth of FGF2-engineered Gram-negative bacteria. The isolated OMV/FGF2 (120.1 nm, -13.7 mV) maintained robust structural integrity in simulated gastric fluid and demonstrated highly favorable cytocompatibility. In a dextran sulfate sodium (DSS)-induced murine colitis model, orally administered OMV/FGF2 significantly attenuated disease severity, mitigating weight loss and colon shortening. Mechanistically, OMV/FGF2 actively restored the intestinal physicochemical barrier by upregulating tight junction proteins (Occludin, ZO-1) and promoting mucus hypersecretion. Furthermore, 16S rRNA analysis revealed that OMV/FGF2 reversed microbial dysbiosis, enhancing α-diversity and enriching beneficial commensals (e.g., Bacteroides, Lactobacillus) while suppressing pathogenic populations. Ultimately, OMV/FGF2 ameliorates intestinal inflammation through a synergistic dual mechanism of fortifying the epithelial barrier and remodeling the gut microbiome. This engineered nanoplatform provides a promising, orally bioavailable therapy for IBD.},
}

@article {pmid42437026,
year = {2026},
author = {Mohidin, AF and Neshat, SA and Santillan, E and Wuertz, S},
title = {Disturbance intensity shapes universal and context-dependent functional traits in anaerobic microbiomes.},
journal = {Environmental science and ecotechnology},
volume = {32},
number = {},
pages = {100729},
pmid = {42437026},
issn = {2666-4984},
abstract = {Trait-based frameworks, notably Grime's competitor-stress-tolerant-ruderal theory, offer a powerful lens for predicting how environmental fluctuations govern community structure. Yet, classical ecological models assume environments combining extreme stress and intense disturbance are non-viable for sustained colonisation, leaving a critical bottleneck in our ability to predict how microbial systems withstand compounded operational pressures. This gap severely hinders the predictive management of engineered microbiomes critical for global waste-to-energy conversion. Here we extend the application of classic ecological frameworks by demonstrating that anaerobic digester microbiomes deploy distinct, predictable life-history strategies across a 182-day compounded gradient of biomass turnover and organic loading. High-intensity single-event disturbances drive severe volatile fatty acid accumulation (propionate reaching 2,955 mg L[-1]), selectively shifting the microbiome toward stress-tolerant and stress-tolerant-ruderal strategies. Traits associated with ribosome function, molecular chaperones, and enzymatic reactive oxygen species detoxification were particularly enriched under highly disturbed conditions. Conversely, intermediate regimes were associated with ruderal strategies that prioritise rapid growth over resource-uptake efficiency, dropping total chemical oxygen demand removal to 41%. Cross-system comparisons encompassing anaerobic digestion, activated sludge, and soil ecosystems, revealed both universal and context-dependent ecological traits. Survival-associated traits linked to cell maintenance and repair, protective mechanisms, and cell motility were universally associated with stress-tolerant or ruderal strategies across ecosystems, whereas nutrient transport and metabolic traits exhibited greater context dependency. These insights establish a gene-resolved framework that reconciles microbial trait selection with ecological theory, providing a roadmap to engineer microbiome resilience against process failures.},
}

@article {pmid42437098,
year = {2026},
author = {Lee, JE and Kim, JS and Do, Y and Park, JK},
title = {Physiological and Skin Microbiome Divergence Among Closely Related Anurans Co-Occurring in Agricultural Wetlands.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e73944},
pmid = {42437098},
issn = {2045-7758},
abstract = {Understanding why endangered amphibian species decline while closely related congeners persist remains a central challenge in conservation biology. Host physiological traits and symbiotic microbial assemblages are increasingly recognized as important mediators of species responses to environmental conditions. Unlike broad comparative studies across geographically separated populations, we compared physiological capacity and skin microbiome characteristics among four anuran species, two endangered species and their respective common congeners from two genera (Dryophytes and Pelophylax), at a fine sympatric scale within shared agricultural wetlands in South Korea. Physiological traits, including body size, corticosterone levels, and bacterial killing ability, were structured primarily at the genus level, with species identity explaining 49.6% of multivariate physiological variation. Skin bacterial alpha diversity tended to be higher in common species, although statistically significant differences were not maintained after correction. Skin bacterial community composition also differed significantly among species (PERMANOVA, R [2] = 0.296), whereas Bd prevalence remained comparable across species (75%-85.7%). Microbial network analysis revealed species-specific differences in topology, with highly connected networks in D. japonicus, fragmented structure in D. suweonensis, and intermediate connectivity in both Pelophylax species. Functional prediction analyzes suggested differences in predicted microbial functions among host species. Together, these findings suggest subtle but structured trait differentiation among sympatric species and support integrating physiology, skin microbiomes, Bd infection, and predicted microbial functions as a complementary trait-based framework for amphibian conservation assessment.},
}

@article {pmid42437521,
year = {2026},
author = {Asemoloye, MD},
title = {Enhancing the Secretion Systems: Genetic Engineering of Super Bioagents for Effective Plant Disease Control.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70303},
pmid = {42437521},
issn = {1097-0290},
abstract = {The escalating threat of plant diseases to global agriculture and food security necessitates innovative and sustainable control strategies. Conventional biological control agents (BCAs), while environmentally friendly, often suffer environmental challenges and secretion of limited/poor antimicrobial compounds. Advances in CRISPR/Cas genome editing, protease engineering, and synthetic biology have enabled precise modifications that improve pathogen targeting and secretion efficiency. Interest should now be shifted on development of "Super Bioagents (SBs)" with enhanced secretion systems (SSs) for plant disease suppression against changing environmental factors. This will create sustainable ecofriendly alternative to chemical pesticides. This review explores a detailed overview of molecular mechanisms of microbial SSs and the potentials of SBs as a frontier in plant disease management. While there are still challenges in mass deployment of BCAs in sustainable agriculture, this review is guided by the hypothesis that rational, quantitative engineering of microbial SSs can transform conventional BCAs into integrated SBs. It synthesizes current advances within a systems‑level bioengineering framework linking secretion efficiency, regulation, and field performance. It further explores possible integration of SBs in plant-microbiome interactions to further enhance their adaptability and effectiveness. Finally, the review dives into recent breakthroughs, current challenges, and future directions for SBs development and application as next-generation plant disease control agents.},
}

@article {pmid42437546,
year = {2026},
author = {Fregolente, LG and Roth, FN and Warncke, JD and Macpherson, AJ and Yilmaz, B and Bassetti, CLA},
title = {The gut-sleep connection: a scoping review into microbiome alterations in sleep-wake and circadian disorders.},
journal = {Sleep medicine},
volume = {147},
number = {},
pages = {109136},
doi = {10.1016/j.sleep.2026.109136},
pmid = {42437546},
issn = {1878-5506},
abstract = {Sleep is fundamental to brain, body, mental, and social health. In parallel, the gut microbiome is increasingly recognized as a key regulator of immune, metabolic, endocrine, and neurophysiological processes. This scoping review explored current evidence on gut microbiome alterations in relation to sleep duration and sleep loss, sleep-wake disorders, and circadian rhythm-related phenotypes. Searches of MEDLINE, Embase, and Cochrane were conducted up to February 2024. Of 2059 records identified, 54 studies met the eligibility criteria. Thirty-eight studies were observational, nine interventional, and seven genome-wide association or Mendelian-randomization studies. The most frequently investigated phenotypes were insomnia (15 studies, 28%), obstructive sleep apnea (12 studies, 22%), circadian rhythm or circadian-misalignment phenotypes (10 studies, 19%), and sleep duration or sleep loss/deprivation (9 studies, 17%). Most studies used 16S rRNA gene sequencing to assess gut microbiota composition and diversity, while shotgun metagenomic sequencing and functional analyses were less common. Across disorders, studies reported alterations in microbial diversity, taxonomic composition, short-chain fatty acid-producing taxa, bile acid-related pathways, inflammatory markers, and cardiometabolic or neurophysiological correlates. However, findings were limited by heterogeneous sleep phenotyping, small sample sizes, cross-sectional designs, variable microbiome methods, and inconsistent control of diet, medication use, body mass index, comorbidities, and stool sampling protocols. Current evidence supports an association between sleep-wake and circadian disturbances and gut microbiome alterations, but causality and disorder-specific microbial signatures remain unresolved. Standardized longitudinal and multi-omics studies are needed to clarify mechanisms and therapeutic potential.},
}

@article {pmid42437561,
year = {2026},
author = {Brar, G and Valle, JW},
title = {Immunotherapy plus chemotherapy in advanced biliary tract cancers: pros and cons.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2026.2701716},
pmid = {42437561},
issn = {1747-4132},
abstract = {INTRODUCTION: Biliary tract cancers (BTC) are highly immunosuppressive 'cold' tumors with limited treatment options. In unresectable or advanced stage disease, the combination of immune checkpoint inhibition with chemotherapy resulted in a modest survival benefit over chemotherapy.

AREAS COVERED: In this review, current obstacles, and strategies to improve the benefit of immunotherapy are highlighted. This includes challenges in optimizing patient selection, understanding the tumor microenvironment and interactions with the gut microbiome, and improving on combination treatment strategies, whether it be with targeted agents, locoregional therapies, or other evolving immune therapies. For this review, we performed a PubMed database search and summarized all relevant clinical studies utilizing ICI in biliary tract cancers from 2019 to current.

EXPERT OPINION: Checkpoint inhibition plus chemotherapy is established as a new standard of care for patients with advanced BTC, with a clinically meaningful subset of patients now achieving durable long-term survival that was previously rare in this disease. The next challenge is to broaden that benefit through biomarker-driven patient selection, use of immunotherapy in earlier stages of disease, and through rational combination strategies. Importantly, these approaches should be grounded in a better understanding of tumor biology as well as the host immune microenvironment.},
}

@article {pmid42437569,
year = {2026},
author = {Strobel, KM and Jaspan, HB and Gibbons, SM and Salas, AA},
title = {Microbial Interactions with Protein Intake and Preterm Infant Body Composition: Secondary Analysis of a Randomized Trial.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101723},
doi = {10.1016/j.tjnut.2026.101723},
pmid = {42437569},
issn = {1541-6100},
abstract = {INTRODUCTION: Enteral protein supplementation improves preterm infant growth, and may impact body composition and the gut microbiota.

OBJECTIVE: To identify effects of additional enteral protein supplementation on the gut microbiota and microbial and clinical drivers of body composition.

METHODS: Secondary analysis of a masked randomized trial of additional enteral protein versus standard fortification in preterm infants born 25-28 weeks gestation (NCT03586102). Stool at weeks 4 and 8 underwent 16S rRNA sequencing; functional potential was predicted by PICRUSt2. Body composition was measured by air-displacement plethysmography at 36 weeks postmenstrual age (PMA). LASSO regression with multivariable linear regression identified body composition predictors.

RESULTS: Among 46 infants, gestational age (p=0.16) and sex (p=0.55) did not differ between groups. The protein group had higher week 4 Shannon diversity than standard fortification (median 1.2 vs. 0.87, p=0.049). Week 4 Shannon diversity was positively correlated with fat-free mass z-score at 36 weeks PMA (r[2]=0.34, p=0.02). Adjusting for covariates, the protein group had higher Peptoniphilus (β=1.6, padj=0.10) and lower Vibrio CLR abundance (β=-0.98, padj=0.10); 62 predicted metabolic pathways were lower in the protein group (FDR<0.20). In combined LASSO models, Bacillus abundance at week 4 was the strongest predictor of fat-free mass z-score (β=-0.17, p<0.001; R[2]=0.80) and fat mass z-score (β=-0.31, p<0.001; R[2]=0.66).

CONCLUSION: Additional protein supplementation was associated with fat-free mass z-score and alterations to the gut microbiota. Clinical variables and microbial variables were key predictors of body composition, suggesting that nutrition, clinical factors, and the gut microbiota jointly contribute to body composition in extremely preterm infants.

NCT03586102, https://clinicaltrials.gov/study/NCT04325308, registered in March 2020.},
}

@article {pmid42437600,
year = {2026},
author = {Pirscoveanu, DF and Papa, MC and Kaltwasser, B and Hermann, DM and Brockmeier, U and Cercel, A and Oliver, A and Gruillari, J and Ionica, MV and Popa-Wagner, A},
title = {Biological limits of lifespan extension: evidence for a shift from pathway leverage to system-level buffering across species.},
journal = {Mechanisms of ageing and development},
volume = {},
number = {},
pages = {112231},
doi = {10.1016/j.mad.2026.112231},
pmid = {42437600},
issn = {1872-6216},
abstract = {Interventions targeting conserved aging pathways can markedly extend lifespan in model organisms, yet their efficacy declines with increasing organismal complexity. While this phenomenon is well documented, the underlying constraints remain poorly defined. Here, we integrate comparative experimental data with mechanistic insights to propose a unifying framework explaining the declining ceiling of lifespan extension. We show that in simple organisms, aging is governed by a limited number of high-leverage pathways, whereas in mammals it emerges from distributed, multi-tissue regulatory systems characterized by redundancy, feedback, and competing physiological constraints. By synthesizing findings from Caenorhabditis elegans, Drosophila melanogaster, and rodent models, we identify key determinants of this transition, including metabolic organization, genetic redundancy, endocrine regulation, microbiome interactions, and pharmacokinetic complexity.},
}

@article {pmid42377935,
year = {2026},
author = {Mueller, KD and Lee, SC},
title = {Yeasts in the gastrointestinal tract.},
journal = {FEMS yeast research},
volume = {26},
number = {},
pages = {},
doi = {10.1093/femsyr/foag029},
pmid = {42377935},
issn = {1567-1364},
support = {//NIH/ ; R01-AI182221/AI/NIAID NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Tract/microbiology ; Inflammatory Bowel Diseases/microbiology/therapy ; *Yeasts/physiology/classification ; *Gastrointestinal Microbiome ; Probiotics ; },
abstract = {The human gastrointestinal (GI) microbiota has come to be recognized as a modulator of health. However, interest in fungi and their function as members of the microbiota has lagged behind interest in bacteria. Despite the lack of historical interest, fungi are prevalent in the human GI tract and have an outsized impact on host immunity. In this review, we aim to examine the associations and potential impact of yeasts on human health outcomes. This review summarizes the associations between yeasts and inflammatory bowel diseases, highlights the predictive service that yeasts may provide in cancer therapy, and explores the possibility of yeasts as therapeutic effectors. There remain significant challenges in data analysis and identifying the relevance of fungal morphology; however, the pathways for clinical translation open to yeasts in the GI tract make these challenges worth overcoming.},
}

Humans
*Gastrointestinal Tract/microbiology
Inflammatory Bowel Diseases/microbiology/therapy
*Yeasts/physiology/classification
*Gastrointestinal Microbiome
Probiotics

@article {pmid42430221,
year = {2026},
author = {Ntamubano, S and Parker, D and Kozik, AJ},
title = {The redefined identity of Prevotella: new implications for oral, respiratory, and vaginal health.},
journal = {Journal of bacteriology},
volume = {},
number = {},
pages = {e0013326},
doi = {10.1128/jb.00133-26},
pmid = {42430221},
issn = {1098-5530},
abstract = {For much of the 20th century, the field of bacteriology was dominated by a pathogen-centric view, which rightly focused scientific resources on identifying, characterizing, and eliminating the agents of infectious disease. However, this perspective has resulted in the relative neglect of abundant yet poorly characterized members of the human microbiota. Few genera embody this oversight more clearly than Prevotella. Despite being consistently found in high abundance across diverse human mucosal sites, including the oral cavity, airways, and vagina, the underlying physiological roles of the genus in both health and disease contexts remain largely unclear. This review traces the evolution of Prevotella research and classification, arguing that the traditional "friend or foe" dichotomy is insufficient. We contend that more mechanistic work at the species level is needed to elucidate the biology of Prevotella, especially after the most recent taxonomic reclassification. The knowledge derived from a mechanistic focus will offer profound benefits for understanding and treating complex polymicrobial diseases across multiple systems, including chronic respiratory infections, oral inflammatory conditions, and recurrent genitourinary dysbiosis.},
}

@article {pmid42430398,
year = {2026},
author = {Correa Orellana, M and Odom, C and Kuzmina, A and Urias-Quiroz, J and Arias, L and Kwiatowski, A and Aitolo, G and Martin, P and Seitze, C and Winfield, M and Frisch, A and Tansiongco, J and Venkatesan, V and La Point, N and Laduc, TJ and Havird, JC},
title = {Comparative analysis of the mucosal and shell microbiota of Trachemys scripta elegans across multiple urban freshwater habitats.},
journal = {PloS one},
volume = {21},
number = {7},
pages = {e0353172},
pmid = {42430398},
issn = {1932-6203},
mesh = {Animals ; *Turtles/microbiology ; *Microbiota/genetics ; Fresh Water ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; *Animal Shells/microbiology ; *Mucous Membrane/microbiology ; Skin Microbiome ; Phylogeny ; },
abstract = {Turtles harbor diverse microbial communities that influence their health, ecology, and interactions with the environment. While sea turtle microbiomes have received growing attention, the microbial communities associated with freshwater turtles, particularly the widely distributed and invasive red-eared slider (Trachemys scripta elegans), remain understudied. Here, we used 16S rRNA gene sequencing to characterize the microbiomes of 42 red-eared sliders across four urban aquatic habitats in Austin, Texas, USA, sampling five body locations: carapace, plastron, skin, oral cavity, and cloaca. A total of 142 samples yielded 20,160 Amplicon Sequence Variants (ASVs), with community composition most strongly structured by body location, but also by geographic habitat. External surfaces (carapace, plastron, skin) were dominated by Cyanobacteria, Proteobacteria, and Deinococcota, while oral and cloacal samples exhibited higher proportions of Bacteroidota and site-specific variation. Alpha diversity differed significantly across habitats of origins but not across body locations, while beta diversity analyses revealed distinct microbial profiles among body regions. Notably, we report the first characterization of the oral microbiome in red-eared sliders, which was dominated by Proteobacteria and Deinococcota-patterns consistent with other reptiles. These findings shed light on microbial communities in invasive freshwater turtles and emphasize the need for broader microbial surveillance in urban aquatic ecosystems where wildlife and humans frequently interact.},
}

Animals
*Turtles/microbiology
*Microbiota/genetics
Fresh Water
RNA, Ribosomal, 16S/genetics
Ecosystem
*Animal Shells/microbiology
*Mucous Membrane/microbiology
Skin Microbiome
Phylogeny

@article {pmid42430437,
year = {2026},
author = {Ansari, AF and Sambamoorthy, G and Alexander, TC and Reddy, YBS and Raut, J and Dixit, NM},
title = {Quartet: Disentangling positive and negative components of microbial interactions.},
journal = {PLoS computational biology},
volume = {22},
number = {7},
pages = {e1014502},
doi = {10.1371/journal.pcbi.1014502},
pmid = {42430437},
issn = {1553-7358},
abstract = {Interspecies interactions are characterized conventionally by the net influence, positive or negative, a species exerts on another. Community ecology theories rely on these net interactions to describe the behaviour of multispecies communities. The net interactions in turn comprise positive and negative components, arising typically from cross-feeding metabolites and competition for resources. The components remain challenging to disentangle, compromising descriptions of community behaviour. Here, we devised a method to estimate the components when metabolic interactions predominate. We conceived a theoretical resource partitioning strategy which when applied to data on species growth rates disentangles the components. Consequently, the net influence a species has on another is decomposed into its positive and negative components. The interactions between a pair of species are thus defined by the 'quartet' of underlying components, specifically the positive and negative components of the net influence of each species on the other. We applied the method to 28 in silico species pairs from a representative oral microbiome and an experimental auxoptroph pair from the literature. We found that positive and negative components had comparable strengths on average. Interestingly, we found species pairs with similar net interactions but disparate components, highlighting the importance of the quartet. Further, weak net interactions could arise from cancellation of strong components. Estimating the quartet helped better understand the complex transitions in community behaviour observed upon varying resource supply in silico and in vitro. The quartet thus offers a more fundamental characterization of interspecies interactions and may help build more reliable community ecology theories, with implications for understanding and design of microbial communities.},
}

@article {pmid42430521,
year = {2026},
author = {Li, R and Li, Y and Yang, Q and Ding, Y and Jiang, G and Xu, Y},
title = {β-caryophyllene gradients act as ecological filters shaping microbial life-history strategies via iron competition.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag181},
pmid = {42430521},
issn = {1751-7370},
abstract = {Plant-emitted volatile organic compounds (VOCs) are increasingly recognized as key mediators of plant-microbe interactions, yet how they shape microbial community assembly and adaptive strategies remains unclear. Here, using the widespread plant sesquiterpene β-caryophyllene as a model VOC, we demonstrate that plant volatiles drive dose-dependent ecological filtering and microbial adaptation, governed by life-history trade-offs and resource availability. Soil microcosm experiments revealed that low concentrations of β-caryophyllene selectively enrich competitive bacterial taxa, whereas high concentrations favor ruderal, fast-growing opportunists, restructuring communities along a competitor-stress tolerator-ruderal (CSR) axis. Focusing on representative taxa, Bacillus subtilis and Pseudomonas aeruginosa, we show that these contrasting ecological outcomes are underpinned by divergent physiological, metabolic, and transcriptional reprogramming. Across both taxa, low-dose β-caryophyllene consistently induces siderophore biosynthesis, identifying iron availability as a central integrator of volatile perception and response. Experimental manipulation of iron reprogrammed growth, carbon utilization, and antibiotic resistance, gating whether β-caryophyllene functions as a signal that primes competition or as a stressor that selects for ruderal traits. Together, our work offers critical insights into the VOC-mediated microbiome management for ecological restoration and sustainable agriculture.},
}

@article {pmid42430532,
year = {2026},
author = {Liu, S and Duan, Y and Sun, F},
title = {Causal association between 473 types of gut microbiota and neonatal bacterial sepsis: a bidirectional two-sample Mendelian randomization study.},
journal = {Journal of infection in developing countries},
volume = {20},
number = {6},
pages = {822-830},
doi = {10.3855/jidc.21933},
pmid = {42430532},
issn = {1972-2680},
mesh = {Humans ; Mendelian Randomization Analysis ; *Neonatal Sepsis/microbiology/genetics ; *Gastrointestinal Microbiome/genetics ; Infant, Newborn ; Genome-Wide Association Study ; },
abstract = {BACKGROUND: Neonatal bacterial sepsis represents a major health threat to newborns, leading to high mortality rates globally. However, the correlation between the gut microbiome and bacterial sepsis in neonates remains unclear.

METHODS: This study utilized publicly available Genome-Wide Association Study data on 473 gut microbiota taxa as exposures. Instrumental variables were rigorously selected, and bidirectional two-sample Mendelian randomization (MR) analyses were performed. The MR and reverse MR analyses results were validated using Bayesian weighted MR (BWMR) analysis. Positive results from MR analysis will be validated through heterogeneity testing, evaluation of horizontal pleiotropy, and univariate sensitivity analysis.

RESULTS: The findings revealed a significant genetic causal association between 18 gut microbial species and neonatal bacterial sepsis, including Acetobacterales (odds ratio [OR]: 159.844; p = 0.04), Campylobacter D (OR: 16.225; p = 0.029), and Firmicutes A (OR: 75.643; p = 0.025). Additionally, both MR and inverse MR analyses confirmed the absence of reverse causation (p < 1e-5), supporting the robustness of the findings (p < 0.05) across five statistical methods. Sensitivity analyses indicated high reliability without significant heterogeneity or pleiotropy (p > 0.05). Furthermore, BWMR analysis highlighted the complex roles of probiotic taxa, including Bacteroides A plebeius (OR: 0.526) and pathogenic bacteria, such as Acetobacterales (OR: 192.449), in neonatal sepsis.

CONCLUSIONS: A causal genetic association exists between gut microbiota and bacterial sepsis in neonates. These results underscore the potential of gut microbiota as biomarkers and therapeutic targets for the prevention and management of neonatal bacterial sepsis.},
}

Humans
Mendelian Randomization Analysis
*Neonatal Sepsis/microbiology/genetics
*Gastrointestinal Microbiome/genetics
Infant, Newborn
Genome-Wide Association Study

@article {pmid42430909,
year = {2026},
author = {Maranho, LT and Geraldo, MR and Nogueira, KDS and Gomes, MP},
title = {Associations between rhizosphere microbial community structure and antibiotic attenuation in a pilot-scale hybrid constructed wetland.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142886},
doi = {10.1016/j.jhazmat.2026.142886},
pmid = {42430909},
issn = {1873-3336},
abstract = {Constructed wetlands are widely used as nature-based solutions for wastewater treatment; however, the role of rhizosphere-associated microbial communities in the attenuation of emerging contaminants remains unclear. In this study, we evaluated the antibiotic removal and microbial community structure in a pilot-scale hybrid constructed wetland treating municipal wastewater by integrating vertical upflow (Sagittaria montevidensis), floating (Salvinia molesta + Lemna gibba), and horizontal subsurface flow (Canna indica) units. Antibiotics from different therapeutic classes were quantified using LC-MS/MS across the treatment compartments. The system achieved high attenuation efficiencies, with removal efficiencies exceeding 98% for the target compounds. The floating macrophyte unit showed the greatest reduction in concentrations relative to the upstream compartments. Microbial community analyses based on 16S rRNA gene sequencing revealed marked shifts in the community structure along the treatment gradient. Alpha diversity indices varied (Shannon index: 1.066-4.954), with higher diversity observed in rhizospheric communities associated with Sagittaria and Canna than in influent wastewater and pre-exposure samples. Beta diversity analysis (Bray-Curtis dissimilarity) showed a clear separation between the wastewater and rhizospheric communities (PERMANOVA, p = 0.001; R[2] = 0.66). Redundancy analysis and correlation-based approaches indicated that variations in dominant groups were statistically associated with antibiotic attenuation patterns across treatment compartments. These relationships represent ecological covariation patterns and should not be interpreted as direct evidence of microbial biodegradation activity. Overall, the results indicate that hybrid CW promote structured rhizosphere microbial communities that co-vary with antibiotic attenuation, supporting the future integration of microbial ecology into nature-based wastewater treatment optimization.},
}

@article {pmid42431062,
year = {2026},
author = {Bai, J and Zhang, Y and Zhao, Z and Zhou, M and Li, W and Guo, J and Duan, R and Yang, Z and Zheng, Y},
title = {Co-occurring ferns orchestrate rhizosphere microbiome assembly driving divergent antimony adaptation at the XKS Mine, China.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120478},
doi = {10.1016/j.ecoenv.2026.120478},
pmid = {42431062},
issn = {1090-2414},
abstract = {The adaptation of native plants to metalliferous environments is associated with intricate plant-microbiome interactions. However, how co-occurring species assemble distinct rhizosphere microbiomes under extreme heavy metal(loid) stress remains unclear. Here, we report a field-based example of ecological divergence among three fern species under extreme antimony (Sb) stress. The Sb-accumulator Pteris multifida showed rhizosphere characteristics consistent with a "Biogeochemical Reactor", including higher abundances of the aioA and anoA genes (3.12- and 4.54-fold, respectively) and elevated Sb(V) content, which were 26.41% and 30.04% higher than those in the excluders. These characteristics coincided with a specialized co-occurrence network which, under high Sb stress, exhibits reduced complexity (16.20% fewer nodes), but an increased proportion of positive interactions, rising from 44.66% to 50.70%. In contrast, the excluder species exhibited characteristics consistent with "Biogeochemical filters," including a 2.91-fold higher abundance of the arsC gene and a reduced proportion of bioavailable Sb. Partial least squares path modeling further identified fern functional type, defined by their Sb accumulation strategy, and Sb valence state as significant direct factors associated with root Sb accumulation. Our findings propose a field-based ecological framework in which host-mediated rhizosphere differentiation may contribute to divergent Sb adaptation strategies, providing a foundation for microbiome-assisted phytomanagement of Sb-contaminated soils.},
}

@article {pmid42431064,
year = {2026},
author = {Zhou, Q and Zheng, K and Deng, H and Pu, Y and Han, Z and Chen, Y and Su, Y},
title = {An aquatic probiotic alleviates lead toxicity in grass carp (Ctenopharyngodon idella) via improved intestinal barrier function and reduced Pb bioaccumulation.},
journal = {Ecotoxicology and environmental safety},
volume = {322},
number = {},
pages = {120491},
doi = {10.1016/j.ecoenv.2026.120491},
pmid = {42431064},
issn = {1090-2414},
abstract = {Probiotics have been used to mitigate heavy metals (HMs) toxicity, however, the mechanisms by which they alleviate HMs toxicity by regulating intestinal microbiota remain unclear in aquatic animals. In this study, the aquatic probiotic Rhodobacter sphaeroides SC01 (RSSC01) was supplemented in the diet of grass carp to investigate its roles in alleviating lead (Pb) toxicity. The results showed that RSSC01 significantly reduced Pb content in the intestine, gills, and kidneys by 25.27%, 55.83%, and 47.42%, respectively, compared with Pb exposure alone. Additionally, it effectively conferred Pb-induced structural damage to the intestine, liver, and kidney. RSSC01 also greatly increased red blood cell count, hemoglobin content, and aminolevulinic acid dehydratase (ALAD) activity. Based on absolute quantification of microbiome sequencing, RSSC01 was found to colonize the intestine and upregulate the absolute abundance of Pb-adsorbing bacteria (Staphylococcus sciuri, Rhodobacter, Chelatococcus, Shinella) and bile acid-transforming bacteria (Clostridium sensu stricto, Streptococcus, Lactobacillales, and Beijerinckiaceae). Correlation analysis showed that these microbiota regulation enhanced the expression of intestinal tight junction proteins, hepatic SOD activity and MDA content. Taken together, these findings demonstrate that RSSC01 effectively mitigates Pb toxicity in grass carp through regulation of intestinal microbiota.},
}

@article {pmid42431194,
year = {2026},
author = {Albano, A and Brasi, L and Loperfido, F and Griffante, G and Cianci, MA and Donati, G and Proserpio, V},
title = {Molecular mechanisms and therapeutic perspectives in vulvodynia: From current evidence to future investigations.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102917},
doi = {10.1016/j.xcrm.2026.102917},
pmid = {42431194},
issn = {2666-3791},
abstract = {Vulvodynia is defined as chronic vulvar pain persisting for at least 3 months without a clear identifiable cause. It affects 10%-16% of women, and despite its high prevalence and the severity of symptoms, vulvodynia remains significantly understudied. Here, we consolidate and analyze the scientific literature from the past 25 years, addressing vulvodynia from a molecular perspective. Following an overview of the female genital anatomy, we use a top-down approach to examine in depth the key determinants associated with this disease from the macroscopic to the microscopic scale, such as cellular components, microbiota diversity, hormones, cytokines, receptors, and genetic predispositions. We summarize existing and potential therapeutic strategies, highlighting the importance of further research. Key functional aspects, such as the interactions between the nervous system, immune system, and microbiota, remain to be elucidated. Across published studies, immune system dysfunction emerges as the most consistently reported factor and may contribute to disease development and maintenance.},
}

@article {pmid42431299,
year = {2026},
author = {Zhang, X and Cai, M and Lin, J and Feng, Z and Wang, W and Jiao, Y and Lu, L},
title = {Multi-year glyphosate exposure impairs soil fertility, microbial communities, nutrient cycling genes, and tea quality in tea plantations.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128689},
doi = {10.1016/j.envpol.2026.128689},
pmid = {42431299},
issn = {1873-6424},
abstract = {Although glyphosate is highly effective for weed control, its potential risks to tea agroecosystems remain a significant concern. Previous studies have shown inhibitory effects on soil microbial communities in tea plantations, yet the multi-year impacts of glyphosate on microbially mediated nutrient cycling remain poorly understood. To address this gap, we conducted a three-year controlled field experiment, applying glyphosate at 0 kg a.i. ha[-1] (CK), 2.3 kg a.i. ha[-1] (G1), and 6.9 kg a.i. ha[-1] (G2), and used metagenomic sequencing to evaluate its effects on soil fertility, microbial communities, nutrient cycling genes, and tea quality. The results showed that glyphosate application significantly increased soil pH but reduced the contents of total organic carbon, total nitrogen, total potassium, available nutrients, and enzyme activities, leading to marked declines in soil fertility. Relative to CK, G2 reduced microbial alpha diversity, with Chao1, Shannon, and Pielou indices decreasing by 33.22%, 14.97%, and 11.50%, respectively. Tea quality was also affected, with free amino acids and caffeine decreasing by 22.67% and 11.30%, respectively, whereas tea polyphenols and the phenol/ammonia ratio increased by 12.16% and 45.08%, respectively. G2 also restructured bacterial communities, including depletion of Actinobacteria and Planctomycetota and more than 70-fold enrichment of Candidatus Rokubacteria. Metagenomic analysis revealed broad suppression of carbon, nitrogen, and phosphorus cycling genes under G2. Overall, these results suggest that repeated glyphosate exposure over three years may alter soil ecological processes and compromise tea quality, highlighting the need for more sustainable weed management strategies and reduced reliance on glyphosate in tea plantations.},
}

@article {pmid42431475,
year = {2026},
author = {Liu, S and Chen, Q and Bai, Y and Li, X},
title = {Harnessing the Microbiome for Head and Neck Cancer Therapy: From Mechanistic Insights to Translational Opportunities.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105484},
doi = {10.1016/j.critrevonc.2026.105484},
pmid = {42431475},
issn = {1879-0461},
abstract = {The human microbiome, particularly the diverse microbial communities in the oral cavity and gut, plays a critical role in the pathogenesis, progression, and treatment response of head and neck squamous cell carcinoma (HNSCC). Emerging evidence indicates that specific microbial communities can bidirectionally modulate cancer therapeutic modalities. Moreover, interventions such as probiotics, prebiotics, and fecal microbiome transplantation have the potential to improve treatment efficacy and alleviate adverse effects. This review outlines the mechanisms underlying oral and gut microbiota in HNSCC development and progression, focusing on their bidirectional regulation of efficacy and toxicity across standard treatments, including surgery, radiotherapy, chemotherapy, targeted therapy, and immunotherapy. We emphasize that microbial signatures not only serve as predictive biomarkers and therapeutic targets but also constitute a fundamental component of personalized oncology in HNSCC, providing a comprehensive framework for integrating microbiota-based strategies into clinical practice.},
}

@article {pmid42431536,
year = {2026},
author = {Dong, Y and Li, M and Qiao, Y and Cheng, Y and Lin, H},
title = {Microbiome restructuring by integrated ryegrass and earthworms accelerates 4-nitrophenol bioremediation in soil.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125239},
doi = {10.1016/j.envres.2026.125239},
pmid = {42431536},
issn = {1096-0953},
abstract = {4-Nitrophenol (4-PNP) is a persistent and ubiquitously distributed industrial pollutant, whose recalcitrance and inhibitory effects on microbial activity impose protracted threats to soil health in the absence of effective remediation strategies. Nevertheless, the interactive mechanisms underlying combined ryegrass-earthworm remediation remain insufficiently elucidated. Herein, we demonstrate that the joint application of ryegrass and earthworms significantly enhances the bioremediation of 4-PNP in contaminated soil. Pot experiment results revealed that the composite treatment achieved a remarkable degradation rate of 82.60% at 40 days, corresponding to a 14.4% increase relative to the indigenous microbial treatment group. The combination operated via complementary pathways: root-derived inputs from ryegrass continuously supplied organic carbon, as corroborated by increased soil organic matter, while earthworm bioturbation enhanced soil aeration, manifested as elevated oxidation-reduction potential. Collectively, these modifications optimized the microhabitat for microbial degradation. This interplay sustained urease activity at 68% of its initial level, elevated catalase activity by 18%, and elicited a distinct mid-phase peak in β-glucosidase activity (125 μg/g/h). Earthworms further augmented bacterial diversity and enriched key degrader taxa, including Sphingomonas and Bacillus. Soil moisture critically governed this process; high moisture suppressed β-glucosidase activity, implying a metabolic shift that subsequently structured the microbial community. The combined system coordinately optimized the temporal dynamics of enzyme activities and microbial composition. Collectively, these findings suggest that ryegrass-earthworm interactions are associated with 4-PNP degradation through multifaceted regulation of the soil environment, offering an actionable framework for the remediation of organic pollution.},
}

@article {pmid42431620,
year = {2026},
author = {Raharjo, AF and Prakoso, HH and Setiawan, A and Aliya, LS and Tasnim, TT},
title = {Prebiotics and asthma: current insights and future directions from a bibliometric analysis.},
journal = {Revista alergia Mexico (Tecamachalco, Puebla, Mexico : 1993)},
volume = {73},
number = {2},
pages = {e165-e177},
doi = {10.29262/ram.v73i2.1616},
pmid = {42431620},
issn = {2448-9190},
mesh = {*Prebiotics ; *Asthma ; Humans ; *Bibliometrics ; Forecasting ; },
abstract = {BACKGROUND: Prebiotics have gained attention as a microbiome-modulating strategy in asthma because they may influence immune regulation through the gut-lung axis. However, evidence on prebiotics and asthma remains distributed across allergy, immunology, nutrition, microbiology, and respiratory medicine.

OBJECTIVES: This study aimed to map global research trends, influential contributors, and thematic development in prebiotics-asthma research using bibliometric analysis.

METHODOLOGY: This bibliometric study analyzed English-language articles and reviews indexed in Scopus. Prebiotic-related and synbiotic-related terms were combined using OR and then linked with asthma-related terms using AND. Eligible records were screened for relevance to prebiotics and asthma. Bibliometric analyses and visualizations were performed using Biblioshiny and VOSviewer to evaluate publication output, leading contributors, citation impact, keyword co-occurrence, and temporal research trends.

RESULTS: A total of 296 publications from 166 sources were included. The earliest eligible publication was published in 2002. Annual scientific production increased over time, with an annual growth rate of 13.66% and the highest output in 2024. Review articles outnumbered original articles. The United States was the leading contributor, followed by Australia, the Netherlands, Italy, and China. Keyword analysis identified three major domains: mechanistic and immunologic studies, early-life allergy prevention, and microbiota-focused modulation. Trend analysis showed a shift toward gut microbiome, short-chain fatty acids, immune dysregulation, and gut-lung axis.

CONCLUSION: Prebiotics-asthma research is a relatively recent but steadily growing field with increasing emphasis on microbiome-mediated and mechanistic pathways. However, asthma-specific translational evidence remains limited, supporting the need for standardized clinical studies and integrative multi-omic approaches.},
}

*Prebiotics
*Asthma
Humans
*Bibliometrics
Forecasting

@article {pmid42431634,
year = {2026},
author = {Fodor, KE and Ritter, AC and Schmieley, RA and Miranda, IC and Ricart Arbona, RJ and Lipman, NS},
title = {Microbiome-Dependent Protection against Corynebacterium bovis-Associated Hyperkeratosis in Nude Mice (Mus musculus).},
journal = {Journal of the American Association for Laboratory Animal Science : JAALAS},
volume = {},
number = {},
pages = {1-15},
doi = {10.30802/AALAS-JAALAS-26-055},
pmid = {42431634},
issn = {2769-6677},
abstract = {Corynebacterium bovis, the causative agent of Corynebacterium-associated hyperkeratosis (CAH), is an important pathogen in immunocompromised mice that is difficult to eliminate and can confound research outcomes. We recently observed that CAH severity varies among outbred athymic nude mouse stocks, but the relative contributions of host genetics and the microbiome remain unclear. We hypothesized that disease course and severity vary based on host genetic stock and/or microbiome composition. Three nude mouse stocks were rederived into the axenic state and either monoinfected with a pathogenic C. bovis isolate (104 CFU) or given sterile media (n = 6/group). Axenic mice were also reassociated with their source microbiome or microbiomes from 3 other stocks with known differences in CAH severity and then inoculated with C. bovis (n = 6) or sterile media (n = 2). In a separate experiment, one axenic stock was used to assess the role of Corynebacterium amycolatum via monoinfection, monoinfection followed by C. bovis challenge, or addition to a nonprotective microbiome followed by C. bovis challenge. Mice were monitored daily for 21 days and scored for skin lesions (0-5). C. bovis monoinfected mice developed disease comparable in severity and timing to conventionally raised controls. Notably, reassociation with Vendor A2's microbiome prevented clinical lesions and reduced histopathologic changes across all stocks. While C. amycolatum as a monoinfection did not cause disease nor reduce disease severity following C. bovis challenge, it delayed the onset and lowered peak scores when added to a nonprotective microbiome. These findings demonstrate that C. bovis can cause CAH as a monoinfection and that both host genetics and microbiome composition influence disease progression and, together with prior work, support its role as the etiologic agent consistent with the Koch postulates. Identifying protective microbiome constituents may inform strategies to reduce disease burden in susceptible mice.},
}

@article {pmid42431711,
year = {2026},
author = {Mao, G and Lan, H},
title = {Concomitant medication reporting should accompany fecal microbiota transplantation plus anti-PD-1 therapy in gastric cancer.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {7},
pages = {},
doi = {10.1136/jitc-2026-015908},
pmid = {42431711},
issn = {2051-1426},
mesh = {Humans ; *Stomach Neoplasms/therapy/drug therapy ; *Fecal Microbiota Transplantation/methods ; *Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors ; Combined Modality Therapy ; },
abstract = {This commentary discusses the phase I study of fecal microbiota transplantation plus anti-programmed cell death protein 1 therapy in refractory microsatellite-stable gastric cancer. We suggest that this strategy should be treated as a pharmacomicrobiomic intervention rather than only as an immunotherapy combination. Evidence from fecal microbiota transplantation trials and microbiome immunotherapy studies indicates that antibiotics, proton pump inhibitors, corticosteroids and other microbiome-modifying exposures may affect donor strain engraftment, immune activation, response assessment and safety. In China and other Asian settings, where acid suppression, Helicobacter pylori history, perioperative antibiotic use and nutritional interventions are common, standardized concomitant medication reporting would make future studies more interpretable and transferable.},
}

Humans
*Stomach Neoplasms/therapy/drug therapy
*Fecal Microbiota Transplantation/methods
*Immune Checkpoint Inhibitors/therapeutic use/pharmacology
*Programmed Cell Death 1 Receptor/antagonists & inhibitors
Combined Modality Therapy

@article {pmid42431872,
year = {2026},
author = {Kaya, NH and Abukhalaf, M and Fuentes, G and Taubenheim, J and Hentschel, U and Tholey, A and Fraune, S},
title = {c-JUN controls microbial colonization via selective phagocytosis in the sea anemone Nematostella.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42431872},
issn = {2041-1723},
support = {CRC 1182, Project B1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC 1182, Project B1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC 1182, Project Z3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC 1182, Project B1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC 1182, Project B1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CRC 1182, Project Z3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
mesh = {Animals ; *Sea Anemones/microbiology/immunology/genetics/metabolism ; *Phagocytosis/immunology ; Immunity, Innate ; Vibrio/immunology ; *Proto-Oncogene Proteins c-jun/genetics/metabolism/immunology ; Microbiota/immunology ; CRISPR-Cas Systems ; Lysosomes/metabolism ; },
abstract = {Innate immunity is traditionally viewed as a broad defense system with limited specificity. However, increasing evidence suggests that innate immune cells can discriminate between distinct microbial partners. How such specificity arises in early-diverging animals remains unclear. Here, we identify in the sea anemone Nematostella vectensis a selective host innate immune mechanism mediated by nematosomes, motile multicellular bodies that differentially process bacterial cells. Nematosomes preferentially engulf non-native Vibrio isolates while showing reduced uptake of native host-associated strains. We identify the transcription factor cJUN as a key regulator of this process. CRISPR/Cas9-mediated knockout of cJUN reduces nematosome abundance, impairs lysosomal response, alters microbiome assembly, and increases susceptibility to bacterial infection. These results link immune gene function to microbial selectivity and demonstrate that even early-diverging animals exhibit sophisticated innate immunity mechanisms for microbiome regulation. Our findings support the idea that immune specificity can arise through repurposing deeply conserved pathways and may have deep evolutionary origin.},
}

Animals
*Sea Anemones/microbiology/immunology/genetics/metabolism
*Phagocytosis/immunology
Immunity, Innate
Vibrio/immunology
*Proto-Oncogene Proteins c-jun/genetics/metabolism/immunology
Microbiota/immunology
CRISPR-Cas Systems
Lysosomes/metabolism

@article {pmid42431880,
year = {2026},
author = {Burke, BI and Valentino, TR and Ismaeel, A and El-Amouri, SS and Goh, J and Scott, LN and Walton, BJ and Joshi, JK and Wood, CR and Burrows-Franco, A and May, JB and Johnson, LA and Flythe, MD and Wen, Y and McCarthy, JJ},
title = {Exercise-associated microbial metabolites prevent skeletal muscle atrophy in adult female mice.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-74852-w},
pmid = {42431880},
issn = {2041-1723},
support = {R01AR084282//U.S. Department of Health & Human Services | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; R21AG071888//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; F31AG087618//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
abstract = {We previously reported that skeletal muscle adaptation to regular exercise requires a healthy gut microbiome, contributing to growing evidence that some exercise benefits are mediated by microbiome-derived metabolites. Here, to identify such exercise-associated microbial metabolites, we transfer cecal contents from exercise-trained female donor mice into exercise-naïve female recipient mice undergoing unilateral hindlimb immobilization. Recipients of cecal material from exercise-trained donors exhibit less muscle atrophy compared with those receiving transfers from sedentary donors. Untargeted metabolomics reveal metabolites enriched in cecal content, serum, and muscle of recipients from exercise-trained donors, consistent with microbial origin. Oral administration of two such metabolites (pipecolic acid and succinate) attenuates muscle atrophy and preserves muscle function in exercise-naïve mice, potentially by enhancing cellular energy status and translational capacity. These findings further define the gut microbiome-skeletal muscle axis and provide evidence that exercise-associated microbial metabolites serve as a novel class of exercise mimetics for treating conditions responsive to physical activity.},
}

@article {pmid42431911,
year = {2026},
author = {Smith, A and Kiwanuka, K and Pessenda, G and Rahmberg, AR and Flynn, JK and Herbert, R and Brenchley, JM and Loke, P},
title = {Hematological consequences of environmental change during dewilding of rhesus macaques.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-75260-w},
pmid = {42431911},
issn = {2041-1723},
support = {ZIAAI001029//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; },
abstract = {The environment shapes immune system development and the regulation of inflammatory responses, however the hematological consequences of a major environmental change, such as those experienced during migration, remain poorly understood. Here, we assess the immunological consequences in male rhesus macaques as they transitioned from an outdoor provisioned environment to an indoor laboratory facility in a process we term 'dewilding.' Dewilding decreased neutrophils and increased lymphocytes, skewing toward a TH1 response and increased T cell activation. In the gut microbiome, fungal abundance decreased while bacterial abundance increased. In the bone marrow, we observed a shift towards the less committed multipotent progenitor cells and increased erythrocyte progenitors, with upregulation of genes involved in hemoglobin control and erythropoiesis. Together, our findings illustrate how dewilding alters immune homeostasis, with implications for understanding immune adaptation in migrants from rural to urban environments and for optimizing immunization strategies during environmental change.},
}

@article {pmid42431976,
year = {2026},
author = {Chattaraj, S and Chatterjee, I and Nandi, R and Mohapatra, PKD and Mitra, P and Mandal, A and Mitra, D and Ganguly, A},
title = {Effect of probiotic Bacillus cereus PKA18 on the overall growth, gut microbiome, and immunity in Clarias magur (Hamilton, 1822).},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57479-1},
pmid = {42431976},
issn = {2045-2322},
abstract = {The current study evaluated the probiotic potential of Bacillus cereus PKA18, isolated from indigenous Clarias batrachus, as a dietary supplement for the cultivation of Clarias magur fingerlings (In India, the species Clarias batrachus was reclassified as the neotype Clarias magur). Prior to application in fish, Bacillus cereus PKA18 was subjected to safety evaluation, which confirmed negative enterotoxin production, non-hemolytic (γ-hemolysis) behavior on sheep, fish, and human blood agar, and the absence of pathogenic effects or adverse impacts on fish growth following intraperitoneal administration. A total of 240 fingerlings (average weight: 4.96 ± 0.06 g) were randomly assigned to four dietary groups (Control, C1, C2, and C3), each in triplicate, and reared for 60 days in continuous-flow chambers (92 × 61 × 92 cm[3]; 516 L; 5 cm bottom mud). The control group received basal feed without any probiotic additives, while treatment groups were administered feed supplemented with increasing concentrations of B. cereus PKA18: C1 (2 × 10[4] CFU), C2 (2 × 10[5] CFU), and C3 (2 × 10[6] CFU) per 100 g of feed. Fish in the C2 group exhibited significantly (p < 0.05) superior performance in terms of specific growth rate (3.14 ± 0.05), protein efficiency ratio (2.15 ± 0.12), and live weight gain (27.77 ± 1.24 g), along with the lowest feed conversion ratio (1.29 ± 0.11). Serum biochemical analyses showed notable enhancement in total proteins and reduction in hepatic enzymes (ALT, ALP, AST) in C2-fed fish. Antioxidant enzyme activities were significantly higher in the C2 group. These included superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-PX). Malondialdehyde (MDA) levels were lowest in this group. Digestive enzyme activities (protease, amylase, cellulase, xylanase, and lipase) were also significantly higher in the C2 group compared to control. Species-level 16 S rRNA gene analysis demonstrated that probiotic-fed Clarias magur exhibited a marked shift in intestinal microbiota, characterized by dominance of beneficial Cetobacterium spp., enrichment of Bacillus spp., and a significant reduction of opportunistic and pathogenic bacteria compared to the control group. Functional profiling further revealed that probiotic supplementation promoted a more metabolically efficient microbial community, with targeted enrichment of core metabolic and genetic information processing pathways despite lower overall functional abundance. Following a pathogenic challenge with Vibrio vulnificus (MTCC 1145), fish in the control and C2 groups were assessed for immune response. Fish fed C2 have demonstrated enhanced activity of respiratory burst, myeloperoxidase, α2-macroglobulin and antiprotease. Additionally, a significant upregulation of immune-related genes (IL-6 and C3a) was observed in the liver, muscle, and intestinal tissues of fish fed with C2. Post-challenge survivability was found to be highest in the C2 group, indicating improved resistance to vibriosis. Overall, the study identifies 2 × 10[5] CFU/100 g feed of B. cereus PKA18 (C2 feed) as the optimal probiotic dose for promoting growth performance, digestive activity, immune functions and disease resistance in Clarias magur. These findings support its potential application in the conservation-oriented aquaculture of this endangered species.},
}

@article {pmid42432192,
year = {2026},
author = {Song, H and Yun, C and Choi, Y and Jeong, W and Kim, Y and Kim, J and Lee, JY and Ryu, D and Park, SW and Oh, CM},
title = {Urolithin A activates mitophagy via the AMPK-mTOR axis and modulates the gut-ceramide axis to ameliorate cardiac remodeling in HFpEF.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42432192},
issn = {2092-6413},
support = {RS-2024-00440824//National Research Foundation of Korea (NRF)/ ; RS-2024-00439685//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; RS-2024-00507256//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; },
abstract = {Heart failure with preserved ejection fraction (HFpEF) accounts for nearly half of all heart failure cases. However, effective therapies targeting its underlying pathophysiological mechanisms remain lacking. Previous studies have indicated mitochondrial dysfunction and impaired mitophagy as key contributors to HFpEF pathophysiology. In this study, we investigated whether urolithin A (UA), a gut microbiome-derived mitophagy-activating compound, can ameliorate HFpEF. A two-hit mouse model was established using a high-fat diet and Nω-nitro-L-arginine methyl ester, and UA was administered during disease progression. In vitro and in vivo experiments, together with multi-omics analyses, showed that UA alleviated diastolic dysfunction, cardiac hypertrophy, and fibrosis in HFpEF mice. These effects were accompanied by restoration of mitochondrial ultrastructure and enhanced mitochondrial respiration and glycolytic capacity. Notably, UA activated AMPK signaling while inhibiting mTOR, promoting ULK1-dependent autophagy initiation and restoring impaired mitophagic flux. These effects were associated with improved mitochondrial quality control and function. Concurrently, multi-omics analyses revealed that UA remodels the gut microbiome-ceramide axis and reduces circulating ceramide accumulation, thereby alleviating lipotoxic stress. Furthermore, single-nucleus transcriptomic analysis revealed that UA treatment leads to the attenuation of fibrosis-related cellular programming in human induced pluripotent stem cell-derived cardiomyocytes. Taken together, these findings indicate that UA improves cardiac remodeling in HFpEF by activating mitophagy-dependent mitochondrial quality control and modulating the gut microbiome-ceramide axis, highlighting its potential as a mechanism-based, mitochondria-targeted therapeutic strategy for HFpEF.},
}

@article {pmid42432305,
year = {2026},
author = {Deveaux, A and Osazuwa-Peters, OL and Kim, YJ and Shi, P and Neish, D and Joshi, A and Duck, V and Williams, A and Gates Kuliszewski, M and Huang, B and Ward, K and Pisu, M and Tucker, T and Previs, R and Berchuck, A and Akinyemiju, T},
title = {Characterizing the composition and diversity of the vaginal microbiome in ovarian cancer.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01771-8},
pmid = {42432305},
issn = {2730-664X},
abstract = {BACKGROUND: Vaginal dysbiosis, characterized by Lactobacillus depletion and anaerobic enrichment, may be relevant to ovarian cancer (OC) outcomes, yet comprehensive microbiome characterization in OC patients remains limited. Here, we characterize the prevalence and predictors of vaginal microbiome dysbiosis among racially diverse OC patients in the US.

METHODS: We performed 16S rRNA gene sequencing on vaginal samples from 132 OC patients recruited as part of the population-based ORCHiD study. Latent Dirichlet Allocation (LDA), a computational topic modeling approach, was applied to identify distinct microbial community signatures representing co-occurring bacterial taxa.

RESULTS: Here, we show that Lactobacillus is detected in only 47.7% of patients. Topic modeling identifies seven distinct microbial signatures spanning Lactobacillus-dominated and anaerobe-enriched community types. Anaerobic bacterial enrichment (Peptoniphilus, Anaerococcus) increases significantly with age (approximately 35% per decade of life, FDR q = 0.019). Racial differences are observed, with non-Hispanic Black patients demonstrating a 5-fold higher prevalence of an Actinomycetaceae-classified amplicon sequence variant (ASV54) compared with non-Hispanic white patients (40.9% vs 8.2%, FDR q = 0.005), while Lactobacillus crispatus is detected only among non-Hispanic white patients (6.4% vs 0%) in this cohort.

CONCLUSIONS: These findings demonstrate a high burden of vaginal microbiome dysbiosis among OC patients and identify age- and race-associated microbial patterns that may be relevant to understanding disparities in OC outcomes.},
}

@article {pmid42432469,
year = {2026},
author = {Liu, L and Fu, M and Peng, J and Duan, T and Ma, X and Liu, H and Sha, R and Yang, Y and Yan, H and Jia, R and Li, X and An, X and Liu, Y and Lu, Q},
title = {Bio-valorization of Caragana korshinskii forage via a synthetic microbial community.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05353-5},
pmid = {42432469},
issn = {1471-2180},
abstract = {Caragana korshinskii represents a critical ecological and feed resource in arid regions, yet its utilization is severely impeded by the recalcitrant lignocellulose barrier. This study established a cross-kingdom synthetic microbial community (SynCom) to synergistically overcome this bottleneck, integrating Lactobacillus plantarum for rapid acidification with the fibrolytic enzyme secretion of Bacillus subtilis and the oxidative delignification potential of Aspergillus niger. We integrated microbiome profiling and functional prediction to decode the fermentation dynamics and metabolic mechanisms. Results demonstrated that the SynCom (LBA) treatment engineered a robust fermentation system, achieving a significantly higher in vitro dry matter digestibility (49.68%) and neutral detergent fiber digestibility (25.65%) compared to the control (P < 0.05). This enhancement was driven by a directed shift in the microbiome, where Lactobacillus abundance surged to > 95%, effectively suppressing spoilage genera like Staphylococcus and Weissella via competitive exclusion. Metagenomic prediction revealed that the SynCom upregulated key metabolic modules, specifically pyruvate metabolism and amino acid biosynthesis pathways, facilitating rapid acidification and protein preservation. These findings delineate a coordinated degradation-fermentation-preservation process driven by a rationally assembled synthetic consortium, offering a promising and sustainable bio-valorization strategy for converting high-fiber woody biomass into high-quality livestock feed.},
}

@article {pmid42432695,
year = {2026},
author = {Li, D and Du, L and Yi, G and Liang, T and Midgley, AC and Shu, G and He, Y and Dong, Y and Li, G and Yao, X},
title = {Extremophyte-derived exosome-like nanovesicles remodel intestinal barrier dysfunction by multi-dimensional intervention: physical barrier repair with immune homeostasis and microbiome regulation.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04800-9},
pmid = {42432695},
issn = {1477-3155},
support = {32302276//National Natural Science Foundation of China/ ; 32472493//National Natural Science Foundation of China/ ; 2023GXLH-078//The Shaanxi Science and Technology association/ ; 2024JC-JCQN-23//The Shaanxi Science and Technology association/ ; },
abstract = {BACKGROUND: Intestinal barrier is the body's largest immune structure and essential for nutrient absorption. Its dysfunction allows the translocation of pathogenic substances into circulation, thereby driving the pathogenesis of inflammatory bowel disease (IBD). Plant-derived exosome-like nanovesicles (ELNs), recognized for their biocompatibility and ability to traverse biological barriers, hold considerable potential for managing intestinal inflammation. Specially, plants cultivated under extreme environmental conditions typically adapt to be stress resistant with greater accumulation of associated biologics, which may in-turn confer unique bioactivities to their respective ELNs.

RESULTS: This study investigated the protective effects and mechanisms of ELNs derived from the extremophyte Rosa roxburghii (R-ELNs) and Artemisia sphaerocephala Krasch (A-ELNs) against intestinal barrier dysfunction. In vitro and in vivo studies indicated that the ELNs, especially R-ELNs, provided enhanced protection against intestinal barrier dysfunction. Specifically, mucus secretion and tight junction protein expression were promoted, and macrophages were polarized toward M2 anti-inflammatory phenotypes. Furthermore, R-ELNs modulated the composition of the intestinal microbiota, thereby promoting a balanced microecological environment. Importantly, the protective effect of R-ELNs was suggested to be through an inhibitory effect on excessive activation of pro-inflammatory signaling proteins (AKT, p38). Notably, exosomes (Exos) derived from R-ELN-treated M2 macrophages had distinct miRNA profiles that can target inflammatory pathway genes (Tgfbr1, Map3k7, Met), enabling anti-inflammatory roles via intercellular communication.

CONCLUSIONS: These findings suggested that R-ELNs can restore intestinal barrier dysfunction via multiple synergistic mechanisms, positioning R-ELNs as a novel and promising preventive strategy for inflammatory bowel disease.},
}

@article {pmid42432727,
year = {2026},
author = {Sheng, Y and Chi, H and Li, C and Huai, B and Song, X and Liu, D},
title = {Dietary patterns and exploratory gut microbiota profiles associated with diabetic retinopathy and cognitive impairment in type 2 diabetes.},
journal = {Nutrition & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12986-026-01167-4},
pmid = {42432727},
issn = {1743-7075},
support = {Grant No. GZY-KJS-SD-2024-059//National Administration of Traditional Chinese Medicine/ ; Grant Nos. 26010132009055 and 26010132009054//Shandong Association for Science and Technology/ ; },
abstract = {BACKGROUND: Diabetic retinopathy (DR) and cognitive impairment are closely related complications of type 2 diabetes mellitus (T2DM). Although dietary patterns and gut microbiota have each been linked to these conditions, their combined associations with co-occurring DR and cognitive impairment remain unclear. This study examined dietary patterns and exploratory gut microbiota profiles in relation to co-occurring DR and cognitive impairment in patients with T2DM.

METHODS: In this cross-sectional study, 306 patients with T2DM were classified into four groups: no DR with normal cognition (DMCN), no DR with cognitive impairment (DMCI), DR with normal cognition (DRCN), and DR with cognitive impairment (DRCI). Dietary patterns were derived using principal component analysis. Gut microbiota composition was assessed using 16 S rRNA sequencing in a subset of 108 participants. Multinomial logistic regression was used to examine associations between dietary patterns and group classification, and microbiome analyses included diversity, taxonomic composition, exploratory differential abundance, and diet-microbiota correlations.

RESULTS: Four dietary patterns were identified. In fully adjusted models, DP-I and DP-II were associated with higher odds of DMCI and DRCI, respectively, whereas DP-III was associated with lower odds of both DMCI and DRCN. DP-IV showed no significant association. Gut microbiota analyses showed modest but statistically significant group-related differences in community structure, with partial overlap across groups. Exploratory LEfSe analysis identified group-associated taxa, including higher relative abundances of Bifidobacterium, Streptococcus, and Dubosiella in DMCN and of Pseudomonas, Bilophila, and Sarcina in DRCI. However, these genus-level differences were not significant after covariate-adjusted MaAsLin2 analysis with false discovery rate (FDR) correction. Nominal diet-microbiota correlations were observed but were not statistically robust after FDR correction.

CONCLUSION: Dietary patterns were associated with clinical group classification based on DR and cognitive impairment in patients with T2DM. Gut microbiota analyses suggested modest, exploratory group-related differences, but diet-microbiota correlations were not statistically robust after FDR correction. These cross-sectional findings should be interpreted as hypothesis-generating and require validation in larger longitudinal studies.},
}

@article {pmid42433106,
year = {2026},
author = {Kerob, D and Salah, S and Dal Belo, SE and Odeimi, J and Clavaud, C and Demessant-Flavigny, A},
title = {A Possible Role of Mycobiome in the Pathophysiology of Acne: Structured Narrative Review and Perspectives.},
journal = {Experimental dermatology},
volume = {35},
number = {7},
pages = {e70308},
doi = {10.1111/exd.70308},
pmid = {42433106},
issn = {1600-0625},
support = {//La Roche-Posay Laboratoire Dermatologique/ ; },
mesh = {Humans ; *Acne Vulgaris/microbiology/physiopathology ; *Malassezia/isolation & purification ; Skin Microbiome ; *Mycobiome ; *Skin/microbiology ; },
abstract = {Acne vulgaris pathogenesis involves complex interactions between sebum hypersecretion, follicular hyperkeratinisation, microbial colonisation and inflammatory cascades. While the bacterial microbiome has been extensively studied, the role of the skin mycobiome, particularly lipophilic Malassezia species, remains less clearly defined in acne-prone sites. To evaluate evidence for skin mycobiome involvement in acne pathogenesis, a structured narrative review was conducted in PubMed/MEDLINE and PMC, synthesising findings from 14 cross-sectional studies involving 1650 participants from diverse geographic and ancestry backgrounds. Across sequencing and culture-based studies, Malassezia was the dominant fungal genus on healthy as well as acne-prone skin; species-level data most often identified M. restricta and M. globosa, with occasional reports of M. furfur. Although significant variations were observed in fungal abundance, discrepancies exist between studies due to differences in study design, sampling methods (surface swabs vs. comedone or pustule contents vs. pore strips), culture media (lipid-supplemented vs. standard), molecular target (ITS1 rDNA vs. other loci) and population demographics. Multiple sequencing studies did not detect significant fungal alpha/beta-diversity differences between acne and non-acne skin while confirming Malassezia species dominance. One study highlighted the potential underdiagnosis of Malassezia folliculitis in acne patients, suggesting that misdiagnosis may occur due to overlapping clinical presentations. Future studies should predefine primary outcomes, adjust for multiplicity, report sampling depth (surface vs. follicular), specify fungal rDNA region sequenced, use specific lipid-supplemented media for Malassezia isolation when culturing, co-profile bacteria and fungi, and add systematic clinical assessment of Malassezia folliculitis.},
}

Humans
*Acne Vulgaris/microbiology/physiopathology
*Malassezia/isolation & purification
Skin Microbiome
*Mycobiome
*Skin/microbiology

@article {pmid42433272,
year = {2026},
author = {Valaei, A and Zahmatkesh, N and Aghaei, R and Maleki, M and Meskini, M and Siadat, SD},
title = {The role of the microbiota in hematological malignancies: A narrative review of mechanisms and therapeutic potential.},
journal = {New microbes and new infections},
volume = {72},
number = {},
pages = {101805},
pmid = {42433272},
issn = {2052-2975},
abstract = {The human microbiota, particularly the gut microbiome, plays a central role in maintaining immune homeostasis, regulating hematopoiesis, and modulating host metabolism through bioactive metabolites such as short-chain fatty acids (SCFAs), bile acids, and tryptophan-derived compounds. Disruption of this microbial ecosystem (dysbiosis) has emerged as a key contributor to the development and progression of hematological malignancies (HMs), including acute and chronic leukemias, lymphomas, and multiple myeloma. This narrative review synthesizes recent evidence (2022-2025) on the complex bidirectional interactions between the microbiota and HMs, highlighting their biological and clinical significance. Current evidence indicates that the microbiota influences hematological malignancies through multiple interconnected mechanisms, including immune regulation, inflammatory signaling, maintenance of hematopoietic homeostasis, and microbial metabolite-mediated modulation of the tumor microenvironment. Dysbiosis has been associated with disease progression, increased susceptibility to infections, impaired treatment tolerance, and inferior clinical outcomes. Conversely, chemotherapy, broad-spectrum antibiotics, and hematopoietic stem cell transplantation profoundly reshape microbial communities, further exacerbating dysbiosis and contributing to complications such as graft-versus-host disease following allogeneic transplantation. Emerging microbiota-targeted interventions, including dietary modulation, probiotics, prebiotics, and fecal microbiota transplantation, show promise for restoring microbial homeostasis and improving therapeutic outcomes. Furthermore, microbiome-derived biomarkers are increasingly being investigated for predicting treatment response, relapse risk, and immunotherapy efficacy. Despite these advances, important challenges remain, particularly in establishing causal relationships, standardizing microbiome profiling, and validating clinical applications through well-designed prospective and randomized studies. Overall, the accumulating evidence supports the microbiota as a critical determinant of hematological cancer biology and treatment response. Integrating microbiome-based diagnostics and therapeutic strategies into precision hematology may offer new opportunities to improve patient management and long-term clinical outcomes.},
}