@article {pmid40844700,
year = {2026},
author = {Alum, EU},
title = {Unlocking the Secrets of Nature: Phytochemicals as Key Players in Longevity and Healthy Aging.},
journal = {Cell biochemistry and biophysics},
volume = {84},
number = {1},
pages = {29-52},
pmid = {40844700},
issn = {1559-0283},
abstract = {BACKGROUND/OBJECTIVE: The global aging population presents significant health and societal challenges, driven by age-related disorders including neurodegeneration, cardiovascular disorders, and metabolic syndromes. Phytochemicals show promise in promoting healthy aging and longevity. This study explores their multifaceted roles in mitigating aging hallmarks through molecular, epigenetic, and gut microbiota interactions. METHODS: A comprehensive review of current literature (2017–2024) published in PubMed and Scopus, using keywords such as phytochemicals, longevity and aging was conducted, focusing on the biological activities of phytochemicals, their molecular mechanisms, and their role in modulating key aging pathways such as AMP-activated protein kinase (AMPK), the mechanistic target of rapamycin (mTOR), and sirtuins. The interaction among phytochemicals and epigenetics, gut microbiome, and their bioavailability challenges were also analyzed. RESULTS: Phytochemicals exhibit potent antioxidant, anti-inflammatory, and senolytic properties, targeting aging characteristics such as oxidative stress and cellular senescence. Compounds like resveratrol and quercetin influence epigenetic regulation, while others modulate gut microbiota, enhancing therapeutic efficacy. Despite their potential, low bioavailability and interindividual variability remain critical challenges. Emerging delivery systems and personalized approaches show promise for optimizing their benefits. CONCLUSION: Phytochemicals offer a natural, integrative strategy to promote longevity and mitigate age-related diseases by targeting fundamental aging mechanisms. Advancements in clinical validation, bioavailability enhancement, and personalized nutrition are essential to harness their full potential, paving the way for transformative applications in healthy aging interventions.},
}

@article {pmid41004017,
year = {2026},
author = {Kaushik, M and Tiku, AB},
title = {Phytochemicals Modulating Redox Homeostasis in Head and Neck Cancer.},
journal = {Cell biochemistry and biophysics},
volume = {84},
number = {1},
pages = {149-162},
pmid = {41004017},
issn = {1559-0283},
abstract = {Reactive oxygen species regulate many biological processes and need constant surveillance and fine-tuning. Oxidative stress can result in the initiation & progression of various cancers including Head and Neck Cancers [HNCs]. The diversity in the structure of the phytochemicals enable them to modulate the redox homeostasis at molecular, biochemical & cellular levels. Understanding the redox regulatory mechanisms induced by phytochemicals is of interest to develop therapeutics against cancers, especially head and neck cancers. Phytochemicals offer multiple benefits compared to synthetic drugs, such as being more affordable, having fewer or no side effects, and being more accessible to the general population. Targeted therapies including immunotherapies, oral microbiome as well as phytochemicals are important factors in the prevention and treatment of HNC. Phytochemicals, besides having chemopreventive & chemotherapeutic role in cancer, can also modulate microbiota indirectly influencing the therapeutic outcome. Despite advancements in therapeutic modalities and emergence of new therapies, management and treatment of HNC is still elusive. Heterogeneity, poor prognosis, invasiveness, and resistance to conventional therapies have been the major road blocks. This review aims to explore and identify new therapeutic approaches for addressing targets linked to redox imbalances. The use of phytochemicals to modulate redox homeostasis at almost all stages of HNC can give a better opportunity for early detection, and prevention leading to improved quality of life for patients. Further development of probes that can detect ROS, for precise therapeutic outcome of phytochemical treatments can also be an important strategy.},
}

@article {pmid41615506,
year = {2026},
author = {Popov, IV and Emelyantsev, SA and Popov, IV and Prazdnova, EV and Berezinskaia, IS and Koroleva, IB and Gorobets, VE and Tsurkova, IS and Aleshukina, AV and Tverdokhlebova, TI and Chikindas, ML and Todorov, SD and Ermakov, AM},
title = {Seasonal Variation in the Mutagenic and Oxidative Properties of Gut Microbiota in Active and Hibernating Common Noctules (Nyctalus noctula).},
journal = {Current microbiology},
volume = {83},
number = {3},
pages = {148},
pmid = {41615506},
issn = {1432-0991},
support = {23-14-00316//Russian Science Foundation/ ; Priority 2030//Southern Federal University/ ; 075-10-2025-017//Ministry of Science and Higher Education of the Russian Federation/ ; },
abstract = {Hibernation induces significant physiological changes in mammals, including suppressed immune responses, metabolic downregulation, and shifts in gut microbiota activity. This study examined seasonal variation in the functional properties of gut microbiota in Nyctalus noctula by assessing the genotoxic and oxidative effects of microbial metabolites using lux-biosensor assays based on Escherichia coli strains carrying stress-inducible promoters: PrecA for detecting DNA damage responses and PkatG for oxidative stress responses. Fifty-eight microbial isolates were obtained from fecal samples collected during hibernation (n = 26) and active (n = 32) periods and evaluated for mutagenic, DNA-protective, antioxidant, and prooxidant activities. Metabolites from isolates collected during hibernation exhibited significantly stronger DNA-protective effects compared to those from active bats, while oxidative stress modulation did not differ significantly between the two groups. A significant negative correlation was observed between bacterial abundance and antioxidant responses, suggesting a possible link between microbial density and functional activity. These results indicate that the physiological state of the host influences the functional output of gut microbiota, particularly in relation to DNA protection. The findings enhance our understanding of seasonal microbiome–host interactions in bats and underscore the relevance of microbial metabolites in shaping host stress responses during hibernation.},
}

@article {pmid41699269,
year = {2026},
author = {Yang, Z and Yu, J and Hong, X and Yin, J and Zhang, T and Song, C and He, C and Mao, S and Yuan, H and Han, P and Li, J and Xiang, X and Li, S and Wang, Z},
title = {Integrated analysis of extrachromosomal circular DNA and transcriptome reveals associations between microbial profiles and Immunoinflammatory markers in hypospadias.},
journal = {World journal of urology},
volume = {44},
number = {1},
pages = {177},
pmid = {41699269},
issn = {1433-8726},
support = {JCYJ20220530145014033//Shenzhen Fundamental Research Program/ ; JCYJ20240813150456073//Shenzhen Fundamental Research Program/ ; JCYJ20240813150456074//Shenzhen Fundamental Research Program/ ; JCYJ20240813150500001//Shenzhen Fundamental Research Program/ ; ZSQYLCKYJJ202317//the Hospital Research Fund of SAHSYSU/ ; 2025A1515012601//Basic and Applied Basic Research Foundation of Guangdong Province/ ; A2301001//Shenzhen Medical Academy of Research and Translation Fund/ ; 592026//Research Start-up Fund of the Seventh Affiliated Hospital, Sun Yat-sen University/ ; 2021B1212040006//Guangdong Provincial Key Laboratory of Digestive Cancer Research/ ; GPKLDCR202206M//Open Fund of Guangdong Provincial Key Laboratory of Digestive Cancer Research/ ; 2023KYPT02//Fundamental Research Funds for the Central Universities, Sun Yat-sen University/ ; ZSQYRSFPD0119//Research Start-up Fund of Post-doctoral of SAHSYSU/ ; 2025M782368//China Postdoctoral Science Foundation/ ; },
abstract = {PURPOSE: Hypospadias, a prevalent congenital anomaly characterized by abnormal urethral opening formation, poses significant psychological and physical challenges to patients. This study aimed to elucidate the function of extrachromosomal circular DNA (eccDNA) found in foreskin tissues of hypospadias patients as well as its association with immunoinflammatory responses and microbial dynamics. METHODS: We used Circle-seq to quantify eccDNA abundance and RNA sequencing for gene expression profiling. Foreskin samples were carefully collected from 54 patients with hypospadias and compared against samples from 59 control individuals with phimosis. The hypospadias cohort was significantly younger (mean 3.2 years) than controls (mean 7.5 years), which might be a major limitation that confounded immune and microbiome findings and limited causal interpretation. Tissue samples were collected after standard surgical disinfection, which may influence microbial detection. RESULTS: Our analysis revealed a striking increase in eccDNA abundance, identifying 2,387,050 eccDNA elements in the hypospadias cohort, contrasted with only 608,545 in the control group. Furthermore, gene expression profiling demonstrated the up-regulation of 541 genes and the down-regulation of 257 genes, with significant enrichment in pathways related to inflammatory responses and lymphocyte differentiation, indicating dysregulated immune responses in hypospadias. Complementary findings of elevated white blood cell counts and inflammatory cytokines underscored the heightened immunoinflammatory response associated with this condition. The activated immunoinflammatory response showed positive associations with eccDNA abundance and sizes. Notably, microbial profiling uncovered that Escherichia coli constituted 43.11% of the foreskin microbiome in hypospadias patients, considerably exceeding levels found in phimosis. Escherichia coli abundance was associated with increased immunoinflammatory response and higher eccDNA levels. CONCLUSION: This study underscores a complex association between immunoinflammatory responses and microbial communities in the pathophysiology of eccDNA dynamics in hypospadias, revealing important implications for future research and potential therapeutic strategies.},
}

@article {pmid41706396,
year = {2026},
author = {Liu, Y and Li, Y and Sun, L and Wu, H and Yin, H and Qin, H and Gu, C and Chang, C and Li, W},
title = {Heterogeneity in Atopic Dermatitis: Ethnic, Anatomical Site, and Age-related Variations.},
journal = {Clinical reviews in allergy & immunology},
volume = {69},
number = {1},
pages = {8},
pmid = {41706396},
issn = {1559-0267},
support = {82273531//National Natural Science Foundation of China/ ; 2021-01-07-00-07-E00078//Key Project of the Innovation Program of Shanghai Municipal Education Commission/ ; 202440121//Clinical Research Funding of Shanghai Municipal Health Commission/ ; 23XD1400400//Program of Shanghai Academic/Technology Research Leader/ ; 23Y31920300//Shanghai Municipal Commission of Science and Technology/ ; },
abstract = {Atopic dermatitis (AD) is a chronic, systematic inflammatory dermatosis with a high prevalence worldwide, characterized by multiple heterogeneities. Recent studies have highlighted variations in the incidence and manifestation of AD among different ethnic populations due to genetic and immunological differences. The severity of AD also varies by anatomical sites, influenced by factors such as regional skin microenvironment, microbiome-immune interaction, and environmental exposure. Notably, head and neck dermatitis (HND) is a refractory phenotype of AD, which responds less well to conventional and novel systemic treatment. Furthermore, distinct susceptibility factors exist across age groups, including food allergies in infants and young children, psychological stress in adults, and aging-related AD in the elderly. The heterogeneity of AD requires further exploration of the pathogenesis in different states, which also poses a significant challenge for therapy. This review synthesizes current evidence on AD heterogeneity, elucidating variations across ethnicities, anatomical sites, and age groups to guide the development of precision treatment.},
}

@article {pmid41735642,
year = {2026},
author = {Arolim, Y and Kumar, H and Hanah, SS and Biswas, TK and Periasamy, K and Chotso, K and Chamuah, JK and Shivanagowda, GP},
title = {A comprehensive review on Mithun (Bos frontalis): a keystone species in sustainable livelihoods of the eastern Himalayas and Indo-Burma region.},
journal = {Tropical animal health and production},
volume = {58},
number = {2},
pages = {},
pmid = {41735642},
issn = {1573-7438},
abstract = {Mithun (Bos frontalis), a unique semi-domesticated bovine of the Eastern Himalayas and Indo-Burma region, plays a critical role in sustaining forest-based agroecosystems and tribal livelihoods, yet remains under-researched. This review synthesizes multidisciplinary research encompassing husbandry, nutrition, reproductive biology, genomic architecture, health management, and ecological adaptations of Mithun. A systematic analysis of published literature, including molecular, physiological, and ethnographic studies, was conducted to identify knowledge gaps and emerging opportunities. Key findings reveal Mithun’s superior meat and milk composition, exceptional adaptation to rugged forest terrains, and valuable genetic traits linked to disease resistance, hypoxia tolerance, and efficient fibre digestion. Technological advances in reproductive biotechnologies (e.g. semen cryopreservation, estrus synchronization), genomic characterization, and microbiome profiling have provided new insights into its productivity and conservation. However, challenges such as habitat loss, genetic erosion, zoonotic risks, and low institutional support constrain its sustainable utilization. This review emphasizes the urgent need to integrate traditional knowledge with modern interventions for conservation breeding, nutrition-sensitive agroforestry systems, and decentralized health management. Strengthening Mithun as a climate-resilient livestock species can enhance both biodiversity preservation and socio-economic resilience in fragile montane ecosystems.},
}

@article {pmid41774153,
year = {2026},
author = {Liu, Y and Zhang, B and Li, H and Si, Y and Qiu, M and Xu, H and Qi, C},
title = {Restoring Firmicutes-Associated Metabolites: A Gut-Brain Axis Approach to Alleviate Neuroinflammation and Oxidative Stress in Intracerebral Hemorrhage.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774153},
issn = {1432-0991},
support = {2021QN14//the Scientific Research Project of Xi'an Medical University/ ; 23JK0641//the Scientific Research Program Funded by Education Department of Shaanxi Provincial Government/ ; 2020JZ-56//the Natural Science Basic Research Program of Shaanxi Province/ ; 2021TD05//the Program for Science and Technology Innovation Team in Xi'an Medical University/ ; 202223//the Science and Technology and Information Bureau, Weiyang district, Xi'an, Shaanxi/ ; 2020JM-608//the General Program of the Natural Science Basic Research Plan in Shaanxi Province/ ; },
abstract = {Intracerebral hemorrhage (ICH), a lethal stroke subtype, lacks therapies targeting gut-brain axis dysregulation. While gut microbiota influences ischemic stroke outcomes, how ICH perturbs microbial-metabolite interactions via the microbiota-gut-brain axis (MGBA) remains unknown. We combined a collagenase-induced ICH mouse model with multi-omics (16S rRNA sequencing, metabolomics) and functional assays (BV2 microglia) to investigate gut dysbiosis and metabolite alterations. Intestinal barrier integrity, neuroinflammation, and oxidative stress were assessed. At the phylum level, the control (CON) group exhibited a microbiome dominated by Firmicutes, Actinobacteriota, and Campylobacterota. In stark contrast, the ICH group displayed a pathological shift toward Bacteroidota, Cyanobacteria, and Proteobacteria. These dysbiotic alterations corresponded to intestinal barrier compromise marked by reduced expression of zonula occludens-1 (ZO-1), occludin, and mucin 2 (MUC2), systemic elevation of pro-inflammatory cytokines including interleukin-1β (Il-1β) and tumor necrosis factor-α (Tnf-α), and depletion of neuroprotective metabolites–specifically oleoyl ethanolamide, linoleoyl ethanolamide, and L-valine–whose levels positively correlated with Firmicutes abundance. Mechanistically, in vitro experiments demonstrated that these metabolites collectively suppressed neuroinflammation and neuronal apoptosis, with l-valine exhibiting unique antioxidant activity through Reactive oxygen species scavenging. Molecular docking studies have shown that linoleoyl ethanolamide (LEA) and oleoylethanolamide (OEA) can inhibit the levels of inflammatory cytokines interleukin-6 (Il-6) and tumor necrosis Tnf-α by binding to key sites. Our findings underscore the critical role of gut microbiota-metabolite crosstalk in ICH pathogenesis and identify microbial metabolites as potential therapeutic targets for preserving gut-brain axis homeostasis.},
}

@article {pmid41790252,
year = {2026},
author = {Shachor, M and Idan, D and Kravarusic, D and Paran, M and Sher, N and Dreznik, Y},
title = {Feeding patterns and the risk of perianal abscess in early infancy: a case-control study.},
journal = {Pediatric surgery international},
volume = {42},
number = {1},
pages = {},
pmid = {41790252},
issn = {1437-9813},
abstract = {BACKGROUND: Breastfeeding is widely recognized as protective against infectious morbidity in infancy, largely through immunologic, anti-inflammatory, and microbiome-mediated mechanisms. Whether exclusive breastfeeding also influences the risk of perianal abscess, a relatively common condition in early infancy, remains unclear. This study aimed to evaluate the association between infant feeding patterns and the development of perianal abscess. METHODS: This retrospective case–control study with age-frequency matching was conducted at a tertiary pediatric surgery center and included male infants aged 0 to 6 months diagnosed with perianal abscess between January 2020 and December 2025. Epidemiologic characteristics, recurrence rates, microbiologic findings, and feeding practices (exclusive breastfeeding, exclusive formula feeding, or mixed feeding) were collected and compared. Logistic regression was used to assess the association between feeding pattern and odds of abscess, adjusting for age and prematurity. RESULTS: Mean age was similar between groups (2.3 vs. 2.5 months). Among infants with perianal abscess, 46% were exclusively breastfed, 23.6% exclusively formula-fed, and 30.3% mixed-fed. In controls, the corresponding rates were 39%, 40%, and 21%, respectively. Overall feeding distribution did not differ significantly (p = 0.056). Exclusive breastfeeding was not associated with reduced odds of abscess (OR 0.81; 95% CI 0.38–1.73), whereas exclusive formula feeding was associated with lower odds compared with mixed feeding (OR 0.40; 95% CI 0.18–0.91). CONCLUSIONS: In this cohort of male infants under six months, exclusive breastfeeding did not appear to protect against perianal abscess. Mixed feeding was more common among affected infants, which may reflect the transient microbiologic shifts that occur during partial weaning or combined feeding.},
}

@article {pmid41879847,
year = {2026},
author = {Kumar, V and Singh, B and Ayyagari, A and Chaudhari, DN and Ahire, JJ},
title = {The Gut-Brain-Cardiac Axis: How Microbiota Influence Cognitive and Cardiovascular Health.},
journal = {Current microbiology},
volume = {83},
number = {5},
pages = {},
pmid = {41879847},
issn = {1432-0991},
abstract = {The gut-brain-heart axis represents a dynamic interplay between the gut microbiota, cognitive function, and cardiovascular health, with profound implications for understanding and managing chronic diseases. In dysbiosis, a disruption in microbial balance contributes to neuro-inflammation, mood disorders, neurodegenerative diseases, and cardiovascular conditions such as atherosclerosis and hypertension. To date, researchers explored different mechanism through which gut microbial communities influence the activities of brain and heart. In order to understand these mechanisms summative, in this review, we focused on key communication pathways between microbiota-gut-brain-heart, such as vagus nerve, gut-derived metabolites, and systemic inflammation. Furthermore, the review discusses the bidirectional nature of these relationships, where cardiovascular and cognitive health mutually influence one another. Therapeutic interventions, including probiotics, dietary modifications, biotechnological approach and lifestyle changes are evaluated for their potential to modulate the gut-brain-heart axis and improve health outcomes. Despite significant advances, challenges remain in understanding the complex interactions within this axis. Future research directions emphasize personalized medicine approaches and the potential of microbiome-targeted therapies to revolutionize the prevention and treatment of cognitive and cardiovascular disorders.},
}

@article {pmid41888496,
year = {2026},
author = {Tsepina, N and Kolesnikov, S and Minnikova, T and Timoshenko, A and Kuzina, A and Evstegneeva, N and Kazeev, K and Minkina, T and Tarigholizadeh, S and Mehmood, N and Rajput, VD},
title = {Assessment of niobium ecotoxicity on biological indicators of chernozem.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {4},
pages = {},
pmid = {41888496},
issn = {1573-3017},
abstract = {The current study employs a controlled model experiment aimed at evaluating niobium (Nb) ecotoxicity through quantitative analysis of temporal variation in biological indicators within Chernozem. The ecotoxicological effects of Nb contamination in black soil across varying doses (3x, 30x and 300x background concentrations) and exposure durations (10, 30 and 90 days) were investigated. The findings demonstrated that elevated Nb concentrations significantly suppressed radish (Raphanus sativus) seed germination and root elongation, reduced Azotobacter sp. abundance and inhibited key enzymatic activities, including catalase, dehydrogenase and cellulolytic activity. The most pronounced inhibitory effects were observed after 30 days of Nb exposure, with all biological indicators reaching their minimum values. Moreover, an extended exposure period of 90 days facilitated recovery of soil biological properties, suggesting a potential resilience or adaptive response within the soil microbiome. Among the assessed parameters, Azotobacter sp. exhibited the highest sensitivity to Nb contamination, while cellulolytic activity emerged as the most robust and informative biomarker for Nb-induced soil toxicity. A critical threshold value of 59 mg/kg Nb was identified beyond which significant ecotoxicological impacts became evident. These findings provided a valuable framework for ecological risk assessment and biomonitoring of Nb-contaminated soils, offering diagnostic indicators for evaluating soil health and further remediation strategies.},
}

@article {pmid41912729,
year = {2026},
author = {Huang, C and Zou, H and Cai, Y and Zhang, H and Zou, X},
title = {Oropharyngeal Microbiota Associated with Sore Throat in Acute Upper Respiratory Tract Infections.},
journal = {Current microbiology},
volume = {83},
number = {5},
pages = {},
pmid = {41912729},
issn = {1432-0991},
support = {No2022YFC3500802//National Key Research and Development Program of China/ ; },
abstract = {Acute upper respiratory tract infections (AURI) can lead to an imbalance in the oropharyngeal microbiome. Specific bacteria may be responsible for a sore throat. We divided 278 AURI patients from outpatient clinics in China into sore throat (ST) and non-sore throat (NST) groups. Then, we performed 16S ribosomal ribonucleic acid (rRNA) gene sequencing on throat swab samples of all patients. And explore whether there are compositional and functional differences between the two groups of microorganisms, and conduct Sparse Correlations for Compositional Data (SparCC) and machine learning analysis. There were no statistically significant differences in age, gender, BMI, or peripheral blood cell counts between patients with sore throat and non-sore throat groups. The composition of OTUs in the two groups was significantly different. Compared to the ST group, the NST group showed an increasing trend in α-diversity. The abundance of Campylobacter, Prevotella, and Actinomycetaceae was higher in the NST group. In terms of functional prediction, the ST group showed a higher expression of non-homologous end-joining repair mechanisms and xenobiotic biodegradation. The Support Vector Machine (SVM) model exhibited the best predictive performance. Machine learning models at the genus level identified Peptostreptococcus as a potential microbial feature associated with sore throat. Notably, further species-level analysis revealed complexity within this genus. The mechanism of sore throat may be related to differences in the oral and pharyngeal microbiota and functional expression.},
}

@article {pmid41940993,
year = {2026},
author = {Xu, Y and Leong, ZN and Huang, Y and Ma, Z and Chan, GCT and Kim, JE},
title = {Impact of brewer's spent grain (BSG) and bio-transformed BSG biscuits on metabolic and gut health in adults with metabolic impairments: a randomized controlled trial.},
journal = {European journal of nutrition},
volume = {65},
number = {3},
pages = {},
pmid = {41940993},
issn = {1436-6215},
support = {A-0008420-00-00//Ministry of Education - Singapore/ ; },
abstract = {BACKGROUND: Brewers’ spent grain (BSG), a fiber-rich by-product of the brewing industry, has high nutritional value. Fermentation with Rhizopus oligosporus further enhances its composition by increasing soluble dietary fiber and releasing antioxidants, potentially conferring superior metabolic regulatory and prebiotic effects. This study evaluated the effect of long-term consumption of BSG or fermented BSG-containing biscuits on metabolic and gut health in Singapore adults with metabolic impairments. METHODS: Thirty-one metabolically impaired subjects were randomized to consume 90 g/day of control biscuits (Control, n = 11), 30% wheat flour substituted autoclaved BSG- (ABSG, n = 10) or fermented BSG-containing biscuits (FBSG, n = 10) for 12 weeks. Anthropometric, blood pressure, dietary intake, glycemic-related biomarkers, lipid-lipoprotein profile, gut microbiome and metabolites were assessed at baseline and after intervention. RESULTS: Total dietary fiber intake increased in both ABSG and FBSG groups (Pinteraction < 0.001). FBSG group showed significant increase of HDL-C after intervention (P = 0.024). BSG-containing biscuits consumption decreased fecal lithocholic acid concentration (Pinteraction = 0.02), which may lower intestinal cytotoxicity. Although α- and β-diversity were unchanged, favorable taxonomic shifts were observed. In the ABSG group, Romboutsia, a genus associated with metabolic dysfunction, decreased while the FBSG group showed increased abundances of the short-chain fatty acids-producing Roseburia and Clostridium scindens, alongside a reduction in Dorea. asa No significant difference was observed in other indicators. CONCLUSIONS: Consumption of BSG-containing biscuits enhances daily dietary fiber intake and modulates gut metabolites and microbiome composition to support gut microbiome homeostasis. Additionally, fermented BSG provides further metabolic benefits, particularly in regulating lipid-lipoprotein metabolism. TRIAL REGISTRATION: ClinicalTrials.gov: NCT05529108.},
}

@article {pmid41968131,
year = {2026},
author = {Gortari, M and Maguire, VG and Ezquiaga, JP and Cicchino, M and Bailleres, M and Escaray, RU and Ruiz, OA and Llames, ME},
title = {Associations between soil microbiomes and carbon stabilization under long-term no-till farming systems in the Argentine Pampas.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47621-4},
pmid = {41968131},
issn = {2045-2322},
support = {PICTs 2018-3723 y 2020-2023//Agencia Nacional de Promoción Científica y Tecnológica , Argentina/ ; PICTs 2018-3723 y 2020-2023//Agencia Nacional de Promoción Científica y Tecnológica , Argentina/ ; PICTs 2018-3723 y 2020-2023//Agencia Nacional de Promoción Científica y Tecnológica , Argentina/ ; PICTs 2018-3723 y 2020-2023//Agencia Nacional de Promoción Científica y Tecnológica , Argentina/ ; PICTs 2018-3723 y 2020-2023//Agencia Nacional de Promoción Científica y Tecnológica , Argentina/ ; PICTs 2018-3723 y 2020-2023//Agencia Nacional de Promoción Científica y Tecnológica , Argentina/ ; PICTs 2018-3723 y 2020-2023//Agencia Nacional de Promoción Científica y Tecnológica , Argentina/ ; PICTs 2018-3723 y 2020-2023//Agencia Nacional de Promoción Científica y Tecnológica , Argentina/ ; PIP CONICET11220210100584CO 2022-2024//Consejo Nacional de Investigaciones Científicas y Técnicas , Argentina/ ; PIP CONICET11220210100584CO 2022-2024//Consejo Nacional de Investigaciones Científicas y Técnicas , Argentina/ ; PIP CONICET11220210100584CO 2022-2024//Consejo Nacional de Investigaciones Científicas y Técnicas , Argentina/ ; PIP CONICET11220210100584CO 2022-2024//Consejo Nacional de Investigaciones Científicas y Técnicas , Argentina/ ; PIP CONICET11220210100584CO 2022-2024//Consejo Nacional de Investigaciones Científicas y Técnicas , Argentina/ ; PIP CONICET11220210100584CO 2022-2024//Consejo Nacional de Investigaciones Científicas y Técnicas , Argentina/ ; PIP CONICET11220210100584CO 2022-2024//Consejo Nacional de Investigaciones Científicas y Técnicas , Argentina/ ; PIP CONICET11220210100584CO 2022-2024//Consejo Nacional de Investigaciones Científicas y Técnicas , Argentina/ ; },
abstract = {Soil microbial communities play a key role in carbon (C) cycling in agroecosystems; however, their long-term responses to contrasting management practices remain poorly understood in agricultural soils. In this study, we evaluated the effects of more than 20 years of no-till farming (NTF) and conventional tillage (CT) on soil physicochemical properties, bacterial and fungal community composition, and inferred functions related to C and nutrient cycling in the Argentine Pampas. We show that NTF increased total organic carbon (TOC) stocks in surface soils and promoted edaphic conditions associated with C stabilization, including higher cation exchange capacity and structural stability. Bacterial communities exhibited high functional redundancy and were primarily structured along sodium-related parameters, whereas fungal communities were more sensitive to management, with NTF favoring ligninolytic and symbiotic fungi that contribute to necromass formation and long-term carbon stabilization. In contrast, CT enriched opportunistic fungal guilds associated with disturbance and short-term nutrient turnover. Phylogenetic analyses revealed community assembly dominated by environmental filtering in both microbial domains. Overall, these results highlight the central role of fungi as mediators of soil C stabilization and suggest that conservation practices such as NTF enhance microbiome contributions to ecosystem services and climate change mitigation in intensively managed agroecosystems.},
}

@article {pmid41986869,
year = {2026},
author = {Fan, S and Yao, J and Yang, L and Chen, Y and Zhou, M and Zhuang, W and Ouyang, G},
title = {Cyclophosphamide alters gut microbiota metabolism and structure in lymphoma-bearing mice: implications for dietary modulation.},
journal = {Irish journal of medical science},
volume = {},
number = {},
pages = {},
pmid = {41986869},
issn = {1863-4362},
support = {2023S142 and 2022S032//Ningbo Municipal Public Welfare Science and Technology/ ; },
abstract = {BACKGROUND: Diffuse large B-cell lymphoma (DLBCL) is a common subtype of non-Hodgkin lymphoma, with a high relapse rate after R-CHOP treatment. Cyclophosphamide (CTX), a key component of R-CHOP, induces gastrointestinal side effects and alters the gut microbiome. This study examined the effect of CTX on gut microbiota metabolism and the role of dietary substrates. METHODS: An in vitro gut fermentation model was used to analyze the fecal microbiota from tumor-bearing mice treated with CTX. We examined microbial metabolites, gas production, short-chain fatty acids (SCFAs), and microbial community structure in response to inulin, tyrosine, and tryptophan. RESULTS: CTX treatment disrupted gut microbiota metabolism, reducing SCFA production (particularly acetate and butyrate) and increasing isovaleric acid from tyrosine metabolism. Inulin utilization was reduced, and gas production (especially hydrogen and CO2) decreased. Tryptophan fermentation increased hydrogen and hydrogen sulfide. CTX also altered microbiota composition, increasing Proteus, Klebsiella, and Enterococcus, which were associated with higher gas production and lower SCFAs. Inulin enhanced beneficial bacteria (Ligilactobacillus) and reduced pathogenic ones (Klebsiella). Correlation analysis showed that inulin fermentation produced more SCFAs with less gas, while tyrosine and tryptophan fermentations promoted gas but limited SCFA formation. CONCLUSION: CTX disrupts gut microbiota metabolism, decreasing SCFA production and altering gas production, which may contribute to gastrointestinal side effects. Dietary interventions like inulin may mitigate these effects by restoring microbial balance.},
}

@article {pmid42046034,
year = {2026},
author = {Yuan, DM and Cao, XG and Chen, J and Zhang, HM and Yu, LF and He, QQ and Mu, J and Liu, Y and Chen, ZF and Yan, LB},
title = {Specificity of the rhizosphere fungal community in Alsophila spinulosa: structure, function, and co-occurrence networks.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05086-5},
pmid = {42046034},
issn = {1471-2180},
support = {2016YFC0502604//the National Key Research and Development Programme for the 13th Five-Year Plan/ ; no. Qian-Ke-He-Ji-Chu-ZK [2023] 111//Guizhou Provincial Basic Research Program (Natural Science)/ ; No. Qian-Ke-He-Basic MS [2025] 662//Guizhou Provincial Basic Research Program (Natural Science)/ ; GNYL[2017]009//Construction Program of Biology First- class Discipline in Guizhou/ ; Guizhou Education and Co-operation Co-Innovation Zi [2014] 01//Guizhou Province Higher Education Institutions Innovation Capability Enhancement Programme Project/ ; Guigengji (2020) No. 27//Talent Introduction Scientific Research Project of Guizhou University/ ; },
abstract = {Through a comparative analysis, this study systematically investigated the assembly mechanisms, functional traits, and interaction networks of the soil fungal community in the rhizosphere of the tree fern Alsophila spinulosa. While the overall structure of the fungal community was similar between the rhizosphere and bulk soil, nuanced differences were observed. Specific taxa (e.g., Perenniporia, Tubulicium) showed relative enrichment in the rhizosphere. Functional prediction further indicated a proportionally higher potential for animal pathogenicity within the community. This pattern suggests that, alongside the dominant saprotrophic functions, the rhizosphere microbiome may influence root health indirectly by mediating soil micro‑food webs. Co‑occurrence network analysis revealed a distinct interaction pattern within the rhizosphere community, wherein keystone taxa such as Arthrinium and Volutella may play important roles in maintaining the network architecture. Collectively, the rhizosphere of A.spinulosa maintains a fungal community with unique functional and structural features, providing a microbiological perspective for understanding the adaptation of this ancient fern to the forest understory habitat. Future studies integrating multi‑omics approaches are warranted to validate the functions of these key fungal groups and elucidate their specific mechanistic roles.},
}

@article {pmid42047719,
year = {2026},
author = {Lawrence, CN and Kohli, H and Brar, K},
title = {Epithelial Barrier Dysfunction in Atopic Dermatitis, Allergic Contact Dermatitis, and Chronic Spontaneous Urticaria and its Therapeutic Implications.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42047719},
issn = {1534-6315},
abstract = {PURPOSE OF REVIEW: Allergic skin diseases arise from complex interactions between epithelial barrier dysfunction and immune dysregulation. This review examines how structural and functional defects in the epidermal barrier predispose to conditions such as atopic dermatitis, allergic contact dermatitis, and chronic spontaneous urticaria, and explores how mechanistic insights into these abnormalities guide therapeutic selection. RECENT FINDINGS: Advances in molecular and genetic research have clarified the roles of filaggrin deficiency, lipid disorganization, altered skin pH, tight junction impairment, antimicrobial peptide imbalance, and microbiome disruption in driving barrier vulnerability and downstream immune activation. Parallel progress in immunology has identified key signaling pathways including JAK-STAT, IL-4/IL-13, OX40, BTK, and KIT that sustain inflammation and disease chronicity. These discoveries have led to the expansion of biologic and small-molecule therapies, with additional agents targeting barrier restoration and immune memory currently in development. Identification of specific epithelial and immune defects has provided a unifying framework for understanding susceptibility, chronicity, and relapse across allergic skin diseases. Ongoing research focused on epidermal barrier biology, microbiome modulation, and translational immunology has the potential to refine therapeutic selection, improve long-term disease control, and guide future drug development.},
}

@article {pmid42062335,
year = {2026},
author = {Silva, LCF and Costa, GXR and da Silva, MAD and Cardoso, LMAB and Sousa, ABM and Rocha, RAR and Machado, MVC and Amaral, LR and Bertarini, PLL and Santos, LD and Gomes, MS},
title = {Microbial community dynamics during Coffea arabica cv. Arara fermentation and their relationship with specialty coffee quality.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44864-z},
pmid = {42062335},
issn = {2045-2322},
support = {2021/06968-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; APQ-04267-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; 400080/2023-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; FINEP-0514/18//Financiadora de Estudos e Projetos/ ; },
abstract = {Fermentation stands out as a promising strategy for the valorization of specialty coffees, directly impacting the sensory profile of the beverage. This study investigated the microbial dynamics during the self-induced anaerobic fermentation (SIAF) of Coffea arabica L. cv. Arara cherries, under different conditions of time (0, 24, 48, and 72 h), temperature (ambient and 27 °C), processing type (solid-state or submerged), and the presence or absence of a starter culture. Metataxonomic analyses (16 S rRNA and ITS1) were performed, revealing significant shifts in the diversity and structure of bacterial and fungal communities throughout the process. A predominance of the genera Lactobacillus and Kazachstania was observed, with fungal diversity being strongly affected, showing a marked reduction within the first 24 h. Decision tree-based predictive models revealed correlations between specific microorganisms and sensory attributes of the beverage, highlighting Leuconostoc, Lactobacillus, and Pichia as potential positive markers. These findings indicate that controlling fermentation conditions enables modulation of the microbiome, promoting desirable sensory profiles and contributing to the development of targeted starter cultures and the standardization of high-quality coffees.},
}

@article {pmid42062386,
year = {2026},
author = {Szklenarik, G and Dora, D and Szincsak, S and Acquah, CK and Biswas, A and Horváth, M and Galffy, G and Lohinai, Z},
title = {The gut mycobiome and inter-kingdom microbial networks are linked to COPD severity in lung cancer patients.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47296-x},
pmid = {42062386},
issn = {2045-2322},
abstract = {Chronic obstructive pulmonary disease (COPD) is increasingly recognized as a systemic disorder affecting host–microbiome interactions beyond the airways. Although bacterial alterations in COPD have been documented, the gut mycobiome and its ecological integration with bacterial communities remain unexplored. In this study, we profiled the gut mycobiome of 61 non-small-cell lung cancer (NSCLC) patients stratified by COPD severity using ITS2 sequencing and analyzed 47 overlapping patients with available metagenomic data to construct cross-kingdom bacterial–fungal networks. Alpha diversity, assessed by Shannon, Simpson, and Chao1 indices, did not differ significantly between patients with and without severe COPD. Partial least squares discriminant analysis (PLS-DA) revealed partial separation of the two groups, with COPD severity explaining 6% of overall compositional variance (R[2]=0.06, p = 0.058). COPD-severe patients exhibited a significantly reduced Ascomycota/Basidiomycota ratio (p = 0.039) and lower relative abundance of Mucoromycota. Analysis of compositions of microbiomes (ANCOM) identified Myrothecium and Lasiodiplodia crassispora enriched in severe COPD, while Helotiales_unclassified and Phallus atrovolvatus were more abundant in non-severe cases. Fungal co-occurrence networks demonstrated reduced connectivity and modularity in severe COPD compared with non-severe COPD. Cross-kingdom analyses integrating bacterial genera revealed strengthened Candida–Enterococcus/Clostridium hubs and weakened Faecalibacterium/Roseburia–yeast associations in severe disease. Keystone analysis showed increased centrality for Candida, Aspergillus, Enterococcus, and Clostridium, and decreased centrality for Akkermansia and Roseburia. A compositional balance classifier achieved high discriminatory power (AUC = 0.88) in distinguishing COPD-severe from non-severe patients. These findings indicate that COPD severity is not characterized by major diversity loss but by guild-specific compositional shifts and extensive network rewiring, favoring oxygen-tolerant, opportunistic taxa over short-chain fatty acid–associated commensals.},
}

@article {pmid42334240,
year = {2026},
author = {Hussain, AN and Fotso, KT and McMurray, MA},
title = {Comparative Analysis of Stress Adaptation in the Yeast Microbiome of Cactus.},
journal = {Yeast (Chichester, England)},
volume = {},
number = {},
pages = {},
doi = {10.1002/yea.70033},
pmid = {42334240},
issn = {1097-0061},
support = {R35GM148198//National Institute of General Medical Sciences of the National Institutes of Health/ ; },
abstract = {Together with other fungi, yeasts make up a significant component of the plant microbiome. As the planet warms, cacti expand their range. Cactus-associated yeasts are known to exhibit signatures of adaptation to the cactus host. Our previous isolation of a wild Saccharomyces paradoxus yeast from a cactus in a forest of oaks populated by S. cerevisiae prompted us to further explore cactus-associated fungi and look for genomic and phenotypic signatures of adaptation. Here we characterize seven yeast isolates, five from cacti and two from adjacent non-cactus plants, among which was a novel species of Coniochaeta isolated from wild grape that we name C. udwismasis. Closely-related isolates from distinct plant hosts exhibited distinct features, including differences in thermotolerance, freeze-thaw tolerance, pigmentation, and predicted septin protein complex assembly, providing new insights into possible mechanisms of cactus adaptation by the yeast microbiome.},
}

@article {pmid42334881,
year = {2026},
author = {Chan Poon, KT and Han, SH and Ilkayeva, O and Muehlbauer, MJ and Newgard, CB and Cotten, CM and Ashley, PL and Seed, PC and Rawls, JF and Younge, NE},
title = {Microbiotas from extremely preterm infants with growth faltering impair postnatal growth and metabolism in mice.},
journal = {JCI insight},
volume = {},
number = {},
pages = {},
doi = {10.1172/jci.insight.199097},
pmid = {42334881},
issn = {2379-3708},
abstract = {Postnatal growth faltering is a pervasive problem among extremely preterm infants that is independently associated with adverse neurodevelopmental outcomes. We previously observed that preterm infants with poor postnatal growth have altered development of the intestinal microbiota relative to preterm infants with appropriate postnatal growth. Here, we used gnotobiotic mice to investigate whether these differences in microbiota development independently contribute to growth faltering. We found that colonization of neonatal mice with microbiotas from extremely preterm infants with poor growth reproduced postnatal growth impairment and induced a metabolic signature of enhanced lipolysis and fatty acid oxidation in the mice, characterized by elevated hepatic acylcarnitines and circulating ketones. In mice colonized at birth with microbiotas from infants with poor growth, postnatal treatment with microbiotas from infants with appropriate growth prevented growth impairment. These results indicate that altered development of the intestinal microbiota contributes to growth faltering in extremely preterm infants, and that microbiota modification can restore postnatal growth.},
}

@article {pmid42334936,
year = {2026},
author = {Anand, U and Rehman, FU and Amponsah, J and Tegg, R and Leo, AE and Balendres, MA and Wilson, CR},
title = {Germinate-to-Exterminate: Pre-Crop Stimulation of Verticillium dahliae Microsclerotia Germination by Root Exudates as a Novel Strategy for Sustainable Control of Verticillium Wilt.},
journal = {Plant disease},
volume = {},
number = {},
pages = {},
doi = {10.1094/PDIS-01-26-0218-FE},
pmid = {42334936},
issn = {0191-2917},
abstract = {Verticillium wilt (VW) is an important soil-borne disease caused by Verticillium species. VW has been reported in nearly 400 plant species from various families, including but not limited to Solanaceae, Brassicaceae, Cucurbitaceae, Fabaceae, Rosaceae, Caprifoliaceae, Malvaceae, Lamiaceae, and Sapindaceae. Potato (Solanum tuberosum L.), belonging to the Solanaceae family, is one of the most important staple crops globally and can be greatly impacted by VW, resulting in more than 40% yield losses in heavily infested commercial fields. VW in potatoes can be caused by infections with Verticillium dahliae (the most damaging species), V. albo-atrum, V. tricorpus, and others. V. dahliae produces microsclerotia (MS), resting structures that can persist in the soil for more than 10 years, even without a host crop, making effective field management challenging. Additionally, the incidence and severity of VW can be increased when root lesion nematodes and V. dahliae co-infect potato crops. Root exudate metabolites facilitate plant-microbial communication, which is also essential for the pathosystems adaptation to environmental change. These can also provide important signals to plant pathogens; for example, to facilitate stimulation of V. dahliae MS germination. A thorough understanding of how root exudates drive plant-pathogen interactions and how this knowledge can be applied to disease suppression will aid in the development of novel biomolecules to manage soil-borne fungal pathogens, thereby reducing or limiting the need for harmful pesticides. In this review article, we examine the current state of knowledge and identify gaps in our understanding of VW and its interactions with root exudates from host plants, highlighting a potential novel strategy for sustainable control of VW in potato crops, known as the germinate-to-exterminate (G2E) approach.},
}

@article {pmid42334937,
year = {2026},
author = {Ma, C and Liu, S and Won, S and Koslicki, D},
title = {MetagenomicKG: a knowledge graph for metagenomic applications.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag421},
pmid = {42334937},
issn = {1367-4811},
abstract = {MOTIVATION: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for the genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities from different databases to standardized identifiers, allowing their interrelations to be captured into a cohesive network regardless of the naming conventions used in each source. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored.

RESULTS: We present MetagenomicKG, a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information on the human microbiome sourced from various databases, and further connects these with existing biomedical KGs to expand the biological network. Through various case studies involving the human microbiome, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction.

CODE AVAILABILITY: The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available on GitHub at https://github.com/KoslickiLab/MetagenomicKG. The data used in this manuscript, including the pre-built files and use case input data, are archived on Zenodo with DOI: 10.5281/zenodo.17546861.

SUPPLEMENTARY INFORMATION: available at Bioinformatics online.},
}

@article {pmid42335165,
year = {2026},
author = {Putz, JC and Wilding, M and Lackner, S and Narrath, M and Schlotmann, D and Sallmutter, MT and Tatzer, J and Brandstätter, A and Lang, JD and Holasek, S and Wenninger, J and Butler, MI and Bengesser, S and Gruber, L and Baranyi, A and Wagner-Skacel, J and Mörkl, S},
title = {Do probiotics modulate dietary intake? Pilot data from a randomized controlled sub-study of the ProBioHRV clinical trial in patients with depression and healthy controls.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350801},
pmid = {42335165},
issn = {1932-6203},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Female ; Male ; Adult ; Pilot Projects ; Double-Blind Method ; Middle Aged ; *Major Depressive Disorder/diet therapy ; Diet ; Gastrointestinal Microbiome/drug effects ; Dietary Supplements ; },
abstract = {BACKGROUND: The gut microbiome plays a central role in human health and is strongly influenced by diet. Probiotics can beneficially modulate the microbiome and, through the gut-brain axis, may affect mood, appetite, and food preferences. This randomized controlled trial examined whether three months of probiotic supplementation could alter dietary intake in individuals with major depression (MD) and healthy controls (HC).

METHODS: In this double-blind, placebo-controlled trial, 53 participants (23 with MD, 30 HC) received either a multi-strain probiotic or placebo twice daily for three months. Dietary intake was assessed at baseline and three follow-ups using the Vienna Food Record (VFR). Nutritional data were analyzed with nut.s® software and evaluated using mixed ANOVAs for repeated measures. These analyses represent additional data collected within the framework of the ProBioHRV study.

RESULTS: Changes across dietary measures were generally small, with only a limited number reaching statistical significance. Significant three-way interactions (time × intervention × diagnosis) emerged for vitamin D intake, dietary variety, folic acid, and diversity. In HC, probiotic supplementation was associated with higher vitamin D intake after one week, while in MD, a similar increase was observed after three months (trend level, p = .058). Conversely, participants receiving probiotics showed lower dietary variety and diversity scores at several time points. Across all time points, folic acid intake was lower in MD compared to HC, independent of intervention.

CONCLUSION: Probiotic supplementation did not produce consistent changes in nutrient intake but showed exploratory, time- and group-dependent patterns for selected measures, including vitamin D intake and dietary variety and diversity. Given the pilot nature of the study, these findings are descriptive and hypothesis- generating. Larger, well-powered studies with objective nutritional and microbiome measures are required.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Female
Male
Adult
Pilot Projects
Double-Blind Method
Middle Aged
*Major Depressive Disorder/diet therapy
Diet
Gastrointestinal Microbiome/drug effects
Dietary Supplements

@article {pmid42335240,
year = {2026},
author = {Barrodia, P and Saw, AK and Jeter-Jones, SL and Chang, CC and Shao, J and Arslan, E and Singh, AK and Satpati, S and Jenq, RR and Rai, K and Piwnica-Worms, H},
title = {Fasting primes small intestinal regeneration after damage via a microbiome-metabolite-chromatin axis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {26},
pages = {e2529215123},
doi = {10.1073/pnas.2529215123},
pmid = {42335240},
issn = {1091-6490},
support = {R01CA269495//HHS | NIH | National Cancer Institute (NCI)/ ; RP220567//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; },
mesh = {Animals ; *Regeneration/physiology ; Mice ; *Intestine, Small/radiation effects/physiology/microbiology/metabolism ; *Chromatin/metabolism ; *Fasting/physiology/metabolism ; *Microbiota ; Epigenesis, Genetic ; Mice, Inbred C57BL ; },
abstract = {Fasting enhances small intestinal regeneration after radiation, but the contribution of the gut microbiome to this process remains uncharacterized. We identify Akkermansia muciniphila (AKK) as a key mediator of this response. AKK was enriched in fasted mice and its antibiotic depletion abrogated radioprotection, whereas reintroduction restored both organismal survival and intestinal integrity. Fasting elevated propionic acid, consistent with AKK's metabolic output. AKK-conditioned medium and propionate induced histone H3 acetylation in intestinal stem cell cultures while in vivo fasting induced AKK-dependent H3K27ac and H3K9ac, remodeling promoter-enhancer landscapes in crypt epithelial cells. Epigenetic profiling revealed a rewired core regulatory program enriched for pioneer transcription factors (Foxa, Gata, Klf), architectural organizers (Ctcf, Boris), and lineage-defining and metabolic regulators (Cdx2, Hnf4). This program supports expansion of a population of primed persister cells characterized by open chromatin accessibility at key stem and regenerative-associated loci including Clu, Olfm4, Lgr5, Ascl2, Lrig1, Sox9, Rnf43, and Axin2. These findings define a fasting-induced microbiome-metabolite-chromatin axis that epigenetically primes highly plastic persister cells for rapid regeneration of the intestinal epithelium following radiation-induced injury.},
}

Animals
*Regeneration/physiology
Mice
*Intestine, Small/radiation effects/physiology/microbiology/metabolism
*Chromatin/metabolism
*Fasting/physiology/metabolism
*Microbiota
Epigenesis, Genetic
Mice, Inbred C57BL

@article {pmid42335290,
year = {2026},
author = {Liu, M and Cai, Y and Wang, Y and Miao, X and Liu, X and Wang, M and Mao, C and Zhao, Y and Niu, L},
title = {Macrophages Intracellularly Gelated With Bioactive Hydrogels for Synergistic Neutralization, Eradication, and Osteopromotion in Periodontitis Treatment.},
journal = {Advanced materials (Deerfield Beach, Fla.)},
volume = {},
number = {},
pages = {e19288},
doi = {10.1002/adma.202519288},
pmid = {42335290},
issn = {1521-4095},
support = {U25A2097//National Natural Science Foundation of China/ ; 82325012//National Natural Science Foundation of China/ ; 2022YFC2405900//National Key Research and Development Program of China/ ; 2022YFC2405901//National Key Research and Development Program of China/ ; 2024M754272//China Postdoctoral Science Foundation/ ; 2024JC-YBQN-0804//Natural Science Basic Research Program of Shaanxi Province/ ; //Hong Kong Jockey Club Charities Trust/ ; },
abstract = {Conventional periodontitis therapy is limited by the lack of an all-in-one material with the desired functions of toxin neutralization, pathogen eradication, and osteopromotion. Exploiting the innate capacity of macrophages to recognize and neutralize pathological stimuli, this study develops novel engineered macrophage-based materials: phytate/Zn[2] [+]-loaded gelated macrophages (PZ-GMs). These materials are fabricated at room temperature by polymerizing polycationic hydrogels and loading phytate/Zn[2] [+] into live macrophages, innovatively integrating the natural immune neutralization function of intact macrophage membranes with the bioactivity of intracellular hydrogels. PZ-GMs are found to eradicate >99.99% of pathogens, remove >90% of bacterial toxins, and eliminate >80% of related inflammatory factors, while simultaneously promoting bone repair through in situ mineralization and osteoinduction. They can be further incorporated into a hydrogel designed for acid-triggered release, ensuring targeted delivery to inflamed sites. In a murine periodontitis model, PZ-GMs facilitate periodontal regeneration via a dual mechanism: transforming the pathological microenvironment induced by bacteria and toxins and fostering the remodeling of an osteogenic microenvironment. Furthermore, oral microbiome homeostasis is restored. Collectively, PZ-GMs represent a promising all-in-one neutralization-eradication-osteopromotion material for highly efficient periodontitis therapy.},
}

@article {pmid42335312,
year = {2026},
author = {Yang, TH and Chang, FM and Chen, PC and Pudasaini, R and Lu, HP and Nai, YS},
title = {Immune Response and Gut Microbiota Shift in the Red Palm Weevil (Rhynchophorus ferrugineus) Infected With Entomopathogenic Fungus, Beauveria bassiana, Reveal Host-Pathogen Interactions.},
journal = {Archives of insect biochemistry and physiology},
volume = {122},
number = {2},
pages = {e70183},
pmid = {42335312},
issn = {1520-6327},
support = {NSTC 113-2313-B-005 -024-MY3//National Science and Technology Council/ ; },
mesh = {Animals ; *Beauveria/physiology ; *Weevils/microbiology/immunology ; *Host-Pathogen Interactions ; Larva/microbiology/immunology ; *Gastrointestinal Microbiome ; },
abstract = {The red palm weevil (RPW), Rhynchophorus ferrugineus (Oliver), is a major pest of palm plants. Entomopathogenic fungi (EPF) are considered promising biocontrol agents against RPW. This study investigated the changes in immune-related gene expression and gut microbiota of RPW larvae infected with Beauveria bassiana (Bb-NCHU-155). In infected larvae, fungal genome copy numbers in the midgut and hindgut were lower than those detected in the fat body, suggesting that infection primarily occurs via the cuticle rather than the digestive tract. Immune-related gene expression in the fat body increased steadily from 3 days post-inoculation (dpi), reflecting a typical host response, whereas digestive tissues exhibited fluctuating patterns. The midgut showed peak induction of C-type lysozyme at 3 dpi and C-type lectin at 6 dpi, while the hindgut displayed the highest expression of serine protease-like protein at 3 dpi. Despite an overall downregulation of immune-related genes, these results indicate tissue-specific immune responses. Although B. bassiana may not infect hosts through the digestive system, gut microbiota composition differed significantly between infected and control groups, with higher relative abundances of Acetobacteraceae, Lactobacillaceae, and Streptococcaceae in the infected larvae. These shifts co-varied with the expression of immune-related genes, such as defensin and C-type lectin, suggesting potential functional links between gut microbiota and host immunity. This study provides fundamental insights into the effects of EPF on gut microbiota and immune gene expression in RPW, supporting further research into the complex interactions underlying microbial control.},
}

Animals
*Beauveria/physiology
*Weevils/microbiology/immunology
*Host-Pathogen Interactions
Larva/microbiology/immunology
*Gastrointestinal Microbiome

@article {pmid42335476,
year = {2026},
author = {Valentino, V and De Filippis, F and Ercolini, D},
title = {Fermented foods: lessons learned from metagenomics.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103545},
doi = {10.1016/j.copbio.2026.103545},
pmid = {42335476},
issn = {1879-0429},
abstract = {Thanks to the standard microbiology protocols of isolation and culturing, hundreds of strains have been isolated from fermented foods throughout the last decades, and phenotypic traits linked with pro-technological properties and health claims have been investigated. However, culture-independent metagenomic analyses have revealed an unexpected microbial diversity in foods fermented spontaneously or by undefined starter cultures. Here, we report the most groundbreaking advancements in the understanding of fermented foods ecology by presenting case studies where metagenomics has been applied, contributing to identifying novel species in silico or to deciphering the microbiome structure associated with spontaneous fermentations. We also highlight the potential of metagenomics in supporting the identification of potential probiotics and discuss the future ahead, particularly focusing on the integration of multi-omics approaches.},
}

@article {pmid42335814,
year = {2026},
author = {Dong, Y and Meng, B and Huang, JH and Mao, K and Liu, Y and Geng, H and Tan, A and Yang, G and Feng, X},
title = {Microbial community restructuring and transcriptional responses to acute stress in duckweed enhance lead phytoremediation.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142796},
doi = {10.1016/j.jhazmat.2026.142796},
pmid = {42335814},
issn = {1873-3336},
abstract = {Lead (Pb) contamination in aquatic ecosystems poses a persistent threat to environmental quality and human health. Duckweed-mediated phytoremediation serves as a valuable model for exploring the short-term physiological endurance of aquatic macrophytes under extreme Pb stress in highly contaminated aqueous environments. However, the integrated mechanisms underlying Pb hyperaccumulation in this system remain insufficiently understood. In this study, we employed a combined physiological, microbiomic, and transcriptomic approach to investigate the acute stress responses of the hyperaccumulating duckweed Landoltia punctata. Non-invasive micro-test technology (NMT) demonstrated that this hyperaccumulation was driven by enhanced, root-specific Pb[2+] uptake, with the Pb-hyperaccumulating genotype exhibiting a 36.08% higher net influx than the non-hyperaccumulating genotype. Meanwhile, Pb exposure induced pronounced kingdom-specific restructuring in the root-associated microbiome, characterized by bacterial specialization for potential detoxification and fungal transitions toward opportunistic saprotrophy. Transcriptomic profiling further revealed a transcriptional shift favoring defense pathways in the host, marked by the upregulation of core stress signaling and the repression of energy-intensive lipid metabolism to sustain essential structural barriers. Collectively, our findings indicate that this short-term physiological endurance involves a complex host-microbiome response, with causal relationships requiring further functional validation. These results provide mechanistic insights and a theoretical framework for future optimization of phytoremediation systems.},
}

@article {pmid42335822,
year = {2026},
author = {He, T and Liu, J and Li, Y and Ohgami, N and Wei, X and Peng, T and Zhang, X and Zhang, R and Du, J and Deng, Y and Jiang, H and Zhang, P and Zhang, Y},
title = {Long-term groundwater arsenic exposure is associated with altered arsenic methylation capacity and gut microbiota composition in a rural Chinese population.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142658},
doi = {10.1016/j.jhazmat.2026.142658},
pmid = {42335822},
issn = {1873-3336},
abstract = {This study investigated the relationship between long-term groundwater arsenic exposure, arsenic methylation capacity, and gut microbiota in adults from rural northern China. Arsenic detoxification relies in part on methylation processes, and growing evidence suggests that the gut microbiome may participate in arsenic biotransformation, yet population-based data integrating exposure, metabolism, and microbial profiles remain scarce. We recruited 258 participants from two neighboring villages supplied by centralized wells with contrasting arsenic levels (control, n = 138; exposure, n = 120). Total urinary arsenic was measured in all participants, and arsenic species were quantified in a subgroup (n = 60) to derive primary and secondary methylation indices (PMI and SMI). Fecal metagenomes were sequenced to characterize taxonomic composition and functional potential based on KEGG and GO annotations. Individuals in the exposure village showed higher levels of urinary inorganic arsenic and methylated metabolites. While PMI was comparable between groups, SMI was significantly reduced among exposed individuals, indicating impaired secondary methylation. Arsenic exposure was also associated with pronounced alterations in gut microbial diversity and community structure. Several anaerobic taxa, largely linked to fermentative metabolism, were positively associated with SMI after multivariable adjustment. Functional analyses further revealed differences in pathways related to transport, environmental sensing, and metabolism. These findings suggest that chronic arsenic exposure is associated with reduced methylation efficiency and shifts in gut microbial composition and function, and that the gut microbiome may contribute to interindividual variability in arsenic metabolism and toxicity.},
}

@article {pmid42335892,
year = {2026},
author = {Tin, CM and Vargas, BC and Abbott, DA and Lohar, AR and Taylor, TC and Valishev, IA and Weinshel, SN and Lian, V and Sullinger, KJ and Butoryak, M and Silverman, MA and Shenhav, L and DePas, WH and Hand, TW},
title = {Single-cell detection and quantification of the microbiota by MicFLY.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.029},
pmid = {42335892},
issn = {1934-6069},
abstract = {The intestinal microbiota regulates multiple host functions, including digestion and immune development. Our knowledge of the microbiota has been shaped by available technology, which primarily measures relative abundance. Quantitative, single-cell bacterial measurements would improve our understanding of microbiome biology, including the dynamics behind shifts in microbiota composition. We present microbiota flow cytometry (MicFLY), a single-cell technology that quantifies absolute bacterial abundance with species-level resolution. Using MicFLY, we can identify the major intestinal taxa, discriminate live from dead bacteria, measure heterogeneous mRNA expression, and concurrently quantify immunoglobulin A (IgA) and IgG binding to intestinal bacteria. Using longitudinal, quantitative microbiota analyses on a small cohort of preterm infants, we find that increases in IgA- and IgG-unbound bacteria from various Enterobacteriaceae species associate with the development of necrotizing enterocolitis (NEC). MicFLY single-cell technology thus enables fine-scale quantitative microbiota measurements for a deeper mechanistic understanding of compositional changes.},
}

@article {pmid42336221,
year = {2026},
author = {Rooney, AM and Li, YY and Barrios, AA and Scherrer, J and Haldimann, K and Diversi, A and Torres, DA and Göller, P and Egli, A},
title = {Self-collected oral swab comparison for supragingival microbiome characterization.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107602},
doi = {10.1016/j.mimet.2026.107602},
pmid = {42336221},
issn = {1872-8359},
abstract = {The oral microbiota is a microbially dense and complex environment with links to local and systemic health outcomes such as periodontitis and cardiovascular disease respectively. Multiple factors may influence microbiome composition, where pre-analytical influence, such as the sample collection method should be minimized. Our aim was to compare three different commercial oral swabs to assess ease-of-use, bacterial DNA yield, and microbiome composition. The Isohelix buccal swab with Dri-Capsules (I), the Omnigene oral swab (O), and the Zymo Research DNA/RNA Shield SafeCollect swab (Z) were evaluated in parallel. Fifteen anonymized volunteers collected supragingival samples. Questionnaires regarding ease-of-use and comfort were completed. Swab samples (n = 45) and negative controls (n = 8) were subject to DNA extraction with the Maxwell RSC Buccal Swab DNA kit and 16S rRNA gene qPCR was performed to measure bacterial DNA yield (limit of detection: 10[-6] ng/μL). DNA was subject to 16S rRNA gene amplicon and ITS sequencing using the QIAseq 16S/ITS Screening Panel on the Illumina MiSeq. The 16S V3-V4 regions were analyzed for genus-level alpha- and beta-diversity and were performed using QIIME2 v.2024.10. Participants preferred O and Z swabs for ease-of-use and comfort, while the I swab had generally negative assessments. The O swab resulted in the highest median bacterial DNA concentration (1.0 ng/μL) followed by the the Z (0.1 ng/μL) and I (0.02 ng/μL) swabs. There was some taxonomic abundance variation between the I and Z swab but these observations were not supported by genus-level differential abundance analysis. There were also no differences in diversity measures at the genus level between swabs. Considering pre-analytical quality is key for oral microbiome studies.},
}

@article {pmid42336239,
year = {2026},
author = {Sanghvi, G and Bishoyi, AK and Joshi, K and Kaneriya, J and Pattani, V},
title = {Precision Nutrition and Chronic Disease: Integrating Genomics, Microbiome, and Digital Health for Personalized Dietary Interventions.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {103422},
doi = {10.1016/j.clnesp.2026.103422},
pmid = {42336239},
issn = {2405-4577},
abstract = {Chronic non-communicable diseases (NCDs), including cardiovascular disease, type 2 diabetes, obesity, and metabolic syndrome, account for more than 70% of global mortality and impose a disproportionate burden on low- and middle-income countries. Traditional, population-level dietary guidelines often fail to address population-level dietary guidelines often fail to account for the considerable inter-individual variability in metabolic responses to food. Personalized nutrition (PN), informed by genomics, metabolomics, gut microbiome composition, and behavioral factors, has emerged as an effective strategy for optimizing dietary interventions for chronic disease prevention and management. This review synthesizes the current evidence on the conceptual foundations, clinical applications, and technological advancements of PN. Important findings from landmark studies have shown that integrating multi-omics profiling, continuous glucose monitoring, and machine-learning algorithms improves the prediction of postprandial glycemic and lipidemic responses, enhances weight-loss outcomes, and supports targeted interventions for type 2 diabetes, obesity, cardiovascular disease, and metabolic syndrome. Phenotype-based approaches, including metabotyping and tissue-specific insulin resistance profiling, further refine dietary recommendations, resulting in superior improvements compared with generic guidelines. Personalized nutrition is an emerging approach with growing evidence suggesting its potential benefits, although its routine clinical application remains limited. Personalized nutrition is a transformative and clinically relevant method with the potential to improve metabolic health and reduce the global burden of chronic diseases.},
}

@article {pmid42336276,
year = {2026},
author = {Chen, H and Tang, Y and Lin, D},
title = {Red Meat, Plant Protein, and Colitis: Emerging Roles for the Gut Microbiome and Bile Acids.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101836},
doi = {10.1016/j.jcmgh.2026.101836},
pmid = {42336276},
issn = {2352-345X},
}

@article {pmid42336336,
year = {2026},
author = {Jiang, J and Wen, L and Liu, H and Liao, X and Liu, Y and Ji, Y and Lu, P and Chen, S and Zhang, L and Yang, W},
title = {The immunomodulatory role of vitamins in tumor: mechanisms and therapeutic implications.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108309},
doi = {10.1016/j.phrs.2026.108309},
pmid = {42336336},
issn = {1096-1186},
abstract = {The tumor microenvironment (TME)-marked by hypoxia, acidosis, and nutrient scarcity-creates a metabolically restrictive niche that undermines sustained antitumor immunity. Within this niche, infiltrating immune cells could become functionally exhausted to limit the efficacy of existing immunotherapies. Recently, metabolic competition between tumor cells and immune cells for nutrients has attracted great attention in immunometabolism to explain the immune dysfunction. Notably, micronutrients, particularly vitamins, have been increasingly revealed to serve as active immunoregulatory agents rather than working solely as metabolic precursors or intermediates. In this review, we highlight the role of vitamins as immune-metabolic modulators that coordinate metabolic reprogramming, epigenetic remodeling, and signal transduction in tumor-infiltrating immune cells. We further discuss how vitamin activity is shaped by tumor-specific metabolic states, molecular forms, microbiome-dependent regulation and microenvironmental conditions, resulting in context-dependent immunological outcomes. By integrating preclinical mechanistic insights with the current landscape of clinical trials, the translational challenges arising from the pleiotropic effects of vitamins have also been evaluated. Finally, we also summarize emerging biomarker-guided and tumor-targeted intervention strategies that may help improve the therapeutic utility of vitamins and overcome immunotherapy resistance.},
}

@article {pmid42336338,
year = {2026},
author = {Su, Z and Huang, Z and Huang, Y and Guo, J and Wang, Q and Xu, S and Kang, Y and Wang, Z and Shi, Y and Jia, B},
title = {Context-Dependent Short-Chain Fatty Acids in Inflammatory Skin Diseases: Immunometabolic Mechanisms, Evidence Boundaries, and Translational Perspectives.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {108318},
doi = {10.1016/j.phrs.2026.108318},
pmid = {42336338},
issn = {1096-1186},
abstract = {Inflammatory skin diseases(ISDs) arise from dynamic interactions among epithelial barrier dysfunction, immune dysregulation, microbial imbalance and metabolic cues. Within gut-skin and skin-microbiome axes, short-chain fatty acids (SCFAs) have attracted attention as microbial metabolites with anti-inflammatory and barrier-regulatory potential. However, treating SCFAs as uniformly beneficial obscures major biological and translational uncertainties. This narrative review synthesizes evidence from mechanistic, preclinical and clinical studies to define how acetate, propionate and butyrate regulate cutaneous immunity and barrier function. SCFAs act through free fatty acid receptors(FFARs), hydroxycarboxylic acid receptor 2(HCAR2), histone deacetylase inhibition(HDAC) and metabolic-substrate effects, but their outcomes depend on species, source, dose, tissue bioavailability, pH, receptor expression, target-cell identity and disease stage. Gut-derived SCFAs are more likely to support systemic immunometabolic regulation and barrier maturation, whereas locally produced cutaneous SCFAs can either maintain microbial and lipid homeostasis or amplify Toll-like receptor-driven inflammation in pilosebaceous niches. We discuss these mechanisms across immune cells, keratinocytes, sebocytes, fibroblasts, adipocytes and endothelial cells, and interpret their relevance to atopic dermatitis, psoriasis, acne vulgaris, rosacea, hidradenitis suppurativa, chronic spontaneous urticaria and contact dermatitis. We further evaluate dietary, prebiotic/probiotic, topical, fecal microbiota transplantation, engineered probiotic, prodrug and delivery-based strategies, distinguishing SCFA-specific causality from broader microbiome remodeling. A context-resolved framework is needed to translate SCFA biology into rational immunometabolic interventions for ISDs.},
}

@article {pmid42336778,
year = {2026},
author = {Arriagada, V and Garrido, A and Madariaga, F and Hasbun, R and Sanfuentes, E},
title = {Functional Diversity and Community Composition of Soil Fungi Associated With Canopy Dieback in Araucaria araucana Forests of Contrasting Edaphic Conditions.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70361},
pmid = {42336778},
issn = {1758-2229},
mesh = {*Soil Microbiology ; Forests ; *Fungi/classification/genetics/isolation & purification/physiology ; Chile ; Biodiversity ; *Tracheophyta/microbiology ; *Plant Diseases/microbiology ; *Mycobiome ; Trees/microbiology ; Soil/chemistry ; Microbiota ; },
abstract = {BACKGROUND: Soil fungal communities play vital roles in forest ecosystem functioning, yet their relationship with tree health remains insufficiently characterized in many endangered species.

AIMS: This study, investigated the composition and functional structure of soil fungi associated with symptomatic and asymptomatic individuals of Araucaria araucana in the Nahuelbuta Coastal Range, Chile.

MATERIALS AND METHODS: Using high-throughput ITS1 sequencing and trait-based annotation, we compared fungal assemblages across two forest sectors with contrasting edaphic conditions.

RESULTS: Marked differences in taxonomic and functional composition were observed between sites, with more even and functionally diverse communities in less restrictive soils. Within this site, where both tree health conditions co-occur, no significant differences in alpha or beta diversity were detected; nevertheless, species-level and functional guild analyses revealed shifts in composition. A shared core microbiome included taxa putatively identified as endophytes, including Cladophialophora minutissima, Fraxinicola europaea, Linnemannia hyalina, saprotrophs (Solicoccozyma terricola, Helicodendron conglomeratum, Pseudogymnoascus roseus) and a plant pathogen (Penicillium excelsum). Symptomatic trees harboured unique stress-tolerant taxa, including cold-adapted saprotrophs and ericoid mycorrhizal fungi, while asymptomatic trees supported lignocellulose decomposers, mutualists and early-successional symbionts.

DISCUSSION: The observed fungal shifts suggest that canopy dieback is associated with a functional reorganization of the rhizosphere microbiome rather than a simple loss of diversity.

CONCLUSION: These findings provide new insights into the fungal ecology of A. araucana forest and contribute to understanding how soil microbiomes respond to forest decline under contrasting edaphic conditions.},
}

*Soil Microbiology
Forests
*Fungi/classification/genetics/isolation & purification/physiology
Chile
Biodiversity
*Tracheophyta/microbiology
*Plant Diseases/microbiology
*Mycobiome
Trees/microbiology
Soil/chemistry
Microbiota

@article {pmid42336793,
year = {2026},
author = {Mohamad, ZA and Bakon, SK and Zakaria, NFS and Mas'ud, NFA and Johari, MZ and Maamor, NH and Abdullah, N and Chemi, N and Muhamad, NA},
title = {Microbiota matters: a cross-sectional study protocol for mapping gut microbiome diversity in Malaysian major depressive disorder cases.},
journal = {BMJ open},
volume = {16},
number = {6},
pages = {e096813},
pmid = {42336793},
issn = {2044-6055},
mesh = {Humans ; Malaysia ; Cross-Sectional Studies ; *Major Depressive Disorder/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Research Design ; Adult ; Male ; },
abstract = {INTRODUCTION: Mental health is now recognised as a major global concern affecting people from diverse backgrounds. There is growing evidence that the gut microbiota plays a crucial role by producing metabolites that significantly influence a person's mood and behaviour. Despite its importance, there is a significant gap in the profiling and understanding of the gut microbiota's influence on mental health among Malaysians. Therefore, this study aims to determine gut microbiome profiles among patients with major depressive disorders (MDD) of different treatment groups attending psychiatric clinics in the state hospitals and compare them to healthy individuals in the community of Klang Valley, Malaysia.

METHODS AND ANALYSIS: This cross-sectional study will be carried out in Klang Valley, Malaysia. Eligibility of the patients will be assessed by the psychiatrists prior to recruitment of patients. Patients with MDD will be categorised into monotherapy and polypharmacy while healthy individuals will be used as a comparison group. Demographic data will be recorded. Stool samples will be subjected to DNA extraction and 16S rRNA gene-sequencing analysis to determine the microbial compositions of the gut microbiome.

ETHICS AND DISSEMINATION: This study will be conducted following the procedure set by the National Medical Research Register Malaysia. The Medical Research Ethics Committee (MREC), Ministry of Health Malaysia, has ratified this study and granted ethical approval to conduct this study (NMRR ID-22-00893-JVW). All the participants will be given an information sheet and will sign a consent form to participate. Participants have the right to withdraw from the study at any time without an explanation. All information gathered will be used for research purposes only and treated as confidential. The results will be submitted to peer-reviewed journals for publication as well as presented at national and international conferences. Informing policy makers at all levels is a crucial aspect of the dissemination and will be done from local to international levels.

TRIAL REGISTRATION NUMBER: This study was registered under National Medical Research Register Malaysia (NMRR ID-22-00893-JVW), a mandatory procedure of the Ministry of Health Malaysia before the start of a research.},
}

Humans
Malaysia
Cross-Sectional Studies
*Major Depressive Disorder/microbiology
*Gastrointestinal Microbiome/genetics
Female
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Research Design
Adult
Male

@article {pmid42336834,
year = {2026},
author = {van Tilburg Bernardes, E and Glatthardt, T and Gutierrez, MW and Nguyen, WNT and Mercer, EM and Ramay, HR and Thomson, CA and Halim, TBA and Gopalakrishnan, N and MacConnell, K and Kalbfleisch, K and Patel, KD and Corrales-Aguilar, E and McCoy, KD and Freedman, SB and Arrieta, MC},
title = {Antibiotic-induced Malassezia expansion in the infant gut promotes early-life immune dysregulation and airway inflammation in mice.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42336834},
issn = {2041-1723},
support = {NI19-1112//Sick Kids Foundation/ ; 1047806//W. Garfield Weston Foundation/ ; },
mesh = {Animals ; *Malassezia/drug effects/immunology/isolation & purification ; *Anti-Bacterial Agents/adverse effects ; Mice ; Humans ; *Asthma/immunology/microbiology ; *Gastrointestinal Microbiome/drug effects/immunology ; Infant ; Female ; Male ; Mycobiome/drug effects ; Respiratory Syncytial Virus Infections/immunology/microbiology ; Prospective Studies ; Inflammation/immunology ; Mice, Inbred C57BL ; },
abstract = {Antibiotics have deleterious consequences for the gut microbiome and can increase the risk of childhood asthma. While the effects of antibiotics on the bacterial microbiome and asthma risk are well characterized, their impact on the fungal microbiome (mycobiome) remains vastly unexplored. We investigated the effect of antibiotic use on the gut mycobiome in an observational, prospective clinical study of young infants. Antibiotic treatment resulted in increased fungal abundance and expansion of the yeast Malassezia spp. in the infant mycobiome. Based on these findings, we colonized germ-free mouse pups with a defined consortium of mouse-derived bacteria (Oligo-MM12) with or without Malassezia restricta. Colonization with this yeast increased myeloid and lymphoid intestinal immune responses deemed critical in atopy development, and elevated airway inflammation in house-dust mite (HDM)-challenged mice and respiratory syncytial virus (RSV)-infected mice. Further evaluation in eosinophil-deficient mice revealed that the observed immune response is partially dependent on this cell type. This translational work demonstrates that expansion of Malassezia spp. is a previously overlooked collateral effect of infant antibiotic use, which may offer a potential strategy to prevent or mitigate pediatric asthma and related conditions.},
}

Animals
*Malassezia/drug effects/immunology/isolation & purification
*Anti-Bacterial Agents/adverse effects
Mice
Humans
*Asthma/immunology/microbiology
*Gastrointestinal Microbiome/drug effects/immunology
Infant
Female
Male
Mycobiome/drug effects
Respiratory Syncytial Virus Infections/immunology/microbiology
Prospective Studies
Inflammation/immunology
Mice, Inbred C57BL

@article {pmid42337002,
year = {2026},
author = {Guéguen, LM and Mathieu, A and Pelletier, S and Woo, A and Misra, N and Moreau, M and Perin, O and Droit, A},
title = {META-DIFF: a k-mer-based pipeline that detects differentially abundant sequences in metagenomics whole genome sequencing.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-59138-x},
pmid = {42337002},
issn = {2045-2322},
abstract = {Traditional case-control metagenomic studies are constrained by their dependence on taxonomic and functional databases. Because annotation occurs before differential analysis, they are limited to known elements and keep function and taxonomy separate. Although binning strategies have emerged to reconstruct genomes and mitigate this issue, they still require an assembly step, preventing the use of all available sequencing data. Here, we introduce META-DIFF, a pipeline based on differentially abundant k-mers independently of any prior annotation. From those k-mers, it reconstructs longer sequences and provides biological context, as well as the best set of unitigs to discriminate between conditions. Across both taxonomy-centric and functionally-centric benchmarks, it showed robust performance and displayed great reproducibility. It also behaved more conservatively than did other univariate methodologies, i.e. it maintained a high precision at the expense of recall, particularly in conditions of low fold-change and limited sequencing depth. The efficacy of META-DIFF was further validated through its application to a real-world colorectal cancer dataset, which produced both confirmatory and novel results compared with those of previous publications. The pipeline is able to exploit all reads and identify differentially abundant elements, including unknown DNA, prior to annotation. With the guidelines provided, META-DIFF provides users with great exploratory power to unravel microbiome changes.},
}

@article {pmid42337031,
year = {2026},
author = {David, P and Oliphant, K and Zhou, C and Wang, A and Andrews, B and Byrne-Bowens, P and Zhu, A and Lewis, D and Cruz Ayala, W and Mohammad, S and Yu, Y and Sulakhe, D and D'Souza, M and Claud, EC},
title = {Associations between fentanyl exposure, gut microbiome and neurodevelopmental outcomes in preterm infants.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {42337031},
issn = {1530-0447},
abstract = {BACKGROUND: Fentanyl, an opioid medication commonly given to hospitalized preterm infants, may alter gut microbiome development and subsequent neurodevelopmental outcomes.

METHODS: We compare a cohort of preterm infants with and without postnatal fentanyl exposure, using their hospitalization stool samples and neurodevelopmental outcomes. The study examines the association between fentanyl exposure, fecal microbiome differences during NICU stay, and neurodevelopmental outcomes up to age 8.

RESULTS: Fentanyl exposure during NICU hospitalization is associated with a decrease in fecal microbiome richness, negative association with the microbial taxa Actinobacteriota and Bacteroidia, increase in constipation, an increase of microbiome derived metabolites involved in inflammation and gastrointestinal (GI) homeostasis, and altered microbial virulence (i.e. factors that contribute to pathogenicity). Increased fentanyl exposure is associated with worse cognitive scores on the Bayley Scales of Infant and Toddler Development at 2 years of age and the intelligence quotient composite score on the Wechsler Preschool and Primary Scale of Intelligence at 3-8 years of age. Virulence factors present in the microbiome mediated the association between fentanyl and cognitive outcomes at 2 years old.

CONCLUSION: Increased duration of postnatal fentanyl exposure in preterm infants is associated with gut microbiome differences (i.e. richness and virulence) and later cognitive impairment.

IMPACT: Postnatal fentanyl exposure of premature infants in the neonatal intensive care unit is associated with microbiome differences that manifest during their hospital stay. Fentanyl-associated microbiome differences during hospitalization include differences in fecal richness, microbial taxa composition, gastrointestinal transit time, microbiome-derived metabolites, and microbial virulence. Early gut fentanyl-associated microbiota differences are associated with worse cognitive outcomes in preterm infants at 2-8 years old.},
}

@article {pmid42337138,
year = {2026},
author = {AbuSalim, JE and Olszewski, K and Youssef, S and Mitchell, SJ and Hunter, CJ and Little, J and Sidebottom, A and Boyer, JA and Knutson, SD and Samarah, LZ and MacArthur, MR and Henneberg, AL and Ryseck, RP and Opitz, CA and MacMillan, DWC and Donia, MS and Pamer, EG and Imam, S and Lehmann, CJ and Odenike, O and Rabinowitz, JD},
title = {Host metabolism can produce many indoles and phenols independently of the microbiome.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {42337138},
issn = {2522-5812},
support = {DP1DK113643//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; F30DK139739//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI172144//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; },
abstract = {Indole and phenol metabolites are typically thought to be products of bacterial digestion of tryptophan (indoles) and phenylalanine or tyrosine (phenols). Interest in controlling gut microbial production of these metabolites has continually grown because they have important physiological impacts, with indoles agonizing aryl hydrocarbon receptor signalling and phenols being associated with healthy body weight. Although there is a growing body of research on which bacteria produce these metabolites, the host contribution to their circulating pools has not been characterized. Here, through stable isotope tracing in cell culture, mice and rats, we show that mammalian cells can make aryl-pyruvates, aryl-lactates, aryl-acetates and aryl-carboxylic acids independently of the microbiome. We demonstrate that circulating levels of these metabolites in mice and human patients are robust to perturbations of the microbiome. By contrast, bacterial metabolism is required to synthesize aryl-propionates and free indole, phenol and p-cresol. Overall, these results suggest that host metabolism is a major contributor to circulating indole and phenol metabolite pools.},
}

@article {pmid42337290,
year = {2026},
author = {Roubalová, R and Luthar, J and Procházková, P and Zadáková, K and Coufalová, K and Kreisinger, J and Semerád, J and Nehasilová, A and Mácha, H and Luptáková, D and Tlaskalová-Hogenová, H and Holanová, P and Lambertová, A and Papežová, H},
title = {Gut microbiota contributions to anorexia nervosa pathogenesis: insights from the activity-based anorexia model.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01055-y},
pmid = {42337290},
issn = {2055-5008},
support = {NU23-04-00381//Ministerstvo Zdravotnictví Ceské Republiky/ ; NU22-04-00010//Ministerstvo Zdravotnictví Ceské Republiky/ ; Talking microbes - understanding microbial interactions within One Health framework (CZ.02.01.01/00/22_008/0004597)//Ministry of Education, Youth, and Sports of the Czech Republic/ ; Cooperatio Program 207038//Univerzita Karlova v Praze/ ; },
abstract = {Anorexia nervosa (AN) is a severe eating disorder that profoundly affects quality of life. Despite increasing understanding of the neurobiological basis of the disease, many patients develop a chronic course of illness accompanied by a variety of physical and psychiatric comorbidities. To investigate the contribution of the gut microbiome to disease progression, we employed the activity-based anorexia (ABA) mouse model of AN. We performed fecal microbiota transplantation using samples from three donor groups: healthy controls, patients with acute AN, and patients with severe and enduring AN (SEAN). We continuously assessed changes in the gut microbiota and fecal metabolites (e.g., short-chain fatty acids, serotonin, and GABA) throughout the experiment, along with behavioral traits across the three groups of mice. Mice colonized with microbiota from acute AN patients exhibited reduced hunger signaling (via NPY, AgRP, MCH, and orexin), accompanied by decreased food intake. In contrast, mice transplanted with microbiota from SEAN patients showed appetite signaling and food consumption comparable to those colonized with microbiota from healthy controls but displayed significantly higher running activity relative to the other groups. However, the distinct microbiota did not affect the development of the ABA phenotype. Overall, our findings suggest that changes in the gut microbiome during disease development contribute to disease progression. Our results also indicate that restoration of a healthy gut microbiome is essential for complete recovery.},
}

@article {pmid42337354,
year = {2026},
author = {Kim, D and Joe, HI and Bae, JW and Wu, GD and Compher, CW and Koo, H},
title = {Fermented food microbiome: influence on oral and gut microbiota, and human health.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42337354},
issn = {1740-1534},
abstract = {The fermented food microbiome comprises live microorganisms, their genetic elements and their metabolites, and represents an established dietary approach for modulating host-microbiome interactions through the consumption of fermented foods. Fermentation enhances food preservation and nutrient bioavailability, and supplies the host with probiotics, prebiotic substrates and postbiotic metabolites. These bioactive compounds can influence the oral and gut microbiota, modulate immune function and support metabolic resilience. Fibre-rich, plant-based fermented foods retain such components within structured matrices that enhance microbial viability and mucosal interactions more consistently than do fermented dairy foods. This Review explores how the fermented food microbiome affects the oral-gut axis via both transient microbial exposure and metabolite-mediated signalling. Drawing on clinical and preclinical evidence, we examine how fermented food intake alters resident microbiota and host physiology throughout the digestive tract. Despite growing evidence, the mechanisms through which fermented food might promote health remain insufficiently defined in humans owing to strain variability, inconsistency in microbial composition across fermented foods, heterogeneous clinical outcomes and regulatory ambiguity. Taking into account these limitations, we propose a roadmap to integrate the fermented food microbiome into precision nutrition as a feasible, personalized, diet-based strategy to promote health and prevent disease.},
}

@article {pmid42337676,
year = {2026},
author = {Gorji, AE and Xue, B and Yan, T and Sadkowski, T and Chen, X and Cristobal-Carballo, O and Morrison, S and Razban, V and Smith, L and Stergiadis, S and Theodoridou, K and Shirali, M},
title = {Apple pomace and hempseed cake can reduce methane intensity (CH4/DMI) and alter the rumen microbiome in dairy cows: a shotgun metagenomic approach.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42337676},
issn = {1674-9782},
support = {Project No. 21/5/01//Department of Agriculture, Environment and Rural Affairs (DAERA)/ ; },
abstract = {BACKGROUND: With growing attention to environmental impacts, the dairy sector is increasingly focused on implementing strategies that lower methane emissions and enhance sustainability while maintaining productivity and economic viability. Utilizing agro-industrial by-products as alternative feed ingredients supports circular economy goals, lowers feed costs, and may benefit rumen fermentation and environmental performance in dairy cows.

METHODS: Forty-five mid-lactation Holstein cows were assigned to three diets, Control, Apple Pomace (AP), or Hempseed Cake (HC) for 24 d. Feed intake, milk yield, rumen fermentation, methane emissions, and nutrient use were measured. Rumen samples underwent shotgun metagenome sequencing and bioinformatics analysis to assess microbial and functional changes.

RESULTS: Values are reported as mean ± SEM. Shotgun metagenomic sequencing revealed that both supplements significantly increased the relative abundance of Bacteroidota (AP: 56.7% ± 2.8%, P = 0.032; HC: 54.5% ± 3.4%, P = 0.048) compared to the Control (48.2% ± 3.1%). Concurrently, Bacillota (formerly Firmicutes) abundance decreased, significantly reducing the Bacillota/Bacteroidota ratio (formerly the Firmicutes/Bacteroidetes ratio) from 0.81 ± 0.06 (Control) to 0.58 ± 0.05 for AP (P = 0.012) and 0.64 ± 0.05 for HC (P = 0.034). Functional analysis showed that AP increased the abundance of Segatella bryantii (2.1-fold, P < 0.01), associated with a 1.52-fold enrichment in propionate metabolism pathways (P = 0.019). Phenotypically, AP significantly reduced the acetate-to-propionate ratio (AP: 2.41 vs. Control: 4.50; P = 0.0075) and methane emissions per unit of dry matter intake (CH4/DMI) (AP: 20.33 vs. Control: 24.27 g/kg; P = 0.016). HC supplementation upregulated fiber-degrading taxa such as Xylanibacter ruminicola (1.6-fold) and enriched xylanase families (GH10: 1.58-fold, P = 0.035), alongside a significant reduction in methane intensity (CH4/DMI). Total methane output, feed intake, and milk yield were not significantly changed by treatments (P > 0.05).

CONCLUSIONS: In this short-term (24-d) controlled feeding study in mid-lactation Holstein cows, AP and HC were associated with distinct microbial and functional shifts alongside lower methane intensity, with AP linked to propanoate-related signals and HC to fiber-degrading functions; however, ruminal H2 concentration and methanogenesis/hydrogen-metabolism markers were not quantified, so the proposed mechanisms should be interpreted as plausible inferences rather than direct physiological evidence.},
}

@article {pmid42337725,
year = {2026},
author = {Jakimowicz, M and Sidorczuk, K and Huyben, D and Hildebrand, F and Napora-Rutkowski, Ł and Hajduk, P and Sztuka, M and Mielczarek, M and Słomian, D and Jarosz, L and Szyda, J},
title = {Supplementation with effective microorganisms in earthen ponds affects common carp growth and abundance of specific bacterial families.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13093-z},
pmid = {42337725},
issn = {1471-2164},
support = {2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; 2021/41/B/NZ9/01409//Narodowe Centrum Nauki/ ; erc-stg-948219/ERC_/European Research Council/International ; erc-stg-948219/ERC_/European Research Council/International ; BB/X011054/1//Quadram Institute Bioscience/ ; BB/X011054/1//Quadram Institute Bioscience/ ; },
abstract = {BACKGROUND: Effective microorganisms are increasingly explored in aquaculture to improve fish health and growth without leaving harmful residues. However, their efficacy in real-world pond environments remains poorly understood. Here, we conducted a 103-day field experiment to assess the effects of supplementation with two effective commercial microorganism products on the microbial communities and growth performance of common carp (Cyprinus carpio).

BACKGROUND: Effective microorganisms were added to the feed and directly to the pond water. Microbial diversity was analysed via 16 S rRNA and whole-genome shotgun sequencing across three environments: water (three time points), sediment (two time points), and fish intestine (one time point) from 25 experimental ponds. Bioinformatics processing was performed using the QIIME2 and MG-TK pipelines with taxonomic classification based on the SILVA database. The results showed that although supplemented bacterial families did not establish significantly in pond environments, fish exposed to specific effective microorganism treatments showed improved growth metrics.

CONCLUSIONS: These findings suggest that effective microorganisms can increase carp growth in aquaculture without significantly altering the resident microbial communities, suggesting a promising residue-free alternative to traditional additives in aquaculture.},
}

@article {pmid42337925,
year = {2026},
author = {Zhu, L and Xu, J and Niu, D and Zhang, X and Jin, C},
title = {Harnessing Gut Microbiota to Enhance Immunotherapy in NSCLC: From Mechanisms to Translational Applications.},
journal = {Cancer medicine},
volume = {15},
number = {6},
pages = {e72061},
pmid = {42337925},
issn = {2045-7634},
support = {ZD202324//Traditional Chinese Medicine Technology Development Plan of Jiangsu Provincial Administration of Traditional Chinese Medicine/ ; ZYYB23//Science and Technology Plan Project of Traditional Chinese Medicine Hospitals from Wuxi Municipal Administration of Traditional Chinese Medicine/ ; XZR2023024//Natural Science Foundation of Nanjing University of Chinese Medicine/ ; },
mesh = {Humans ; *Lung Neoplasms/therapy/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; *Immunotherapy/methods ; *Carcinoma, Non-Small-Cell Lung/therapy/immunology/microbiology ; Tumor Microenvironment/immunology ; Animals ; Translational Research, Biomedical ; Precision Medicine ; },
abstract = {The gut microbiome has emerged as a pivotal regulator of immunotherapy efficacy in non-small cell lung cancer (NSCLC), with mounting evidence demonstrating that microbial-immune crosstalk significantly influences therapeutic responses. Current research reveals that commensal bacteria modulate host immunity through complex metabolic and immunological pathways, yet the precise mechanisms underlying these interactions remain incompletely characterized. Meanwhile, the substantial heterogeneity of microbial ecosystems across individuals and the lack of standardized protocols for microbiota-based therapeutic interventions pose significant barriers to clinical translation. Furthermore, unresolved questions persist regarding the safety profiles and reproducibility of clinical outcomes associated with microbial modulation. Addressing these knowledge gaps could provide transformative insights into immunotherapy resistance while enabling the development of precision medicine approaches. This narrative review synthesizes current knowledge on the clinical impact of gut microbiota on the immunotherapy response in NSCLC, mechanistic insights into the interactions between gut microbiota and the lung cancer immune microenvironment, and the challenges in clinical translation. By integrating these perspectives, we develop a practical framework for implementing microbiota-based strategies to enhance immunotherapy efficacy, with the hope of addressing current limitations in biomarker development, intervention protocols, and personalized treatment approaches to bridge the gap between research and clinical practice in precision oncology.},
}

Humans
*Lung Neoplasms/therapy/immunology/microbiology
*Gastrointestinal Microbiome/immunology
*Immunotherapy/methods
*Carcinoma, Non-Small-Cell Lung/therapy/immunology/microbiology
Tumor Microenvironment/immunology
Animals
Translational Research, Biomedical
Precision Medicine

@article {pmid42338083,
year = {2026},
author = {Arooj, S and Zubair, A and Batool, SZ and Niaz, G and Ali, M and Waheed, Y and Elsharkawy, ER and Afghan, N},
title = {Lung Microbiome Diversity, Infection Dynamics, and Microbe-Mediated Cross-Protection.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70349},
pmid = {42338083},
issn = {2045-8827},
support = {//The authors extend their appreciation to Northern Border University, Saudi Arabia, for supporting this work through project number (NBU-CRP-2026-249)/ ; },
mesh = {*Microbiota ; Humans ; *Lung/microbiology/immunology ; Animals ; Bacteria/classification/isolation & purification ; *Respiratory Tract Infections/microbiology/immunology ; *Host Microbial Interactions/immunology ; },
abstract = {Modern technological advances have revealed that the lungs, once believed to be sterile, actually harbor a diverse community of microorganisms. A normal lung microbiome possesses its own characteristic microbial community, although it is largely influenced by the microbiota of the upper respiratory tract. The lung microbiome is distinct from that of other organs due to unique selective pressures, including mechanical clearance through coughing, the activity of pulmonary macrophages, the coordinated movement of respiratory cilia, and the antimicrobial effects of alveolar surfactant. Although recent research has largely concentrated on the pulmonary bacteriome, comparatively little attention has been given to the lung mycobiome and virome. Various databases such as PubMed, Scopus/Web of Science, Google Scholar, and Medline for literature research up to December 2025. This updated review discusses the origin, composition, and functional significance of the lung microbiome, with particular emphasis on its protective role against respiratory pathogens through host-microbe interactions. The review primarily focuses on respiratory disorders such as asthma, along with a range of viral and bacterial infections. Special attention is given to current evidence on how lung microbial communities influence susceptibility to pulmonary infections, as well as how the lung microbiome contributes to host defense during infectious conditions.},
}

*Microbiota
Humans
*Lung/microbiology/immunology
Animals
Bacteria/classification/isolation & purification
*Respiratory Tract Infections/microbiology/immunology
*Host Microbial Interactions/immunology

@article {pmid42338163,
year = {2026},
author = {Delaroque, C and O'Mahony, L and Kortekaas Krohn, I and Mortz, CG and Ollert, M and Desai, MS},
title = {Diet-Microbiome-Immune Interactions at the Gut Mucosa in Food Allergy: Mechanisms, Gaps, and Therapeutic Implications.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70426},
pmid = {42338163},
issn = {1398-9995},
abstract = {Mucosal surfaces are sites of highly dynamic interactions among epithelial and immune cells, environmental exposures, particularly dietary inputs, and the diverse microbial communities and their metabolites. These elements continually influence each other to maintain homeostasis and ensure appropriate immune discrimination between pathogens and innocuous stimuli, such as commensal microbes and dietary antigens. When this balance is disrupted, immune tolerance breaks down, leading to maladaptive responses characteristic of food allergy. Targeting mucosal interactions to restore homeostasis, therefore, holds substantial promise for preventing and treating food allergies and other atopic diseases. However, the complexity of the interconnected networks linking host factors, the microbiome, and diet presents major challenges. In this review, we synthesize recent advances in understanding the mechanisms governing mucosal crosstalk in both health and allergic disease. We provide an in-depth examination of the intestinal mucus layer and its components as active mediators of microbiota-host communication and potential initiators of allergic responses. We also discuss emerging mechanistic and therapeutic insights into how diet, food-derived molecules or treatments shape mucosal immunity, and highlight key knowledge gaps that warrant further investigation to clarify how disruptions in these interactions contribute to allergic sensitization.},
}

@article {pmid42338230,
year = {2026},
author = {Vu, NT and Shen, X and Gibson-Kueh, S and Carrai, M and Terence, C and Poon, ZWJ and Nelson, SP and Senapin, S and Dong, HT and Loh, JY and Jerry, DR and Domingos, JA},
title = {Microbiome and Pathobiome Characterization in Farmed Barramundi (Lates calcarifer) During and Post Scale Drop Disease Outbreaks.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70225},
doi = {10.1111/jfd.70225},
pmid = {42338230},
issn = {1365-2761},
support = {//Singapore Food Agency/ ; },
abstract = {Large-scale double-digest RAD sequencing (ddRADseq) datasets generated for genotyping are increasingly available in aquaculture, yet their unmapped reads remain largely unexplored for pathogen surveillance. Here, we evaluated the utility and limitations of repurposing unmapped ddRADseq reads to examine pathogen-associated and disease-associated microbiome-pathobiome patterns during scale drop disease (SDD) outbreaks in farmed barramundi (Lates calcarifer). Using fin clips ddRADseq datasets from 4593 barramundi across four commercial sea-cages, we profiled bacterial and viral communities by taxonomic classification of unmapped reads. Fish sampled during active outbreaks consistently exhibited strong enrichment of scale drop disease virus (SDDV-associated signals; 76.3%-80.5%), frequently co-occurrence with infectious spleen and kidney necrosis virus (ISKNV; 0%-13.4%), along with a marked microbial shift towards Vibrio-dominated bacterial communities, particularly reads classified within the Vibrio harveyi clade. In contrast, clinically healthy post-outbreak fish showed consistently low viral signals and were characterized by distinct, more diverse microbial profiles dominated by Alphanudivirus, Cyvirus, Stenotrophomonas and Burkholderia, indicating a comparatively stable microbiome state in the absence of active disease outbreaks. Treating normalized pathogen read counts as proxy traits, exploratory quantitative genetic analyses indicated low overall heritability estimates for SDDV-associated signal (h[2] = 0.08), with higher cohort-specific estimates (up to 0.23), consistent with strong environmental or co-infection effects and complex co-infection dynamics in open-sea farming systems. While ddRADseq-based pathogen detection is inherently biased by restriction-enzyme site representation, host-DNA dominance and the lack of absolute quantification, consistent patterns observed across thousands of fish tissues across multiple cohorts and outbreak stages provide biological meaningful population-level insights into farm-associated microbiome and pathobiome dynamics. Together, our results support that the use of unmapped ddRADseq reads as a cost-effective, complementary tool for retrospective pathogen screening and hypothesis generation in aquaculture, alongside targeted surveillance and diagnostic approaches.},
}

@article {pmid42338329,
year = {2026},
author = {Araujo, G and Thomas, T and Montoya, JM and Webster, NS and Lurgi, M},
title = {Towards Key Principles of Host-Associated Microbiome Assembly.},
journal = {Ecology letters},
volume = {29},
number = {6},
pages = {e70433},
pmid = {42338329},
issn = {1461-0248},
support = {RPG-2022-114//Leverhulme Trust/ ; },
mesh = {Animals ; *Microbiota ; *Symbiosis ; *Models, Biological ; *Porifera/microbiology ; Humans ; *Host Microbial Interactions ; },
abstract = {Symbiotic relationships between microbes and hosts frequently involve the assembly of complex microbial communities. Community-level patterns influence life-history traits, ecological trajectories of partners, and are often critical for host health. These patterns are driven by mechanisms acting at the individual level, including microbial dispersal, host selection, and microbe-resource interactions. Critically, we still lack a clear picture of how these mechanisms interact to shape microbiome assembly. We present a model that describes how distinct community structures arise from those underlying mechanisms. To illustrate the approach, we simulate microbiome data from marine sponges, thereby bridging mechanistic models and empirical patterns. We further apply the model to human data to explore its relevance across systems, proposing that a small set of general mechanisms may govern diverse patterns of diversity and abundance. Our findings advance ecological theory by linking individual-level processes to community-scale patterns, illuminating key drivers of microbiome assembly.},
}

Animals
*Microbiota
*Symbiosis
*Models, Biological
*Porifera/microbiology
Humans
*Host Microbial Interactions

@article {pmid42338389,
year = {2026},
author = {Coyne, S and Ghergurovich, R and Sacco, F and Lombardi, F and Paar, K and DeMartino, J and Kenfack, AA and Stack, TMM},
title = {Gut Bacterial 20-Hydroxysteroid Dehydrogenases Modify Endogenous Glucocorticoids and Corticosteroid Drugs.},
journal = {Biochemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.biochem.5c00661},
pmid = {42338389},
issn = {1520-4995},
abstract = {Bacterial 20-hydroxysteroid dehydrogenases (20-HSDHs) from the human gut are known to reduce the C-20 carbonyl group of cortisol, producing either 20α- or 20β-dihydrocortisol. Two 20-HSDHs from Bifidobacterium adolescentis L2-32 and Agathobaculum desmolans ATCC 43058, both members of the short-chain dehydrogenases/reductases superfamily, are known to produce 20β-dihydrocortisol, while the 20-HSDH from Clostridium scindens ATCC 35704, belonging to the zinc-containing alcohol dehydrogenase family, produces 20α-dihydrocortisol. These three enzymes were characterized for their activity toward cortisol and structurally related therapeutic corticosteroids. Kinetic analyses revealed narrow substrate specificity, with all enzymes preferring cortisol but maintaining significant activity for prednisone and prednisolone (kcat/KM values between 10[3]-10[6] M[-1] s[-1] for the 20β-HSDH enzymes), and some detectable activity of the 20β-HSDHs to reduce triamcinolone. The 20β-HSDHs exhibited pH-dependent substrate inhibition, influencing their activity profile. Structural docking studies indicated that suitable substrates occupy a single productive binding mode within the 20β-HSDH enzyme active site. Our findings show that enzymes in the gut microbiome can metabolize corticosteroid drugs by reducing the 20-keto group, which could have implications for drug efficacy and side effects. This work highlights the importance of gut microbial enzymes in the biotransformation of both endogenous and therapeutic steroids, informing future research into drug-microbiome interactions and personalized medicine.},
}

@article {pmid42338436,
year = {2026},
author = {Govindarajan, S and Ramamurthy, J},
title = {Evaluation of the relationship between subgingival microbiome in obese and nonobese clinically healthy and periodontitis patients - An experimental study.},
journal = {Journal of Indian Society of Periodontology},
volume = {30},
number = {1},
pages = {135-140},
pmid = {42338436},
issn = {0972-124X},
abstract = {BACKGROUND: This study investigates the association between obesity and the prevalence of periodontopathic bacteria in obese/overweight individuals and healthy/normal-weight individuals, focusing mainly on the red complex organisms in individuals with and without periodontitis.

MATERIALS AND METHODS: A cross-sectional study was conducted with 14 participants (7 obese/overweight and 7 healthy weight individuals), further categorized into periodontitis and healthy periodontium groups. Body mass index and waist-to-hip ratio were measured, total cholesterol level was determined, and probing pocket depth was determined. Subgingival plaque samples were obtained and examined for the presence of Tannerella forsythia, Porphyromonas gingivalis, and Treponema denticola through the quantitative real-time polymerase chain reaction analysis.

RESULTS: Obese patients had a significant association with P. gingivalis. In contrast, T. forsythia and T. denticola numbers were not statistically significant. Five out of seven obese participants had periodontitis, compared to four out of seven participants in the healthy weight group.

CONCLUSION: Within the limitations of this pilot cross-sectional study, obesity was associated with an increased prevalence of P. gingivalis in individuals with periodontitis. These findings suggest that obesity may have a possible association with alterations in the subgingival red complex bacterial profile. However, results should be interpreted cautiously, and larger longitudinal studies are required to confirm these observations.},
}

@article {pmid42338576,
year = {2026},
author = {Mansour, SR and Khalaf, MA and Moustafa, MA and Moustafa, MA and Moustafa, AA},
title = {Exploring the gut-brain axis: dietary influences on Alzheimer's disease pathogenesis.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1639904},
pmid = {42338576},
issn = {2813-4338},
abstract = {Alzheimer's disease (AD) is one of the most diagnosed neurodegenerative disorders worldwide and presents a significant challenge for both affected individuals and their caregivers. Alzheimer's disease is characterized by the accumulation of amyloid plaques and dysfunctional tau protein in the brain, along with the final development of dementia. Recently, in addition to the strongly developing ischemic etiology of AD, it is suggested that the gut and oral microbiota may also participate in the development of this disease. This involvement may stem from an unbalanced diet and the consumption of foods containing harmful chemical additives. An unhealthy diet can compromise the integrity of the gut barrier, facilitating the translocation of bacterial pathogens and leading to a pro-inflammatory T-cell response mediated by innate immune cells. This inflammatory response can disrupt systemic homeostasis and may contribute to neuroinflammation. The brain and gut interact through a complex network known as the "gut-brain-microbiota axis," and emerging studies suggest that the intestinal microbiota and their metabolites may play a significant role in the pathogenesis of Alzheimer's disease. Moreover, these inflammatory mediators and microbial metabolites can reach the brain via the gut-brain axis, potentially exacerbating neurodegenerative processes. Preclinical and limited clinical evidence indicates that low-fiber diets are associated with alterations in intestinal microbiota composition, which may contribute to the onset and progression of Alzheimer's disease. This review aims to explore the potential connections between AD and the gut microbiome, emphasizing the significance of dietary factors in shaping these relationships. A comprehensive understanding of the interactions between the human microbiome and the brain, particularly in the context of diet and its ingredients, may enhance our understanding of AD etiology and inform the development of preventative strategies, through dietary modifications or therapeutic interventions. This area of research holds promise for identifying novel approaches to prevent or slow the progression of AD.},
}

@article {pmid42338577,
year = {2026},
author = {Pal, E and Omidi Arjenaki, N and Lu, Y and Xia, J and Chalifour, L},
title = {Acute myocardial infarction induces sex-specific, time-dependent remodeling of the gut microbiome and intestinal immune compartment in retired breeder C57BL/6N mice.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1818652},
pmid = {42338577},
issn = {2813-4338},
abstract = {INTRODUCTION: The gut microbiome influences cardiovascular health through metabolite production and immune modulation. Gut microbial dynamics and cardiovascular outcomes are also shaped by biological sex. However, sex-specific responses to myocardial infarction (MI) that involve the gut microbiome and intestinal milieu remain poorly defined, particularly in older hosts. Here, we characterize gut microbiome structure and function alongside physiological and immune responses to MI across multiple tissues in aging male and female mice.

METHODS: MI was induced by permanent LAD ligation and confirmed by echocardiography in C57BL/6N retired breeder mice. Sham surgery (SH) and no surgery (NoSx) groups served as controls. Gut microbiota and the cecal metabolome were characterized using 16S rRNA sequencing and untargeted UPLC-MS, respectively. Immune cells in the small intestine, heart, bone marrow, and spleen were quantified by flow cytometry, and small intestinal morphology was assessed on H&E-stained sections.

RESULTS: Sex-specific differences were evident at baseline. Following MI, pronounced time- and sex-specific differences in gut microbial and immune cell populations were observed, peaking on day 3 (D3) and absent in SH and NoSx controls. Early increases in Bacteroidaceae, Tannerellaceae, and Marinifilaceae were present in both sexes, with sex-specific enrichment of Bacteroidaceae in males and Akkermansiaceae in females. Metabolomic analyses identified increased secondary bile acid derivatives, including cholylvaline in males and 12-oxo-lithocholic acid in females. Integration of microbiota-metabolome data revealed MI-responsive and homeostatic taxa with opposing metabolite signatures, while functional analyses indicated enrichment of propanoate and amino acid metabolism pathways. These changes were temporally aligned with acute MI-induced expansion of intestinal MHCII[+]CD11c[+] dendritic cells and TCRαβ[+]CD4[+], TCRαβ[+]CD8αβ[+], and CD25[+]FoxP3[+] regulatory T cells on D3 in both sexes. Males alone exhibited marked increases in intestinal TCRγδ[+] T cells, while females showed increased accumulation of innate immune cells.

DISCUSSION: Convergence of peak physiological, immunological, and microbial responses on day 3 after MI reveals coordinated responses across the gut-heart axis that are fundamentally influenced by sex. Our findings highlight the need for personalized, sex-specific perioperative strategies and identify the gut microbiome as a potential therapeutic target to improve outcomes after MI.},
}

@article {pmid42338620,
year = {2026},
author = {Kris-Etherton, PM and Li, Z and Matthan, NR and Rajaram, S and Sabaté, J and Reboussin, DM and Ford, N and Barnes, S and Petersen, KS},
title = {The Habitual Diet and Avocado Trial (HAT): A Collaborative Multicenter Model for Large-Scale, Privately Funded Nutrition Research Consortia.},
journal = {Current developments in nutrition},
volume = {10},
number = {6},
pages = {107713},
pmid = {42338620},
issn = {2475-2991},
abstract = {The research model used to conduct the Habitual Diet and Avocado Trial (HAT), a large multicenter clinical trial (n = 1008 participants) designed to evaluate the effect of consuming 1 avocado/d for 6 mo on visceral adiposity in individuals with an increased waist circumference, has been a long-term productive collaboration. The primary outcome analysis showed that intake of 1 avocado/d did not affect visceral adiposity compared with habitual dietary intake. Secondary and ancillary analyses showed improvements in diet quality, LDL cholesterol, and red blood cell fatty acid composition, as well as the gut microbiome with avocado intake. These findings are relevant to a large proportion of the United States population because of the study sample characteristics. The aim of this paper is to summarize the research protocol and implementation of the HAT as well as the findings. This approach could be used by consortia supported by nongovernmental entities. Notably, there is still ongoing research being conducted by the investigators using the data collected from the HAT. Moreover, HAT samples and data are available, pending an approved request, to scientists interested in conducting avocado health research. The collaborative commitment of the investigators, their collegial spirit, along with strong leadership and ongoing support from the coordinating center and funding agency representatives, has created a productive research consortium. This consortium has furthered knowledge about the health effects of avocados, and the approach has maximized the return on the research investment from a single large clinical trial.},
}

@article {pmid42338630,
year = {2026},
author = {Phongphattarawat, S and Songvorawit, N},
title = {Bacterial communities associated with the blue dragon nudibranch Glaucilla marginata from Phuket, Thailand.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21462},
pmid = {42338630},
issn = {2167-8359},
mesh = {Animals ; Thailand ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Bacteria/genetics/classification/isolation & purification ; *Gastropoda/microbiology ; Phylogeny ; DNA, Bacterial/genetics ; },
abstract = {Sampling neustonic nudibranchs is challenging because they live in the open-ocean surface layer, which restricts available microbiome reference data. On July 12, 2025, a mass stranding of the blue dragon nudibranch (Glaucilla marginata) at Karon Beach, Phuket, Thailand, provided a rare opportunity for microbiome sampling. We generated a 16S rRNA gene amplicon dataset from whole-body homogenates of stranded individuals. Ten specimens were sequenced as five pooled samples (two individuals per pool) targeting the V3-V4 region on an Illumina MiSeq. After processing, the dataset contained 43 amplicon sequence variants, dominated by a small number of taxa; most samples were enriched in Firmicutes, largely represented by Mycoplasma. This low bacterial richness suggests host-mediated filtering, potentially driven by host-produced antibacterial compounds or competitive exclusion mediated by resident microbes. In addition, six culturable bacterial isolates were obtained and identified by near full-length 16S rRNA gene sequencing. Some isolates were not detected in the amplicon data, underscoring the importance of integrating culture-dependent and -independent approaches to better characterize host-associated assemblages.},
}

Animals
Thailand
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Bacteria/genetics/classification/isolation & purification
*Gastropoda/microbiology
Phylogeny
DNA, Bacterial/genetics

@article {pmid42338684,
year = {2026},
author = {Teng, NMY and Vijayakumar, B and Smith, DJF and Tonkin, J and Orton, CM and Garner, JL and Harker, JA and Lloyd, CM and Molyneaux, PL and Shah, PL},
title = {Investigating the lasting effects of SARS-CoV-2 infection and the lung microbiome: no persistent microbial alterations in recovered COVID-19 patients with persistent radiological or respiratory abnormalities.},
journal = {Access microbiology},
volume = {8},
number = {6},
pages = {},
pmid = {42338684},
issn = {2516-8290},
abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was a global pandemic where infected individuals experienced mild or severe disease. Unfortunately, some patients who experienced severe disease also had lasting abnormalities. The lung microbiome of 38 adult coronavirus disease 2019 (COVID-19) patients with persistent respiratory symptoms and/or radiological abnormalities was analysed. The aim was to investigate whether the lasting radiological abnormalities reported in this cohort were associated with an altered airway. Thirty-six bronchoalveolar lavage fluid samples from patients underwent 16S rRNA gene amplicon sequencing and were compared to 28 non-fibrotic control samples from a previously published study. COVID-19 patients had statistically significantly greater number of genera but at uneven abundances, though not statistically significant compared to non-fibrotic controls. Permutational ANOVA (PERMANOVA) suggested that COVID-19 can influence the lung microbiome composition after accounting for multivariate dispersion. Further analysis showed differences in the relative abundances of Actinomyces, Neisseria, Haemophilus, Rothia and Gemella. Indicator species analysis showed that a COVID-19 lung microbiome profile could be driven in part by differences in Fusobacterium, Actinomyces, Catonella, Oribacterium and Mycobacterium. Associations with clinical parameters were lacking apart from CT lung opacification, which revealed a significant negative association with the number of genera. Differential abundance analysis with MaAsLin2 pointed towards Porphyromonas as a potential explaining genus, though this was not significant after post hoc corrections. DESeq2 revealed enriched oral taxa in the BAL samples, suggesting potential oral-translocation reflective of a disease state. Our findings suggest that individuals with persistent radiological abnormalities following SARS-CoV-2 infection have experienced subtle shifts in their microbiome profile, but these are not strongly associated with clinical phenotypes and, therefore, unlikely of significance.},
}

@article {pmid42338687,
year = {2026},
author = {Ramalingam, C and Ansbro, K and Pratten, J and Bradshaw, D and Stafford, GP},
title = {Effect of sialidase inhibitors on a plaque community biofilm model.},
journal = {Access microbiology},
volume = {8},
number = {6},
pages = {},
pmid = {42338687},
issn = {2516-8290},
abstract = {The oral microbiome is a diverse ecosystem that plays a critical role in health and disease and contains numerous bacterial species capable of metabolizing host-derived glycans, particularly sialic acids. Sialidase enzymes can be produced by both commensal and pathogenic bacteria influencing biofilm formation and host interactions. To investigate how sialidase activity might influence the oral microbiome, we conducted a series of in vitro polymicrobial biofilm experiments and assessed community composition using 16S rRNA sequencing. As a first step, we tested modified Oxford Nanopore Technology (ONT) primers using an in-house sequencing workflow and compared them to the standard Illumina MiSeq primers. Through in silico and in vitro assessments, we identified primer bias in the standard ONT 16S primers and designed human oral microbiome (HOM) modified primers (HOM_27F-YM/1492R-D) to improve taxonomic resolution, achieving results comparable to the gold-standard Illumina 16S primers particularly for key oral genera. These HOM-optimized primers had an overall lower error rate (3.4%) and generated community profiles that closely matched those produced by Illumina. We then used the same ONT workflow and modified 16S primers to evaluate the effects of the sialidase inhibitors oseltamivir and 2,3-dehydro-2-deoxy-N-acetylneuraminic acid on hydroxyapatite-coated minimum biofilm eradication concentration assay plate-derived plaque biofilms from a whole-plaque community model. Inhibitor-treated biofilms exhibited differences in relative abundance depending on the inhibitor combination used, with increased abundance of Streptococcus with oseltamivir alone and Fusobacterium with both inhibitors combined (Kruskal-Wallis cutoff=0.05, LDA>2). These findings demonstrate that ONT-based 16S sequencing with HOM-modified primers suggests that sialidase activity can modulate microbial community structure in plaque biofilms.},
}

@article {pmid42338719,
year = {2026},
author = {Dai, L and Wang, X and Zhang, H and Gong, R and Pang, J and Pan, J and Xu, Q and Duan, Y},
title = {Integrative multi-omics analysis identifies a robust 14-metabolite signature and reveals microbiome-metabolite-host interactions in atherosclerosis.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1849138},
pmid = {42338719},
issn = {2297-055X},
abstract = {BACKGROUND: Atherosclerosis (AS) is a complex metabolic and inflammatory disease in which interactions between host metabolism and gut microbiota play critical roles. However, robust metabolic biomarkers and their integration with microbial and host factors remain incompletely understood.

METHODS: We performed untargeted metabolomics to characterize metabolic alterations between AS patients and healthy controls (HC). Differential metabolites were identified and subjected to pathway enrichment analysis. Three machine learning models, including random forest (RF), least absolute shrinkage and selection operator (LASSO), and support vector machine (SVM), were applied to identify key metabolite signatures. Gut microbiota composition was analyzed using 16S rRNA sequencing, and correlation analyses were conducted to explore microbiome-metabolite interactions. In addition, inflammatory and senescence-related markers were assessed to evaluate host responses.

RESULTS: A total of 122 differential metabolites were identified between AS and HC, primarily enriched in amino acid-related pathways, including tryptophan, phenylalanine, and methionine metabolism. Machine learning integration revealed a robust panel of 14 overlapping metabolites with strong discriminative performance. Among them, Trimethylamine N-oxide, 3-Hydroxyhippuric acid, and Cholesteryl sulfate showed the highest diagnostic potential. Despite limited differences in gut microbial composition, several microbiota-derived metabolites and significant correlations between specific genera and metabolites were observed, suggesting functional alterations in the microbiome. Furthermore, senescence markers P16 and P21 were significantly elevated in AS and were associated with key metabolites and microbial taxa, whereas classical inflammatory markers showed no significant differences.

CONCLUSION: This study identifies a robust metabolite signature associated with AS and highlights a coordinated microbiome-metabolite-host interaction network. These findings provide new insights into the metabolic mechanisms underlying AS and suggest potential biomarkers and therapeutic targets for disease diagnosis and intervention.},
}

@article {pmid42338795,
year = {2026},
author = {Chen, J and Wei, J and Liu, T and Chen, J and Yuan, Y and Zhang, F and Zhang, J},
title = {Gut microbiome dynamics in autism: a prospective nested case-control study demonstrates microbial-clinical associations following rehabilitation interventions.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1820904},
pmid = {42338795},
issn = {1662-4548},
abstract = {BACKGROUND: Children with autism spectrum disorder (ASD) commonly exhibit gut microbiota dysbiosis and metabolic abnormalities, yet the mechanisms linking these changes to clinical symptoms remain unclear.

OBJECTIVE: This study employed a nested case-control design and multi-omics approaches to evaluate the effects of rehabilitation intervention on clinical symptoms and gut microbiota in children with ASD, identify distinct microbial-metabolic signatures, and explore their mechanistic links with sleep disorders and developmental abilities.

METHODS: Within a prospectively established pediatric cohort (n = 45), we implemented a nested case-control design including 26 ASD children (18 males, 8 females; mean age 61.79 ± 11.15 months) and 19 age- and sex-matched healthy controls. All ASD participants received standardized rehabilitation therapy (2 h/day, 5 days/week for 6 months) comprising occupational therapy and cognitive-linguistic training. Primary outcomes included comprehensive clinical assessments [Griffiths Development Scales-Chinese (GDS-C), Children's Sleep Habits Questionnaire (CSHQ), Autism Behavior Checklist (ABC), Childhood Autism Rating Scale (CARS)] and longitudinal multi-omics analysis (metagenomic sequencing and LC-MS-based metabolomics). Association analyses were performed with FDR correction (q < 0.05).

RESULTS: Following the 6-month rehabilitation intervention, significant clinical improvements were observed in sleep quality (CSHQ total and subscores) and developmental performance (GDS-C). Multi-omics profiling revealed distinct biological signatures in ASD children compared to healthy controls, characterized by elevated Intestinibacter_bartlettii and reduced levels of ornithine and siderophore nonribosomal peptide biosynthesis. Crucially, correlation analysis demonstrated that, after FDR correction, ornithine levels were significantly positively correlated with multiple GDS-C developmental domains, while tyrosine was associated with parasomnias. These findings establish a potential mechanistic link where amino acid metabolism connects gut microbial shifts to clinical phenotypes.

CONCLUSION: This study demonstrates that rehabilitation intervention synchronously ameliorates clinical symptoms and modulates the gut-metabolic profile in ASD. The identified associations between specific metabolites (ornithine and tyrosine) and clinical outcomes suggest a metabolic mechanism underlying the gut-brain axis, highlighting the potential of these metabolites as biomarkers for therapeutic monitoring. Further large-scale studies are needed to validate these findings.},
}

@article {pmid42338883,
year = {2026},
author = {Goktas, NT and Guven, S and Dinleyici, EC},
title = {The combination of Lactobacillus acidophilus DSMZ 26280 and Limosilactobacillus reuteri DSMZ 25441 has an impact on clinical course and gut microbiota of children with acute infectious diarrhea.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1792126},
pmid = {42338883},
issn = {1664-302X},
abstract = {INTRODUCTION: Previous studies and society guidelines have proposed probiotics as a complementary therapy for acute infectious diarrhea, which may shorten the disease course, yet strain-specific effects and microbiome correlates remain incompletely defined. We aim to evaluate the effect of a combination of Lactobacillus acidophilus and Limosilactobacillus reuteri on the duration of diarrhea and gut microbiota composition in children with acute infectious diarrhea.

PATIENT AND METHODS: In a prospective, randomized, controlled, open-label trial at a tertiary pediatric emergency department (March-August 2024), children aged 1-6 years with acute infectious diarrhea lasting less than 24 h were allocated 1:1 to standard therapy (oral rehydration ± intravenous fluids) with or without 5-day probiotic (L. acidophilus DSMZ 26280; 108 CFU) and (L. reuteri DSMZ 25441; 108 CFU). Primary outcomes were duration of diarrhea and the proportion diarrhea-free at 72 h. The secondary outcome measures included the proportion of diarrhea-free children during first 10th day of the study. A subgroup analysis for gut microbiota composition at Day 0, 10th and 30th days of the study have been performed.

RESULTS: Of 145 enrolled children, 79 in the probiotic group (34 girls, 45 boys) and 66 in the control (30 girls and 36 boys); baseline demographics were comparable. The duration of diarrhea was significantly reduced in the probiotic group compared to the control group (46.4 ± 29.6 h vs. 81.6 ± 38.5 h, p < 0.001). The percentage of diarrhea-free children was significantly larger in the probiotic group at 72 h compared to the control (86.0% vs. 33.3%, p < 0.001). Persistence of diarrhea was lower in the probiotic group at 24, 48, and 96 h (all p < 0.001) and at day 6 (2.5% vs. 15.1%; p < 0.05); by days 7-10, persistence was rare in both groups. The probiotic combination is well-tolerated, and no adverse events have been reported. Alpha diversity indices were unchanged within/between groups. Bray-Curtis and Jaccard PCoA showed no between-group separation; unweighted UniFrac revealed differences within the probiotic group (day 1 vs. day 30) and between groups at day 30 (p < 0.05). LEfSe indicated enrichment of taxa associated with recovery in the probiotic arm and control group, and there is difference between group at Day 30.

CONCLUSION: This study evaluates a specific combination of L. acidophilus DSMZ 26280 and L. reuteri DSMZ 25441 in a randomized controlled setting, adding to the growing body of strain-specific probiotic research in pediatric acute infectious diarrhea. Adding probiotics to treatment is well-tolerated and reduces the duration of diarrhea by approximately 35 h when it starts in the early hours of infection. This probiotic combination use is associated with modest phylogenetics shifts in gut microbiota composition, with enrichment of certain taxa that have been previously associated with gut homeostasis in other contexts; however, their functional and clinical significance in this setting remains unclear. Larger blinded trials are warranted to confirm durability and detailed metagenomic analysis including metabolomics.},
}

@article {pmid42338886,
year = {2026},
author = {Gong, H and Lv, X and Zhang, H and Kuang, G and Huang, J and Yu, R},
title = {Development and validation of embedded multilayer attention graph convolution neural network models for predicting gut microbe-disease associations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1851283},
pmid = {42338886},
issn = {1664-302X},
abstract = {INTRODUCTION: Identifying associations between gut microbes and diseases is crucial for uncovering disease mechanisms and advancing precision medicine. However, experimentally validated microbe-disease associations remain scarce due to time-consuming and costly validation. Existing computational methods face three measurable challenges: (1) severe class imbalance (positive associations constitute only 1.89-2.56% of all possible pairs); (2) difficulty in capturing nonlinear relationships inherent in microbial community interactions; and (3) limited capacity for propagating information across heterogeneous networks with sparse connectivity (graph density < 0.03).

METHODS: To address these limitations, we propose MAGMDA, a graph convolutional neural network embedded with a multi-layer attention mechanism. MAGMDA integrates known microbe-disease associations, microbial functional similarity, and disease semantic similarity into a heterogeneous network. A graph convolutional encoder learns low-dimensional embeddings of microbes and diseases, while a multi-head additive attention mechanism (8 attention heads) is incorporated into each convolutional layer. Attention weights are computed via softmax normalization over layer-wise embeddings and shared across all nodes to preserve input feature contributions and mitigate information decay. A linear decoder reconstructs the association matrix, and the model is optimized using a weighted binary cross-entropy loss to enhance sensitivity to positive associations.

RESULTS: Evaluated on the HMDAD dataset and independently validated on the Disbiome dataset (4,351 associations between 218 diseases and 1,052 microbes), MAGMDA achieves average AUC improvements of 1.87% (HMDAD) and 1.44% (Disbiome) over the second-best method, with an average AUPR improvement of 1.83% (HMDAD). Case studies on asthma and type 2 diabetes-both closely linked to gut microbiota-show that the top 30 predicted microbes are strongly supported by published literature. Preliminary external validation using real-world clinical data (290 osteoarthritis patients vs. 290 healthy controls) and animal experiments (6 rabbits per group for osteoarthritis; 6 mice per group for diabetic cardiomyopathy) provides supporting evidence for the model's ability to identify gut microbes associated with osteoarthritis and diabetic cardiomyopathy, though further large-scale validation is needed.

DISCUSSION: MAGMDA offers a robust computational framework for prioritizing gut microbe-disease associations, with strong potential to guide hypothesis-driven research and reduce the burden of experimental validation in microbiome studies.},
}

@article {pmid42338911,
year = {2026},
author = {Huang, Y and Chen, F and Yu, Z and Sheng, X and Wen, S and Zhang, X and Tang, W and Huang, M},
title = {Integrated analysis of physicochemical properties, microbiome, and flavor profiles for differentiating two aroma grades of sauce-flavor Daqu.},
journal = {Food chemistry: X},
volume = {37},
number = {},
pages = {104092},
pmid = {42338911},
issn = {2590-1575},
abstract = {Aroma characteristics are critical indicators for evaluating sauce-flavor Daqu quality. This study systematically compared physicochemical properties, enzyme activities, microbiomes, and flavor profiles of first-grade (GF) and second-grade (GS) aroma Daqu. GF had higher total acidity, amino nitrogen content, acid protease activity, a lower pH, and was correlated with enrichment of bacteria potentially associated with flavor precursor production such as Kroppenstedtia guangzhouensis and Kroppenstedtia eburnea. GS showed higher liquefying/cellulase activities and pH, and was associated with dominance by hydrolytic fungi such as Paecilomyces variotii and off-odor-related Oceanobacillus. HS-SPME-GC-MS combined with VIP and OAV analyses identified 11 differential volatile compounds. Aldehydes were strongly correlated with positive aroma grading and may serve as potential indicators associated with grade differentiation, while GS accumulated dimethyl trisulfide correlating with off-odors. The findings reveal the relationships between multi-omics characteristics and aroma grade differentiation of Daqu, and provide theoretical support for Daqu quality evaluation and production regulation.},
}

@article {pmid42338931,
year = {2025},
author = {Kaochari, S and Dehnel, A and Ntiri, E and Wong, ACN},
title = {Taste sensitivity and consumption responses to sucrose and artificial sweeteners in Drosophila melanogaster and the impact of the microbiome.},
journal = {Journal of undergraduate research (Gainesville, Fla.)},
volume = {27},
number = {},
pages = {},
pmid = {42338931},
issn = {2638-0668},
abstract = {Artificial sweeteners may alter taste sensitivity and feeding behavior, but their effects compared to natural sugars and the role of the gut microbiome in modulating these responses remain unclear. This study compares taste sensitivity and consumption responses to erythritol (Truvia), sucralose (Splenda), and sucrose in flies with a gut microbiome (conventional) and without a microbiome (axenic). Taste sensitivity was assessed using the proboscis extension response (PER) assay, while the capillary feeder (CAFE) assay was used to measure consumption. PER results revealed that sucrose elicited a significantly stronger taste response than Splenda or Truvia, with response rates increasing at higher concentrations. CAFE assays indicated fly aversion to Truvia, and axenic flies consuming significantly more Truvia compared to conventional flies, suggesting a significant microbiome effect. In the Splenda trials, axenic flies consumed significantly more yeast than those in the sucrose treatment, suggesting a potential compensatory feeding response due to the lack of calories in artificial sweeteners.},
}

@article {pmid42339027,
year = {2026},
author = {Shivanand, S and Tiwari, R and Joon, A and Mustafa, M and Shetty, C and Bennadi, D},
title = {Microbial dynamics in primary and refractory apical periodontitis: Next-generation 16S rRNA sequencing reveals selective shifts and reduced diversity.},
journal = {Journal of conservative dentistry and endodontics},
volume = {29},
number = {6},
pages = {667-671},
pmid = {42339027},
issn = {2950-4708},
abstract = {CONTEXT: Apical periodontitis (AP) is an inflammatory condition caused by root canal infection. Primary AP (PAP) arises from untreated necrotic pulp and is typically polymicrobial, whereas persistent or refractory AP (RAP) occurs after root canal treatment (RCT) and may reflect selective microbial survival.

AIM: The study aimed to compare the root canal microbiomes in PAP and persistent AP using 16S rRNA gene sequencing in a standardized mandibular molar cohort.

SETTINGS AND DESIGN: Comparative, observational, cross-sectional study conducted at a tertiary care dental institution.

MATERIALS AND METHODS: Intracanal samples were collected from 45 systemically healthy adults (30 RAP, 15 PAP) with chronic asymptomatic mandibular molars (Periapical Index 2-4). Samples were processed using Illumina MiSeq sequencing targeting the V3-V4 region. Bioinformatics analysis was performed using QIIME 2 and DADA2 pipelines.

STATISTICAL ANALYSIS USED: Alpha diversity was analyzed using the Mann-Whitney U-test. Beta diversity was assessed using permutational multivariate analysis of variance (PERMANOVA). Differential abundance was evaluated using DESeq2 with Benjamini-Hochberg false discovery rate (FDR) correction.

RESULTS: RAP exhibited significantly reduced alpha diversity (P ≤ 0.003) and a distinct microbial community structure compared with PAP (PERMANOVA, P ≤ 0.003). Persistent cases showed enrichment of Gram-positive taxa, particularly Enterococcus faecalis (38.5% vs. 2.1%; Log2 fold change +4.2, FDR < 0.001), whereas primary cases demonstrated higher abundance of anaerobic Gram-negative taxa such as Fusobacterium nucleatum and Porphyromonas gingivalis.

CONCLUSIONS: Persistent AP is associated with reduced microbial diversity and enrichment of Gram-positive organisms, particularly E. faecalis. These findings may reflect selective survival of resistant taxa and/or secondary colonization following RCT.},
}

@article {pmid42339158,
year = {2026},
author = {Tashiro, K and Shinzawa, N and Ishino, T and Saito, R and Shirogane, Y and Suzuki, T},
title = {Strengthening infectious disease surveillance and control through long-term international collaboration: Insights from the Ghana- Japan partnership.},
journal = {GHM open},
volume = {6},
number = {1},
pages = {40-43},
pmid = {42339158},
issn = {2436-2956},
abstract = {West Africa remains a global epicenter for emerging and re-emerging infectious diseases, yet data on pathogen diversity and transmission dynamics remain fragmented. This communication summarizes 21 years of longitudinal research collaboration between the Institute of Science Tokyo (formerly Tokyo Medical and Dental University) and the Noguchi Memorial Institute for Medical Research (NMIMR) in Ghana. Our integrated surveillance framework encompasses: i) defining environmental virulence factors for Mycobacterium ulcerans to refine Buruli ulcer risk assessment; ii) uncovering the "masked" circulation of Dengue and SARS-CoV-2 through molecular epidemiology; iii) investigating biological determinants, including gut microbiome profiles, of reduced Rotavirus vaccine efficacy in low-income settings; iv) characterizing the environmental reservoirs and fitness costs of carbapenemase-producing Enterobacteriaceae; and v) analysis of the interaction of malaria parasites between symbionts in vector mosquitoes and vaccine development. By aligning basic research on infectious diseases with clinical data and human resource development, this partnership provides a scalable model for strengthening global health security and addressing the unique infectious disease challenges of the "post-viral" era.},
}

@article {pmid42339293,
year = {2026},
author = {Zheng, H and Chen, W},
title = {Baseline gut microbiome features associated with fecal calprotectin response to exclusive enteral nutrition in pediatric Crohn's disease.},
journal = {Frontiers in pediatrics},
volume = {14},
number = {},
pages = {1833193},
pmid = {42339293},
issn = {2296-2360},
abstract = {BACKGROUND AND AIMS: Exclusive enteral nutrition is an established induction therapy for pediatric Crohn's disease, but biochemical response varies across patients. We assessed whether baseline gut microbiome features were associated with fecal calprotectin response and whether treatment-related taxonomic shifts could be interpreted alongside reported fecal biochemical summaries.

METHODS: We re-analyzed a public pediatric cohort (PRJEB14084). Paired baseline and end-of-treatment microbiome profiles were summarized as within-subject genus-level changes. Reported stool biochemical summaries were used as contextual data. Baseline model performance was explored by repeated nested cross-validation with calibration assessment. An independent pediatric cohort (PRJEB33603) was used only for summary-level external comparison.

RESULTS: Several genera changed consistently during treatment. Stool biochemical summaries showed lower total amino acids and tryptophan and higher secondary bile-acid proportion and hydrophobicity index at the end of treatment. The baseline model showed modest discrimination with broad uncertainty (mean area under the receiver operating characteristic curve, 0.655; 95% confidence interval, 0.450-0.850). In the external comparison, 7 of 12 overlapping genera showed concordant directions.

CONCLUSION: In this public cohort, baseline microbiome features showed an exploratory association with fecal calprotectin response, but the estimates were imprecise. External comparison was limited to published summary tables, and all inferences remain association-based.},
}

@article {pmid42339334,
year = {2025},
author = {Yaprak Çolak, E and Duran, N},
title = {Correction: Synergistic antibacterial effects of postbiotics combined with linezolid and amikacin against nosocomial pathogens.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1750002},
doi = {10.3389/fcimb.2025.1750002},
pmid = {42339334},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2025.1616501.].},
}

@article {pmid42339375,
year = {2026},
author = {Tomasi, N and Banchi, E and Manna, V and Celussi, M},
title = {Surface sediments prokaryotic communities: five years of 16S rRNA amplicon sequencing data from the northernmost part of the Mediterranean Sea.},
journal = {Data in brief},
volume = {67},
number = {},
pages = {112971},
pmid = {42339375},
issn = {2352-3409},
abstract = {Surface sediments harbour diverse prokaryotic communities that play a key role in biogeochemical cycling and provide valuable insights when compared with water column communities, allowing for a more comprehensive understanding of marine ecosystem functioning. Specifically, this dataset presents prokaryotic community data from 16 surface sediment samples collected seasonally from June 2020 to May 2025 at the C1-LTER station (45°42'2.99″ N, 13°42'36.00″ E; DEIMS.iDhttps://deims.org/96969205-cfdf-41d8-979f-ff881ea8dc8b) in the Gulf of Trieste, located in the northeastern Adriatic Sea (Mediterranean Sea). Extracted DNA was sequenced following the 16S Metagenomic Sequencing Library Preparation protocol and run on an Illumina NovaSeq 6000 System. Raw reads were filtered and denoised with DADA2, and taxonomic assignment was performed against the Silva 138.2 99% reference database. The dataset provides useful insights into prokaryotic communities and their seasonal variability over five years. Moreover, a focus on specific taxa is provided, such as Cyanobacteriota and Archaea, highlighting patterns of community variability in the sediment. Finally, it shows seasonal stability and generally consistent taxa distribution over time, as indicated by the high proportion of shared taxa at each taxonomic level. The raw data, deposited in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA1442017, include two sets of sequencing reads obtained from surface sediment samples using the Illumina MiSeq and Illumina NovaSeq 6000 sequencing platforms, for a total of 27 16S rRNA gene sequencing FASTQ files. Overall, these data provide valuable insight into the surface sediment community in the northernmost part of the Mediterranean Sea, contributing to long-term research on sediment prokaryotic communities.},
}

@article {pmid42339384,
year = {2026},
author = {Hussain, M and Ahmed, N and Yang, Z and Xie, X and Xing, W and Su, H and Peng, Q and Zhu, Z},
title = {From green to red: metabolic reprogramming and bacterial community succession underpin cherry tomato fruit ripening and quality formation.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1843442},
pmid = {42339384},
issn = {1664-462X},
abstract = {Tomato fruit ripening is accompanied by profound biochemical and microbial-associated changes that collectively shape fruit flavor, quality, and susceptibility to (a)biotic stresses. However, integrated insights into the co-varying effect of metabolic reprogramming and fruit-associated microbiome across ripening stages remain limited. Here, we employed a multi-omics approach to investigate stage-dependent shifts in the metabolome and bacteriome of cherry tomato fruits across three ripening stages: mature green, pink, and red ripe. Fruit quality analysis revealed a significant increase in soluble sugars, lycopene, and ascorbic acid from the green to the red stage. Untargeted metabolomics showed extensive metabolic reprogramming during ripening, characterized by the marked accumulation of lipids, amino acids, carbohydrates, terpenoids, and flavonoids in red ripe fruits, alongside a decline in defensive alkaloids such as tomatine. High-throughput 16S rRNA amplicon sequencing showed that bacterial diversity and community composition shifted significantly with ripening, with red ripe fruits harboring higher diversity and enrichment of gram-positive taxa, including Bacillus, Clostridium, Enterococcus, Lactiplantibacillus, Litchfieldia, and Pediococcus, whereas Pseudomonas was enriched in the mature green stage. Correlation analysis revealed a strong association between specific bacterial taxa and ripening-related metabolites, suggesting a link between microbial succession and metabolic remodeling. Together, these findings demonstrate that tomato fruit ripening involves tightly coupled metabolic and microbial dynamics, providing new insights into fruit quality formation and postharvest ecology for sustainable agriculture.},
}

@article {pmid42339597,
year = {2026},
author = {da Costa, TB and Vaz, JDS and Pieniz, S},
title = {The infant gut microbiota: a narrative review about development and external determinants.},
journal = {Journal of developmental origins of health and disease},
volume = {17},
number = {},
pages = {e26},
doi = {10.1017/S2040174426100488},
pmid = {42339597},
issn = {2040-1752},
mesh = {Humans ; Infant ; *Breast Feeding ; *Gastrointestinal Microbiome/physiology ; Infant, Newborn ; Female ; Infant Formula ; *Infant Nutritional Physiological Phenomena ; },
abstract = {This narrative review examines the development of the infant gut microbiota during the early months of life, highlighting the impact of delivery mode and feeding practices on microbial colonization and overall infant health. The search was conducted using the Virtual Health Library and PubMed databases, with the descriptors "gut microbiota" combined with "breastfeeding" (BF) and "infant formula." After screening, 18 articles were selected for final analysis. Findings indicate that cesarean section reduces initial gut microbial diversity by 30%-50% and decreases Bifidobacterium colonization, while increasing the abundance of Enterobacteriaceae and Clostridium. In contrast, exclusive BF supports a more favorable microbial profile, enriched in bifidobacteria, and contributes to immune system maturation. The literature also highlights the importance of other genera, including Lactobacillus, Veillonella, and Firmicutes, in regulating inflammation, producing short-chain fatty acids, and protecting against pathogens. Supporting vaginal birth and exclusive BF emerges as a key strategy to promote a more resilient and health-promoting gut microbiota during infancy.},
}

Humans
Infant
*Breast Feeding
*Gastrointestinal Microbiome/physiology
Infant, Newborn
Female
Infant Formula
*Infant Nutritional Physiological Phenomena

@article {pmid42339722,
year = {2026},
author = {Kanika, NH and Guo, Z and Mandal, RN and Hanif, MS and Bao, X and Chen, X and Wang, J and Wang, C},
title = {Multi-Omics Analysis Reveals Impacts of SCARB1, TYR, and TYRP1 Knockouts on Pigmentation and Metabolic Pathways in Oujiang Color Common Carp.},
journal = {Animal genetics},
volume = {57},
number = {4},
pages = {e70140},
doi = {10.1002/age.70140},
pmid = {42339722},
issn = {1365-2052},
support = {32172959//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Pigmentation/genetics ; *Carps/genetics/metabolism/physiology ; Multiomics ; *Metabolic Networks and Pathways/genetics ; *Scavenger Receptors, Class B/genetics ; *Oxidoreductases/genetics ; *Fish Proteins/genetics/metabolism ; *Protein-Tyrosine Kinases/genetics ; Microbiota ; Intramolecular Oxidoreductases ; },
abstract = {Gene knockout (KO) techniques are important for understanding gene function and their impact on organismal traits. This study investigates the effects of targeted KO of SCARB1, TYR, and TYRP1 genes in Oujiang Color common carp, focusing on pigmentation changes, metabolic dysregulation, and host-microbiome interactions. Our multi-omics approach revealed that SCARB1 KO led to complete loss of red pigmentation, while TYR and TYRP1 KOs resulted in hypopigmentation and altered pigmentation patterns. Transcriptomic analysis identified seven key genes (PLA2G4, C3, F2, ERN1, UGP2, purA, and GRIN2A), linked to major pathways: glycerophospholipid metabolism, biosynthesis of cofactors, autophagy, and neuroactive ligand-receptor interaction. Notably, we observed significant upregulation of phosphatidylethanolamine (PE) and disruptions in glycolysis and tyrosine metabolism. Histological analysis showed reductions in epithelial and goblet cells, and microbiome profiling indicated shifts in microbial diversity, including significant changes in Firmicutes, Bacteroidetes, and genera such as Pseudomonas, Rhodobacter, Bacillus, and ZOR0006. These findings uncover pigmentation genes as pivotal players in regulating pigmentation, cellular stress, metabolism, and the microbiota. This study improves our understanding of pigmentation regulation in common carp and provides potential molecular targets for color trait improvement in aquaculture species.},
}

Animals
*Pigmentation/genetics
*Carps/genetics/metabolism/physiology
Multiomics
*Metabolic Networks and Pathways/genetics
*Scavenger Receptors, Class B/genetics
*Oxidoreductases/genetics
*Fish Proteins/genetics/metabolism
*Protein-Tyrosine Kinases/genetics
Microbiota
Intramolecular Oxidoreductases

@article {pmid42339741,
year = {2026},
author = {Moutsoglou, D and Jarrah, M and Jaques, J and Aguilar, L and Shahi, SK and Mangalam, AK and Mokadem, M},
title = {Roux-en-Y gastric bypass alters microbial circadian rhythms with links to metabolic improvement.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00440.2025},
pmid = {42339741},
issn = {1522-1547},
support = {BX004774-05//U.S. Department of Veterans Affairs (VA)/ ; 1I01CX002212//U.S. Department of Veterans Affairs (VA)/ ; I01BX006112//U.S. Department of Veterans Affairs (VA)/ ; RG-2407-43720//National Multiple Sclerosis Society/ ; HT94252510562//U.S. Department of Defense (DOD)/ ; },
abstract = {The circadian clock and gut microbiome are integral regulators of metabolic homeostasis, with disruptions in either system contributing to obesity pathogenesis. Roux-en-Y gastric bypass (RYGB) effectively treats severe obesity, yet the mechanisms underlying its benefits remain incompletely characterized. We investigated the impact of RYGB on cecal gut microbial composition and function using 16S rRNA sequencing in relation to host circadian gene expression and metabolic parameters in diet-induced obese mice. Diet-induced obese mice underwent RYGB or sham surgery and were compared with lean controls across multiple circadian Zeitgeber time (ZT) points (ZT3, ZT9, ZT15, ZT21). Principal component analysis at the ASV level revealed significant differences in all ZT points (ZT3, ZT9, ZT15, and ZT21) in the lean and sham-operated mice; however, only a significant difference between ZT9 and ZT21 was observed in RYGB mice. Microbial gene counts and microbial pathways were also different between RYGB and sham-operated mice, with several correlating with hepatic Clock and Bmal1 gene expression. Notably, specific taxa showed differential associations with glucose homeostasis, independent of surgical intervention. These findings demonstrate that RYGB alters the gut microbiome and host circadian rhythms, suggesting an association between microbial remodeling, circadian gene expression, and metabolic improvement following bariatric surgery.},
}

@article {pmid42339814,
year = {2026},
author = {Haewou, N and Khwanbua, E and Khaengraeng, C and Kuncharoen, N and Kasem, S and Chatnaparat, T},
title = {Compartment-Specific Bacterial Communities in Turmeric and Their Association with Suppression of Ralstonia pseudosolanacearum.},
journal = {Phytopathology},
volume = {},
number = {},
pages = {},
doi = {10.1094/PHYTO-03-26-0066-R},
pmid = {42339814},
issn = {0031-949X},
abstract = {Bacterial wilt caused by Ralstonia pseudosolanacearum poses a significant threat to turmeric (Curcuma longa L.) production in many growing regions. Although plant-associated microbial communities may contribute to disease suppression, the ecological roles of rhizosphere and endosphere microbiomes in turmeric are still underexplored. Here, we characterized rhizosphere and endosphere bacterial communities using 16S rRNA gene amplicon sequencing and evaluated their antagonistic activity against bacterial wilt pathogen of turmeric R. pseudosolanacearum strain RalsTur1. Microbiome profiling revealed compartment-specific patterns in turmeric-associated bacterial communities, with rhizosphere communities strongly structured by geographic location and endosphere communities comparatively stable across field sites. The endosphere core microbiome was dominated by bacterial members in the family Enterobacteriaceae, particularly Enterobacter, along with Pseudomonas, whereas rhizosphere communities included diverse taxa such as Bacillus and members of the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium group. Interbacterial competition assays showed that several turmeric-associated isolates reduced RalsTur1 populations in vitro. However, in planta assays using tissue-cultured turmeric plants revealed that only the endosphere-derived bacterial community, including Chryseobacterium gleum (ED4), Pseudomonas laurentiana (ED4-21), and Pantoea sp. (WEH1), significantly reduced pathogen populations, resulting in a two-log reduction in pathogen abundance. These findings suggest that colonization within plant tissues may contribute to suppression of vascular pathogens and highlight endophytic bacteria as candidates for further investigation in microbiome-based management of bacterial wilt.},
}

@article {pmid42340023,
year = {2026},
author = {Pei, T and Nwanade, CF and Liang, X and Zhang, Y and Wang, Z and Liu, Z and Dai, Y and Zhang, X and Yu, Z},
title = {Environmental Low Temperatures Dynamically Reshape the Microbial Diversity and Community Structure of the Vector Tick Haemaphysalis longicornis.},
journal = {Archives of insect biochemistry and physiology},
volume = {122},
number = {2},
pages = {e70182},
pmid = {42340023},
issn = {1520-6327},
support = {2026ZD01909100//National Science and Technology Major Project/ ; 32071510//National Natural Science Foundation of China/ ; },
mesh = {Animals ; Female ; Male ; Bacteria/classification/genetics ; *Cold Temperature ; *Haemaphysalis longicornis/microbiology ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Arachnid Vectors/microbiology ; },
abstract = {Low temperature is a key abiotic factor shaping tick-associated microbial communities, which in turn influence host physiology, vector competence, and environmental adaptation. However, the impact of prolonged cold exposure, such as overwintering conditions, on the microbiome of the invasive tick Haemaphysalis longicornis remains insufficiently characterized in terms of its microbial response. In this study, unfed adult ticks were subjected to a gradient of low temperatures (8°C, 4°C, 0°C, -4°C) for 7 days, while a control group was maintained at 27°C. The bacterial communities of whole ticks were characterized using Illumina NovaSeq-based 16S rRNA gene sequencing, followed by comprehensive bioinformatics analyses to evaluate alpha diversity, beta diversity, taxonomic composition, and differentially abundant taxa. The results showed that cold exposure markedly reshaped the microbial community structure, with an overall increase in alpha diversity (Shannon index) observed in several treatment groups. Across all samples, the dominant bacterial phyla included Proteobacteria, Firmicutes, and Bacteroidota. Notable shifts were detected at the genus level, particularly in Coxiella endosymbiont and Pseudomonas, whose relative abundances changed substantially under low-temperature conditions. In addition, microbial responses exhibited clear sex-specific patterns: Escherichia-Shigella and Serratia were enriched in certain cold-treated groups, whereas Staphylococcus showed a reduction in males exposed to low temperatures. The endosymbiont Coxiella was significantly enriched in male ticks at 8°C (p = 0.009). Beta diversity analysis further demonstrated distinct clustering of the -4°C male group relative to all other groups. Collectively, these findings indicate that sustained low temperatures drive pronounced and sex-dependent restructuring of the bacterial microbiome in H. longicornis. The enrichment of specific taxa, including putative nutritional symbionts such as Coxiella, under cold stress conditions suggests a potential role for microbial communities in facilitating host adaptation to low-temperature environments, thereby providing new insights into the ecological dynamics and adaptive capacity of this invasive vector species.},
}

Animals
Female
Male
Bacteria/classification/genetics
*Cold Temperature
*Haemaphysalis longicornis/microbiology
*Microbiota
RNA, Ribosomal, 16S/genetics
*Arachnid Vectors/microbiology

@article {pmid42340049,
year = {2026},
author = {Mao, H and Wang, X and Pang, Y and Lu, Y and Wang, H and Li, H and Ni, Y and Jia, W},
title = {The Gut Microbiome-Endocrine Axis in Obesity: Mechanisms and Therapeutics.},
journal = {Journal of gastroenterology and hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jgh.70511},
pmid = {42340049},
issn = {1440-1746},
support = {C2406002//Shenzhen Medical Research Fund/ ; 92357305//Major Research Plan of National Natural Science Fund of China (NSFC)/ ; 24HAA01325//Excellent Young Scientists Fund of the National Natural Science Foundation of China (Overseas)/ ; },
abstract = {Obesity, a major global health challenge and a key risk factor for metabolic diseases, represents a state of dysregulated energy homeostasis. The gut microbiome has emerged as a critical mediator of obesity pathogenesis, yet the precise endocrine mechanisms linking microbial signals to metabolic dysfunction remain incompletely understood. Therefore, at the perspectives of gut microbiome-endocrine axis encompassing gut-brain, gut-adipose, and gut-pancreas axes, this review elucidates how gut microbiota and their metabolites influence systemic endocrine homeostasis through energy intake, fat storage, and hormonal secretion. Mechanistic studies highlight the roles of short-chain fatty acids, bile acids, and microbial peptides in modulating obesity control and related metabolic health. We further summarize the current therapeutics targeting gut microbiome in the gut-endocrine axis, including prebiotics, probiotics, synbiotics, postbiotics, fecal microbiota transplantation, and lifestyle approaches and highlight their mechanistic and translational relevance. The major challenges of gut microbiome studies are discussed, including obscure phenotyping, insufficient cross-organ integration, and limited causal inference. Overcoming these limitations by precise obesity measurement, integrated cross-organ models, and AI-driven causal modeling could advance the pathophysiological insight and management of obesity.},
}

@article {pmid42340359,
year = {2026},
author = {Bandopadhyay, S and Danczak, RE and Patel, KF and Beilsmith, KR and Weisenhorn, PB and Spanbauer, TL and Reichart, NJ and Weintraub, MN and Bailey, VL},
title = {Soil microbial ecology and microbiome-metabolite linkages improve understanding of ecosystem states along terrestrial-aquatic interfaces.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag066},
pmid = {42340359},
issn = {1574-6941},
abstract = {Coastal soils are dynamic systems where unique microbial niches are shaped by the intensity and duration of flooding between the terrestrial and aquatic boundaries of the terrestrial-aquatic interface (TAI). We aimed to understand the soil microbial community (16S rRNA gene) along the TAIs of a freshwater versus estuarine region and how it relates to organic matter (OM, FTICR-MS). We studied the TAI gradients along a transect from upland (forested), transition (stressed forest), to wetland at three sites in each of the Lake Erie (freshwater) and Chesapeake Bay (estuarine) regions. Microbial communities differed significantly by region, transect position, and site. Contrary to expectations, given their dynamic hydrologies, transitions represented midpoints in microbial richness and diversity. We identified a core microbiome conserved across all transect positions within a region, highlighting potential microbial functions most resilient to environmental change. Indicator taxa unique to each transect position defined specific niches shaped by soil biogeochemistry. Co-expression networks of feature-level β-nearest-taxon indices revealed positive relationships in bacterial and OM feature contributions to community assembly. Our study provides critical insights into microbial communities at the forefront of hydrological changes in coastal areas that connect the land to lakes and oceans and remain vulnerable to changing weather patterns.},
}

@article {pmid42340370,
year = {2026},
author = {Sayyed, R and Al-Zharani, M and Mubarak, M and Anca Șuțan, N and Egamberdieva, D and Sharma, A and Rebouh, NY and Barasarathi, J},
title = {Integrating Epigenetic Memory and Plant Growth-Promoting Rhizobacteria -Mediated Signaling for Climate-Resilient Agriculture.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag149},
pmid = {42340370},
issn = {1365-2672},
abstract = {AIMS: Climate change is shifting agriculture toward multifactorial abiotic stresses (drought, heat, and salinity). This study aims to characterize emergent, non-additive plant responses to combined stresses and to define the epigenetic and microbial frameworks that govern environmental memory and adaptive plasticity.

METHODS AND RESULTS: We conducted a meta-synthesis of molecular and ecological studies, evaluating high-throughput data on DNA methylation, histone modifications, and ncRNA profiles. We further analyzed the plant holobiont to determine how rhizosphere and endosphere microbiota influence host stress imprinting. The analysis revealed that stress combinations trigger distinct transcriptomic and metabolic signatures, which are stabilized by an "epigenetic toolkit" such as RNA-directed DNA methylation and chromatin remodeling. Furthermore, plant-associated microbiota serve as an extrinsic regulatory layer, modulating host epigenetic states to prime plants for compound stress. While translational pathways such as epigenetic editing, CRISPR-mediated epigenome editing, and microbiome engineering show promise, their field-scale stability remains context-dependent.

CONCLUSION: Building climate resilience requires a paradigm shift from traditional single-trait breeding toward multi-scale regulatory approaches. Harnessing the synergy between the plant epigenome and the microbiome enables the development of 'primed' crop varieties-an integrated strategy vital for safeguarding global food security amid intensifying environmental volatility.},
}

@article {pmid42340445,
year = {2026},
author = {Wang, Y and Li, G and Liu, Y and Liu, J and Li, G and Li, Y and Zhou, N},
title = {Dynamic changes in oral microbiome composition during early childhood caries management.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13928-5},
pmid = {42340445},
issn = {1432-0614},
support = {2023Y0822//Scientific Research Foundation of Yunnan Provincial Department of Education/ ; D2019-007//by Academic Leader Project of Yunnan Province/ ; XDYC-YLWS-2023-0047//Xingdian Talent Support Plan of Yunnan Province-Medical and Health Talents Special Project/ ; 2022GZ001//clinical research grant from the School and Hospital of Stomatology, Kunming Medical University/ ; },
abstract = {Early childhood caries (ECC) is a prevalent dental disease with significant public health burdens. Oral microbiota plays a key role in caries development. Although several studies have compared the oral microbiota before and after caries treatment, few have investigated the dynamic changes in oral microbial communities beyond 3 months. This 6-month prospective study monitored dynamic changes in the dental plaque microbiome, salivary pH, and oral hygiene status among children with ECC undergoing caries management. The outcomes were assessed at baseline (T0), immediately post-treatment (T1), and at 1-month, 3-month, and 6-month follow-ups (T2-T4). Children's oral hygiene status improved significantly after ECC management (p < 0.001). Their salivary pH levels increased at T1 but returned to the initial level during follow-up visits. Higher Chao1 scores were observed at T2, T3, and T4 when compared to T0 and T1 (p < 0.001). The principal coordinate analysis revealed distinct clustering patterns between baseline and post-treatment visits. Significant differences were observed in the relative abundance of Corynebacterium (p < 0.01), Corynebacterium matruchotii (p < 0.01), and Selenomonas noxia (p < 0.05) during the study period. The relative abundance of Corynebacterium and Corynebacterium matruchotii was significantly higher at T3 and T4 when compared to T1 (p < 0.01). Additionally, Saccharibacteria was positively correlated with children's dmfs scores and negatively correlated with children's salivary pH values. The above findings possibly indicated that comprehensive ECC management might be associated with dynamic changes in the oral microbiome. Further well-designed randomized controlled trials are warranted to determine the impact of dental treatment on oral microbiota dynamics. KEY POINTS: • Dynamic changes observed in the oral microbiome following dental treatment • Abundance of Saccharibacteria associated with children's caries status and salivary pH values • Children's oral health-related behaviors improved after comprehensive dental management.},
}

@article {pmid42340489,
year = {2026},
author = {Manna, P and Ganguly, SC and Chatterjee, A and Mondal, B and Maity, A and Chatterjee, S and Guria, T and Chakraborty, M},
title = {Targeting microbiota-gut-brain axis with phytochemicals: a mechanistic roadmap for dementia.},
journal = {Metabolic brain disease},
volume = {41},
number = {1},
pages = {},
pmid = {42340489},
issn = {1573-7365},
mesh = {Humans ; *Phytochemicals/therapeutic use/pharmacology ; *Dementia/drug therapy/metabolism/microbiology ; Animals ; *Brain/drug effects/metabolism ; *Gastrointestinal Microbiome/drug effects/physiology ; *Brain-Gut Axis/drug effects/physiology ; Dysbiosis/drug therapy/metabolism ; },
abstract = {Dementia is a growing global health concern, with limited therapeutic options. Treating dementia is a crucial but often overlooked part of neurological care for the elderly. The gut microbiota plays an essential role in the bidirectional interaction between the gut and the brain. Growing evidence suggests that gut microbes, which can influence neural development, modulate neurotransmission, and affect behaviour, may contribute to the development and pathophysiology of various neurodevelopmental, neuropsychiatric, and neurological disorders like dementia. This underscores the need for new interventions targeting the gut-brain axis(GBA). This review highlights the role and application of phytochemicals in treating dementia by modifying the GBA. We outline the harmful relationship between dementia and microbial dysbiosis, focusing on abnormal tryptophan- kynurenine metabolism, impaired SCFA synthesis, disruption of the BBB, and altered microglial activation states. Nevertheless, the potential of different phytochemicals, such as flavonoids, alkaloids, terpenoids, and polyphenols, to enhance neuroprotective metabolite production, restore microbial balance, regulate inflammatory signalling (e.g., NF- κb, Nrf 2, MAPK, and TLR 4), and improve synaptic plasticity via pathways like BDNF-CREB, is under investigation. Key bioactive compounds like berberine, resveratrol, and curcumin are being tested for their efficacy concerning molecular targets and outcomes in both preclinical and clinical models of cognitive decline. In addition to specific phytochemicals, probiotic and prebiotic synergistic approaches may enhance gut homeostasis and cognitive resilience, opening avenues for functional food- based treatments. Although promising, challenges to clinical application remain, such as low bioavailability, standardisation issues, and interindividual microbiome variability. This review emphasises prospects for precision nutrition and microbiome- targeted therapies in dementia, discusses translational barriers, and summarises recent data on phytochemical modulation of the GBA in dementia.},
}

Humans
*Phytochemicals/therapeutic use/pharmacology
*Dementia/drug therapy/metabolism/microbiology
Animals
*Brain/drug effects/metabolism
*Gastrointestinal Microbiome/drug effects/physiology
*Brain-Gut Axis/drug effects/physiology
Dysbiosis/drug therapy/metabolism

@article {pmid42340499,
year = {2026},
author = {Lin, LX and Chen, WJ and Li, SX and Zheng, FY and Huang, XG and Liu, FJ and Luo, JY and Huang, ZJ and Zhang, WJ and Zhuo, YB and Long, X},
title = {Exploring gut microbiota responses to low-dose thallium exposure via food chain transfer: insights from soil-plant-human systems.},
journal = {Environmental geochemistry and health},
volume = {48},
number = {9},
pages = {},
pmid = {42340499},
issn = {1573-2983},
support = {22574071//National Natural Science Foundation of China/ ; },
mesh = {Humans ; Male ; Adult ; Female ; *Gastrointestinal Microbiome/drug effects ; *Thallium/toxicity/analysis ; *Soil Pollutants/toxicity ; *Food Chain ; Feces/microbiology ; Bacteria/classification/drug effects/genetics ; Soil Microbiology ; Young Adult ; },
abstract = {Thallium (Tl) is a toxic metal and priority pollutant, its soluble Tl levels in soil drive Tl accumulation in edible plants, posing health risks to gut microbiota via dietary exposure even at low doses. This study investigated Tl accumulation in sweet potatoes (4.45-32.87 µg/kg dry weight, 0.2442-1.7368 µg/kg wet weight) from soils (282.89-699.50 µg/kg) and its impact on a single pooled microbial community derived from fecal samples of three healthy adults (2 females, 1 male, 20-30 years) using an in vitro digestion-colon fermentation model. Low-dose Tl exposure drove significant, dose- and time-dependent genus-level restructuring of the pooled microbial community (Kruskal-Wallis, P = 0.001; PERMANOVA, P = 0.001, R[2] = 0.783-0.980), without altering phylum-level alpha diversity (Kruskal-Wallis, P > 0.05), indicating compositional shifts rather than richness loss. Genus-level shifts included proliferation of harmful taxa (Escherichia_Shigella, Enterococcus) and reduction of beneficial taxa (Bacteroides, Prevotella, Akkermansia, Bifidobacterium, Blautia). Significant correlations (p < 0.05, 0.6883 < R[2] < 0.9850) linked Tl content to Bacteroides, Prevotella, Escherichia_Shigella, and Enterococcus abundances. These findings demonstrate exposure-relevant microbiome shifts within this single pooled microbial community even at Tl concentrations below regulatory limits (300 µg/kg) via food chain transfer. However, as this in vitro model lacks host-microbe interactions (e.g., immune signaling, peristalsis) and the results reflect the response of one mixed inoculum from three donors rather than inter-individual variability, chronic in vivo studies are essential to validate these shifts and their metabolic and immune implications, informing soil-plant-human safety and public health strategies for low-dose dietary Tl exposure.},
}

Humans
Male
Adult
Female
*Gastrointestinal Microbiome/drug effects
*Thallium/toxicity/analysis
*Soil Pollutants/toxicity
*Food Chain
Feces/microbiology
Bacteria/classification/drug effects/genetics
Soil Microbiology
Young Adult

@article {pmid42340677,
year = {2026},
author = {Yang, R and Li, Y and Sankaran, K and Mace, TA and Hart, PA and Ma, Q and Wang, XW and Ke, S},
title = {Prevalence aware feature selection improves biomarker identification in microbiome studies.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag371},
pmid = {42340677},
issn = {1367-4811},
abstract = {MOTIVATION: Identifying robust microbial biomarkers is crucial for disease diagnosis and prediction, elucidation of biological mechanisms, and development of targeted therapies. Machine learning-based approaches, particularly the random forest model, have been widely used for biomarker identification during sample stratification. However, those biomarkers often vary considerably for the same disease, limiting their practical applicability. A robust framework for reliable biomarker identification in microbiome research is needed. To address this gap, we proposed a prevalence-aware feature selection framework (ParSlet) that incorporates a universal scaling relationship between taxon prevalence and selection frequency.

RESULTS: We first identified a universal exponential scaling law linking the probability of a taxon being consistently recognized as a biomarker versus its prevalence. Then, we integrated this scaling law with taxa prevalence into the biomarker identification using random forest. We systematically evaluated this approach in both simulated microbiome datasets and real-world microbiome datasets and compared it with existing methods, finding that our integrated approach generally improved feature stability and reproducibility of biomarker identification. In colorectal cancer (CRC) datasets, our method robustly identified well-established microbial biomarkers such as Ruminococcus, Clostridium_XVIII, and Faecalibacterium. Integrating a prevalence-based scaling adjustment into feature importance enhances the stability of microbiome biomarker identification. This approach holds promise for enabling more reliable disease diagnostics, uncovering generalizable microbial signatures across cohorts, and guiding the development of targeted microbiome-based interventions.

AVAILABILITY: ParSlet is available at https://github.com/KelabatOSU/Feature_selection.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.},
}

@article {pmid42340852,
year = {2026},
author = {Racine, KC and Iglesias-Carres, L and Herring, JA and Lambirth, KC and Kay, CD and Tessem, JS and Neilson, AP},
title = {Epicatechin and High-Molecular Weight Fraction Do Not Recapitulate the Antiobesity and Antidiabetes Activities of Whole Cocoa Extract.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c05001},
pmid = {42340852},
issn = {1520-5118},
abstract = {Cocoa flavanols show promise for inhibiting type 2 diabetes (T2D). The components responsible for this remain poorly understood. We compared cocoa extract (CE) supplementation against matched epicatechin (EC) or a high-molecular-weight fraction (HMW) in a T2D mouse model induced by high-fat (HF) plus streptozotocin (STZ). Mice were fed HF diet with STZ alone or with CE, EC, or HMW. HF + STZ animals fed CE had blunted weight gain and reduced insulin resistance compared to HF + STZ control as measured by the homeostasis model assessment of insulin resistance. However, these improvements are driven by reduced fasting glucose and insulin, as peripheral insulin resistance was not observed in the model when accounting for the fasting glucose. HF + STZ-induced dysbiosis was partially reversed by CE and HMWs. These findings demonstrate the beneficial effects of CE on the gut microbiome and cardiometabolic markers, which were not fully achieved by EC or HMW, suggesting synergistic effects of flavanols.},
}

@article {pmid42341025,
year = {2026},
author = {Wohl, DL and Belder, PT and Mitchell, BD},
title = {A comparative analysis of the oral microbiome of Amish and non-Amish individuals to strengthen our understanding of variation within the oral microbiome.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0350558},
pmid = {42341025},
issn = {1932-6203},
mesh = {Humans ; *Microbiota/genetics ; *Mouth/microbiology ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; *Amish ; Female ; Male ; Oral Health ; Adult ; Middle Aged ; Dental Plaque/microbiology ; Bacteria/genetics/classification ; },
abstract = {More than 700 phylotypes associated with the oral cavity collectively comprise the oral microbiome. Study of microbiomes has advanced our understanding of human health. Little is known about the oral microbiome of the Old Order Amish population, a distinct ethnoreligious group who choose to stay separate from mainstream society to preserve their traditional, faith-based way of life. This research was to generate a novel characterization of the Amish oral bacterial microbiome and, using a comparative study design, provide metagenomic analyses of potential variations between generated profiles of the Amish and non-Amish. Next-generation sequencing of 16S rRNA genes of supragingival plaque and saliva samples was used. Analysis between oral health habits from surveys (e.g., fluoride use, frequency of dental visits) and markers within the microbiomes were used to assess the extent of variation due to oral health habits or other factors. Samples were analyzed from 14 Amish and 13 non-Amish individuals. Using non-parametric analyses, alpha and beta diversity were measured to assess core microbiomes, abundance, and sample dissimilarity. Compared to non-Amish, Amish experienced significantly lower frequency of dental visits (p < 0.001) and fluoride use (p < 0.001), but no difference in frequency of teeth brushing (p = 0.198) was observed. Alpha-diversity of observed species differed significantly between Amish and non-Amish samples (H = -3.89, p = 0.002). Beta-diversity which accounted for relative taxon abundance and presence, as well as other metadata such as fluoride use, frequency of dental visits, and teeth brushing indicated, for both saliva and plaque, samples clustered by grouping and their covariates. The five primary phyla typically associated with the oral microbiome were the dominant phyla in both Amish and non-Amish individuals, although Proteobacteria were proportionally fewer in Amish samples. We conclude the oral microbiome between the Old Order Amish and rural non-Amish are distinctly different, which may reflect observed differences in lifestyle and oral health habits.},
}

Humans
*Microbiota/genetics
*Mouth/microbiology
RNA, Ribosomal, 16S/genetics
Saliva/microbiology
*Amish
Female
Male
Oral Health
Adult
Middle Aged
Dental Plaque/microbiology
Bacteria/genetics/classification

@article {pmid42341424,
year = {2026},
author = {Tsuboi, I and Inoue, S and Hirayama, T and Mitsui, Y and Watanabe, M and Hirakawa, H and Sadahira, T},
title = {Gut, vaginal, and urinary microbiome alterations in women with genitourinary syndrome of menopause: A systematic review.},
journal = {Maturitas},
volume = {211},
number = {},
pages = {109031},
doi = {10.1016/j.maturitas.2026.109031},
pmid = {42341424},
issn = {1873-4111},
abstract = {BACKGROUND AND OBJECTIVE: Genitourinary syndrome of menopause (GSM) is a chronic condition caused by estrogen deficiency, encompassing vaginal dryness, dyspareunia, and urinary symptoms. Alterations in the vaginal, urinary, and gut microbiome may contribute to GSM pathophysiology. We synthesize the evidence on microbiome composition and diversity across these compartments in postmenopausal women with GSM.

METHODS: PubMed, Scopus, and Embase were searched from inception to April 2026 for studies assessing the microbiome in postmenopausal women with GSM using 16S rRNA gene sequencing, metagenomics, or culture-based methods.

RESULTS: Twenty-three studies (5027 participants) were included: 15 examined the vaginal microbiome, seven the urinary microbiome, and one the gut microbiome. Postmenopausal women consistently showed reduced Lactobacillus abundance and increased microbial diversity. Estrogen therapy partially restored Lactobacillus dominance but did not uniformly improve symptoms. In the SWAN cohort (n = 1320), sexual pain was the only GSM symptom independently associated with a specific community state type (CST IV-C1; OR 2.26, 95% CI 1.20-4.23). Specific species showed associations with distinct symptom domains: Prevotella with urinary symptoms, Finegoldia magna with recurrent urinary tract infection, and Streptococcus with sexual pain. Parallel Lactobacillus depletion and pathobiont enrichment across all three compartments pointed toward a vaginal-bladder-gut axis, potentially linked through estrobolome disruption and bacterial translocation.

CONCLUSION: The postmenopausal genitourinary microbiome is characterized by Lactobacillus depletion and increased diversity, but microbiome restoration alone does not predict symptom resolution. The shared microbial alterations across compartments suggest a vaginal-bladder-gut axis that may collectively drive GSM, but this requires multi-compartment longitudinal validation. PROSPERO registration: CRD420261335478.},
}

@article {pmid42341476,
year = {2026},
author = {Yang, Y and Gao, F and Jia, X and Jin, D and Haddi, K and Li, Z and Zhao, Z},
title = {Gut-microbiota reshaping by environmental oxytetracycline residues threatens life-history traits in a polyphagous fruit fly.},
journal = {Journal of hazardous materials},
volume = {514},
number = {},
pages = {142788},
doi = {10.1016/j.jhazmat.2026.142788},
pmid = {42341476},
issn = {1873-3336},
abstract = {The persistence and overuse of oxytetracycline (OTC) have been associated with environmental contamination, ecological toxicity, and the emergence of antimicrobial resistance. Beyond its direct antimicrobial activity, environmental residues of OTC may disrupt non-target organisms by affecting life-history traits. In this study, the oriental fruit fly (Bactrocera dorsalis) was chronically exposed to OTC to assess gut microbiota shifts and associated life-history responses. Our results demonstrated that environmental OTC residues prolonged larval development, reduced pupal weight, and suppressed ovarian maturation in B. dorsalis. Microbiome analysis revealed that OTC exposure decreased beneficial bacteria while increasing opportunistic taxa, with multiple opportunistic taxa enriched under OTC exposure. Such OTC-induced microbial compositional changes might be associated with reduced availability of specific amino acids, which may contribute to cascading effects on pupal mass and ovarian development. Importantly, both lactic acid bacteria (Lactiplantibacillus plantarum and Levilactobacillus brevis) replenishment and amino acids (leucine, isoleucine, and glutamic acid) supplementation significantly alleviated OTC-induced impairments. Overall, our findings demonstrate that residual OTC exposure reshapes gut microbiota composition and metabolic function. Finally, we propose a conceptual framework illustrating how OTC-driven microbiota reorganization may be associated with cross-kingdom effects on insect life-history traits, providing insight into the ecological risks of environmental antibiotic residues.},
}

@article {pmid42341715,
year = {2026},
author = {Zhang, Z and Geng, C and Ho, SXY and Lu, Y and Liu, SQ},
title = {Medicinal plants fermentation: current knowledge and perspectives.},
journal = {Current opinion in biotechnology},
volume = {100},
number = {},
pages = {103544},
doi = {10.1016/j.copbio.2026.103544},
pmid = {42341715},
issn = {1879-0429},
abstract = {Fermentation improves medicinal plants in functional foods, nutraceuticals, and phytomedicine. Many plants have bioactive compounds trapped in complex matrices, limited by low bioavailability, toxins, anti-nutritional compounds, bitterness, astringency, and/or off-flavors. Recent studies show fermentation enhances plant value through bioactivity modulation, detoxification, safety, and sensory optimization. Effects are achieved via the release of bound phytochemicals, polyphenol transformation, new metabolites, reduction of toxins, microbe control, and reshaping of aroma and taste. Emerging systems like moringa, noni, and chaga show microbial biotransformation that addresses substrate challenges and supports product development. However, raw material variability, inconsistent protocols, unclear mechanisms, and limited validation restrict progress. Future studies should emphasize standardized systems, multi-omics-based mechanism analysis, host and microbiome evaluation, precision fermentation, and product design with regulatory considerations. Overall, fermentation provides a promising framework for functional products with improved bioactivity, safety, sensory quality, and translational potential.},
}

@article {pmid42341762,
year = {2026},
author = {Pekel, S and Karcher, N and Essex, M and Springer, F and Romano, S and Ducarmon, QR and Schudoma, C and Larralde, M and Lupatin, A and Zeissig, S and Zimmermann, M and Zeller, G},
title = {Meta-analysis reveals microbiome signatures for colorectal cancer that are universal across age groups and sequencing methods.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.030},
pmid = {42341762},
issn = {1934-6069},
abstract = {Numerous studies have linked gut microbiome alterations to colorectal cancer (CRC), but limited sample sizes and study heterogeneity have hampered cross-study comparisons and subgroup analyses. Here, we present a comprehensive single-disease gut microbiome meta-analysis based on consistently re-computed and re-analyzed shotgun and amplicon sequencing profiles (n = 6,779 samples, 27 studies). Association and machine-learning analyses delineate CRC microbiome signatures, which are robustly generalizable across studies and sequencing approaches and nearly identical between early- and late-onset cases. Meta-analysis of the tumor-resident microbiome reveals characteristic tumor-enriched microbes in concordance with fecal signatures that are clearly detectable in early-stage tumors, although their detection in feces becomes moderately higher in late-stage and distal tumors, possibly due to dilution effects in stool. The unified fecal CRC signature inversely associates with dietary fiber intake and is modifiable by dietary interventions. Finally, genome-resolved functional analysis reveals variation in virulence factor carriage and geographic enrichment across Fusobacterium subspecies.},
}

@article {pmid42341885,
year = {2026},
author = {Abuqwider, J and Pasolli, E and Scidà, G and Corrado, A and Vitale, M and Giosuè, A and Filippis, F and Ercolini, D and Annuzzi, G and Rivellese, AA and Bozzetto, L},
title = {Ultra-processed food intake and its associations with atherogenic dyslipidemia, glycemic control, and gut microbiome features in adults with type 1 diabetes from Southern Italy.},
journal = {Diabetes research and clinical practice},
volume = {},
number = {},
pages = {113373},
doi = {10.1016/j.diabres.2026.113373},
pmid = {42341885},
issn = {1872-8227},
abstract = {AIMS: To examine the associations between ultra-processed food (UPF) intake, glycemic control, cardiovascular risk factors, and gut microbiome in adults with type 1 diabetes (T1D).

METHODS: In 253 adults with T1D, diet was assessed using the EPIC food-frequency questionnaire, and UPFs classified according to NOVA. Evaluations included lipid profile, HbA1c, and continuous glucose monitoring metrics. In a subgroup (n = 103), gut microbiota composition/function was analyzed using shotgun metagenomic sequencing and beta-diversity assessed by PERMANOVA. Associations were examined using multivariable regression models adjusted for age and Mediterranean diet adherence.

RESULTS: Mean UPF intake was 15.5 % of total food intake. Higher UPF intake was independently associated with higher triglycerides (β per 20 g/1000 kcal = 3.62 mg/dL; 95 %CI 1.16-6.08) and lower HDL-cholesterol (β =  - 0.98 mg/dL; 95 %CI - 1.72 to - 0.24). Sugar/artificially sweetened beverages were positively associated with triglycerides and animal-based UPFs inversely associated with HDL cholesterol. In participants on multiple daily injections or open-loop systems, ready-to-eat mixed dishes were positively associated with HbA1c. Microbiome beta-diversity significantly differed according to UPF intake. Triglycerides positively associated with microbial pathways (ketogluconate, tetrapyrrole, and acetate metabolism).

CONCLUSION: Higher UPF intake was associated with atherogenic dyslipidemia, poorer glycemic control in selected groups, and gut microbiome alterations in adults with T1D. The study was registered at ClinicalTrials.gov with the identifier NCT05936242.},
}

@article {pmid42341992,
year = {2026},
author = {Subramaniyan, B and Lu, F and Li, H and Paiboonrungruang, C and Li, Y and Xiong, Z and Zhang, GF and Chen, X},
title = {Precision metabolic therapy for propionic acidemia.},
journal = {Biochemical pharmacology},
volume = {251},
number = {Pt 2},
pages = {118187},
doi = {10.1016/j.bcp.2026.118187},
pmid = {42341992},
issn = {1873-2968},
abstract = {Propionic acidemia (PA) is a rare autosomal recessive metabolic disorder caused by a deficiency of mitochondrial propionyl-CoA carboxylase, leading to the accumulation of propionyl-CoA and toxic metabolites that disrupt TCA cycle flux and ammonia detoxification. Propionyl-CoA is generated from gut microbiome-derived propionate, propiogenic amino acids, odd-chain fatty acids, and cholesterol side chains. Its accumulation produces downstream metabolites such as propionylcarnitine and methylcitrate and promotes histone propionylation. These alterations collectively contribute to mitochondrial dysfunction, oxidative stress, and multi-organ pathology. Current clinical management focuses on reducing propionyl-CoA burden through dietary restriction and supportive therapies, but long-term outcomes remain suboptimal due to poor tolerability and progressive complications. Although liver transplantation improves hepatic metabolism, it does not fully correct extrahepatic disease. Gene-based approaches, including mRNA-based enzyme replacement and viral vector-mediated gene delivery, show promise but face challenges related to delivery efficiency, durability of expression, and immune responses. Emerging small-molecule strategies aim to reprogram metabolism by restoring the balance between propionyl-CoA and acetyl-CoA while replenishing cellular CoA pools. Precision metabolic therapy may combine acetate supplementation and NRF2 activation to enhance acetyl-CoA production and mitochondrial resilience, while suppressing propionyl-CoA formation through ACSS3 inhibition and propiogenic amino acid restriction. In parallel, CoA availability may be increased through activation of PANK1-3, inhibition of PANK4, and supplementation with CoA precursor compounds. We propose that rational combination therapy targeting multiple nodes of short-chain fatty-acid metabolism and CoA homeostasis will provide a more effective strategy than single-agent approaches for correcting metabolic imbalance in PA.},
}

@article {pmid42342136,
year = {2026},
author = {Sınır, B and Ortan, P and Sayin, SS and Uzel, A},
title = {Relationship Between Changes in Intestinal Desulfovibrio Levels and Oxygen Desaturation in Patients With Obstructive Sleep Apnea Syndrome.},
journal = {Respiratory medicine},
volume = {},
number = {},
pages = {108986},
doi = {10.1016/j.rmed.2026.108986},
pmid = {42342136},
issn = {1532-3064},
abstract = {PURPOSE: Obstructive sleep apnea syndrome (OSAS) causes intermittent hypoxia and sleep fragmentation, which may alter gut microbiota composition. We primarily aimed to compare intestinal Desulfovibrio detection/abundance between patients with moderate-to-severe OSAS and healthy controls. Secondarily, we evaluated the association between Desulfovibrio and polysomnographic oxygen desaturation parameters, including ODI and minimum SpO2.

METHODS: In this prospective cross-sectional study, 30 patients with moderate or severe OSAS and 20 healthy volunteers were included. All participants followed a balanced diet for 15 days before overnight polysomnography and fecal sampling. Fecal samples collected the morning after polysomnography were stored at -80 °C and analyzed by quantitative real-time PCR. Between-group comparisons and associations with polysomnographic parameters were evaluated.

RESULTS: Desulfovibrio was detected in 11 of 50 participants (6 patients, 5 controls). Although bacterial concentration was numerically higher in the OSAS group, the difference was not statistically significant. No significant differences in demographic characteristics or sleep parameters were observed according to Desulfovibrio presence. Among patients with OSAS, Desulfovibrio was not significantly associated with apnea-hypopnea index or oxygen desaturation-related parameters.

CONCLUSION: This is, to our knowledge, the first human study to examine whether intestinal Desulfovibrio colonization is increased in OSAS and related to intermittent hypoxia. In this cohort, Desulfovibrio colonization did not differ significantly between OSAS and control groups and was not associated with polysomnographic desaturation indices. Larger, adequately powered studies with broader microbiome profiling are needed.},
}

@article {pmid42342142,
year = {2026},
author = {Kolovou, M and Bachtsevani, E and Bekris, F and Pedrinho, A and Omirou, M and Nicol, GW and Hazard, C and Papadopoulou, ES and Karpouzas, DG},
title = {Using species sensitivity distributions to assess the toxicity of pesticides on nitrifiers and broader microbial groups: from single-species tests to soil amplicon sequencing.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128640},
doi = {10.1016/j.envpol.2026.128640},
pmid = {42342142},
issn = {1873-6424},
abstract = {Soil microorganisms are essential for ecosystem functioning, yet their responses to pesticides are inadequately captured by conventional ecotoxicological tests. Recent studies identify ammonia-oxidizing microorganisms (AOM) as soil microbial indicators of chemical stress. Building on previous single-species tests with AOM, we investigated the effects of pyraclostrobin, glyphosate and metsulfuron-methyl on nitrification. The more consistent impact of metsulfuron-methyl led us to focus on its effects on the abundance and diversity of AOM and broader microbial groups. An integrated approach combining amplicon sequencing with species sensitivity distributions (SSDs) was applied to derive thresholds relevant for risk assessment. Metsulfuron-methyl showed negative effects on AOM and prokaryotes, while fungi were more tolerant. SSDs based on single-species AOM data and soil microcosm amplicon sequencing yielded hazard concentration 5% (HC5) values of 0.001 and 0.06 mg kg[-1], respectively, verifying the conservative nature of the former. SSDs constructed from amplicon sequencing provided HC5 values of 0.042 and 0.1 mg kg[-1] for prokaryotes and fungi, respectively. Calculated predicted no-effect concentrations (PNEC) suggested a potential risk only for AOM when based on single-species data, whereas no risk was indicated using soil-derived data. These findings support the complementary use of SSDs derived from single-species and soil-based approaches in pesticide risk assessment for soil microbes.},
}

@article {pmid42342144,
year = {2026},
author = {Cheng, D and Shen, G and Pathiranage, JC and Zhao, Y and Xie, J and Wang, Q and Ferreira, CR and Zheng, Q and Yuan, C and Wang, W},
title = {Perfluorooctanoic Acid Exposure Disrupts Gut Microbiota and Aggravates Experimental Colitis.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128646},
doi = {10.1016/j.envpol.2026.128646},
pmid = {42342144},
issn = {1873-6424},
abstract = {Perfluorooctanoic acid (PFOA), a prevalent and environmentally persistent compounds in the per- and polyfluoroalkyl substance (PFAS) family, is ubiquitously detected in the food chain and has been epidemiologically linked to inflammatory bowel disease (IBD). However, the actions and mechanisms by which PFOA exposure influences colonic inflammation under colitis conditions remain incompletely understood. In this study, we investigated the impact of dietary PFOA exposure on colitis severity using a dextran sulfate sodium (DSS)-induced colitis model. Our results suggest that dietary PFOA exposure exacerbated colitis severity, as reflected by increased loss in body weight, colon shortening, and histopathological damage. Notably, PFOA exposure promoted colonic neutrophil infiltration and activation, characterized by increased expression of neutrophil markers, upregulation of neutrophil-recruiting chemokines, and enhanced expression of oxidative enzymes. PFOA also led to goblet cell depletion and reduced E-cadherin expression in colitis mice, indicating compromised integrity of epithelial barrier. Furthermore, fecal microbiome and metabolomic analyses revealed that PFOA exposure altered gut microbial composition and fecal metabolic profiles, which could be associated with the enhanced inflammatory outcomes observed during acute colitis. Collectively, these findings indicate that dietary PFOA exposure aggravates experimental colitis through coordinated neutrophil-mediated inflammation, epithelial barrier disruption, and microbiome-associated alterations. Our results highlight the potential role of PFOA as an environmental exacerbator of IBD and provide mechanistic insight into how its exposure influences host-microbiome interactions.},
}

@article {pmid42342152,
year = {2026},
author = {Gray, SM and Wood, MC and Mulkeen, SC and Ahmed, S and Thaker, SD and Chen, B and Sander, WR and Bibeva, V and Zhang, X and Yang, J and Herzog, JW and Moss, AD and Zhang, S and Dogan, B and Simpson, KW and Sartor, RB and Montrose, DC},
title = {Dietary protein source mediates colitis pathogenesis through bacterial modulation of bile acids.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101825},
doi = {10.1016/j.jcmgh.2026.101825},
pmid = {42342152},
issn = {2352-345X},
abstract = {BACKGROUND AND AIMS: Evidence-based dietary recommendations for individuals with inflammatory bowel diseases (IBD) are limited. Red meat consumption is associated with increased IBD incidence and relapse in patients, suggesting that switching to a plant-based diet may limit gut inflammation. However, the components and mechanisms underlying the differential effects of these diets remain poorly understood. This study investigated the differential impact of dietary protein source on experimental colitis and related mechanisms.

METHODS: Isocaloric synthetic diets containing protein isolates from beef (BP), egg whites (EP), casein (CP), soy (SP) or pea (PP) were tested in acute (dextran sodium sulfate-induced) and chronic (Il10-deficient) murine colitis models. Gut resident microbes were quantified with 16S-sequencing and their role evaluated by antibiotic depletion, germ-free, selectively colonized gnotobiotic, and fecal microbiota transplant mouse studies.

RESULTS: Mice fed a BP diet exhibited the most severe colitis, while mice fed PP developed mild inflammation. The colitis-promoting effects of BP were microbially-mediated. In the absence of colitis, BP-feeding reduced abundance of Lactobacillus johnsonii and Turicibacter sanguinis and expanded Akkermansia muciniphila, which localized to the mucus in association with decreased mucus thickness and quality. BP-fed mice had elevated primary and conjugated fecal bile acids (BAs), and taurocholic acid administration to PP-fed mice worsened colitis. Dietary psyllium protected against BP-mediated inflammation, restored BA-modulating commensals and normalized BA ratios.

CONCLUSIONS: These data suggest that the protein component of red meat may be responsible, in part, for the colitis-promoting effects of this food source and provide insight into dietary factors that may influence IBD severity.},
}

@article {pmid42342198,
year = {2026},
author = {Gonzalez, JAC and Brant, CF and Pigossi, SC and Wiegand, A and Sabino-Silva, R and Massignan, C and Zanatta, RF},
title = {Is Erosive Tooth Wear a Truly Non-Bacterial Condition? A Scoping Review.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {106859},
doi = {10.1016/j.jdent.2026.106859},
pmid = {42342198},
issn = {1879-176X},
abstract = {OBJECTIVE: This scoping review examined the current knowledge on oral biofilm ecology and erosion-associated dysbiosis, proposing pathways by which the oral microbiome may contribute to erosive tooth wear (ETW).

DATA: The PRISMA-ScR guidelines were followed (OSF platform, doi: 10.17605/OSF.IO/KM4JQ). Primary research articles (in vitro, in situ, or clinical trials) that investigated ETW associated with oral biofilm ecology, erosion-associated dysbiosis, or microbiome pathways were included.

SOURCES: A systematic search of PubMed/MEDLINE, Scopus, Web of Science, Embase, and the Cochrane Library was conducted up to April 2026 using predefined terms.

STUDY SELECTION: A total of 2355 records were identified. After screening, 16 full texts were eligible, and 7 studies were included for data extraction. The included studies were highly heterogeneous in design [including observational (3), randomized (1), and in situ/ex vivo (3) models], outcomes, and biological targets. Two studies evaluated the biofilm´s protective effect against erosive challenge, showing reduced enamel erosion but limited protection of dentin. Two studies assessed bioactive compounds' influence on microbiome, demonstrating reduced bacterial adhesion, altered pellicle structure, and improved erosion protection. Three studies investigated microbial ecology directly with inconsistent findings: one found no significant differences in microbial counts, another reported similar alpha- and beta-diversity but taxon-level differences, and a third showed lower microbial diversity, proteolytic protein degradation, altered gene expression, and metabolic profiles compatible with acid-adapted and proteolytic communities.

CONCLUSIONS: The findings suggest that the oral microbiome may act as an ecological modifier of ETW by influencing biofilm organization, and local metabolic behavior, but current evidence is insufficient to determine whether ETW is truly a non-bacterial condition.

CLINICAL SIGNIFICANCE: The oral microbiome can influence erosive tooth wear, which impacts risk assessment and prevention strategies.},
}

@article {pmid42342479,
year = {2026},
author = {Bergers, MD and Goté, TA and Armstrong, Z},
title = {The role of glycan modifications in health and disease.},
journal = {Trends in biochemical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibs.2026.05.013},
pmid = {42342479},
issn = {0968-0004},
abstract = {Glycans are polymeric carbohydrate chains that often decorate proteins and lipids present on cell surfaces and in the extracellular space, thereby influencing cell interactions, immune responses, and host-microbiome relationships. Glycans are highly dynamic and can undergo a plethora of post-synthetic modifications, including O-acetylation, sulfation, and sulfamation. In this review, we examine how these glycan modifications are established and how they influence human health, from cell signaling to host-pathogen dynamics. We propose terming these glycan modifications, which give rise to a greater diversity of glycans, collectively as the epiglycome. Despite their biological importance, glycan modifications are considerably less well studied than the underlying glycans and proteins. However, advances in chemical and biochemical tools are enabling greater insights into their roles and translational potential.},
}

@article {pmid42342541,
year = {2026},
author = {Slater, E and Yang, WJ and Skoufou-Papoutsaki, N and Renshaw, SA and Owens, RM and Zilbauer, M},
title = {Transcriptomic and functional profiling of human intestinal organoids identifies enhanced calcium signalling and thrombospondin-2 activity in cystic fibrosis.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.06.007},
pmid = {42342541},
issn = {1873-5010},
abstract = {BACKGROUND: Although gastrointestinal symptoms of cystic fibrosis (CF) have long been overlooked, patients with CF have an unexplained 5-fold increased risk of colorectal cancer. Much of our understanding of the disease has relied on two-dimensional cell lines and animal models. However, the primary changes occurring in human CF epithelial cells remain largely unclear.

METHODS: Donor-matched wild-type (WT) and CFTR knockout (KO) human intestinal organoid (HIO) lines were employed to dissect epithelial cell-intrinsic responses to CFTR dysfunction. Knockout was confirmed at the molecular level by qPCR and immunostaining, and functionally by the forskolin-induced swelling assay. Bulk RNA sequencing was then performed to assess key transcriptional differences between WT and KO organoids under steady state conditions and after IFNγ stimulation, and to evaluate the therapeutic potential of calcium channel blockade. Relevant changes were functionally validated using organoid-derived monolayers.

RESULTS: Loss of CFTR expression alone was sufficient to induce profound changes in gene expression across all conditions. Notably, CFTR KO organoids showed higher baseline MUC2 expression and increased THBS2 in an inflamed context. Calcium channel blockade with verapamil reversed these disease-associated changes at the RNA and protein levels.

CONCLUSIONS: By utilising gene-edited HIOs derived from the same donor, we reveal epithelial cell-intrinsic mechanisms downstream of CFTR loss. These findings, enabled by our experimental approach, offer important insights into the role of the intestinal epithelium in CF, independent of immune cells, the microbiome, and inflammation. They also lend support for therapeutic targeting of calcium signalling to reverse disease-associated transcriptomic changes.},
}

@article {pmid42342711,
year = {2026},
author = {Mou, E and Guo, R and Yi, Y and Li, Y and Yao, Y and Xu, J},
title = {Beyond estrobolome 1.0: unraveling endocrine-microbiome axis as a driver and therapeutic target in hormone-driven cancers.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01074-9},
pmid = {42342711},
issn = {2055-5008},
abstract = {The endocrine-microbiome axis extends the estrobolome concept, recognizing gut microbes as active endocrine partners. Bacteria modulate estrogen recycling via diverse enzymes and produce SERM-like metabolites, while host hormones shape microbial communities. This bidirectional crosstalk influences hormone-driven carcinogenesis through inflammation, genomic instability, and epigenetic changes. Therapeutic opportunities include precision probiotics and selective enzymatic inhibition. Advancing the field requires causal models, multi-omics integration, and sex as a biological variable.},
}

@article {pmid42342913,
year = {2026},
author = {Ahmad, S and Wu, T and Arnold, M and Hankemeier, T and Ghanbari, M and Roshchupkin, G and Uitterlinden, AG and Borkowski, K and Neitzel, J and Kraaij, R and , and van Duijn, CM and Ikram, MA and Kaddurah-Daouk, R and Kastenmüller, G},
title = {The blood metabolome of brain health in midlife and influences of genes, microbiome and exposome.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {42342913},
issn = {2662-8465},
support = {U19AG063744//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; RF1AG058942//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; RF1AG059093//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U01AG061359//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; RF1AG057452//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG063744//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; RF1AG058942//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG063744//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; RF1AG058942//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01AG059093//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; RF1AG057452//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; R01AG046171//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; RF1AG051550//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U01AG061359//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; 536691227//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; #733050814//ZonMw (Netherlands Organisation for Health Research and Development)/ ; },
abstract = {Metabolic alterations are increasingly implicated in neurological disorders, including Alzheimer's disease (AD), highlighting the relevance of the peripheral metabolome, shaped by genetic and environmental exposures, for brain health. We examined the relation of 991 blood metabolites with cognition and magnetic resonance imaging (MRI) measures cross-sectionally in 1,082 dementia-free middle-aged participants of the population-based Rotterdam Study and quantified contributions of genetic variation, lifestyle, comorbidities, medication and gut microbiota to metabolite variance. Cognition-associated metabolites were replicated in two independent cohorts of older adults and tested for associations with incident AD longitudinally in one cohort. Twenty-two metabolites were associated with MRI measures. Fourteen metabolites showed replicated associations with cognition, with ergothioneine exhibiting the largest effect. The metabolite signature of cognition mirrored that of incident AD. Lifestyle, clinical variables and medication were the strongest determinants of cognition-associated and MRI-associated metabolites, explaining up to 28.6% of their variance. Antacid use was associated with worse cognition and lower ergothioneine levels, which mediated 31.5% of the negative medication effect, suggesting implications for AD prevention.},
}

@article {pmid42342926,
year = {2026},
author = {Sharma, A},
title = {Voices of microbiome researchers in an artificial intelligence era.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41564-026-02359-7},
pmid = {42342926},
issn = {2058-5276},
}