@article {pmid41777393,
year = {2026},
author = {Zhang, B and Liu, Y and Zhou, D and Lv, Y and Cao, M and Li, H and Yang, Z and Liu, Z and Yin, H and Wang, X and Huang, Z and Meng, D},
title = {The role of quorum sensing in rhizosphere community regulation during bacterial wilt pathogen invasion.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1685007},
pmid = {41777393},
issn = {1664-462X},
abstract = {Bacterial wilt, caused by the soil-borne pathogen Ralstonia solanacearum is a major threat to solanaceous crops worldwide. The onset of this disease is frequently associated with disruptions in the rhizosphere microbial community. Quorum sensing (QS), a key mechanism for microbial communication, plays a critical role in regulating microbial interactions and maintaining community structure. However, whether and how QS is involved in reshaping the rhizosphere microbiome during R. Solanacearum infection remains poorly understood. In this study we compared QS-related genes, signaling pathways, and network structures in metagenomes of healthy and wilt-infected rhizospheres. The results show QS-related genes of the plant beneficial bacterial were significantly down-regulate, whereas QS-related genes of pathogenic R. Solanacearum were up-regulated in wilt-infected rhizosphere. The up-regulated QS genes of pathogens belong to eight QS signaling pathways (AI-1, GABA, PapR, NprX, Phr, cCF10, and DSF). Network analysis showed a simplified structure in the wilt-infected rhizosphere. It is also found the number of connectors in the QS gene co-occurrence network was reduced in wilt-infected rhizosphere network. This is due to the upregulation of QS system allows the pathogen to mediate the rhizosphere microbial ecology network, and leads to destabilization of rhizosphere community. These findings demonstrate that QS system contributes to bacterial wilt infection by suppressing the QS-based interactions among plant beneficial microbes, thereby triggering community function disruption.},
}

@article {pmid41777263,
year = {2026},
author = {Wang, X and He, J and Ding, G and Tang, Y and Wang, Q},
title = {Artificial Intelligence-Enabled Multi-Omics for Predicting Immune Checkpoint Inhibitor Response and Resistance.},
journal = {Journal of multidisciplinary healthcare},
volume = {19},
number = {},
pages = {572089},
pmid = {41777263},
issn = {1178-2390},
abstract = {Immune checkpoint inhibitors (ICIs) have reshaped oncology, yet overall response rates remain modest and resistance is common, driven by tumor heterogeneity and evolving tumor-immune crosstalk. Established biomarkers (PD-L1, tumor mutational burden, microsatellite instability) provide incomplete prediction. Multi-omics profiling across genomic, transcriptomic, proteomic, epigenomic, metabolomic and microbiomic layers offers a systems-level view of malignant and immune states, uncovering determinants of ICI efficacy such as lineage plasticity, stromal remodeling, immunometabolic reprogramming and microbiome-associated immune modulation. Artificial intelligence (AI) is uniquely positioned to fuse these heterogeneous data, learn non-linear cross-layer signatures, and enable interpretable predictions using approaches such as SHAP and Grad-CAM. Representative models link routine histology or imaging to molecular phenotypes, stratify patients beyond single biomarkers, and may nominate rational combinations that target oncogenic pathways, lactate-driven immune suppression, or the gut microbiome. In this narrative review, we synthesize recent AI-multi-omics advances for response modeling, immune-relevant tumor subtyping, and clinical translation, including radiomics/pathomics integration and liquid-biopsy-based monitoring, as well as emerging applications in toxicity risk prediction. We also discuss barriers to implementation-platform heterogeneity, limited prospective validation, bias, interpretability and cost-and outline future directions, including single-cell and spatial multi-omics integration, federated learning and generative modeling to improve robustness and equity of precision immunotherapy.},
}

@article {pmid41777157,
year = {2026},
author = {Popova, PV and Loboda, AA and Liaudanski, A and Sitkin, SI and Anopova, AD and Vasukova, EA and O Isakov, A and Tkachuk, AS and Nemikina, IS and Akhmatova, M and Eriskovskaya, AI and Vasilieva, EY and Galyautdinov, IV and Babenko, A and Zgairy, S and Rubin, E and Even, C and Turjeman, S and Pervunina, TM and Kostareva, AA and Vatian, AS and Mohan, V and Grineva, EN and Koren, O and Shlyakhto, EV},
title = {Maternal Gut Microbiome as a Predictor of Insulin Therapy Requirement in Gestational Diabetes.},
journal = {Journal of diabetes science and technology},
volume = {},
number = {},
pages = {19322968261426025},
doi = {10.1177/19322968261426025},
pmid = {41777157},
issn = {1932-2968},
abstract = {BACKGROUND: Gestational diabetes mellitus (GDM) often requires pharmacological intervention beyond lifestyle modification to achieve optimal glycemic control. This study aimed to develop machine learning models that integrate clinical and gut microbiome data to predict the need for insulin therapy (IT) in women with GDM.

METHODS: We characterized 205 pregnant women with GDM from the Genetic and Epigenetic Mechanisms of Developing Gestational Diabetes Mellitus and its Effects on the Fetus study, collecting clinical parameters, lifestyle questionnaires, self-monitored blood glucose records, and gut microbiome profiles based on 16S rRNA gene sequencing. Gradient-boosting models were trained to predict IT, basal insulin (BI), and prandial insulin (PI) requirements. Model discrimination was assessed using repeated stratified five-fold cross-validated area under the curve-receiver operating characteristic (AUC-ROC) (nested cross-validation). Feature importance and interpretability were evaluated with SHapley Additive exPlanations and permutation analyses. Differential microbial abundance was analyzed by ANCOM-BC2 (analysis of composition of microbiomes with bias correction, version 2), and metabolic pathways were predicted via PICRUSt2.

RESULTS: Women requiring insulin were older and had higher pre-pregnancy body mass index (BMI), fasting plasma glucose, 1-hour oral glucose tolerance test glucose, and glycated hemoglobin than diet-treated women (P < .05 for all). Adding microbiome data improved AUC-ROC for IT prediction from 0.63 (95% CI = 0.43, 0.83) to 0.70 (0.50, 0.89), BI from 0.77 (0.59, 0.95) to 0.82 (0.65, 0.99), and for PI from 0.69 (0.50, 0.88) to 0.70 (0.51, 0.89). Key influential features included glycemic markers, BMI, and microbial taxa, such as Phascolarctobacterium faecium, Alistipes ihumii, Cloacibacillus evryensis, Ruthenibacterium lactatiformans, and Methanosphaera stadtmanae, and the predicted microbial metabolic pathway PWY-5823.

CONCLUSION: Our findings demonstrate that integrating gut microbiome characteristics with clinical data improves the prediction of insulin treatment needs in GDM, particularly for BI initiation.},
}

@article {pmid41777065,
year = {2025},
author = {Zhang, Y and Zhang, T and Wang, H},
title = {[Research Progress on the Regulatory Mechanism of Respiratory Microbiota in the Comorbidity of Chronic Obstructive Pulmonary Disease and Lung Cancer].},
journal = {Zhongguo fei ai za zhi = Chinese journal of lung cancer},
volume = {28},
number = {12},
pages = {939-947},
doi = {10.3779/j.issn.1009-3419.2025.106.33},
pmid = {41777065},
issn = {1999-6187},
abstract = {Both chronic obstructive pulmonary disease (COPD) and lung carcinoma (LC) are major public health challenges in China. With the continuous advancement of microbial detection methods, the role of the respiratory microbiome in the pathogenesis and progression of respiratory diseases has become increasingly prominent. This article systematically reviews the dynamic characteristics of the respiratory microbiome during the progression of COPD and LC, then explores its crucial bridging role in COPD-LC comorbidity through mechanisms such as persistently driving chronic inflammation, mediating genomic damage, and participating in immune regulation. The aim is to deepen the understanding of the respiratory microbiome, and to provide new perspectives for optimizing existing treatment strategies, exploring microbial biomarkers for early cancer screening, and improving the clinical management of chronic respiratory diseases. .},
}

@article {pmid41777057,
year = {2026},
author = {Singh, A and Bhardwaj, A and Midha, V and Sood, A},
title = {Deciphering the diet-inflammatory bowel disease relationship: knowledge gaps and future perspectives.},
journal = {Intestinal research},
volume = {},
number = {},
pages = {},
doi = {10.5217/ir.2025.00278},
pmid = {41777057},
issn = {1598-9100},
abstract = {Diet is increasingly recognized not as a passive exposure but as a dynamic determinant of inflammatory bowel disease (IBD) pathogenesis, progression, and treatment response. This review article redefines diet as a multidimensional modifier acting through complex interactions with genetics, microbiota, intestinal barrier function, and environmental exposures. Beyond nutrient composition, we highlight how age, sex, habitual diet, cooking methods, contaminants, and lifestyle collectively shape disease trajectories. We also identify key research priorities: incorporation of long-term, mechanistically anchored trials; development of digital, biomarker-informed dietary assessment tools; and integration of polygenic, microbial, and metabolic data to inform individualized therapy. Emerging evidence also calls for culturally tailored and patient-centered frameworks that ensure real-world adherence and equity in dietary interventions. Reframing diet as a biological, behavioral, and environmental nexus shifts it from the periphery to the forefront of IBD care, transforming it from a confounder in research to a therapeutic frontier in clinical practice.},
}

@article {pmid41776947,
year = {2026},
author = {Mitchell, A and Hayes, C and Hudson, CJ and Connell, SD and Harvey, BP and Agostini, S and Jolly, J and Ravasi, T and Booth, DJ and Nagelkerken, I},
title = {Marine Heatwaves, Ocean Warming and Acidification Reshape Reef Fish Gut Microbiomes.},
journal = {Molecular ecology},
volume = {35},
number = {5},
pages = {e70275},
doi = {10.1111/mec.70275},
pmid = {41776947},
issn = {1365-294X},
support = {DP230101932//Australian Research Council/ ; JPJSCCA20210006//Japan Society for the Promotion of Science/ ; 23K26924//Japan Society for the Promotion of Science/ ; },
abstract = {Extreme climatic events and gradual climate change are increasingly anticipated to interact and reshape ecological communities. However, the combined effects of ocean warming, acidification and marine heatwaves on host-associated microbial communities and their potential role in host adaptation remain poorly understood. Here, we assessed shifts in gut microbiome communities and their associations with physiological performance in one tropical (Abudefduf vaigiensis) and one subtropical (Microcanthus strigatus) reef fish species, across three temperate reefs representing natural analogues of climate change: a present-day baseline ('cool reef'), a chronically warmed reef ('warm reef') and a reef experiencing combined warming and extreme acidification ('extreme reef'). We also examined gut microbiome changes in A. vaigiensis before and during a severe marine heatwave. A. vaigiensis had lower gut microbiome evenness and diversity at the warm (43% and 44% decrease, respectively) and extreme (38% and 31% decrease) reefs compared to the cool reef, and its gut microbiome community shifted at the extreme reef with a 122% increase in abundance of opportunistic bacteria Vibrio. A. vaigiensis also had lower gut microbiome richness at the warm (42% decrease) and extreme (52% decrease) reefs during the heatwave compared to pre-heatwave individuals. In contrast, M. strigatus showed higher microbiome evenness (99% increase) and diversity (98% increase) at the warm reef compared to the cool reef; however, these gains were lost at the extreme reef, with microbiome diversity and evenness returning to cool reef levels. Microbiome changes in both species were generally not associated with their physiological performance (protein content, oxidative stress, antioxidant capacity or body condition). Our findings suggest that marine heatwaves, ocean warming and acidification can reshape reef fish gut microbiomes, driving simplification in Abudefduf vaigiensis but distinct restructuring in Microcanthus strigatus. We conclude that climate-driven microbiome reshuffling may alter host-microbiome relationships and functions in fishes in a future ocean.},
}

@article {pmid41776819,
year = {2026},
author = {Holstein, T and Verschaffelt, P and Van Den Bossche, T and Van de Vyver, S and Martens, L and Mesuere, B and Muth, T},
title = {The Peptonizer2000: Bringing Confidence to Metaproteomics.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.5c00567},
pmid = {41776819},
issn = {1535-3907},
abstract = {Metaproteomics, the large-scale study of proteins from microbial communities, faces challenges in identifying species due to similarities in protein sequences across different organisms. Current methods often rely on simple counting of matches between proteins and taxa, which can lead to low accuracy. We introduce the Peptonizer2000, a new tool that uses advanced modeling to provide more precise taxonomic identifications along with confidence scores. It combines peptide scores from any proteomic search engine with peptide-to-taxon links from the Unipept database. By applying statistical models, the Peptonizer2000 improves taxonomic resolution and delivers more reliable results. We validate its performance using publicly available data sets, demonstrating its ability to produce high-confidence identifications. Our results suggest that the Peptonizer2000 improves the specificity and confidence of taxonomic assignments in metaproteomics, providing a valuable resource for the study of complex microbial communities.},
}

@article {pmid41776759,
year = {2025},
author = {Fernhout, L and Lambrechts, H and van Zyl, JHC},
title = {Ovine balanoposthitis: observations on the microbiome and immunoglobulin response.},
journal = {Journal of the South African Veterinary Association},
volume = {96},
number = {2},
pages = {73},
doi = {10.36303/JSAVA.679},
pmid = {41776759},
issn = {2224-9435},
abstract = {The incidence of ulcerative balanoposthitis (UB) in rams contributes to significant economic losses in the national sheep population. Understanding the immune response in the reproductive tract can aid in developing preventive measures. This study aimed to characterise the immunoglobulin profiles and microbial diversity in the reproductive tract of rams affected by UB, providing insight into the immune responses to this disease. Serum and glans tissue samples from healthy and UB-affected rams were analysed using an ELISA approach to quantify IgG, IgA, and IgM levels. The microbial diversity in nasal, penile swabs, and smegma samples was assessed using an ARISA approach. Significant differences (p ≤ 0.001) were observed between the systemic and localised immune responses. UB-affected rams exhibited higher IgG and IgM levels but lower IgA levels in both serum and glans tissue compared to healthy rams. The study confirmed UB-induced shifts in the microbiome, with significant differences in microbial diversity indices in nasal, penile, and smegma samples. Specifically, there were changes in the nasal fungi Shannon (p = 0.047) and Simpson (p = 0.038) indices, the penile Shannon (p = 0.015) and Simpson (p = 0.006) bacterial indices, and the smegma bacterial species number index (p = 0.042). Correlations between microbial populations and immunoglobulin profiles indicated an interactive immune response in different health statuses. This study highlights the need to understand the immune system of the lower reproductive tract and its interaction with commensal organisms to develop therapeutic immunomodulators for preventing UB in sheep.},
}

@article {pmid41776699,
year = {2026},
author = {Song, Y and Wen, S and Guan, LL},
title = {Unraveling the dynamic changes in the intestinal microbiome: impacts on pre-weaning calf health and productivity.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41776699},
issn = {1674-9782},
abstract = {The early life gut microbial colonization in pre-weaning calves plays a pivotal role in shaping their health, growth, and productivity. This review delves into the dynamic changes of intestinal microbiota during early life, emphasizing key factors such as colostrum management, feeding strategies, roughage supplementation, and microbial interventions including probiotics, prebiotics, and fecal microbiota transplantation (FMT), and non-nutritional stressors that can shape the early life microbial colonization. We highlight the microbiota's critical functions in nutrient metabolism, immune development, gut barrier integrity, and gut-brain axis regulation. Additionally, the consequences of microbial dysbiosis on calf health and its long-term effects on production performance in beef and dairy cattle are discussed. While current research has provided valuable insights, understanding causal mechanisms remains a challenge. This review aims to guide practical strategies for targeted microbial management, offering a pathway to optimize early-life interventions for improved calf health and productivity.},
}

@article {pmid41776621,
year = {2026},
author = {Yadav, B and Banerjee, G and Srivastava, A and Madan, AK and Kumar, R and Banerjee, P},
title = {Host-microbiome interplay supports heat stress resilience in zebu calves.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00539-8},
pmid = {41776621},
issn = {2524-4671},
}

@article {pmid41776571,
year = {2026},
author = {Ni, Z and Wang, G and Li, Q and Wu, X and Song, Z and Yu, H and Yu, P and Chen, Y and Li, L and Chen, H and Hou, H and Hu, Q},
title = {Sex-specific metabolic and microbial remodeling in a rotenone-induced rat model of Parkinson's disease following nicotine administration.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00865-1},
pmid = {41776571},
issn = {2042-6410},
support = {2023100CC0190//the Science and Technology Project of Beijing Life Science Academy/ ; 2024100CC0090//the Science and Technology Project of Beijing Life Science Academy/ ; 2024100CC0100//the Science and Technology Project of Beijing Life Science Academy/ ; },
abstract = {BACKGROUND: Parkinson's disease (PD) is a neurodegenerative disorder with established sex differences in incidence and progression. Epidemiological evidence suggests nicotine may confer protection against PD, but its mechanisms, particularly regarding sex-specific effects, remain unclear. This study investigated the neuroprotective mechanisms of nicotine in a rotenone-induced PD rat model, with a specific focus on evaluating sex-dependent modulation across behavioral, pathological, and gut-related outcomes.

METHODS: Male and female Sprague-Dawley rats were administered rotenone (2 mg/kg/day, s.c.) for four weeks to induce PD. Nicotine (0.5 mg/kg/day, s.c.) was administered 30 min after rotenone. Motor function was assessed using rotarod and CatWalk XT gait analysis. Neuropathology in the substantia nigra was evaluated via immunofluorescence for α-synuclein and tyrosine hydroxylase (TH). Gut pathology was analyzed through colon histopathology (H&E staining) and ELISA for IL-6 and α-synuclein. Gut microbiota composition was assessed by 16 S rDNA sequencing, and serum metabolomics was performed using UPLC-MS/MS. Data were analyzed by two-way ANOVA with Tukey's post-hoc test.

RESULTS: Nicotine significantly attenuated rotenone-induced motor impairments: males showed a superior response in balance-related parameters, while females exhibited enhanced efficacy in dynamic gait metrics. Pathologically, nicotine reduced nigral α-synuclein accumulation and TH depletion in both sexes, with males showing greater α-synuclein accumulation following rotenone exposure. Crucially, nicotine exclusively ameliorated colon histopathology, reduced plasma α-synuclein, and suppressed colon IL-6 in females, while attenuating intestinal α-synuclein accumulation in both sexes. Microbiota analysis revealed sex-divergent taxonomic shifts with nicotine treatment. Metabolomics showed significantly more extensive metabolic reprogramming in females, particularly affecting indole derivatives. Pearson correlations revealed significant sex-specific associations between altered serum indole derivatives and gut microbiota genera.

CONCLUSIONS: Nicotine exerts neuroprotection in PD through sex-dependent modulation of multiple pathological pathways, primarily involving the gut-microbiota-metabolite axis. Females benefit from enhanced gastrointestinal protection and metabolic reprogramming, while males show preferential motor balance restoration. These findings underscore the critical importance of sex-stratified therapeutic strategies for PD.},
}

@article {pmid41776310,
year = {2026},
author = {Kim, M and Wang, J and Pilley, SE and Lu, RJ and Xu, A and Kim, Y and Liu, M and Fu, X and Booth, SL and Mullen, PJ and Benayoun, BA},
title = {Estropausal gut microbiota transplant improves measures of ovarian function in adult mice.},
journal = {Nature aging},
volume = {},
number = {},
pages = {},
pmid = {41776310},
issn = {2662-8465},
support = {#00034120//Pew Charitable Trusts/ ; T32 AG052374/AG/NIA NIH HHS/United States ; No. 58-1950-7-707//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; },
abstract = {The decline in ovarian function with age affects fertility and is associated with increased risk of age-related diseases, including osteoporosis and dementia. Notably, earlier menopause is linked to shorter lifespan, yet the molecular mechanisms underlying ovarian aging remain poorly understood. Recent evidence suggests the gut microbiota may influence ovarian health. Here we show that ovarian aging is associated with distinct gut microbial profiles in female mice and that the gut microbiome can directly influence ovarian health. Using fecal microbiota transplantation from young or estropausal female mice, we demonstrate that heterochronic microbiota transfer remodels the ovarian transcriptome, reduces inflammation-related gene expression and induces transcriptional features consistent with ovarian rejuvenation. These molecular changes are accompanied by enhanced ovarian health and increased fertility. Integrating metagenomics-based causal mediation analyses with serum untargeted metabolomics, we identify candidate microbial species and metabolites that may contribute to the observed effects. Our findings reveal a direct link between the gut microbiota and ovarian health.},
}

@article {pmid41776177,
year = {2026},
author = {Liu, J and Li, J and Li, Y and Gao, Z and Wang, L and Song, Q and Ye, Y and Liang, J},
title = {Mechanism of Morchella polysaccharide in anti-fatigue: the role of the gut microbiota-metabolite axis in mice.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00763-1},
pmid = {41776177},
issn = {2396-8370},
support = {2023-ZJ-904T//Science and Technology Plan Project of Qinghai Province/ ; },
abstract = {This study aims to investigate the anti-fatigue effects of crude Morchella polysaccharide (MP) extracted from the Qinghai-Tibet Plateau region in mice, and to preliminarily explore its potential mechanisms based on the gut microbiota-metabolite axis. Chemical analysis indicates that MP exhibits typical characteristics of crude polysaccharides: it consists of multiple monosaccharides (primarily glucose at 72.33%, along with mannose, galactose, etc) and possesses a broad molecular weight distribution (dispersion index (Mw/Mn) of 30.97). To investigate its material basis, we further isolated and purified the primary water-soluble neutral fraction MP1-1. Structural characterization confirmed MP1-1 as a homogeneous glucan composed solely of glucose units, with a backbone linked via →4)-α-D-Glcp-(1 → 4)-type bonds. A negative control group (NC), a positive control group (PC, Rhodiola glycoside,100 mg/kg), and low-, medium-, and high-dose MP groups (50, 100, 200 mg/kg) were established, with continuous gavage for four weeks. Following the final gavage, a weight-bearing swimming test was conducted to record the time to exhaustion and establish a fatigue model. Subsequently, fatigue-related biochemical indicators, gut microbiota composition, and metabolite changes were assessed. The results indicate that MP intervention is significantly associated with an anti-fatigue phenotype. This may occur through regulating the gut microbiota by enriching beneficial bacteria (such as Lactobacillus and Bifidobacterium) and suppressing harmful bacteria (such as Desulfovibrio and Helicobacter), thereby reshaping the intestinal microbiome. These alterations were associated with changes in the host's metabolic profile, particularly the upregulation of energy metabolism pathways (e.g., β-alanine metabolism, pentose phosphate pathway, glycerolipid metabolism) and the disruption of inflammation- and oxidative stress-related metabolic pathways. Ultimately, the MP intervention group exhibited increased glycogen reserves, enhanced antioxidant capacity (elevated SOD and GSH-Px; reduced MDA), and reduced systemic inflammation (decreased IL-6 and TNF-α; increased IL-10). Collectively, these effects delayed fatigue onset, promoted recovery, and significantly prolonged swimming duration. In summary, this study suggests that the polysaccharide extract from Morchella elata, native to the Qinghai-Tibet Plateau, may exert anti-fatigue effects by regulating the "gut microbiota-metabolite-host physiological phenotype" network, providing preliminary experimental evidence for its application in the functional food sector.},
}

@article {pmid41776098,
year = {2026},
author = {Xiang, X and Zhu, J and Jiang, J and Ding, P and Zhu, Y and Cheng, K and Ming, Y},
title = {Unique gut microbiota and metabolomic profiling as biomarker of post-transplant recovery in acute-on-chronic liver failure after liver transplantation.},
journal = {Applied microbiology and biotechnology},
volume = {110},
number = {1},
pages = {},
pmid = {41776098},
issn = {1432-0614},
support = {81771722 and 82570782//National Natural Science Foundation of China/ ; },
abstract = {Acute-on-chronic liver failure (ACLF) is a severe condition arising from chronic liver disease, characterized by acute decompensation, organ failure, and high short-term mortality. Poor outcomes have also been observed in patients with ACLF after liver transplantation (LT). Emerging evidence, including a study from our center, suggests that gut microbiota plays an important role in ACLF. Patients who underwent LT at our center between October 2022 and June 2024 were included. Fecal samples were collected within 1 month post-LT for 16S rRNA and untargeted metabolomic sequencing. In this study, 144 samples from 69 patients with ACLF, cirrhosis, or hepatocellular carcinoma (HCC) were analyzed. Distinct microbiota and metabolic profiles were observed among the groups. ACLF patients exhibited significantly altered beta diversity, with notable depletion of g__Anaerostipes. Metabolomic analysis revealed substantial differences, including enrichment of tangeritin and depletion of candesartan in the ACLF group. Network analysis identified g__Anaerostipes as a key node linking differential taxa and metabolites. A random forest model based on these features effectively distinguished patient groups, with the highest classification accuracy observed in HCC. Multi-omic signatures were also associated with early allograft dysfunction (EAD), particularly g__Lachnoclostridium. Several microbial and metabolic features, including g__Lachnoclostridium, showed significant correlations with clinical indicators. The gut microbiome after LT is closely associated with ACLF. This study offers valuable insights for further investigation into the pathogenesis and post-LT prognosis. KEY POINTS: • ACLF patients have a unique gut microbiota and metabolic profile after LT • g__Anaerostipes is the prominent biomarker of ACLF's multi-omics signature • g__Lachnoclostridium is a promising indicator of recovery after LT.},
}

@article {pmid41776009,
year = {2026},
author = {Kumar, Y and Xu, B},
title = {A critical review on the roles of natural products in shaping oral microbiota and preventing chronic diseases.},
journal = {Natural products and bioprospecting},
volume = {16},
number = {1},
pages = {},
pmid = {41776009},
issn = {2192-2195},
support = {UICR0400015-24B//Beijing Normal-Hong Kong Baptist University/ ; UICR0400016-24B//Beijing Normal-Hong Kong Baptist University/ ; },
abstract = {The oral microbiome plays a central role in maintaining both oral and systemic health, and disruptions in its balance can contribute to a wide range of diseases. This review brings together current evidence on how natural products modulate oral microbial communities, promote microbial equilibrium, and help prevent conditions such as dental caries, periodontitis, and chronic systemic disorders linked to oral dysbiosis. Recent studies highlight that phytochemicals particularly polyphenols, terpenoids, saponins, and alkaloids exert antimicrobial, anti-inflammatory, and antioxidant effects that influence bacterial adhesion, biofilm development, gene expression, and acid production. These compounds not only inhibit key oral pathogens but also support beneficial species, helping to sustain a stable and resilient microbiome. Evidence was gathered from PubMed, Scopus, ScienceDirect, and Google Scholar using relevant keywords and focusing on literature from 2015 to 2025. Insights into microbial diversity, environmental influences, host genetics, and advanced sequencing tools further strengthen understanding of oral microbial dynamics. While natural products show strong potential, challenges related to safety, bioavailability, regulatory clarity, and clinical translation remain to explore. This review outlines current progress and future directions needed to transform natural compounds into effective, evidence-based strategies for improving oral and systemic health through microbiome modulation.},
}

@article {pmid41776008,
year = {2026},
author = {Ticinesi, A and Maggi, S and Nouvenne, A and Zuliani, G and Franceschi, C},
title = {The gut microbiome and ageing trajectories: mechanisms and clinical implications.},
journal = {Nature reviews. Endocrinology},
volume = {},
number = {},
pages = {},
pmid = {41776008},
issn = {1759-5037},
abstract = {This Review discusses the current state of knowledge on the contribution of the gut microbiome as a potential key actor in defining how we age. The gut microbiome is a complex ecosystem that establishes lifelong dynamic interactions with the host at multiple levels (several gut-organ axes), differently influencing ageing patterns and age-related disease onset and progression across populations. Accordingly, the definition of a 'normative' gut microbiome remains elusive, depending largely on the interaction with the external environment. In this complex scenario, the causal role of the gut microbiome in defining the ageing trajectory and its precise contribution to various organ-specific age-related diseases is still uncertain in clinical terms and could be context specific. Multiparametric and uniqueness indexes within a given population have shown a certain capacity for predicting disability and mortality. However, the gut microbiome is shaped over time by exposure to different intrinsic and environmental factors, resulting in a high degree of inter-individual variability, a key phenomenon that should be considered to develop novel personalized strategies to counteract age-related disease and frailty.},
}

@article {pmid41775773,
year = {2026},
author = {Chowdhury, SF and Sarkar, MMH and Al Sium, SM and Naser, SR and Hossain, MS and Habib, MA and Akter, S and Banu, TA and Goswami, B and Jahan, I and Chakrovarty, T and Molla, MMA and Nafisa, T and Yeasmin, M and Ghosh, AK and Khan, MS},
title = {Metatranscriptomic insights into host-microbiome interactions underlying asymptomatic COVID-19 cases.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40563-x},
pmid = {41775773},
issn = {2045-2322},
support = {GOB 224125200//Ministry of Science and Technology, Government of the People's Republic of Bangladesh/ ; },
}

@article {pmid41775715,
year = {2026},
author = {Zhu, B and Wang, J and Zhang, X and Zhang, B and Li, Z and Hao, L},
title = {A bacteria community sequencing data set from pothos (Epipremnum aureum).},
journal = {Scientific data},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41597-026-06677-7},
pmid = {41775715},
issn = {2052-4463},
abstract = {Pothos, with the scientific name of Epipremnum aureum, is a popular ornamental plant widely utilized for indoor greening, which is adaptable to both soil-based and hydroponic cultivation. Plant-associated microorganisms significantly influence plant health and productivity by facilitating nutrient acquisition and enhancing stress tolerance. Pothos, which is tolerant to low-nutrient conditions, is thus a suitable model plant to study plant-microorganisms interaction. However, knowledge about the microbiome of pothos is lacking, especially under hydroponic cultivation conditions. In this study, we recorded the dynamic changes of the bacterial communities associated with pothos during a transition from soil-based to hydroponic growth conditions in a 86-day cultivation. Bacterial communities from root tissues, hydroponic solutions, leaves, and soils were characterized through 16S rRNA gene amplicon sequencing, generating 98 community composition profiles. Significant shifts in microbial diversity and composition were observed during the transition, highlighting specific bacterial taxa associated with hydroponic adaptation. Across sample types, Proteobacteria dominated, with Actinobacteriota as the second most abundant group, while Bacteroidota and Firmicutes were present at lower relative abundances. This is the first high resolution and comprehensive data set of the pothos microbiome, offering a foundational resource for studying plant-microbe interactions in aquatic systems.},
}

@article {pmid41775278,
year = {2026},
author = {Kim, YS and Woo, SY and Ha, E and Ahn, SH and Kim, E and Kim, SI and Lim, WJ and Kim, SY},
title = {Role of Gut Microbiota in Psychiatric Disorders: From Mechanistic Insights to Therapeutic Strategies.},
journal = {Journal of Korean medical science},
volume = {41},
number = {8},
pages = {e78},
pmid = {41775278},
issn = {1598-6357},
support = {/NRF/National Research Foundation of Korea/Korea ; },
abstract = {Mental health disorders are a global health challenge, and the underlying biological mechanisms remain unclear. Recent evidence has linked gut microbiota to psychiatric symptoms through complex bidirectional interactions along the gut-brain axis, which involve neural, endocrine, and immune pathways. This narrative review aims to synthesize current findings on how gut microbiota contributes to the pathophysiology of major psychiatric disorders, and explore microbiota-based therapeutic interventions, and discusses emerging strategies for personalized treatment. Relevant literature up to July 2025 was reviewed using targeted keywords in major databases, including PubMed and Google Scholar. Rather than applying formal systematic review criteria, we focused on selecting influential and high-impact studies, and the findings were synthesized thematically to provide a comprehensive overview. Consistent findings across psychiatric conditions include a decreased abundance of short-chain fatty acid-producing bacteria and an increased presence of pro-inflammatory taxa. These shifts correlate with heightened systemic inflammation, disrupted neurotransmitter synthesis, and dysregulation of the hypothalamic-pituitary-adrenal axis. Thus, the gut microbiota is increasingly recognized as playing a potential role in the pathophysiology of psychiatric disorders through multifaceted mechanisms involving the gut-brain axis. Probiotics, prebiotics, and dietary modifications show promise in modulating gut microbiota and alleviating psychiatric symptoms, although clinical outcomes remain heterogeneous. Emerging precision medicine strategies indicate promising potential for personalized microbiota-based treatments. Although microbiota-targeted therapies offer promising adjunctive strategies, large-scale, mechanistically informed clinical trials remain warranted. Future research should leverage artificial intelligence and multi-omics tools to develop personalized interventions tailored to individual microbiome profiles.},
}

@article {pmid41775266,
year = {2026},
author = {Han, Z and Sun, Z and Zhao, Q and Du, L and Zhen, D and Liu, X and Jiang, S and Liu, YY and Zhang, J},
title = {Competition and compromise between exogenous probiotics and native microbiota.},
journal = {Cell systems},
volume = {},
number = {},
pages = {101516},
doi = {10.1016/j.cels.2025.101516},
pmid = {41775266},
issn = {2405-4720},
abstract = {Probiotic interventions are effective strategies to modulate the gut microbiome, but how exogenous probiotics compete with native gut microbiota remains elusive. Here, we use a mouse model and a well-documented probiotic, Bifidobacterium animalis subsp. lactis V9 (BV9), to mechanistically investigate its competitive strategies. We perform metagenomic and whole-genome sequencing of stool samples and isolated BV9, longitudinally collected from 24 mice orally administered with BV9 and different diets. Results show that a high-fiber diet most effectively supports the colonization of BV9, where BV9 selectively competes with Parabacteroides distasonis (P. distasonis), rather than extensively with other gut bacteria. By comparing the genomic structures of BV9 and P. distasonis isolated during the washout period, we infer their co-evolution mechanisms, highlighting their competition and compromise in utilizing inulin-derived glucose. Finally, our in vitro co-culture experiments validate such competitive dynamics. This study fills a critical gap in our understanding of niche competition in colonization.},
}

@article {pmid41775198,
year = {2026},
author = {Xiao, J and Wang, Y and Chen, H and Bu, F and Xu, W and Qiu, S and Kang, Y and Wang, D and Wu, H and Hu, Z and Zhang, J and Guo, Z},
title = {Overlooked fate and associated pathogens of antimicrobial resistance in the Yellow River Delta, China.},
journal = {Journal of hazardous materials},
volume = {506},
number = {},
pages = {141645},
doi = {10.1016/j.jhazmat.2026.141645},
pmid = {41775198},
issn = {1873-3336},
abstract = {The spread of antibiotic resistance genes (ARGs) within terrestrial inputs and marine dispersal in estuarine deltas has posed significant environmental challenges, exacerbated by diverse microbial habitats, estuarine eutrophication, and other anthropogenic impacts. However, the precise mechanisms governing persistence and associated risks of ARGs in this region remain poorly understood. In this study, the distribution, mobility, removal and hosts of ARGs in wetlands and rivers of the Yellow River Delta (YRD) region were systematically investigated through metagenomic approaches. A total of 23 antibiotics were detected in water (0.07-4.67 ng/L) and 14 antibiotics in sediment (0.0042-0.4768 ng/g). Following wetland treatment, despite a 67.5% reduction in antibiotic concentrations, the relative abundance of antibiotic resistance genes decreased by only 7.60%, indicating substantial persistence of genetic resistance. Moreover, Proteobacteria were identified as primary hosts for ARGs. ARGs carried by resistant pathogens, especially ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.), also showed a significant reduction in the abundance and diversity throughout the wetland. Notably, total nitrogen in water (Water-TN) greatest shaped the composition of the resistome and microbiome, while the presence of antibiotics exerted stronger selective pressure on ARGs in wetland than in river. Collectively, this study highlights the associated risks of ARGs in YRD, offering insights for controlling antimicrobial resistance in deltas.},
}

@article {pmid41634593,
year = {2026},
author = {Narem, RSR and Mathakala, V and Sallabathula, ST and Peddiboyina, VL and Palempalli, UMD},
title = {Probiotics as emerging adjuncts in metabolic associated fatty liver disease therapy-a systemic review.},
journal = {BMC gastroenterology},
volume = {26},
number = {1},
pages = {},
pmid = {41634593},
issn = {1471-230X},
abstract = {Metabolic associated fatty liver disease (MAFLD), a leading cause of chronic liver disorders globally, is closely linked with the dysbiosis of the gut. These microbial imbalances contribute to pathogenesis of MAFLD through intestinal barrier dysfunction, systemic inflammation, and hepatic fat accumulation. This review aims to provide an in-depth analysis of the complex interaction between the gut microbiome and MAFLD, through literature search of articles published in open access journals of two electronic data bases PubMed, Medline from January 2015 to May 2025. Among 602 publications identified initially, 54 studies were considered based on inclusion and exclusion criteria as per the PRISMA guidelines. The results assimilate the findings from both preclinical models and human clinical trials, highlighting the influence of probiotic strains on key metabolic pathways. Lactobacillus and Bifidobacterium species were shown to regulate lipid metabolism, normalize liver enzyme activity, reduce insulin resistance, and attenuate hepatic inflammation. These effects are mediated through multiple mechanisms, including enhancement of gut barrier integrity, modulation of bile acid metabolismsuppression of endotoxemia and modulation of gut–liver axis. By summarizing emerging insights, this review offers an updated perspective on the role of probiotic interventions as a promising adjunct strategy in the prevention and management of MAFLD.},
}

@article {pmid41775960,
year = {2024},
author = {Liu, Y and Du, Z and Lu, Y and Ma, Y and Yang, Y and Osmanaj, F and Zhang, Y and Guo, X and Qin, Y and Yang, X and Hua, K},
title = {Gut microbiota metabolism disturbance is associated with postoperative atrial fibrillation after coronary artery bypass grafting.},
journal = {NPJ cardiovascular health},
volume = {1},
number = {1},
pages = {},
pmid = {41775960},
issn = {2948-2836},
support = {82100295//National Natural Science Foundation of China/ ; CI2021A04110//China Academy of Chinese Medical Sciences/ ; 7222049//Beijing Natural Science Foundation of China/ ; },
abstract = {Postoperative atrial fibrillation (POAF) is a common complication after coronary artery bypass grafting (CABG) surgery. Gut microbiota and its metabolites have been implicated in the development of AF. However, whether the gut-host metabolic interaction contributes to POAF is still unknown. This study aimed to investigate the POAF-associated gut microbiota metabolism biomarkers and related risk model. The POAF (N = 30) patients and non-POAF (N = 60) patients from the discovery cohort exhibited significantly different microbiome and metabolome profiles. The differentiated features were mainly implicated in the bile acids (BAs) and short-chain fatty acids metabolism, inflammation, and oxidative stress. Random forest analysis identified the combination of five secondary BAs showed a powerful performance on predicting POAF in the discovery cohort, highlighting significant values of area under the curve (AUC = 0.954) and correct classification rate (CCR, 93.3%). In addition, the five secondary BAs-based risk model also exhibited good performance in differentiating the POAF (N = 114) and non-POAF individuals (N = 253) in an independent validation cohort (AUC = 0.872; CCR = 90.4%). This work revealed perturbed microbial and metabolic traits in POAF, providing potential avenues for the prediction and prevention of POAF after CABG.},
}

@article {pmid41774605,
year = {2026},
author = {Wang, T and Lu, S and Sun, L and Cheng, Y},
title = {Skin Barrier Compromise: A Central Early Event in Ultraviolet Radiation-Induced Skin Pathogenesis.},
journal = {Dermatology (Basel, Switzerland)},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000551027},
pmid = {41774605},
issn = {1421-9832},
abstract = {Ultraviolet radiation (UVR) is a major environmental stressor to the epidermal barrier, extending beyond erythema or photoaging. Emerging evidence reframes barrier impairment as an early and central event, integrating DNA and oxidative injury with inflammatory, immune, and microbial disturbances in a self-reinforcing cycle of fragility. This perspective challenges the traditional view of UVR damage as isolated mechanisms and highlights the need for barrier-focused research. Sunscreens remain essential, and recent formulations now extend beyond optical filtering by incorporating biologically active components such as antioxidants and photolyase that enhance photostability and support DNA lesion clearance. Emerging research also suggests that microbiome-preserving compositions may help maintain commensal balance during UVR exposure. Together, these developments point to a shift toward multifunctional photoprotection, although evidence is still accumulating. This review synthesizes recent advances alongside remaining gaps in the field. By integrating mechanistic evidence on UVR-induced barrier injury, it identifies directions that can support the design of more biologically grounded photoprotective strategies and delineates priority topics for future research.},
}

@article {pmid41774204,
year = {2026},
author = {Gulumbe, BH and Alum, EU and Abdulrahim, A and Abubakar, TM and Bagwai, MA and Ali, M},
title = {The Role of the Environmental Microbiome in Modulating the Spread of Antimicrobial Resistance.},
journal = {Current microbiology},
volume = {83},
number = {4},
pages = {},
pmid = {41774204},
issn = {1432-0991},
abstract = {Antimicrobial resistance (AMR) poses an escalating global health challenge with important environmental dimensions. While the environment is well known as a reservoir and conduit for antibiotic resistance genes (ARGs), the regulatory role of environmental microbiomes in modulating ARG dissemination remains inadequately studied. This review synthesizes current knowledge on how environmental microbiomes influence the spread of AMR by acting as buffers, amplifiers, or gatekeepers of ARG flow in natural and human-impacted ecosystems. We synthesize findings from metagenomic analyses, ecological experiments, and theoretical frameworks to evaluate how microbial diversity, community composition, and ecological interactions shape the persistence and horizontal transfer of ARGs in the environment. Evidence suggests that diverse and resilient microbial communities can inhibit ARG persistence and limit gene transfer, whereas environmental disturbances and biodiversity loss may facilitate ARG propagation. These dynamics highlight the importance of microbial ecosystem structure in shaping AMR trajectories. Understanding the ecological role of environmental microbiomes in AMR dissemination offers new perspectives for antimicrobial stewardship within the One Health framework. Integrating this knowledge into practical interventions, such as engineered microbial consortia and bioremediation can help manage environmental sources of resistance and strengthen global efforts against AMR.},
}

@article {pmid41774188,
year = {2026},
author = {Yadav, A and Melkani, GC},
title = {Microbes, mood, and metabolism/obesity: Pharmacological insights into the gut-obesity-depression triad.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00018-025-06022-y},
pmid = {41774188},
issn = {1420-9071},
support = {AG065992//National Institute of Aging/ ; },
}

@article {pmid41773937,
year = {2026},
author = {Wang, A and Dao, LQ and Ramos-Gomez, F and Wang, Y},
title = {Maternal influences on oral microbiome development and implications for early childhood health: a systematic review.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0058525},
doi = {10.1128/iai.00585-25},
pmid = {41773937},
issn = {1098-5522},
abstract = {A deeper understanding of how maternal-infant interactions shape the establishment and diversification of the oral microbiome could have significant clinical applications; however, relatively few studies emphasize early maternal-infant microbial connections. This systematic review provides a longitudinal analysis of oral microbiome development from birth to five years, focusing on the relationship between maternal and infant microbiomes. We conducted a systematic search (June 2025) using keywords "mother," "children," "oral microbiome," and "longitudinal" across PubMed, Cochrane Library, and Embase. Twelve studies fulfilled the inclusion criteria: longitudinal design, healthy mother-child dyads, saliva sample collection, and relevant age range. We excluded review articles, non-English publications, and studies with overlapping data. Results were synthesized by developmental stage and topic. Overall, current literature agrees that the mother is an important source of exposure for initial colonization of the newborn's oral microbiome. Several studies indicated that the oral microbiome at birth is diverse and unspecialized, composed mostly of maternally derived strains. Rapid selection occurs over the first few weeks, as the relative abundances of typical oral bacterial species increase. Throughout the first year, increases in diversity strengthen the resemblance between infant and maternal microbiomes. The microbiome appears to stabilize around 3-5 years. In conclusion, maternal-infant connections play a significant role in influencing oral microbiome development during the first 5 years of life. This review highlights the need for future studies to incorporate larger, longitudinal designs with metadata and advanced tools to clarify the roles of delivery mode, tooth eruption, and parental lifestyle habits in shaping early oral microbiome development.},
}

@article {pmid41773902,
year = {2026},
author = {Vidal, VM and Montes-Cobos, E and Canto, FB and Bozza, MT},
title = {The different meanings of tolerating the gut microbiome.},
journal = {mBio},
volume = {},
number = {},
pages = {e0173624},
doi = {10.1128/mbio.01736-24},
pmid = {41773902},
issn = {2150-7511},
abstract = {Multicellular life arose in a world dominated by microorganisms, a reality that has imposed a constant and pervasive selective pressure on all subsequent complex organisms. The immune system has been historically defined by its role in pathogen clearance through resistance mechanisms. However, a complementary and equally critical strategy is to enable the peaceful and inevitable coexistence with microorganisms, allowing each host species to shelter a unique associated microbiome. The term tolerance holds multiple meanings in immunology, yet all underlie a balanced and cooperative host-microorganism relationship. Each represents a different aspect of how the immune system limits tissue damage while maintaining functionality in the presence of microbial or inflammatory stimuli. Using the intestinal mucosa as a paradigm, we explore how epithelial barrier integrity, toxin neutralization, tissue repair, and stress response underpin disease tolerance; how microbial exposure calibrates innate immunity via epigenetic and metabolic reprogramming (LPS tolerance); and how the gut microenvironment fosters the generation of tolerogenic antigen-presenting cells and microbe-specific regulatory T cells to enforce immunological tolerance. We further explore how the microbiota itself is a potent inducer of these tolerogenic pathways and highlight IL-10 as a major hub, connecting different tolerogenic circuits. Finally, we examine the hygiene hypothesis, arguing that lifestyle changes during the Anthropocene disrupt these finely tuned tolerance mechanisms, thereby contributing to the rising incidence of immune-mediated diseases. We posit that these tolerance programs are fundamental prerequisites for engendering host-microbiota symbiosis, a relationship forged over millennia of co-evolution and endangered in the contemporary world.},
}

@article {pmid41773862,
year = {2026},
author = {Makori, TO and Gicheru, ET and Mburu, MW and Sada, MS and Nyawa, O and Mutunga, M and Lewa, C and Cheruiyot, R and Kiguli, S and Olupot-Olupot, P and Muhindo, R and Mogaka, C and Williams, TN and Agoti, CN and Maitland, K and Sande, CJ},
title = {Nasopharyngeal Microbiome Composition and its Clinical Correlates in Children Hospitalized with Severe Pneumonia in East Africa.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag093},
pmid = {41773862},
issn = {1537-6613},
support = {P46493//Imperial College London/ ; //Medical Research Council Department for International Development/ ; MR/L004364/1/WT_/Wellcome Trust/United Kingdom ; 102231/WT_/Wellcome Trust/United Kingdom ; },
abstract = {BACKGROUND: Pneumonia remains the leading cause of infectious mortality in children under 5, with the highest burden in sub-Saharan Africa. Dysbiosis in nasopharyngeal (NP) microbiota may influence pneumonia susceptibility and progression, but little is known about its composition or clinical relevance in low- and middle-income countries. We characterized the NP microbiota of children hospitalized with severe pneumonia in East Africa and investigated associations with clinical outcomes.

METHODS: We performed 16S rRNA partial gene sequencing of NP swabs collected at hospital admission from 876 children enrolled in the COAST trial across 5 sites in Kenya and Uganda. Clinical, demographic, and virological data were prospectively collected. Microbial profiles were analyzed using hierarchical clustering, nonmetric multidimensional scaling, and multivariable regression to assess associations with respiratory viral infections, sepsis, cyanosis, bacteremia, coma, HIV status, malnutrition, sickle cell disease, malaria, and mortality.

RESULTS: The NP microbiome was structured in 6 distinct clusters, each dominated by different genera, including Staphylococcus, Streptococcus, Haemophilus, Dolosigranulum, Corynebacterium, and Moraxella. Multivariable models adjusting for study site and age showed a positive association between Corynebacterium and early mortality. Temporal analysis showed elevated Corynebacterium abundance in children who died within 48 hours of admission, then declined over longer 56 survival intervals, approaching levels observed in survivors. However, time-continuous models did not support this persistent association, suggesting a subgroup effect.

CONCLUSIONS: We provide one of the largest high-resolution surveys of the pediatric upper airway microbiome in Africa, identifying microbial patterns associated with viral infection, HIV status, early death, and bacteremia.},
}

@article {pmid41773858,
year = {2026},
author = {Vijayakumar Padmavathy, B and Shanmugavel, AK and Shanmugam, S and Narayanan, M},
title = {Dissecting the effect of single- and co-infection of TB and COVID-19 pathogens on the sputum microbiome.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0222025},
doi = {10.1128/spectrum.02220-25},
pmid = {41773858},
issn = {2165-0497},
abstract = {UNLABELLED: Tuberculosis (TB) and COVID-19 are both respiratory diseases, and understanding their interaction is important for effective co-infection management. Although some studies have investigated TB and COVID-19 co-infection in terms of immune responses, microbial dysbiosis in such cases remains unexplored. In this study, we understand the interface between TB and COVID-19 by systematically inspecting the microbial composition of sputum samples collected from four groups of individuals: TB only, COVID-19 only, and both TB and COVID-19 (TBCOVID) infected patients, and uninfected group (Controls). Besides metagenomic analysis of the microbiome of these sputum samples, we also performed whole-genome sequencing analysis of a subset of TB-positive samples. Different bioinformatic analyses ensured data quality and revealed significant differences in the microbial composition between Control vs disease groups. To understand the effect of COVID-19 on TB, we compared TBCOVID vs TB samples and observed (i) higher read counts of TB-causing bacteria in the TBCOVID group, and (ii) differential abundance of several taxa, including Capnocytophaga gingivalis. Functional profiling with PICRUSt2 revealed elevated pathways, including the pulmonary surfactant lipid metabolism pathway (with a fold change of 7.46) in the TBCOVID group. Further clustering of these pathways revealed a sub-cluster of individuals with adverse treatment outcomes. Two individuals in this sub-cluster had a respiratory pathogen, Stenotrophomonas maltophilia-knowing such information on key respiratory pathogens in a patient can help personalize the patient's antibiotic regimen. Overall, our study reveals the effect of COVID-19 on the airway microbiome of TB patients and encourages the use of co-microbial/co-pathogen profiling to personalize TB treatment.

IMPORTANCE: The community of microbes in an individual's airway tract can play a complex role in respiratory diseases like tuberculosis (TB) and COVID-19. Although changes in microbial composition in TB and COVID-19 patients have been studied separately, we present a first-of-its-kind investigation of the airway-tract microbiome of individuals simultaneously infected with TB and COVID-19 pathogens. Our results highlight that co-infection with COVID-19 in TB patients alters the abundance of certain bacterial species and their related pathways. For instance, Capnocytophaga gingivalis is abundant in co-infected patients, but not in TB-only patients. This species and other differentially abundant species we identified in the co-morbid condition, if replicated in independent cohorts, can help explain how COVID-19 could exacerbate the severity of lung infection in TB patients. Our study also stimulates future longitudinal studies using expanded data sets to understand the role of concomitant pathogens and assess whether adjusting the antibiotic regimen accordingly can improve TB treatment outcomes.},
}

@article {pmid41773303,
year = {2026},
author = {Ma, H and Hu, K and Wang, Y},
title = {Dynamic changes of cervical microbiome during pregnancy for preterm birth risk prediction: A prospective cohort study.},
journal = {African journal of reproductive health},
volume = {30},
number = {4},
pages = {50-63},
doi = {10.29063/ajrh2026/v30i4.5},
pmid = {41773303},
issn = {1118-4841},
abstract = {This prospective cohort study investigated the dynamic changes in the cervical microbiome during pregnancy and developed a predictive model for preterm birth risk. Ninety-three singleton pregnant women were enrolled, including 41 with preterm birth and 52 with term delivery. Cervical secretions were collected at four gestational stages and analyzed using 16S rRNA sequencing, alongside ELISA testing for inflammatory markers. The preterm group exhibited significantly lower microbial diversity and a progressively increasing ratio of Lactobacillus iners to Lactobacillus crispatus throughout pregnancy. Early pregnancy IL-6 levels were also significantly elevated in this group. Logistic regression identified the L. iners/L. crispatus ratio, IL-6, history of preterm birth, and short cervical length as independent risk factors. The integrated prediction model demonstrated high accuracy (AUC 0.847), with even stronger performance in predicting births before 34 weeks (AUC 0.892). These findings suggest that microbiome patterns and inflammatory markers can effectively predict preterm birth risk, supporting early clinical intervention.},
}

@article {pmid41773092,
year = {2026},
author = {Lamanna, OK and Hu, R and Khemmani, M and Wolfe, AJ and Groah, SL and Forster, CS},
title = {Differential Effects of Uropathogenic and Non-Uropathogenic E. coli on the Mouse Urobiome and Urine NGAL Levels.},
journal = {Research and reports in urology},
volume = {18},
number = {},
pages = {580953},
pmid = {41773092},
issn = {2253-2447},
abstract = {OBJECTIVE: To determine whether urine neutrophil gelatinase-associated lipocalin (uNGAL) or urobiome alterations can differentiate urinary tract infections (UTI) from asymptomatic bacteriuria (ASB).

METHODS: Female 8-week-old C57BL/6 mice were instilled with either Escherichia coli CFT073 (UTI model, n=12), E. coli 83972 (ASB model, n=12), or saline (control, n=3). uNGAL was measured daily for 3 days post-instillation. Urobiome composition was assessed pre- and post-instillation using 16S rRNA sequencing. At day 3, kidneys were harvested for culture. Comparisons were made across groups for uNGAL levels and urobiome diversity.

RESULTS: Baseline β diversity did not differ between groups. Post-instillation, β diversity significantly differed across groups (p=0.01), driven by increased relative abundance of E. coli in UTI mice compared to ASB mice. Median uNGAL levels increased significantly in both UTI and ASB groups relative to controls, but no significant difference was observed between UTI and ASB groups.

CONCLUSION: Introduction of a uropathogenic E. coli strain reduced urobiome diversity, while a non-uropathogenic strain did not, suggesting strain-specific effects on microbial ecology. Bladder instillation itself also altered the urobiome. Elevated uNGAL levels were observed in both UTI and ASB models, indicating that while uNGAL reflects bacterial exposure, it does not distinguish between uropathogenic and non-uropathogenic E. coli. These findings highlight urobiome analysis as a potential tool for differentiating UTI from ASB, whereas uNGAL alone is insufficient.},
}

@article {pmid41772961,
year = {2026},
author = {Li, M and Zong, H and Yang, X and Liu, Q and Wang, J and Wang, M and Wu, D and Zheng, S and Wang, H and Long, Q},
title = {A flavonoid-rich medicinal herb extract ameliorates high-fat diet-induced obesity and insulin resistance in mice.},
journal = {Acta biochimica et biophysica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.3724/abbs.2026007},
pmid = {41772961},
issn = {1745-7270},
abstract = {Obesity has emerged as a critical global health challenge, contributing to severe metabolic and neoplastic complications. However, most existing anti-obesity drugs exhibit significant adverse effects, necessitating the development of safer therapeutic alternatives. In this study, we evaluate the efficacy and safety of a flavonoid-rich medicinal herb extract (MHE) in a high-fat diet (HFD)-induced murine obesity model. Daily oral administration of MHE does not alter food intake or induce hepatic injury but significantly attenuates HFD-induced weight gain (P < 0.05) and adiposity accumulation. Furthermore, MHE treatment improves systemic insulin sensitivity and glycemic control. Notably, MHE enhances whole-body energy expenditure, as evidenced by elevated oxygen consumption (VO 2), carbon dioxide production (VCO 2), and heat generation (P < 0.01). Mechanistically, MHE selectively promotes the proliferation of beneficial gut microbiota, including Lactobacillus, Akkermansia, and Bifidobacterium species, resulting in increased production of the short-chain fatty acid propionate (PA). Elevated circulating PA levels subsequently stimulate the browning/beiging of inguinal white adipose tissue (iWAT) and upregulate thermogenic pathways. Collectively, our findings demonstrate that MHE exerts anti-obesity effects through gut microbiota modulation and adipose tissue remodeling, offering a promising natural alternative for obesity management.},
}

@article {pmid41772824,
year = {2026},
author = {Ndhlovu, A and von der Heyden, S},
title = {Spatial Patterns and Overlap of Sedimentary and Rhizosphere Microbiomes of the Seagrass Zostera capensis.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70313},
pmid = {41772824},
issn = {1758-2229},
support = {//African Research Universities Alliance/ ; //National Research Foundation/ ; },
abstract = {Seagrasses are important nature-based solutions for climate change mitigation and adaptation due to their carbon stocks and ecosystem service co-benefits. Characterising microbial communities in seagrass sediments and rhizospheres is essential for understanding their roles in biogeochemical cycling, seagrass health, and potential contributions to ecosystem functioning. However, the extent to which seagrass microbiomes are shared at different spatial scales is not well understood. We utilised 16S rRNA metabarcoding to characterise prokaryotic communities in the sediments of the seagrass Zostera capensis at three estuaries spanning the environmental gradient of South Africa. In addition, we characterised the rhizosphere microbiome (rhizobiome) to better understand rhizosphere and sediment community dynamics. Overall, after accounting for community in adjacent seawater, we found that Z. capensis sediment and rhizosphere microbiomes largely overlap, sharing 34 genera but also harbour core genera. The sediment microbiome and rhizobiome showed significant spatial variability, suggesting that both local-scale and broader estuary-specific factors shape site-level microbial signatures. Further, predictive functional analysis showed that the rhizobiome was enriched for nutrient cycling pathways potentially beneficial to Z. capensis. Our findings support the exploration of sediment and rhizosphere microbial communities for monitoring ecosystem health and assessing impacts from threats such as pollution and climate change.},
}

@article {pmid41772743,
year = {2026},
author = {He, J and Wang, MN and Chen, HJ and Zuo, GY and Li, JL and Yin, WF and Pan, XG and Cheng, YC and Xia, CY and Xu, JK and Zhang, WK},
title = {Muribaculum intestinale alleviates depressive-like behaviors by inhibiting Th17 cell differentiation and M1 microglia polarization.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02354-4},
pmid = {41772743},
issn = {2049-2618},
support = {ZRZC2025-KCC03//National High Level & Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; 2025-NHLHCRF-JBGS-A-WZ-10; ZRJY2024-BJ01//National High Level & Elite Medical Professionals Project of China-Japan Friendship Hospital/ ; 82474100//National Natural Science Foundation of China/ ; 82474100, 82273815, 82273809, 82073731//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Gut microbiota dysbiosis has been implicated in the pathogenesis of depression. Our previous studies identified loganin as a potential antidepressant agent; however, its oral bioavailability is low. Whether loganin alleviates depression via modulation of the gut microbiota remains unclear.

METHODS: Chronic unpredictable stress mice model was used to evaluate the antidepressant-like effects of loganin. To determine the role of gut microbiota, mice were treated with an antibiotic cocktail (ABX) to deplete microbiota. Fecal microbiota transplantation (FMT) from loganin-treated donors and Muribaculum intestinale (M. intestinale) were performed to assess microbial contributions.

RESULTS: Loganin exerted antidepressant-like effects by modulating gut microbiota, as evidenced by reduced efficacy in ABX-treated mice and behavioral improvements in recipients of FMT from loganin-treated donors. Loganin modulated gut microbiota composition particularly increasing the abundance of Muribaculum, and increased short-chain fatty acids (SCFAs). M. intestinale alleviated depressive-like behaviors, prompted the butyrylation of RORγt, inhibited Th17 cells differentiation, and suppressed M1 microglia polarization. Importantly, overexpression of RORγt attenuated the behavioral benefits of M. intestinale.

CONCLUSION: Loganin exerts antidepressant-like effects by enriching Muribaculum and SCFAs, thereby inhibiting Th17 cell differentiation and M1 microglia polarization. M. intestinale may represent a promising microbial-based therapeutic strategy for depression.},
}

@article {pmid41772715,
year = {2026},
author = {Merenstein, C and Litichevskiy, L and Thaiss, C and Collman, RG and Bushman, FD},
title = {Dynamics of gut bacteriophage in diversity outbred mice studied over lifespan and during extreme caloric restriction.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02362-4},
pmid = {41772715},
issn = {2049-2618},
support = {F31 HL170550/NH/NIH HHS/United States ; T32 HG000046/NH/NIH HHS/United States ; DP2 AG067492/NH/NIH HHS/United States ; U54 AG089323/NH/NIH HHS/United States ; U19 AI174998/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: The majority of bacteria in the vertebrate gut harbor integrated bacterial viruses ("bacteriophages" or "phages"; integrated phage are termed "prophages"). To probe phage replication strategies in the mammalian gut microbiome, we investigated phage activity in a large longitudinal study of diversity outbred mice (913 animals) undergoing extreme dietary restriction with detailed phenotypic characterization across lifespan.

RESULTS: We assembled 54,119 candidate DNA viral genomes from 2997 longitudinal metagenomes, forming 6462 viral operational taxonomic units (vOTUs). Over 85% of vOTUs annotated as novel. Viruses annotated predominantly as prophages in the Caudoviricetes class. We detected no eukaryotic DNA viruses, and none of the strictly lytic Crassvirales order that is abundant in human gut. The most prevalent phages had the widest predicted host ranges. The relative abundance of most phages was highly correlated to that of their inferred host bacteria, suggesting quiescent prophages dominate viral metagenomes, consistent with "piggyback-the-winner" dynamics. After accounting for close phage-bacterial covariation, we did identify a subset of phages changing in relative abundance and prevalence relative to their hosts in response to dietary restriction and aging. In particular, phages with larger genomes become less common in diets with restricted calories, potentially reflecting a higher fitness cost to their host. Generalist phages were enriched for a gene encoding a single-strand DNA binding protein which is reportedly involved in DNA repair and protection from nucleases encoded by host cells. Lytic phages became more common with aging, and we observed a reduction in phage richness with age, both findings previously observed in human cohorts.

CONCLUSION: These studies enrich our understanding of DNA phage dynamics in gut while emphasizing the predominance of "piggyback-the-winner" strategies.},
}

@article {pmid41772405,
year = {2026},
author = {Luo, H and Kamer, AR and Xu, Z and Qi, X and Liu, R and Wu, B},
title = {Moderating Effects of Oral Bacteria and Tooth Loss on Cognitive Performance.},
journal = {JDR clinical and translational research},
volume = {},
number = {},
pages = {23800844261423487},
doi = {10.1177/23800844261423487},
pmid = {41772405},
issn = {2380-0852},
abstract = {INTRODUCTION: The oral microbiome may influence brain health and contribute to cognitive decline. However, little evidence exists on the potential modifying role of the oral microbiome in the relationship between tooth loss and cognitive performance. This study aimed to investigate the interaction effects between tooth loss and oral dysbiotic status on cognitive performance.

METHODS: Data were from the 2011-2012 National Health and Nutrition Examination Survey. The sample included 677 adults aged 60 to 69 y. Cognitive performance was assessed by the Consortium to Establish a Registry for Alzheimer's Disease, the Animal Fluency Test (AFT), and the Digit Symbol Substitution Test. Significant tooth loss was defined as a loss of ≥10 permanent teeth out of 28. A high dysbiotic index was defined as being in the upper tertile of the ratio of periodontal disease-associated bacteria (Treponema, Porphyromonas, and Tannerella) to healthy bacteria (Rothia and Corynebacterium).

RESULTS: A multivariable linear regression model showed a significant interaction effect between tooth loss and dysbiotic index on the AFT (b = -1.87, P = 0.03), indicating that participants with a higher dysbiosis index and fewer missing teeth scored lower on the AFT.

CONCLUSIONS: The effect of tooth loss on verbal fluency depends on oral bacterial imbalances: if there is significant tooth loss, bacterial imbalances may not be important. However, when fewer teeth are lost, high bacterial imbalances may account for lower verbal fluency. These findings suggest that maintaining periodontal health aimed at decreasing oral dysbiosis should be promoted among older adults in the community.Knowledge Transfer Statement:Our findings highlight the importance of preserving the health of the teeth and not just retaining the teeth. Oral health awareness and good oral hygiene practice should be further promoted among older adults in the community.},
}

@article {pmid41771971,
year = {2026},
author = {Deng, S and Wu, X and Xu, W and Wu, X and Cai, H and Wang, S and Liu, J and Cao, J},
title = {Multi-dimensional immunoprotection of Ganoderma lucidum spore oil in immunosuppressed mice via microbiome-proteome-metabolome network analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40137-x},
pmid = {41771971},
issn = {2045-2322},
support = {JCYJ20220530153201003//Science and Technology Planning Project of Shenzen Municipality/ ; GDRC202119//Natural Science Foundation of Top Talent of SZTU/ ; 82104362//National Natural Science Foundation of China/ ; 20211063010055//Research Founding of Post-doctor who came to Shenzhen/ ; SDAIT-20-05//Shandong Province Traditional Chinese Medicine Industry Project/ ; 2022ZDJS119//Guangdong Province Key Discipline Construction Research Project/ ; },
}

@article {pmid41771954,
year = {2026},
author = {Nicotra, D and Mosca, A and Dimaria, G and Tessitori, M and Vetukuri, RR and Catara, V},
title = {Temporal dynamics of the tomato rhizosphere microbiome in response to synthetic communities of plant growth-promoting rhizobacteria.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41771954},
issn = {2045-2322},
abstract = {UNLABELLED: The rhizosphere microbiome plays a crucial role in plant health and productivity, yet intensive agriculture has diminished soil microbial diversity, increasing reliance on chemical inputs. Plant growth-promoting rhizobacteria offer a sustainable alternative, enhancing nutrient uptake, stress tolerance, and pathogen resistance. While single-strain inoculants have shown promise, microbial consortia may improve resilience through functional diversity. However, their impact on resident microbial communities remains understudied. In this study, three SynComs (four, six, and ten strains) were assembled from taxonomically diverse native PGPR strains identified as part of the tomato core microbiome, including Bacillus, Pseudomonas, Glutamicibacter, Paenarthrobacter, Chryseobacterium and Leclercia. All consortia significantly enhanced tomato growth, with the six- and ten-strain SynComs (containing Pseudomonas) exhibiting the most pronounced effects, increasing plant height by up to 94% in the indeterminate-growth variety ‘Proxy’. High-throughput sequencing revealed that while temporal factors were the primary drivers of community assembly, SynCom application triggered dynamic, time-dependent shifts specifically targeting the bacterial “rare biosphere”. Early-stage (T1) responses were characterized by the enrichment of rare bacterial taxa involved in key biogeochemical processes, such as the sulphur (Sulfurovum, Desulfosporosinus) and nitrogen (Azospirillum) cycles. By four weeks post-inoculation, community responses converged, primarily through the depletion of rare taxa and a predicted functional redirection toward xenobiotic degradation pathways. While SynCom strains showed a decline in absolute abundance over time, the persistence of growth-promoting effects suggests that these consortia act through early-stage indirect microbiome modulation rather than long-term high-density colonization. Furthermore, the consortia exerted a subtle cross-kingdom influence, modulating fungal succession by sustaining Basidiomycota and Mucoromycota populations. These findings demonstrate that small, host-derived, taxonomically diverse SynComs can enhance tomato growth and restructure rhizosphere microbial communities, especially impacting rare bacterial taxa and metabolic potential of the communities, with Pseudomonas-containing consortia exerting the most pronounced effects. These insights support the use of tailored, core-based microbial communities to improve crop productivity and soil health, though further research is needed to optimize SynCom design for agricultural applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-41114-0.},
}

@article {pmid41771940,
year = {2026},
author = {Li, Y and Azman, EA and Ismail, R and Deng, X and Dhar, S and Noviardi, R and Citraresmini, A and Zi, T and Yang, L},
title = {Effect of root promoter on tobacco (Nicotiana tabacum L.) growth and nutrient accumulation at Hunan Province, China.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-40215-0},
pmid = {41771940},
issn = {2045-2322},
}

@article {pmid41771883,
year = {2026},
author = {Mao, C and Jin, W and Dou, L and Guo, T and Huang, J and Wang, Y and Liu, X and Wu, S and Qiao, W and Xiang, Y and Zhu, Y and Wu, J and Yeung, KWK},
title = {Bioengineered ROS-tolerant probiotic reshapes gut microbiota-host axis to ameliorate type 2 diabetes in male mice.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-70138-3},
pmid = {41771883},
issn = {2041-1723},
support = {2023YFB3810200//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 21200592//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; 22210832//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; 23220952//Food and Health Bureau (Food and Health Bureau of the Government of the Hong Kong Special Administrative Region)/ ; },
abstract = {The pandemic-scale progression of type 2 diabetes mellitus (T2DM) necessitates innovative interventions targeting the pathogenic triad of insulin resistance, dysregulation of lipid metabolism, and gut microbiome dysbiosis. Here, we report a synthetically bioengineered probiotic consortium (REcN-F/Ca) developed through directed metabolic adaptations of Escherichia coli Nissle 1917 (EcN) under iterative hydrogen peroxide selection, subsequently functionalized with fructooligosaccharide-calcium carbonate composites. REcN-F/Ca exhibits enhanced reactive oxygen species tolerance through upregulated antioxidant enzymes and hydrogen sulfide-mediated redox balancing, alongside improved gastrointestinal survivability. In high-fat diet-induced obese male mice, REcN-F/Ca restores gut microbiota diversity, enriches butyrogenic taxa (Lachnospiraceae and Blautia), and rescues short-chain fatty acids depletion. Transcriptomic profiling reveals PPAR signaling activation, driving lipid metabolism and suppressing adipose inflammation. These effects translate to systemic metabolic improvements with attenuated weight gain (-25.4%), restored glucose homeostasis, and reduced insulin resistance (HOMA-IR: -73.2%) in the obesity and T2DM murine model. Our findings establish REcN-F/Ca as a synthetically engineered probiotic that simultaneously corrects intestinal ecological perturbations and reverses host metabolic dysfunction, proposing a paradigm for metabolic syndrome management.},
}

@article {pmid41771597,
year = {2026},
author = {Payne, T and Shaw, A and Hanjani, LS and Homes, R and Giddens, F and Ravuri, HG and Yap, CX and Walsh, J and Kumar, V and Garton, FC and Rhee, H and Huang, A and Francis, RS and Reid, N and McAdams-DeMarco, M and Gordon, E and Midwinter, M and Hubbard, R},
title = {ReFIT study (reversing frailty in transplantation): protocol for a longitudinal study to assess clinical and biomedical changes in frailty through kidney transplantation.},
journal = {BMJ open},
volume = {16},
number = {3},
pages = {e100158},
doi = {10.1136/bmjopen-2025-100158},
pmid = {41771597},
issn = {2044-6055},
abstract = {INTRODUCTION: Losses of functional reserve across multiple physiological systems have been identified in frail patients, yet the exact aetiology of frailty remains unclear. Although strongly associated with chronological age, frailty often develops at a younger age in patients with organ failure. Frailty is prevalent in patients with kidney failure; however, individuals experience improvements in physical frailty measures following kidney transplantation. This makes younger patients with kidney failure a unique population for studying both the accelerated onset of frailty and its reversal. This research project aims to test the hypothesis that frailty secondary to organ failure and age-related frailty are associated with similar molecular and physiological measures.

METHODS AND ANALYSIS: This longitudinal study will recruit 150 patients in three groups. Group A (kidney transplant recipients aged ≥40 years; n=50) and Group B (patients aged ≥40 years active on the kidney transplant waitlist; n=50) will comprise younger adults with frailty from organ failure. Group C (adults aged ≥65 years (or ≥55 years for Aboriginal and Torres Strait Islander patients); n=50) will comprise older community dwellers. The primary outcome is the Frailty Index (FI). Secondary outcomes include the change in FI over time, and at baseline when considering various clinical metadata, immune parameters, kidney function and nutrition intake which will be measured at baseline and 12-month time points. Longitudinal changes in frailty will be analysed using linear mixed models with multiple testing corrections for false discovery rates.Endocrine profiles and metabolomics, measures of immune function and microcirculatory dysfunction, will be measured by liquid chromatography-mass spectrometry and/or gas chromatography-mass spectrometry. The gut microbiome will be sequenced via shotgun metagenomics (Illumina NextSeq500, 150 bp paired-end, [3]Gbp/sample). Circulating cell-free DNA/mitochondrial DNA will be quantified through droplet digital PCR. Microcirculation will be assessed via sublingual dark field videomicroscopy with glycocalyx markers measured by ELISA.

ETHICS AND DISSEMINATION: This study will be conducted with all stipulations of this protocol, and the conditions of the ethics committee approval. Ethical principles have their origin in the Declaration of Helsinki, all Australian and local regulations and in the spirit of the standard of Good Clinical Practice (as defined by the International Conference on Harmonisation). Organs/tissues will be sourced ethically and will not be sourced from executed prisoners or prisoners of conscience or other vulnerable groups.Ethics approval was received by the Metro South Health Research Ethics Committee (HREC/2023/QMS/95392) and ratified by the University of Queensland.Results will be disseminated through peer-reviewed publications, academic conferences, participant newsletters and health organisation collaboration.},
}

@article {pmid41771438,
year = {2026},
author = {Lynch, SV and Nagler, CR and Rachid, R},
title = {Microbial Therapeutics for the Prevention and Treatment of Food Allergy.},
journal = {The journal of allergy and clinical immunology. In practice},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaip.2026.02.024},
pmid = {41771438},
issn = {2213-2201},
abstract = {Food allergy affects approximately 8% of children and 11% of adults in the United States. Available treatment including oral immunotherapy and anti-IgE are not known to lead to remission. There is now increasing evidence implicating the gut microbiome as a key regulator of allergic inflammation. Distinct microbial and metabolomic alterations characterize food-allergic individuals, and gnotobiotic mouse models show that fecal microbiota from food-allergic donors transfers allergic sensitization, whereas microbiota from healthy donors protects from anaphylaxis through induction of tolerogenic Foxp3[+]RORγt[+] regulatory T cells. Goblet cell-derived resistin-like molecule beta (RELM β) induces food allergy through modulation of the gut microbiome and depletion of indole-producing species. These findings have inspired the development of five microbial therapeutics approaches: probiotics, rationally defined bacterial consortia, fecal microbiota transplantation, metabolite-based approaches, and biologics targeting dysbiosis-associated pathways. Early-phase clinical studies support feasibility, yet long-term safety, durability, and reproducibility remain uncertain. Major challenges include inter-individual variability, ecological complexity, and regulatory standardization. Microbiome-directed therapeutics hold promise to transform food allergy management from temporary desensitization toward remission and durable immune tolerance. The application of systems biology approaches integrating metabolomics, transcriptomics, and immune phenotyping will be essential to unravel the complex host-microbial interactions that underlie the efficacy of these approaches.},
}

@article {pmid41771260,
year = {2026},
author = {Vaughn, SN and Pavlovsky, JC and Jackson, CR},
title = {Bacterial Communities in Sand and Seawater of Northern Gulf Coast Beaches: Temporal, Spatial, and Environmental Influences.},
journal = {Environmental microbiology reports},
volume = {18},
number = {2},
pages = {e70309},
pmid = {41771260},
issn = {1758-2229},
support = {//U.S. Department of the Treasury/ ; //Mississippi Department of Environmental Quality/ ; //Mississippi Based RESTORE Act Center of Excellence/ ; },
abstract = {Coastal microbial communities play critical roles in marine food webs and biogeochemical cycling, yet their diversity and function remain poorly characterised in many regions. This is especially evident along the northern Gulf coast, a dynamic system with substantial freshwater influences. We used high throughput 16S rRNA sequencing to characterise bacterial communities in sand and seawater collected every 3 months (March 2024 through March 2025) from 10 beaches along a 53 km stretch of the Mississippi coast. The diversity and composition of these communities were related to environmental variation and to biogeochemical function as determined from the activity of enzymes related to carbon, nitrogen, and phosphorus mineralisation. Our findings revealed distinct bacterial communities in sand and seawater, with the microbiome of each habitat showing greater temporal variation over the course of the study than spatial variation between beaches. Patterns in bacterial community structure and proportions of abundant taxa were strongly linked to physicochemical variables, while enzyme activities suggested how microbial communities may contribute to biogeochemical processes in these habitats. Collectively, these findings provide critical information for understanding microbial ecology in this system and highlight the central role of bacteria in mediating ecosystem function along a dynamic and understudied coastline.},
}

@article {pmid41771225,
year = {2026},
author = {Maria-Alexia, P and Cristina, R and Andreea-Ramona, T and Octavian, A and Viorica, R},
title = {Familial colorectal cancer: risk factors, screening strategies and personalized medicine.},
journal = {Cancer genetics},
volume = {302-303},
number = {},
pages = {166-175},
doi = {10.1016/j.cancergen.2026.02.008},
pmid = {41771225},
issn = {2210-7762},
abstract = {Colorectal cancer (CRC) remains a leading cause of cancer-related mortality worldwide, with approximately 25-30 % of cases exhibiting a familial component driven by germline mutations in DNA mismatch repair genes (Lynch syndrome) or the APC gene (familial adenomatous polyposis). Despite advances in screening and early detection, significant challenges persist in identifying at-risk individuals, optimizing surveillance strategies and addressing disparities in access to genetic testing and preventive care. This narrative review synthesizes current evidence on the genetic underpinnings, modifiable risk factors and personalized screening approaches for familial CRC. We highlight the critical interplay between hereditary predisposition and environmental exposures including diet, obesity, smoking and gut microbiome alterations, which cumulatively influence disease penetrance and clinical outcomes. Emerging predictive models integrating family history, polygenic risk scores and proteomic biomarkers offer unprecedented opportunities for risk stratification, enabling tailored screening initiation and intervals that balance clinical efficacy with cost-effectiveness. Novel non-invasive biomarkers, such as circulating tumor DNA and stool RNA tests, demonstrate promising sensitivity and specificity, potentially enhancing patient adherence while complementing gold-standard colonoscopy. Furthermore, artificial intelligence-assisted endoscopy and comprehensive genetic panels are reshaping precision oncology by improving adenoma detection rates and guiding targeted therapies. Addressing social determinants of health and implementing structured genetic counseling remain essential to achieving equitable CRC prevention. By transitioning from age-based to individualized, risk-adapted screening paradigms, healthcare systems can significantly reduce CRC incidence and mortality, particularly among genetically predisposed populations.},
}

@article {pmid41771203,
year = {2026},
author = {Khan, SM and Hussain, JM and Khan, B and Saad, A and Mehboob, J and Rukh, G and Manzoor, M and Mughal, AW and Kayani, A and Baig, MA and Khan, SRM and Saleem, Z and Hashim, R},
title = {Dark side of nocturnal eating: Unraveling the emerging axis between meal timing, gut microbiota, and early-onset cancer risk.},
journal = {Nutrition research (New York, N.Y.)},
volume = {148},
number = {},
pages = {1-14},
doi = {10.1016/j.nutres.2026.01.007},
pmid = {41771203},
issn = {1879-0739},
abstract = {The worldwide increase in early-onset metabolic disorders and digestive system cancers has elicited serious concern about lifestyle and diet as contributors to chronic disease risk. Disruption of circadian rhythms, particularly through nocturnal eating, is implicated in the development of various malignancies. This narrative review explored the emerging interplay between nocturnal eating, gut microbiota disruption, and early-onset cancer risk. Literature was sourced from PubMed, Scopus, Google Scholar, and Elsevier databases, emphasizing mechanistic studies and key findings in chrononutrition, microbiome research, and oncology. Nocturnal eating desynchronizes central and peripheral clocks, alters clock-gene expression, and provokes gut dysbiosis and inflammatory signaling that promote tumorigenic pathways. In contrast, daytime-aligned time-restricted eating (TRE) has shown potential to restore circadian synchrony, enhance metabolic resilience, and improve gut health even in the absence of caloric restriction. While TRE's role in cancer prevention remains hypothetical, its circadian benefits warrant further investigation. Overall, meal timing represents a modifiable factor influencing metabolic health and possibly early carcinogenesis. Aligning eating behavior with intrinsic circadian rhythms may help mitigate cancer risk and improve long-term well-being.},
}

@article {pmid41771182,
year = {2026},
author = {Carrillo, MP and Berrojalbiz, N and Sánz, C and Iriarte, J and Trilla-Prieto, N and Calbet, A and Saiz, E and Barata, C and Dachs, J and Vila-Costa, M},
title = {Copepod-associated microbiome responses to organophosphate ester plasticizers and other bioaccumulative organic pollutants in the ocean.},
journal = {Water research},
volume = {296},
number = {},
pages = {125640},
doi = {10.1016/j.watres.2026.125640},
pmid = {41771182},
issn = {1879-2448},
abstract = {Organic pollutants pose a growing threat to ocean ecosystems, largely due to their persistence, bioaccumulation potential, and toxicity. Yet, directly measuring the full spectrum of pollutants in situ remains unfeasible, and thus there is a dearth of alternative indicators of exposure. Host-associated microbiomes offer a promising but underexplored approach to fill this gap. Along a latitudinal transect of the Atlantic Ocean (40°N - 52°S), we observed significant correlations between the relative abundance of Enterobacterales in copepod-associated bacterial communities and seawater concentrations of organophosphate esters (OPEs), polycyclic aromatic hydrocarbons (PAHs) and with some perfluoroalkyl acids (PFAAs). All these chemicals bioaccumulate in marine zooplankton. Laboratory exposures of the copepod Paracartia grani to environmentally relevant OPE concentrations revealed similar microbiome composition shifts and decreased fecundity, revealing active depuration processes, including microbial degradation and fecal pellet production. These findings establish the basis for exploring host-associated microbiomes as sensitive indicators of bioaccumulative contaminant exposure in marine ecosystems, offering a novel avenue for large-scale pollution monitoring.},
}

@article {pmid41770930,
year = {2026},
author = {Bai, X and Li, Z and Chen, B and Qian, X and Guo, Y and Wang, Q and Chen, C and Chen, W and Shen, X and Liu, J and Jin, J and Zhang, W and Liu, Q and Chen, S and Yang, S and Xu, L and van der Heijden, MGA and Tiedje, JM and Jiao, S and Wei, G},
title = {High bacterial diversity drives the suppression of a soilborne plant disease.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {10},
pages = {e2509303123},
doi = {10.1073/pnas.2509303123},
pmid = {41770930},
issn = {1091-6490},
abstract = {The rhizosphere microbiome plays a crucial role in the resistance to soilborne plant diseases. However, the principles needed to explain and predict which microbiota will be effective against soilborne pathogens are still lacking due to the complexity of the soil microbial community. We hypothesized that, independent of particular microbial strains, a high diversity is associated with, or increases the probability of, effective suppression. We tested this hypothesis by demonstrating that random combinations of rhizosphere microbial isolates, with the same bacterial diversity, had an equal impact on suppressing root diseases. The incidence of root rot was significantly reduced when soil bacterial diversity was high. We further investigated how high-diversity bacterial communities suppress root rot by constructing synthetic bacterial communities (SynComs). The results suggest that high bacterial diversity suppresses pathogens through mechanisms potentially including nutrient competition and the formation of physical barriers on the root surface. Our study highlights that high bacterial diversity is beneficial for suppressing soilborne plant diseases, offering a nonchemical and sustainable approach for crop disease management.},
}

@article {pmid41770903,
year = {2026},
author = {Wang, X and Sun, H and Tan, Y and Xu, S and Liu, Z and Ji, K and Qiu, D and Deng, J and Feng, B and Wu, X and Iwakura, Y and Chen, M and Feng, R and Huang, C and Tang, C},
title = {Colonic Engyodontium fungus triggers neutrophil antimicrobial activity to suppress Lactobacillus johnsonii-derived glutamic acid-maintained Tregs.},
journal = {The Journal of clinical investigation},
volume = {},
number = {},
pages = {},
doi = {10.1172/JCI196788},
pmid = {41770903},
issn = {1558-8238},
abstract = {Isolating commensal fungi from mouse intestines has been challenging, limiting our understanding of their role in intestinal immune homeostasis and diseases. Using an Fc fusion protein of the C-type lectin Dectin-2, we successfully purified the commensal Ascomycota fungus Engyodontium sp. from mouse feces. Engyodontium enhances the antimicrobial activity of colonic neutrophils via CARD9 pathway, and exacerbates colitis by impairing the colonization of intestinal Lactobacillus johnsonii (L. johnsonii) WXY strain. L. johnsonii produces high levels of L-glutamic acid by expressing the glutaminase-encoding gene glsA to facilitate Treg expansion via enhancing IL-2 receptor signaling. Patients with Crohn's disease (CD) and ulcerative colitis harbored increased Engyodontium and decreased L. johnsonii abundance. Engyodontium directly induced calprotectin in human colonic neutrophils, and CD patients exhibited lower levels of L-glutamic acid which also promoted human Treg expansion. These findings highlight the Engyodontium-calprotectin axis against the Lactobacillus-glutamate-Treg cascade to aggravate colitis, suggesting commensal Engyodontium-triggered signaling as a therapeutic target for mucosal inflammatory diseases.},
}

@article {pmid41770693,
year = {2026},
author = {Lin, A and Bik, EM and Costello, EK and Dethlefsen, L and Haque, R and Relman, DA and Singh, U},
title = {Correction: Distinct Distal Gut Microbiome Diversity and Composition in Healthy Children from Bangladesh and the United States.},
journal = {PloS one},
volume = {21},
number = {3},
pages = {e0343568},
pmid = {41770693},
issn = {1932-6203},
abstract = {[This corrects the article DOI: 10.1371/journal.pone.0053838.].},
}

@article {pmid41770447,
year = {2026},
author = {Sosanya, ME and Temple, JL},
title = {Two Sides of a Coin: Molecular, metabolic, and Phenotypic Convergence in Pediatric Undernutrition and Obesity.},
journal = {Current obesity reports},
volume = {15},
number = {1},
pages = {},
pmid = {41770447},
issn = {2162-4968},
abstract = {PURPOSE OF REVIEW: This narrative review juxtaposes the metabolic and molecular consequences of pediatric under- and overnutrition, highlighting the similarities and differences between these two nutritional states occurring simultaneously in different parts of the world.

RECENT FINDINGS: Numerous biological changes in pediatric acute undernutrition and obesity have been linked to elevated risks of chronic metabolic disorders. We summarize recent evidence on pathophysiological pathways and outcomes common to both conditions. Despite etiological divergence, early-life nutritional imbalances converge on shared mechanisms and consequences with intergenerational implications.

SUMMARY: Both acute undernutrition and obesity in childhood have intersecting long-term outcomes including insulin resistance, type 2 diabetes, cardiovascular diseases, hepatic steatosis, cancers, and others, mediated through endocrine, immunological, epigenetic, and gut microbiome pathways, albeit via diverse specific mechanisms. Robust, longitudinal studies in varied geopolitical settings are needed to further elucidate the complex mechanisms, long-term phenotypic consequences, and therapeutic effects in these twin conditions.},
}

@article {pmid41770016,
year = {2026},
author = {Martins, I and Silva, JM and Almeida, JR},
title = {HYMET: A Hybrid Metagenomic Pipeline for Accurate and Efficient Taxonomic Classification.},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag024},
pmid = {41770016},
issn = {2047-217X},
abstract = {BACKGROUND: Reliable taxonomic classification of metagenomic sequences remains constrained by high mutation rates, fragmented assemblies, and large heterogeneous reference databases. HYMET (Hybrid Metagenomic Tool) was developed to overcome these challenges through a two-stage hybrid design combining adaptive Mash-based screening with Minimap2 alignment and a coverage-weighted Lowest Common Ancestor (LCA) classifier. Its sample-adaptive thresholds and on-the-fly reference database construction enable efficient, domain-agnostic classification while maintaining accuracy across divergent genomes.

RESULTS: Across seven CAMI assembly datasets in contig mode, HYMET achieved a mean F1 of 83.89%, with genus-level F1 of 76.75% and species-level F1 of 60.18%, while averaging 115.93 s runtime and a mean peak memory of 6.24 GB. Performance remained stable under mutation rates up to 30% for most domains (F1 ≥ 0.8), with viral sequences showing the expected decline (F1 ≈ 0.5 at 30%). Read and contig inputs produced nearly identical results when sharing reference caches, and real-world datasets confirmed robustness with the human gut metagenome reproduced typical anaerobic profiles, while in the ZymoBIOMICS mock community HYMET recovered all bacterial members; a further ground-truth evaluation on the ZymoBIOMICS Gut Microbiome Standard (D6331) yielded near-perfect genus-level concordance (Pearson r = 0.998, Bray-Curtis =0.04) across bacteria, fungi, and archaea.

CONCLUSIONS: HYMET achieves a practical balance of accuracy, efficiency, and scalability for metagenomic classification. Its adaptive candidate selection, alignment-anchored taxonomy, and reproducible reference caching collectively enhance performance across domains. HYMET source code is fully available at https://github.com/ieeta-pt/HYMET.},
}

@article {pmid41769660,
year = {2026},
author = {He, X and Chen, C and Shen, L and Su, X and Xie, H and Yang, M and Jiang, W},
title = {Retrospective insights into probiotic and prebiotic interventions: associations with gut microbiota profiles and nutritional outcomes.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1729480},
pmid = {41769660},
issn = {2296-861X},
abstract = {BACKGROUND: Probiotics and prebiotics are known to regulate the gut microbiota, however, their relations with the metabolic and nutritional outcomes in adults are under-investigated in practical environments.

OBJECTIVE: To provide light on microbiome-targeted metabolic health initiatives, this retrospective study investigates relationships among probiotic and prebiotic therapies, gut microbiota profiles, and nutritional outcomes.

METHODS: Clinical and nutritional history (n = 350 adults) in probiotic (n = 140), prebiotic (n = 120), and control (n = 90) were compared. The microbiota data were obtained with the help of 16S rRNA sequencing in the stool samples at baseline and 4-12 weeks of the intervention. Alpha (Shannon, Simpson) and beta diversity (Bray-Curtis) was evaluated by means of PERMANOVA, and the relative abundance of the main taxa (Lactobacillus spp., Bifidobacterium spp., Faecalibacterium prausnitzii) was determined. The adjusted ANCOVA and multivariate regression models adjusted to the difference between baseline were used to analyze the anthropometric and biochemical outcomes, including body mass index (BMI) and lipid profiles.

RESULTS: Alpha diversity (Shannon index: probiotics 3.4-4.2, p < 0.01; prebiotics 3.3-4.0, p < 0.01) and beta diversity clustering (PERMANOVA R2 = 0.12, p < 0.001 in probiotics) were significantly increased by the use of probiotics and prebiotics, respectively. Lactobacillus (2.1-4.8%, p < 0.01) and Bifidobacterium (3.5-7.9%, p < 0.001) were increased due to probiotic supplementation, whereas Bifidobacterium (3.7-6.8%, p < 0.001) and F. prausnitzii (6.1-8.3%, p = 0.04) were increased due to prebiotics supplementation. The two interventions were better than controls in terms of BMI and lipid levels (reduction of BMI: probiotics -1.6 + - 0.4 kg/m2, prebiotics -2.0 + - 0.5 kg/m2; total cholesterol: probiotics -18 + -5 mg/dL, prebiotics -17 + -6 mg/dL; all p < 0.05).

CONCLUSION: The use of probiotic and prebiotic supplementation was found to be related to an augmented gut microbial and better metabolic results in grown-ups. Such results point to possible advantages of the dietary microbiota modulation, but due to the retrospective design, it is not possible to make causal conclusions.},
}

@article {pmid41769659,
year = {2026},
author = {Alhodieb, FS},
title = {Microbial biofortification of fermented foods: a review of probiotic-mediated nutrient enhancement.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1754233},
pmid = {41769659},
issn = {2296-861X},
abstract = {Microbial biofortification via probiotic fermentation is a unique solution to reducing micronutrient deficiencies worldwide and it is a sustainable approach to prevention and German fermentation is widely applicable for plant-based diets as these micronutrients, such as B12 and K, are hardly present. Fermentative microbes such as Lactobacillus, Bifidobacterium, Propionibacterium synthesis of the vitamins like folate, riboflavin, vitamin K. They also facilitate the accessibility of minerals and increase the quality of proteins in many foods. This process not only enhances vitamins and minerals as a result of antinutrient such as phytate breakdown, but also bioactive peptides and short-chain fatty acids are produced. These are beneficial compounds for gut health and are helpful to the health of the immune system. Studies in labs, animals, and humans indicate that consumption of biofortified fermented foods increases micronutrient levels, promotes gut microbial balance, and increases immunity. In order to exploit this approach to its fullest potential, there are hurdles to overcome, ensuring that the strain remains viable, enhancing product taste, and overcoming regulatory hurdles. Future advances will require engineering strains of probiotics to produce even greater amounts of vitamins and implementing personalized microbiome information, as well as their public health interventions, in resource-limited situations.},
}

@article {pmid41769655,
year = {2026},
author = {Ray, S and Shankaran, P},
title = {Nutrition and the gut microbiome: a symbiotic dialogue influencing health and disease.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1761992},
pmid = {41769655},
issn = {2296-861X},
abstract = {The gut microbiome, a complex consortium of trillions of microorganisms, significantly influences human health through its metabolic activities, immune modulation, and interaction with the nervous system. Diet plays a significant role in shaping the gut microbiome, with plant-based diets promoting the colonization of beneficial bacteria and fiber fermentation, whereas meat-based diet may encourage harmful microbial shifts associated with systemic inflammation. Gut bacteria produce short-chain fatty acids (SCFAs) from dietary fibers and those are crucial for energy metabolism, intestinal integrity, and immune modulation. Certain neurotransmitters like GABA and serotonin produced by gut bacteria, play a vital role in the gut-brain axis. Dysbiosis in the gut microbiota have been linked to various psychiatric and neurological disorders like anxiety, depression, bipolar disorder, Schizophrenia, Alzheimer's and Parkinson's. Beyond neurological implications, the gut microbiota also linked to metabolic and cardiovascular diseases, including obesity, hypertension, and coronary artery disease, as well as colorectal cancer. Imbalances in bacterial ratios, such as Firmicutes to Bacteroidetes, can impact metabolism and inflammation. This review (i) elucidates the complex interplay between nutrition and the gut microbiome, emphasizing its implications for human health and disease; (ii) critically examines the methodological and analytical limitations inherent in current metagenomic studies; and (iii) proposes an integrated, multi-layered, systems-level framework for developing predictive models of host-microbe interactions and their pathological significance.},
}

@article {pmid41769611,
year = {2026},
author = {Li, X and Xu, S and Li, Y and Wang, R and Qin, C and Wang, X},
title = {Research Progress on the Mechanisms of Gut Microbiota Dysbiosis Associated With Idiopathic Pulmonary Fibrosis: A Review.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e102429},
pmid = {41769611},
issn = {2168-8184},
abstract = {Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive fibrotic interstitial lung disease with an incompletely understood pathogenesis. In recent years, growing evidence has highlighted the critical role of gut microbiota dysbiosis in the onset and progression of IPF. This review comprehensively summarizes the characteristics of gut microbiota alterations associated with IPF, explores the underlying mechanisms driving these changes, and examines their impact on disease development. Particular emphasis is placed on the emerging concept of the "gut-lung axis," which elucidates the bidirectional communication between the intestinal microbiome and pulmonary health. The review further discusses microbial metabolites and immune modulation as key mediators linking gut dysbiosis to pulmonary fibrosis. Additionally, current advances in microbiota-targeted therapeutic strategies, including probiotics, prebiotics, and fecal microbiota transplantation, are analyzed for their potential in IPF management. By systematically integrating recent findings, this article aims to deepen the understanding of IPF pathophysiology and provide a theoretical foundation for novel treatment targets centered on gut microbiota regulation.},
}

@article {pmid41769608,
year = {2026},
author = {Beniwal, P and Singla, M and Kar, DP and Bhargava, V and Chandra, N and Sinha, DK and Ruhela, V and Jha, R and Joseph, R and Rs, V and Bhosle, N and Mehta, K and Bajpai, S},
title = {Multispecies Probiotic Supplementation in Chronic Kidney Disease (CKD): Insights From Indian Nephrology Experts.},
journal = {Cureus},
volume = {18},
number = {1},
pages = {e102520},
pmid = {41769608},
issn = {2168-8184},
abstract = {Chronic kidney disease (CKD) is a progressive condition leading to the accumulation of uremic toxins and systemic complications, eventually resulting in loss of kidney function. One of the major mechanisms behind the CKD complications is gut dysbiosis, a commotion in the gut micro-ecology that aggravates systemic inflammation and worsens the CKD management. Probiotics, through their ability to restore gut micro-ecology, strengthen the intestinal barrier integrity, modulate the immune system, and mitigate systemic inflammation, offer a promising add-on therapy to traditional CKD therapies. Specific probiotic strains, including Streptococcus thermophilus, Lactobacillus acidophilus, Bifidobacterium longum, and Bacillus coagulans, have demonstrated antimicrobial effects by promoting commensal bacterial growth and inhibiting pathogenic bacterial growth. Studies indicate that these probiotics reduce uremic toxin levels, such as indoxyl sulfate and p-cresyl sulfate, blood urea nitrogen, urea, and creatinine levels, enhance gut integrity, alleviate inflammation, and are beneficial for patients with CKD stages 3 to 5. While the evidence for probiotic supplementation is promising, further studies are required to establish their long-term benefits, especially in patients with immune deficiency or kidney transplants. Overall, this consensus article provides insights from Indian nephrology experts on the potential benefits of multispecies probiotic supplementation in CKD patients, focusing on improving their quality of life, delaying disease progression, and ultimately augmenting survival outcomes.},
}

@article {pmid41769348,
year = {2026},
author = {Sun, M and Zang, D and Zhou, H and Che, YL and Chen, J},
title = {Epistemic compression in large language model explanations of the gut-liver axis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1773593},
pmid = {41769348},
issn = {2235-2988},
abstract = {BACKGROUND: The gut-liver axis integrates intestinal barrier function, microbial ecology, metabolism, immune regulation, and hepatic feedback, yet remains causally non-closed and strongly context dependent. As large language models (LLMs) increasingly mediate biomedical explanation, their ability to preserve evidentiary structure within such epistemically open frameworks requires systematic evaluation.

METHODS: We conducted a cross-platform, mixed-methods infodemiology analysis of five widely accessible LLMs. Twenty clinically grounded questions spanning five hierarchical domains from basic mechanisms to intervention and evaluation generated 100 single-turn responses. Linguistic accessibility was assessed using seven established readability indices, while epistemic integrity was evaluated using the Journal of the American Medical Association Benchmark Criteria, Global Quality Score, and a modified DISCERN framework.

RESULTS: Linguistic complexity increased as prompts progressed toward intervention and evaluation, without corresponding gains in transparency, reliability, or educational quality. Informational integrity clustered primarily by platform rather than domain. Readability indices showed strong internal concordance, whereas integrity metrics aligned only moderately and correlated weakly with readability. Item-level analysis revealed consistently high narrative clarity but systematic under-signaling of source attribution and uncertainty, resulting in over-coherent explanations that compressed conditional associations into mechanism-like claims.

CONCLUSIONS: LLM explanations of the gut-liver axis are susceptible to epistemic compression driven by narrative fluency rather than factual error. Readability does not reliably indicate epistemic robustness in decision-adjacent contexts. These findings support shifting evaluation and governance from platform comparison toward concept-conditioned requirement engineering that enforces provenance, calibrated uncertainty, and explicit separation of correlation, mechanism, and actionability as generative outputs approach clinical relevance.},
}

@article {pmid41769343,
year = {2026},
author = {Yan, X and Zhang, X and Wang, L and Song, W and Qi, T and Wang, Z and Tang, Y and Sun, J and Xu, S and Yang, J and Shao, Y and Chen, Y and Wang, J and Chen, J and Zhang, R and Liu, L and Shen, Y},
title = {Gut microbiota alterations and microbial translocation in HIV/SARS-CoV-2 co-infected patients.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1688580},
pmid = {41769343},
issn = {2235-2988},
abstract = {OBJECTIVE: To characterize gut microbiome alterations and microbial translocation in human immunodeficiency virus (HIV)/severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) co-infected patients and identify microbial signatures associated with COVID-19 severity.

METHODS: In this cohort study, blood and fecal samples from 38 HIV/AIDS patients (20 SARS-CoV-2 co-infected [PC group]; 18 SARS-CoV-2-negative [NC group]) were analyzed. The PC group was stratified by COVID-19 severity: mild-to-moderate (PC1, n=13), severe-to-critical (PC2, n=3), and mixed infections (PC3, n=4). Serum lipopolysaccharide (LPS), soluble CD14 (sCD14), and zonulin levels were measured to assess microbial translocation and gut barrier integrity. Fecal metagenomic profiling was performed via whole-genome shotgun sequencing (Illumina NovaSeq/HiSeq).

RESULTS: Co-infected patients exhibited significantly elevated plasma LPS (78.09 vs 48.72 pg/mL, p=0.032) and sCD14 (2667 vs 1927 ng/mL, p=0.0015) compared to controls. Although no differences in α-diversity or overall taxonomic abundance were observed between the PC and NC groups, 329 PC-unique and 216 NC-unique microbial species were identified. Nine genera demonstrated diagnostic potential for co-infection [Area Under the Curve (AUC), >0.7] with Akkermansia showing the highest predictive value (AUC = 0.811). Critically, Blautia abundance was significantly reduced in severe-to-critical cases (PC2) versus mild-moderate cases (PC1, p=0.043) and controls (NC, p=0.006). Besides, our function prediction for gut microbiota suggested that SARS-CoV-2 may exacerbate lipid metabolic dysregulation in HIV-infected individuals.

CONCLUSIONS: HIV/SARS-CoV-2 co-infection is characterized by heightened microbial translocation and species-specific microbiota alterations rather than global dysbiosis. Blautia depletion may correlate with COVID-19 severity.},
}

@article {pmid41769336,
year = {2026},
author = {Wu, Y and Han, B and Zhang, B and Li, J and Ren, B and Su, Z},
title = {Metabolic crosstalk between oral microbiota and the host in OSCC: emerging roles of microbial metabolites in tumor initiation and progression.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1778329},
pmid = {41769336},
issn = {2235-2988},
abstract = {Oral squamous cell carcinoma (OSCC) is an aggressive malignancy characterized by profound metabolic reprogramming and a persistently poor clinical outcome. Beyond genetic and environmental risk factors, growing evidence indicates that dysbiosis of the oral microbiome is associated with metabolic perturbations observed in OSCC and may contribute to tumor initiation and progression. Microbiome-derived metabolites represent a previously underappreciated layer of cancer metabolism, linking microbial activity to host metabolic states, epigenetic regulation, and immune dysfunction within the tumor microenvironment. In this review, we provide a comprehensive synthesis of current evidence highlighting how microbial metabolites shape metabolic vulnerabilities in OSCC through the microbiome-metabolite-host axis. We focus on key metabolite classes, including short-chain fatty acids, tryptophan-derived metabolites, sulfur-containing compounds, and other emerging metabolic intermediates, and discuss their roles in modulating cellular energy metabolism, epigenetic remodeling, oxidative stress responses, and immune evasion. Particular emphasis is placed on the context-dependent and often dualistic functions of metabolites such as butyrate, which can exert tumor-suppressive or tumor-promoting effects depending on microbial source, concentration, and local inflammatory conditions. By integrating insights from metabolomics, microbial functional profiling, and mechanistic studies, this review underscores microbial metabolism as an integral component of OSCC pathobiology. Recognizing microbial metabolites as active metabolic regulators rather than passive byproducts provides a conceptual framework for identifying novel biomarkers and metabolic intervention strategies in OSCC.},
}

@article {pmid41769334,
year = {2026},
author = {Zhong, L and Zhou, X and Su, J and Zhang, Y and Zhang, D and Wan, H},
title = {Microbiome dysbiosis and therapeutic restoration in atopic dermatitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1693905},
pmid = {41769334},
issn = {2235-2988},
abstract = {Atopic dermatitis (AD) is increasingly recognized as a chronic inflammatory skin disease driven by a self-reinforcing vicious cycle involving skin barrier dysfunction, immune dysregulation, and cutaneous microbiome dysbiosis. A hallmark of this dysbiosis is the overrepresentation of pathogens like Staphylococcus aureus and Malassezia species, alongside a marked loss of microbial diversity, particularly during disease flares. This review systematically dissects the host-derived factors-such as altered lipid profiles, reduced antimicrobial peptides, and elevated skin pH-that facilitate S. aureus colonization. We further examine how bacterial virulence factors amplify type 2 inflammation and impair barrier integrity, thereby sustaining the pathological loop. We also explore the emerging roles of the skin virome, particularly the phageome, and discuss how microbiome-targeted interventions, including bacteriotherapy with commensal bacteria and precision phage therapy, offer promising avenues for ecological restoration. Finally, we argue that future research must leverage multi-omics to understand strain-specific functions, ultimately guiding the development of personalized microbiome interventions for AD.},
}

@article {pmid41768933,
year = {2025},
author = {Ameer, A and Saleem, F and Keating, C and Afzal, F and Irshad, H and Ahmed, K and Sattar, S and Ijaz, UZ and Javed, S},
title = {Avian cecal microbiome response and resilience to Newcastle disease are dictated by breed background.},
journal = {Frontiers in systems biology},
volume = {5},
number = {},
pages = {1659648},
pmid = {41768933},
issn = {2674-0702},
abstract = {A wide range of viral infections threaten the long-term sustainability of poultry production. Newcastle disease (ND), caused by Newcastle disease virus (NDV), is endemic in most Asian countries, including Pakistan, causing 50%-100% mortality in young and mature chickens. Some local chicken breeds show resistance to certain diseases and have greater survival probability. The chicken gut microbiome is linked to immune response against infections and to production performance parameters. The present study aims to comprehend disease resistance patterns in multiple chicken breeds with respect to gut microbial communities. Day-old Naked Neck, Black Australorp, Rhode Island Red, white layer, and broiler chicks were raised on an antibiotic-free diet in a semi-controlled setup. Vaccinated and non-vaccinated birds were challenged with NDV. Disease onset was delayed in breeds other than broilers, in which disease symptoms appeared at day 3 post-challenge with maximum severity and mortality. Other breeds, irrespective of vaccination, survived through the challenge period. Naked Neck showed the least variation in clinical features and growth parameters. A lower diversity in broiler groups with a significant decrease after NDV challenge was revealed by 16S rRNA amplicon sequencing of cecal DNA. Furthermore, broiler cecal core microbiome membership was found to be more variable than other breeds. Moreover, differentially abundant genera were observed across treatment groups and breeds with a similar effect on the predicted metabolic pathways, indicating varied energy metabolism responses. Shotgun metagenomics revealed a higher abundance of functional genes, including antimicrobial resistance (AMR) genes, stress genes, virulence genes, and amino acid degradation genes in the broiler NDV-infected group compared to the control group. The gut microbiota in chickens affects immunity to infections, health, and productivity. Compared to broilers, local chicken breeds, specifically Naked Neck, are found to have high immune competence in resisting ND while maintaining most performance metrics. Broilers show lower alpha diversity with an unstable core microbiome. Therefore, stable core microbiome maintenance may help the birds cope with the viral infection. The results support the farming of resistant chicken breeds over broilers to reduce production losses from NDV outbreaks.},
}

@article {pmid41768524,
year = {2026},
author = {Hirano, T and Wagatsuma, K and Shimomori, Y and Akita, K and Nakamura, T and Yamakawa, T and Yokoyama, Y and Kurumi, H and Ishigami, K and Nagaishi, K and Nakase, H},
title = {Loss of Nonhematopoietic Osteopontin Weakens the Intestinal Barrier and Alters the Microbiome and Metabolome in Mice.},
journal = {Gastro hep advances},
volume = {5},
number = {4},
pages = {100883},
pmid = {41768524},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Inflammatory bowel disease (IBD) is characterized by intestinal barrier disruption and dysregulated interactions between host immunity and gut microbiota. Osteopontin (OPN) is considered a proinflammatory mediator in IBD, but nonhematopoietic cell-derived OPN may exert barrier-protective functions. This study aimed to determine the effects of OPN in a murine model of acute colitis.

METHODS: We examined wild-type and OPN knockout mice under steady-state conditions and in dextran sulfate sodium-induced colitis, including bone marrow chimeras to distinguish the effects of hematopoietic and nonhematopoietic OPN.

RESULTS: Overt colitis did not occur under steady-state conditions. Compared with wild-type mice, OPN knockout mice exhibited crypt elongation, goblet cell hyperplasia, and increased epithelial proliferation. Gene expression analysis revealed reduced interleukin (IL)-22, IL-23, and IL-13 levels alongside increased interferon-γ, IL-1β, and IL-17A levels. 16S rRNA sequencing revealed increased alpha diversity, expansion of Akkermansia and Prevotellaceae, and reduced Lactobacillus abundance. Functional prediction identified enrichment of microbial sulfur metabolism pathways, and metabolomic analysis demonstrated increased L-proline and L-(-)-fucose levels and reduced β-sitosterol levels. These shifts indicate enhanced mucinolytic activity and altered energy metabolism, consistent with a latent "preinflammatory state." Bone marrow chimera experiments demonstrated that OPN deficiency in the recipients reproduced changes in the microbiota composition and lipocalin-2 expression at the steady state and conferred heightened susceptibility to dextran sulfate sodium-induced acute colitis, irrespective of donor genotype.

CONCLUSION: These findings indicate that nonhematopoietic cell-derived "guardian-type" OPN preserves barrier integrity, sustains IL-22/IL-23 production, and maintains microbiota-metabolome balance, whereas its loss induces a preinflammatory state that predisposes to acute mucosal injury. These findings provide a conceptual basis for stage- and source-specific therapeutic strategies in IBD.},
}

@article {pmid41768503,
year = {2025},
author = {Lundberg, HE and Kafel, J and Holo, H and Larsen, SE},
title = {Daily cheese intake positively affects serum osteocalcin levels, vitamin K status and bone turnover markers in elderly men and women.},
journal = {BMJ nutrition, prevention & health},
volume = {8},
number = {2},
pages = {e000933},
pmid = {41768503},
issn = {2516-5542},
abstract = {INTRODUCTION: Daily intake of vitamin K2-rich Jarlsberg cheese is shown to positively affect bone turnover markers (BTMs) in fertile women. How do postmenopausal women and adult men respond to a cheese intervention?

PURPOSE: To estimate the optimal daily efficacy dose (OED) of Jarlsberg cheese to increase serum osteocalcin level in postmenopausal females and males past 55 years of age and estimate the effect on BTMs.

METHODS: Ten expected healthy postmenopausal females and 10 healthy males past 55 years voluntarily participated in a two-dimensional response surface pathway designed dose-response study with three design levels. The duration of each design level was 4 weeks. Blood samples were taken at baseline and the end of each design level for measurements of osteocalcin (OC), vitamin K2, the BTMs procollagen type 1 N-terminal propeptide (P1NP) and serum cross-linked C-telopeptide type I collagen (CTX-1) and other biochemical parameters.

RESULTS: In the female group, the OC level increased significantly (p<0.01) during the first design level but decreased slightly during the second and third design levels. Among males, the OC level increased monotonously during the study and significantly in the second and third design levels (p<0.01). There was no significant change in P1NP, but CTX decreased significantly (p≤0.05) in both sex groups. The ratio P1NP/CTX increased significantly (p≤0.05) in the female group. S-phosphate and s-urea increased significantly (p≤0.02) while s-calcium and s-magnesium were unchanged. After the study, four of the participating women received a diagnosis of osteoporosis.

CONCLUSION: Estimated OED of Jarlsberg cheese was 47 and 67 g/day for postmenopausal females and adult males, respectively. The development in OC and BTMs suggests an anabolic effect of Jarlsberg cheese on bone tissue.},
}

@article {pmid41768492,
year = {2025},
author = {Vignal, L and de Lahondès, R and Gillibert, A and Tavolacci, MP and Prifiti, E and Formstecher, E and Ribet, D and Quillard, M and Coeffier, M and Déchelotte, P},
title = {Metagenomic analysis of salivary microbiota in patients with anorexia nervosa and association with functional digestive disorders (ORMICAN pilot study).},
journal = {BMJ nutrition, prevention & health},
volume = {8},
number = {2},
pages = {e001112},
pmid = {41768492},
issn = {2516-5542},
abstract = {BACKGROUND: Patients with anorexia nervosa (AN) have intestinal dysbiosis and are frequently affected by oral and upper gastrointestinal disorders. Until now, no metagenomic sequencing data were available on oral microbiota in AN.

DESIGN: This observational study enrolled 46 patients with restrictive/purging AN and 20 controls. Salivary samples were performed after fasting. DNA of oral microbiota from salivary samples was analysed by whole genome shotgun deep sequencing. The primary objective was to compare the diversity of oral microbiota between patients with AN and healthy individuals. Secondary endpoints were to assess the associations between the diversity of oral microbiota and the severity of functional digestive disorders, between patients with a restrictive type of AN and patients with a mixed/purging type and between the diversity of oral microbiota and the severity of AN.

RESULTS: We observed not only a significant decrease in the alpha diversity of oral microbiota in AN patients (4.47 (4.05; 4.75)) versus controls (4.81 (4.68; 5.04)) (p=0.001) but also in gene richness (p=0.00023). There was no significant correlation (95% CI) between oral microbiota diversity and functional digestive disorders nor between patients with a restrictive type of AN and patients with a mixed/purging type of AN, nor between the diversity of oral microbiota and the severity of AN. In addition, we observed four bacterial taxa that were decreased in AN patients.

CONCLUSION: Our study highlights a decreased diversity of oral microbiota in AN patients. Future larger studies may help identify the prognostic and therapeutic value of oral microbiota in AN.},
}

@article {pmid41768489,
year = {2025},
author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Iwasaki, M and Dinassing, A and Senthilkumar, R and Preethy, S and Abraham, SJK},
title = {Randomised trial of Aureobasidium pullulans-produced beta 1,3-1,6-glucans in patients with Duchenne muscular dystrophy: favourable changes in gut microbiota and clinical outcomes indicating their potential in epigenetic manipulation.},
journal = {BMJ nutrition, prevention & health},
volume = {8},
number = {2},
pages = {e000776},
pmid = {41768489},
issn = {2516-5542},
abstract = {OBJECTIVE: Duchenne muscular dystrophy (DMD) is an X-linked neuromuscular disorder that leads to increasing muscle weakening and early death. Steroids, the standard treatment of choice in slowing down disease progression, are plagued with adverse effects. Anti-inflammatory, antifibrotic effects and enhancement of muscle regeneration biomarkers after oral consumption of Aureobasidium pullulans strain N-163-produced beta 1,3-1,6-glucan (Neu REFIX) having been demonstrated in clinical and preclinical studies of DMD; in this study, we have investigated the effects on the gut microbiome in patients with DMD.

DESIGN: Twenty-seven patients with DMD were included in the study (control (n=9), N-163 (n=18)). Whole-genome metagenomic sequencing was performed in pre-N-163 and post-N-163 intervention faecal samples of each of these participants.

RESULTS: After N-163 beta-glucan administration, the constitution of the gut microbiome in all the participants was modified to one with positive outcomes on health. There was an increase in butyrate-producing species such as Roseburia and Faecalibacterium prausnitzii. There was a decrease in harmful bacteria associated with inflammation such as enterobacteria and Alistipes.

CONCLUSION: Beneficial reconstitution of the gut microbiome after Neu REFIX beta-glucan administration and its safety have been confirmed. These outcomes correlating with the anti-inflammatory, anti-fibrotic effects along with increase in dystrophin in skeletal muscle and plasma, reported earlier make us recommend further in-depth exploration on its role in epigenetic manipulation which when found encouraging might help other genetic diseases as well.

TRIAL REGISTRATION NUMBER: CTRI/2021/05/033346.},
}

@article {pmid41768415,
year = {2026},
author = {Panda, A and Adhikari, M and Nasker, SS and Nayak, AK and Das, D and Nayak, SK and Dash, SK and Nayak, S},
title = {Enhanced formulation of precision probiotics through active machine learning.},
journal = {Biology methods & protocols},
volume = {11},
number = {1},
pages = {bpag007},
pmid = {41768415},
issn = {2396-8923},
abstract = {The human gut microbiome is crucial to health, with dysbiosis increasingly linked to disease. Precision probiotics offer a promising approach to restoring microbial balance, but ensuring probiotic viability through gastrointestinal transit remains a challenge. This study applies an advanced active machine learning (ML) approach to predict how excipients affect the growth of Lactobacillus plantarum, a commonly used probiotic. State-of-the-art experiments were carried out to complement the ML study. Starting with five known excipient-probiotic interactions, we apply active ML over three rounds to predict the effects of 116 excipients, iteratively refining model certainty and accuracy. Five ML models-neural networks, gradient boosting, logistic regression, random forest, and support vector machines-were trained and evaluated, with the final model achieving certainty levels close to 90%. Unlike previous methods, which retrained new models per iteration, our approach continuously optimized a single model, enhancing prediction stability and reducing uncertainty spread. These results highlight the potential of active ML to support accurate excipient selection in probiotic formulations.},
}

@article {pmid41768127,
year = {2026},
author = {Alsaid, F and Davila, B and He, B},
title = {Plant-derived extracellular vesicles and nanoparticles: origins, functions, and applications.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1758558},
pmid = {41768127},
issn = {2296-4185},
abstract = {Plant-derived extracellular vesicles (PDEVs) and plant-derived nanoparticles (PDNPs) are emerging plant-based nanomaterials with growing relevance in biotechnology, agriculture, and health. Although often grouped together, they arise from distinct origins: PDEVs are actively secreted vesicles with selective cargo loading, whereas PDNPs form during tissue disruption and reflect the lipid-metabolite composition of plant biomass. This review summarizes recent progress in distinguishing these systems, including advances in biogenesis, isolation, biomarkers, and functional characterization. We highlight mechanistic insights into PDEV-mediated cross-kingdom RNA communication in plant immunity and the strong translational potential of PDNPs in oral drug delivery, immunomodulation, and microbiome regulation. Remaining challenges include standardization, scalable purification, and deeper mechanistic clarity. By clarifying their differences and complementary strengths, this review outlines a foundation for developing reliable plant-derived nanovesicle technologies.},
}

@article {pmid41768053,
year = {2026},
author = {Lv, M and Tian, D and Wang, G and Hou, C and Fan, T and Li, W},
title = {Salinity gradients alter root-zone soil microbiome structure and nitrogen-related functional potential in alfalfa (Medicago sativa L.): a pot experiment.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1753229},
pmid = {41768053},
issn = {1664-462X},
abstract = {INTRODUCTION: Soil salinization constrains agricultural sustainability in arid and semi-arid regions. This study examined integrated soil-plant-microbe responses of alfalfa (Medicago sativa L.) to a salinity gradient.

METHODS: A pot experiment was conducted with control, low-, and moderate-salinity treatments. Root-zone soil and plants were sampled to measure soil EC, pH, and inorganic nitrogen forms, and to assess plant growth traits. Shotgun metagenomics was used to characterize microbial community composition and metagenome-inferred functional potential.

RESULTS: Salinity increased soil EC and pH and altered inorganic nitrogen forms, with higher NO3 [-]-N under moderate salinity and lower NH4 [+]-N under salinity compared with the control. Plant height peaked under low salinity, whereas fresh and dry biomass decreased under both salinity treatments. Microbial β-diversity differed among treatments, while α-diversity showed limited responses. Functional annotations indicated treatment-associated trends in nitrogen- and stress-related categories and KEGG level 3 pathways; however, most differences were not significant after FDR correction.

DISCUSSION: This integrative root-zone assessment links salinity-driven soil chemistry changes with alfalfa performance and suggests coordinated shifts in soil chemistry, microbiome structure, and plant growth under salinity stress.},
}

@article {pmid41767851,
year = {2026},
author = {Khanehzar, E and Shams, F and Jafari, A and Poustforoosh, A},
title = {Next-generation AI-assisted drug design against cancer: large language models meet conventional in silico methods.},
journal = {In silico pharmacology},
volume = {14},
number = {1},
pages = {76},
pmid = {41767851},
issn = {2193-9616},
abstract = {UNLABELLED: Cancer remains a leading cause of death, with limited effective therapies. The AXL-GAS6 pathway promotes tumor growth, invasion, metastasis, and resistance to apoptosis. Large Language Models (LLMs) can predict drug-target interactions, generate novel molecular scaffolds, and optimize lead compounds. This study aims to design novel small molecules through a computational pipeline integrating commercial LLMs, molecular docking, molecular dynamics (MD), and ADMET evaluation. We combined DeepSeek LLM with conventional computational methods to design AXL inhibitors via three strategies: natural product-based, microbiome-derived, and FDA-approved drug-inspired scaffolds. Structured prompt engineering generated novel candidates, filtered for drug-likeness, synthetic feasibility, and docking score (Glide, Schrödinger). Top hits underwent 100 ns MD simulations and ADMET evaluation (SwissADME, ADMETLab3). AIC1 showed the highest binding affinity (- 10.079 kcal/mol), surpassing clinical-stage bemcentinib (- 8.234 kcal/mol). MD confirmed stable complexes (RMSD < 3 Å), with AIC1 and AIC4 forming extensive hydrogen bonds. ADMET profiling indicated favorable pharmacokinetics for all, with AIC2 exhibiting the lowest toxicity (hERG inhibition: 34.2%, hematotoxicity: 36.8%) and optimal drug-like properties. This work pioneers LLM-driven in silico design of AXL inhibitors, offering a scalable blueprint for accelerated anticancer drug development.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40203-026-00582-y.},
}

@article {pmid41767845,
year = {2026},
author = {Ortutu, BF and Okin, AO and Darkwah, KO and Onuorah, UM and Maigoro, AY and Iheme, GO},
title = {Gut microbiota and brain aging: a comparative review of African and western populations.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1740408},
pmid = {41767845},
issn = {1663-4365},
abstract = {As the population ages, cognitive decline and neurodegenerative diseases have become major public health concerns. The human gut microbiota plays a major role in regulating neurodevelopment, neuroinflammation, and cognitive decline through the gut-brain axis. Emerging evidence reveals a possible association between alterations in gut microbial diversity and age-related neurological disorders, including Alzheimer's disease and neurodegeneration. Regional and dietary differences shape the gut microbiome. These variations may, in turn, be associated with differences in brain aging across populations. Several cross-sectional studies indicate that rural African communities consuming predominantly fiber-rich diets exhibit distinct gut microbiota profiles characterized by increased abundance of genera, including Prevotella, Faecalibacterium, and Ruminococcus. These microbial configurations have been associated with improved gut barrier integrity, reduced systemic inflammation, and enhanced production of short-chain fatty acids in some preclinical and human studies. All these factors have been studied as potential mechanisms linked to delayed brain aging. Furthermore, epidemiological reports suggest lower prevalence rates of dementia and other neurodegenerative disorders in these populations, although such comparisons may be influenced by differences in study design, diagnosis, and case ascertainment across regions. This narrative review synthesized current understanding of the gut microbiota's role in brain aging, summarized available data on gut microbiota composition in African versus Western populations, and explored the pathways by which traditional African diets may contribute to neuroprotection. By critically examining this evidence and highlighting major research gaps, the review advocates for region-specific investigations and future longitudinal studies to validate causal links.},
}

@article {pmid41767840,
year = {2026},
author = {Kost, E and Kundel, D and Barthel, M and Conz, RF and Werner, RA and Ghiasi, S and Bublitz, TA and Mäder, P and Krause, HM and Six, J and Hartmann, M and Mayer, J},
title = {Drought increases root and rhizodeposition carbon inputs into soils.},
journal = {Plant and soil},
volume = {519},
number = {1},
pages = {103-127},
pmid = {41767840},
issn = {0032-079X},
abstract = {AIMS: Increasing droughts affect crop yield and health. Plants can respond to drought by adapting their root biomass, root morphology, and quality and quantity of rhizodeposition to improve water and nutrient uptake. Besides droughts, agricultural management influences roots and rhizodeposition; however, it is not well studied how agricultural management can affect the response of roots and rhizodeposition to drought.

METHODS: A semi-continuous [13]CO2 isotope labelling experiment was performed in a long-term field experiment comparing biodynamic, mixed conventional, and mineral conventional cropping systems. Rainout shelters were installed to induce drought. Root, net rhizodeposition, and the rhizosphere microbiome were determined at ripening of wheat.

RESULTS: Drought enhanced the total root carbon mainly through the increase of fine roots. Fine root carbon under drought was primarily enhanced in the mixed conventional and biodynamic cropping system, both receiving farmyard manure, whereas no increase was measured in the mineral fertilized conventional system. Net rhizodeposition carbon was enhanced in all cropping systems under drought, particularly in the first 0.25 m. While some plant-growth-promoting genera such as Streptomyces and Rhizophagus showed relative increases under drought, other plant growth-promoting genera often involved in nitrogen fixation such as Rhodoferax and Mesorhizobium were decreased.

CONCLUSION: This field trial suggests that drought increases total belowground carbon input via fine root and net rhizodeposition carbon inputs. Since fine root carbon increased under drought in cropping systems with farmyard manure, adding manure under future drought periods could be advantageous to increase soil carbon inputs and improve nutrient foraging.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-025-08021-1.},
}

@article {pmid41767763,
year = {2026},
author = {Samara, P and Athanasopoulos, M and Athanasopoulos, I},
title = {Benign, persistent, and invasive: mechanistic and translational approaches to middle‑ear cholesteatoma.},
journal = {Exploration of targeted anti-tumor therapy},
volume = {7},
number = {},
pages = {1002359},
pmid = {41767763},
issn = {2692-3114},
abstract = {Acquired middle-ear cholesteatoma is a histologically benign keratinizing squamous epithelial lesion that paradoxically exhibits locally destructive, recurrent, and invasive behavior, often resulting in ossicular erosion, hearing loss, labyrinthine fistula, and, rarely, intracranial complications. Surgical excision remains the primary management strategy; however, recurrence is common due to persistent microenvironmental drivers. Recent mechanistic studies-including single-cell transcriptomics, spatial proteomics, and epigenetic profiling-reveal a multifactorial pathogenesis orchestrated by chronic inflammation, proteolytic extracellular-matrix remodeling, osteoclast activation via RANKL and activin A, epithelial plasticity with partial epithelial-to-mesenchymal transition (EMT), and a dysbiotic, biofilm-forming microbiome. Emerging evidence further implicates oxidative stress, RNA and epigenetic modifications, miRNA dysregulation, and immune cell infiltration as central modulators of lesion chronicity and bone resorption. Collectively, these processes establish a self-sustaining pro-osteolytic microenvironment that drives bone erosion and postoperative recurrence. Cholesteatoma recapitulates several features of malignant lesions-hyperproliferation, local invasion, and stromal/immune cell recruitment-yet remains fundamentally benign, lacking metastatic potential and genomic instability. Its aggression is ecological rather than genetic, highlighting the potential for microenvironment-directed, precision-based strategies. Adjunctive approaches may include local delivery of modulatory agents, targeted interference with inflammatory, proteolytic, osteoclastogenic, and microbial axes, and biomarker-guided patient stratification. Preclinical and early-phase experimental studies assessing target engagement, radiologic stabilization, and molecular surrogates of efficacy could inform safer, mechanism-driven interventions that complement surgery, reduce recurrence, and preserve hearing. Integrating molecular pathobiology with clinical strategy positions cholesteatoma as a model for benign yet locally aggressive, microenvironment-driven disease, providing a roadmap for translational therapies with direct relevance to surgical practice.},
}

@article {pmid41767584,
year = {2025},
author = {Dang, Y and Xu, S and Huang, J and Peng, X and Yang, Y and Wang, Y and Yan, Y and Jiang, F and Wang, J and Liu, J},
title = {Comprehensive identification of microbial and metabolomic factors impacting ICC recurrence.},
journal = {Frontiers in oncology},
volume = {15},
number = {},
pages = {1703182},
pmid = {41767584},
issn = {2234-943X},
abstract = {INTRODUCTION: Intrahepatic cholangiocarcinoma (ICC) originates from intrahepatic bile duct epithelial cells and its global incidence is rising. Surgery remains the primary treatment, but postoperative recurrence rates remain high.

METHODS: We analyzed ICC patients' gut microbiota at four stages (preoperative, 7 days postoperative, 1 month postoperative, and during recurrence) using 16S rRNA sequencing and their serum metabolome via LC-MS/MS. Correlations among gut microbiota, metabolome, and clinical indicators were investigated, and candidate microorganisms and metabolites were integrated for multiomics clustering and staging.

RESULTS: This revealed significant increases in Bacteroides, Veillonella, and Enterococcus in ICC patients compared to healthy controls across all stages, suggesting these bacteria as potential markers of ICC progression. Microbial and metabolite changes were observed, with gut microbes influencing ICC development through kynurenic acid, linoleic acid, creatine, cholic acid, L-arginine, and the tumor microenvironment. Multiomics analysis showed that cholangiocarcinoma staging improves patient prognosis, particularly highlighting bile acids' role in type II hepatic phenotypes related to cholesterol metabolism.

DISCUSSION: Our study provides insights into ICC microbiome and metabolome associations with clinical features and survival.},
}

@article {pmid41767576,
year = {2026},
author = {Luppi, S and Topouzova, GA and Campisciano, G and Giolo, E and Bulfone, T and Rossi, F and Zito, G and Ricci, G and Comar, M and Andreuzzi, E},
title = {Impact of hormonal treatments for endometriosis on the reproductive microbiome: a systematic review.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1755725},
pmid = {41767576},
issn = {1664-302X},
abstract = {INTRODUCTION: The reproductive microbiome plays a key role in disease progression and fertility in women with endometriosis. Vaginal and endometrial dysbiosis has been increasingly linked to inflammation, impaired reproductive outcomes, and symptom severity. Although estro-progestins, progestins, and GnRH agonists are widely used, their impact on microbial communities remains poorly understood, highlighting the need to clarify microbiome-therapy interactions. This systematic review aims to comprehensively synthesize current evidence on how hormonal therapies influence the reproductive microbial environment and to offer insights for optimizing clinical management of endometriosis.

METHODS: Literature screening and data extraction followed PRISMA guidelines using PubMed, Scopus, and Google Scholar. The search combined terms on endometriosis, hormonal therapy, and reproductive microbiome. Non-English studies, reviews, and those without original data were excluded. Risk of bias was assessed with ROBINS-I-V2, and microbial composition and diversity were analyzed and synthesized qualitatively.

RESULTS: The literature search retrieved 577 publications, of which 6 met eligibility criteria and were analyzed. The evidence collected through sequencing or culture-based methods suggested that the use of hormonal therapies to treat endometriosis may impact both vaginal and endometrial microbiome, favoring the colonization of bacterial species associated with infertility. GnRHa resulted to foster the dominance of potentially pathogenic bacteria, as Gardnerella and Streptococcaceae, in the endometrium, and supporting bacterial vaginosis by increasing intermediate flora (Nugent score 4-6). A similar effect on the vaginal environment has been reported upon the use of oral contraceptive pills, which was shown to prompt the increase of Prevotella, Ureaplasma, Streptococcus anginosus and Streptococcus agalactiae, among other pathogenic microbes, and to enhance the Bacillota/Bacteroidota ratio.

DISCUSSION: Despite affected by several limitations and heterogeneity of included studies, this review provides a preliminary overview of the possible pejorative effect of hormonal therapy on the reproductive microbiome of endometriosis patients. While further investigations are required to consolidate these findings, the observations raised offer a valuable basis for opening a discussion about improving management strategies for affected women. By highlighting confounding factors overlooked in the selected papers, the present work will also be functional to optimize the design of future studies.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251042858, identifier PROSPERO (CRD420251042858).},
}

@article {pmid41767572,
year = {2026},
author = {Pattapulavar, V and S, SK and Ramanujam, S and Subburaj, S and John, GC},
title = {Probiotic-based therapeutics for a One Health future: redefining antibiotic dependency to combat antimicrobial resistance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1736436},
pmid = {41767572},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) has become a major One Health concern, affecting the interconnected microbial systems shared by humans, animals, and the environment. Decades of antibiotic-driven control have disturbed ecological stability and contributed to the expansion of the global resistome. This Perspective approaches AMR mitigation through an ecological restoration lens, outlining a three-part strategy that brings together probiotic therapeutics, microbiome-focused public awareness, and integrated surveillance. Probiotics are presented as biologically compatible tools that promote microbial stability through competitive niche occupation, immune support, and environmental biodegradation, thereby reducing selective pressures that favor resistance. In parallel, strengthening microbiome literacy can guide behavioral choices that support stewardship and reduce unnecessary antimicrobial use. The proposed One Health Microbiome Intelligence Framework (OH-MIF) adds a data-driven layer by linking genomic, clinical, agricultural, and environmental information through AI-enabled analytics. Together, these components form an adaptable system that shifts AMR management from reactive dependence on antibiotics toward a more resilient, coexistence-based approach. By aligning ecological interventions with education and policy intelligence, this Perspective positions microbial balance as a practical foundation for sustainable AMR control within broader planetary health goals.},
}

@article {pmid41767565,
year = {2026},
author = {Doku, TE and Belford, JDE and Sylverken, AA},
title = {Rhizosphere microbiome assembly drives metal sequestration in Leucaena leucocephala during tailing phytoremediation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1745018},
pmid = {41767565},
issn = {1664-302X},
abstract = {INTRODUCTION: Ghana's water and soil resources face severe challenges due to heavy metal contamination from gold mining operations. Although Leucaena leucocephala exhibits potential for phytoremediation, little is known about the contribution of its rhizosphere microbiomes to metal uptake and tolerance in multiple-metal contaminated tailings in field conditions.

METHODS: We investigated the rhizosphere bacterial community dynamics in L. leucocephala across three soil treatments (garden soil, 1:1 soil-tailings mixture, and pure tailings) using 16S rRNA amplicon sequencing and atomic absorption spectrophotometry. Briefly, transplanted seedlings of L. leucocephala were harvested at three-month intervals for three consecutive harvests to assess metal accumulation and changes in the microbiome.

RESULTS AND DISCUSSION: Leucaena leucocephala demonstrated notable tolerance to elevated metal concentrations (>10,000 mg/kg Fe and Mn) under acidic conditions (pH 4.57-5.97). Maximum metal uptake occurred at final harvest, with Fe reaching 14,605 ± 1.40 mg/kg in shoots and Mn reaching 12,279 ± 1.13 mg/kg in roots. The elevated concentrations of metals reduced overall bacterial diversity, except for selected metal-tolerant Actinobacteria, Proteobacteria, and Acidobacteria, which dominated bacterial communities across all treatments. The initial proliferation of Nocardioides and Streptomyces corroborated nutrient and metal-induced stress, while key genera such as Arthrobacter, Gaiella, Skermanella, and Chelatococcus showed strong positive associations with metal accumulation and maintained essential ecological functions.

CONCLUSION: Rhizosphere bacterial communities undergo stress-specific assembly processes, with specific taxa facilitating L. leucocephala's exceptional phytoremediation capacity. These findings provide insights into microbiome-enhanced strategies for mine site rehabilitation.},
}

@article {pmid41767558,
year = {2026},
author = {Song, L and Yu, QY},
title = {Stratified management of residual gastric cancer risk after Helicobacter pylori eradication.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779490},
pmid = {41767558},
issn = {1664-302X},
abstract = {Despite the established efficacy of Helicobacter pylori eradication in reducing gastric cancer (GC) incidence, a significant residual risk persists in successfully treated individuals, driven by lasting pathological alterations termed "oncogenic memory," including irreversible mucosal damage (e.g., intestinal metaplasia), residual pro-inflammatory and epigenetic "molecular scars," and gastric microbiome dysbiosis. This perspective synthesizes current evidence to advocate for a paradigm shift from a singular focus on pathogen clearance towards a comprehensive, risk-adapted management strategy. We propose a novel, dual-dimensional framework centered on a multidimensional risk assessment that integrates OLGA/OLGIM staging, demographic, lifestyle, and genetic factors to stratify post-eradication individuals into distinct risk categories. The framework subsequently outlines tailored surveillance protocols-specifying endoscopy frequency and advanced biomarker application-leverages technological support from AI-assisted endoscopy and molecular testing, and details differentiated resource allocation models based on regional GC incidence and economic development. This integrated approach provides a practical roadmap for implementing precision prevention, aiming to mitigate the lingering GC risk and ultimately reduce the global disease burden through a dynamic, lifelong management system beyond eradication. To facilitate implementation, we provide a user-ready risk calculator that operationalizes the multidimensional score for cohort-level application.},
}

@article {pmid41767542,
year = {2026},
author = {Effendi, RMRA and Witkam, WCAM and Dwiyana, RF and Suwarsa, O and Kraaij, R and Murad, C and Thio, HB and Nijsten, T and Pardo, LM},
title = {Profiling skin microbiota in an underrepresented population: Indonesian children with atopic dermatitis and controls.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1697420},
pmid = {41767542},
issn = {2296-858X},
abstract = {INTRODUCTION: The skin microbiome plays a central role in the pathogenesis of atopic dermatitis (AD), but most studies have focused on high-income populations of European ancestry. Microbiome data from tropical and developing regions remains limited. In Asia, microbiome research has similarly centered around developed countries, leaving populous developing countries like Indonesia underrepresented. The aim was to profile the cutaneous bacterial microbiota of children with AD from Indonesia and compare it with controls.

METHODS: Skin swabs were collected from lesional sites of 111 children aged 4-18 years with AD and from the forearms of 107 controls, all attending Pediatric Dermatology Clinic of Dr. Hasan Sadikin General Hospital, an urban tertiary-care referral center in Bandung, West Java, Indonesia. AD was diagnosed using Hanifin-Rajka criteria, while controls had non-atopic, non-inflammatory dermatological conditions. Cutaneous bacterial microbiota was profiled using 16S rRNA sequencing with amplicon sequence variant (ASV) level analysis using DADA2 pipeline. Data was analyzed after quality control to estimate alpha and beta diversities, the later using, permutational multivariate analysis of variance (PERMANOVA) to assess contribution of individual variables to the variation in microbiota composition. Univariable differential abundance was done to analysis the composition of specific bacteria in cases versus controls. Analysis of core microbiota compositions and phylogenetic relationships were explored to identify key taxa associated with AD.

RESULTS: Most children came from families with higher household incomes, and children with AD were younger than controls (mean age 8.35 ± 3.51 vs. 9.91 ± 3.79 years, P = 0.002). Lesional AD skin showed a significantly reduced alpha diversity and a marked overrepresentation of Staphylococcus aureus and Staphylococcus epidermidis. Less commonly reported genera, including Acetobacter and Gluconobacter, were enriched in cases, potentially reflecting environmental exposure in this cohort. PERMANOVA revealed that case-control status, family income, maternal atopy, maternal education and DNA concentration significantly influenced microbial composition. Phylogenetic analysis showed a clear lineage-level distinction between Staphylococcus ASVs.

CONCLUSION: Our findings reveal distinct microbial profiles in children with AD from a tropical, underrepresented population with predominantly higher household incomes, and underscore the role of environmental and sociodemographic factors associated with skin microbiota. While generalizability to lower-income or rural populations may be limited, the value of ASV-level analysis lies in its ability to capture both known and less characterized microbial signals.},
}

@article {pmid41767378,
year = {2026},
author = {Xu, Y and Cao, Y and Zou, L and Wulanna, and Liu, X and Yan, S and Liu, C and Gao, M and Zhan, J and Wang, Q and Wu, C},
title = {Protective role of aqueous Coriandrum sativum seed extract in diet-induced glucolipid metabolic disorder through gut-liver axis regulation.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1744741},
pmid = {41767378},
issn = {1664-2392},
abstract = {OBJECTIVE: To elucidate the protective effects of aqueous Coriandrum sativum seed extract against high-fat, high-sugar diet (HSFD)-induced glucolipid metabolic disorder in mice, with particular focus on gut-liver axis regulation involving hepatic metabolism, oxidative stress, inflammation, and gut microbiota composition.

METHODS: Male mice were fed an HSFD and orally treated with Coriandrum sativum seed extract (1.0 or 2.0 g/kg/day) for eight weeks. Biochemical parameters, histopathology, hepatic gene expression, oxidative stress markers, and gut microbial profiles were assessed via standard assays, RT-qPCR, Western blot, histological staining, and full-length 16S rRNA gene sequencing with functional prediction.

RESULTS: The extract significantly ameliorated HSFD-induced metabolic impairments, including hyperglycemia, hyperlipidemia, insulin resistance, and hepatic steatosis. Histological improvements were observed in the liver, pancreas, and colon. Hepatic expression of FAS, NF-κB, and IL-6 was suppressed, while PPARα and LDLR expression was restored. Antioxidant defenses were enhanced by reducing malondialdehyde and increasing superoxide dismutase activity. Microbiota analysis revealed partial restoration of beneficial taxa such as Lactobacillus murinus and Lachnospiraceae_UCG-006, alongside enrichment of microbial pathways related to energy and carbohydrate metabolism.

CONCLUSION: Aqueous Coriandrum sativum seed extract exerts systemic metabolic benefits in diet-induced glucolipid dysregulation by targeting the gut-liver axis. Its multi-targeted actions on hepatic metabolism, inflammatory signaling, oxidative balance, and gut microbiota composition support its potential as a natural therapeutic agent for metabolic disorders.},
}

@article {pmid41767368,
year = {2026},
author = {De Pasquale, C and Harrison, LC},
title = {Early-life antibiotic exposure and type 1 diabetes risk: a systematic review and meta-analysis.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1764522},
pmid = {41767368},
issn = {1664-2392},
abstract = {OBJECTIVE: Antibiotic exposure impacts the gut microbiome and potentially, in an infant, the developing immune system, with implications for the emergence of immune disorders such as type 1 diabetes (T1D). Reports of early-life antibiotic exposure on risk for T1D are inconsistent. We aimed to perform a systematic review and meta-analysis of the association between antibiotic exposure in early life and the development of T1D.

METHODS: Observational studies were assembled that reported an association between early-life antibiotic exposure and the development of T1D. Four early-life periods were covered: 12 months preconception, prenatal (in pregnancy), neonatal and up to 24 months postnatal. Medline, Embase, Web of Science Core Collection, and Scopus were searched from inception to August 28, 2024. All records were imported into Covidence for automated deduplication, abstract screening and full-text screening by two independent reviewers. Data from 20 studies and 10, 960 T1D cases were extracted and analysed using a random effects meta-analysis. Pooled odds ratios (ORs) and hazard ratios (HRs) with associated 95% confidence intervals (CIs) were calculated.

RESULTS: In the preconception period, maternal exposure to macrolide (OR = 1.23 [95% CI: 1.02-1.48]), sulfonamide/trimethoprim (OR = 1.34 [95% CI: 1.07-1.69]) or tetracycline (OR = 1.26 [95% CI: 1.11-1.44]) antibiotics was associated with an increased odds of T1D. Prenatal, neonatal and postnatal antibiotic exposure was not significantly associated with T1D.

CONCLUSION: Preconception exposure to specific antibiotic classes may represent a modifiable maternal risk factor for T1D in the offspring. This would have implications for antibiotic prescribing guidelines but requires validation by the further study of defined antibiotic classes and their exact timing of preconception exposure.

The protocol was pre-registered on PROSPERO (CRD42024589374) and followed PRISMA guidelines.},
}

@article {pmid41767236,
year = {2026},
author = {Tavassol, ZH and Farsi, F and Ettehad-Marvasti, F and Ejtahed, HS and Hasani-Ranjbar, S},
title = {Gut Microbiota Alterations in Hypothyroidism: A Pilot Study Revealing Increased Abundance of Specific Bacterial Genera.},
journal = {Journal of nutrition and metabolism},
volume = {2026},
number = {},
pages = {9988966},
pmid = {41767236},
issn = {2090-0724},
abstract = {BACKGROUND: Hypothyroidism (HT) is a prevalent thyroid disorder characterized by insufficient thyroid hormone production, leading to metabolic complications. Emerging research suggests a link between gut microbiota and thyroid regulation, positing that alterations in gut bacterial populations may contribute to HT's development and progression. This study aimed to investigate these associations by comparing gut microbiota compositions between individuals with HT and healthy adults, potentially refining diagnostic tools and therapeutic strategies.

METHODS: In this pilot study conducted between 2019 and 2023, 15 hypothyroid patients and 15 age- and gender-matched healthy controls participated in the study. Exclusion criteria were applied to eliminate confounding factors. Anthropometric data were collected, and stool samples underwent microbial analysis. Total bacterial DNA was extracted, and quantitative real-time PCR targeting 16S rRNA genes across eight bacterial genera was performed. The Mann-Whitney U test was used for statistical analyses.

RESULTS: No significant differences were observed in baseline demographic and anthropometric characteristics between groups. However, hypothyroid patients exhibited significantly elevated levels of Bacteroides, Bifidobacterium, Escherichia, Fecalibacterium, and Prevotella (p values < 0.001-0.030). No significant differences were found in levels of Akkermansia, Lactobacillus, or in the Bacteroides/Prevotella ratio.

CONCLUSION: This pilot study provides preliminary indications of a possible role of gut microbiota in the pathophysiology of HT. Variations in bacterial composition suggest a significant influence of gut health on thyroid regulation. Future studies with larger cohorts are needed to explore the biological pathways linking the gut microbiome to thyroid function, which may lead to novel microbiota-targeted therapeutic approaches.},
}

@article {pmid41767117,
year = {2026},
author = {Hu, T and Chen, Z and Yin, Z and Zhou, L and Chen, Q and Han, Y and Li, K},
title = {New concept in wound infection management: From bacterial eradication to microbiome modulation.},
journal = {APL bioengineering},
volume = {10},
number = {1},
pages = {010901},
pmid = {41767117},
issn = {2473-2877},
abstract = {Wound infection represents a significant challenge in clinical practice. Traditional wound management, targeting sterility and relying on strategies of broad-spectrum bactericidal activity and antibiotic dependence, achieves partial infection control but induces severe complications, including exacerbated bacterial resistance and skin microbiota dysbiosis. With the continuous advancement of microbiome research, a novel consensus has emerged: the key to wound healing lies not in the complete eradication of all microorganisms but in maintaining the dynamic balance of the microbial ecosystem. This review aims to elaborate on the paradigm shift from "bactericidal eradication" to "microbial modulation" in wound care, analyze the inherent limitations of conventional antibacterial strategies, and systematically summarize the critical roles of skin commensal microbiota in promoting wound healing through core mechanisms such as competitive inhibition, metabolic regulation, and immune modulation. Furthermore, it proposes that the core strategy of future wound care should focus on precision microbial modulation and discusses the application prospects of cutting-edge technologies, including probiotics, postbiotics, and individualized precision interventions. The innovative significance of this paradigm in wound dressing design is envisaged, emphasizing the development of novel materials integrating microbiota-specific regulatory capabilities and smart responsive functions. This work provides theoretical support for the precision prevention and control of wound infections, the improvement of healing quality, and technological innovation in the field of wound care.},
}

@article {pmid41767020,
year = {2026},
author = {Alachraf, K and Trouten, P and Thayer, J},
title = {Zoonotic Streptococcus canis Bacteremia Following a Dog Scratch in an Elderly Patient With a Nonconditional Pacemaker.},
journal = {Case reports in infectious diseases},
volume = {2026},
number = {},
pages = {2485747},
pmid = {41767020},
issn = {2090-6625},
abstract = {Streptococcus canis is a β-hemolytic Group G streptococcus commonly found in the microbiome of dogs and cats and is an uncommon cause of invasive human infection. Although typically regarded as a veterinary pathogen, S. canis has been reported to cause bacteremia, endocarditis, and other severe infections in humans, particularly in older adults with significant comorbidities or implanted medical devices. We describe a case of Streptococcus canis bacteremia in an 89-year-old woman with multiple comorbidities and a nonconditional permanent pacemaker who presented with fever, dyspnea, and severe lower back pain. Blood cultures grew S. canis, identified using standard microbiologic techniques. The clinical course raised concern for metastatic infection and pacemaker involvement. Imaging of the thoracic and lumbar spine demonstrated no evidence of discitis or osteomyelitis, and both transthoracic and transesophageal echocardiography showed no valvular or pacemaker lead vegetations. Further history revealed a dog scratch several weeks prior to presentation that resulted in skin disruption, representing a plausible portal of entry. The patient was treated with intravenous ceftriaxone with rapid clinical improvement, resolution of hypoxia, clearance of bacteremia, and declining inflammatory markers. She was discharged to inpatient rehabilitation to complete a 2-week course of antimicrobial therapy and recovered without evidence of recurrent infection. This case underscores Streptococcus canis as an uncommon but clinically relevant zoonotic pathogen and highlights the importance of detailed exposure history, appropriate microbiologic identification, and careful evaluation for device-related infection in high-risk patients.},
}

@article {pmid41766754,
year = {2026},
author = {Devinsky, O and Leitner, DF and Kamondi, A and Wisniewski, T},
title = {Epilepsy and Alzheimer Disease: Epidemiologic, Clinical, Molecular, and Neuropathologic Convergences and Divergences.},
journal = {Neurology. Clinical practice},
volume = {16},
number = {2},
pages = {e200589},
pmid = {41766754},
issn = {2163-0402},
abstract = {PURPOSE OF REVIEW: Alzheimer disease (AD) and epilepsy are major causes of neurologic disability and are reciprocally related: epileptiform discharges, subclinical seizures, and epilepsy are more prevalent in patients with AD compared with controls; progressive cognitive impairment commonly afflicts epilepsy patients; and late-onset epilepsy patients have higher rates of new-onset dementia.

RECENT FINDINGS: Epidemiologic studies support shared risk factors (e.g., genetic variants, vascular disease, sleep disorders, microbiome) with notable divergences. AD and epilepsy have some overlapping anatomic (e.g., hippocampus, entorhinal, and association cortex), clinical (e.g., memory, attentional, and executive) impairments, and neuropathologic (e.g., amyloid, tau, neurofibrillary tangles) features. Shared clinical and translational challenges include underlying mechanisms (e.g., genetic variants, neuroinflammation, metabolic and mitochondrial dysfunction, excitatory/inhibitory imbalance, microbiome, and sociodemographic factors) and identifying valid and reliable biomarkers (e.g., total tau and phosphorylated tau (p-tau), amyloid deposition, Aβ42/Aβ40 ratio) to assess disease progression, predict outcomes, and assess potentially disease-modifying interventions.

SUMMARY: Identifying convergences and divergences between epilepsy and AD may inform our understanding. The clinical, neurophysiologic, neuropathologic, and molecular pathologic changes in AD and epilepsy may reveal pathophysiologic insights and therapeutic opportunities.},
}

@article {pmid41766731,
year = {2026},
author = {Peddle, SD and Cando-Dumancela, C and Costin, S and Davies, T and Doane, MP and Edwards, RA and Hodgson, RJ and Krauss, SL and Liddicoat, C and Breed, MF},
title = {Soil Microbial Functions Indicate Persistent Agricultural Legacies and Potential Alternative States Following Restoration Plantings.},
journal = {Ecology and evolution},
volume = {16},
number = {3},
pages = {e73172},
pmid = {41766731},
issn = {2045-7758},
abstract = {Soil microbiomes are fundamental ecosystem components that are increasingly used to monitor the efficacy of restoration efforts. However, given high levels of functional redundancy among soil microbial taxa and the subsequent lack of definitive taxa-function links, taxonomic assessments (e.g., via metabarcoding) alone are limited for inferring ecological recovery. Here, we used shotgun metagenomics on soils from six post-agricultural restoration sites in southwest Western Australia to test whether soil microbial functional potential recovers following restoration plantings. We compared taxonomic and functional gene diversity and composition across degraded, passively regenerated, revegetated, and remnant land conditions. Effective number of functions (alpha diversity) did not differ across land conditions. However, functional composition (beta diversity) differed between remnant and revegetated conditions and associated with altered soil abiotic properties, especially elevated phosphorus. Remnant soils supported a greater diversity of phosphorus metabolism functions despite lower available phosphorus, indicating a microbial adaptation to nutrient limitation in phosphorus deficient soils. Rather than indicating a lack of functional recovery, these results suggest a functional response to persistent agricultural legacies that may reflect a shift toward an alternative state. Restoration interventions that aim to target the soil microbiome (e.g., soil inoculations) or directly address abiotic legacies (e.g., phosphorus mining plants) may therefore be required to facilitate recovery of the soil microbial functions and the wider ecosystem.},
}

@article {pmid41766653,
year = {2026},
author = {Jiang, Z and Zhai, C and He, C and Shen, L and Tang, G and Xu, L and Yang, H and Hu, H and Han, J},
title = {Effects and mechanisms of probiotics supplement on hypertension.},
journal = {Journal of hypertension},
volume = {},
number = {},
pages = {},
doi = {10.1097/HJH.0000000000004258},
pmid = {41766653},
issn = {1473-5598},
abstract = {The global population of individuals suffering from hypertension is estimated to surpass 1.28 billion. Uncontrolled hypertension makes contributions to the development of cardiovascular and cerebrovascular diseases. Emerging evidence indicates a significant correlation between hypertension and gut microbiota. As an intestinal regulator, which could confer health benefits to the host in adequate amounts, probiotics may become a novel approach to regulating blood pressure without side effects. Therefore, we overview the antihypertensive effects and the potential mechanisms of probiotics supplement on hypertension.},
}

@article {pmid41766520,
year = {2026},
author = {Wallander, K and Beijer, G and Eliasson, E and Giske, CG and Ponzer, S and Söderquist, B and Eriksen, J},
title = {Is current guidance for cloxacillin prophylaxis dosages in hip and knee arthroplasty adequate? Evidence from a prospective Swedish cohort.},
journal = {The Journal of antimicrobial chemotherapy},
volume = {81},
number = {3},
pages = {},
doi = {10.1093/jac/dkag067},
pmid = {41766520},
issn = {1460-2091},
support = {//Region/ ; FoUI-954900//Stockholm/ ; FoUI-973467//Stockholm/ ; FoUI-974859//Stockholm/ ; 2021-02699//Stockholm/ ; OLL-983304//Region Örebro County/ ; },
abstract = {OBJECTIVES: Perioperative antibiotic prophylaxis is crucial for preventing detrimental postoperative prosthetic joint infections (PJIs). Guidelines aim to prevent infection with methicillin-susceptible staphylococci-in Sweden through administering cloxacillin, at fixed doses with minimal consideration to kidney function or patient weight. Over- and under-dosing could have adverse effects, negative effects on the microbiome, or increase the risk of PJI. We aimed primarily to evaluate whether the current uniform prophylactic regimen of cloxacillin in hip and knee arthroplasty is adequate.

PATIENTS AND METHODS: Patients subjected to elective prosthetic joint surgery (N = 204) were included in a prospective study. Free plasma concentrations of cloxacillin were measured on three occasions throughout arthroplasty surgery. Samples were analysed using a validated HPLC-MS/MS method. A free concentration of <2 mg/L was deemed a theoretically appropriate concentration to suppress growth of methicillin-susceptible staphylococci in bone. A sensitivity analysis with values of 1 and 4 mg/L was included.

RESULTS: Potentially subtherapeutic concentrations (≤2 mg/L) at the end of surgery were found in 31 cases (15%). The corresponding numbers for 1 and 4 mg/L were 3 and 88 (1% and 43%). In multivariable logistic regression analysis, an ASA (American Association of Anesthesiologists physical status) score of I (relatively healthy patients), estimated glomerular filtration rate >90 mL/min/1.73 m2, body weight >100 kg and long duration of surgery significantly predicted suboptimal concentrations.

CONCLUSIONS: Current cloxacillin dosing in hip and knee arthroplasty surgery results in a risk for subtherapeutic levels in patients with high body weight and preserved renal function. Therefore, dosing guidelines for cloxacillin prophylaxis in arthroplasty should be reviewed.},
}

@article {pmid41766340,
year = {2026},
author = {Kovner, A and Kapushchak, Y and Pakharukova, M},
title = {Liver flukes and kidney injury: systematic review of human and animal data (from 1950 to 2025).},
journal = {Journal of helminthology},
volume = {100},
number = {},
pages = {e24},
doi = {10.1017/S0022149X26101187},
pmid = {41766340},
issn = {1475-2697},
support = {grant number 24-44-00048//Russian Science Foundation/ ; },
abstract = {Foodborne trematodes, particularly from families Opisthorchiidae and Fasciolidae, significantly impact human health. Research on trematode-related diseases has primarily focused on the hepatobiliary system and carcinogenic potential of these flukes. Nonetheless, chronic infection by these parasites likely affects other organ systems. This review emphasises the need to expand studies beyond the hepatobiliary system to fully understand the pathogenesis of liver fluke infections and advocates for a systematic approach to the management of affected humans. This review analyses scientific data from 1950 to 2025, including studies on laboratory animals, wild animals, and humans. Databases such as PubMed, Google Scholar, WHO, IARC, Rospotrebnadzor, and eLibrary were utilised. Common kidney injuries from trematode infections include glomerular and tubular damage, interstitial inflammation, and fibrosis. These injuries are influenced by liver damage and gut microbiome imbalances. Interspecies differences highlight the complexity of host-parasite interactions. Research indicates that foodborne-trematode-associated nephropathy exists in both humans and animals and involves immune complexes, oxidative stress, and biomarkers like KIM1. The documented renal damage underscores the need for further investigation into the mechanisms of the trematode-associated renal pathologies.},
}

@article {pmid41766326,
year = {2026},
author = {Troielli, P and Moreno, J and Cortes, A and Cardenas, P and Kerob, D and Gamarra, A and Dreno, B},
title = {Integrating Dermocosmetics Into Acne Care in Latin America.},
journal = {Journal of cosmetic dermatology},
volume = {25},
number = {3},
pages = {e70776},
pmid = {41766326},
issn = {1473-2165},
support = {//La Roche-Posay Laboratoire Dermatologique, L'Oreal Dermatological Beauty Division/ ; },
abstract = {BACKGROUND: Prescription acne products have proven efficacy and safety, yet management can pose a challenge. This review discusses the benefits of adding dermocosmetics to acne management.

METHODS: We add expert consensus with review of the literature to provide guidance for clinicians managing patients with acne in Latin America.

RESULTS: There is increasing evidence that dermocosmetics (over-the-counter cleansers, moisturizers, and sunscreens that contain acne-targeting ingredients) can be a good alternative to prescription acne treatments as well as adjuncts. Milder forms of acne may be present in any age patient, but prepubertal acne and acne cosmetica may be particularly well suited to a dermocosmetic approach. More severe acne may need a dermocosmetic added if there is sensitive skin or poor tolerance to prescription medications, and when the patient or family does not wish to use antibiotics or other acne prescription treatments. Dermocosmetics may be used as adjuncts to any type of prescription therapy, but may be most effective when used with products associated with skin irritation such as topical retinoids or benzoyl peroxide. Appropriate dermocosmetics can also fortify the skin barrier and help to protect the skin microbiome.

CONCLUSIONS: Acne management is complex and there can be adherence, tolerability, and efficacy problems. Dermocosmetics alone can be used in milder forms of acne or in maintenance post treatment, as a good compromise between efficacy and tolerability. As adjuncts, dermocosmetics can also decrease skin irritation and thereby increase adherence, can enhance the efficacy of prescription therapies, and can normalize dysbiosis in acne.},
}

@article {pmid41766111,
year = {2026},
author = {Zhao, C and Ye, S and Chen, M and Qian, J and Xu, J},
title = {First-line immunotherapy for advanced HER2-negative gastric cancer: differences between Asian and non-Asian patients.},
journal = {Cancer biology & medicine},
volume = {},
number = {},
pages = {},
doi = {10.20892/j.issn.2095-3941.2025.0398},
pmid = {41766111},
issn = {2095-3941},
support = {2024ZD0520600//Non-communicable Chronic Diseases-National Science and Technology Major Project/ ; },
abstract = {Emerging evidence suggests that the efficacy of immunotherapy in patients with advanced HER2-negative gastric cancer differs between Asian and non-Asian populations. This review examines potential factors contributing to these disparities, including differences in demographic and clinicopathologic characteristics, somatic mutations, molecular subtypes, tumor immunity, Helicobacter pylori (H. pylori) infection, dietary habits, and gut microbiome composition. These factors may serve as predictors of immunotherapy response in gastric cancer patients. For example, the prevalence of molecular subtypes and somatic mutations have been linked to variations in immunotherapy efficacy between Asian and non-Asian populations. In addition, differences in H. pylori infection rates, dietary habits, and gut microbiota composition may influence systemic immune responses, and consequently, immunotherapy outcomes. Understanding the factors contributing to these disparities in immunotherapy response is crucial for optimizing treatment strategies and improving outcomes for patients with gastric cancer. Further research into the mechanisms underlying racial and ethnic disparities in immunotherapy response is needed to identify potential biomarkers predictive of immunotherapy response in diverse patient populations.},
}

@article {pmid41766018,
year = {2026},
author = {You, Y and Peng, H and Gu, A and Liu, Y},
title = {High-throughput sequencing-based profiling of endophytic bacterial community composition and diversity in seeds of Yunnan cytoplasmic male-sterile rice.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {3},
pages = {},
pmid = {41766018},
issn = {1572-9699},
support = {Y20240210, QN2021105002L//the National Foreign Expert Program of China/ ; 20250484961, 20220484220//the Beijing Nova Program/ ; FM2025-09//the Opening Project of Food Microbiology Key Laboratory of Sichuan Province/ ; },
abstract = {As an important food crop in China, hybrid rice is of significant importance for national food security and supply. Cytoplasmic male-sterile (CMS) rice is a key component of hybrid rice technology, while plant endophytes, especially seed endophytes, play a crucial role in promoting plant growth and reproduction. Therefore, understanding the diversity and community structure of seed endophytes in CMS rice is essential for hybrid rice technology. However, relevant research in this area remains scarce. This study systematically analyzed the diversity and community structure characteristics of seed endophytic bacteria in 14 Yunnan CMS rice varieties (totaling 42 samples) based on Illumina NovaSeq 6000 high-throughput sequencing technology, aiming to elucidate the core microbial community structure and diversity. A total of 503 operational taxonomic units (OTUs) were identified. At the phylum level, the dominant microbial groups in all samples were Proteobacteria (relative abundance 91.53-99.95%). At the genus level, the core microbial community consisted of Pantoea (64.29-93.11%), Xanthomonas (1.08-16.97%), and Kosakonia (0.46-12.66%). Both α- and β-diversity analyses revealed no significant inter-line differentiation, indicating a highly stable and conserved endophytic bacterial community across the Yunnan CMS rice germplasm. This study provides the first comprehensive characterization of the seed-associated core microbiome of Yunnan CMS rice lines.},
}

@article {pmid41765557,
year = {2026},
author = {Wang, M and Zhao, J and Gao, J and Cai, S and Gu, Y and Liu, Y and Gao, L and Xu, Y and Wu, Y and Zhou, Z and Zhang, J and Tian, W},
title = {Deciphering the potential of Bacillus cereus HS-9 in cadmium bioremediation and ensuring rice safety.},
journal = {Journal of environmental sciences (China)},
volume = {162},
number = {},
pages = {573-583},
doi = {10.1016/j.jes.2025.05.044},
pmid = {41765557},
issn = {1001-0742},
abstract = {Cadmium (Cd) contamination in agricultural soils poses significant environmental and health risks due to its non-degradable and bio-magnifying nature. With the global imperative for eco-friendly Cd remediation strategies, microbial bioremediation emerges as a promising approach. Here, Bacillus cereus HS-9 was isolated from Cd-contaminated paddy soil using LB medium supplemented with 5 mg/L of Cd. HS-9 exhibited an impressive Cd removal efficiency of 95.44 % at a concentration of 5 mg/L. A rice pot experiment was conducted using Cd-contaminated soil, with HS-9 inoculation as the treatment group and non-inoculated soil as the control. The treatment group resulted in a 38.99 % reduction in soil Cd availability and a 34.33 % decrease in rice Cd content without affecting rice yield. The microbial community of the rice rhizosphere was analyzed using metagenome sequencing. The results revealed an increased abundance of czcA, frnE, and irlS genes in the soil microbiome, indicating enhanced Cd resistance and efflux capabilities. Microbial community showed significant shifts towards a beneficial microbial consortium, particularly marked by increases in Lysobacter and Sphingomonas genera which are known for their roles in heavy metal resistance and bioremediation. B. cereus HS-9 demonstrated significant potential for the bioremediation of Cd-contaminated soil. This study provides foundation for the development of microbial-based strategies for the eco-friendly remediation of heavy metal-polluted agricultural lands.},
}

@article {pmid41765175,
year = {2026},
author = {Clarke, BC and Ordinola-Zapata, R and Noblett, WC and Gould, M and Staley, C},
title = {Taxonomy and Virulence Factors in the Root Canal Microbiome: Metagenomic Insights by Lesion Size and Clinical Factors in Primary Endodontic Infections.},
journal = {Journal of endodontics},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.joen.2026.02.016},
pmid = {41765175},
issn = {1878-3554},
abstract = {INTRODUCTION: This study aimed to investigate the taxonomic and functional profiles of the root canal microbiome in teeth with large versus small periapical lesions, examining the influence of clinical variables on microbial composition and functional pathways.

METHODS: Samples from 25 teeth with large (>8mm) and 20 with small periapical lesions (<2mm) were analyzed. Quantitative PCR, 16S next-generation and whole genome sequencing (WGS) were used to assess microbial load, diversity, and composition. Functional predictions were performed using the KEGG and MetaCyc databases. Alpha diversity was calculated using Shannon and Chao1 indices. Beta diversity was assessed using ANOSIM and PERMANOVA. Significant variables were explored using MaAsLin3. Kruskal-Wallis tests were used for univariate comparisons.

RESULTS: Teeth with large lesions exhibited significantly higher bacterial load (p = 0.011), but comparable alpha diversity and number of species per group in 16S and Whole genome analysis (P > 0.05). Lesion size showed significance by ANOSIM (p = 0.04) but not in PERMANOVA (p = 0.36). Age was significant in both beta diversity tests, but the effect size only explained 3.6% of the variance. All clinical variables were not significant in 16S analysis for beta diversity. MetaCyc pathway analysis identified percussion sensitivity as the most influential clinical variable in both tests (ANOSIM R = 0.182, p = 0.012; PERMANOVA R[2] = 0.063, p = 0.046). MaAsLin3 modeling revealed enrichment of enzymatic pathways involved in methionine and cysteine-related metabolism.

CONCLUSIONS: Large periapical lesions contain significantly higher bacterial load, but similar diversity compared to small lesions. Functional predictions suggest bacterial metabolic activity may contribute to mechanical allodynia in endodontic infections.},
}

@article {pmid41765047,
year = {2026},
author = {Himmerich, H and Keeler, JL and King, JA and Ehrlich, S and Kaufmann, LK and Bulik, CM and Cohen-Woods, S and Wade, T and Steiger, H and Booij, L and Monteleone, P and Cascino, G and Monteleone, AM and Cuntz, U and Voderholzer, U and Tessema, SA and Lewis, YD and Sjögren, M and Hebebrand, J and Seitz, J and Tyszkiewicz-Nwafor, M and Karpenko, O and Mutwalli, H and Fetissov, SO and Mack, I and Dhopatkar, N and Mörkl, S and Kan, C and Uribe, MM and Yoshiuchi, K and Abuobeid, N and Kapogiannis, D and Stein, D and Bektas, S and Müller, DJ and Gorwood, P and Duriez, P and Montcel, CTD and Paszyńska, E and McElroy, SL and Wranik, WD and Fernandez-Aranda, F and Mehler, PS and Papežová, H and Roubalová, R and Procházková, P and Morris, R and Lewczuk, P and Hiemke, C and Berk, M and Karwautz, A and Treasure, J and Kasper, S and , and , },
title = {World Federation of Societies of Biological Psychiatry (WFSBP) consensus statement on candidate biomarkers for anorexia nervosa.},
journal = {The world journal of biological psychiatry : the official journal of the World Federation of Societies of Biological Psychiatry},
volume = {},
number = {},
pages = {1-92},
doi = {10.1080/15622975.2026.2626934},
pmid = {41765047},
issn = {1814-1412},
abstract = {OBJECTIVES: This World Federation of Societies of Biological Psychiatry (WFSBP) consensus paper aims to summarise and evaluate the published study results on objectively measurable biological markers associated with anorexia nervosa (AN).

METHODS: The relevant literature was reviewed by the WFSBP Task Forces on Eating Disorders and on Biological Markers, and a consensus regarding the significance of the published evidence was reached.

RESULTS: Candidate biological markers that have been associated with AN include clinical (e.g. body weight), molecular (e.g. genetic, epigenetic, hormonal, immunological, metabolomic), cellular (e.g. leukocytes), neuroimaging (e.g. structure, function, connectivity), digital, cardiac and neurophysiological parameters. Some clinical and laboratory parameters are risk markers in clinical practice. Biological markers have pathophysiological relevance in understanding the biological and metabolic pathophysiology of AN and its physical health consequences. Few studies have examined pharmacogenetics or therapeutic drug monitoring as tools to monitor and guide the treatment of AN.

CONCLUSIONS: Biological markers will hopefully soon enable clinicians to intervene earlier in a more targeted manner to mitigate treatment resistance. However, the current scientific basis for most biological markers are group comparisons only. Studies on sensitivity, specificity and the prognostic value of these markers are lacking.},
}

@article {pmid41764962,
year = {2026},
author = {Kong, J and Han, C and Shao, G and Feng, K and Song, C and Xie, Q},
title = {Virulence attenuation of intestinal pathogenicity via combined gene deletion in duck enteritis vaccine strain restores gut microbiota balance and enhances safety.},
journal = {Poultry science},
volume = {105},
number = {5},
pages = {106633},
doi = {10.1016/j.psj.2026.106633},
pmid = {41764962},
issn = {1525-3171},
abstract = {There is an increasing need for a new generation of effective and safe vaccines, in the context of large-scale poultry farming and the prevalence of infectious diseases. With this in mind, we developed, for the first time, a duck enteritis virus (DEV) mutant, ΔTK-ΔgI/gE-ΔgG/gJ, through the deletion of multiple virulence genes. The resulting gene-deletion strain exhibited replication kinetics similar to those of the parent strain and was found to be safe in various animal models, offering a strategy for rapidly generating attenuated DEV strains. Previously, our team reported that DEV infection leads to intestinal dysbiosis; however, the impact of DEV vaccines on the gut microbiota remains unclear. This study aimed to characterize the gut microbiota of ducks, chicks, and mice immunized with DEV strains using microbiome analysis, assess the effects on microbial composition, and compare the outcomes. Both two strains caused significant shifts in gut microbiota diversity. Both strains restored the diversity of the microbiota, whereas the parental vaccine caused the enrichment of potential pathogens in chicks. Moreover, the conventional DEV vaccine disrupted gut microbiota and morphology, but the gene-deleted strain largely reversed these changes. These findings may improve the safety of vaccine through gene editing, thereby enhancing the protection of target animals.},
}

@article {pmid41764831,
year = {2026},
author = {Peng, X and Zhang, L},
title = {Advances and challenges in the application of metagenomic sequencing for the diagnosis and treatment of infectious diseases: from pathogen spectrum identification to personalized antimicrobial strategies.},
journal = {Diagnostic microbiology and infectious disease},
volume = {115},
number = {2},
pages = {117321},
doi = {10.1016/j.diagmicrobio.2026.117321},
pmid = {41764831},
issn = {1879-0070},
abstract = {Infectious diseases remain a major global public health concern, demanding rapid and accurate identification of pathogens. Although conventional diagnostic methods such as culture, PCR, and immunological assays are widely used, they are limited by long processing times, narrow detection scopes, and poor capability for identifying unknown pathogens. untargeted shotgun metagenomic sequencing (mNGS), as a non-targeted, high-throughput detection technology, enables broad-spectrum identification of diverse microorganisms and functional gene annotation, making it an increasingly important complement in infectious disease diagnostics. This review summarizes the clinical value of mNGS in key scenarios such as neurological, respiratory, and bloodstream infections. It also discusses its utility in antimicrobial resistance (AMR) monitoring and personalized therapy, highlights current challenges in sensitivity, bioinformatics analysis, and result interpretation, and briefly explores future directions involving artificial intelligence (AI), multi-omics integration, and healthcare information system integration. The goal is to provide a reference for the standardized application of mNGS in infectious disease diagnosis and treatment.},
}

@article {pmid41764596,
year = {2026},
author = {Yao, W and Du, H and Kulyar, MF and Pan, H and Ren, H and Luo, Q and Bhutta, ZA and Liu, S and Fang, R and Li, J},
title = {Probiotic efficacy of Bacillus amyloliquefaciens TL106 from Tibetan pigs in metabolic syndrome: modulation of gut microbiota and metabolic in sows and suckling piglets.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-025-02328-y},
pmid = {41764596},
issn = {2049-2618},
abstract = {BACKGROUND: Metabolic syndrome disrupts metabolic resilience in periparturient sows and compromises piglet growth. As intestinal microbes govern host energy homeostasis, microbiome-directed feed additives represent a practical solution. We therefore evaluated the Tibetan‑pig isolate Bacillus amyloliquefaciens TL106, previously validated in weanlings for its capacity to alleviate sow-associated metabolic syndrome.

RESULTS: In a 43‑day trial (20 sows per group), dietary TL106 (5 × 10[9] CFU kg[-1]) increased digestibility of crude fiber (+ 12.5%, p < 0.05) and crude fat (+ 9.3%, p < 0.01), lowered serum IL‑1β (- 34%) and TNF‑α (- 28%), and boosted antioxidant enzymes and immunoglobulins (all p < 0.05). Litter performance improved, with a two‑thirds reduction in diarrhea and heavier piglets at 21 days (+ 15%, aggregate n = 300). Multi‑omics profiling revealed higher cecal α‑diversity, enrichment of butyrate‑producing Ruminococcus and Butyricicoccus (log2C 2.1 and 1.8; FDR < 0.05), and activation of histidine‑metabolism and ABC‑transporter pathways (q ≤ 0.03) in piglets, while pathways for amino‑acid biosynthesis, lipid utilization, and steroidogenesis were favored in sows.

CONCLUSIONS: Bacillus amyloliquefaciens TL106 simultaneously enhanced maternal metabolic health and neonatal development by reshaping gut microbiota and host metabolism, positioning it as a micro‑ecological tool for managing metabolic syndrome in Landrace × Yorkshire sows and Duroc × Landrace × Yorkshire suckling piglets. Video Abstract.},
}

@article {pmid41764594,
year = {2026},
author = {Geng, M and Zheng, Y and Tang, S and Fang, Z and Wang, T and Li, K and Chen, H and Zhang, J and Zhou, N and Wei, X and Yang, J},
title = {Gut T cell-microbiota crosstalk orchestrates antibacterial immunity and mucosal homeostasis in teleost.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02370-4},
pmid = {41764594},
issn = {2049-2618},
support = {2025T180854//China Postdoctoral Science Foundation/ ; 24ZR1419700//Natural Science Foundation of Shanghai Municipality/ ; 32373165//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: T cells cooperate with the intestinal microbiota to coordinate antimicrobial defense, but whether this crosstalk arose as an independent innovation in mammals or represents an evolutionarily conserved feature of vertebrate immunity remains unknown.

RESULTS: Using the teleost Nile tilapia as a model, we demonstrate that both systemic and localized infection with Edwardsiella piscicida induce enteritis, correlated with robust intestinal T cell responses. Selective T cell depletion triggered excessive expression of proinflammatory cytokines, impaired mucosal architecture, and diminished host resistance to infection, underscoring the essential role of T cells in gut immunity. Strikingly, T cell depletion also caused profound alterations in gut microbial composition, characterized by a sharp decline in beneficial taxa such as Cetobacterium and the expansion of opportunistic pathogens including Klebsiella and Acinetobacter, indicating that T cells are required to maintain microbiome homeostasis. Conversely, broad-spectrum antibiotic eradication of the microbiota provoked hyperproliferation of intestinal T cells and barrier disruption, revealing reciprocal regulation between T cells and commensals. From the gut content, we isolated a C. somerae strain SH518, whose dietary supplementation for 6-8 weeks enhanced the activation, proliferation, and effector function of intestinal T cells, preserved mucosal homeostasis during E. piscicida challenge, and even boosted systemic T cell immunity in the spleen.

CONCLUSIONS: Collectively, these findings demonstrate that teleost T cells engage in bidirectional interactions with gut microbiota to orchestrate both antimicrobial defense and mucosal homeostasis. We therefore propose that T cell-microbiota cooperation represents an evolutionarily ancient strategy predates terrestrial adaptation, offering new insights into the coevolution of mucosal T cell immunity and microbiome. Video Abstract.},
}

@article {pmid41764576,
year = {2026},
author = {Li, J and Ren, J and Xu, J and He, J and Xu, J and Yin, Q and Yao, J and Wu, S},
title = {Ability of the Chinese herbal residue to alleviate short-distance transportation stress in sheep through the remodeling of the rumen microbiome-metabolism axis.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {41764576},
issn = {1674-9782},
support = {2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 32573272//National Natural Science Foundation of China/ ; 2024//Shaanxi Province's Elite Recruitment Initiative: The Three Qin Talents Program - Regional Young Talent Project/ ; },
abstract = {BACKGROUND: Transportation is a common stressor in sheep production that is capable of inducing oxidative stress and impairing sheep health and production performance. This study aimed to investigate the alleviating effects of the traditional formula Siji Antiviral Mixture residue after water extraction, which still contains active ingredients, including fiber, polyphenols, and flavonoids, on short-distance transport stress in sheep, as well as its mechanism of action in regulating oxidative stress through the rumen microbiota‒metabolism axis.

RESULTS: Twenty first-lambing East Friesian × Hu sheep hybrids weighing 54.49 ± 7.94 kg were randomly assigned to a control group (CON, basal diet) or a Chinese herbal residue group (CMR, basal diet + 50 g/d CMR) feeding at 4 h after approximately 300 km of short-distance transport. Results indicated that 4 h of short-distance transport significantly elevated serum reactive oxygen species (ROS) levels in sheep. Supplementation with Chinese herbal medicine residues markedly reduced serum ROS and lactate dehydrogenase levels while increasing glutathione peroxidase and immunoglobulin G levels. Metagenomic results revealed significantly increased abundance of bacteria such as Selenomonas ruminantium in the rumen of the CMR group, along with substantial increases in CAZymes, including AA7, GH113, and GH84. Metabolomic analysis revealed differentially expressed metabolites in plasma and rumen fluid that were enriched in metabolic pathways such as glycerophospholipid metabolism, α-linolenic acid metabolism, and drug metabolism-cytochrome P450. Correlation network analysis further revealed that Selenomonas ruminantium was significantly negatively correlated with ROS and positively correlated with ruminal LysoPC (16:1(9Z)/0:0), plasma phosphatidylcholine, and key glycerophospholipid metabolism enzymes (e.g., EC 3.1.4.3, PLC). Glycerophospholipid metabolism exhibited synergistic regulatory interactions with arachidonic acid metabolism and drug metabolism-cytochrome P450 pathways.

CONCLUSION: This study confirmed that 4 h of short-distance transport can induce oxidative stress in sheep. Supplementing feed with Siji Antiviral Mixture herbal residue effectively alleviated transport stress and enhanced immune function. The mechanism of action involved rumen microbial conversion of the herbal residue, which substantially increased the abundance of Selenomonas ruminantium. Related metabolites then regulated host arachidonic acid metabolism and cytochrome P450 drug metabolism indirectly through the glycerophospholipid metabolic pathway and the rumen microbiota-metabolism axis, thereby synergistically exerting antioxidant effects.},
}