@article {pmid41682924,
year = {2026},
author = {Songel-Sanchis, B and Morales-Fernández, L and García-Bardera, J and Güemes-Villahoz, N and Martínez-de-la-Casa, JM and García-Feijoo, J},
title = {The Ocular and Gut Microbiome Axis in Understanding Glaucoma: A Systematic Review.},
journal = {Journal of clinical medicine},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/jcm15031245},
pmid = {41682924},
issn = {2077-0383},
abstract = {Background: Glaucoma is a neurodegenerative disease and the second leading cause of irreversible blindness in developed countries. It is characterized by progressive loss of retinal ganglion cells (RGCs) and optic nerve axons, leading to permanent vision impairment. Although elevated intraocular pressure (IOP) is the main recognized risk factor, recent evidence suggests that ocular and gut microbiota may play a significant role in the onset and progression of glaucoma. Objectives: This study aimed to characterize ocular and gut microbiota alterations in patients with different types of glaucoma. Methods: Five searches were conducted between June and September 2025 using selected keywords. A total of 121 articles were identified, of which 14 met the inclusion criteria following the PRISMA 2020 guidelines. Results: Findings indicate a Mendelian genetic predisposition influencing microbiota composition associated with glaucoma development. Patients treated with benzalkonium chloride (BAK) showed increased Gram-negative and Alphaproteobacteria on the ocular surface, along with enhanced lipopolysaccharide synthesis. Compared with controls, glaucoma patients exhibited reduced Corynebacterium mastiditis and Actinobacteria and increased Firmicutes, Proteobacteria, and Verrucomicrobiota. Dysbiosis was more pronounced in patients with concurrent dry eye disease, characterized by higher Gram-negative taxa and pro-inflammatory microbial activity. Conclusions: Significant differences in ocular and gut microbiota were observed between glaucoma patients and controls, as well as among glaucoma subtypes such as pseudoexfoliation and primary open-angle glaucoma. Age-related dysbiosis and epigenetic factors appear to contribute to disease development. Microbiota profiling may offer new opportunities for improved prediction, management, and treatment of glaucoma.},
}

@article {pmid41682832,
year = {2026},
author = {Maslennikov, R and Gosteeva, E and Ananeva, V and Korshunova, L and Kravtsowa, A and Poluektova, E and Ulyanin, A and Sigidaev, A and Kikhasurova, P and Ivashkin, V},
title = {Strain-Specific Systematic Review with Meta-Analysis of Probiotics Efficacy in the Treatment of Irritable Bowel Syndrome.},
journal = {Journal of clinical medicine},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/jcm15031152},
pmid = {41682832},
issn = {2077-0383},
abstract = {Background: Many probiotic strains have been studied in relation to irritable bowel syndrome (IBS). The aim of this study was to identify probiotic strains demonstrating efficacy in the management of IBS based on meta-analyses of randomized placebo-controlled trials (RPCTs). Methods: This systematic review was registered in the PROSPERO database (CRD420251047092). Searches were conducted in PubMed and Scopus on 8 April 2025. Additional completed studies with available results were identified through ClinicalTrials.gov. An additional search of the Cochrane Central Register of Controlled Trials (CENTRAL), including records indexed in EMBASE, was conducted in December 2025 and did not identify any additional studies. RPCTs were included if they evaluated single-strain probiotics without additional active components compared with a placebo in patients with IBS. Studies whose results could not be meta-analyzed were excluded. Results: A total of 2643 records were identified; 32 articles evaluating 10 probiotic strains were included in the meta-analyses. Meta-analyses demonstrated the efficacy of Bifidobacterium longum (formerly Bifidobacterium infantis) 35624, Lactobacillus rhamnosus GG, Lactiplantibacillus plantarum 299v (DSM 9843), Saccharomyces cerevisiae CNCM I-3856, and Bacillus coagulans Unique IS2 (MTCC 5260) in improving key IBS symptoms. Meta-analyses also demonstrated that Bacillus coagulans MTCC 5856 improved quality of life for those with IBS. Conflicting results were observed for Saccharomyces boulardii CNCM I-745. Meta-analyses did not demonstrate the efficacy of Escherichia coli Nissle 1917, Lactobacillus gasseri BNR17, or Lactobacillus casei Shirota. Conclusions: Several probiotic strains demonstrated efficacy in the treatment of IBS in meta-analyses of RPCTs.},
}

@article {pmid41682824,
year = {2026},
author = {Biesiadecki, S and Janeczko, M and Kozak, J and Homaj-Siudak, M and Szarpak, L and Rahnama-Hezavah, M},
title = {Advanced Diagnostic Technologies and Molecular Biomarkers in Periodontitis: Systemic Health Implications and Translational Perspectives.},
journal = {Journal of clinical medicine},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/jcm15031142},
pmid = {41682824},
issn = {2077-0383},
abstract = {Background/Objectives: Periodontitis is a chronic inflammatory disease with marked inter-individual heterogeneity and well-established links to cardiometabolic and other systemic conditions. Conventional clinical diagnostics remain indispensable. However, they provide limited real-time insight into molecular activity and host-response biology. This review aimed to synthesize recent advances in point-of-care diagnostics and emerging molecular biomarkers relevant to periodontal disease and its systemic associations. Methods: We performed a state-of-the-art narrative review of literature published between 2018 and 2026. The focus was on point-of-care biosensing technologies and molecular biomarkers assessed in oral and related biological matrices. These included saliva, gingival crevicular fluid, blood, and dental plaque. Evidence was prioritized based on analytical performance, clinical validity, and translational readiness. Results: Substantial progress has been made in multiplex optical and electrochemical point-of-care platforms. These include microfluidic systems and early intraoral wearable sensors. Such technologies enable quantification of host-response proteins, including MMP-8, cytokines, and chemokines. In parallel, omics-derived biomarkers are emerging as clinically informative adjuncts for diagnosis and monitoring. MicroRNAs, cell-free DNA, extracellular vesicle-derived signals, proteomic profiles, and microbiome classifiers demonstrate promising discrimination. They also provide mechanistic links to systemic inflammation. Clinical translation remains limited by study heterogeneity, spectrum bias, and insufficient external validation. Conclusions: Near-term clinical value lies in adjunctive risk stratification and longitudinal disease monitoring. Replacement of conventional periodontal examination is not currently justified. Meaningful clinical and public-health impact will require standardized disease definitions. Harmonized sampling and reporting protocols are essential. Multicenter validation across comorbidity strata is needed. Regulatory-grade evidence must be generated for in vitro diagnostics and artificial intelligence software classified as medical devices.},
}

@article {pmid41682795,
year = {2026},
author = {Zych-Krekora, K and Sylwestrzak, O and Krekora, M},
title = {The Effect of Oral Supplementation with a Multi-Strain Probiotic Preparation on Group B Streptococcus (GBS) Carriage in Pregnant Women-A Pilot Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/jcm15031113},
pmid = {41682795},
issn = {2077-0383},
abstract = {Background/Objectives: Maternal rectovaginal carriage of Group B Streptococcus (GBS, Streptococcus agalactiae) is a major risk factor for vertical transmission and early-onset neonatal infection. Intrapartum antibiotic prophylaxis reduces early-onset disease but does not address antenatal carriage and may affect the maternal-neonatal microbiota. Microbiota-directed interventions, including probiotics, are being explored as complementary strategies. Methods: This prospective, single-centre, open-label pilot intervention study included 10 pregnant women (18-40 years) with singleton pregnancies and a positive vaginal and/or rectal GBS swab, without pre-gestational or gestational diabetes and without antibiotic use in the 4 weeks before enrolment. Participants received OMNi-BiOTiC[®] FLORA plus (multi-strain lactic acid bacteria, including Lactobacillus crispatus) orally at 2 × 2 g/day from the 15th to the 34th gestational week. Microbiological swabs were obtained at qualification (12-15 weeks), mid-pregnancy (22-25 weeks), and late pregnancy (34-35 weeks). Outcomes were described descriptively. Results: Among 56 screened pregnant women, 10 were GBS-positive (17.9%) and enrolled. All participants were GBS-positive at baseline. At 22-25 weeks, 5/10 (50%) had a negative GBS result. At 34-35 weeks, 9/10 (90%) were GBS-negative, while 1/10 (10%) remained colonised. Time to first negative result ranged from 7.6 to 20.2 weeks from supplementation start (median 8.6 weeks). No recurrences (negative-to-positive transitions) were observed between the second and third sampling points. No adverse events related to supplementation were reported. In contrast, among the 46 women who were GBS-negative at screening and did not receive probiotic supplementation, 14 (30.4%) were found to be GBS-positive at routine screening performed at 35-37 weeks of gestation. Conclusions: In this pilot single-arm study, oral supplementation with a multi-strain probiotic preparation during pregnancy was associated with a time-dependent reduction in rectovaginal GBS carriage and was well tolerated. These preliminary findings support the feasibility of larger randomised controlled trials incorporating microbiome profiling and neonatal outcomes.},
}

@article {pmid41682620,
year = {2026},
author = {Martínez-Galindo, R and Campuzano-Pérez, M and Konstantouli, A and Aguilar-Ramírez, MDP and Rodríguez, JAM and Abad-López, P and Shabaka, A and Cansino, R},
title = {Clinical Approaches and Emerging Therapeutic Horizons in Primary Hyperoxaluria.},
journal = {Journal of clinical medicine},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/jcm15030940},
pmid = {41682620},
issn = {2077-0383},
abstract = {Primary hyperoxalurias (PHs) are rare autosomal recessive disorders characterized by overproduction of oxalate, a metabolic end product that readily forms calcium oxalate crystals. Excess hepatic oxalate leads to recurrent kidney stones, nephrocalcinosis, and progressive renal injury, often culminating in end-stage kidney disease (ESKD). Once renal clearance declines, systemic oxalate accumulation can cause multisystem deposition. PH encompasses three types-PH1, PH2, and PH3-caused by deficiencies in the hepatic enzymes AGT, GRHPR, and HOGA1, respectively, resulting in accumulation of glyoxylate and subsequent oxalate overproduction. Clinical presentation varies from infantile oxalosis to adult-onset recurrent nephrolithiasis, with PH1 generally being the most severe. Diagnosis relies on urinary oxalate measurements, plasma oxalate in advanced chronic kidney disease, urinary metabolite profiling, imaging, and genetic testing. Management includes hyperhydration, citrate supplementation, pyridoxine for responsive PH1 patients, dialysis and transplantation when required, while RNA interference therapies targeting glycolate oxidase or LDHA have demonstrated substantial biochemical efficacy in PH1 and represent promising emerging therapeutic options, although long-term clinical outcome data remain limited and broader applicability to other PH types is still under investigation. Future strategies focus on modulating intestinal oxalate absorption, gut microbiome therapies, oxalate-degrading enzymes, and novel gene-editing approaches. Early diagnosis and individualized management are critical to prevent kidney injury and systemic oxalosis. In this review, we summarize the genetic, biochemical, and clinical features of PH and discuss current and emerging therapeutic strategies.},
}

@article {pmid41682213,
year = {2026},
author = {Ciongaru, DN and Piţuru, SM and Păunică, S and Giurgiu, MC and Bujdei-Tebeică, I and Dumitriu, AS},
title = {Comparative Analysis of Oral Bacterial Profiles in Parkinson's Disease According to Periodontal Status: A Clinical Case Series.},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {3},
pages = {},
doi = {10.3390/healthcare14030362},
pmid = {41682213},
issn = {2227-9032},
abstract = {Introduction: Parkinson's disease can influence oral health by impairing motor function and altering salivary composition, potentially affecting the oral microbiome. Materials and Methods: The objectives of this study are fourfold: (a) to compare the prevalence of bacterial species associated with periodontal disease in patients with and without Parkinson's disease (PD), (b) to assess whether the coexistence of periodontal disease in PD patients contributes to an imbalance in the oral microbiome, (c) to evaluate the correlation between periodontal clinical indices (plaque index, tartar index, bleeding index, and probing depth) and the concentrations of specific periodontopathogenic bacterial species, and (d) to explore the potential implications of these evidences for clinical management and preventive strategies in Parkinson's patients. The main objective of this study is to compare periodontal clinical indices (plaque index, tartar index, bleeding index, and probing depth) and the bacterial profile of patients with periodontal and Parknson's disease. Two groups were included: 15 patients with periodontal disease (control group) and 16 patients with both periodontal and Parkinson's disease (study group). Microbial samples were collected from the periodontal pockets at baseline and analyzed using the Polymerase Chain Reaction (PCR) Perio-Ident 12 kit to detect major periodontal pathogens. Results: Periodontal indices showed no statistically significant differences between groups, although the study group presented lower mean tartar index (49.31% vs. 67.4%, p = 0.069), bleeding on probing (44.31% vs. 56.67%, p = 0.137), and plaque index (66% vs. 68.93%, p = 0.754). Median bacterial loads were generally higher in control group, with Tannerella forsythia, but without statistically significant difference (p = 0.072). Significant correlations between plaque index and multiple pathogens occurred only in control gorup, suggesting disrupted plaque-pathogen dynamics (p < 0.05). Conclusions: The results highlight the potential value of integrating clinical and microbiological assessment when managing periodontal disease in patients with Parkinson's disease.},
}

@article {pmid41681995,
year = {2026},
author = {Hah, YS and Lee, SJ and Hwang, J and Kwag, SJ},
title = {The Vesicular Intersection Layer: A Framework for Cross-Kingdom Extracellular Vesicle Signaling That May Connect Gut Dysbiosis to Skeletal Muscle Wasting in Colorectal Cancer Cachexia.},
journal = {Cancers},
volume = {18},
number = {3},
pages = {},
doi = {10.3390/cancers18030522},
pmid = {41681995},
issn = {2072-6694},
support = {2025-RISE-16-001//Regional Innovation System & Education (RISE) program through the RISE Center, Gyeongsang-nam-do, funded by the Ministry of Education (MOE) and the Gyeongsangnam-do Provincial Government, Republic of Korea/ ; GNU-NFRSG-0041//New Faculty Research Support Grant from Gyeongsang National University in 2025/ ; GNUHBRIF-2025-0001//Biomedical Research Institute Fund from the Gyeongsang National University Hospital/ ; },
abstract = {Colorectal cancer (CRC) cachexia is a multifactorial, treatment-limiting syndrome characterized by progressive loss of skeletal muscle with or without loss of fat mass, accompanied by systemic inflammation, anorexia, metabolic dysregulation, and impaired treatment tolerance. Despite decades of work, cachexia remains clinically underdiagnosed and therapeutically underserved, in part because canonical models treat tumor-derived factors and host inflammatory mediators as a largely 'host-only' network. In parallel, CRC is strongly linked to intestinal dysbiosis, barrier disruption, and microbial translocation. Extracellular vesicles (EVs)-host small EVs, tumor-derived EVs, and bacterial extracellular vesicles (including outer membrane vesicles)-may provide a mechanistically plausible, information-dense route by which these domains could be coupled. Here, we synthesize emerging evidence suggesting that cross-kingdom EV signaling may operate as a vesicular ecosystem spanning gut lumen, mucosa, circulation, and peripheral organs. We propose the "vesicular intersection layer" as a unifying framework for how heterogeneous EV cargos converge on shared host decoding hubs (e.g., pattern-recognition receptors and stress-response pathways) to potentially contribute to muscle catabolism. We critically evaluate what is known-and what remains unproven-about EV biogenesis, trafficking, and causal mechanisms in CRC cachexia, highlight methodological constraints in microbial EV isolation and attribution, and outline minimum evidentiary standards for cross-kingdom claims. Finally, we translate the framework into actionable hypotheses for EV-informed endotyping, biomarker development (including stool EV assays), and therapeutic strategies targeting shared signaling nodes (e.g., TLR4-p38) and endocrine mediators that are predominantly soluble but may be fractionally vesicle-associated (e.g., GDF15). By reframing CRC cachexia as an emergent property of tumor-host-microbiota vesicular communication, this review provides a roadmap for mechanistic studies and clinically tractable interventions.},
}

@article {pmid41681968,
year = {2026},
author = {Caramella, I and Abeni, C and Cherri, S and Ogliosi, C and Morena, T and Galvagni, G and Meriggi, F and Zaniboni, A},
title = {Decoding Microbiota in Genitourinary Oncology: Biological Mechanisms and Clinical Implications-A Narrative Review.},
journal = {Cancers},
volume = {18},
number = {3},
pages = {},
doi = {10.3390/cancers18030497},
pmid = {41681968},
issn = {2072-6694},
abstract = {Genitourinary malignancies are characterized by marked heterogeneity in tumor biology, clinical behavior and therapeutic outcomes. Despite significant progress in surgical and systemic treatments, resistance to therapy remains a major challenge, highlighting the need to identify additional host-related determinants of disease progression and treatment response. Within this framework, converging experimental and clinical evidence indicates that host-associated microbial ecosystems may influence key biological processes involved in tumor-host interactions, including immune modulation, metabolic regulation and inflammatory pathways. Altered microbial profiles have been associated with oncogenic signaling, changes in the tumor microenvironment and differences in clinical benefit from systemic therapies, particularly immunotherapeutic approaches. This review brings together preclinical, translational and clinical evidence on the involvement of microbiota in renal, prostate, bladder and testicular cancers, with attention to biological mechanisms and clinically meaningful correlations with disease characteristics. While current data are largely observational, early interventional studies suggest that modulation of microbial ecosystems may influence therapeutic activity in selected clinical settings. Collectively, these findings support microbiota as a relevant component of genitourinary cancer biology with potential implications for precision medicine approaches.},
}

@article {pmid41681904,
year = {2026},
author = {Munteanu, C and Nadhan, R and Turti, S and Prifti, E and Achim, L and Basu, S and Ferraresi, A and Ha, JH and Isidoro, C and Dhanasekaran, DN},
title = {LncRNAs at the Crossroads of Precision Nutrition and Cancer Chemoprevention.},
journal = {Cancers},
volume = {18},
number = {3},
pages = {},
doi = {10.3390/cancers18030430},
pmid = {41681904},
issn = {2072-6694},
support = {W81XWH-22-1-0415//United States Department of Defense/ ; P30GM154635/GM/NIGMS NIH HHS/United States ; P30CA225520/CA/NCI NIH HHS/United States ; },
abstract = {Cancer remains a leading cause of morbidity and mortality worldwide, and effective strategies for cancer prevention are urgently needed to complement therapeutic advances. While dietary factors are known to influence cancer risk, the molecular mechanisms that mediate inter-individual responses to nutritional exposures remain poorly defined. Emerging evidence identifies long non-coding RNAs (lncRNAs) as pivotal regulators of gene expression, chromatin organization, metabolic homeostasis, immune signaling, and cellular stress responses, the core processes that drive cancer initiation and progression and are highly sensitive to nutritional status. In parallel, advances in precision nutrition have highlighted how variability in genetics, metabolism, microbiome composition, and epigenetic landscapes shape dietary influences on cancer susceptibility. This review integrates these rapidly evolving fields by positioning lncRNAs as molecular conduits that translate dietary exposures into transcriptional and epigenetic programs governing cancer development, progression, and therapeutic vulnerability. We provide mechanistic evidence demonstrating how dietary bioactive compounds and micronutrients, including polyphenols [such as curcumin, resveratrol, epigallocatechin gallate (EGCG)], flavonoids, alkaloids such as berberine, omega-3 (ω-3) fatty acids, folate, vitamin D, probiotic metabolites (such as butyrate and propionate), and trace elements (such as selenium and zinc), modulate oncogenic and tumor-suppressive lncRNAs. These nutrient-lncRNA interactions influence cancer-relevant pathways controlling proliferation, epithelial-mesenchymal transition (EMT), inflammation, oxidative stress, and metabolic rewiring. We further discuss emerging lncRNA signatures that reflect nutritional and metabolic states, their potential utility as biomarkers for individualized dietary interventions, and their integration into liquid biopsy platforms. Leveraging multi-omics datasets and systems biology, we outline AI-driven frameworks to map nutrient-lncRNA regulatory networks and identify targetable nodes for cancer chemoprevention. Finally, we address translational challenges, including compound bioavailability, inter-individual variability, and limited clinical validation, and propose future directions for incorporating lncRNA profiling into precision nutrition-guided cancer prevention trials. Together, these insights position lncRNAs at the nexus of diet and cancer biology and establish a foundation for mechanistically informed precision nutrition strategies in cancer chemoprevention.},
}

@article {pmid41681750,
year = {2026},
author = {Liepina, EE and Sivina, E and Jurkane, L and Daneberga, Z},
title = {Baseline Gut Microbiome and Metabolite Profiles Associate with Treatment Response in Breast Cancer Patients Undergoing Neoadjuvant Chemotherapy.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/diagnostics16030433},
pmid = {41681750},
issn = {2075-4418},
abstract = {Background/Objectives: Response to neoadjuvant chemotherapy (NAC) varies substantially among breast cancer patients and is only partially explained by tumor-intrinsic factors. The gut microbiome has emerged as a potential modulator of chemotherapy efficacy, yet its role in breast cancer remains underexplored. This study aimed to characterize gut microbial composition, functional potential, and microbially derived metabolites in breast cancer patients undergoing NAC. Methods: baseline stool samples from 39 chemotherapy-naïve breast cancer patients undergoing NAC were analyzed using shotgun metagenomic sequencing and targeted metabolomics. Patients were stratified by pathological complete response (pCR, n = 17; no pCR, n = 22). Microbial taxonomic and functional profiles, short-chain fatty acids (SCFAs) and bile acids were assessed, with subgroup analysis performed in triple-negative breast cancer (TNBC). Results: Patients achieving pCR exhibited significantly higher baseline microbial richness compared to non-responders (p = 0.040). Differential abundance analysis revealed enrichment of Dialister, Kineothrix, and Jutongia in responders, whereas Rothia, Leuconostoc, Klebsiella, Jingyaoa, Cuneatibacter, Youxingia, and Bittarella were enriched in non-responders. SCFAs (acetate, propionate and butyrate) positively correlated with microbial glucose catabolic pathways, while caproate was negatively associated with multiple amino acid, lipid, vitamin, and cell wall biosynthesis pathways, including peptidoglycan maturation. Metabolomic analysis identified higher deoxycholic acid (DCA) levels in non-responders and increased C6 levels in responders, although these associations did not remain significant after multiple testing correction. Similar trends were observed in the TNBC subgroup (n = 15). Conclusions: Baseline gut microbiome diversity, taxonomic composition, and functional metabolic potential are associated with response to neoadjuvant chemotherapy in breast cancer, supporting the gut microbiome and its produced metabolites as a potential biomarker of treatment efficacy.},
}

@article {pmid41681613,
year = {2026},
author = {Halifu, S and Zhang, S and Liu, G and Yang, L and Deng, X},
title = {Changes in the Microbial Communities of Picea schrenkiana Needles Following Lirula macrospora Infection.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/plants15030449},
pmid = {41681613},
issn = {2223-7747},
support = {LH2023C105//Heilongjiang Provincial Natural Science Foundation Project/ ; Hei, 2023, TG19; Hei, 2024, TG04//Central Finance Forestry Science and Technology Promotion and Demonstration Projects/ ; RCZK2021B23//Shihezi University High-Level Talent Research Start-up Project/ ; ZZZC2022009//Shihezi University Independent Funding Support Special Project/ ; },
abstract = {Picea schrenkiana is a keystone species in Central Asian ecosystems currently threatened by climate-driven disease outbreaks. Here, we investigated the causal agent of needle blight and characterized the associated microbial dynamics. By integrating tissue isolation, Koch's postulates, and high-throughput amplicon sequencing across a disease severity level, we confirmed Lirula macrospora as the etiological agent. Community analysis revealed that disease severity is the primary driver of succession, with alpha diversity peaks at the moderate infection stage. Notably, the abundance of Lirula surged from 2.56% in healthy needles to 65.10% in severe cases, displacing the core endophyte Phaeococcomyces, while potentially beneficial bacteria like Sphingomonas showed only transient enrichment. Furthermore, cross-kingdom co-occurrence network analysis revealed marked topological restructuring whereby the system reached a complex ecological "tipping point" during moderate stage before undergoing significant simplification. As the disease progressed, L. macrospora shifted from a peripheral node to a central hub, effectively dismantling the native microbial network. We conclude that L. macrospora infection triggers a cascading collapse of the needle microbiome, driving a phase shift from a healthy homeostasis to a pathogen-dominated state. These findings elucidate the critical mechanisms of pathogen-microbiome interactions and provide a theoretical basis for the ecological management of P. schrenkiana forests.},
}

@article {pmid41681589,
year = {2026},
author = {Zou, J and Wang, Q and Zhang, H and Meng, Q and Li, J and Chen, A and Liu, X and Luo, Y and Guo, Z},
title = {Effect of Deep Placement Fertilization on Soybean (Glycine max L.) Development in Albic Black Soil.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/plants15030424},
pmid = {41681589},
issn = {2223-7747},
support = {2022YFD1500800//National Key Research and Development Program of China/ ; },
abstract = {Maximizing the agricultural output on inherently infertile land and minimizing the environmental cost remain central research imperatives. Albic black soil typifies such infertility. Conventional practice relies on fertilization and straw incorporation, but the albic layer's impermeability funnels applied nutrients into adjacent aquatic systems. Therefore, this study developed deep placement fertilization by lodging fertilizer directly within the albic layer to block hydrologic loss. The feasibility of mechanization was first validated in pot experiments. Soybeans were allocated to six treatments simulating fertilizer placement at different soil depths: control (C), control and fertilizer (CF), surface soil mixing (SM), surface soil mixing and fertilizer (SMF), plow pan soil mixing (PM), and plow pan soil mixing and fertilizer (PMF). The treatments used 20 cm tillage, and the data were collected after 15, 25, and 35 days and at harvest. Integrative transcriptomic, proteomic, metabolomic, and soil microbiome profiling revealed that fertilizer positioned at 25 cm in the albic layer increased yield, restructured the rhizobiont community and promoted arbuscular mycorrhizal fungal colonization. Among the fertilizer treatments, CF had the best growth, and SMF was inhibited by a nutrient shortage. SMF and PMF lost water faster than CF. Abscisic acid (ABA) conveyed the subterranean fertilization signal to the leaf. The enrichment of Vicinamibacterales, Xanthobacteraceae, and Glomeromycota in soil lowered the ABA content in the roots, which upregulated thymidine kinase and peroxidase upon arrival in the leaf, increasing yield. These findings provide a transferable benchmark for any parent material exhibiting poor hydraulic conductivity.},
}

@article {pmid41681579,
year = {2026},
author = {Amin, U and Shabbir, M and Long, D and Wang, Z and Chen, M},
title = {Molecular Interactions Between Soil-Borne Oomycetes and Plants: Infection Mechanisms, Host Resistance, and Implications for Sustainable Agriculture.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/plants15030416},
pmid = {41681579},
issn = {2223-7747},
support = {2024J01210; 2020J05177//the Natural Science Foundation of Fujian Province/ ; MFK24031//the Research Project of Fashu Foundation/ ; },
abstract = {Soil-borne oomycetes, such as Phytophthora and Pythium species, are highly destructive pathogens responsible for severe diseases in crops, ornamentals, and natural ecosystems. These pathogens can persist in soil for many years, making them particularly difficult to control. To establish infection, they deploy a diverse arsenal of effector proteins that manipulate host immune responses, disrupt vital cellular functions, and may influence the rhizosphere microbiome to facilitate successful colonization. Phytophthora relies heavily on RxLR effectors to disrupt intracellular immunity, while Pythium species predominantly deploy necrosis-inducing NLPs and cell wall-degrading enzymes, with no confirmed canonical RxLR effectors, suggesting distinct evolutionary strategies. This review aims to explore the detailed mechanisms of plant-pathogen interaction. In recent years, significant progress has been made in understanding the molecular dialogue between pathogens and their hosts, particularly how pathogenic species such as Phytophthora and Pythium manipulate plant immunity through effector secretion, and how plants counteract by activating defense mechanisms at molecular, cellular, and biochemical levels, including changes in hormone signaling, reactive oxygen species (ROS) dynamics, and defense gene expression. The review also outlines emerging disease management strategies and integrative approaches guided by effector biology and microbiome insights.},
}

@article {pmid41681578,
year = {2026},
author = {Ji, L and Fang, X and Chen, S and Ai, Z and Ni, K and Yang, Y and Ruan, J},
title = {Tea Cultivar Genotype Shapes Rhizosphere Microbiome Assembly Through Metabolic Differentiation.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
doi = {10.3390/plants15030414},
pmid = {41681578},
issn = {2223-7747},
abstract = {Tea cultivar genotype plays a critical role in shaping rhizosphere microbiome assembly, yet the underlying mechanisms remain poorly understood. This study employed a controlled pot experiment with five widely cultivated Chinese tea cultivars (Camellia sinensis) to investigate how cultivar-specific variation influences rhizosphere microbial communities and their assembly processes. Rhizosphere soil microbiomes (bacterial and fungal communities) and metabolomes were characterized using 16S rRNA and ITS2 amplicon sequencing combined with untargeted metabolomics. Significant differences in rhizosphere metabolite composition, primarily organic acids, fatty acids, and carbohydrates, were observed among cultivars, which corresponded to distinct bacterial and fungal community structures. Redundancy analysis (RDA) revealed that rhizosphere metabolites explained 19.87% of bacterial and 21.63% of fungal community compositional variation, second only to soil physicochemical properties. Neutral community model and modified stochasticity ratio analyses indicated that microbial assembly across cultivars was predominantly deterministic, and rhizosphere metabolite profiles were strongly correlated with microbial community structure. Notably, arbuscular mycorrhizal fungi made up about 11% of the fungal communities in minimally fertilized pot systems, contrasting sharply with their near-absence in conventionally managed systems plantations. These findings demonstrate that tea cultivar genotype significantly shapes rhizosphere microbiome assembly through metabolic differentiation, providing a theoretical foundation for integrating microbiome considerations into tea breeding programs and developing cultivar-specific management strategies.},
}

@article {pmid41681493,
year = {2026},
author = {Pavanello, C and Franchini, M and Romanzin, A and Tat, L and Bovolenta, S and Corazzin, M},
title = {Rumen Microbial Composition and Fermentation Variables Associated with Methane Production in Italian Simmental Dairy Cows.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030510},
pmid = {41681493},
issn = {2076-2615},
support = {Agritech Missione 4 Componente 2, Investimento 1.4 - D.D. 1032 17/06/2022, CN00000022; PNRR M4C2, DM352/2022 in collaboration with Le Tenute Marianis farm//PNRR/ ; },
abstract = {The study investigated differences in ruminal and fecal microbiota composition, fermentation traits, and volatile organic compounds (VOC) in Simmental dairy cows classified as high (HME) or low (LME) methane emitters. Methane emissions from 48 cows were quantified using the Laser Methane Smart portable gas detector. The 12 animals with the highest and lowest emissions were selected and assigned to the HME and LME groups, respectively, balanced for body weight, days in milk, and body condition score. Rumen fluid and fecal samples were analyzed for pH, ammonia, volatile fatty acids (VFA), VOC, and microbiota composition. As expected, CH4 emissions were significantly higher in HME than in LME cows (22.5 vs. 13.2 g/kg DMI; 16.9 vs. 8.4 g/kg FCM). The neutral detergent fiber digestibility was higher in HME cows (51.4% vs. 47.9%). The valeric acid concentration and the acetate-to-propionate ratio were significantly higher in HME cows (3.53 vs. 3.31). The VOC profiles significantly differed between groups in both feces and rumen fluid. The microbiota analysis revealed a significant difference between groups at the order and genus levels (Bray-Curtis dissimilarity). The Shannon index was higher in LME cows (2.08 vs. 1.95). HME cows exhibited a higher abundance of Methanosphaera and Methanobacteriales. Overall, the results indicate that re-shaping the rumen microbial community can play a key role in reducing methane emissions, strengthening the case for microbiome-driven approaches and offering insights that can support mitigation strategies across dairy production systems.},
}

@article {pmid41681417,
year = {2026},
author = {Yan, M and Liu, Z and Liu, M and Liu, H and Li, Z and Yang, Z and Lu, Y and Feng, W and Chen, X and Cheng, S and Yang, Y and Zhang, C and Wang, X and Cui, H},
title = {Dynamics and Health Risks of Fungal Bioaerosols in Confined Broiler Houses During Winter.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030437},
pmid = {41681417},
issn = {2076-2615},
support = {YJ2023038//the special project of introducing talents for scientific research in Hebei Agricultural University/ ; HBCT2024270204//the Hebei Agriculture Research System/ ; CARS-41-Z13//the China Agriculture Research System/ ; 246Z6604G//the Central government guided local science and technology development fund projects/ ; },
abstract = {Fungal bioaerosols play a critical ecological and health role in intensive poultry production systems. However, their dynamic characteristics and community succession patterns in confined cage environments during winter remain poorly understood. This study investigated a typical confined broiler house in Hebei Province, China, during winter. A combined approach of Andersen six-stage sampling, colony counting, and Internal Transcribed Spacer (ITS) high-throughput sequencing was employed to comprehensively analyze the concentration, particle size distribution, diversity, and community composition of fungal bioaerosols across three key growth stages: 7 days (brooding phase), 21 days (growing phase), and 35 days (finishing phase). The results revealed a significant increasing trend in fungal aerosol concentration as the rearing cycle progressed, increasing from 1125 ± 125 CFU/m[3] at day 7 to 3872 ± 565 CFU/m[3] at day 35 (p < 0.001), reaching high-risk exposure levels in the later stages. Small-sized fungal bioaerosols (<4.7 μm) were dominant across all stages (54.35-65.50%), with the highest proportion observed at day 21, indicating their potential for deep respiratory deposition and long-distance airborne transmission. The number of Operational Taxonomic Units (OTUs), along with Chao1 and Shannon indices, increased significantly with bird age (p < 0.001), demonstrating a clear community succession from early-stage yeast-dominated forms (e.g., Diutina, Blumeria) to mid- and late-stage assemblages dominated by filamentous fungi (e.g., Aspergillus, Cladosporium, Alternaria). Notably, several zoonotic pathogenic genera were detected throughout all rearing stages, highlighting the potential risks of airborne fungi to animal health, occupational exposure, and environmental safety under winter ventilation restrictions. This study characterizes a stage-dependent pattern of increasing airborne fungal concentrations accompanied by shifts in particle size distribution and community composition under winter confined conditions. The findings provide a crucial scientific basis for optimizing winter ventilation and environmental management strategies, improving environmental control technologies, establishing airborne biosafety standards, and developing targeted fungal monitoring and prevention technologies.},
}

@article {pmid41681414,
year = {2026},
author = {Mohammed, EAH and Fehér, M and Bársony, P and Teye-Gaga, C and Czeglédi, L and Freytag, C and Váradi, A and Ahmed, AEM and Pál, K},
title = {Growth Performance, Gut Integrity and Intestinal Microbiome Responses of Juvenile Common Carp (Cyprinus carpio L.) to Probiotic and Prebiotic Supplementation.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030433},
pmid = {41681414},
issn = {2076-2615},
abstract = {The aim of this study was to examine the impact of the probiotics Saccharomyces cerevisiae (SC) and Pediococcus acidilactici (PA), as well as the prebiotic yeast cell wall extract (Cyberlindnera jadinii and S. cerevisiae) (YP), on the growth parameters, intestinal histomorphology, liver and gills normality, and gut microbiome of common carp (Cyprinus carpio L.). These feed supplements were subjected to a 60-day experimental period, during which 120 fish (26.4 ± 5.2 g) were distributed into four groups, with each group comprising 30 fish. The feed supplements were administered at a rate of 1 g/kg of body weight. Before the trial, the fish were acclimatized for two weeks, then injected with Passive Integrated Transponder (PIT) tags. The results showed that none of the feed supplements exhibited a significant effect (p > 0.05) on growth indices. In contrast, the villi length, villi width, muscular thickness, and crypt depth in the anterior, mid, and posterior intestine of the SC group exhibited significant (p < 0.05) improvements compared to the other groups. No alteration or abnormal growth were noticed in the gills and livers. The most dominant microbe genera in all groups, with abundances greater than 60% of the total, were Cetobacterium and Aeromonas. However, Polynucleobacter, Nordella, Mycoplasma, Romboutsia, and Staphylococcus species were present at lower abundances. The presence of Actinobacteria has been observed only in the intestine of fish that have been fed a diet supplemented with PA. It can be concluded that the tested probiotics and the yeast cell wall prebiotic have the potential to produce a remarkable improvement in intestinal morphology and a considerable change in the gut microbiome without notable effect on growth, livers, or gills of common carp.},
}

@article {pmid41681409,
year = {2026},
author = {Kowalczyk-Jabłońska, I and Jundziłł-Bogusiewicz, P and Kaleta, T},
title = {The Role of Olfaction in Dogs: Evolution, Biology, and Human-Oriented Work.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030427},
pmid = {41681409},
issn = {2076-2615},
support = {The publication was financed by Institute of Animal Sciences, Warsaw University of Life Sciences - SGGW//Institute of Animal Sciences, Warsaw University of Life Sciences - SGGW/ ; },
abstract = {Dogs show exceptional olfactory sensitivity and are widely used in medical, rescue, military, and forensic applications, yet the determinants of individual and breed-level scent-work performance remain incompletely characterized. This review integrates evidence from the anatomy and physiology of the canine olfactory organ, neurobiological mechanisms of odor transduction and coding, and links between olfaction, memory, and emotion, alongside molecular genetics, evolution, domestication, and selective breeding. We synthesize findings indicating that complex nasal turbinates and specialized airflow patterns enhance odorant capture, while olfactory bulb circuitry and downstream connections to limbic and frontal networks support discrimination, learning, and affective modulation. Comparative and breed-focused studies suggest that skull morphology and breeding priorities can alter olfactory capacity, with shortened nasal anatomy associated with reduced functional potential in some lines. In applied contexts, detection success is strongly shaped by behavioral traits such as motivation, persistence, independence, and reward value, as well as by physical condition and environmental stressors that can impair search efficiency. Emerging literature further suggests that the gastrointestinal and upper airway microbiome, together with diet, housing, temperature, and workload, may influence sensory and cognitive readiness, although direct causal links to detection outcomes remain limited. Overall, canine olfactory performance reflects interactions among genetic-anatomical capacity, neurobehavioral factors, and environment, underscoring the value of standardized selection, training, welfare management, and future integrative research.},
}

@article {pmid41681369,
year = {2026},
author = {Dallavalle, G and Secchi, G and Mancini, A and Cologna, N and Vrhovsek, U and Angeli, A and Aprea, E and Zambanini, J and Solovyev, P and Bontempo, L and Betta, E and Biasioli, F and Zanon, T and Franciosi, E},
title = {Grape Stalks as a Sustainable Feed Supplement for Dairy Cows: A Preliminary In Vivo Study on Milk Microbiota and Cheese Quality.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030388},
pmid = {41681369},
issn = {2076-2615},
support = {ECS00000043//NextGenerationEU (PNRR), Interconnected Nord-Est Innovation Ecosystem (iNEST)/ ; PE00000003//NextGenerationEU (PNRR), ONFoods/ ; },
abstract = {In the Trentino Alto Adige region, disposal of grape stalks (GS) represents a major cost for wineries, despite their content of phenolic and tannin-rich compounds with potential functional value in ruminant nutrition. This study evaluated whether dietary GS supplementation could influence milk microbiota and cheese quality, supporting local circular-economy strategies. GS from three red cultivars (L-GS, CS-GS, M-GS) were dried, milled, and assessed for safety; their average total polyphenol content was approximately 15 g/kg DM. 3 Holstein cows underwent a 7-week trial consisting of alternating control (CTRL) and GS-supplemented periods (2% DM). Weekly milk samples (n = 21) and corresponding mini-cheeses (n = 21) were analyzed. GS supplementation did not affect milk coliforms (2.3-2.5 log CFU/mL), while total mesophilic counts were significantly lower in M-GS (2.8 ± 0.46 log CFU/mL) than in CTRL (4.5 ± 0.71; p < 0.05). Acinetobacter dominated the milk microbiota but decreased from 34.0% in CTRL to 18.0% in L-GS. Cheese total polyphenols were highest in CS-GS (224 ± 34 mg/kg). [1]H-NMR and VOCs profiling indicated cultivar-dependent shifts in carbohydrate-related metabolites and short-chain fatty acids. Overall, GS supplementation subtly modulated cheese biochemical and aromatic traits without impairing technological performance, supporting the valorization of winery by-products within integrated dairy-viticulture systems.},
}

@article {pmid41681352,
year = {2026},
author = {Zhou, X and Cao, J and Feng, G and Li, Y and Liu, D and Liu, G},
title = {Commensal Microbiota and Reproductive Health in Livestock: Mechanisms, Cross-System Crosstalk, and Precision Strategies.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030371},
pmid = {41681352},
issn = {2076-2615},
support = {2024-XPY-00-008//Department of Agriculture and Rural Affairs of Guangdong Province/ ; },
abstract = {Reproductive performance in livestock and poultry is a core determinant of economic efficiency in the animal industry. While traditional research has primarily focused on genetics, endocrinology, and immune regulation, emerging microbiome studies reveal that commensal microbiota within the gut and reproductive tracts play an underestimated yet pivotal role in host reproductive health. This review systematically synthesizes recent advances regarding the relationship between the microbiome and reproductive functions in major livestock species (cattle, pigs, sheep, and chickens). We first delineate the theoretical basis and mechanisms of the "gut-reproductive axis," highlighting cross-system communication mediated by microbial metabolites, including short-chain fatty acids (SCFAs), indoles, and bile acids. Subsequently, we provide an in-depth comparative analysis of the microecological features of both female (vagina/uterus) and male (semen/epididymis) reproductive systems, examining their impacts on fertility, sperm quality, and pregnancy outcomes. Furthermore, we explore the molecular and systemic mechanisms governing microbial regulation of reproduction, encompassing the modulation of the hypothalamic-pituitary-gonadal (HPG) axis, the balance of local mucosal immunity and inflammation, and epigenetic regulation. Finally, we address current challenges-such as causal validation and the scarcity of multi-species databases-and propose future directions, including spatial multi-omics, AI-integrated analysis, and microbial intervention strategies. Ultimately, this review aims to offer a theoretical foundation and translational insights for elucidating reproductive regulatory networks and developing microbiome-driven precision strategies to enhance reproductive performance.},
}

@article {pmid41681340,
year = {2026},
author = {Belenguer, A and Moroni, F and Naya-Català, F and Holhorea, PG and Domingo-Bretón, R and Calduch-Giner, JÀ and Pérez-Sánchez, J},
title = {Autochthonous and Allochthonous Gut Microbes May Work Together: Functional Insights from Farmed Gilthead Sea Bream (Sparus aurata).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {3},
pages = {},
doi = {10.3390/ani16030360},
pmid = {41681340},
issn = {2076-2615},
support = {PRTR-C17.I1//Ministerio de Ciencia, Innovación y Universidades/ ; PID2023-146990OB-I00//Ministerio de Ciencia, Innovación y Universidades/ ; THINKINAZUL/2021/024//Generalitat Valenciana/ ; },
abstract = {In fish gut microbiome studies, there are no standardized protocols regarding sampling region or post-feeding time, nor clear consensus on whether analyses should target resident (autochthonous) or transient (allochthonous) bacteria. This study examined the dynamics and interactions of both microbial communities in the anterior and posterior intestine of farmed gilthead sea bream and evaluated the resident microbiome at 24 and 48 h post-feeding. Microbial DNA was sequenced using the Oxford Nanopore Technology platform. Data were analyzed through statistical and discriminant approaches, as well as a Bayesian network framework to assess bacterial interactions. Transient communities showed higher richness and diversity, regardless of intestinal section, suggesting a more specialized and stable microbial environment in the mucus layer. The two communities differed markedly in structure and composition. Variations associated with intestinal region were less pronounced, particularly for autochthonous bacteria, and post-feeding fluctuations in the resident microbiome were minimal. Functionally, results indicated relevant synergies between communities. Protein metabolism pathways were enriched in autochthonous bacteria, whereas allochthonous microorganisms contributed mainly to bile acid and carbohydrate metabolism. Overall, resident and transient bacteria constitute distinct communities in the gut of gilthead sea bream, with numerous genera present in both but most being differentially represented and interconnected.},
}

@article {pmid41681112,
year = {2026},
author = {Hao, X and Yuan, R and Guo, Y and Chen, G and Guo, Y and Liu, L and Lu, F and Bai, Y and Tian, Y},
title = {Host Oxidative Response Capacity Determines Longevity Outcomes of Microbial Interventions.},
journal = {Aging cell},
volume = {25},
number = {2},
pages = {e70418},
doi = {10.1111/acel.70418},
pmid = {41681112},
issn = {1474-9726},
support = {2022YFA1303000//National Key Research and Development Program of China/ ; 32225025//National Natural Science Foundation of China/ ; 32321004//National Natural Science Foundation of China/ ; 32430025//National Natural Science Foundation of China/ ; 32225038//National Natural Science Foundation of China/ ; YSBR-076//CAS Project for Young Scientists in Basic Research/ ; //New Cornerstone Science Foundation/ ; },
mesh = {Animals ; *Longevity/genetics ; *Caenorhabditis elegans/microbiology/genetics ; *Oxidative Stress ; Caenorhabditis elegans Proteins/genetics/metabolism ; Oxidation-Reduction ; Quantitative Trait Loci/genetics ; Microbiota ; DNA-Binding Proteins ; Transcription Factors ; },
abstract = {Microbial communities profoundly influence host aging, yet how natural genetic variation determines microbiota-driven longevity remains unclear. By screening root-derived bacterial isolates across genetically diverse Caenorhabditis elegans strains, we identified striking phenotypic heterogeneity, ranging from lifespan extension to accelerated aging. Combining classical genetic analysis, quantitative trait locus (QTL) mapping and CRISPR-Cas9 allelic recapitulation, we identify skn-1 (Nrf2) and gsy-1 (glycogen synthase) as key host determinants. We demonstrate that strains with mutations or specific natural variants in these loci exhibit a compromised redox buffering capacity, leading to systemic oxidative stress, loss of tissue integrity, and premature death upon microbial challenge. Conversely, robust hosts utilize the same microbial signals to promote longevity. Notably, lifespan defects in susceptible individuals were rescued by antioxidant supplementation. These findings establish redox homeostasis as a central axis in host-microbe-aging interactions and provide a mechanistic framework for precision microbiome interventions tailored to host genetic backgrounds.},
}

Animals
*Longevity/genetics
*Caenorhabditis elegans/microbiology/genetics
*Oxidative Stress
Caenorhabditis elegans Proteins/genetics/metabolism
Oxidation-Reduction
Quantitative Trait Loci/genetics
Microbiota
DNA-Binding Proteins
Transcription Factors

@article {pmid41681011,
year = {2026},
author = {Werneburg, GT and Gross, MD and Hettel, DR and Lyon, M and McSweeney, S and Jeong, SH and Knorr, JM and Adler, A and Dang, T and Orji, P and Ramanujan, S and Slopnick, E and Goldman, HB and Vasavada, SP and Miller, AW},
title = {Urinary Fungal Microbiome and Associations With Overactive Bladder, Antibiotics and Therapy Response.},
journal = {Neurourology and urodynamics},
volume = {},
number = {},
pages = {},
doi = {10.1002/nau.70227},
pmid = {41681011},
issn = {1520-6777},
abstract = {OBJECTIVE: To characterize and compare the fungal urinary microbiome ("mycobiome") in healthy women and those with overactive bladder (OAB), and secondarily compare the mycobiome by comorbidities, recent antibiotic exposure, and response to OAB therapy.

MATERIAL AND METHODS: DNA was isolated from urine of those with and without OAB and underwent internal transcribed spacer (ITS) sequencing to detect fungi. Alpha- and beta-diversity, and relative abundance of fungal taxa were analyzed and compared by patient characteristics including OAB status. Fungal-bacterial interactions were identified.

RESULTS: A total of 152 participants were included and fungi were detected in 98% of samples. The most abundant fungal phyla were Basidiomycota and Ascomycota. The most abundant genera were Malassezia, Candida, and Aspergillus. Candida was more abundant in the urine of individuals without OAB (p = 0.01) and Debaryomyces was more abundant in individuals with OAB (p = 0.02). Beta diversity differed between individuals with and without OAB and by diabetes mellitus status (p < 0.05). Relative abundance of fungal genera differed by OAB phenotype, diabetes mellitus status, antibiotic use, and response to OAB treatment (p < 0.05). Fungal-bacterial interaction networks demonstrated a central role of fungi in the interkingdom community structure.

CONCLUSIONS: The study provides new insights into the fungal composition of urine in the physiological state as well as in the context of OAB. Fungi appear to play a central role in interkingdom fungal-bacterial interaction networks. The findings pave the way for future investigations to assess the role of urinary fungi in urologic health and disease, and its modulation to augment therapy.},
}

@article {pmid41680945,
year = {2026},
author = {Yu, Q and Huang, C and Bao, P and Li, N and Zhang, M and Wang, T and Ma, C and Deng, J and Cao, X and Jia, J and Yan, P},
title = {Lactobacillus fermentum supplementation modulates jejunal microbiota, metabolome, and morphology in yaks under high-energy feeding.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {17},
pmid = {41680945},
issn = {2524-4671},
support = {2022KJ137//National Beef Cattle Industry Technology and System (CARS-37)/ ; ZR2023MC164//Shandong Natural Science Foundation/ ; TCYC-TP2023//Xinjiang Tianchi Talent Research Program/ ; TZYC-TP2023//Tingzhou Talent Research Program/ ; KCXFZ20201221173205015//Shenzhen Science and Technology Program/ ; },
abstract = {UNLABELLED: Concentrated supplementary feeding is an effective strategy for addressing nutritional deficiencies in yaks during the cold-season grazing period. However, limited research has investigated whether long-term implementation may alter the gut microbiota and metabolite profiles of yaks, potentially posing health risks to the host. This study investigated the regulatory role of Lactobacillus fermentum in host metabolism through the gut microbiota, employing a “nutrition-gut-metabolism” perspective. Eighty healthy male Pamir yaks with similar body conditions were randomly divided into four groups (n = 20 per group), including Control (Con), Medium Energy (ME), High Energy (HE), and Medium Energy plus Lactobacillus fermentum (MEJ). Body weight was recorded every 30 days during the 150-day trial. Jejunal tissues and contents from nine yaks per group were collected for subsequent analyses. Key findings revealed that the HE group showed significantly increased crypt depth and elevated relative abundance of Clostridium_sensu_stricto_1 (P < 0.05). In contrast, the MEJ group reversed the decline in villus height and width observed in the ME group, while significantly enhancing muscularis thickness. Notably, MEJ yaks exhibited higher abundance of Paeniclostridium, Romboutsia and Treponema (P < 0.05) and markedly increased short-chain fatty acids concentrations (P < 0.001). Metabolomic analysis identified upregulated pathways, including D-amino acid metabolism and Neuroactive ligand-receptor interaction. Furthermore, comparative analyses pinpointed five critical microbial taxa (e.g., vadinBE97, Lachnospiraceae_UCG-008) and 18 key metabolites (e.g., 15-Deoxyprostaglandin J2, Lasalocid A) associated with these effects. In conclusion, Lactobacillus fermentum supplementation improved yak growth performance and mitigates metabolic risks linked to excessive energy intake. These findings provided a theoretical foundation for optimizing yak feeding strategies and advancing precision nutrition in ruminant production.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-025-00479-9.},
}

@article {pmid41680823,
year = {2026},
author = {Ma, PJ and Li, M and Hu, WT and Yang, D and Liang, YK and Chen, L and Wang, X and Pan, Y and Wang, Y},
title = {L-kynurenine reshapes immune microenvironment to alleviate methamphetamine-induced chronic lung injury through gut-lung axis.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02348-2},
pmid = {41680823},
issn = {2049-2618},
support = {81973404//National Natural Science Foundation of China/ ; 2024-N012-07 (YJXM-202448)//Medical Education Research Project of Liaoning Province/ ; },
abstract = {BACKGROUND: Long-term abuse of methamphetamine (MA) is strongly associated with severe lung injury. Microbiome metabolites are one way to understand the interactions between microbes and disease. Although gut microbes and their metabolites play a crucial role in the gut-lung axis, the microbial mechanism by which MA induces lung injury is unclear. The purpose of this work was to identify the omics characteristic factor associated with MA abuse and explore its immune regulatory mechanism by 16 s rDNA sequencing, LC-MS/MS non-targeted metabolomics analysis, hemodynamics, flow cytometry, and some methods of cellular and molecular biology and morphology.

RESULTS: Based on the joint analysis of the gut microbiome and metabolomics, it was found that MA abuse disrupted the structure of the gut microbiome and drove the reprogramming of metabolites, leading to a reduction in Lactobacillus rhamnosus and its metabolite L-kynurenine (L-KYN). Activated Lactobacillus increased L-KYN level in MA-administrated mice. L-KYN, as a product of Lactobacillus, is a key omics signature factor for MA abuse, which has been further confirmed in vivo. L-KYN induced Treg cells differentiated from CD4[+] T cells and reshaped the immune microenvironment. L-KYN induced the secretion of IL-10 by Treg cells, mediated the communication between Treg cells and alveolar epithelial cells (AEC) through IL-10, and alleviated MA-induced lung inflammation and alveolar barrier damage through the IL-10/JAK1/STAT3 pathway.

CONCLUSIONS: From the perspective of intestinal microbiome-metabolite-immune network regulation, the omics characteristic factor L-KYN reshaped the immune microenvironment and alleviated methamphetamine-induced chronic lung injury through the gut-lung axis, providing a new theoretical and experimental basis for the prevention and treatment of MA-induced chronic lung injury. Video Abstract.},
}

@article {pmid41680605,
year = {2026},
author = {Wang, M and Qu, Y and Ma, X and Fan, Y and Zhang, C and Li, J and Liu, X and Wang, Z and Li, J and Wang, Y and Zhang, T and Chu, D and Liu, J and Li, Y},
title = {Temporal dynamics of the fecal microbiome in wintering seagulls: a One Health perspective.},
journal = {BMC genomics},
volume = {27},
number = {1},
pages = {191},
pmid = {41680605},
issn = {1471-2164},
support = {2024SKLVPHS06//State Key Laboratory of Veterinary Public Health and Safety/ ; 2021YFC0863400//National Key Research and Development Program of China/ ; 32100002//National Natural Science Foundation of China/ ; },
}

@article {pmid41680567,
year = {2026},
author = {Chen, L and Hong, C and Xie, Y},
title = {Bridging the gap between microbiome function and clinical benefit in sarcopenia.},
journal = {Aging clinical and experimental research},
volume = {38},
number = {1},
pages = {76},
pmid = {41680567},
issn = {1720-8319},
mesh = {Humans ; *Sarcopenia/microbiology/therapy/physiopathology ; *Gastrointestinal Microbiome/physiology ; Probiotics/therapeutic use ; Aged ; Muscle Strength ; },
abstract = {We read the recent systematic review and meta-analysis on nutrition-based, gut microbiota-targeted interventions for sarcopenia in older adults with great interest. While the evidence suggests that probiotics and fiber-enriched diets may improve surrogate outcomes such as muscle strength and gait speed, we highlight two priorities to strengthen future mechanistic and clinical translation. First, microbiome measurements in existing trials are often limited to genus-level taxonomic shifts, which can be biologically misleading because a single genus may include members with divergent immunomodulatory properties. Even species-level profiling may be insufficient, as strains within the same species can differ markedly in genetic content and metabolic capacity. Moreover, taxonomic composition does not necessarily reflect functional output due to functional redundancy across microbial communities. We therefore recommend transitioning to whole-genome shotgun metagenomics to enable strain-level resolution and functional profiling, allowing investigators to quantify pathways and metabolites relevant to muscle preservation, including short-chain fatty acids and vitamin biosynthesis. Second, we argue that improvements in sarcopenia-defining parameters should be linked to patient-centered clinical benefit. Future randomized controlled trials should be adequately powered to assess hard endpoints, including falls, fractures, hospitalization rates, and functional independence, alongside muscle mass and performance measures, to establish whether microbiota modulation delivers meaningful reductions in healthcare burden.},
}

Humans
*Sarcopenia/microbiology/therapy/physiopathology
*Gastrointestinal Microbiome/physiology
Probiotics/therapeutic use
Aged
Muscle Strength

@article {pmid41680533,
year = {2026},
author = {Géniès, C and Maître, M and Baradat, S and Froliger, M and Turlier, V and Mercadié, A and Simcic-Mori, A and Gravier, E and Lauze, C and Huyghe, C and Alvarez-Georges, S and Chansard, N and Marinescu, R and Reygagne, P and Bessou-Touya, S and Mengeaud, V and Duplan, H},
title = {Metabolomics in Scalp Seborrheic Dermatitis Evidenced Key Changes in Inflammatory Markers Following a 10-Week Scalp Care Scheme with an Anti-dandruff Shampoo.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {41680533},
issn = {2193-8210},
abstract = {INTRODUCTION: Mild-to-moderate scalp seborrheic dermatitis (SD) is commonly managed by using anti-SD shampoos containing antifungal, anti-inflammatory, and keratolytic agents. A newly formulated anti-SD shampoo containing the patented combination of two antifungal actives has shown good clinical efficacy and tolerability in a previous two-phase randomized controlled trial.

METHODS: A specific analysis of scalp SD-associated metabolome was conducted to identify molecular markers involved in SD symptoms, and examine the impact of the anti-SD shampoo on these compounds. The intervention scheme involved a 2-week phase of intensive product use (three times a week), followed by an 8-week parallel-group maintenance phase consisting of the test group using the study shampoo once a week, and the control group using a neutral shampoo.

RESULTS: Following the intensive phase of the intervention, a significant decrease in the levels of SD markers (cathepsin S, interleukin-8, and histamine), inflammatory lipids (arachidonic acid, linoleic acid, and oxylipins), and metabolites involved in tryptophan metabolism (indolacetate and indolelactate) was observed. These changes were sustained during the maintenance phase in the test group only, supporting the clinical efficacy of the anti-SD shampoo. The integrated analysis of metabolome and fungal microbiome data suggested a positive correlation between the level of Malassezia fungi and that of two oxylipins (9,10,13-triHOME and 9-HODE), highlighting the pivotal role of these lipolytic fungi in SD conditions, and the involvement of newly identified proinflammatory lipid mediators. These oxylipins could be used as novel targets for developing alternative anti-SD strategies.

CONCLUSION: This approach allowed us to better characterize specific interactions within the scalp ecosystem providing deeper insights and unravelling new therapeutic pathways in SD like pro-inflammatory oxylipins.

GOV IDENTIFIER: NCT06578962 (retrospectively registered on August 28, 2024).},
}

@article {pmid41680341,
year = {2026},
author = {Karjee, A and Chatterjee, S and Chakraborty, R},
title = {Genomic and functional insights into a novel Lactococcus sp. AK05 from Cirrhinus mrigala with potent antagonism against Aeromonas hydrophila.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {87},
pmid = {41680341},
issn = {1573-0972},
}

@article {pmid41680322,
year = {2026},
author = {Li, Y and Wu, J and Wu, Y and Liu, Z and Zhang, J and Qian, T and You, J and Ma, B and Zuo, L and Luo, E and Bai, Y and Sun, X and He, Y and Xu, W and Peng, J},
title = {How gut microbiome and blood metabolites drive ossification of the posterior longitudinal ligament of the spine: a genome-wide association study based on the East Asian population.},
journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society},
volume = {},
number = {},
pages = {},
pmid = {41680322},
issn = {1432-0932},
support = {L242042//Beijing Natural Science Foundation/ ; },
}

@article {pmid41680178,
year = {2026},
author = {Tak, EJ and Goo, BJ and Lee, JY and Han, JE and Jeong, YS and Joe, HI and Sung, H and Kim, HS and Bae, JW},
title = {Dysbiosis of oral and gut microbiomes characterized by elevated Lactococcus in a mouse model of oral squamous cell carcinoma.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00934-8},
pmid = {41680178},
issn = {2055-5008},
abstract = {Oral microorganisms contribute to the progression of oral squamous cell carcinoma (OSCC), and the gut microbiome may also influence OSCC by modulating systemic immunity. This study investigated oral and gut microbial changes in a 4-nitroquinoline N-oxide (4-NQO)-induced OSCC mouse model. After 16 weeks of 4-NQO exposure, significant alterations were observed in the beta diversity of both oral and gut microbiomes. Notably, the relative abundance of Lactococcus increased, especially in oral microbiomes, from week 6 to 16, followed by a decline at week 22, suggesting a 4-NQO-induced niche favorable to its proliferation. Absolute quantification revealed a 4-NQO-induced increase in total bacterial load in the oral cavity, accompanied by elevated absolute abundance of Lactococcus. Unexpectedly, oral administration of Lactococcus strains isolated from 4-NQO-treated mice mildly alleviated inflammation. In vitro, lysates from these strains exhibited protein-dependent cytotoxicity against murine OSCC cells. These results suggest that Lactococcus strains may exert protective effects during OSCC progression.},
}

@article {pmid41680172,
year = {2026},
author = {Lu, Q and Wang, K and Gu, S and Ma, J and Cui, D and Chi, Z and Li, B and Zai, X and Wang, N and Wang, T and Dou, Z and Zhang, F and Geisen, S and Raaijmakers, JM and Song, C and Zuo, Y},
title = {Siderophore-producing Bacillus and free-living nematodes are associated with soil suppressiveness to banana root-knot nematodes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-69647-y},
pmid = {41680172},
issn = {2041-1723},
support = {No. 32372810//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 32302668//National Natural Science Foundation of China (National Science Foundation of China)/ ; No. 42577142//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {The control of soil-borne diseases is crucial for ensuring global food security. Here, we investigate the impact of the root-knot nematode (Meloidogyne) on banana continuous cropping over a period of 11 years. The results show significant root infestation initially, but disease incidence declined markedly from the 7th cropping year onwards. Soil community profiling revealed that this intriguing onset of nematode suppressiveness was associated with changes in free-living nematode populations and rhizosphere microbiome composition. Rhizosphere microbiome analyses and strain isolation pinpointed Bacillus velezensis as a keystone taxon in soil suppressiveness to Meloidogyne. Genomics, metabolomics and bioassays validated the suppressive effects of B. velezensis against Meloidogyne and identified the siderophore bacillibactin as key metabolite with repellent and nematicidal activities. By integrating long-term field studies with multi-omics approaches, this study uncovered co-occurring increases in specific rhizobacterial genera and free-living nematodes associated with reduced root-parasitic nematode populations, offering valuable insights for sustainable agriculture.},
}

@article {pmid41680006,
year = {2026},
author = {Yang, W and Shi, X and Xie, L and Zhang, H and Shen, L and Pan, L and Feng, S and Mao, X and Wu, X},
title = {The brain-lung axis: bridging neurological and respiratory disorders via neural-immune-microbial dialogue.},
journal = {Chinese journal of traumatology = Zhonghua chuang shang za zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cjtee.2025.10.006},
pmid = {41680006},
issn = {1008-1275},
abstract = {The human brain maintains intricate interconnections with various peripheral organs. Recent scientific inquiry has substantiated the existence of the gut-brain axis; nevertheless, emerging evidence suggests that the brain and lungs engage in bidirectional communication through multiple pathways, thereby giving rise to the conceptualization of a brain-lung axis. Studies indicate the presence of crosstalk between the central nervous system and the lungs, mediated by the lung microbiome, neural pathways, metabolite signaling, and immune pathways. This bidirectional communication between the brain and lungs is further implicated in the pathogenesis of several diseases: traumatic brain injury, stroke, and other cerebral disorders can precipitate pulmonary injury; conversely, severe pulmonary conditions, such as acute respiratory distress syndrome and chronic obstructive pulmonary disease, can exacerbate neuroinflammation, intensify brain damage, impair neurological function, and contribute to adverse prognoses. Exploring the brain-lung axis not only facilitates a multifaceted understanding of disease progression, but also unveils critical targets for therapeutic intervention. Research into the brain-lung axis provides novel perspectives for deciphering underlying pathological mechanisms, developing diagnostic methodologies, and formulating treatment strategies. It further establishes a theoretical foundation for cross-organ targeted therapies, holding promise for ameliorating patient outcomes and promoting the advancement of integrated diagnostic and therapeutic approaches for respiratory and neurological disorders.},
}

@article {pmid41679750,
year = {2026},
author = {Lamont, RF and Jørgensen, JS},
title = {The Influence of the Vaginal Microbiome on the Prediction and Prevention of Preterm Birth.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.70173},
pmid = {41679750},
issn = {1471-0528},
abstract = {BACKGROUND: Spontaneous preterm labour that leads to preterm birth is known to be associated with vaginal dysbiosis, particularly bacterial vaginosis, and this may explain why progress has been slow in the last few decades. Bacterial vaginosis was considered enigmatic with unknown aetiology, difficulty in diagnosis, different response to treatment, be that persistence or recurrence, and different phenotypic outcomes.

METHODOLOGY: A narrative review.

RESULTS: New information from the Human Microbiome Project using molecular-based, culture-independent technology has added important new knowledge to our understanding of vaginal eubiosis and dysbiosis. While this metagenomics are currently mainly research tools, we hope further studies will better elucidate the full profile of dysbiosis. This will hopefully aid the choice of antibiotic to suit each dysbiotic profile identified rather than for a single organism. By measuring abundance and diversity of the vaginal microbiome, we can develop molecular means of differentiating eubiosis and dysbiosis to predict preterm birth. We can also choose which antibiotic is appropriate for different dysbiotic subtypes, the local subtype of milieu created by that microbiota, the host response, and the phenotypical outcomes of which preterm birth is paramount. In addition, we can develop suitable probiotic species of lactic acid producing bacteria to aid in the prevention of preterm birth.},
}

@article {pmid41679688,
year = {2026},
author = {Tibi, MF and Argote, YM and Walker, AC and Pandey, S and Puente, C and Ellward, GL and Safwat, A and Rincon-Limas, DE and Czyż, DM},
title = {Modulation of Host Proteostasis by Prevotella corporis via Induction of the Heat Shock Response.},
journal = {Cell stress & chaperones},
volume = {},
number = {},
pages = {100150},
doi = {10.1016/j.cstres.2026.100150},
pmid = {41679688},
issn = {1466-1268},
abstract = {Neurodegenerative protein conformational diseases (PCDs) are progressive, currently incurable disorders driven by toxic protein aggregation that leads to neuronal death. Emerging evidence supports a microbial role in PCDs, including the most prevalent: Alzheimer's and Parkinson's disease. While metagenomic studies consistently associate gut dysbiosis with these disorders, the mechanisms by which microbes influence host proteostasis remain poorly understood. In particular, considerable attention has been given to proteotoxic bacteria, but the mechanisms by which commensal microbes confer proteoprotection remain largely unexplored. We have previously employed Caenorhabditis elegans models to characterize the role of over 220 bacterial isolates on host proteostasis. Strikingly, members of the Prevotella genus exhibited proteoprotective effects. Most notably, transient exposure to P. corporis uniquely induced Hsp70, a critical molecular chaperone that maintains proteostasis, and significantly reduced aggregation of polyglutamine (polyQ), Aβ1-42, and α-synuclein. In the present study, we expand on these findings, demonstrating that among 13 Prevotella species tested, P. corporis robustly activates the heat shock response (HSR) and confers conserved aggregate-suppressing activity in Drosophila melanogaster. We further demonstrate that transient exposure to P. corporis results in the activation of protective stress pathways and promotes disaggregation of existing intestinal polyQ aggregates in C. elegans, leading to a general enhancement of global proteostasis. This is supported by significantly improved survival and enhanced thermotolerance. Together, our findings reveal a beneficial niche for P. corporis in activating the HSR to enhance organismal proteostasis and support a microbe-mediated gut-proteostasis axis. This work underscores the therapeutic potential of targeting the gut microbiota for the management of PCDs, highlights the importance of species-level resolution in microbiome studies, and supports the emerging view of the intestine as a proteostasis-modulating organ.},
}

@article {pmid41679638,
year = {2026},
author = {Feng, X and Jiang, S and Yin, Q and Wang, K and Wang, C and Gao, W and Lei, L and Du, X and Wang, Z and Li, X and Song, Y and Liu, G},
title = {Effects of Fructus Ligustri Lucidi supplementation on energy metabolism, immunity, and rumen microbiome in peripartum cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27166},
pmid = {41679638},
issn = {1525-3198},
abstract = {The aim of this study was to evaluate the effect of Fructus Ligustri Lucidi (FLL) supplementation on energy metabolism, immunity, and the rumen microbiome in peripartum cows. Twenty healthy multiparous Holstein dairy cows were enrolled in the trial based on expected calving date, parity, and previous lactation milk yield. They were randomly assigned to either a control diet (Con; n = 10) or the control diet supplemented with 150 g/d per cow of FLL (FLL; n = 10). The trial spanned 6 wk, from 3 wk prepartum to 3 wk postpartum. Cows were milked thrice daily at 0500, 1100, and 1700 h, with milk yield and SCC recorded. Blood samples were collected from each cow at -3, -2, -1, 0, 1, 2, and 3 weeks relative to calving to evaluate the metabolic, inflammatory, and oxidative profiles. Peripheral blood neutrophils were isolated to measure reactive oxygen species (ROS), phagocytic activity, and neutrophil extracellular traps (NET). Rumen liquid was obtained via esophageal tubing at -3, 0, and 3 wk to investigate microbial biodiversity. Results indicated that FLL supplementation did not significantly affect the milk yield or SCC within 3 wk postpartum. Notably, FLL ameliorated negative energy balance from 1 wk to 3 wk, mitigated inflammation from calving day to 3 wk, and reduced oxidative stress at both -1 and 1 wk. The FLL treatment enhanced neutrophil phagocytosis from calving day to 1 wk, increased NET release at -1 wk, and reduced neutrophil ROS levels on calving day. Moreover, FLL increased rumen microbial α-diversity on calving day. At the phylum level, Firmicutes abundance was higher in the Con group on calving day compared with 3 wk pre- and postpartum, whereas Bacteroidota exhibited the opposite trend; FLL maintained stable Firmicutes and Bacteroidota abundances throughout the peripartum period. At the genus level, Prevotella abundance decreased in both groups on calving day but rebounded by 3 wk, with significantly higher Prevotella levels in the FLL group on calving day. The level 2 Kyoto Encyclopedia of Genes and Genomes pathway prediction further indicated divergent metabolic profiles: lipid metabolism pathways were less active in the FLL group than in the Con group on calving day and at 3 wk, whereas immune-related pathways were enriched in the FLL group. Energy metabolism pathway activity was higher in the FLL group on calving day but lower by 3 wk compared with the Con group. Correlation analysis indicated that rumen microbiome shifts were associated with energy metabolism, immunity, and oxidative stress. In conclusion, this study elucidates the dynamic changes in rumen microbiome during the peripartum period and highlights the beneficial effects of FLL supplementation on energy metabolism, immune function, and rumen microbial homeostasis in peripartum dairy cows.},
}

@article {pmid41679623,
year = {2026},
author = {Wang, Y and An, M and Lv, Y and Hou, Y and Li, Z and Dai, J and Ni, W and Hu, S},
title = {Genomic and functional characterization of probiotic strains from traditional fermented dairy products in alleviating dextran sulfate sodium-induced colitis.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27589},
pmid = {41679623},
issn = {1525-3198},
abstract = {Traditional fermented dairy products constitute a rich reservoir of probiotics and are closely associated with the maintenance of gut microbiome homeostasis and host health. However, the diversity and functional properties of probiotics in these products remain incompletely characterized. In this study, we aimed to isolate and identify novel probiotic strains from traditional fermented dairy products and systematically evaluate their probiotic attributes and mechanisms of action. Three previously uncharacterized strains-Lacticaseibacillus rhamnosus L.r1, Lacticaseibacillus rhamnosus L.r2, and Lactiplantibacillus plantarum ssp. plantarum L.p-were isolated and identified. Their probiotic features were assessed through acid and bile salt tolerance tests, survival in simulated gastrointestinal fluids, cell surface hydrophobicity, and autoaggregation capacity. Additionally, cell-free supernatants from these isolates exhibited broad-spectrum antimicrobial activity against several pathogenic bacteria. Whole-genome sequencing and comparative genomic analysis revealed the presence of an LPH homolog gene implicated in anti-inflammatory processes, along with gene clusters encoding secondary metabolites such as RiPP-like and terpene-precursor compounds. In a dextran sulfate sodium-induced murine colitis model, administration of L.r1, L.r2, or L.p significantly ameliorated colon damage, upregulated the expression of ZO-1, occludin, and IL-10, and downregulated IL-6. Fecal microbiome sequencing and functional prediction indicated that intervention with these strains restored gut microbiota balance, promoted the enrichment of beneficial genera including Akkermansia, Pediococcus, and Bacteroides, and suppressed microbial pathways related to antibiotic resistance and carbohydrate transport. These findings demonstrate that the isolated strains alleviate colitis through multifaceted mechanisms and hold strong potential as next-generation probiotics, providing both a theoretical foundation and microbial resources for developing functional foods.},
}

@article {pmid41679496,
year = {2026},
author = {Jing, M and Zhang, X and Li, X and Tan, L and Niu, Z and Ma, Y},
title = {Direct Evidence of Microplastic-Mediated Microbial Migration Across the River-Sea Transition via a Novel Field-Laboratory Coupled Approach.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123973},
doi = {10.1016/j.envres.2026.123973},
pmid = {41679496},
issn = {1096-0953},
abstract = {Large amounts of microplastics (MPs) are transported annually from river into the ocean. Biofilm-covered MPs, termed as the "plastisphere", may mediate microbial transfer. Previous studies have mostly focused on the evolution of the plastisphere itself, covering field experiments and its transformation during migration. Direct evidence for their impact on marine communities is still limited. To address this, we combined field and laboratory experiments to directly evaluate the effects of MPs on marine microbial communities along the river-sea shift. MPs were incubated for 0, 28, and 140 days in freshwater. They were then transferred to a laboratory-simulated marine micro-ecosystem constructed with a fresh seawater microbiome to allow the microbial communities to acclimate, and then further incubated in the laboratory for 1, 3, and 7 days. Microbial community dynamics were examined using metagenomic analysis. Long-term incubated plastispheres (140 days) rapidly shifted marine community structure toward plastisphere-like composition as early as Day 1. However, this overall structural change faded by Day 7. Interestingly, the presence of 28-day and 140-day plastispheres led to a consistent increase in microbial species diversity and a higher number of antibiotic resistance genes (ARGs) and virulence factors (VFs), this effect persisted through Day 7. Additionally, salt-tolerant, potentially pathogenic bacteria were also detected, reflecting the as carrier roles of plastispheres. This study provides direct evidence that plastispheres mediate microbial transfer, thereby enhancing diversity and spreading ARGs and VFs, contributing to a better understanding of the potential ecological and environmental risks of microplastics.},
}

@article {pmid41679417,
year = {2026},
author = {Dash, S and Zhao, D and Schuppe-Koistinen, I and Du, J},
title = {Female reproductive microbiome in fertility care.},
journal = {Fertility and sterility},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.fertnstert.2026.02.015},
pmid = {41679417},
issn = {1556-5653},
abstract = {The microbiome has emerged as a critical determinant of female reproductive health and fertility outcomes. While conventional infertility evaluations, encompassing medical history, ovulation assessment, uterine and tubal evaluation, genetic screening, hormonal profiling, and reproductive tract imaging, provide essential diagnostic information, a substantial proportion of infertility cases remain unexplained, prompting increased attention to microbial factors. This review provides a comprehensive, critical evaluation of methods for assessing the female reproductive microbiome, spanning traditional culture-based microbiology to contemporary molecular approaches. We systematically discuss the diagnostic performance, clinical utility, and established techniques, including microscopic examination, Nugent scoring, and Amsel criteria, alongside modern molecular methods such as quantitative PCR panels, 16S rRNA gene sequencing, shotgun metagenomics, and other multi-omics. Critically, we evaluate the current microbiome testing platforms in clinical validity and utility. We identify significant gaps between research-grade methodologies and clinically actionable diagnostics, including a lack of standardized protocols, inconsistent reporting of absolute bacterial loads versus relative abundances, and limited validation against reproductive outcomes. We propose evidence-based criteria for selecting appropriate diagnostic approaches based on clinical context and discuss emerging technologies, including multi-omics integration for implementing microbiome assessment in fertility care.},
}

@article {pmid41679348,
year = {2026},
author = {Odermatt, A and Morris, DJ},
title = {What can we learn from the history of steroid metabolites and the ongoing identification of novel biologically active steroid metabolites?.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {106954},
doi = {10.1016/j.jsbmb.2026.106954},
pmid = {41679348},
issn = {1879-1220},
abstract = {Historically, it was thought that primary steroids released from endocrine glands exert their hormonal effects through corresponding receptors in peripheral tissues, and that their metabolism then inactivates them, followed by excretion. However, the metabolism of primary steroids is not just a way of inactivating and excreting them, but generates a variety of metabolites with different biological properties. In this review, we outline how various active steroid metabolites were discovered, describe some of the ways they are generated, and how they can in a non-classical way act on receptors or alter the activity of steroid metabolizing enzymes, thereby indirectly affecting receptor activities. Examples include the 5α-reduced ring-A metabolites of 11-deoxycorticosterone (DOC) and progesterone that are formed in the brain, act as neurosteroids and exert effects through the GABA-A membrane receptor. Another example is 11-ketoprogesterone that potently activates mineralocorticoid receptors (MR), but not glucocorticoid receptors (GR), and is more potent than its 11β-hydroxylated form, in contrast to glucocorticoids. Moreover, we discuss the microbiome as important source of bioactive metabolites, exemplified by the 11β-hydroxylated 5α-reduced ring-A corticosteroid and progesterone metabolites that were shown as potent 11β-hydroxysteroid dehydrogenase 2 (11β-HSD2) inhibitors. 11β-HSD2 inhibition results in cortisol-induced MR activation, sodium retention and hypertension. Furthermore, microbial 17,20-desmolase activity can convert glucocorticoids to androgens, potentially influencing diseases and therapeutic outcomes. There are still many knowledge gaps regarding bioactive steroid metabolites. Identifying additional bioactive steroid metabolites and characterizing their genomic and non-genomic effects should help uncovering their cell-specific functions and contributions to the maintenance of homeostatic regulation.},
}

@article {pmid41679285,
year = {2026},
author = {Hussain, U and Cambon, MC and Crampton, B and Subramaniam, S and Kajamuhan, A and Ordoñez, A and Downie, J and Finch, J and Beckmann, M and Brown, N and Elison, A and Brady, C and Vanguelova, E and Denman, S and McDonald, JE},
title = {Microbial communities in semi-mature oak trees are resilient to drought, nutrient limitation, and pathogen challenge.},
journal = {Cell host & microbe},
volume = {34},
number = {2},
pages = {344-358.e5},
doi = {10.1016/j.chom.2026.01.009},
pmid = {41679285},
issn = {1934-6069},
mesh = {*Quercus/microbiology/physiology ; *Droughts ; *Microbiota ; Animals ; Trees/microbiology ; Forests ; Plant Roots/microbiology ; Plant Leaves/microbiology ; Rhizosphere ; Bacteria/classification/genetics/isolation & purification ; Stress, Physiological ; Nutrients/metabolism ; Coleoptera ; Ecosystem ; Plant Diseases/microbiology ; },
abstract = {Global forest biomes face increasing stressors and disease outbreaks that threaten ecosystem health. Tree-associated microbiota are vital for tree resilience, yet their responses to biotic and abiotic stressors in mature trees remain poorly understood. Using an experimental woodland plot of 144 Quercus petraea trees subjected to drought (rain exclusion), nutrient stress (ringbarking), and biotic treatments (bacterial pathogens and beetle larvae) to simulate acute oak decline, we tracked microbial communities in leaf, stem, and root/rhizosphere tissues across four time points over 2 years. Oak trees hosted distinct microbial communities across tissue types, which remained largely stable under stress. Rain exclusion significantly altered microbiota composition, though these changes explained less than 1% of total variance. Actinobacteriota, linked to drought tolerance, increased in the root/rhizosphere of rain-excluded trees. These findings reveal a surprising resilience of oak-associated microbial communities to environmental and biotic disturbances, highlighting their potential role in forest ecosystem stability.},
}

*Quercus/microbiology/physiology
*Droughts
*Microbiota
Animals
Trees/microbiology
Forests
Plant Roots/microbiology
Plant Leaves/microbiology
Rhizosphere
Bacteria/classification/genetics/isolation & purification
Stress, Physiological
Nutrients/metabolism
Coleoptera
Ecosystem
Plant Diseases/microbiology

@article {pmid41679283,
year = {2026},
author = {Rojer, Z and Hendry, TA},
title = {Seeing the forest: Microbiome resilience in mature trees.},
journal = {Cell host & microbe},
volume = {34},
number = {2},
pages = {195-197},
doi = {10.1016/j.chom.2026.01.014},
pmid = {41679283},
issn = {1934-6069},
mesh = {*Microbiota ; *Quercus/microbiology ; *Forests ; *Trees/microbiology ; Stress, Physiological ; },
abstract = {In this issue of Cell Host & Microbe, Hussain et al.[1] demonstrate surprising microbiome resilience in oak trees under abiotic and biotic stress. In contrast to work on herbaceous plants or saplings, it was found that mature oak trees growing in situ experienced little microbiome change under stress, across both time and tissue type.},
}

*Microbiota
*Quercus/microbiology
*Forests
*Trees/microbiology
Stress, Physiological

@article {pmid41679282,
year = {2026},
author = {Ma, L and Shu, L},
title = {Protist predators engineer bacterial metabolic cooperation.},
journal = {Cell host & microbe},
volume = {34},
number = {2},
pages = {192-194},
doi = {10.1016/j.chom.2026.01.011},
pmid = {41679282},
issn = {1934-6069},
mesh = {*Bacteria/metabolism ; Gastrointestinal Microbiome ; Ecosystem ; Animals ; *Eukaryota/physiology ; *Microbial Interactions ; },
abstract = {In the current issue of Cell Host & Microbe, Liu et al. establish a scalable framework and find that protist predation drives bacterial metabolic cooperation. This study offers insights for investigating similar cross-kingdom interactions in other ecosystems, such as sustainable agriculture and the gut microbiome.},
}

*Bacteria/metabolism
Gastrointestinal Microbiome
Ecosystem
Animals
*Eukaryota/physiology
*Microbial Interactions

@article {pmid41679274,
year = {2026},
author = {Liu, H and Hao, J and Han, X and Xu, S and Wang, X and Zhang, Q and Guo, T and Luo, C and Hu, L and Zhang, W},
title = {Rumen microbiota and fermentation parameters in Tibetan semi-fine wool sheep reflect growth stages and potential nutritional adaptations.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.250616},
pmid = {41679274},
issn = {2765-0189},
abstract = {OBJECTIVE: The rumen microbiota plays a pivotal role in fermenting plant biomass, which is essential for nutrient conversion. Although extensive research has examined the intestinal microbiome of Tibetan livestock, the rumen microbiota of semi-fine wool sheep (SF-sheep) remains poorly characterized. This study aimed to profile age-related changes in the rumen microbiota and fermentation parameters of SF-sheep to uncover potential microbial-mediated adaptations to different growth stages.

METHODS: Full-grazing male SF-sheep were randomly assigned into three age groups: two-month-old lambs, yearling sub-adults, and approximately 50-month-old adults. 16S rRNA gene sequencing and high-performance liquid chromatography were used to analyze the rumen microbiota composition and short-chain volatile fatty acids (SCVFAs).

RESULTS: Age-dependent differences were observed in ruminal NH₃-N concentrations, with sub-adult sheep exhibiting higher levels than young and adult individuals, whereas SCVFAs concentrations remained relatively stable. With age, the rumen microbial community structure tended to become more homogeneous, whereas microbial diversity and complexity showed a marked increase during adulthood. At the phylum level, Saccharibacteria and Succiniclasticum were enriched in sub-adults, whereas Euryarchaeota and Prevotellace_UCG_001 were more abundant in adults; no microbial biomarkers were detected in young sheep. Correlation analyses indicated that age and NH₃-N concentrations were the primary factors shaping the rumen microbiota. SCVFAs, including acetate, butyrate, and propionate, were positively associated with fibrolytic and polysaccharide-degrading bacteria such as Prevotella_1, Treponema_2, and Selenomonas_1. The rumen microbial communities were classified into two enterotypes. Enterotype 1, predominantly observed in young SF-sheep, showed higher abundances of KEGG Orthologs (e.g., K00656, K00239, K01966) associated with acetate, propionate, and butyrate synthesis.

CONCLUSION: The rumen microbial ecosystem of SF-sheep undergoes pronounced age-dependent restructuring in microbial composition and diversity, accompanied by nitrogen metabolism. These changes reflect dynamic microbial adaptation to the host's physiological state and potential developmental shifts in nutrient requirements, offering valuable insights for age-specific nutritional management strategies.},
}

@article {pmid41679270,
year = {2026},
author = {Saba, N and Moniruzzaman, M and Toung, DTC and Chin, S and La Min, LL and Karthikeyan, A and Lee, DI and Chun, JY and Min, T},
title = {Insights into nanostructured lipid carriers for the effective delivery of bioactives in swine and poultry health: review.},
journal = {Animal bioscience},
volume = {},
number = {},
pages = {},
doi = {10.5713/ab.250901},
pmid = {41679270},
issn = {2765-0189},
abstract = {Nanostructured lipid carriers (NLCs) are promising in target and efficient delivery of bioactive compounds with high loading capacity of bioactives, better physical stability, better encapsulation efficiency, solubility and bioavailability in comparison to the conventional delivery systems for lipophilic and hydrophobic bioactives such as essential oils and phytochemicals as well as functional feed ingredients. There are different types of NLCs combining solid lipid and liquid lipid in a single nanoparticulate matrix that have advantages over other drug delivery systems. The NLCs can be synthesized in form of imperfect, amorphous, oil-enriched, surface modified or functionalized, hybrid or composite and multiple-compartment or double-shell NLCs. Moreover, the synthesized NLCs safety, efficacy, toxicity, encapsulation efficiency, drug loading and releasing capacity, reproducibility in large scale were evaluated. The application of NLCs for the effective and target delivery of bioactive compounds are widely reported in biomedical and therapeutic studies. However, utilization of NLCs for the effective delivery of bioactive compounds is very limited in swine and poultry health. There are some recent studies reported that NLCs with can enhance growth, antioxidant capacity, immunity, gut health and microbiome as well as disease resistance in swine and poultry. This review focuses on recent developments and future prospects of utilizing NLCs in swine and poultry health management. Regardless of the potential beneficial effects of NLCs in nanodelivery of bioactive compounds, further research on long-term field oriented studies in livestock and poultry farms and economic analysis of manufactured NLCs should be carried out.},
}

@article {pmid41679088,
year = {2026},
author = {Leducq, JB and St-Amand, LP and Ross, D and Kembel, SW},
title = {A phylogenomic and metagenomic meta-analysis of bacterial diversity in the phyllosphere lifts a veil on hyphomicrobiales dark matter.},
journal = {Systematic and applied microbiology},
volume = {49},
number = {2},
pages = {126697},
doi = {10.1016/j.syapm.2026.126697},
pmid = {41679088},
issn = {1618-0984},
abstract = {The phyllosphere, or above-ground part of plants, hosts diverse bacterial communities that play critical ecological roles and provide beneficial functions for the plant. The Hyphomicrobiales (Alphaproteobacteria) are a highly diverse and ecologically important clade known to be key members of the plant microbiome, in particular in association with plant roots, but their diversity remains largely uncharacterized in the phyllosphere. Using a meta-analysis combining metabarcoding, metagenomics and phylogenomics, we explored the diversity of leaf-associated Hyphomicrobiales. We confirmed Methylobacterium was ubiquitous in the phyllosphere and revealed the dominance of two under-characterized Hyphomicrobiales taxa: Lichenihabitantaceae, a lichen-associated family previously identified as "1174-901-12" in taxonomic databases, and RH-AL1, an undescribed lineage of bacteria related to Beijerinckiaceae. Despite their abundance in the phyllosphere, Lichenihabitantaceae and RH_AL1 could not be properly identified by 16S rRNA gene barcoding, due in part to limitations of short read sequencing leading to a lack of recognition of certain Hyphomicrobiales genera, and to incongruencies in the assignment of genera to families among existing taxonomic databases. A significant proportion of Lichenihabitantaceae were detected in association with lichens and in environments with harsh conditions like exposed surfaces, air and snow. Overall, our study stresses the need to agree on a common systematic framework to properly classify and identify key leaf-associated Hyphomicrobiales taxa, and to move toward metagenomics and culturomics to increase their representation in reference databases, to provide a better understanding of the evolutionary and functional mechanisms underpinning bacteria adaptations to living on plants.},
}

@article {pmid41679036,
year = {2026},
author = {Lu, L and Jian, X and Lin, S and Li, Z and Tang, Q and Xiao, Y and Zhang, Y and Wang, D},
title = {The cNED framework: modeling core microbial communities and metabolic functions with SHAP-interpretable environmental thresholds in large rivers.},
journal = {Water research},
volume = {294},
number = {},
pages = {125531},
doi = {10.1016/j.watres.2026.125531},
pmid = {41679036},
issn = {1879-2448},
abstract = {Microbial communities in river ecosystems regulate biogeochemical cycling and serve as natural bioremediators for environmental pollutants. However, accurately predicting their dynamic responses to changing conditions remains a significant scientific challenge because of the complexity of microbial interactions and ecosystem-scale feedbacks. Here, a novel compositional neural encoder-decoder (cNED) framework was developed, coupling environmental variables with microbial profiles based on an extensive collection of 473 samples from the upper Yangtze River. A total of 157 core bacterial OTUs were identified from 27,932 OTUs by the occupancy-frequency method, which were predominantly governed by deterministic assembly processes. The identified core microbiome demonstrated significant functional associations with carbon and nitrogen cycling. Compared with conventional modeling approaches (multilayer perceptron, random forests, linear regression), the cNED framework demonstrated superior predictive performance, achieving high accuracy in taxonomic prediction and functional profile prediction (carbon cycling: R[2] = 0.85; nitrogen cycling: R[2] = 0.52). The Shapley additive explanations (SHAP) analysis identified spatial gradients and temperature as key environmental drivers. Generalized Additive Models uncovered phylum- and function-specific tipping points: Proteobacteria exhibited a dual-threshold thermal niche (20.5-27 °C), while functions like methylotrophy and nitrogen fixation responded nonlinearly to temperature and TN, revealing unimodal or monotonic transitions. The cNED framework developed in this study establishes an interpretable predictive framework for forecasting microbial community and functional responses to environmental perturbations, offering valuable insights for evidence-based river ecosystem management and climate adaptation strategies.},
}

@article {pmid41679031,
year = {2026},
author = {Lin, L and Zhu, X and Lin, X and Zhao, Z and Wang, H and Yan, H and Ju, F},
title = {Nitrogen-removal collapse and recovery: Integrative meta-omics insights into seasonal microbiome dynamics and cold-adaptive mechanisms in a full-scale activated sludge system.},
journal = {Water research},
volume = {294},
number = {},
pages = {125478},
doi = {10.1016/j.watres.2026.125478},
pmid = {41679031},
issn = {1879-2448},
abstract = {The underlying mechanisms by which seasonal cooling impairs nitrogen removal in ambient-temperature bioreactors remain largely unresolved. Here, we monitored a full-scale livestock wastewater activated sludge (LWAS) system throughout the summer-winter transition, integrating meta-omics analyses to link process performance with microbial community dynamics and intracellular functional adaptation. Nitrogen-removal rate fell from averaged 92.7 g N/m[3]/d in summer to zero in autumn, then partially recovered in winter. Concurrently, the microbial Shannon diversity of nitrogen-metabolizing communities declined in autumn and rebounded in winter. Seasonal cooling increased influent immigration and compressed the niche space of nitrogen-metabolizing guilds. Denitrification remained functionally robust, with Pseudomonas and Corynebacterium supplanted summer-dominant Thauera and Thiobacillus. In contrast, ammonia-oxidizing bacteria (AOB) were strongly inhibited: both species abundance and ammonia monooxygenase activity declined in autumn. During winter, Nitrosomonas eutropha_B LWAS_194 dominated and maintained ammonium oxidation at 4°C by up-regulating genes for post-translational modification, energy generation, cryoprotectant production, membrane fluidity, and antioxidant defense. These findings highlight the cold-induced inhibition of AOB as the key limitation for nitrogen removal. Strategies including AOB-specific carriers, bioaugmentation with cold-adapted AOBs and thermal insulation offer practical solutions. This multiscale microbiome-engineering framework is broadly applicable to wastewater and ecological systems experiencing seasonal cold stress.},
}

@article {pmid41678952,
year = {2026},
author = {Chandrasekar, GH},
title = {Unraveling immune evasion in the tumor microenvironment: Mechanisms, therapeutic strategies, and future directions in cancer immunotherapy.},
journal = {Molecular immunology},
volume = {191},
number = {},
pages = {70-78},
doi = {10.1016/j.molimm.2026.01.013},
pmid = {41678952},
issn = {1872-9142},
abstract = {The immune evasion that is encouraged by the tumor microenvironment (TME) is a key factor in the failure of cancer immunotherapies. This review addresses how tumor cells avoid immune surveillance, which is critically dependent on cellular and molecular events associated with immune checkpoint signaling, the capture of immune surveillance cells, metabolic restructuring, and physical and hypoxic barriers. We also discuss the latest therapeutic options, including immune checkpoint blockers, metabolic and angiogenic combination therapies, and Macrophage reprogramming of tumors. Nonetheless, such challenges as therapeutic resistance and patient heterogeneity are still significant challenges. In the future, individualized immunotherapy with the use of precision oncology tools that integrate multi-omics profiling, artificial intelligence, and manipulation of the gut microbiome a promising opportunity. A better understanding of the dynamic TME and the individualized immune landscape is the key to effective immunotherapy and the attainment of durable clinical responses to various types of cancers.},
}

@article {pmid41678593,
year = {2026},
author = {Chen, HC and Tang, TWH and Pasaribu, SNN and Wu, DC and Rey, FE and Hsieh, PCH},
title = {Gut-Heart Axis in Myocardial Repair: Mechanisms, Cross-Organ Networks, and Therapeutic Opportunities.},
journal = {Circulation research},
volume = {138},
number = {4},
pages = {e326978},
doi = {10.1161/CIRCRESAHA.125.326978},
pmid = {41678593},
issn = {1524-4571},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Animals ; *Myocardium/metabolism/pathology ; *Regeneration ; *Heart/physiology ; },
abstract = {Cardiovascular diseases remain the leading global cause of morbidity and mortality, placing an escalating burden on health care systems and economies. While the gut microbiota is well recognized in atherosclerosis and cardiometabolic disorders, its influence on myocardial injury, repair, and regeneration is only beginning to emerge. Growing evidence reveals that gut microbes and their metabolites regulate myocardial health through intricate cross-organ networks, including the gut-brain-heart, gut-liver-heart, and gut-lung-heart axes. These findings suggest that the heart plays a key role in systemic host-microbe communication. Advances in metagenomics, metabolomics, and single-cell transcriptomics are now defining the molecular and cellular pathways by which microbial metabolites modulate immune tone, endothelial integrity, metabolic resilience, and cardiomyocyte survival. Studies in gnotobiotic models have established causal links between specific microbial taxa and myocardial outcomes while illuminating their roles in fibrosis resolution, angiogenesis, and regeneration. In this review, we synthesize current knowledge on the bidirectional gut-heart dialogue, emphasizing immunometabolic signaling, cross-organ integration, and regenerative mechanisms. We propose that coupling high-resolution multiomics with mechanistic modeling in controlled microbial systems will be pivotal for next-generation, microbiota-informed diagnostics, and therapeutics. We explore the emerging role of the gut-myocardium axis as both a driver of disease and as a promising modifiable therapeutic target and highlight a new frontier in precision cardiovascular medicine, with the potential to transform strategies for prevention, repair, and tissue regeneration.},
}

Humans
*Gastrointestinal Microbiome/physiology
Animals
*Myocardium/metabolism/pathology
*Regeneration
*Heart/physiology

@article {pmid41678114,
year = {2026},
author = {Dash, HR},
title = {Advanced molecular techniques in distinguishing monozygotic twins for forensic applications.},
journal = {Genes & genomics},
volume = {},
number = {},
pages = {},
pmid = {41678114},
issn = {2092-9293},
abstract = {Despite significant advancements in the forensic DNA analysis techniques, one of the major limitations is the availability of a gold standard genetic technique to distinguishing the monozygotic (MZ) twins. NGS mediated deep sequencing approach is capable of detecting the rare post-zygotic mutations. Despite having a similarity DNA profile, tiny differences in the personality, living habits and disease susceptibility, leads to the observance of epigenetic changes. Both DNA methylation and histone acetylation have demonstrated scientific approach of distinguishing MZ twins. The stable non-coding RNAs, i.e., miRNA, circRNA, and tsRNA have been targeted in most of the studies to differentiate the MZ twins based on their differential expression. The inception of MPS technology allows the rapid sequencing of whole mtDNA genome. It allows the identification of rare mutational events as well as the heteroplasmic DNA to accurately distinguish the MZ twins. Emergence of IRs like TCRβCDR3 have also shown promise as a potential biomarker in distinguishing MZ twins. Analysis of the relatively more stable molecules by proteomics, metabolomics, and microbiome analysis have also demonstrated their MZ twins' differential capability. The present article highlights the technological advancements in the forensic differentiation of the MZ twins and their respective pros and cons.},
}

@article {pmid41677895,
year = {2026},
author = {Zhang, W and Wang, J and Wu, P and Pang, Y and Dai, S and Zhang, X and Xu, S and Gao, B and Chen, Y and Huang, Z},
title = {Development of biocontrol agents for cotton verticillium wilt using microbiome analysis.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {184},
pmid = {41677895},
issn = {1432-072X},
mesh = {*Gossypium/microbiology ; *Plant Diseases/microbiology/prevention & control ; Soil Microbiology ; *Microbiota ; Plant Roots/microbiology ; Rhizosphere ; *Verticillium/physiology ; *Biological Control Agents ; Bacteria/classification/isolation & purification/genetics ; Antibiosis ; Fungi/classification/isolation & purification/genetics ; },
abstract = {Verticillium wilt is one of the most devastating diseases of cotton, yet effective biocontrol strains remain scarce. This study aimed to guide the selection of efficient biocontrol strains by comparing the microbiomes of healthy and diseased cotton plants. Our results revealed that Verticillium dahliae V991 (V991) significantly altered the bacterial and fungal communities in the cotton roots, rhizosphere soil and bulk soil. Compared to diseased cotton in the V991 inoculation group (D), both healthy cotton in the V991 inoculation group (H) and non-inoculated control cotton (C) suppressed Verticillium and Fusarium and enriched Bacilli, Clostridia, Archacosporales, Glomerales, unclassified Basidiomycota and unclassified Glomeromycota in the roots, enriched Burkholderiales in the rhizosphere soil, enriched Archaeosporales and Verrucomicrobiota in the bulk soil. A total of 20 strains with antagonism against V991 were screened, most isolated from roots of the C group. Bacillus amyloliquefaciens M9 (BM), isolated from rhizosphere soil, exhibited the strongest antifungal activity, while Bacillus cereus R19 (BR), isolated from root, showed weaker activity. Pot experiments demonstrated that application of BR and BM (10[9] CFU/mL) reduced disease incidence by 44.82% and 24.14%, respectively, compared to the control. Field experiments showed that BR reduced disease incidence by 88.46%, while BM achieved a 50.01% reduction. These findings confirm that comparative microbiome analysis is a powerful strategy for selecting highly effective biocontrol strains.},
}

*Gossypium/microbiology
*Plant Diseases/microbiology/prevention & control
Soil Microbiology
*Microbiota
Plant Roots/microbiology
Rhizosphere
*Verticillium/physiology
*Biological Control Agents
Bacteria/classification/isolation & purification/genetics
Antibiosis
Fungi/classification/isolation & purification/genetics

@article {pmid41677879,
year = {2026},
author = {Nolan, L and O'Toole, PW},
title = {Soy and the gut microbiome: a bi-directional relationship shaping nutrition and health.},
journal = {European journal of nutrition},
volume = {65},
number = {2},
pages = {53},
pmid = {41677879},
issn = {1436-6215},
}

@article {pmid41677827,
year = {2026},
author = {Sharma, S and Sati, B and Pant, D and Basu, S},
title = {Culturable rhizospheric microbiota of Lactuca sativa cultivars during nutrient-film farming reveals potential biocontrol and plant-growth promoting traits against commonly infesting fungal pathogens.},
journal = {Archives of microbiology},
volume = {208},
number = {4},
pages = {185},
pmid = {41677827},
issn = {1432-072X},
support = {UCOST Grant RND/8/2024 - DPT 26319//UCOST/ ; UPES: UPES/R&D- SoHST/10042024/71//University of Petroleum and Energy Studies/ ; },
mesh = {*Rhizosphere ; *Lactuca/microbiology/growth & development ; *Bacteria/classification/isolation & purification/genetics/growth & development ; *Fungi/isolation & purification/classification/genetics ; *Microbiota ; Soil Microbiology ; *Plant Diseases/microbiology/prevention & control ; Plant Roots/microbiology/growth & development ; Hydroponics ; Fusarium ; },
abstract = {Solar-powered hydroponics farming of edible crops is gaining prominence as a sustainable cultivation method. However, growing evidence indicates a significant risk of pathogen emergence in commercial settings, potentially arising from waterborne sources or plant physiological stress. Nevertheless, there is a paucity of understanding the potential of plant-growth promoting and biocontrol traits among microorganisms colonizing the rhizosphere of hydroponically grown crops. In this study, we investigated the culturable rhizosphere microbial communities of three different Lactuca sativa cultivars in controlled green-house hydroponics employing the circulating nutrient-film farming technique with coconut coir as substrate. Over an 8-week growth period, ~ 250 bacterial and fungal strains were isolated. By week 7, the presence of Alternaria sp. SSSB_F2 and Fusarium sp. SSSB_F1 was detected from infected leaves and confirmed to be pathogenic to all L. sativa cultivars. Notably, fungal infections were accompanied by a marked decline in cultivable rhizosphere microbes, suggesting a disruption of root-associated microbial communities. Further, biochemical characterisation of rhizosphere strains followed by 16SrRNA and ITS sequencing led us to identify eight promising biocontrol and plant-growth promoting bacterial strains belonging to Stenotrophomonas, Bacillus, Pseudomonas, Micrococcus, Exiguobacterium, Staphylococcus, and two fungal strains as Trichoderma and Simplicillium. A plant-probiotics consortium was thus formulated based on mutual compatibility and tested for its effects on seedling germination, plant development, and pigmentation. Preliminary trials performed using this consortium to prime L. sativa seeds enhanced seedling germination and plant growth in coconut coir. These findings underscore the importance of harnessing beneficial rhizosphere microbiota enriched during controlled environment agriculture, such as hydroponics, and their potential to enhance plant-growth as well as disease resilience.},
}

*Rhizosphere
*Lactuca/microbiology/growth & development
*Bacteria/classification/isolation & purification/genetics/growth & development
*Fungi/isolation & purification/classification/genetics
*Microbiota
Soil Microbiology
*Plant Diseases/microbiology/prevention & control
Plant Roots/microbiology/growth & development
Hydroponics
Fusarium

@article {pmid41677795,
year = {2026},
author = {Gaio, D and Tackmann, J and Perez-Molphe-Montoya, E and Näpflin, N and Patsch, D and Malfertheiner, L and Peluso, ME and von Mering, C},
title = {Enhanced semantic classification of microbiome sample origins using Large Language Models (LLMs).},
journal = {GigaScience},
volume = {},
number = {},
pages = {},
doi = {10.1093/gigascience/giag015},
pmid = {41677795},
issn = {2047-217X},
abstract = {Over the past decade, central sequence repositories have expanded significantly in size. This vast accumulation of data holds value and enables further studies, provided that the data entries are well annotated. However, the submitter-provided metadata of sequencing records can be of heterogeneous quality, presenting significant challenges for re-use. Here, we test to what extent large language models (LLMs) can be used to cost-effectively automate the re-annotation of sequencing records against a simplified classification scheme of broad ecological environments with relevance to microbiome studies, without fine-tuning. This effort directly contributes to improving the FAIRness-Findability, Accessibility, Interoperability, and Reusability-of microbiome sequencing metadata, thereby enhancing their "AI readiness" for downstream computational analyses. We focused on sequencing samples taken from the environment, for which metadata is important. We employed OpenAI Generative Pre-trained Transformer (GPT) models, and assessed scalability, time- and cost-effectiveness, as well as performance against a diverse, hand-curated benchmark with 1,000 examples, that span a wide range of complexity in metadata interpretation. Annotation performance markedly outperformed that of a baseline, manually curated, non-ML keyword-based approach. Changing models (or model parameters) has only minor effects on performance, but prompts need to be carefully designed to match the task. Furthermore, when we compared proprietary OpenAI models with open-weight alternatives (e.g., Qwen, meta-Llama, and microsoft-phi-4), we found comparable accuracy for both biome and sub-biome classification, indicating that open-weight architectures can match the performance of proprietary models for large-scale ecological metadata re-annotation. We validated the pipeline with 1,000 hand-curated samples, and we applied the optimized pipeline to 2 million sequencing records from the environment, providing coarse-grained yet standardized sample origin annotations covering the globe. Our work demonstrates the effective use of LLMs to simplify and standardize annotation from complex biological metadata.},
}

@article {pmid41677682,
year = {2026},
author = {Lee, DY and Liu, J and Lamichhane, G and Swayze, A and Zhang, G and Kim, TY and Egan, JM and Kim, Y},
title = {Fermented Red Ginseng Restores Age-Associated Insulin Homeostasis and Gut Microbiome Balance in Mice.},
journal = {Biology},
volume = {15},
number = {3},
pages = {},
pmid = {41677682},
issn = {2079-7737},
support = {1-156214//Oklahoma State University/ ; 1-511773//BTC Corporation/ ; },
abstract = {Biological aging disrupts liver-gut intercommunication, resulting in the development of insulin resistance and type 2 diabetes, coupled with the imbalance of gut microbiome composition known as gut dysbiosis. Fermented red ginseng (FRG) is a renowned functional food substance showing its notable anti-inflammatory and anti-diabetic effects owing to its unique bioactive compounds known as ginsenosides. However, whether FRG could impact biological aging and age-related metabolic dysfunction is still unclear. The current study aimed to determine the health benefits of FRG in improving age-associated impaired insulin homeostasis and gut dysbiosis in 19-month-old male mice. Mice were fed with a normal chow diet (NCD) or NCD with FRG (300 mg/kg) for 14 weeks. FRG supplementation significantly improved insulin homeostasis by activating the hepatic protein kinase B (AKT) and proline-rich AKT substrate of 40 kDa (PRAS40). We also observed suppressed mRNA expression of proinflammatory cytokines and diminished inflammatory infiltrates in the liver of FRG-fed mice compared with NCD-only controls. Furthermore, alongside a decreased ratio of Firmicutes to Bacteroidetes, FRG administration enriched beneficial genera, including Muribaculaceae, Borkfalkiaceae, Parasutterella, and Clostridia vadin BB60 group, whereas FRG reduced the abundance of Erysipelotrichaceae and Dubosiella at the genus level. In summary, we suggest that FRG can be a potential anti-aging dietary supplement to manage age-driven dysregulation of insulin homeostasis and gut microbiota composition.},
}

@article {pmid41677269,
year = {2026},
author = {Rhodes, K},
title = {mSphere of Influence: Missing the trees for the forest.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0073725},
doi = {10.1128/msphere.00737-25},
pmid = {41677269},
issn = {2379-5042},
abstract = {Katherine Rhodes is a bacteriologist working in the field of host-microbe interaction. In this mSphere of Influence article, she reflects on how two papers, "Spatial ecology of the human tongue dorsum microbiome" by S. Wilbert, J. Mark Welch, and G. Borisy and "Novel peptide from commensal Staphylococcus simulans blocks methicillin-resistant Staphylococcus aureus quorum sensing and protects host skin from damage" by M. Brown et al., impact her research on Neisseria commensalism and host adaptation.},
}

@article {pmid41677228,
year = {2026},
author = {Galbraith, NJ and White, MG and Smith, JJ},
title = {Translating Microbiome Science Into Surgical Oncology: Insights From Global Colorectal Cancer Studies.},
journal = {Diseases of the colon and rectum},
volume = {69},
number = {3},
pages = {326-329},
doi = {10.1097/DCR.0000000000004037},
pmid = {41677228},
issn = {1530-0358},
}

@article {pmid41677194,
year = {2026},
author = {Simm, NM and Williams, GM and Fowler, S and Barlow, K and Carter, B and Talley, NJ and Keely, S and Duncanson, K and Hoedt, EC},
title = {A Scoping Review of Methods Used to Investigate Relationships between Dietary Intake and the Gastrointestinal Microbiome.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuaf306},
pmid = {41677194},
issn = {1753-4887},
support = {//Australian Government Research Training Program Scholarship/ ; //Australian NSW Health Round 5 Early-Mid Career Grant/ ; },
abstract = {The gastrointestinal (GI) microbiome is intrinsically linked to human health and disease, with dietary intake being a major modifiable variable contributing to microbial colonization and fermentation. Diet-microbiome studies are heterogeneous in the methods used to assess and record dietary intake, to sequence the microbiome data, and to analyze associations. To capture the extent of these inconsistencies, we performed a systematic scoping review to synthesize the information on methods used to assess and compare relationships between diet and the GI microbiome in human studies. Our search identified papers with metrics of both dietary intake and the GI microbiome (using either 16S rRNA or metagenomic shotgun sequencing) and specific diet-microbiome associative analysis. The databases searched were MEDLINE, EMBASE, CINAHL, Cochrane, and Google Scholar, and the search produced 22, 228 unique records after de-duplication. After full-text screening, 1,262 articles were selected for full extraction. A subset of 295 studies captured whole dietary intake and investigated associations with the GI microbiome. This subset assessed diet using 84 different food frequency questionnaires, 12 alternative surveys, and 4 types of diet recalls or diaries ranging from 1 to 14 days. Fifty-five percent (n = 163) of studies investigated habitual dietary intake, 35% (n = 101) investigated recent dietary intake, and 10% (n = 30) used methods to assess both. Eighty-one percent of studies employed 16S rRNA sequencing, with wide variation in extraction, sequencing, pre-processing, and annotation methods. Gaps in the reporting of the methods for each step of the sequencing and analysis process were evident, limiting future comparison of study outcomes. Microbiome-specific statistical methods were used in 11% of the subset-predominantly correlational methods that are not recommended for microbiome data. In conclusion, this review revealed extensive inconsistencies within the exploratory diet-microbiome studies, despite the existence of recommendations to assist researchers. Collaborative efforts to develop consensus in methods and reporting are needed to substantially progress the obtaining of high-quality evidence and meta-analysis in the diet-microbiome research field.},
}

@article {pmid41676974,
year = {2026},
author = {Poczta, Z and Leśniak, C and Podeszwa, A and Różycka, MA and Włoch, O and Siejek, A and Dobrowolska, A and Zawada, A},
title = {The Relationship between Diabetes Complications and the Intestinal Microbiota.},
journal = {Current diabetes reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115733998408978251206123827},
pmid = {41676974},
issn = {1875-6417},
abstract = {INTRODUCTION: The increasing prevalence of diabetes mellitus (DM) has intensified research into its mechanisms and complications. Alterations in gut microbiota are considered an environmental factor influencing the onset, progression, and complications of diabetes. This review summarizes current evidence on the role of microbiota in diabetes and its outcomes.

METHODS: This literature review was conducted using English-language articles from PubMed and Google Scholar, focusing on original research and reviews, primarily published within the last 10 years. Key search terms included "type 1 diabetes mellitus," "type 2 diabetes mellitus," "gut microbiota dysbiosis," and related metabolic and complication terms. Both animal and human studies were included.

RESULTS: Current studies reveal a strong correlation between gut microbiota alterations and diabetes and its complications. Dysbiosis, characterized by reduced bacterial diversity, is observed in both type 1 (T1DM) and type 2 diabetes (T2DM) patients. In T1DM, dysbiosis may contribute to immune dysregulation and increased intestinal permeability. In T2DM, lower bacterial diversity is linked to insulin resistance and obesity. Dysbiosis is also directly associated with diabetic retinopathy and contributes to nephropathy, neuropathy, and ischemic heart disease.

DISCUSSION: These findings suggest that gut microbiota alterations may play a role in diabetes pathogenesis and its complications, indicating potential targets for therapeutic modulation. However, causal relationships remain to be fully clarified.

CONCLUSION: Although progress has been made, the precise role of gut bacteria in diabetes remains unclear. A better understanding of these mechanisms is crucial for developing diagnostic and therapeutic strategies, and further human studies are needed to confirm findings from animal models.},
}

@article {pmid41676861,
year = {2026},
author = {Tzanetakis, GN and Markou, ME and Koletsi, D and Nagendrababu, V and Duncan, HF},
title = {Bacterial Diversity of Deep Carious Lesions Analysed by Next-Generation Sequencing Approaches Associated With Different Pulp Diagnoses: A Systematic Review.},
journal = {International endodontic journal},
volume = {},
number = {},
pages = {},
doi = {10.1111/iej.70114},
pmid = {41676861},
issn = {1365-2591},
abstract = {AIM: This systematic review aimed to synthesise evidence on the microbiome of deep or extremely deep caries associated with a range of different pulp conditions, by analysing studies using next-generation sequencing (NGS) approaches.

METHODOLOGY: The review reported according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 guidelines and protocol was registered prospectively at the Open Science Framework (https://osf.io/vnwjh/). A literature search was carried out in the following databases: MEDLINE via PubMed, Scopus, Cochrane Database for Systematic Reviews (CDSR), Web of Science, the clinicaltrials.gov, and the Open Science Framework, in English language without time restriction. The last search was performed on May 1st 2025. An additional online search of the four major journals in the field of endodontics (International Endodontic Journal, Journal of Endodontics, Australian Endodontic Journal and the European Endodontic Journal) was also carried out independently starting from January 1st, 2010 to May 1st 2025. Only original research articles that used an NGS approach and investigated the microbiome of deep or extremely deep caries associated with different pulp diagnoses, assessed preoperatively, were included. The Johanna Brigg's Institute (JBI's) Critical Appraisal Instrument for Studies Reporting Prevalence Data was used to assess the risk of bias of included studies.

RESULTS: Among 1914 articles initially identified, four were considered eligible for inclusion and further assessed for certain parameters. The overall risk of bias of the three and one included studies was characterised as 'unclear' and 'high'. Firmicutes were the most prevalent phylum in all cases. In cases of irreversible pulpitis, Firmicutes prevalence increased compared with cases of normal pulp and reversible pulpitis, while the prevalence of Actinobacteria, Proteobacteria and Bacteroidetes decreased. Lactobacillus was the most abundant genus in all cases, with its abundance in cases of symptomatic irreversible pulpitis increasing substantially.

CONCLUSIONS: The NGS studies evaluated in this review create a preliminary, but comprehensive map of the microbiome of deep caries associated with a range of pulpal diagnoses. Α shift in microbiome as the asymptomatic cases become progressively symptomatic seems to occur, which may be relevant to management of deep caries in terms of complete or selective caries removal.},
}

@article {pmid41676651,
year = {2026},
author = {Charron-Lamoureux, V and Xing, S and Patan, A and Walker, C and Monter, RA and Abiead, YE and Zhao, HN and Patel, L and Weng, Y and Gonzalez, A and Ackermann, G and Deleray, V and Gandhi, V and Mohanty, I and Caraballo-Rodriguez, AM and Kvitne, KE and Zuffa, S and Norman, A and Martin, A and Chin, L and Paz-Gonzalez, R and Sala-Climent, M and Suryawinata, N and Zemlin, J and Gouda, H and Hu, Z and Norton, G and Rajkumar, P and Molina, AJ and Bergstrom, J and Pinner, M and Giddings, S and Aron, AT and Liang, L and Dahesh, S and Lamichhane, S and Reilly, ER and Nizet, V and Skrip, A and Lukowski, AL and Shore, SFH and Ghoshal, S and Engevik, MA and Horvath, TD and Renwick, S and Agongo, J and Marco, ML and Mazmanian, SK and Wang, M and Yang, H and McDonald, D and Guma, M and Stegmann, E and Hernandez Perez, N and Stincone, P and Kemen, E and Pakkir Shah, AK and Bode, L and Petras, D and Siegel, D and Raffatellu, M and Patterson, AD and Devkota, S and Jinich, A and Knight, R and Zengler, K and Dorrestein, PC},
title = {A searchable metadata network graph for microbiome metabolomics.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.04.703849},
pmid = {41676651},
issn = {2692-8205},
abstract = {Establishing the biological context of microbial metabolites remains a major challenge. We present microbiomeMASST, a metadata-driven network graph that maps metabolites across 467 available datasets with 144,424 mass spectrometry files from humans, animals, and microbial culture systems. MicrobiomeMASST integrates monocultures, synthetic communities, and host-associated samples across multiple body sites and plants. MS/MS spectra can be queried to trace occurrence across hosts, experimental conditions, and interventions, enabling cross-study integration. We demonstrate this framework by contextualizing microbial-conjugated bile acids and interrogating microbiome-mediated drug metabolism. Screening gut bacteria revealed deprolylation of the angiotensin-converting enzyme (ACE) inhibitor prodrug enalapril. Using microbiomeMASST, we traced this metabolite across human cohorts, microbial isolates, environmental samples, and in Gorilla gorilla . Structural modeling and enzymatic assays showed that microbial deprolylation abolishes ACE inhibition, thereby inactivating its therapeutic effect. Together, microbiomeMASST links MS/MS spectra to biological context, converting isolated observations into an interpretable microbiome map for cross-study analysis.},
}

@article {pmid41676579,
year = {2026},
author = {Pakkir Shah, AK and Griesshammer, A and Stincone, P and Kalinski, JC and Walter, A and Wang, M and Maier, L and Petras, D},
title = {A Functional Metabolomics Framework to Track Microbiome Drug Metabolism.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.30.702925},
pmid = {41676579},
issn = {2692-8205},
abstract = {Understanding how gut microbes transform drugs, and how this influences microbiome composition and function, remains a key question to better understand the efficacy and side effects of pharmaceuticals. To accelerate the discovery of microbiome-derived drug metabolites, we developed a functional metabolomics workflow that combines the use of synthetic microbial communities (SynComs) with a time-series resolved molecular networking approach and advanced computational metabolite annotation. We demonstrate how this framework can be used to illuminate chemical transformation dynamics in a gut SynCom (Com20) with 50 clinical drugs. Our results highlight a multitude of drug metabolites, including multi-step metabolic cascades, some of which correlated to shifts in microbial taxa, suggesting functional links between microbiome composition and biochemical transformations. Our computational data analysis workflow is publicly available through the GNPS2 ecosystem at chemprop.gnps2.org, which can be used to prioritize biotransformations and other (bio)chemical reactions in various biological and abiotic systems.},
}

@article {pmid41676568,
year = {2026},
author = {Thurman, M and Chokkavelu, V and Johnson, SD and Olwenyi, OA and Kathamuthu, GR and Yu, J and Adeniji, S and Hong, KY and Johnston, M and Bose, D and Pandey, K and Gao, H and Shen, X and Montefiori, D and Wong, PT and Baker, JR and Villinger, F and Kane, M and Abdel-Mohsen, M and Byrareddy, SN},
title = {Intranasal Delivery of HIV/SIV Antigens with NE/AS01B Adjuvants Enhances Cellular Immunity and Reduces Viral Loads in SHIV-Challenged Macaques.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.04.703720},
pmid = {41676568},
issn = {2692-8205},
abstract = {UNLABELLED: The primary route of HIV transmission is across mucosal tissues; therefore, developing a protective mucosal vaccine is a top priority. In a pilot study, using a macaque model, we delivered HIV gp140 envelope glycoprotein and SIVmac239 P55 Gag and Nef antigens using heterologous prime/boost via the intranasal route with a soybean oil-based nanoemulsion (NE) adjuvant and through the intramuscular route with the AS01B adjuvant system to generate enhanced cell-mediated immunity. We used a NE adjuvant to promote gut-homing cell-mediated immunity and the AS01B system to enhance humoral immune responses. Following intrarectal challenge with SHIV 4MTF.tHy, vaccinated macaques acquired the virus but experienced lower viral loads in plasma (P=0.003) and CSF (P=0.001), and potent polyfunctional gag-specific (CD107a+, IFNγ, TNFα+) responses across diverse lymph nodes. Significant antibody-dependent complement deposition (ADCD) and antibody-dependent cellular phagocytosis (ADCP) responses were induced, and gut-microbiome crosstalk could be modulated and showing reduced SHIV-dysbiosis. Notably, vaccination preserved mucosal all-trans retinoic acid levels (atRA) (p<0.05). However, no significant differences were observed for antibody responses between vaccinated and unvaccinated macaques. In summary, the induced gut-homing properties by the NE adjuvant are effective at generating cell-mediated immunity and reducing viral set points and warrant further investigations as a mucosal adjuvant in HIV vaccine design.

IMPORTANCE: Three major non-mucosal vaccine trials (RV144, HVTN702, and 706) failed to reduce HIV infection rates. Therefore, new approaches in developing a mucosal vaccine remain an effective strategy to attempt to control HIV infection. Coherent vaccine approaches against HIV were focused on immune correlates related to viral loads, persistent reservoirs, and antibody responses. As a proof-of-principle, we developed a vaccine regimen consisting of AS01B and an adjuvanted oil-in-water NE cleaved HIV clade C gp140 protein and non-cleaved Gag, and nef particles administered through intranasal, subcutaneous, and intramuscular routes, followed by intrarectal challenge with clade C SHIV. This vaccine elicited strong ADCD and ADCP responses, modulated immune-microbiome crosstalk, and reduced susceptibility to SHIV-infection-associated dysbiosis. Additionally, it preserved mucosal all trans retinoic acid (atRA) levels, suggesting a potential role for this approach in HIV vaccine development.},
}

@article {pmid41676551,
year = {2026},
author = {Zhang, Y and Mead, EA and Ni, M and Ksiezarek, M and Liu, Y and Cao, L and Chen, H and Fan, Y and Qiao, W and Li, Y and Zuluaga, L and Deikus, G and Sebra, R and Brody, R and Yong, RL and Badani, KK and Zhang, XS and Fang, G},
title = {Critical assessment of intratumor and low-biomass microbiome using long-read sequencing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.02.02.703393},
pmid = {41676551},
issn = {2692-8205},
abstract = {The detection of low-biomass microbial DNA in human tissues is often confounded by contamination, as demonstrated in the debates over the existence of microbiomes in the placenta, brain, blood, and tumors. Here we show that genomic DNA fragment length serves as an informative discriminator: while genuine microbiome genomes have long genomic DNA fragments, contaminant DNA is typically short and fragmented. Using germ-free mouse tissues with bacterial spike-ins and human cell lines, we developed Median Length-Adjusted (Median(L)adj), a metric that normalizes microbial read length to host read length, facilitating the differentiation between genuine microbiome and contamination. Applying the metric across multiple human tumor and normal tissues, we found genuine microbiome signals are largely limited to biopsy sites with natural microbial exposure (e.g., gastrointestinal tract, cervix, vagina and skin), while sterile tissues, including kidney, brain, lung, blood, and placenta, showed no evidence of resident microbiome. These findings support DNA fragment length as an informative metric for quality controlling low-biomass microbiome profiling, offering a framework to clarify the ongoing debates and strengthen future studies of resident microbiome in tissues.},
}

@article {pmid41676488,
year = {2026},
author = {Sen, O and Wang, PH and Saingam, P and Godfrey, BJ and Himmelfarb, J and Xiong, Y and Pan, C and Winkler, MKH},
title = {Biochemical mechanism of p-cresol removal by Thauera aminoaromatica S2.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.01.30.702948},
pmid = {41676488},
issn = {2692-8205},
abstract = {Protein-bound uremic toxins are inefficiently cleared by dialysis and contribute to complications in chronic kidney disease, motivating approaches that target their gut-derived precursors. Here we investigate anaerobic p-cresol metabolism by the environmental denitrifier Thauera aminoaromatica S2, a pathway originally evolved for aromatic pollutant degradation. Proteomic stable isotope probing with [13] C-labeled p-cresol reveals strong incorporation of labeled carbon into T. aminoaromatica proteins, whereas parallel incubations with human fecal microbiomes show minimal incorporation, indicating limited intrinsic gut capacity for p-cresol utilization. Label-enriched proteins enable reconstruction of the anaerobic p-cresol degradation pathway and identification of key enzymes synthesized during growth on p-cresol. Moreover, hydrogel-encapsulated T. aminoaromatica remains active during co-incubation with the gut microbiome, achieving complete removal of 0.3 mM p-cresol in less than 10 hours, a timescale compatible with typical intestinal transit in the colon. Together, these findings establish a biochemical basis for repurposing environmental aromatic degradation pathways for gut-localized p-cresol removal.},
}

@article {pmid41676451,
year = {2025},
author = {Yang, G and Yu, G and Cui, Q and Huang, X and Guo, K and Jia, S},
title = {BioMGCore: A toolkit for detection of biological metabolites in microbiome.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70036},
pmid = {41676451},
issn = {2996-9514},
abstract = {The keyword matching and gene proximity principles were used to accurately identify core gene clusters in microbial genomes. The metabolic gene clusters can be classified into different taxonomic groups according to Domain, Phylum, Class, Order, Family, Genus, and Species. BioMGCore can achieve batch statistics for secondary metabolites prediction.},
}

@article {pmid41676450,
year = {2025},
author = {Zhang, L and Liu, Y and Wang, S and Ching, JY and Tam, WH and Leung, TF and Leung, TY and Chan, PKS and Mak, JWY and Cheung, CP and Tun, HM and Chang, EB and DeLeon, O and Huang, Q and Chen, X and Huo, H and Miao, Y and Cheong, PK and Ip, KL and Yeung, YL and Chang, MK and Lyu, C and Yang, H and Li, B and Fan, Y and Sun, Y and Jiang, S and Ng, SC and Chan, FKL},
title = {MOMMY study profile: An integrative early-life multi-omics cohort in China.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70068},
pmid = {41676450},
issn = {2996-9514},
abstract = {Large-scale, prospective birth cohorts capturing the complex interplay between the gut microbiome, host biology, and environmental exposures are crucial to understanding early-life health but remain scarce, particularly within Asian populations. To address this gap, we established the MOMMY cohort (The MOther-infant Microbiota transmission and its link to long terM health of babY), a large, prospective birth cohort uniquely designed to investigate maternal-paternal-infant microbiota transmission and its impact on child health within the understudied Chinese population. MOMMY aims to recruit 20,000 families from three geographically and economically diverse regions across China. This cohort prospectively follows pregnant mothers, fathers, and their infants, with children up to 7 years of age. Since September 2019, we have systematically collected a comprehensive repository of longitudinal biospecimens-including maternal and infant stool, breast milk, cord blood, and parental blood-stored in an accredited biobank. This is complemented by extensive data on environmental exposures, diet, and health outcomes gathered through validated questionnaires and physician assessments. The MOMMY cohort's unique value lies in its unprecedented scale, geographic diversity, and its integrative multi-omics design, which will combine metagenomic, metabolomic, immunologic, and epigenetic data. By creating this unique resource, MOMMY will elucidate how early-life microbial and molecular trajectories, shaped by genetic and environmental factors, influence child development and disease risk, thereby filling a critical gap in global microbiome research.},
}

@article {pmid41676449,
year = {2025},
author = {Wang, H and Peng, Z and Zhang, C and Kang, C and Zhang, Y and Guo, X and Wang, Y and Yang, G and Xiang, Z and Zhou, L and Jing, Z and Liu, D and Wang, S and Huang, L and Guo, L},
title = {The combined influence of microbiome and soil environment contributes to the chemotype differentiation in Atractylodes lancea.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70058},
pmid = {41676449},
issn = {2996-9514},
abstract = {Atractylodes lancea, a traditional Chinese medicinal herb, is divided into two chemotypes based on the production of volatile bioactive compounds: the geo-authentic Maoshan chemotype (MSA, rich in atractylon and atractylodin) and the non-authentic Hubei chemotype (HBA, dominated by hinesol and β-eudesmol). However, the mechanisms underlying the differentiation of these chemotypes remain poorly understood. By sequencing analysis of wild and cultivated A. lancea samples from multiple provinces in China, we revealed that the genetic divergence into Maoshan-Dabie Mountains group (MA) and Qinling-Taihang Mountains group (SA) was occurred along altitudinal and climatic gradients, but the chemotype was not solely genetically determined. Interestingly, both MA and SA genotypes in the MSA-favorable or HBA-conducive soil could develop into the MSA or the HBA chemotype, respectively, indicating a role of the soil microbiome. Critically, specific rhizosphere microbiomes were indicated as key mediators-core in this process, including Streptomyces in MSA formation and Paenibacillus in HBA formation. Shared endophytic core genera, such as Rhodococcus, Ralstonia, Sphingomonas, and Bradyrhizobium, further contributed to this divergence through species-level functional variation. Using piecewise structural equation modeling, we further confirmed that altitude, climate, and soil properties directly or indirectly influenced the chemotype formation via genotype-microbiome interactions. Taken together, this study highlights the central role of soil and microbes in the chemotype differentiation of A. lancea and provides new insights into its underlying mechanisms. The regulatory role of microbes in the production of volatile bioactive compounds offers a theoretical foundation for the microbial breeding strategies to improve medicinal quality and clinical efficacy.},
}

@article {pmid41676445,
year = {2025},
author = {Xu, T and Niu, Y and Deng, C and Cheung, Y and Li, Y and Hu, Z and Sun, S and Chen, Y and He, F and Yang, G and Chen, F and Duan, C and Huang, Y and Deng, X},
title = {Saliva MicroAge: A salivary microbiome based machine learning model for noninvasive aging assessment and health state prediction.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70040},
pmid = {41676445},
issn = {2996-9514},
abstract = {Saliva MicroAge is a machine learning-based model designed to estimate biological age and assess health status using globally sourced salivary microbiome data. Trained on 4532 healthy samples, the model achieves high accuracy in predicting chronological age and captures health-related deviations (MicroAgeGap) in various diseases. Taxonomic and functional analyses of key microbial features reveal biological relevance to aging processes, offering a noninvasive and scalable approach for aging monitoring and precision health assessment.},
}

@article {pmid41676442,
year = {2025},
author = {Chaboy-Cansado, R and Talavera-Marcos, S and Gallego-Simón, R and Cobeta, P and Roscales, G and Rastrojo, A and de Cárcer, DA},
title = {Modular automated high-throughput isolation and phylogenetic identification of bacteria from complex microbiomes.},
journal = {iMetaOmics},
volume = {2},
number = {4},
pages = {e70037},
pmid = {41676442},
issn = {2996-9514},
abstract = {Metagenomic analysis can generate hypotheses about microbiome interactions and function, yet mechanistic understanding is only possible through precise experimentation manipulating its microbiota composition. The high-throughput isolation of microbiome members thus represents a core resource in this field of research.},
}

@article {pmid41676136,
year = {2026},
author = {Ni, FX and Wang, HX and Hu, J and Chen, PS and Xu, P and Chen, HH and Jiang, ZB and Huang, DH},
title = {The gut-lung axis in COPD: immunomodulatory roles of gut microbiota and novel therapeutic strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1733726},
pmid = {41676136},
issn = {1664-3224},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/therapy/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; *Lung/immunology/microbiology/metabolism ; Animals ; Dysbiosis/immunology ; Probiotics/therapeutic use ; Immunomodulation ; Prebiotics ; Fecal Microbiota Transplantation ; },
abstract = {Chronic Obstructive Pulmonary Disease (COPD) is a progressive respiratory disorder characterized by persistent airflow limitation and systemic inflammation, with accumulating evidence implicating gut microbiota dysbiosis as a key modulator of disease pathogenesis via the gut-lung axis. This review synthesizes current knowledge on the bidirectional communication between the gut and lungs, highlighting how microbial metabolites-particularly short-chain fatty acids (SCFAs), tryptophan derivatives, and bile acids-regulate pulmonary immunity through G-protein-coupled receptors, histone deacetylase inhibition, and aryl hydrocarbon receptor signaling. Dysbiosis-driven disruptions in these pathways exacerbate neutrophilic inflammation, impair regulatory T-cell function, and sustain TLR4/NF-κB activation, amplifying lung tissue damage and remodeling. Therapeutic strategies targeting the gut-lung axis show promise in restoring microbial homeostasis and mitigating COPD progression. Probiotics (e.g., Lactobacillus and Bifidobacterium), prebiotics (e.g., inulin), and dietary interventions (e.g., high-fiber diets) enhance SCFA production, strengthen epithelial barriers, and suppress pro-inflammatory cytokines. Advanced approaches, including fecal microbiota transplantation, nanotechnology-enabled metabolite delivery (e.g., dendrimer-complexed indole-3-acetic acid), and traditional Chinese medicine (TCM) formulations (e.g., the postbiotic formulation Qipian), demonstrate efficacy in preclinical and clinical studies by synchronizing gut-lung microbiota and inhibiting inflammatory pathways. Despite these advances, challenges remain in translating findings to clinical practice, including methodological heterogeneity, antibiotic and corticosteroid confounding, and inter-individual microbiota variability. Future research must integrate multi-omics technologies, validate biomarkers (e.g., Bacteroidales/Lactobacillus ratio, SCFA levels), and develop personalized interventions to bridge the bench-to-bedside gap. Harnessing the gut-lung axis offers transformative potential for COPD management, shifting the paradigm from symptomatic treatment to disease-modifying strategies rooted in microbiome immunology.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/therapy/immunology/microbiology/metabolism
*Gastrointestinal Microbiome/immunology
*Lung/immunology/microbiology/metabolism
Animals
Dysbiosis/immunology
Probiotics/therapeutic use
Immunomodulation
Prebiotics
Fecal Microbiota Transplantation

@article {pmid41676130,
year = {2024},
author = {Yousuf, S and Luo, H and Zeng, M and Chen, L and Ma, T and Li, X and Zheng, M and Zhou, X and Chen, L and Xi, J and Lu, H and Cao, H and Ma, X and Bian, B and Zhang, P and Wu, J and Gan, R and Jia, B and Sun, L and Ju, Z and Gao, Y and Malik, WA and Ma, C and Lyu, H and Li, Y and Hou, H and Zhou, Y and Bai, D and Wang, Y and Yang, H and Xun, J and Du, S and Zhang, T and Wan, X and Peng, K and Xu, S and Wen, T and Chen, T and Liu, YX},
title = {Unveiling microbial communities with EasyAmplicon: A user-centric guide to perform amplicon sequencing data analysis.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e42},
pmid = {41676130},
issn = {2996-9514},
abstract = {The advent of next-generation sequencing has revolutionized microbiome research, enabling in-depth exploration of microbial communities through amplicon sequencing. The widespread adoption of sequencing across diverse fields, coupled with decreasing costs, underscores the critical need for validated, fully automated, reproducible, and adaptable analysis pipelines. However, analyzing these high-throughput datasets often necessitates extensive bioinformatics expertize, hindering accessibility for many researchers. To address this challenge, in 2023 we developed EasyAmplicon, a comprehensive, user-friendly pipeline that integrates popular tools such as USEARCH and VSEARCH, offering a streamlined workflow from raw data to results. Remarkably, EasyAmplicon has garnered significant recognition within a year, as evidenced by 127 citations to date. To further facilitate the researchers and enhance usability, we present a detailed protocol with a video recording that guides users through each step of the pipeline, including data preprocessing (quality filtering, chimera removal), amplicon sequence variant analysis, diversity analysis, and data visualization. The protocol is designed for ease of use, with each step documented, allowing researchers to execute the workflow without requiring complex scripting skills. The EasyAmplicon pipeline is freely available on GitHub (https://github.com/YongxinLiu/EasyAmplicon).},
}

@article {pmid41676126,
year = {2024},
author = {Li, Y and Lyu, H and Yang, H and Ju, Z and Ma, C and Hou, H and Wang, Y and Zhou, Y and Gao, Y and Yang, J and Xu, S and Bai, D and Luo, H and Yousuf, S and Zhang, T and Xun, J and Zeng, M and Qi, H and Chen, T and Liu, YX},
title = {FoodMicroDB: A microbiome database for composition and time-series research in food.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e40},
pmid = {41676126},
issn = {2996-9514},
abstract = {Microorganisms are crucial for food fermentation, preservation, and safety, directly impacting human health. The number of studies on the food microbiome has surged recently, along with a substantial increase in data. However, there is a notable lack of databases specialized for this field. To address this gap, we developed Food Microbiome Database (FoodMicroDB), a platform aimed at enhancing the reusability and accessibility of food microbiome data through comprehensive data management and data visualization tools. FoodMicroDB aggregates 6358 amplicon data from 108 meta-taxonomic projects covering 62 foods, and harbors 4710 taxa of bacteria, archaea, and fungi. The collected data were consistently analyzed and curated, then visualized using versatile utilities, including unique tools for visualizing microbial composition and time-series microbiome data. It also includes advanced modules for microbial abundance analysis, cross-host abundance comparison, and cross-food analysis. FoodMicroDB will be a valuable resource platform for the food microbiome research field. The database is freely accessible at: https://www.bic.ac.cn/FoodMicro/.},
}

@article {pmid41676120,
year = {2024},
author = {Ling, Y and Liu, Z and Han, S and Wu, H and Mu, C and Zhu, W},
title = {Integrated omics revealed the altered colonic microenvironment after inhibition of peripheral serotonin synthesis by LP533401.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e34},
pmid = {41676120},
issn = {2996-9514},
abstract = {Gut-derived 5-hydroxytryptamine (5-HT), known as serotonin, plays a crucial role in regulating gastrointestinal functions. However, the impact of disruptions in gut-derived 5-HT synthesis on the early gut microbiome and intestinal microenvironment remains unclear. In this study, LP533401, an inhibitor targeting peripheral 5-HT synthesis, was administered orally to neonatal rats starting at 4 days post-birth. By day 11, inhibition of gut-derived 5-HT resulted in altered colonic morphology, characterized by increased crypt depth and reduced myenteric thickness. To investigate the mechanisms underlying these alterations, we employed a combination of metagenomics, mucosal transcriptome, and untargeted metabolomics on colonic samples. Metagenome profiling revealed an upregulation in the microbial two-component system (ko02020) and tyrosine metabolism (ko00350), with minimal effects on taxa abundances. Transcriptome profiling analysis indicated the discriminant expression of genes enriched in pathogen infection-responsive signaling (e.g., Salmonella and Yersinia infection) and the Wnt signaling pathway that affected stem cell proliferation. Consistent with increased crypt depth, marker genes related to cell proliferation were excessively activated. Metabolomics analysis indicated lower ascorbate level and higher succinic acid level, correlating with 5-HT concentrations and increased crypt depth. Additionally, altered metabolic pathways (e.g., nucleotide metabolism, signal transduction, metabolism of cofactors and vitamins) suggested an impact on the colonic function. In summary, early inhibition of gut-derived 5-HT may unfavorably reshape the colonic microenvironment, affecting gut morphology, microbial function, stem cell proliferation, and mucosal metabolism.},
}

@article {pmid41676124,
year = {2024},
author = {Xie, Y and Xu, S and Xi, Y and Li, Z and Zuo, E and Xing, K and Bai, L and Li, K},
title = {Global meta-analysis reveals the drivers of gut microbiome variation across vertebrates.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e35},
pmid = {41676124},
issn = {2996-9514},
abstract = {Shifts in gut microbial diversity and structure are one route by which vertebrate hosts adapt to local environmental conditions. However, recent studies have mostly been limited to a single species, small sample sizes, or restricted geographic ranges. Therefore, drawing a global picture of vertebrate gut microbiome diversity, community structure, and determinants for their adaptive shifts remains to be elucidated. We here collected 6508 samples from 113 vertebrate species covering diverse classes, feeding behaviors, and host habitats based on 16S rRNA gene sequencing. The results showed that host diet pattern had a significant impact on gut microbiome variation, which might drive taxonomic and functional contents of gut microbiome across vertebrates. Of note, the phylum Fusobacteria were enriched in carnivorous vertebrate gut while herbivorous vertebrate gut selectively increased the abundance of Verrucomicrobia. Also, climate factors were strongly associated with gut microbiome variation across vertebrates. Interestingly, we found that the abundance of microbiota belonging to Bacteroidetes increased gradually while the members from Proteobacteria showed a decreasing trend from high- to low-latitude zones, potentially contributing to vertebrate adaptation to local climate condition. Additionally, we comprehensively deciphered the common antibiotic resistomes and their potential mobility between terrestrial vertebrate gut microbiome (n = 487) and their sympatric soil biological environment samples (n = 203) by integrating metagenomic sequencing datasets. Particularly, potential horizontal antibiotic resistance genes (e.g., bacA) transfers were detected between vertebrates gut microbiome and their sympatric soil biological environment. Together, our findings provide new evidence of how external environmental factors affect vertebrate gut microbiome variation.},
}

@article {pmid41676117,
year = {2024},
author = {Shi, P and Xu, S and Yang, Z and Wang, L and Wu, Y and Li, Y and Zhu, Z},
title = {Harnessing gut microbiota for longevity: Insights into mechanisms and genetic manipulation.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e36},
pmid = {41676117},
issn = {2996-9514},
abstract = {The gut microbiota is pivotal in maintaining health, with most microorganisms being beneficial, except for a few pathogens. Emerging evidence suggests a link between the gut microbiome and aging, hinting at its potential role in longevity. However, understanding the relationship is challenging due to the microbiota's complexity. This perspective summarizes the mechanisms by which gut microbes regulate host lifespan and explores genetic manipulation strategies to promote healthy aging in the elderly.},
}

@article {pmid41676129,
year = {2024},
author = {Zhou, Y and Xu, Z and Zhang, H and Liu, T and Zhou, J and Bi, Y and Han, Y and Tan, Y and Yuan, J and Yang, R},
title = {When the microbiome meets One Health principle: Leading to the Holy Grail of biology and contributing to overall well-being and social sustainability.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e30},
pmid = {41676129},
issn = {2996-9514},
abstract = {The convergence of microbiome science with the One Health principle heralds a transformative era in biology, prioritizing the collective well-being of humans, animals, and the environment. This review delves into the intricate dance between microbiomes and their hosts, revealing their profound impact on health, nutrient cycles, and climate change. Championing a unified approach to health issues across diverse kingdoms of life, One Health emerges as a holistic strategy, underscored by a proposed universal balance theory, "Balance of Dynamic Factors." This theory spotlights the equilibrium within microbial and human-animal-environment interactions, offering a revolutionary pathway to global health and social well-being. It paves the way for disease prevention, health equity, and sustainability, all of which are purviews of a balanced ecological system. We navigate the challenges and opportunities of this integrative approach, culminating in a call for action for the incorporation of microbiome science into health policies, precision medicine, legislation, eco-health projects, and education, thereby setting the stage for harmonious coexistence with our planet.},
}

@article {pmid41676125,
year = {2024},
author = {Xia, JJ and Zhong, Q and Li, ZM and Wei, QZ and Jiang, LY and Duan, C and Jia, HJ and Tan, YM and Han, LY and Krutmann, J and Wang, J and Liu, X},
title = {Culture dependent and independent approaches reveal the role of specific bacteria in human skin aging.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e26},
pmid = {41676125},
issn = {2996-9514},
abstract = {Skin aging is a dynamic process involving a spectrum of phenotypic changes, making it an attractive model for studying microbiome-phenotype interactions. Therefore, 822 facial microbial samples and 14 skin phenotypes from corresponding areas were assessed in a Chinese cohort. Porphyrins and the chronological age exhibited the most significant microbial variability. We further profiled the dynamics of the skin microbiome associated with age and aging phenotypes. Using a multiple linear regression model, we predicted premature/delayed aging-related microbial species, mainly Moraxella osloensis and Cutibacterium acnes. We also validated the biological functions of the host-microbe interactions in vitro. Moraxella osloensis isolated from healthy skin regulates collagen metabolism and extracellular matrix assembly, and promotes cell senescence in human keratinocytes and fibroblasts, making it potentially applicable in the development of antiaging interventions.},
}

@article {pmid41676123,
year = {2024},
author = {Cheng, S and Shi, Y and Hu, W and Liu, F},
title = {Arabidopsis multiomics reveals the role of autophagy in root microbiome assembly.},
journal = {iMetaOmics},
volume = {1},
number = {2},
pages = {e28},
pmid = {41676123},
issn = {2996-9514},
abstract = {Upon mutation of the core autophagy protein ATG5, disrupted autophagy pathways result in alterations in several biological processes important for plant-root microbe interaction mechanisms, including the expression of cell wall- and defense-related proteins and the secretion of root metabolites, all of which affect the root microbial community diversity.},
}

@article {pmid41676100,
year = {2026},
author = {Liu, C and Chen, Y},
title = {The current consensus on ulcerative colitis, and the evidence and perspectives on the influence of gut microbiota on it.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1735850},
pmid = {41676100},
issn = {2296-858X},
abstract = {Ulcerative colitis (UC) is a chronic non-specific inflammatory disease, the pathogenesis is not clear, there is no clinical cure. The number of cases of UC has increased worldwide in recent years due to industrialization and social pressures. At present, the therapeutic effectiveness of UC remains controversial. Although researchers have conducted certain studies on the pathogenesis of UC, its pathogenesis and anti-UC pathogenesis have not been fully revealed. Previous studies have found a close relationship between human gut microbes and UC, and may be the most important measure of UC for clinical judgment. Many studies have linked UC to disruption of the gut microbiome, which is one of the most important features of UC. This paper reviews the clinical characteristics, pathogenesis and current treatment strategies of UC, and reviews the interaction between intestinal flora and UC as well as the therapeutic effects of intestinal flora, providing reference for the prevention and treatment of UC.},
}

@article {pmid41676065,
year = {2026},
author = {Liu, Y and Huang, S and Zhang, Y and Zhang, Y and Xu, Y and Tang, Y and Guo, S and Zhang, Z},
title = {Microbial dysbiosis in cholangiocarcinoma.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1727736},
pmid = {41676065},
issn = {1664-302X},
abstract = {Cholangiocarcinoma (CCA) is a highly aggressive malignancy of the biliary epithelium, with its incidence and mortality rates continuing to rise worldwide. Advances in high-throughput sequencing and metabolomic technologies have intensified interest in elucidating the role of the microbiome in CCA. Microbial dysbiosis may contribute to tumor initiation and progression by inducing chronic inflammation, altering metabolic pathways, and modulating the immune microenvironment. Moreover, these microbial alterations have been associated with therapeutic resistance, underscoring their potential impact on disease progression and treatment outcomes. This review summarizes the potential origins of intratumoral microorganisms and the microbiome alterations associated with distinct CCA subtypes. Crucially, we critically evaluate the methodological challenges inherent to low-biomass biliary samples-including contamination risks and confounding factors such as cholestasis and medical interventions-and distinguish between associative and causal evidence in current literature. Collectively, this work aims to provide a rigorous theoretical framework and novel insights for microbiome-based strategies in the early diagnosis and treatment of CCA.},
}

@article {pmid41676061,
year = {2026},
author = {Qiao, X and Yan, X and Dong, C and Tao, L and Aili, A and Waheed, A},
title = {From microbiome collapse to recovery: a roadmap for microbiome-informed grassland restoration under global change.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1741287},
pmid = {41676061},
issn = {1664-302X},
abstract = {Grassland ecosystems depend on soil- and plant-associated microbiomes that regulate nutrient cycling, soil structure formation, plant health, and stress tolerance. This review synthesizes recent progress on how grassland microbiomes are assembled across rhizosphere, endosphere, and bulk soil niches, and how degradation drivers (e.g., overgrazing, drought, salinization, and nutrient enrichment) disrupt microbial diversity, network stability, and functional guilds, often shifting communities toward reduced mutualist capacity and greater disease risk. We then evaluate restoration strategies that aim to re-establish beneficial microbial functions through practices such as organic amendments, inoculation with mycorrhizae or plant growth-promoting microbes, and management approaches that promote habitat recovery and microbial recolonization. Despite rapid advances in sequencing and observational studies, major gaps remain: (i) limited causal evidence linking microbiome changes to process rates (e.g., nitrification, phosphorus mobilization) across field gradients; (ii) underrepresentation of soil viral ecology and its consequences for microbial regulation and ecosystem function; (iii) inconsistent persistence and context-dependence of introduced inoculants; and (iv) a lack of standardized, outcome-oriented indicators for "restoration-ready" microbiomes. Future research should integrate multi-omics with process-based measurements and long-term field experiments, develop locally adapted microbial consortia with monitoring of non-target effects, and strengthen risk assessment and governance frameworks to enable safe, scalable microbiome-informed grassland restoration under global change.},
}

@article {pmid41676058,
year = {2026},
author = {Sivamaruthi, BS and Kesika, P and Chaiyasut, C and Ragu Varman, D},
title = {Gut dysbiosis in neurodevelopmental disorders: linking microbiota signatures to cognitive rigidity in autism spectrum disorder.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1760635},
pmid = {41676058},
issn = {1664-302X},
abstract = {Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental condition characterised not only by social-communication difficulties but also by restricted interests, stereotyped behaviours, and marked cognitive rigidity. Over the past decade, converging lines of evidence have implicated gut dysbiosis, an imbalance in intestinal microbial composition and function, as a potentially important modulator of these behavioural phenotypes via the microbiota-gut-brain axis. In this narrative review, we integrate preclinical and clinical data to examine how specific microbial signatures, metabolic pathways, and immune and synaptic mechanisms may contribute to inflexible cognition in ASD. The manuscript outlines the organisation of the microbiota gut-brain axis in neurodevelopment and summarises reproducible microbial alterations reported in ASD cohorts. We then discuss how microbial metabolites, including short-chain fatty acids and tryptophan-derived neuroactive molecules, as well as immune mediators and neurotransmitter precursors, converge on pathways regulating excitatory-inhibitory balance, synaptic plasticity, and corticostriatal circuit function. Evidence from germ-free, genetic, and environmental rodent models provides causal support for microbiota-dependent modulation of repetitive and rigid behaviours, whilst clinical studies reveal associations between dysbiosis, metabolomic profiles, gastrointestinal symptoms, and ASD severity. Finally, we consider the translational landscape of microbiota-targeted interventions, probiotics, prebiotics, dietary strategies, and faecal microbiota transplantation and highlight key methodological and ethical challenges for moving toward precision microbiome-based therapies. Taken together, current data support gut dysbiosis as both a mechanistic contributor and a tractable therapeutic target for cognitive rigidity in ASD.},
}

@article {pmid41675883,
year = {2026},
author = {Amjad, A and Batool, ST and Ali, U and Mahato, RK},
title = {Gut microbiome metaproteomics for colorectal cancer risk stratification: moving from taxonomic signatures to functional protein biomarkers.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {2112-2113},
doi = {10.1097/MS9.0000000000004567},
pmid = {41675883},
issn = {2049-0801},
}

@article {pmid41675866,
year = {2026},
author = {Mehmood, MS and Qamar, T and Amjad, F and Danaf, N},
title = {Bacterial co-infection as a catalyst in HPV-associated cervical carcinogenesis.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {1176-1177},
pmid = {41675866},
issn = {2049-0801},
abstract = {Cervical cancer remains a preventable yet persistent global burden, with more than 660 000 new cases and 360 000 deaths reported in 2024. While high-risk HPV is the central driver of malignant transformation, growing evidence shows that bacterial co-infection can intensify HPV persistence and promote genomic instability. Meta-analyses now indicate that pathogens such as Chlamydia trachomatis, Mycoplasma genitalium, Gardnerella vaginalis, and diverse anaerobic microbiota markedly increase the risk of persistent HPV infection and cervical lesions. These microbes disrupt epithelial barriers, fuel chronic inflammation, and enhance the oncogenic activity of HPV E6/E7. Studies also show that Lactobacillus-depleted vaginal communities carry higher viral loads and increased CIN2[+] progression. A 2024 review from sub-Saharan Africa further highlights frequent bacterial co-infections among HPV-positive women, particularly in settings with limited vaccination and screening. Together, these findings support a dual-pathogen model of cervical carcinogenesis and underscore the need to integrate microbiome-focused strategies into prevention efforts.},
}

@article {pmid41675854,
year = {2026},
author = {Imtiaz, E and Mahato, RK and Tahir, A},
title = {Patient-specific precision microbiome modulation: rethinking therapeutic strategies in IBD.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {2138-2139},
pmid = {41675854},
issn = {2049-0801},
}

@article {pmid41675847,
year = {2026},
author = {Ali, MR and Devi, S and Jawed, M and Irshad, NUN and Imran, SB},
title = {Gut-brain axis in neurology: microbiome as a modifiable risk factor for multiple sclerosis.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {2158-2159},
pmid = {41675847},
issn = {2049-0801},
}

@article {pmid41675768,
year = {2026},
author = {Beniwal, SS and Janu, Y and Cummings, K and Syed, S and Everton Assunção Ribeiro da Costa, R and Dahiya, P and Jeong, Y and Cabe Cacas, A and Mwaanga, C and Kotaich, J},
title = {Sex steroid receptors in colorectal cancer: implications for tumor progression, therapeutic opportunities, and sex-specific outcomes.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {1427-1436},
pmid = {41675768},
issn = {2049-0801},
abstract = {Colorectal cancer (CRC) is a common malignancy with high incidence and mortality. Hormone signaling pathways, including estrogen, progesterone (P4), and androgen receptors (ARs), influence tumor development and progression and offer potential therapeutic opportunities. This study investigates the role of sex steroid receptors in CRC, explores therapeutic strategies, and considers sex-specific implications. Multiple cohort studies were analyzed based on gender, age, clinical stage, and tumor location. A structured literature search was conducted across PubMed, Web of Science, and Google Scholar, selecting studies with relevant sex-specific data and study designs. ERβ exhibits antitumor effects, with lower levels linked to tumors in females, while ERα and AR promote growth, particularly in postmenopausal women. Progesterone receptors (PGRs) are associated with poorer prognosis, though P4 treatment inhibits CRC cell proliferation. Malignant tissues show increased ERα and AR but decreased ERβ and PGR. ER isoforms' mRNA is lower in malignant females, and AR expression is higher in males. Women more often develop proximal colon tumors (reduced ERβ) and men develop distal tumors, reflecting nuanced gene transcription modulation by ERα, ERβ, and G-protein coupled estrogen receptor (GPER). The mechanism of P4's protective effect remains unclear. Variability in cell lines, hormone concentrations, receptor expression, and hormone replacement therapy outcomes complicates interpretation, as do interactions between cytokines and estrogen signaling in the tumor microenvironment. Future strategies include combined ERβ and PGR activation, sequential estrogen-P4 therapy for early stage CRC, and simultaneous therapy for advanced cases. Research should clarify sex hormone roles, advance prognostic markers, explore selective estrogen receptor modulators, target ERβ pharmacologically, and investigate gut microbiome influences for tailored interventions.},
}

@article {pmid41675731,
year = {2026},
author = {Mehmood, MS and Iqbal, I and Hajj, F},
title = {Microbial metabolites from gut bacteria as novel anti-cancer agents.},
journal = {Annals of medicine and surgery (2012)},
volume = {88},
number = {2},
pages = {2096-2097},
pmid = {41675731},
issn = {2049-0801},
abstract = {Recent evidence highlights the potential of gut microbial metabolites as promising anticancer agents, with mechanisms distinct from those of conventional chemotherapeutics. Short-chain fatty acids, particularly butyrate, exhibit histone deacetylase inhibitory activity, leading to apoptosis and cell-cycle arrest in colorectal and breast cancers. Reuterin, a redox-active metabolite of Lactobacillus reuteri, selectively induces oxidative stress and suppresses tumo growth in vivo. Likewise, secondary bile acids such as lithocholic acid demonstrate dose-dependent antineoplastic properties, while inosine has been shown to potentiate PD-1 blockade efficacy by enhancing T-cell activation. Additionally, bacteriocins derived from lactic acid bacteria reveal selective cytotoxicity and immunomodulatory effects, representing biocompatible therapeutic scaffolds. The novelty of these metabolites lies in their ability to target epigenetic, metabolic, and immune pathways simultaneously, offering a multidimensional approach to tumor control. Harnessing these microbial molecules through synthetic optimization, delivery innovations, and integrative clinical trials could revolutionize cancer therapeutics by merging microbiome science with precision oncology.},
}

@article {pmid41675714,
year = {2025},
author = {Wang, C and Lin, J and Duan, M and He, J and Halizere, S and Chen, N and Chen, X and Jiao, Y and He, W and Dyar, KA and Yang, F and Zhu, S},
title = {Multi-omics reveals different signatures of obesity-prone and obesity-resistant mice.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e59},
pmid = {41675714},
issn = {2996-9514},
abstract = {Obesity-prone (OP) and obesity-resistant (OR) individuals demonstrate significant metabolic differences, potentially influenced by variations in the gut microbiome. However, the influence of host-microbiota interactions on obesity susceptibility remains unknown. We performed an integrative multi-omics approach to explore microbial, metabolic, and genetic differences in high-fat diet (HFD)-fed OP and OR mice, with additional analyses of gut microbiota variations in humans. In OP mice, the dynamic gut microbiota was characterized by a stable presence of Longibaculum, while Kineothrix predominated in OR mice. We termed both as keystone bacteria. Beyond these, eight dominant bacterial genera were significantly associated with bile acid metabolites and amino acids. Three of these genera were also identified in OR humans and showed positive correlations with genes that may support intestinal barrier function. We identified 22 specific amino acid profiles as potential biomarkers for obesity susceptibility, along with significantly increased levels of ten non-12-OH bile acids in fecal of OR mice. In vivo, mouse experiments demonstrated that ursodeoxycholic and hyodeoxycholic acids could reduce HFD-induced obesity. Additionally, the colon of OP mice displayed a higher presence of inflammatory cells. These findings suggest that host-microbiota interactions may contribute to phenotypic differences between OP and OR. Our study offers insights into crucial intestinal markers associated with obesity, providing a valuable resource for advancing the understanding of obesity-prone and obesity-resistant phenotypes.},
}

@article {pmid41675707,
year = {2025},
author = {Wu, J and Yang, X and Zhao, L and Li, Z and Zhao, G and Zhang, L},
title = {Systematic characterization of horizontally transferred biosynthetic gene clusters in the human gut microbiota using HTBGC-Finder.},
journal = {iMetaOmics},
volume = {2},
number = {1},
pages = {e62},
pmid = {41675707},
issn = {2996-9514},
abstract = {The human gut microbiota contains biosynthetic gene clusters (BGCs) that encode bioactive secondary metabolites, which play pivotal roles in microbe-microbe and host-microbe interactions and serve as a rich source of pharmaceutical lead compounds. Understanding the horizontal transfer of BGCs can reveal insights into microbial adaptation, resource utilization, and evolutionary mechanisms, thereby advancing biotechnological applications. Despite its importance, horizontal transfer of BGCs within the gut microbiota remains poorly understood. In this study, we introduce a novel tool, the Horizontally Transferred Biosynthetic Gene Clusters Finder (HTBGC-Finder), designed to systematically identify potential horizontally transferred BGCs (HTBGCs) within the extensive human gut microbiota. Using HTBGC-Finder, we identified 81 potential HTBGCs, underscoring the prevalence and significance of horizontal gene transfer in shaping the genetic landscape of the gut microbiome. Remarkably, ribosomally synthesized and post-translationally modified peptides (RiPPs) constituted the majority of these HTBGCs (76 out of 81, 93.83%), exhibiting a significantly higher transfer rate compared to non-RiPPs (Chi-squared test, p < 0.001). Upon detailed examination of BGCs, cyclic-lactone-autoinducer (CLA) and RiPP recognition element (RRE)-containing BGCs were predominant, representing nearly three-quarters of the total (45, or 55.56%, and 14, or 17.28%, respectively). Notably, CLA BGCs also demonstrated a higher transfer rate than non-CLA BGCs (Chi-squared test, p < 0.001). Taxonomy profiling revealed that horizontal BGC transfer occurred exclusively in the phyla Bacteroidota (synonym Bacteroidetes) and Bacillota (synonym Firmicutes), with 50 and 31 instances, respectively. Furthermore, cross-phylum transfer events were observed, highlighting the complex interactions between the gut microbiota and host health. These findings offer valuable insights into the horizontal transfer dynamics of BGCs within the gut microbiome and their potential implications for host-microbiota interactions.},
}

@article {pmid41675303,
year = {2026},
author = {Siani, R and Si, Y and Thaqi, SK and Stabl, G and Gutjahr, C and Schloter, M},
title = {Loss of the flagellar regulator FlhC changes the transcriptional response of plant-associated Acidovorax delafieldii strains to metabolites from Rhizophagus irregularis-colonized Lotus japonicus roots.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycaf235},
pmid = {41675303},
issn = {2730-6151},
abstract = {Acidovorax is a cosmopolitan bacterial genus comprising both beneficial and pathogenic plant-associated species. In plant-associated bacteria, flagella can facilitate colonization but also trigger plant immune responses driving mutation or loss of flagella in some strains. FlhC is an important transcriptional regulator of flagella assembly genes. Here, we investigated whether it modulates root colonization and the transcriptional response of plant-commensal Acidovorax strains to different plant cues. As model cues, we used root extracts from Lotus japonicus that forms symbioses with arbuscular mycorrhiza fungi (AMF), which strongly change root metabolism and add their own metabolites. To offer different stimuli to Acidovorax bacteria, we used extracts from L. japonicus roots colonized or not with the AMF Rhizophagus irregularis. We investigated two Acidovorax delafieldii strains with almost identical genomes but differences in the presence or absence of flhC. Overall, loss of flhC resulted in distinct expression profiles and a more modular transcriptional network. Pathway analysis linked flhC to genes associated with stress tolerance, nutrient mobilization, biofilm formation, secretion, surface attachment, and quorum sensing. Root extracts from mycorrhizal roots induced increased expression of genes associated with substrate preference and downregulation of genes involved in biofilm formation and secretion. flhC-deficient strains also responded with increased expression of genes related to surface attachment and vitamin biosynthesis. The absence of flhC correlated with increased root colonization and influenced the response of Acidovorax to R. irregularis in planta. Our findings highlight that a flagellar regulator in root-associated bacteria influences root colonization and transcriptional responses to host cues.},
}

@article {pmid41675273,
year = {2025},
author = {Yue, H and Shen, P and Huang, Q and Lin, S and Shen, J and Wang, Y and Sun, Z and Qi, X and Jiang, Y and Yuan, C and Zou, D and Zheng, Y and Yang, C},
title = {Associations Between Dietary Habits, Oral Microbiota, and Dental Caries in Adolescents.},
journal = {Phenomics (Cham, Switzerland)},
volume = {5},
number = {6},
pages = {633-645},
pmid = {41675273},
issn = {2730-5848},
abstract = {UNLABELLED: Suboptimal dietary habits, such as excessive consumption of sugary foods and beverages, have been associated with a higher risk of dental caries. While known cariogenic species enrichment in the oral microbiome correlating with dental caries, the complex interactions between dietary habits, the oral microbiota, and dental caries among adolescents remain underexplored. Here, we examined the comprehensive associations between dietary habits, oral microbiota, and dental caries among 421 adolescents (mean age: 12.9 years, 28% having dental caries). The dietary data were collected via a food frequency questionnaire, dental health was examined by a skilled dentist, and the saliva microbiota was profiled by 16S ribosomal RNA sequencing. Significant difference in the oral microbial composition was observed between participants with and without dental caries (p-value < 0.05), which was replicated in an external adult population (n = 580). The relative abundances of 19 genera were associated with dental caries in adolescents independent of gender (all FDR-adjusted p-values < 0.20). For example, dental caries was linked with a higher abundance of Prevotella and Veillonella, both of which were also enriched in higher consumer of sugary food and beverage. In mediation analysis, certain caries-related genera, including Staphylococcus and Paludibacteraceae F0058, might partially mediate the associations between dietary habits and dental caries (p-mediation < 0.05). This research highlighted the role of oral microbiota in the association between dietary intakes and dental caries and may explain the potential mechanisms by which diet affects dental caries.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-024-00208-3.},
}

@article {pmid41675168,
year = {2025},
author = {Qin, F and Zhang, M and Yang, Q and Wu, L and Mao, T and Zhou, X and Li, J and Lai, M},
title = {Interactions between Parabacteroides goldsteinii CCUG 48944 and diet ameliorate colitis in mice via regulating gut bile acid metabolism.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70008},
pmid = {41675168},
issn = {2996-9514},
abstract = {Inflammatory bowel disease (IBD) is a chronic disorder linked to an increased risk of colorectal cancer (CRC) and is characterized by significant dysbiosis in the gut microbiota. The commensal bacterium Parabacteroides goldsteinii (P. goldsteinii) has shown potential in modulating host metabolism and inflammatory responses. In this study, we investigated the probiotic properties of P. goldsteinii and its mechanism of action in IBD models, with a particular focus on bile acid metabolism and diet-microbiota interactions. Fecal samples from patients with ulcerative colitis (n = 14), Crohn's disease (n = 22), and healthy controls (n = 13) were analyzed to assess P. goldsteinii relative abundance. In dextran sulfate sodium (DSS)-induced colitis and azoxymethane (AOM)/DSS-induced CRC mouse models, administration of P. goldsteinii significantly attenuated inflammation and tumorigenesis, particularly under fiber-free diet conditions. Metabolomic profiling revealed an enrichment of secondary bile acids in P. goldsteinii-treated mice, suggesting a link between bile acid metabolism and its anti-inflammatory effects. Further mechanistic studies using bile salt hydrolase inhibitors and Tgr5 knockout mice confirmed the role of bile acid regulation in mediating the therapeutic benefits of P. goldsteinii. Additionally, we found that dietary factors significantly influenced the colonization and metabolic activity of P. goldsteinii, thereby modulating its probiotic efficacy. This highlights the potential for microbiome-based therapies tailored to specific dietary contexts in the treatment of IBD. Our findings demonstrate that P. goldsteinii can modulate gut bile acid metabolism to alleviate colitis, making it a promising candidate for probiotic applications in IBD management, with dietary modulation enhancing its therapeutic potential.},
}

@article {pmid41675166,
year = {2025},
author = {Shao, MW and Chen, HJ and Huang, AQ and Zheng, L and Li, CJ and Qin, D and Sun, YH and Lin, Z and Fu, G and Chen, YH and Li, YJ and Dong, ZY and Cheng, P and Pramono, H and Yu, GH and Xu, ZM and Miao, S and Hyde, KD},
title = {Modulation of rhizosphere microbiota by Bacillus subtilis R31 enhances long-term suppression of banana Fusarium wilt.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70006},
pmid = {41675166},
issn = {2996-9514},
abstract = {Continuous cropping of bananas leads to Fusarium wilt, affecting crop health, yet employing biocontrol bacteria to modulate rhizosphere microbial communities may offer effective disease suppression. This study revealed the secondary succession characteristics of rhizosphere microbiota in banana fields after more than 5-year continuous cropping and assessed the suppressive effects induced by biocontrol strain Bacillus subtilis R31. Through high-throughput sequencing, we observed a convergent enrichment of core bacterial genera Burkholderia-Dyella and Arthrobacter-Ralstonia in naturally suppressive and R31-treated suppressive soils, indicating broad-spectrum disease-suppressive soil traits induced by R31. R31 significantly enhanced associations between Streptomyces and the rhizosphere core community while weakening Burkholderia's linkage with membrane transport and energy metabolism pathways; moreover, it strengthened positive correlations between Rhizobium and terpenoid and polyketide metabolism (r = 0.65, p < 0.01). Culture-dependent assays showed that among 46 isolates from root and rhizosphere, those with high activities of indole-3-acetic acid, protease, cellulase, chitinase, and β-1,3-glucanase exhibited pronounced antagonistic activities against Fusarium oxysporum. Although R31 was undetectable in the rhizosphere in the second year, its modulation of rhizosphere function persisted, displaying a "legacy effect" consistent with the priority effects theory, whereby early colonizing beneficial communities resist subsequent pathogen invasions. R31 induced functional bacteria colonization in nascent banana root hair tissues, establishing new microbiome patterns that contributed to long-term disease suppression. Pot experiments further indicated that endophytic bacteria within roots exhibited stronger Fusarium wilt control than rhizosphere isolates. However, single-strain treatments frequently led to sheath rot co-infection, suggesting that synergistic actions of multiple strains might be more effective for disease suppression. This study highlighted R31's potential to sustainably modulate the rhizosphere microbiome, enhance enzyme activity, and promote beneficial bacteria colonization, laying the groundwork for constructing efficient synthetic bacterial communities for biocontrol.},
}

@article {pmid41675162,
year = {2025},
author = {Lyu, Y and Shen, J and Che, Y and Dai, L},
title = {Skin microbiome engineering: Challenges and opportunities in skin diseases treatment.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70012},
pmid = {41675162},
issn = {2996-9514},
abstract = {The skin microbiome, consisting of a vast array of microorganisms, is essential for human skin health, aiding in barrier protection, immune regulation, wound repair, and defense against pathogens. Disruptions in this microbial balance are closely linked to the onset and worsening of various skin disorders. This review evaluates the potential of skin microbiome engineering as a therapeutic strategy for treating skin diseases. We discuss nontargeted approaches like probiotics and fecal microbiota transplantation that aim to reshape the microbial community, as well as targeted methods such as phage therapy, phage lysins, and engineered bacteria, which specifically modulate microbial populations or influence the skin environment. These approaches open new avenues for personalized dermatological treatments. Despite significant progress, challenges remain in the clinical translation of microbiome-based therapies. Safety, standardization, regulatory approval, and long-term ecological stability must be addressed to ensure efficacy and reproducibility in clinical settings, underscoring the critical need for further research in their dermatological applications.},
}

@article {pmid41675159,
year = {2025},
author = {Zhang, Q and Wang, N and Zhang, F and Chen, B and Wang, Y and Wang, Z and Zhao, C and Jin, C and Sheng, D and Yue, K and Jiang, D and Gao, L and Zhang, H and Kang, Z and Cheng, M and Ma, X and Wang, H and Hu, D and Wang, J and Liu, Y and Zhou, C and Yao, M and Zhao, G and Wang, Y and Wang, Z and Ning, K and Zhang, L},
title = {Transfer learning identifies bacterial signatures for cross-regional diagnosis of type 2 diabetes and enable stage-sensitive dietary fiber intervention.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70021},
pmid = {41675159},
issn = {2996-9514},
abstract = {DeepMicroFinder is a deep learning framework designed to update the existing disease diagnosis model to generate a transfer model by leveraging region-specific microbiome datasets and transfer learning approach. This framework effectively overcomes the limitation of regional effects in the gut microbiome, enabling accurate cross-regional disease detection. Microbial markers related to type 2 diabetes (T2D) were identified by DeepMicroFinder, and subsequently validated in independent T2D cohorts undergoing dietary fiber interventions.},
}

@article {pmid41675154,
year = {2025},
author = {Liu, Y and Li, Z and Zhang, C and Li, B and Jiang, W and Li, H and Zhang, L and Zhen, H and Bao, S and Li, X and Liu, Y and Chen, X and Du, J and Xia, J and Wang, J and Guo, R and Sun, Y and Pan, B and Lei, W and Xiao, L and Zhao, J and Jin, X and Zhang, W and Liu, X and Wang, J and Chen, M and Liao, W and Fang, W and Nie, C and Pan, W},
title = {A human skin microbiome reference catalog and the skin microbial landscape of plateau adults.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70000},
pmid = {41675154},
issn = {2996-9514},
abstract = {Comprehensive reference genomes are needed for the classification and functional characterization of the human skin microbiota. Here, we established human skin microbiome genome (HSMG) and protein (HSMP) catalogs by integrating 739 newly sequenced and 2,520 published samples, along with two published microbial genome catalogs. The HSMG includes 3547 prokaryotic species, of which 1556 (43.87%) are unidentified, and the HSMP contains 39,283,339 nonredundant proteins, with 64.8% of which are poorly characterized. Using the HSMG as a reference, we identified distinct features and biogeographical traits of the skin microbiome in plateau adults, revealing significant differences between sebaceous and dry skin, with 1784 of 3547 inferred prokaryotes showing considerable variation. Additionally, host characteristics, skincare, and daylight habits were found to shape the skin microbiome. This work expands our understanding of the diversity of uncultured skin bacteria and provides a comprehensive characterization of the human skin microbiome in plateau environments.},
}

@article {pmid41675153,
year = {2025},
author = {Ye, L and Hu, Q and Zang, T and Wang, Y and Heng, H and Chan, EWC and Chen, S},
title = {Deciphering comprehensive profiles of pathogenies and resistome of pork using integrating metagenomic and isolation strategies.},
journal = {iMetaOmics},
volume = {2},
number = {2},
pages = {e70004},
pmid = {41675153},
issn = {2996-9514},
abstract = {The pork microbiome was investigated using an integrated approach combining isolation and metagenomic sequencing methods to comprehensively analyze the pathogens and resistome on pork surfaces. The study revealed a large number and diversity of pathogens and resistance genes, potentially originating from air, transportation, water, or cross-contamination. These findings underscore the importance of implementing multifaceted food surveillance strategies to monitor and mitigate these risks effectively.},
}