@article {pmid41614121,
year = {2025},
author = {Shi, M and Guo, A and Qin, S and Kang, Y and Zhang, W and Yang, X},
title = {Metagenomic insights into short-term legume rotation: modulating potato rhizosphere microbiota to enhance tuber yield and quality.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1680056},
pmid = {41614121},
issn = {1664-302X},
abstract = {OBJECTIVE: This study aims to investigate the effects of legume crop rotation on the rhizosphere microbiota and its potential to improve potato (Solanum tuberosum L.) productivity and tuber quality. We specifically focus on the microbial functional potential revealed through metagenomic sequencing under different legume rotation systems in the intensive agricultural region of the Chinese Loess Plateau.

METHODS: A five-year field experiment (2018-2022) was conducted to establish three cropping systems: (1) continuous potato monocropping for 5 years (CK), (2) continuous potato cropping for 3 years followed by one-year pea rotation and one-year potato cropping (T1), and (3) continuous potato cropping for 3 years followed by one-year faba bean rotation and one-year potato cropping (T2). The impacts of these rotation regimes on potato yield formation, tuber quality, and rhizosphere microbial communities were systematically evaluated, with a focus on microbial diversity and functional potential, using metagenomic sequencing and network analysis.

RESULTS: Metagenomic analysis demonstrated that legume rotation, particularly the T2 system, significantly enriched the relative abundances of Actinobacteria (38.31%) and Proteobacteria (28.40%) in the potato rhizosphere while reducing Acidobacteria (10.03%). Functional annotation further revealed that T2 promoted the expression of microbial genes involved in carbon fixation (K00626, K01895, etc.), nitrogen assimilation (narB, narA, etc.), and sulfur metabolism (cysNC, cysN, etc.), enhanced potential for nutrient cycling. Co-occurrence networks revealed Actinobacteria and Acidobacteria as keystone taxa forming robust interaction modules potentially linked to soil ecological stability. Compared to CK, T2 increased the commercial tuber rate by 85.82%, overall tuber yield by 28.38%, starch content by 34.85%, and vitamin C content by 30.79%, while reducing sugar levels decreased by 9.35%.

CONCLUSION: Faba bean-potato rotation (T2) effectively mitigated the adverse impacts caused by continuous potato cropping by altering the rhizosphere microbial structure and enhancing microbial functional pathways related to nutrient cycling. This study provides a detailed metagenomic perspective on the microbial mechanisms underlying the benefits of crop rotation and offers a theoretical basis for developing microbiome-informed ecological management strategies to mitigate continuous cropping obstacles in potato production on the Loess Plateau.},
}

@article {pmid41613796,
year = {2026},
author = {Pawłowska, M and Jarek, D and Milanowski, J and Szewczyk-Golec, K},
title = {Parasitic Infections and Carcinogenesis: Molecular Mechanisms, Immune Modulation, and Emerging Therapeutic Strategies.},
journal = {Oncology research},
volume = {34},
number = {2},
pages = {8},
pmid = {41613796},
issn = {1555-3906},
mesh = {Humans ; Animals ; *Parasitic Diseases/immunology/complications/parasitology ; *Neoplasms/immunology/parasitology/therapy/etiology ; *Carcinogenesis/immunology ; Tumor Microenvironment/immunology ; Host-Parasite Interactions/immunology ; Immunomodulation ; },
abstract = {Parasitic infections are increasingly recognized as contributors to cancer development, yet the underlying oncogenic mechanisms remain insufficiently understood. Growing evidence from molecular oncology, immunology, and microbiome research suggests that chronic parasitic infections may drive tumorigenesis through sustained inflammation, deregulated signaling pathways, genomic instability, and the release of parasite-derived exosomes that reshape the tumor microenvironment. These insights underscore the need to integrate parasitology with cancer biology to understand infection-associated malignancies better. The aim of this narrative review is to synthesize current knowledge on how selected parasites contribute to cancer development and to highlight emerging therapeutic and diagnostic opportunities. We examine pathogens such as Schistosoma haematobium, Opisthorchis viverrini, Toxoplasma gondii, Plasmodium falciparum, and Leishmania spp., detailing their roles in chronic inflammation, immune modulation, and interactions with tumor-associated immune cells. The review further discusses parasite-induced immunosuppression, coinfections, and their cumulative impact on cancer risk. Additionally, we explore novel therapeutic approaches, including pathway inhibitors, epigenetic drugs, microbiome modulation, and engineered parasites. Future perspectives emphasize parasite-based immunotherapies, long-term epigenetic consequences of infection, and AI-driven multi-omics strategies for identifying oncogenic signatures. This review integrates advances from parasitology and oncology to provide new insights into biomarkers, targeted therapies, and mechanisms of infection-induced tumorigenesis. The literature search covered studies indexed in PubMed, Scopus, and Web of Science up to July 2025.},
}

Humans
Animals
*Parasitic Diseases/immunology/complications/parasitology
*Neoplasms/immunology/parasitology/therapy/etiology
*Carcinogenesis/immunology
Tumor Microenvironment/immunology
Host-Parasite Interactions/immunology
Immunomodulation

@article {pmid41613795,
year = {2026},
author = {Liu, K and Xue, X and Qin, H and Zhu, J and Jin, M and Dai, D and Tang, Y and Bukhari, I and Liu, H and Qiu, C and Ren, F and Zheng, P and Mi, Y and Chen, W},
title = {Gut Associated Metabolites Enhance PD-L1 Blockade Efficacy in Prostate Cancer.},
journal = {Oncology research},
volume = {34},
number = {2},
pages = {23},
pmid = {41613795},
issn = {1555-3906},
mesh = {Male ; Humans ; Animals ; *Prostatic Neoplasms/metabolism/drug therapy/pathology/immunology ; *B7-H1 Antigen/antagonists & inhibitors/metabolism/genetics ; Mice ; *Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Cell Line, Tumor ; Exosomes/metabolism ; Mice, Transgenic ; Disease Models, Animal ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a critical modulator of cancer immunotherapy response. However, the mechanisms by which gut-associated metabolites influence checkpoint blockade efficacy in prostate cancer (PC) remain not fully explored. The study aimed to explore how gut metabolites regulate death-ligand 1 (PD-L1) blockade via exosomes and boost immune checkpoint inhibitors (ICIs) in PC.

METHODS: We recruited 70 PC patients to set up into five subgroups. The integrated multi-omics analysis was performed. In parallel, we validated the function of gut microbiome-associated metabolites on PD-L1 production and immunotherapy treatment efficacy in PC cell lines and transgenic adenocarcinoma of the mouse prostate (TRAMP) models.

RESULTS: We identified two metabolites, 16(R)-Hydroxyeicosatetraenoic acid (16(R)-HETE) and 6-Keto-Prostaglandin E1 (6-Keto-PGE1), that positively correlated with the plasma exosomal PD-L1 levels. The in vitro experiments found that both 16(R)-HETE and 6-Keto-PGE1 can enhance PD-L1 expression at the mRNA, protein, and exosome levels in both human and mouse PC cell lines, which were also validated in vivo based on subcutaneous mouse models. Both metabolites significantly promoted the anti-PD-L1 efficacy against PC in situ on a TRAMP mouse model.

CONCLUSIONS: Targeting the "gut-tumor metabolic axis" is a promising strategy to improve the efficacy of immune checkpoint inhibitors in tumors.},
}

Male
Humans
Animals
*Prostatic Neoplasms/metabolism/drug therapy/pathology/immunology
*B7-H1 Antigen/antagonists & inhibitors/metabolism/genetics
Mice
*Immune Checkpoint Inhibitors/pharmacology/therapeutic use
*Gastrointestinal Microbiome
Cell Line, Tumor
Exosomes/metabolism
Mice, Transgenic
Disease Models, Animal

@article {pmid41613600,
year = {2025},
author = {Li, L and Zhang, Q and Zhang, L and Wei, R and Qin, Y and Zhao, J and Wu, H},
title = {A cross-sectional study of salivary and gut microbiomes in hemodialysis patients with heart failure with preserved ejection fraction.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1683657},
pmid = {41613600},
issn = {2235-2988},
mesh = {Humans ; *Heart Failure/microbiology/physiopathology ; Cross-Sectional Studies ; *Saliva/microbiology ; *Gastrointestinal Microbiome ; Male ; Female ; Aged ; *Renal Dialysis/adverse effects ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Dysbiosis/microbiology ; Bacteria/classification/genetics/isolation & purification ; Stroke Volume ; DNA, Bacterial/genetics/chemistry ; },
abstract = {BACKGROUND: Heart failure (HF) is a primary cause of death in patients on maintenance hemodialysis (MHD), yet the role of microbial dysbiosis is poorly defined. This study characterized the salivary and gut microbiomes of MHD patients with heart failure with preserved ejection fraction (HFpEF), those without HF (NHF), and healthy controls (CON).

METHODS: In this cross-sectional study (n=88), we compared the salivary and fecal microbiomes of HFpEF (n=30), NHF (n=30), and CON (n=28) groups using 16S rRNA gene sequencing. Microbial community structure and composition were analyzed.

RESULTS: Alpha diversity and Beta diversity analysis revealed a distinct salivary microbial structure, which effectively distinguished the MHD group from the Con group (P < 0.05). Conversely, the overall gut community structure showed no significant separation. At the genus level, both MHD groups showed depletion of salivary Veillonella and gut Faecalibacterium compared to controls. Notably, LEfSe analysis highlighted salivary Anaerocolumna as a promising candidate feature associated with the HFpEF group.

CONCLUSION: Our analyses suggest that HFpEF in MHD patients may be associated with structural alterations in the oral microbiome, which appear more pronounced than those in the gut. Specific oral microbial signatures, particularly the enrichment of Anaerocolumna, showed associations with the HFpEF cohort in our study. This preliminary evidence positions the oral microbiome as an area worthy of further investigation for its potential role in this high-risk population.},
}

Humans
*Heart Failure/microbiology/physiopathology
Cross-Sectional Studies
*Saliva/microbiology
*Gastrointestinal Microbiome
Male
Female
Aged
*Renal Dialysis/adverse effects
Middle Aged
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Dysbiosis/microbiology
Bacteria/classification/genetics/isolation & purification
Stroke Volume
DNA, Bacterial/genetics/chemistry

@article {pmid41613599,
year = {2025},
author = {Lu, S and Wu, Z and Zhao, Y and Tang, T and Dong, Y and Wu, M and Zhang, P and Ma, Z},
title = {Comprehensive microbiome and metabolome analysis revealed the changes of semen microbial characteristics and metabolic phenotypes in patients with idiopathic oligoasthenozoospermia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1741184},
pmid = {41613599},
issn = {2235-2988},
mesh = {Humans ; Male ; *Semen/microbiology/metabolism ; *Metabolome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Adult ; Metabolomics/methods ; *Oligospermia/microbiology/metabolism ; Phenotype ; Biomarkers ; Bacteria/classification/genetics/isolation & purification/metabolism ; *Asthenozoospermia/microbiology/metabolism ; Case-Control Studies ; },
abstract = {BACKGROUND: The etiology and pathogenesis of idiopathic oligoasthenospermia (IOA) remain unclear, and current treatment options yield suboptimal outcomes. Consequently, there is an urgent need to identify novel biomarkers and develop diagnostic tools to improve patient identification and clinical management. Multi-omics technologies offer a promising pathway toward achieving this goal in the future.

METHODS: This study included 40 untreated patients with idiopathic oligoasthenospermia (IOA) and 30 healthy fertile males (HP) as controls. Semen samples were analyzed using 16S rRNA gene sequencing (microbiome) and non-targeted metabolomics (GC-MS/LC-MS coupled). A microbe-metabolite association network was integrated at the genus level based on Spearman correlation algorithms.

RESULTS: Semen microbiome analysis revealed that both microbial composition and species richness differed between IOA patients and HP controls. Non-targeted metabolomics further demonstrated characteristic metabolic dysregulation in seminal plasma of IOA patients, with a metabolic signature effectively distinguishing cases from controls (VIP > 1, FDR < 0.05). KEGG pathway enrichment analysis indicated that differentially expressed metabolites primarily involved amino acid metabolism, carbohydrate metabolism, and related signaling pathways (corrected p-value < 0.05). Construction of a Spearman correlation network between microbiota and metabolites (|r| > 0.6) identified significant interactions between core bacterial genera such as Dialister, Prevotellaceae_NK3B31_group, Lawsonella, and Blautia with seminal plasma metabolites, suggesting potential involvement of the microbiota-metabolite axis in the pathological process of IOA.

CONCLUSION: The microbial community structure and metabolic profiles in the semen of IOA patients exhibit significant disruption. Diagnostic models constructed based on combined microbial-metabolite features demonstrate potential for effectively distinguishing disease phenotypes. The core dysregulated bacterial genera, associated metabolites, and related pathways may serve as early diagnostic biomarkers and therapeutic intervention targets.},
}

Humans
Male
*Semen/microbiology/metabolism
*Metabolome
RNA, Ribosomal, 16S/genetics
*Microbiota
Adult
Metabolomics/methods
*Oligospermia/microbiology/metabolism
Phenotype
Biomarkers
Bacteria/classification/genetics/isolation & purification/metabolism
*Asthenozoospermia/microbiology/metabolism
Case-Control Studies

@article {pmid41613399,
year = {2025},
author = {Gao, Y and Wei, Y and Zeng, D and Zhang, J and Dong, J and Gao, X and Yuan, H and Li, X and Qiu, D and Burford, M},
title = {Restructuring of the epiphytic microbiome and recruitment of algicidal bacteria by Vallisneria natans for the suppression of Microcystis.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1731742},
pmid = {41613399},
issn = {1664-462X},
abstract = {The effective suppression of cyanobacteria by submerged macrophytes is a key mechanism underlying the successful restoration of aquatic vegetation in some eutrophic water bodies. However, the responses and functional roles of epiphytic microorganisms in this process remained largely unclear, limiting a clear understanding of how macrophytes inhibit cyanobacterial growth. In this study we investigated the temporal dynamics of the epiphytic microbiome on Vallisneria natans before, during and after exposure to toxic cyanobacterium Microcystis, corresponding to three distinct physiological stages of the plant: pre-stress, stress, and recovery. It was observed that the diversity of epiphytic bacteria and eukaryotic algae increased during the stress stage, while that of other eukaryotes, particularly fungi and protozoa, decreased. The complexity and stability of the epiphytic microbiome were enhanced, with bacteria emerging as central hubs in the co-occurrence network in response to Microcystis stress. More importantly, a selective enrichment and recruitment of potential algicidal bacteria, particularly Streptomyces, Pseudomonas and Chryseobacterium, occurred on macrophyte surfaces during the stress phase. Their abundance peaked under Microcystis stress and returned to baseline levels during the plant recovery phase. Our findings demonstrate that V. natans did not function alone, but rather actively recruited and sustained a beneficial microbiome to enhance its suppressive effects on Microcystis. This study revealed a previously neglected macrophyte-epiphytic microbiome synergy, providing novel mechanistic insights into how submerged vegetation effectively suppresses harmful cyanobacteria.},
}

@article {pmid41613388,
year = {2025},
author = {Fasipe, B and Laher, I},
title = {Obesity and metabolic disease in migrants: a role for the gut microbiome?.},
journal = {Frontiers in clinical diabetes and healthcare},
volume = {6},
number = {},
pages = {1745885},
pmid = {41613388},
issn = {2673-6616},
abstract = {Migration, while often motivated by safety, education, or economic opportunity, often heightens the risk of obesity and metabolic syndrome. Resettlement in industrialized nations is associated with sedentary lifestyles, irregular sleep schedules, and Westernized dietary patterns rich in ultra-processed, high-fat, and high-sugar foods. These changes disrupt metabolic homeostasis through endocrine and circadian dysregulation, promoting insulin resistance, visceral adiposity, and systemic inflammation. Migration alters the composition and diversity of the gut microbiome, suggesting that the characteristics of the microbiome could be important in linking migration to changes in health outcomes after resettlement. However, the precise mechanisms underlying these microbiome-mediated effects remain poorly understood. We propose that a dynamic metabolic interface is reshaped via a rapid "microbiome acculturation", which is a process by which the gut microbiome rapidly adapts to a new cultural and environmental milieu, such as caused by migration, shifting from traditional, fiber-rich microbial profiles to Westernized, Bacteroides-dominant communities associated with metabolic dysfunction. This is characterized by the depletion of fiber-fermenting Prevotella and enrichment of Bacteroides species, leading to reduced short-chain fatty acid production, impaired gut barrier function, and increased endotoxemia. Dietary transitions, chronic psychosocial stress, circadian disruption to night-shift work, and reduced physical activity experienced by immigrants reshapes gut microbial composition and function to a pro-inflammatory milieu and enhancing insulin resistance. Thus, gut dysbiosis serves as both a biomarker and mechanistic driver of post-migration metabolic deterioration, integrating dietary, behavioral, and environmental stressors into a unified pathogenic pathway. Effective prevention should target the gut-brain-metabolic axis using multidimensional strategies: restoring microbial diversity using high-fiber, prebiotic, and probiotic nutrition; promoting physical activity and circadian alignment; and addressing social determinants of health such as work patterns, food access, and acculturation stress.},
}

@article {pmid41613338,
year = {2025},
author = {Qian, T and He, Y and Yan, R and Yu, S and Chen, Y and He, W},
title = {Recurrent urinary tract infections and psychological burden: mechanisms and integrative perspectives.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1721343},
pmid = {41613338},
issn = {2296-858X},
abstract = {Recurrent urinary tract infections (rUTIs) remain a global health concern with significant physical and psychological impacts, particularly in women. Recent evidence indicates a strong bidirectional association between rUTIs and psychological burden, yet the underlying mechanisms remain incompletely understood.This review integrates findings from biomedical and traditional Chinese medicine (TCM) perspectives to elucidate potential pathways linking rUTIs with anxiety and depression. Four major mechanisms-immune dysregulation, endocrine imbalance, microbiome alteration, and neuroendocrine dysfunction-are proposed to explain this complex interaction. In addition, TCM conceptualizes this relationship through the theory of the "coexistence of disease and depression syndromes" emphasizing that emotional regulation is a key determinant of both urinary and systemic health. By synthesizing these insights, this narrative review underscores the importance of integrative approaches in preventing and managing rUTIs while addressing concurrent psychological distress.},
}

@article {pmid41613307,
year = {2025},
author = {Lee, J and Song, H and Kim, KY},
title = {Association of lifestyle, physiological factors, and body composition with the facial skin microbiota in acne vulgaris.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1679925},
pmid = {41613307},
issn = {2296-858X},
abstract = {INTRODUCTION: The skin microbiota plays a crucial role in maintaining skin health and overall well-being. The composition of this microbial community is influenced by various host factors, including lifestyle habits, physiological parameters, and body composition.

METHODS: 1,053 participants were included in this study. The composition of the skin microbiota was determined by analysing facial skin microbiome collection, obtained after the consent of participants. Also, physical characteristics of each participant were evaluated using answers from questionnaire. Potential microorganisms that contribute to acne vulgaris development were investigated. Statistical analysis was then performed based on the characteristics of the patient and normal groups, and the differences in the bacterial ratio grade assigned to each individual.

RESULTS: C. acnes, S. aureus, and S. epidermidis were significantly correlated with acne vulgaris. Several characteristics of the participants were closely correlated with the composition of the skin microbiota. There was significant differences among the participants' characteristics.

DISCUSSION: By analyzing the body composition and daily life of the study subjects, we identify associations of acne vulgaris and suggest specific lifestyle modifications that may be beneficial for acne sufferers.},
}

@article {pmid41613170,
year = {2026},
author = {Siziya, IN and Seo, MJ and Park, CS and Jung, DH},
title = {Bacterial fructan-metabolizing enzymes: modular architecture and biotechnological potential.},
journal = {3 Biotech},
volume = {16},
number = {2},
pages = {85},
pmid = {41613170},
issn = {2190-572X},
abstract = {Bacterial fructan-metabolizing enzymes exhibit substantial structural and mechanistic diversity to support their biotechnological uses. Recent findings on glycoside hydrolase (GH) families 32 and 68 emphasize the conserved catalytic triads, calcium-binding motifs, and domain architectures that define their reaction frameworks. Differences in carbohydrate-binding modules (CBMs), extended loops, and accessory domains contribute to variations in substrate affinity, polymer length, and the balance between polymerization and hydrolysis. Aggregated data shows that GH68 enzymes generally exhibit higher catalytic efficiencies on sucrose, while GH32 hydrolases display stronger preferences for inulin and short-chain fructooligosaccharides (ScFOS). In gut commensals, distinct fructan utilization operons provide the basis for substrate-driven cross-feeding interactions, with ScFOS typically exhibiting shorter fermentation times compared to high molecular-weight levans. Rapid progress in artificial intelligence for structural predictions, molecular dynamics simulations, and CRISPR-enabled pathway engineering now supports the rational redesign of fructan-active enzymes, enabling the generation of catalysts with customized product profiles, enhanced stability, or altered chain-length distributions. This review provides a comprehensive overview of bacterial fructan-metabolizing enzymes, integrating structural, biochemical, and ecological perspectives to establish a foundation for applying fructan-modifying enzymes to prebiotic production, food texturization, microbiome modulation, and emerging oral enzyme therapeutics.},
}

@article {pmid41613163,
year = {2026},
author = {Ganamurali, N and Sabarathinam, S},
title = {Bidirectional interplay between the gut microbiota and GLP-1 receptor agonists: towards Microbiome-Mediated therapeutics in type 2 diabetes mellitus.},
journal = {Journal of diabetes and metabolic disorders},
volume = {25},
number = {1},
pages = {44},
pmid = {41613163},
issn = {2251-6581},
abstract = {Type 2 diabetes mellitus (T2DM) is a complex chronic disease characterized by progressive β-cell dysfunction and insulin resistance. Glucagon-like peptide-1 receptor agonists (GLP-1RAs) are widely used in T2DM management due to their ability to lower HbA1c, promote weight loss, and offer cardiovascular and renal protection. However, inter-individual variation in therapeutic response has been observed, potentially influenced by gut microbiota composition. A brief review was conducted to explore current evidence on the interaction between GLP-1RAs and gut microbiotatermed the "pharmaco-gut axis." Literature was examined to understand how specific microbial populations affect drug efficacy and insulin sensitivity. Studies suggest that certain gut microbes, including Bacteroides species, Akkermansia muciniphila, and those producing short-chain fatty acids (SCFAs), enhance GLP-1RA efficacy by improving insulin sensitivity and stimulating endogenous GLP-1 secretion. Conversely, dysbiosis characterized by reduced microbial diversity and increased lipopolysaccharide (LPS)-producing pro-inflammatory bacteria correlates with poor therapeutic response. Furthermore, GLP-1RAs may exert beneficial modulatory effects on the gut microbiota itself, indicating a bidirectional relationship. The interaction between GLP-1RAs and gut microbiota introduces a novel pharmaco-gut interface, emphasizing the role of microbial composition in drug response. This emerging concept has the potential to enhance precision medicine in diabetes care by utilizing microbiome profiling to guide GLP-1RA therapy and improve clinical outcomes.},
}

@article {pmid41613132,
year = {2025},
author = {Sîrbu, AE and Gradisteanu Pircalabioru, G and Deaconu, DM and Andronic, O and Gheorghe, DC},
title = {The pediatric nasal microbiome and its role in chronic ENT disorders: a narrative review.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1699707},
pmid = {41613132},
issn = {1664-3224},
mesh = {Humans ; *Microbiota/immunology ; Chronic Disease ; Child ; *Otorhinolaryngologic Diseases/microbiology/immunology ; },
abstract = {The human microbiome is increasingly recognized as a key factor in immune development and disease susceptibility, especially in early life. Nasal microbiome has emerged as a critical element in upper airway health, yet its role in pediatric otorhinolaryngological conditions remains underexplored. This narrative review synthesizes current evidence on the microbial nasopharyngeal patterns in healthy children compared with children suffering from chronic ENT conditions such as otitis media, allergic rhinitis, chronic rhinosinusitis, adenoid and tonsillar hypertrophy associated with obstructive sleep apnea. A structured search of Web of Science, PubMed, Google Scholar and CrossRef databases was conducted for peer-reviewed articles published in the past ten years. Nasal microbiota of healthy children was proved to be dominated by commensal protective taxa such as Dolosigranulum and Corynebacterium which contribute to mucosal immune stability. In contrast, patients with chronic ENT pathologies exhibited reduced diversity and increased prevalence of potential pathogens microbial species such as Haemophilus, Streptococcus and Staphylococcus. Several extrinsic factors appear to play an important role in modulating the nasal microbiota such as environmental exposure, delivery mode, feeding practices and antibiotic treatment. Growing evidence supports the predictive and modulatory potential of the nasal microbiome, however methodological variability, limited pediatric-specific studies and unclear causal relationships remain challenging components. This review highlights key microbial patterns, outlines the limitations of current research and suggests future directions for clinical integration of nasal microbiome analysis in pediatric ENT standard of care as it may hold promising utilisation of biomarkers for disease risk stratification and targeted therapeutic or preventative interventions in early life.},
}

Humans
*Microbiota/immunology
Chronic Disease
Child
*Otorhinolaryngologic Diseases/microbiology/immunology

@article {pmid41613128,
year = {2025},
author = {Koh, JH and Park, S and Kang, M and Park, JI and Lee, J and Cho, H and Kim, JE and Nam, H and Kim, D and Li, M and Park, S and Moon, KC and Kim, HJ and Kim, YS and Kim, DK and Lee, H},
title = {Altered acetate metabolism and signaling in IgA nephropathy: an integrated gut microbiome and glomerular spatial transcriptome analysis.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1665585},
pmid = {41613128},
issn = {1664-3224},
mesh = {Humans ; *Glomerulonephritis, IGA/metabolism/microbiology/genetics ; *Gastrointestinal Microbiome ; Male ; Adult ; Gene Expression Profiling ; Female ; *Transcriptome ; Middle Aged ; *Acetates/metabolism ; Signal Transduction ; *Kidney Glomerulus/metabolism/pathology ; Feces/microbiology/chemistry ; RNA, Ribosomal, 16S/genetics ; },
abstract = {INTRODUCTION: IgA nephropathy (IgAN) is the most common primary glomerulonephritis, and emerging evidence implicates the gut microbiome in its pathogenesis. Additional studies focusing on the molecular mechanisms linking gut microbial signals to intraglomerular changes are warranted.

METHODS: We performed 16S rRNA-based microbial profiling of fecal samples of 172 IgAN patients, 51 healthy controls, and other glomerular disease controls including 15 diabetic nephropathy, 35 minimal change disease, and 63 membranous nephropathy cases. Serum and fecal acetate levels were measured by liquid chromatography-mass spectrometry. Glomerular spatial transcriptomic profiling was performed with the GeoMx Digital Spatial Profiler. DESeq2 analysis was performed to identify differentially expressed genes, followed by gene ontology annotations.

RESULTS: Beta diversity differed significantly between IgAN and healthy controls (p = 0.001). While no single taxon showed consistent differences in abundance, the methanogenesis from acetate pathway was significantly enriched in IgAN, accompanied by an increased proportion of major acetate-producing gut microbial genera. Serum acetate levels were elevated in IgAN (p = 0.03), while fecal acetate levels were comparable to those in healthy controls. In glomerular transcriptomes, functional annotations of 1,227 upregulated and 1,078 downregulated genes in IgAN indicated decreased activities of G protein-coupled receptors, short-chain fatty acid transporters, and beta-1,3-galactosyltransferases.

DISCUSSION: IgAN is characterized by gut microbial enrichment in acetate metabolism and increased systemic acetate levels, along with altered intraglomerular expression of metabolic and signaling genes. These findings suggest a gut microbiome-glomerular signaling axis contributing to disease pathogenesis.},
}

Humans
*Glomerulonephritis, IGA/metabolism/microbiology/genetics
*Gastrointestinal Microbiome
Male
Adult
Gene Expression Profiling
Female
*Transcriptome
Middle Aged
*Acetates/metabolism
Signal Transduction
*Kidney Glomerulus/metabolism/pathology
Feces/microbiology/chemistry
RNA, Ribosomal, 16S/genetics

@article {pmid41613126,
year = {2025},
author = {Zhang, R and Li, Z and Liu, X and Qiu, Z and Li, Y and Gao, C and Guo, C},
title = {Intratumoral microbiota: synergistic reshaping of lung cancer microenvironment via inflammation and immunity.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1653727},
pmid = {41613126},
issn = {1664-3224},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Lung Neoplasms/immunology/microbiology/therapy/pathology/metabolism ; *Microbiota/immunology ; Animals ; *Inflammation/immunology/microbiology ; Immunotherapy/methods ; },
abstract = {As high-throughput sequencing tools have advanced in recent years, scientists have discovered that lung cancer tissues are not sterile. The intratumoral microbiota exists in the tumor parenchyma and stroma in a low-biomass form. This finding has overturned the traditional concept of "sterile tumors" and brought the intratumoral microbiota to the forefront of tumor research. In this review, we focus on elucidating the mechanisms by which intratumoral microbiota influence lung cancer cells and the tumor microenvironment (TME), with the aim of clarifying their role in lung cancer progression. The intratumoral microbiota does not exist as a passive resident. Instead, it may actively induce and maintain a chronic inflammatory state through the secretion of metabolites, activation of signaling pathways, immune suppressor cell recruitment, and upregulation of immune checkpoint molecule expression, thereby promoting tumor cell proliferation, invasion, and immune evasion. From a clinical translation perspective, we explore the potential of using intratumoral microbiota characteristics to predict immunotherapy efficacy. Additionally, we assess the application prospects of engineered bacteria and targeted nanobiotics, which are based on synthetic biology, in reshaping the immune microenvironment. However, the field still faces significant challenges, particularly as the low biomass nature of lung tissues makes sequencing data highly susceptible to reagent contamination and batch effects. Additionally, the synergistic role of non-bacterial components such as fungi and viruses in the tumor ecosystem is often overlooked. Future research needs to establish rigorous quality control standards and integrate multi-omics technologies to comprehensively analyze the dynamic interaction network between the microbiota and host immunity, which will drive the clinical implementation of microbiome-based precision diagnostic and therapeutic strategies for lung cancer.},
}

Humans
*Tumor Microenvironment/immunology
*Lung Neoplasms/immunology/microbiology/therapy/pathology/metabolism
*Microbiota/immunology
Animals
*Inflammation/immunology/microbiology
Immunotherapy/methods

@article {pmid41613079,
year = {2025},
author = {Martínez-Ortiz, IC and Garcia-Atutxa, I and Sanchez-Villamil, JI and Machain-Williams, C and Reyes-López, MA and Villanueva-Flores, F},
title = {Predictive multi-omic biomarkers for urban zoonotic spillover detection: an integrative review.},
journal = {Frontiers in public health},
volume = {13},
number = {},
pages = {1720300},
pmid = {41613079},
issn = {2296-2565},
mesh = {*Zoonoses/diagnosis/epidemiology ; Humans ; Animals ; *Biomarkers/analysis ; Animals, Wild/microbiology ; Multiomics ; },
abstract = {Urban wildlife is an overlooked yet critical component of zoonotic disease surveillance, especially in biodiversity hotspots where human-animal interfaces accelerate spillover risk. This review synthesizes five complementary omics layers: Host microRNAs, host-pathogen genetic markers, bacterial microbiome profiling, viromics, and host transcriptomics into a single predictive framework for early spillover detection. Across taxa and pathogen classes, we highlight convergent molecular signatures of infection, from receptor polymorphisms and shifts in MHC diversity to pathogen-responsive miRNAs, high-risk bacterial genera, novel viral sequences, and transcriptomic profiles associated with pathogen tolerance. By integrating these biomarkers into a cross-validated, multi-omics architecture, we outline a workflow from non-invasive sampling to predictive modeling that enhances sensitivity for detecting both known and cryptic pathogens. We also identify key barriers, including Field preservation, cross-species assay standardization, and bioinformatics capacity, and propose practical solutions, such as interoperable pipelines and open-access databases. This integrative approach shifts surveillance from reactive detection to anticipatory risk profiling, providing a transformative tool for One Health strategies aimed at forecasting and preventing zoonotic epidemics.},
}

*Zoonoses/diagnosis/epidemiology
Humans
Animals
*Biomarkers/analysis
Animals, Wild/microbiology
Multiomics

@article {pmid41612732,
year = {2026},
author = {Ma, ZS},
title = {How Host Phylogeny and Diet Shape the Specificity and Specificity Diversity of Animal Gut Microbiomes.},
journal = {Environmental microbiology reports},
volume = {18},
number = {1},
pages = {e70253},
pmid = {41612732},
issn = {1758-2229},
support = {//Bullard Fellowship/ ; 72274192//National Natural Science Foundation of China/ ; //Prosperous Yunnan Talent Support Program/ ; },
mesh = {Animals ; *Phylogeny ; *Gastrointestinal Microbiome ; *Host Specificity ; *Diet ; *Bacteria/classification/genetics/isolation & purification ; Species Specificity ; Biodiversity ; },
abstract = {The forces shaping host specificity in the animal gastrointestinal microbiome (AGM) are often studied through separate lenses: community-level patterns (phylosymbiosis) or lineage-level histories (cophylogeny). Furthermore, traditional diversity metrics fail to capture compositional heterogeneity from host-specific distributions. We bridge these gaps using our SSD (Species Specificity and Specificity Diversity) framework, a recent conceptual and computational advance that quantifies host specificity across scales via: (i) Species Specificity (SS), locating species on the specialist-generalist continuum; (ii) Specificity Diversity (SD), quantifying community compositional heterogeneity; and (iii) statistical tests for identifying unique/enriched species. Applying SSD to 4903 AGM samples from 318 species, we identified unique and enriched microbial species in specific host taxa and diets, demonstrating that host phylogeny and diet jointly shape these patterns. A PTSD (Phylogenetic Timeline-Specificity Diversity) power-law model reveals the evolution of more complex microbiome structures in modern species. One surprising finding is the high similarity amongst animal AGMs, with only 252 microbial species being exclusively unique at the animal class level-somewhat analogous to the high genomic similarity between humans and primates. Our findings demonstrate a unified quantitative approach to dissecting the eco-evolutionary forces that shape microbial specificity and specificity heterogeneity, with potential synthesis with established phylosymbiosis and cophylogeny frameworks.},
}

Animals
*Phylogeny
*Gastrointestinal Microbiome
*Host Specificity
*Diet
*Bacteria/classification/genetics/isolation & purification
Species Specificity
Biodiversity

@article {pmid41612514,
year = {2026},
author = {Enagbonma, BJ and Pierneef, RE and Modise, DM and Babalola, OO},
title = {Effects of legume-based rotation on subsequent sorghum rhizosphere microbial communities and their drought tolerance-related genes.},
journal = {Environmental microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40793-025-00829-9},
pmid = {41612514},
issn = {2524-6372},
support = {CRP/ZAF22-03//ICGEB/ ; },
abstract = {INTRODUCTION: The impacts of incorporating legumes into cereal crops on soil microbial structure, composition, functional genes involved in nitrogen, carbon and phosphorus cycling, signaling pathways and hydraulic conductivity adaptations have been well studied. However, the same cannot be said for functional genes that increase drought tolerance.

OBJECTIVES: Here, we examined the changes in microbial community structure and functional genes involved in drought tolerance in response to legume‒cereal rotation and cereal‒cereal rotation. This study provides a preliminary, exploratory characterization of microbial community and functional gene shifts, without direct evidence of functional impact on plant physiology or productivity.

METHODS: DNA extracted from soil samples collected across cowpea-sorghum treatment (CS) or maize-sorghum treatment (MS) was sequenced via shotgun sequencing.

RESULTS: Nonmetric multidimensional scaling analysis revealed that the microbial communities in the CS treatment significantly differed from those in the MS treatment. Compared with the MS rotation, the CS rotation increased the relative abundances of Pseudomonadota, Acidobacteriota, Chloroflexota, Gemmatimonadota, Euryarchaeota, and Candidatus Bathyarchaeota and reduced the abundances of Actinomycetota, Ascomycota, and Nitrososphaerota at the phylum level. Furthermore, the CS rotation increased the abundance of microbial genera such as Solirubrobacter, Sphingomonas, Nitrosocosmicus, Nitrosotenuis Aspergillus, and Metschnikowia when related to the MS rotation. STAMP analysis revealed that in the CS rotation, genes involved in trehalose biosynthesis, biofilm formation, oxidative stress mitigation (e.g., sodA, katG), stress signaling (e.g., rpoS, ipdC), nutrient provisioning (e.g., nifH, pqqC), membrane fluidity (desA, desB), dormancy (spo0A, spoVF), and ion homeostasis (nhaB, kup) predominated. In the MS rotation, proline biosynthesis (proA, proB, and proC), glycine betaine synthesis (betA and betB), aquaporin (aqpZ), and structural integrity genes (murA and murC) were predominant. The RDA results revealed that crop rotation influenced the soil physicochemical parameters, which in turn impacted both the microbial communities and drought tolerance genes in both treatments, probably creating a favorable environment for resilience under drought.

CONCLUSION: These research findings provide insight into the relationships between cowpea cropping sequences and the soil microbiome and drought-tolerant functional genes fundamental for the productivity of successive crops and this understanding guides sustainable crop selection.},
}

@article {pmid41612472,
year = {2026},
author = {Wang, Y and Shen, Y and Shen, J and Bi, J and Xu, J and Wei, T and Wang, R and Wu, X and Li, F and Bai, J and Jie, Z and Hou, D and Song, Y},
title = {Airway microbiome dysbiosis in severe pneumonia: metagenomic evidence of pathogen expansion and commensal depletion.},
journal = {European journal of medical research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40001-026-03892-1},
pmid = {41612472},
issn = {2047-783X},
support = {ZD2021CY001//Shanghai Municipal Science and Technology Major Project/ ; GWVI-11.1-18//Shanghai Three-year Action Plan to Strengthen the Construction of Public Health System/ ; 82130001//National Natural Science Foundation of China/ ; 2024YFC3044400//National Key Research and Development Program of China/ ; GZNL2024A02003//R&D Program of Guangzhou National Laboratory/ ; W2020-013//The Construction of Multi-Disciplinary Treatment System for Severe Pneumonia/ ; 22Y11900800//Science and Technology Commission of Shanghai Municipality/ ; shslczdzk02201//Shanghai Municipal Key Clinical Specialty/ ; },
abstract = {BACKGROUND: The pulmonary microbiome is increasingly recognized as a key determinant of pneumonia severity, yet its clinical implications remain incompletely understood. Disruption of microbial ecology, or dysbiosis, may impair host immune responses and exacerbate disease progression. This study aimed to characterize microbiome alterations associated with severe pneumonia and their correlation with host inflammatory and coagulative parameters.

METHODS: In this multicenter, prospective observational cohort study conducted across nine hospitals in Shanghai (2021-2025), bronchoalveolar lavage fluid (BALF) samples from 306 patients with clinically diagnosed pulmonary infections were analyzed using metagenomic next-generation sequencing (mNGS). Patients were stratified into severe (n = 196) and non-severe (n = 110) groups using WHO-derived severe pneumonia criteria at the time of bronchoalveolar lavage (BAL). Microbial taxonomic profiles, diversity indices, co-occurrence networks, and correlations with clinical markers were comprehensively assessed using standard bioinformatic and statistical approaches.

RESULTS: Severe pneumonia was associated with marked microbial dysbiosis, including reorganization of co-occurrence network topology with centrality shifting away from commensals toward opportunistic taxa in severe disease, characterized by reduced α-diversity, altered β-diversity, and enrichment of opportunistic Gram-negative pathogens including Acinetobacter and Klebsiella. In contrast, commensals such as Rothia and Prevotella were depleted. Co-occurrence network analysis revealed fragmentation of microbial interactions in severe cases, with centrality shifting from commensals to opportunists like Corynebacterium striatum. Shannon diversity negatively correlated with SOFA scores, and specific taxa positively associated with systemic inflammation (CRP, PCT) and coagulation abnormalities. Nearly all samples demonstrated polymicrobial infection, with distinct microbial patterns observed across monomicrobial and polymicrobial subgroups.

CONCLUSION: Our multicenter observational analysis suggests that severe pneumonia is associated with marked ecological disruption of the lower-airway microbiome, characterized by commensal loss, opportunist expansion, and fragmented interspecies networks, and with concurrent inflammatory and coagulative abnormalities. These hypothesis-generating findings warrant external validation in independent, multi-region cohorts and longitudinal sampling to test directionality and causality before informing clinical decision-making.},
}

@article {pmid41612446,
year = {2026},
author = {Kwon, HJ and Ahn, JH and Won, MH and Kim, DW},
title = {Chronic periodontitis and systemic inflammation in the elderly: implications for neurodegeneration.},
journal = {Journal of neuroinflammation},
volume = {23},
number = {1},
pages = {43},
pmid = {41612446},
issn = {1742-2094},
support = {NRF-2021R1A6A3A01086738//Ministry of Education/ ; NRF-2021R1F1A1048079//Ministry of Science and ICT, South Korea/ ; },
mesh = {Humans ; *Inflammation ; *Chronic Periodontitis/complications/microbiology ; *Neurodegenerative Diseases ; Aged ; Animals ; *Aging/pathology ; Dysbiosis ; },
abstract = {Chronic periodontitis is increasingly recognized as a potential upstream contributor to neurodegenerative processes through sustained systemic inflammation, microbial dysbiosis, and blood-brain barrier (BBB) alterations. This review synthesizes human and experimental evidence linking periodontal pathogens-including but not limited to Porphyromonas gingivalis as well as broader dysbiotic consortia such as Tannerella forsythia, Treponema denticola, and other keystone oral taxa-to neuroinflammatory cascades associated with cognitive decline. Mechanistic insights highlight the roles of glial activation, proinflammatory cytokines, and polymicrobial virulence-mediated neuronal stress in bridging oral and brain pathology, while age-related factors such as immunosenescence and microbiome imbalance amplify systemic vulnerability. Human biomarker and imaging studies support an association between chronic periodontal inflammation and neurovascular dysfunction, suggesting that oral disease may act as a persistent peripheral amplifier of central immune activation. Recent research has expanded into biomarker discovery and translational implementation, yet progress remains limited by population heterogeneity, methodological variability, and regulatory complexity. Promising interventions-including anti-inflammatory therapies, oral hygiene optimization, probiotic or dietary modulation, and molecular strategies such as polymicrobial-targeted approaches, gingipain inhibition, and microRNA-based modulation-are discussed within emerging multi-omics and precision-medicine frameworks. Although standardization and longitudinal validation are still required, integrative approaches combining inflammatory, microbial, and genetic profiling may enable individualized risk assessment and targeted prevention. As global populations age, addressing the oral-brain axis offers a practical and modifiable pathway to lessen the burden of neurodegenerative diseases and support healthier cognitive aging.},
}

Humans
*Inflammation
*Chronic Periodontitis/complications/microbiology
*Neurodegenerative Diseases
Aged
Animals
*Aging/pathology
Dysbiosis

@article {pmid41612376,
year = {2026},
author = {Sánchez-Morán, M and Valverde-Benítez, I and Corcuera Tejada, J and Velasco, O and Aurrekoetxea-Oribe, J and Saso-Jiménez, L and Martinez de Lapiscina, I and Castaño, L and , },
title = {Oral microbiota assessment at different time points during the first year of life: delivery mode and breastfeeding shape the bacterial community.},
journal = {International breastfeeding journal},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13006-026-00813-0},
pmid = {41612376},
issn = {1746-4358},
abstract = {BACKGROUND: The assembly of the oral microbiota during the first year of life is a critical process that may influence long-term health and immunological development. While the gut microbiome has been extensively studied, early oral colonization patterns remain less understood. This study aimed to characterize the oral microbial succession in infants and to evaluate the impact of two primary clinical factors-delivery mode and breastfeeding practices-on microbial composition from birth through the first 12 months of life.

METHODS: Forty-eight newborns were prospectively recruited between January and June 2022 through the Basque Health Service (Osakidetza, Spain). Oral samples were collected at five time points (4-10 days, 1 month, 4 months, 6 months, and 12 months). Feeding status was categorized as exclusive breastfeeding (EBF) or mixed feeding (MF) for the first 4 months, after which the EBF group transitioned to a "Breast milk -No Formula" (BM-NF) group to account for the complementary feeding. Microbial communities were assessed via 16S rRNA amplicon sequencing. To compare alpha diversity (Shannon, Chao1, ACE, Simpson, Observed, and Fisher indices) between groups, Mann-Whitney or Kruskal-Wallis tests were employed. Beta diversity was evaluated via non-metric multidimensional scaling (NMDS) based on Bray-Curtis distances. PERMANOVA was employed to assess community shifts over time, and relative abundance differences across delivery and lactation type´s groups were analyzed using Mann-Whitney tests.

RESULTS: Oral bacterial diversity increased significantly over time as the oral cavity transitioned towards a more complex community. Streptococcus, Ralstonia, Gemella, and Rothia were the primary early colonizers. Significant taxonomic shifts were associated with birth and feeding modes. C-section infants exhibited a higher abundance of Veillonella and Neisseria during the first days of life. Regarding nutrition, mixed feeding (MF) infants showed higher proportions of Rothia, Prevotella, and Veillonella during the initial months. Conversely, Streptococcus remained significantly predominant in infants receiving breast milk (EBF/BM-NF) at the 6-month mark.

CONCLUSIONS: These findings demonstrate that delivery mode and lactation significantly shape the neonatal oral ecosystem. Specific microbial signatures up to 12 months suggest that early-life factors and feeding choices are key in establishing the mature oral microbiota.},
}

@article {pmid41470031,
year = {2025},
author = {Ge, T and Fang, D and Zhong, L and Pang, S and Hua, LB and Chen, J and Zhao, J and Huang, H},
title = {The dysbiosis of intestinal microbiota associated with isolated tricuspid valve regurgitation.},
journal = {Journal of cardiothoracic surgery},
volume = {21},
number = {1},
pages = {56},
pmid = {41470031},
issn = {1749-8090},
support = {No.2022YFC2407406//National Key Research and Development Program of China/ ; No. 2023B03J0596//the Guangzhou Science and Technology Planning Project/ ; No. 2023A031004//the Science and Technology Foundation of Guangzhou Health/ ; No. KD022023019//the 2023 Stability Support for Innovative Capacity Building of Guangdong Provincial Scientific Research Institutions/ ; No.2023FTJCZ0011//the Health Commission of Guangdong Province/ ; No.82270373//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Isolated tricuspid regurgitation (TR) is an increasingly recognized yet frequently underappreciated valvular disorder that adversely affects both survival and quality of life, with progressively worse outcomes as severity increases. Advances in high-throughput sequencing technologies have considerably expanded our understanding of the human microbiome, uncovering its close associations with a range of cardiovascular diseases, including atherosclerosis, heart failure, and hypertension. However, the potential role of intestinal dysfunction and the gut–heart axis in TR pathophysiology remains largely unexplored.

METHODS: A total of 20 patients diagnosed with TR and 10 healthy age- and gender-matched patients were enrolled in this study. Fecal samples were collected before the operation and subjected to 16 S rDNA gene sequencing.

RESULTS: The gut microbiomes of TR and healthy patients were significantly different in terms of alpha-diversity and beta-diversity analysis. Indicator analysis further showed 9 indicative bacterial genera and 2 bacterial species. Genera known to produce short-chain fatty acids (SCFAs), including Faecalibacterium, Blautia, and Ruminococcus were depleted, whereas Lactobacillus and Veillonella were enriched. Their correlations with clinical features using Pearson analysis showed that Ruminococcus, Lactobacillus, and Veillonella were potentially involved in the pathophysiology of TR. Functional predictions indicated enrichment of pathways related to carbohydrate, lipid, and nucleotide metabolism, as well as immune and cardiovascular diseases, whereas pathways linked to amino acid and vitamin metabolism were reduced. Notably, pathways involving D-arginine and D-ornithine metabolism and Staphylococcus_ aureus infection were upregulated.

CONCLUSIONS: Patients with tricuspid regurgitation (TR) exhibit gut dysbiosis, characterized by significant alterations in taxonomic composition. These findings suggest a dysregulation of the gut-host interaction in TR.},
}

@article {pmid41466244,
year = {2025},
author = {Blomqvist, M and Mørch, MB and Ghafouri, B and Wåhlén, K and Shannon, O and Davies, JR},
title = {Immunomodulatory effects of eubiotic and dysbiotic multi-species biofilms on oral keratinocytes.},
journal = {BMC oral health},
volume = {26},
number = {1},
pages = {203},
pmid = {41466244},
issn = {1472-6831},
abstract = {BACKGROUND: Elucidating host‒microbe interactions is essential for understanding oral health and disease. In periodontitis, the host inflammatory response to accumulated plaque shifts eubiotic biofilm communities toward dysbiosis, with enrichment of proteolytic bacterial species. The first line of host defence in the subgingival niche involves oral keratinocytes, which communicate with immune cells in the mucosa. Host responses to individual bacterial species have been widely characterized, but in this study, we used a co-culture model to better understand how changes in the multispecies biofilm phenotype affect keratinocyte effector function as well as the effects on inflammatory cells.

METHODS: Biofilms representative of eubiotic (HA) or dysbiotic (DA) bacterial communities were developed on nitro-cellulose membranes over 7 days and then co-cultured with oral keratinocytes for 6 h. Biofilm proteolytic activity was measured with a fluorescent substrate. Multiplex cytokine analysis of the co-culture medium was used to study keratinocyte responses and the activation of inflammatory cells was investigated via flow cytometry.

RESULTS: Proteolytic activity was greater in the DA biofilms than in the HA biofilms, most likely due to gingipains from Porphyromonas gingivalis. Keratinocytes released a range of cytokines, chemokines and growth factors, and the response to DA was more pro-inflammatory than that to HA biofilms, with relatively high levels of factors such as MIP-3a, IL-8, GM-CSF and IL-17 C. Co-culture medium from both the HA and DA biofilms elicited strong monocyte and neutrophil activation responses, although the effect of the DA biofilms was greater for monocytes than for neutrophils.

CONCLUSIONS: In this study, we show that keratinocytes have distinct response profiles to HA as compared to DA periodontal biofilm communities. The combination of products from the biofilm and the activated keratinocytes generated significant activation of inflammatory cells. This in vitro model thus provides insight on the complex host-microbiome interactions during development of periodontal disease.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12903-025-07576-w.},
}

@article {pmid41457283,
year = {2025},
author = {Sadeghi, N and Shams, S and Mirlohian, RS and Haerifar, F and Bakhshi-Kashi, M and Ghaderi, A},
title = {The effect of probiotics on anxiety, depression, nicotine dependence, and metabolic biomarkers in smokers: a randomized clinical trial.},
journal = {BMC complementary medicine and therapies},
volume = {26},
number = {1},
pages = {36},
pmid = {41457283},
issn = {2662-7671},
support = {401110//Kashan University of Medical Sciences/ ; },
abstract = {BACKGROUND: Cigarette smoking (CS) has long been associated with both metabolic disturbances and psychological dysfunction. Recent evidence suggests that the gut microbiome may play a role in these processes. This study examined whether probiotic supplementation could influence metabolic markers, nicotine dependence, and symptoms of anxiety and depression in smokers.

METHODS: In this randomized, double-blind, placebo-controlled clinical trial, seventy-four adult smokers were recruited (Kashan, Iran) and randomly assigned to receive either probiotic capsules containing Lactobacillus acidophilus, Bifidobacterium longum, Bifidobacterium bifidum, and Bifidobacterium lactis (1.8 × 10⁹ CFU/day; n = 36) or a matching placebo (n = 38) for 12 weeks. Primary endpoints included changes in depressive symptoms (Beck Depression Inventory-II; BDI-II), anxiety (Beck Anxiety Inventory; BAI), and nicotine dependence (Nicotine Dependence Syndrome Scale; NDSS). Secondary endpoints included changes in metabolic, inflammatory, and oxidative stress biomarkers.

RESULTS: After 12 weeks, participants receiving probiotics showed significant reductions in fasting plasma glucose, triglycerides, very-low-density lipoprotein (VLDL) cholesterol, and C-reactive protein (CRP) compared with the placebo group (p = 0.025, p = 0.022, p = 0.026, and p = 0.004, respectively). High-density lipoprotein (HDL) cholesterol levels also increased significantly in the probiotic group (p = 0.007). No significant changes were observed in insulin, HOMA-IR, total cholesterol, LDL cholesterol, total antioxidant capacity, plasma nitric oxide, malondialdehyde, glutathione, or in scores for anxiety, depression, and nicotine dependence.

CONCLUSIONS: Twelve weeks of probiotic supplementation produced favorable effects on fasting glucose, some lipid profile, and CRP levels in smokers, though no measurable benefits were observed for anxiety and depression symptoms or nicotine dependence. These findings highlight a potential metabolic benefit of probiotics in populations exposed to cigarette smoking.

TRIAL REGISTRATION: This trial was registered at the Iranian Registry of Clinical Trials (IRCT20170420033551N13; registration date: December 6, 2022).},
}

@article {pmid41612192,
year = {2026},
author = {Li, L and Wang, H and Gao, Y and Zhang, B and Chen, Y},
title = {Integrative profiling of gut microbiome, bacteriophagenome, and predicted metabolome in obese adults: novel insights into intervention targets.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04682-1},
pmid = {41612192},
issn = {1471-2180},
support = {2023QN03043//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 2025ZD034//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; 2025TYL08//First-Tier Team of the Yingcai Xingmeng Project/ ; },
}

@article {pmid41612181,
year = {2026},
author = {Zhang, J and Deng, J and He, B and Wang, H and Lin, D and Li, J and Zhong, Q and Chen, Y and Liao, S and Wang, J and Wang, Y and Su, M and Guo, X},
title = {The study on the identification of cross-boundary microbiome enterotypes between high-altitude and coastal populations and their predictive value.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-025-04578-0},
pmid = {41612181},
issn = {1471-2180},
support = {2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; 2024B03J0562//the Science and Technology Program of Guangzhou/ ; },
}

@article {pmid41612134,
year = {2026},
author = {Bracken, AK and Malarney, KP and Chang, PV},
title = {Chemical Proteomics Reveals Regulation of Bile Salt Hydrolases via Oxidative Post-translational Modifications.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c18912},
pmid = {41612134},
issn = {1520-5126},
abstract = {The gut microbiome is the vast, diverse ecosystem of microorganisms that inhabits the human intestines and provides numerous essential functions for the host. One such key role is the metabolism of primary bile acids that are biosynthesized in the host liver into a plethora of secondary bile acids produced by gut bacteria. These metabolites serve as both antimicrobial and chemical signaling agents within the host. The critical microbial enzyme that plays a gatekeeping role in secondary bile acid metabolism is bile salt hydrolase (BSH), a cysteine hydrolase that is primarily known for its deconjugating and reconjugating activities on bile acid substrates. Despite the crucial nature of these biotransformations, regulation of BSH activity is not well understood. Here, we found that the catalytic cysteine 2 (Cys2) within the BSH active site exists in multiple sulfur oxidation states including sulfenic acid (Cys-SOH). Importantly, we show this reversible oxidative post-translational modification (oxPTM) ablates BSH catalytic activity. We have leveraged this discovery to develop a chemoproteomic platform featuring a sulfenic acid-reactive bile acid probe to profile BSH Cys2 oxPTMs throughout the gut microbiome. Our results reveal that though most gut microbiota-associated BSHs exist in the active Cys2-SH state, some are preferentially and reversibly inactivated in the Cys2-SOH state. This reversible oxidation of Cys2 may serve as a general mechanism to regulate BSH activity in vivo in response to a changing physiological environment.},
}

@article {pmid41612130,
year = {2026},
author = {Dimmers, F and Reichert, D and Wigmann, C and Trullàs, C and Piquero-Casals, J and Brown, A and Foyaca, M and Esser, C and Krutmann, J},
title = {Effects of solar-simulated (UVB plus UVA) radiation on the skin microbiome: An exploratory study.},
journal = {Photochemistry and photobiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/php.70078},
pmid = {41612130},
issn = {1751-1097},
support = {//ISDIN, Barcelona, Spain/ ; },
abstract = {This exploratory in vivo study investigated the impact of solar-simulated ultraviolet (UV) radiation (UVB plus UVA) on the composition of the human skin microbiome in healthy male volunteers. Thirty Caucasian men were exposed to suberythemal and erythemal doses of UV radiation (0.5, 0.7, and 1.0 minimal erythema dose, MED) on defined areas of the lower back. Skin swabs were collected from both irradiated (n = 243) and nonirradiated control sites (n = 81) 30 min, 24 h, and 96 h postexposure. The microbial profiles were generated using flow cytometry, and the data were analyzed via the open-access bioinformatic platform FlowSoFine™. The results revealed pronounced alterations in the microbial composition, with changes already detectable 30 min after exposure. Although partial recovery was observed over time, certain microbial shifts persisted. Further analysis indicated dose-dependent trends in microbiome changes, suggesting a potential relationship between the extent of microbial alteration and the applied UV dose. These results suggest that even low, nonerythematous exposure to solar-simulated UV radiation can rapidly alter the microbial balance of the skin and emphasize the role of UV radiation as a potent modulator of the skin microbial homeostasis.},
}

@article {pmid41612069,
year = {2026},
author = {Sun, G and Cheng, H and Yin, M},
title = {Oral hygiene and cancer risk: emerging evidence and public health perspectives.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-026-04527-x},
pmid = {41612069},
issn = {2730-6011},
support = {22JR5RA916//the Gansu Province Natural Science Foundation Project/ ; ldyyyn2020-46//the In-House Fund of Lanzhou University First Hospital/ ; 2020-ZD-92//the Science and Technology Development Plan Project of Lanzhou City/ ; CYXZ2023-06//the Scientific Research Cultivation Program for Cuiying Scholars, Second Hospital of Lanzhou University/ ; },
}

@article {pmid41611923,
year = {2026},
author = {Costa-Santos, M and Sario, S and Mendes, RJ and Santos, C},
title = {Seasonal dynamics and core stability of the bacterial microbiome of a Drosophila suzukii wild population.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-37656-y},
pmid = {41611923},
issn = {2045-2322},
support = {2021.06319.BD//Fundação para a Ciência e a Tecnologia/ ; PTDC/ASP-PLA/4477/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/ASP-PLA/4477/2020//Fundação para a Ciência e a Tecnologia/ ; PTDC/ASP-PLA/4477/2020//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {Drosophila suzukii (spotted-wing drosophila, SWD) is an invasive pest with pronounced sexual dimorphism and seasonal polyphenism. While seasonal morphotypes are well documented, how these phenotypic traits shape the SWD microbiome remains poorly understood. Here, we investigate how sex and seasonal phenotypes shape microbiome composition in SWD. We hypothesize that these factors drive microbial shifts, with some taxa varying between phenotypes and others forming a stable core. Understanding these patterns may reveal microbiome-associated adaptations relevant to SWD ecology and management. To investigate this, we monitored SWD microbiome dynamics over one year by collecting individuals during spring, summer, and autumn of 2022 and winter of 2023 from an organic farm in northern Portugal. Bacterial communities were compared using 16 S rRNA amplicon sequencing. This SWD population retained a core bacterial community, highly represented by Gluconobacter, Pseudomonas, Commensalibacter and Pantoea, consistent with other SWD Portuguese populations. Moreover, microbiome composition varied significantly across seasons but not between sexes, although females exhibited higher microbial alpha diversity. Linear discriminant analysis of relative abundance (LEfSe) revealed enrichment of Morganella, Methanosaeta, Serratia, Duganella, Frateuria, Suttonella, and Janthinobacterium in winter groups. However, functional prediction analyses revealed no significant differences in microbiome functional potential across seasons, suggesting functional redundancy despite taxonomic variation. This study offers baseline insights into the seasonal stability and plasticity of the D. suzukii microbiome, contributing to a deeper ecological understanding of this invasive pest.},
}

@article {pmid41611306,
year = {2026},
author = {Shen, Y and Solís-Lemus, C},
title = {Bayesian chain graph models to characterize microbe-environment dynamics.},
journal = {Mathematical biosciences and engineering : MBE},
volume = {23},
number = {2},
pages = {499-546},
doi = {10.3934/mbe.2026020},
pmid = {41611306},
issn = {1551-0018},
mesh = {Bayes Theorem ; Algorithms ; Computer Simulation ; *Microbiota ; Linear Models ; Humans ; Computational Biology ; Gastrointestinal Microbiome ; Models, Biological ; Models, Statistical ; },
abstract = {Microbiome data require statistical models that can simultaneously decode microbes' reaction to the environment and interactions among microbes. While a multiresponse linear regression model seems like a straight-forward solution, we argue that treating it as a graphical model is problematic given that the regression coefficient matrix does not encode the conditional dependence structure between response and predictor nodes. This observation is especially important in biological settings when we have prior knowledge on the edges from specific experimental interventions that can only be properly encoded under a conditional dependence model. Here, we propose a chain graph model with two sets of nodes (predictors and responses) whose solution yields a graph with edges that indeed represent conditional dependence, thus agreeing with the experimenter's intuition on the average behavior of nodes under treatment. The solution to our model is sparse via the Bayesian linear regression (LASSO). In addition, we propose an adaptive extension so that different shrinkages can be applied to different edges to incorporate edge-specific prior knowledge. Our model is computationally inexpensive through an efficient Gibbs sampling algorithm and can account for binary, counting, and compositional responses via an appropriate hierarchical structure. We test the performance of our model in a variety of simulated datasets, thereby showing superior performance to state-of-the-art approaches. We further apply our model to human gut and soil microbial compositional datasets, and we highlight that CG-LASSO can estimate biologically meaningful network structures in the data. Our software is available as an R package at https://github.com/YunyiShen/CAR-LASSO.},
}

Bayes Theorem
Algorithms
Computer Simulation
*Microbiota
Linear Models
Humans
Computational Biology
Gastrointestinal Microbiome
Models, Biological
Models, Statistical

@article {pmid41611115,
year = {2026},
author = {Kuribayashi, S and Naik, N and Miller, AW and Lundy, SD},
title = {Micro-Management: How the Male Reproductive Microbiome Shapes Male Fertility.},
journal = {Fertility and sterility},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.fertnstert.2026.01.019},
pmid = {41611115},
issn = {1556-5653},
abstract = {IMPORTANCE: One in six couples worldwide experience infertility, and male factors contribute to at least half of these cases. The pathophysiology of male infertility is complex and often multifactorial, and the male reproductive microbiome has now been implicated as a potentially critical component in male reproductive health and disease.

OBJECTIVE: To summarize the emerging evidence describing the male reproductive microbiome with a focus on clinically relevant aspects within spermatogenesis and reproductive outcomes.

EVIDENCE REVIEW: We performed a librarian-led search of MEDLINE, Embase, and Web of Science and a targeted PubMed search for antibiotic and probiotic trials, focusing on human studies that reported male reproductive microbiome data together with semen parameters, oxidative, DNA-damage, or inflammatory indices, or assisted reproduction outcomes. Given heterogeneity in design and laboratory methods, we conducted a narrative synthesis and integrated relevant mechanistic animal work.

FINDINGS: Across heterogeneous cohorts, anaerobe-leaning seminal profiles (often with Prevotella or Atopobium) are more often linked to higher oxidative stress, greater sperm DNA fragmentation, and lower motility or total motile count. In contrast, Lactobacillus-rich profiles more often align with better redox status and DNA integrity. Couple-level data show rapid and robust partner microbiome exchange that can shift semen over short periods. Work on the gut-testis axis has identified a link between gut dysbiosis and systemic inflammation with semen quality via the gut-testis axis. Proposed mechanisms underlying the effect of the microbiome on fertility include local inflammation, oxidative injury, altered seminal rheology (e.g., viscosity/viscoelastic properties of seminal plasma), adherence/biofilms, and immune-metabolic crosstalk. Small trials to date using antibiotics and/or probiotics show variable benefits; durability and reproductive endpoints remain limited.

CONCLUSION AND RELEVANCE: Emerging evidence supports a role for the male reproductive microbiome in sperm function and fertility and highlights it as a potential target for clinical intervention. However, predominantly small, cross-sectional studies and methodological heterogeneity limit causal inference and immediate translation, underscoring the need for longitudinal, couple-integrated cohorts and adequately powered randomized trials of targeted microbiome modulation.},
}

@article {pmid41611114,
year = {2026},
author = {Young, RB and Correia, GDS and MacIntyre, DA},
title = {Host, microbial and environmental drivers of vaginal microbiota composition.},
journal = {Fertility and sterility},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.fertnstert.2026.01.020},
pmid = {41611114},
issn = {1556-5653},
abstract = {The human vagina harbours a microbial community that differs markedly in compositional structure from all mammals, including closely related primates. Lactobacilli are the most abundant vaginal species, and their dominance in this niche are associated with protection against adverse health outcomes including preterm birth, sexually transmitted infections and bacterial vaginosis. However, the vaginal environment can also support compositions of diverse anaerobic bacteria, which have been linked to poor reproductive health outcomes. Here, we review current knowledge on host and microbial determinants that influence microbial community structure within the vaginal niche, emphasising the interplay between host physiology, immune and metabolic interactions as well as lifestyle factors. This integrated understanding provides a foundation for linking vaginal microbiome compositions to clinically relevant phenotypes and highlights mechanisms that could be exploited to promote improved reproductive health.},
}

@article {pmid41611056,
year = {2026},
author = {Saeed, Q and Lu, X and Farooqi, ZUR and Ghafoor, A and Naveed, M and Maqsood, N and Kareem, HA and Mustafa, A},
title = {Root Traits and Rhizosphere Responses as Emerging Bioindicators of Microplastic Pollution in Agricultural Soils: A review.},
journal = {Environmental research},
volume = {},
number = {},
pages = {123866},
doi = {10.1016/j.envres.2026.123866},
pmid = {41611056},
issn = {1096-0953},
abstract = {In agricultural soils, crop roots are central to regulating soil health, nutrient cycling, and long-term carbon sequestration through rhizosphere-driven processes such as root exudation, microbial modulation, and litter decomposition. However, the increasing prevalence of microplastics (MPs) in farmlands arising from mulching films, sewage sludge, composts, and atmospheric deposition is increasingly recognized as a pervasive threat to root-soil-microbe interactions. This review focused on how crop root traits (architecture, chemistry, turnover) are influenced by MPs and explores their cascading impacts on rhizosphere functionality, with a specific focus on their potential as emerging bioindicators of MPs pollution in agricultural soils. MPs disrupt root morphology, alter microbial communities, reduce carbon inputs as exudates, and interfere with organo-mineral associations, and reshape rhizosphere responses that govern soil aggregation, nutrient availability, and microbial carbon stabilization. These responses vary across crop functional types, including grasses, legumes, vegetables, and fodder crops, reflecting differences in root architecture, turnover, and rhizosphere regulation. Collectively, these trait-based responses provide integrative and sensitive indicators of MPs stress in agroecosystems. We highlight future research strategies emphasizing rhizosphere engineering such as microbiome manipulation, exudation modulation, breeding for resilient root traits, and multi-indicator integration, to mitigate MPs stress and enhance overall ecosystem resilience. Collectively, this review underscores the potential of root-based bioindicators and rhizosphere responses as robust tools for monitoring MPs pollution and supporting sustainable soil management in plastic-impacted agroecosystems.},
}

@article {pmid41610908,
year = {2026},
author = {Barash, JR and Sambol, SP and Skinner, AM and Johnson, S and Gerding, DN},
title = {Clostridioides difficile colonization of Twin Patients Recovering From Infant Botulism.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103022},
doi = {10.1016/j.anaerobe.2026.103022},
pmid = {41610908},
issn = {1095-8274},
abstract = {OBJECTIVES: The prevalence of Clostridioides difficile co-colonization of 107 California patients with suspect infant botulism (IB) was studied over a two-year period. One set of twins with lab-confirmed IB and C. difficile co-colonization was followed longitudinally and their isolated C. difficile was typed by restriction endonuclease analysis (REA).

METHODS: Stool specimens sent to California Department of Public Health for routine IB diagnostic testing were cultured for C. botulinum and C. difficile. After diagnostic testing identified twin IB patients, their stools collected at weekly and monthly intervals were cultured to determine duration of C. botulinum and C. difficile co-colonization until three consecutive specimens were culture negative for each organism.

RESULTS: Twins X and Y were colonized by C. botulinum for a duration of nearly three and four months, followed by C. difficile for eight and seven months, respectively. Continuous colonization by C. difficile was identified in each twin as C. botulinum colonization was waning. They sequentially shared four identical REA types, three toxigenic and one non-toxigenic, including epidemic strain type J9. Neither twin developed C. difficile illness and colonization ceased spontaneously in each.

CONCLUSIONS: C. difficile co-colonization of laboratory-confirmed IB patients is infrequently encountered. IB in both twins was followed by asymptomatic C. difficile colonization. Risk factors for their respective co-colonization remain unknown, including if previous illness with IB was a potential contributing factor. Although the environmental source of the colonizing strains was not determined, this study highlights the ability of C. difficile to spread to close contacts and persist in the infant intestinal microbiome.},
}

@article {pmid41610853,
year = {2026},
author = {Weiler, BA and Kron, N and Bonacolta, AM and Vermeij, MJA and Baker, AC and Del Campo, J},
title = {Temporal transcriptional rhythms govern coral-symbiont function and microbiome dynamics.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.01.004},
pmid = {41610853},
issn = {1934-6069},
abstract = {Diel rhythms align physiological processes with light/dark cycles, driving predictable oscillations in gene expression and protein activity through tightly controlled transcriptional-translational feedback loops. This study presents in situ transcriptomic analyses of the stony coral Pseudodiploria strigosa and its photosymbionts, Breviolum sp., at key daily time points. P. strigosa shows precise transcriptional control: dawn triggers a molecular reset marked by RNA metabolism and protein turnover; midday emphasizes anabolic and phosphate-regulated pathways; dusk reflects transitional lipid and amino acid metabolism; and midnight reveals stress responses, mRNA catabolism, and mitochondrial organization. Photosymbionts display subtler diel patterns, with photoprotection at dawn, metabolite transport and nitrogen cycling through midday/dusk, and cell cycle and ion homeostasis at night. Microbial communities show time-dependent restructuring of co-occurrence networks, driving diel-related functional consequences like changes in microbial metabolism. These findings present a system-level molecular framework of diel regulation across the coral-photosymbiont-microbe holobiont, revealing time-specific transcriptional control of coordinated function and homeostasis.},
}

@article {pmid41610813,
year = {2026},
author = {Ramos-Madrigal, J},
title = {The potential of plant palaeogenomic research.},
journal = {Current opinion in plant biology},
volume = {90},
number = {},
pages = {102856},
doi = {10.1016/j.pbi.2025.102856},
pmid = {41610813},
issn = {1879-0356},
abstract = {Plant palaeogenomics has transformed the way we study plant evolution. After a slow start, the last decade has seen a shift from the study of a few genomic markers to genome-wide data and complete genomes across multiple species. These studies have changed fundamental ideas about plant domestication and evolution. The field still has great potential to unlock. Emerging approaches promise to recover genomic information from both plants and their associated microbes from macrobotanical remains, providing a new perspective to study deep-time plant-microbiome coevolution. Environmental DNA preserved in ancient sediments may soon yield complete plant genomes, expanding our ability to study population dynamics well before the rise of agriculture. Ancient genomes also provide a reservoir of lost genetic diversity that we could exploit to improve crop resilience and adaptation.},
}

@article {pmid41610734,
year = {2026},
author = {Widyarman, AS and Bur, R and Udawatte, NS and Agaristi, PM and Razari, I and Bahri, S and Richi, M and Astoeti, TE and Seneviratne, CJ},
title = {Mouthrinses differentially rewire salivary virus-microbiome interaction dynamics in COVID-19 patients: A randomized controlled trial.},
journal = {Archives of oral biology},
volume = {184},
number = {},
pages = {106524},
doi = {10.1016/j.archoralbio.2026.106524},
pmid = {41610734},
issn = {1879-1506},
abstract = {OBJECTIVE: In this randomized clinical trial (RCT) we evaluated the efficacy of mouthrinses containing sodium chlorite (NaClO2), povidone iodine (PVP-I), cetylpyridinium chloride (CPC) compared to sterile water control in modulating salivary SARS-CoV-2 viral load and the oral microbiome in COVID-19 patients.

METHODS: Forty PCR-confirmed COVID-19 patients were randomly allocated to four groups (n = 10 each) and rinsed with 10 ml of their assigned solution for 30 s. Saliva was collected pre-rinse and at 5-min, 3-hour, and 6-hour post-rinse. Viral load was quantified via RT-qPCR targeting N and ORF1ab genes, and oral microbiome was analyzed using 16S rRNA sequencing.

RESULTS: CPC reduced viral load by 1.5-fold (P = 0.12), PVP-I by 1.2-fold (P = 0.18), and NaClO2 by 1.1-fold (P = 0.34) at 6-hour, though not statistically significant. Overall oral microbiome diversity and composition remained stable (P = 0.67), although CPC and PVP-I significantly altered specific taxa such as Leptotrichia sp. and Lautropia mirabilis. Moreover, CPC and PVP-I disrupted the salivary microbiome network with SARS-CoV-2 genes, namely N and ORF1ab genes.

CONCLUSION: This study to provide new insight into the modulation dynamics of mouthrinses on salivary SARS CoV-2 and oral microbiome, suggesting that CPC and PVP-I may provide potential health benefits by reducing viral load and modulating microbiome-virus networks.},
}

@article {pmid41610732,
year = {2026},
author = {Chen, S and Li, H and Ning, M and Yu, BYM and Wu, S and Cheng, WY and Li, Y and Yeung, WF},
title = {The association between gut microbiota and insomnia: A systematic review and meta-analysis.},
journal = {Sleep medicine reviews},
volume = {86},
number = {},
pages = {102236},
doi = {10.1016/j.smrv.2026.102236},
pmid = {41610732},
issn = {1532-2955},
abstract = {Emerging evidence suggests interactions between gut microbiota and sleep regulation, but specific associations with insomnia remain unclear. This systematic review evaluated alterations in gut microbiota in patients with insomnia compared with healthy controls. A systematic literature search was performed on eight databases from inception to June 2025. Case-control, cohort, and cross-sectional studies examining gut microbiota in adults with insomnia versus healthy controls were included. Fourteen studies encompassing 9036 participants (58.4 % female) were included. Alpha diversity was reduced in patients with insomnia in most of the included studies, among which observed species significantly decreased (SMD: 0.90, 95 % CI: 1.39, -0.40, k = 5). Beta diversity analysis revealed a consistently distinct microbial community structure between individuals with insomnia and healthy controls. Taxonomically, insomnia correlated with shifted Firmicutes-to-Bacteroidetes ratios. Meta-analyses revealed alterations in key genera, including significantly decreased Faecalibacterium and Lachnospira, and significantly increased Blautia and Eubacterium hallii. Changes in gut microbiota were also correlated with inflammatory markers and metabolic disturbances. In summary, gut microbiota dysbiosis was associated with insomnia and characterized by reduced microbial diversity and altered bacterial composition. These findings suggest potential applications for microbial biomarkers in insomnia diagnosis and subtyping, and the development of personalized microbiota-targeted interventions.},
}

@article {pmid41610646,
year = {2026},
author = {Kumar, S and Srivastava, S and Tan, CS and Abohashrh, M and Malviya, R},
title = {Correlation between oral disease and neurodegenerative disorders: Role of biological proteins for the modulation of oral-brain axis and gut-brain axis.},
journal = {Colloids and surfaces. B, Biointerfaces},
volume = {262},
number = {},
pages = {115480},
doi = {10.1016/j.colsurfb.2026.115480},
pmid = {41610646},
issn = {1873-4367},
abstract = {Biological proteins play a crucial role at the intersection of oral health and neuroscience, offering promising opportunities for improved diagnosis, prevention, and treatment. This review highlights the molecular, inflammatory, and biochemical pathways linking oral diseases, particularly periodontal disease and microbial dysbiosis, with neurodegenerative disorders such as Alzheimer's and Parkinson's disease. Key inflammatory, neuroprotective, and tissue-repair proteins play a crucial role in maintaining both oral integrity and neural function. Advances in proteomics and molecular imaging have clarified how protein misfolding, aggregation, and immune responses drive neuroinflammation and cognitive decline. Emerging therapies include protein-based biomaterials, such as hydrogels, nanocarriers, and protein-polymer hybrids, for delivering neuroprotective and regenerative agents through oral and nasal routes. Early diagnosis is being transformed by salivary proteomics and transcriptomics, enabling non-invasive detection of neurodegenerative biomarkers. Host-defense peptides and antimicrobial proteins also show promise in controlling oral infections that may exacerbate brain inflammation. Integrating oral biology, biomaterials science, and neuroscience is accelerating clinical translation through the development of innovative scaffolds and smart delivery systems. Despite challenges in biomarker validation and clinical application, advances in artificial intelligence, bioinformatics, and protein engineering are driving the future of personalized regenerative and preventive medicine. Overall, biological proteins provide a critical molecular link between oral and neural health, paving the way for novel non-invasive diagnostic and therapeutic strategies.},
}

@article {pmid41610568,
year = {2026},
author = {Yousaf, MW and Nadeem, AH and Nadeem, MF and Qaisar, R},
title = {The role of artificial intelligence in sarcopenia: Advances, applications, and future directions.},
journal = {Computational biology and chemistry},
volume = {122},
number = {},
pages = {108930},
doi = {10.1016/j.compbiolchem.2026.108930},
pmid = {41610568},
issn = {1476-928X},
abstract = {Sarcopenia, the gradual loss of skeletal muscle mass, strength, and function, is a growing concern in aging populations. Early detection is vital to reduce the risk of frailty, disability, and mortality, yet traditional diagnostic methods such as imaging and physical performance tests are often costly, inconsistent, or difficult to implement in routine care. Artificial intelligence (AI), including machine learning (ML) and deep learning (DL), is emerging as a powerful tool in sarcopenia research and clinical practice. This review explores how AI is being applied to early detection, imaging-based diagnosis, prediction of functional outcomes, and personalized monitoring. Models trained on large datasets, such as NHANES, have demonstrated strong predictive performance using standard clinical variables. DL has enabled automated analysis of CT scans for muscle segmentation, reducing the need for manual interpretation. At the same time, ML systems integrated with wearable devices allow real-time tracking of physical function. Emerging approaches such as explainable AI, federated learning, and the integration of diverse data sources, including omics and microbiome profiles, are expanding opportunities for individualized care. Despite these advances, significant challenges remain, including variability in data quality, limited model transparency, algorithmic bias, and ethical concerns. Regulatory oversight and clinician engagement will be key to successful implementation. AI offers a promising path toward proactive, scalable, and personalized management of sarcopenia.},
}

@article {pmid41610179,
year = {2026},
author = {Singh, D and Liu, J and Luo, J and Huang, L and Huang, QS and Yang, L and Zhou, Z},
title = {Sugar-sweetened orange beverages: A silent risk factor for colorectal cancer?.},
journal = {Nutrition and health},
volume = {},
number = {},
pages = {2601060251383198},
doi = {10.1177/02601060251383198},
pmid = {41610179},
issn = {2047-945X},
abstract = {BackgroundEriodictyol is a flavonoid primarily found in citrus fruits for dietary consumption. Laboratory studies have shown that it has antioxidant and anti-inflammatory properties, which help prevent colorectal cancer (CRC). However, consuming eriodictyol through citrus drinks and added sugars may increase the risk of CRC. These beverages can raise blood sugar levels and disrupt the gut microbiome, potentially increasing the risk of CRC.AimThis study aims to evaluate the relationship between dietary intake of eriodictyol flavonoid, commonly consumed through citrus drinks or sugar-sweetened orange beverages, and the increased risk of CRC, as well as its connection with diabetic patients.MethodsData from 53,914 participants in the Prostate, Lung, Colorectal, and Ovarian Cancer Screening Trial were analyzed using Dietary Questionnaire (DQX) and Dietary History Questionnaire (DHQ). LASSO regression identified significant associations, while restricted cubic spline analysis examined nonlinear relationships between eriodictyol intake and CRC risk.ResultsDiabetes was confirmed as a significant risk factor for CRC in both the DHQ and DQX cohorts. Additionally, higher eriodictyol intake was associated with increased CRC risk in the DQX group, suggesting a possible link between diabetes, elevated eriodictyol consumption, and CRC development. The primary source of dietary eriodictyol in the USA is sugar-sweetened beverages.ConclusionsThe findings show that hyperglycemic patients have a notably higher risk of CRC, and this increased risk remains even with dietary intake of eriodictyol, a flavonoid commonly found in citrus fruits and increasingly consumed through citrus beverages in industrialized countries.},
}

@article {pmid41609982,
year = {2026},
author = {Rustamova, N and Wali, A and Litao, N and Movlanov, J and Davranov, K and Yili, A},
title = {Characterization and biological activities of endophytic bacteria from Vernonia anthelmintica flowers.},
journal = {Folia microbiologica},
volume = {},
number = {},
pages = {},
pmid = {41609982},
issn = {1874-9356},
support = {2019-FPGGRC-004 and 2019-FPGGRC-005//West Light Foundation of the Chinese Academy of Sciences Grant/ ; },
abstract = {Endophytic bacteria associated with medicinal plants are a vital component of the plant microbiome and represent a valuable biological resource. This study investigates the diversity and biological activities of endophytic bacteria isolated from the flowers of Vernonia anthelmintica, a medicinal plant native to China. The research focuses on evaluating the cytotoxic, antimicrobial, antioxidant, and antidiabetic properties of natural products derived from these bacteria, as well as their effects on melanin synthesis and tyrosinase activity in B16 cells. A total of 32 bacterial strains were isolated and cultured, of which eight crude extracts exhibiting antimicrobial activity were selected for further analysis. These isolates. belong to four genera: Bacillus, Streptococcus, Priestia and Paenibacillus. Among them, Priestia megaterium XJB-41 demonstrated the most substantial pharmacological potential, warranting further investigation to optimize its culture conditions for enhanced bioactive compound production. The optimal growth conditions for P. megaterium XJB-41 were determined to be LB and Nutrient Broth (NB) media, with peptone as the carbon source and yeast extract as the nitrogen source, under 24 h of incubation. These conditions significantly enhanced both bacterial growth and metabolite yield. Moreover, two secondary metabolites: cyclo(D-leu-L-pro) [1] and 2-benzoxazolone [2] were isolated for the first time from the ethyl acetate fraction of P. megaterium XJB-41. This strain shows promise for further investigation as a potential source of therapeutic agents.},
}

@article {pmid41609895,
year = {2026},
author = {Moreiras-Arias, N and Nieto-Fontarigo, JJ and Salgado, FJ and González-Vilas, D and Paredes-Suárez, C and Combo-García, E and Rodríguez-Otero, C and Flórez, Á},
title = {Novel Therapeutic Strategies for Atopic Dermatitis: Biomarker Modulation and Clinical Implications. A Systematic Review.},
journal = {Clinical reviews in allergy & immunology},
volume = {69},
number = {1},
pages = {4},
pmid = {41609895},
issn = {1559-0267},
mesh = {Animals ; Humans ; *Biomarkers/metabolism ; Chemokine CCL17/metabolism ; *Dermatitis, Atopic/diagnosis/drug therapy/therapy/metabolism/etiology/immunology ; Janus Kinase Inhibitors/therapeutic use ; },
abstract = {Advances in the understanding of atopic dermatitis (AD) pathogenesis have driven the development of innovative systemic therapies targeting key immunologic pathways. This systematic review summarizes current evidence on the impact of biologic agents, Janus kinase (JAK) inhibitors, and other emerging treatments on AD-related biomarkers and their correlation with clinical outcomes. A comprehensive literature search was conducted across PubMed, Embase, Scopus, and Web of Science for studies published between 2014 and 2024. Eighty studies met the inclusion criteria. Dupilumab was the most extensively investigated therapy, followed by tralokinumab, JAK inhibitors, and novel agents such as amlitelimab, stapokibart, and tezepelumab. Across drug classes, consistent reductions in CCL17/TARC, LDH, and total IgE levels were observed, generally paralleling clinical improvement in EASI and SCORAD scores. Transcriptomic and proteomic analyses revealed normalization of Th2/Th22 inflammatory signatures and restoration of barrier-related gene expression, while microbiome studies showed a reduction in Staphylococcus aureus colonization. Despite these advances, the heterogeneity of study designs and analytical techniques limits the comparability of results. CCL17 and LDH currently represent the most reliable biomarkers associated with disease severity and treatment response, although their limited specificity restricts clinical applicability. Future research should aim to validate integrated biomarker panels combining immunologic, transcriptomic, and microbiomic data to enable precision medicine approaches in atopic dermatitis management.},
}

Animals
Humans
*Biomarkers/metabolism
Chemokine CCL17/metabolism
*Dermatitis, Atopic/diagnosis/drug therapy/therapy/metabolism/etiology/immunology
Janus Kinase Inhibitors/therapeutic use

@article {pmid41609714,
year = {2026},
author = {Koch, BL and Singla-Rastogi, M and Innes, RW},
title = {Extracellular Vesicles and Extracellular RNAs in Plant-Microbe Interactions.},
journal = {Annual review of plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-arplant-063025-110704},
pmid = {41609714},
issn = {1545-2123},
abstract = {Plants and microbes exchange macromolecules such as RNA and proteins. How this exchange is accomplished is poorly understood, but extracellular vesicles (EVs) have been proposed as likely vehicles. Here, we review recent work on the biogenesis and functions of plant EVs and the current evidence in support of and against their role in cross-kingdom RNA interference. Plant EVs, like EVs from other kingdoms of life, are released in part by the fusion of multivesicular bodies with the plasma membrane, a complex and conserved mechanism involving lipid-modifying proteins, the exocyst complex, and Rab GTPases. Though some plant EV subpopulations are involved in immunity, it appears unlikely that plant EVs contribute to cross-kingdom RNA interference. Recent work has shown that plants secrete extravesicular RNA, including small RNAs and long noncoding RNAs, into the leaf apoplast and onto leaf surfaces, while very little RNA is found inside of EVs. We propose that these free extracellular RNAs play a central role in maintaining a healthy leaf microbiome.},
}

@article {pmid41609616,
year = {2026},
author = {Han, SH and He, MT and Baek, KW and Kim, HY and Lee, S and Lee, AY},
title = {Protective Effect of Luteolin Isolated from Taraxacum coreanum Against Neuroinflammatory Responses Induced by Lipopolysaccharide: Involvement of Gut-Brain Axis.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c12437},
pmid = {41609616},
issn = {1520-5118},
abstract = {Neuroinflammation can be brought on by intestinal inflammatory agents and metabolites generated by the gut microbiota that can pass across the blood-brain barrier. Taraxacum coreanum is rich in the bioactive compound luteolin (LT), a molecule known for its potent antioxidant and anti-inflammatory activities. The current research investigated whether LT prevents inflammatory responses and barrier dysfunction in the brain and gut of lipopolysaccharide (LPS)-injected mice. LT (10 and 20 mg/kg/day) effectively lowered the brain levels of pro-inflammatory mediators and cytokines triggered by LPS stimulation. Moreover, occludin and ZO-1 are two tight junction proteins whose expression was markedly elevated by LT. In the intestine, LT not only attenuated the levels of inflammatory mediators but also markedly upregulated tight junction protein expression relative to the LPS-treated group. LT markedly reversed LPS-induced dysbiosis by increasing beneficial taxa such as Bacteroidota, Actinobacteriota, Murivaculaceae, and Lactobacillus. In addition, LT reduced the relative abundance of Firmicutes and Desulfovibrio. Collectively, LT from Taraxacum coreanum may attenuate neuroinflammation and maintain blood-brain barrier integrity by suppressing inflammatory responses, protecting the gut barrier, and modulating the gut microbiome.},
}

@article {pmid41609448,
year = {2026},
author = {Koçak, Ö and Sharafi, P and Gökdemir, Ş and Görkem, Ü and Al-Kaleel, A and Taylan Özkan, A},
title = {[Changes in Gut Microbiome Profile in Pregnant Women with Hyperemesis Gravidarum: A Comparative Study Based on 16S rRNA Sequencing].},
journal = {Mikrobiyoloji bulteni},
volume = {60},
number = {1},
pages = {53-71},
doi = {10.5578/mb.2026018},
pmid = {41609448},
issn = {0374-9096},
mesh = {Humans ; Female ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome/genetics ; *Hyperemesis Gravidarum/microbiology ; Adult ; Feces/microbiology ; Case-Control Studies ; *Bacteria/classification/genetics/isolation & purification ; DNA, Bacterial/chemistry/genetics ; },
abstract = {Hyperemesis gravidarum (HEG) is a pregnancy complication characterized by severe nausea, vomiting more than four times a day and dehydration, especially occurring in the first trimester of pregnancy. In recent years it has been shown that the intestinal bacterial microbiome profile may be associated with a wide range of diseases. The aim of this study was to determine whether the intestinal bacterial microbiome profiles differ between pregnant women diagnosed with hyperemesis gravidarum (HEG) and those with healthy pregnancies. Fresh stool samples were collected from 15 pregnant women diagnosed with HEG and 14 healthy pregnant women who did not have any complaints in the first trimester. After DNA isolation from the samples, 16S rRNA gene-based microbial profiling was performed with next-generation sequencing. The 16S rRNA V3-V4 region was sequenced with paired-end reads (2×250 base pair) on the Illumina MiSeq platform. The average sequence number for each sample was similar (HEG= ~2.54 million, control= ~1.48 million; p> 0.05). After quality filtering, reads obtained from all samples were analyzed by rarefaction at equal depth. Alpha diversity measures were found to be significantly higher in the HEG group compared to the control group (Shannon, ACE, and Chao1 indices; p< 0.05 for all). In the beta diversity analysis, it was observed that the gut microbiome compositions of the two groups were separated; In the Principal Coordinates Analysis plot, the groups were clearly clustered and the group difference was found to be statistically significant by PERMANOVA test (p< 0.01). Significant differences were also found in the comparisons at the taxonomic level. At the class level, the relative abundance of Clostridia was significantly higher in the HEG group (p< 0.05), while the class Bacilli was dominant in the control group (p< 0.05). At the family level, the abundances of Lachnospiraceae and Prevotellaceae were found to be significantly higher in the HEG group than in the control group (p< 0.05). In contrast, at the family level, the rates of Enterobacteriaceae and at the genus level, the rates of Escherichia-Shigella were found to be significantly higher in the control group (p< 0.05). Some bacterial taxa detected only in the HEG group samples were also noteworthy: Collinsella, Blautia, and Dialister genera, which are only found in the intestines of patients with HEG, were not detected in the control group. In conclusion, these findings reveal that there are significant differences between the intestinal microbiome profiles of pregnant women with HEG and healthy pregnant women. The high microbial diversity observed in the HEG group and changes in certain bacterial groups suggest that processes related to lipid and carbohydrate metabolism may play a role in the pathogenesis of HEG. In the future, the clinical significance and possible therapeutic targets of these differences can be evaluated with more comprehensive studies aiming at clarifying causality.},
}

Humans
Female
Pregnancy
RNA, Ribosomal, 16S/genetics
*Gastrointestinal Microbiome/genetics
*Hyperemesis Gravidarum/microbiology
Adult
Feces/microbiology
Case-Control Studies
*Bacteria/classification/genetics/isolation & purification
DNA, Bacterial/chemistry/genetics

@article {pmid41609372,
year = {2026},
author = {Motta, EVS and Seong, J and Dickey, M and Ellis, JT and Rangel, J},
title = {Divergent microbiome signatures between managed and wild honey bee (Apis mellifera) populations in South Texas.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0339425},
doi = {10.1128/spectrum.03394-25},
pmid = {41609372},
issn = {2165-0497},
abstract = {UNLABELLED: Animal microbiomes are shaped by a complex interplay of host genetics, environment, and lifestyle. Transitions of animals from wild to managed or domesticated conditions can impact the structure and function of their microbiomes. Among insects, the Western honey bee (Apis mellifera) is a promising model for studying these dynamics, given its long history of domestication and importance in agriculture. Despite extensive research on managed honey bee microbiomes, direct comparisons with wild populations remain scarce. Here, we compared the gut microbiomes of wild honey bee colonies from the Welder Wildlife Refuge in South Texas, which have remained unmanaged for over 30 years, with those from the closest managed apiary, located approximately 40 miles away. Using quantitative PCR and 16S ribosomal RNA gene sequencing, we found that managed bees harbored significantly higher bacterial loads but lower microbial diversity than wild bees. Although both groups shared a conserved microbiome dominated by core bacterial genera, distinct amplicon sequence variants and predicted metabolic pathway profiles differentiated them. Managed bee microbiomes were enriched in amino acid interconversion and antibiotic resistance-associated pathways, whereas wild bee microbiomes exhibited broader metabolic versatility, including amino acid biosynthesis and aromatic compound degradation. PCR screening further revealed a higher prevalence of tetracycline resistance markers in managed bees. Together, these findings indicate that long-term absence of human management and distinct ecological pressures shape honey bee gut microbiomes, influencing community composition and potentially functional capacity, underscoring the importance of natural environments to maintain microbial diversity and resilience.

IMPORTANCE: Understanding how human management shapes the microbiomes of domesticated species is essential for predicting their resilience to environmental stressors. Honey bees (Apis mellifera) are critical pollinators whose health and productivity are closely tied to their gut microbiota, but nearly all microbiome studies have focused on managed colonies. This study leverages the Welder Wildlife Refuge in South Texas, one of the few documented and well-studied sites in the United States where honey bee colonies have persisted unmanaged for decades, to directly compare managed and wild populations. We show that managed bees harbor higher bacterial loads but reduced microbial diversity and greater antibiotic resistance potential. These findings demonstrate that long-term absence of human intervention can preserve microbial diversity, offering insights into how domestication, antibiotic exposure, and environmental simplification influence the evolution and ecology of host-associated microbiomes.},
}

@article {pmid41609371,
year = {2026},
author = {Panattoni, A and De Boeck, I and Wittouck, S and Deffner, P and Lillie-Jaschniski, K and Stadler, J and Lebeer, S and Theuns, S},
title = {Exploring the functional microbiome of pigs within the porcine respiratory disease complex: viral-bacterial co-infections and virulence factor profiling.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0191025},
doi = {10.1128/spectrum.01910-25},
pmid = {41609371},
issn = {2165-0497},
abstract = {Respiratory infections are among the most impacting on pigs' health and economic productivity. Despite this, detailed insights into the microbial community of the lower respiratory tract (LRT) are currently lacking, mainly because of difficulties in the processing of respiratory samples. In this study, we characterized the microbiota of the LRT of finisher pigs aged 3-5 months with respiratory symptoms for both the viral and bacterial components, using a previously validated metagenomic diagnostic assay and a full-length 16S rRNA gene sequencing approach, respectively. Functional characterization was carried out using metagenomic shotgun sequencing, revealing the presence of specific virulence factors (VFs). Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and swine Influenza A Virus (swIAV) were the most prevalent viruses, being detected in 30% and 23% of the tested samples, respectively. Mesomycoplasma hyopneumoniae, Glaesserella parasuis, and Pasteurella multocida were the three most abundant bacterial taxa based on both sequencing approaches, while other detected bacterial taxa consisted mainly of Streptococcus, Clostridium, and Rothia species. Detected virulence factors belonged mainly to Mesomycoplasma and Pasteurella and consisted of adhesion factors such as p102, p97, p146, mhp108, mhp107 and the hemolysin-encoding gene hlyA for Mesomycoplasma, and adhesin-encoding ptfA and endoxtoxin-related gene lpxC for Pasteurella. Our data show how the microbial community of the lower respiratory tract in pigs with respiratory symptoms includes key viral (PRRSV, swIAV) and bacterial pathogens (M. hyopneumoniae, G. parasuis, and P. multocida), along with specific virulence factors likely contributing to disease.IMPORTANCEThe obtained results offer insights into the composition of the swine respiratory tract microflora, opening new perspectives on its correlation with viral infections, functional characteristics, and overall health conditions. Moreover, the present study provides technical advancement on the possibility of extracting and amplifying bacterial DNA from low-biomass respiratory samples, with the resulting possibility of identifying virulence factors and better understanding their contribution to the disease state. These discoveries pave the way for future studies aimed at improving diagnostic accuracy and treatment strategies for respiratory disease in both veterinary and human medicine.},
}

@article {pmid41609355,
year = {2026},
author = {Li, Y and Li, Q and Quan, K and Xie, Y and Yang, N and Ma, T and Zheng, L and Zhou, W and Li, Y and Jin, H and Sun, Z and Chen, Y and Kwok, L-Y and Lu, N and Zhu, W and Liu, W and Zhang, H},
title = {Adjunctive probiotic therapy sustains symptom relief in gastroesophageal reflux disease through gut microbiome-metabolome remodeling.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0156825},
doi = {10.1128/msystems.01568-25},
pmid = {41609355},
issn = {2379-5077},
abstract = {Proton pump inhibitors (PPIs) are standard therapy for gastroesophageal reflux disease (GERD), but long-term use causes dysbiosis, gastrointestinal side effects, and symptom relapse after discontinuation. Probiotics may offer adjunctive benefits by modulating the gut ecosystem. The study aimed to evaluate the efficacy of a multi-strain probiotic (Lihuo) with rabeprazole in GERD and its impact on gut microbiota and metabolome. A randomized, double-blind, placebo-controlled trial was conducted in 120 GERD patients assigned to receive rabeprazole with either Lihuo (n = 64) or placebo (n = 56) for 8 weeks, followed by 4 weeks of probiotic or placebo alone. The primary outcome was change in the Reflux Disease Questionnaire (RDQ) score. Secondary outcomes included Gastrointestinal Symptom Rating Scale, endoscopic healing, and multi-omics profiling (shotgun metagenomics, phageome, and untargeted/targeted metabolomics). Compared with the placebo group, the probiotic group exhibited a pronounced 36.51% reduction in RDQ scores after 12 weeks of intervention (P = 0.017), alongside a higher numerical endoscopic healing rate (36.84% vs 12.50%; P = 0.365). Metagenomics revealed enrichment of Bifidobacterium animalis, Lactiplantibacillus plantarum, and Clostridium sp900540255, with reductions in Bacteroides uniformis and Clostridium Q fessum. Metabolomics showed increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids levels, with interesting microbe-metabolite correlations such as Bifidobacterium animalis-γ-aminobutyric acid and Bacteroides fragilis-succinate (r ≥ 0.30, P < 0.01). Our findings support that adjunctive probiotic therapy sustains post-PPI symptom relief, associated with targeted modulation of gut microbiota and bioactive metabolites.IMPORTANCELong-term proton pump inhibitor use in gastroesophageal reflux disease (GERD) may disrupt gut microbiota and cause symptom relapse after discontinuation. We found that adjunctive probiotic therapy sustained reflux reduction post-proton pump inhibitor. Probiotic use enriched beneficial taxa (Bifidobacterium and Lactiplantibacillus plantarum) and increased γ-aminobutyric acid, succinate, citrulline, and short-chain fatty acids. Strong correlations linked microbial shifts to metabolic and clinical improvements. This study demonstrates that adjunctive probiotic therapy enhances symptom control and supports microbial-metabolic homeostasis in GERD.CLINICAL TRIALSThis study is registered with the Chinese Clinial Trial Registry as ChiCTR2000038409.},
}

@article {pmid41609167,
year = {2026},
author = {Koo, WLY and Thng, KX and Tiew, PY and Chotirmall, SH},
title = {The Airway Microbiome in Chronic Obstructive Pulmonary Disease (COPD): A Guide for Clinicians.},
journal = {British journal of hospital medicine (London, England : 2005)},
volume = {87},
number = {1},
pages = {50163},
doi = {10.31083/BJHM50163},
pmid = {41609167},
issn = {1750-8460},
support = {MOH-001636//National Research Foundation Singapore/ ; MOH-001356//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000710//Singapore Ministry of Health's National Medical Research Council/ ; MOH-001275-00//Singapore Ministry of Health's National Medical Research Council/ ; MOH-000955//Singapore Ministry of Health's National Medical Research Council/ ; RT1/22//Singapore Ministry of Education/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/therapy ; *Microbiota ; Dysbiosis/microbiology ; *Lung/microbiology ; Disease Progression ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is a progressive and debilitating respiratory condition marked by chronic symptoms and frequent exacerbations, contributing to significant morbidity and mortality. The advent of molecular microbiology and next-generation sequencing (NGS) has expanded our understanding of the lung microbiome, and integration of microbiome datasets with other omics reveals important microbial-metabolic-immuno-inflammatory interactions that influence COPD pathogenesis. Recent studies have highlighted dysbiosis of the airway microbiome, with shifts in bacterial, viral, and fungal communities playing a crucial role in disease progression, exacerbations and clinical outcomes. Moreover, microbiome changes are observed in COPD associated overlap syndromes, complicating diagnosis and treatment. This review synthesizes current microbiome research in COPD, focusing on its clinical relevance, including its potential as a diagnostic and prognostic tool. We additionally discuss the challenges of integrating microbiome data into clinical practice, emphasizing the need for personalized, precision medicine approaches to optimize COPD management and improve patient outcomes.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/therapy
*Microbiota
Dysbiosis/microbiology
*Lung/microbiology
Disease Progression

@article {pmid41609081,
year = {2026},
author = {Yang, J and Wang, B and Yu, Y and Zhang, H and Zhou, X and Wu, G and Liu, Y and Shi, X},
title = {Gut Microbiota and Metabolome Dynamics Along Gastric Cancer Progression: An Exploratory Multi-Omics Analysis.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {1},
pages = {46553},
doi = {10.31083/FBL46553},
pmid = {41609081},
issn = {2768-6698},
support = {//2023 Chizhou City major science and technology special project/ ; },
mesh = {Humans ; *Stomach Neoplasms/microbiology/metabolism/pathology ; *Gastrointestinal Microbiome ; *Metabolome ; Disease Progression ; Metabolomics/methods ; Male ; Middle Aged ; Female ; Feces/microbiology ; Aged ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Multiomics ; },
abstract = {BACKGROUND: Gastric cancer (GC) remains a major global health burden, particularly in East Asia, with complex etiologies involving Helicobacter pylori infection, diet, host genetics, and environmental exposures. GC development follows the Correa sequence (CS), a multistep cascade from gastritis to atrophy, erosion, and carcinoma. Although gut microbiota (GM) dysbiosis and metabolic reprogramming have each been implicated in GC, their integrated dynamics across CS remain incompletely defined.

METHODS: We recruited participants across five groups: normal controls (G1), gastritis (G2), atrophy (G3), erosion (G4), and GC (G5). Fecal and gastric tissue samples were analyzed using 16S rRNA sequencing and untargeted metabolomics under both ion modes. Microbial diversity was assessed by α- and β-diversity indices, linear discriminant analysis effect size (LEfSe), and functional prediction. Metabolic features were profiled by UHPLC-Q Exactive Orbitrap MS, and differential metabolites were identified using t-tests and partial least squares discriminant analysis (PLS-DA). Diagnostic potential was evaluated using receiver operating characteristic (ROC) curves.

RESULTS: Microbial α-diversity decreased significantly with progression, particularly in G3, while compositional shifts included depletion of Bacteroides and Faecalibacterium alongside enrichment of Actinobacteria, Peptostreptococcaceae, and Lachnoclostridium. LEfSe identified Bifidobacterium and Oscillospiraceae as potential biomarkers of advanced stages. ROC analyses demonstrated strong discriminatory power, with the class Actinobacteria achieving an area under the ROC curve (AUC) of 0.935 in distinguishing controls from GC. Fecal metabolomics revealed reductions in anti-inflammatory short-chain fatty acids (SCFAs) and increases in pro-inflammatory metabolites emerging at G3, while tissue metabolomics showed broader reprogramming in GC involving amino acid, nucleotide, lipid, and energy metabolism. Notably, erosion (G4) exhibited transitional features, whereas atrophy (G3) marked a distinct metabolic "breakpoint".

CONCLUSIONS: By integrating GM and metabolomic data, this study delineates stage-specific microbial and metabolic alterations along the CS. Atrophy represents a pivotal inflection point in the transition from homeostasis to carcinogenesis, while erosion serves as a transitional state. Combined microbiota-metabolite signatures hold promise for non-invasive early detection, disease stratification, and mechanistic insights into metabolic dependencies in GC.},
}

Humans
*Stomach Neoplasms/microbiology/metabolism/pathology
*Gastrointestinal Microbiome
*Metabolome
Disease Progression
Metabolomics/methods
Male
Middle Aged
Female
Feces/microbiology
Aged
RNA, Ribosomal, 16S/genetics
Dysbiosis/microbiology
Multiomics

@article {pmid41609075,
year = {2026},
author = {Wang, Z and Ma, Y and Li, M and Jiang, X and Pan, Q and Deng, M and Guo, L},
title = {Akkermansia muciniphila Ameliorates Chronic Sleep Deprivation-Induced Glucose Intolerance and Inflammatory Cytokine Activation.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {1},
pages = {45680},
doi = {10.31083/FBL45680},
pmid = {41609075},
issn = {2768-6698},
support = {BJ-2022-145//National High Level Hospital Clinical Research Funding/ ; 82200928//National Natural Science Foundation of China/ ; 2021-N-03//China Endocrinology and Metabolism Young Scientific Talent Research Project/ ; },
mesh = {Animals ; *Sleep Deprivation/complications/microbiology ; *Cytokines/metabolism/blood ; Mice ; Male ; *Akkermansia/physiology ; *Glucose Intolerance/etiology/microbiology/therapy ; Gastrointestinal Microbiome ; Zonula Occludens-1 Protein/metabolism/genetics ; Mice, Inbred C57BL ; Mucin-2/metabolism/genetics ; *Verrucomicrobia ; Disease Models, Animal ; Lipopolysaccharides/blood ; },
abstract = {OBJECTIVE: Emerging evidence indicates that Akkermansia muciniphila (A. muciniphila or AKK) regulates host glucose metabolism through multiple pathways. In this study, we examined the therapeutic effects of A. muciniphila on chronic sleep deprivation (CSD)-induced glucose dysregulation and the underlying mechanisms.

METHODS: A modified multiplatform water environment method was used to generate a mouse model of CSD. The mice were divided into three groups: the control (CON) group (ad libitum sleep), the CSD group (subjected to sleep deprivation), and the CSD+AKK group (CSD mice were supplemented with A. muciniphila at 3 × 10⁸ CFU per mouse, three times per week). After an 8-week intervention, glucose metabolism was assessed. Serum concentrations of lipopolysaccharide (LPS), interleukin-6 (IL-6), interleukin-1β (IL-1β) and tumor necrosis factor α (TNF-α) were measured. The mRNA expression and protein expression of mucin 2 (MUC2) and zonula occludens-1 (ZO-1) in the colon tissue were analyzed. Goblet cells in colon tissues were quantified using Alcian Blue-Periodic Acid-Schiff (AB-PAS) staining. Additionally, changes in gut microbiome diversity and composition among groups were compared.

RESULTS: CSD induced significant glucose intolerance and insulin resistance, evidenced by increased area under the curve (AUC) of the oral glucose tolerance test (OGTT), homeostatic model assessment of insulin resistance (HOMA-IR), and fasting insulin levels compared to the CON group (all p < 0.05). This was accompanied by a marked impairment of the colonic mucosal barrier, characterized by a profound loss of goblet cells and downregulation of key barrier components, MUC2 and ZO-1, at both the mRNA and protein levels (all p < 0.05). Intervention with A. muciniphila significantly ameliorated CSD-induced glucose intolerance, insulin resistance and colonic barrier damage. Furthermore, CSD elevated serum levels of LPS, IL-6, TNF-α, and IL-1β (all p < 0.05), which were effectively mitigated by A. muciniphila intervention. 16S rDNA sequencing confirmed the successful colonization of A. muciniphila, as its absolute abundance was significantly greater in the CSD+AKK group than in the CSD group. In addition, A. muciniphila intervention affected the abundance of Burkholderiales bacterium, Lactococcus garvieae, and other bacterial strains in the intestine.

CONCLUSION: A. muciniphila supplementation effectively ameliorated CSD-induced glucose intolerance, reduced the serum levels of LPS and proinflammatory cytokines (IL-6, TNF-α, and IL-1β), and restored intestinal barrier integrity by upregulating MUC2 and ZO-1 expression in colon tissues.},
}

Animals
*Sleep Deprivation/complications/microbiology
*Cytokines/metabolism/blood
Mice
Male
*Akkermansia/physiology
*Glucose Intolerance/etiology/microbiology/therapy
Gastrointestinal Microbiome
Zonula Occludens-1 Protein/metabolism/genetics
Mice, Inbred C57BL
Mucin-2/metabolism/genetics
*Verrucomicrobia
Disease Models, Animal
Lipopolysaccharides/blood

@article {pmid41608923,
year = {2025},
author = {Polena, H and Callejon, S and Salvert, M and Abric, E and Buisson, A and Cadars, B and Giraud, F and Scalia, J and Remoue, N and Ardiet, N and Sayag, M and Trompezinski, S and Prestat-Marquis, E and Dreno, B and Graizeau, C},
title = {An innovative ecobiological wound repair cream that restores the microbiome.},
journal = {European journal of dermatology : EJD},
volume = {35},
number = {6},
pages = {508-518},
doi = {10.1684/ejd.2025.4979},
pmid = {41608923},
issn = {1952-4013},
mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota/drug effects ; *Skin Cream/pharmacology/therapeutic use ; *Skin/microbiology/drug effects ; Male ; Female ; Middle Aged ; Adult ; Aged ; },
abstract = {Small everyday wounds would benefit from optimal healing conditions, and the role of the microbiome in this process is being increasingly discussed. Objectives: To evaluate a wound repair cream (Cicabio Crème+, NAOS Ecobiology Company, Bioderma, France), assessing its effects on the skin microbiome and wound healing. The impact on the microbiome was evaluated by monitoring restoration of diversity after disinfection. The efficacy of the repair complex was assessed ex vivo using a 3D wound-healing human skin model to analyse closure and protein expression. Short-term evaluation of adherence, gas permeability, wound protection, and hydration was assessed. In vivo efficacy was examined through two clinical studies: one on healing erosive areas and another after chemical peel. After disinfection, the cream accelerated restoration of microbiome diversity (+31%, p=0.001) without promoting pathogenic/commensal bacteria or altering the level of Staphylococcus epidermidis (p=0.193). In a 3D wound-healing model, the repair complex enhanced wound closure, promoting protein expression (Ki67, loricrin, CD44, collagen XVII, VII, III) and re-epithelialisation. The cream adhered to the skin, allowed gas exchange, and provided protection and hydration. In vivo, the cream reduced transepidermal water loss (day 4: p=0.016; day 7: p=0.014), erythema (day 7: p=0.023), and functional signs (day 4: p=0.032) of erosive wounds. Following chemical peels, the cream reduced inflammation (day 7: p=0.037), visible damage (day 7: p=0.029), and skin pH (day 1: p<0.001). We demonstrate, for the first time, protection of microbiome diversity, stimulation of wound closure, and preservation of skin pH using a wound repair cream.},
}

Humans
*Wound Healing/drug effects
*Microbiota/drug effects
*Skin Cream/pharmacology/therapeutic use
*Skin/microbiology/drug effects
Male
Female
Middle Aged
Adult
Aged

@article {pmid41608868,
year = {2026},
author = {Mahen, KK and Massey, WJ and Orabi, D and Brown, AL and Jaramillo, TC and Burrows, A and Horak, AJ and Dutta, S and Mrdjen, M and Mouannes, N and Varadharajan, V and Osborne, LJ and Ye, X and Yarbrough, DM and Grubb, T and Zajczenko, N and Hohe, R and Banerjee, R and Linga, P and Laungani, D and Hajjar, AM and Sangwan, N and Dwidar, M and Buffa, JA and Swanson, GR and Wang, Z and Brown, JM},
title = {Gut microbe-derived trimethylamine shapes circadian rhythms through the host receptor TAAR5.},
journal = {eLife},
volume = {14},
number = {},
pages = {},
pmid = {41608868},
issn = {2050-084X},
support = {R01 DK130227/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; P50 AA024333/AA/NIAAA NIH HHS/United States ; RF1 NS133812/NS/NINDS NIH HHS/United States ; 10.58275/aha.24post1178494.pc.gr.190863//American Heart Association/ ; },
mesh = {*Methylamines/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology ; *Circadian Rhythm/physiology ; Mice ; *Receptors, G-Protein-Coupled/metabolism/genetics ; Mice, Inbred C57BL ; Male ; Mice, Knockout ; },
abstract = {Elevated levels of the gut microbe-derived metabolite trimethylamine N-oxide (TMAO) are associated with cardiometabolic disease risk. However, the mechanism(s) linking TMAO production to human disease are incompletely understood. Initiation of the metaorganismal TMAO pathway begins when dietary choline and related metabolites are converted to trimethylamine (TMA) by gut bacteria. Gut microbe-derived TMA can then be further oxidized by host flavin-containing monooxygenases to generate TMAO. Previously, we showed that drugs lowering both TMA and TMAO protect mice against obesity via rewiring of host circadian rhythms (Schugar et al., 2022). Although most mechanistic studies in the literature have focused on the metabolic end product TMAO, here we have instead tested whether the primary metabolite TMA alters host metabolic homeostasis and circadian rhythms via trace amine-associated receptor 5 (TAAR5). Remarkably, mice lacking the host TMA receptor (Taar5[-/][-]) have altered circadian rhythms in gene expression, metabolic hormones, gut microbiome composition, and diverse behaviors. Also, mice genetically lacking bacterial TMA production or host TMA oxidation have altered circadian rhythms. These results provide new insights into diet-microbe-host interactions relevant to cardiometabolic disease and implicate gut bacterial production of TMA and the host receptor that senses TMA (TAAR5) in the physiologic regulation of circadian rhythms in mice.},
}

*Methylamines/metabolism
Animals
*Gastrointestinal Microbiome/physiology
*Circadian Rhythm/physiology
Mice
*Receptors, G-Protein-Coupled/metabolism/genetics
Mice, Inbred C57BL
Male
Mice, Knockout

@article {pmid41608696,
year = {2025},
author = {Liu, Y and Rong, L and Cheng, Y and Wang, M and Min, S and Xiao, F and Zhang, Z and Yang, Z and Zhang, Q and Zheng, X},
title = {Topographic controls on soil organic carbon partitioning and enzyme dynamics in nutrient-poor soils.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1735665},
pmid = {41608696},
issn = {1664-302X},
abstract = {INTRODUCTION: Understanding the dynamics of soil organic carbon (SOC) in sloping farmlands is critical, as they play a vital role in the global carbon cycle and soil health. Although prior research has focused on physical carbon loss due to erosion, the biological mechanisms by which slope gradients affect microbial carbon cycling remain poorly understood.

METHODS: Soil samples were collected from maize fields with three slope gradients (30°, 45°, and 60°) across different growth stages. Key indicators were determined as follows: SOC by potassium dichromate oxidation (external heating method); DOC by ultrapure water extraction (1:5 ratio) and organic carbon analyzer; POC by sodium hexametaphosphate dispersion, 53-μm sieving, and chromic acid oxidation; soil Ca[2+], Mg[2+], and Cl[-] by EDTA complexometric titration and silver nitrate titration, respectively; invertase (SUC) by 3,5-dinitrosalicylic acid colorimetry; polyphenol oxidase (SPPO) and peroxidase (SPOD) by commercial kits with L-dopa as substrate. Statistical analyses were performed using IBM SPSS 26 (One-way ANOVA with LSD post-hoc test, Pearson correlation analysis) and Origin 2024 (Principal Component Analysis, PCA). Normality of data was verified prior to analysis, and significance was set at P < 0.05.

RESULTS: Results showed that SOC levels decreased with increasing slope steepness, while DOC peaked at 45°. SPPO and SPOD activities (involved in recalcitrant carbon decomposition) were significantly elevated at 60°. SUC activity was positively correlated with DOC, while oxidase activities were positively associated with POC and negatively with Mg[2+].

DISCUSSION: This study identifies a critical slope threshold (30°-45°) for DOC loss: DOC availability on steeper slopes stimulates microbial synthesis of SPPO and SPOD, enhancing recalcitrant carbon degradation and potentially intensifying long-term SOC depletion. The identification of this threshold provides insights for designing microbiome-informed strategies to mitigate soil degradation and safeguard ecological security.},
}

@article {pmid41608689,
year = {2025},
author = {Yan, W and Du, N and Zhang, K and Yang, P and Guo, J and Xu, L},
title = {Bilirubin-microbiota interaction: molecular mechanisms and therapeutic strategies in neonatal jaundice.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1749152},
pmid = {41608689},
issn = {1664-302X},
abstract = {Recent studies have revealed a complex interplay between bilirubin metabolism and the gut microbiota. Bilirubin functions as a potent antioxidant and signaling molecule in humans, and its concentration-dependent effects on distinct microbial taxa indicate that the compound exerts selective pressure on the gut ecosystem. The gut microbiota modulates bilirubin metabolism by altering intestinal pH, producing and activating Bilirubin metabolic enzyme, and bile acids. Because perturbations in bilirubin handling are especially common-and potentially neurotoxic-in neonates, a concise synthesis of recent progress is warranted. Here we review how microbial communities reshape bilirubin flux, how bilirubin and its conjugates, in turn, sculpt microbial ecology, and how the dynamic equilibrium between conjugated and unconjugated bilirubin in hyperbilirubinaemia is influenced by the microbiome. Regulating gut microbiota to accelerate bilirubin clearance or attenuate its toxicity may therefore offer a tractable therapeutic avenue.},
}

@article {pmid41608686,
year = {2025},
author = {Sun, Y and Ding, M and Zheng, W and Zhang, H and Lu, Z and Zhang, J and Zhao, G},
title = {Manganese-oxidizing Exiguobacterium acetylicum 4-3-1 reduces cadmium accumulation in spinach.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1734825},
pmid = {41608686},
issn = {1664-302X},
abstract = {Cadmium (Cd) accumulation in edible plants is a significant global concern. This research explores the potential of a manganese-oxidizing rhizobacterium, Exiguobacterium acetylicum 4-3-1, to promote spinach growth while reducing Cd uptake. The bacterium produces indole-3-acetic acid and siderophores and effectively removed 73.74% of free CdCl2. Under Cd stress (10.5 mg/kg), E. acetylicum 4-3-1 significantly increased spinach biomass by 184.3% (dry weight) and chlorophyll content by 33.99%, while decreasing the Cd concentration in spinach leaves by 53.07% through both intrinsic and extrinsic mechanisms. Intrinsically, E. acetylicum 4-3-1 inoculation up-regulated pathways related to photosynthesis and energy metabolism in spinach, while down-regulating genes linked to heavy metal transport. Extrinsically, it oxidizes Mn(II) to form manganese oxides that may immobilize Cd. Moreover, inoculation with strain 4-3-1 altered the rhizosphere microbiome of spinach, increasing the presence of beneficial bacteria like Bacillales. A synthetic community (SynCom) composed of Bacillus subtilis and E. acetylicum 4-3-1 demonstrated synergistic effects on spinach growth under Cd stress. Thus, E. acetylicum 4-3-1 has the potential for Cd bioremediation in crops and promotes sustainable agriculture.},
}

@article {pmid41608653,
year = {2026},
author = {Yang, RL and Lu, Q and Liang, EM and Luo, HC},
title = {Strengthening causal inference and analytical rigor in the Wumei Pills-Lactobacillus reuteri-intestinal stem cell axis for chemotherapy-induced mucositis.},
journal = {World journal of stem cells},
volume = {18},
number = {1},
pages = {114114},
pmid = {41608653},
issn = {1948-0210},
abstract = {A recent preclinical study reported that Wumei Pills (WMP) and Lactobacillus reuteri (L. reuteri) mitigate 5-fluorouracil-induced intestinal mucositis by promoting intestinal stem cell (ISC)-mediated repair via Wnt/β-catenin signaling. The mechanistic interpretation rests largely on systemic inflammation readouts, correlative microbiota changes, and immunohistochemistry of pathway markers. From a clinical standpoint, chemotherapy-induced mucositis remains a common and burdensome toxicity that leads to dose reductions, treatment delays, and infection risk; current care is largely supportive and does not directly restore ISC-mediated repair. This unmet need motivates rigorous appraisal of the proposed "WMP → L. reuteri → ISC/Wnt" axis. To highlight key methodological considerations that may affect causal inference and analytical rigor in the proposed "WMP → L. reuteri → ISC/Wnt" pathway. This letter critically appraises the study's design, endpoints, and analyses against current best practices in mucositis biology, microbiome causality testing, Wnt/β-catenin pathway validation, and preclinical statistics, and synthesizes concrete, literature-grounded remedies. Six issues with potential impact on interpretation were identified: (1) Reliance on serum cytokines/lipopolysaccharide to infer local mucosal inflammation, with limited tissue-level indices (e.g., myeloperoxidase, interleukin-1β, immune-cell infiltration); (2) Absence of necessity/sufficiency tests to verify microbiota mediation (e.g., L. reuteri depletion, WMP-donor fecal microbiota transplantation, probiotic add-back); (3) Pathway evidence tiering - Wnt/β-catenin activation not confirmed by β-catenin nuclear translocation or downstream targets (Axin2, c-Myc, cyclin D1), and Lgr5 quantification/specificity insufficient; (4) Statistical design under-specified (power justification, blinded assessment, control of multiple comparisons) and potential cage effects unmodeled; (5) Limited dose-response and safety profiling for WMP/L. reuteri; and (6) Constrained generalizability (single sex/strain/age, lack of ABX-only controls, single time-point). The reported benefits of WMP and L. reuteri in chemotherapy-induced mucositis are promising, but stronger causal and analytical foundations are needed. Incorporating tissue-level inflammation readouts, microbiota loss-/gain-of-function designs, definitive Wnt/β-catenin activation assays, rigorous statistical practices (including mixed-effects models for cage clustering and multiplicity control), dose-response/safety evaluation, and broader experimental scope (sex/age/strain, ABX-only controls, time-course) will yield more robust and translationally relevant conclusions.},
}

@article {pmid41608632,
year = {2026},
author = {Zhang, X and Zhang, Z and Peng, Q and Huang, X and Liu, M and Bai, D and Yang, R and Zhang, Y and Yang, C},
title = {The Immunogenetic Landscape of Allergic Rhinitis: from Cellular Effectors to Gene Regulation and Targeted Therapies.},
journal = {International journal of biological sciences},
volume = {22},
number = {3},
pages = {1322-1345},
pmid = {41608632},
issn = {1449-2288},
mesh = {Humans ; *Rhinitis, Allergic/genetics/immunology/therapy ; Animals ; Signal Transduction ; Gene Expression Regulation ; },
abstract = {Allergic Rhinitis (AR) is a highly prevalent type 2 inflammatory disease driven by a complex immunogenetic background. This review aims to systematically delineate the immunogenetic landscape of AR, elucidating the complete knowledge chain from macroscopic cellular interactions and microscopic molecular regulation to precision targeted therapies. The article first dissects the two core immune axes driving the pathological process of AR: one is the classic adaptive immune pathway, centered on Th2 cells, which mediates IgE production, eosinophil infiltration, and mucus hypersecretion through the secretion of cytokines such as IL-4, IL-5, and IL-13; the other is the innate immune initiation pathway, in which nasal epithelial cells act as "sentinels" by releasing "alarmins" like TSLP and IL-33, leading to the rapid activation of type 2 innate lymphoid cells (ILC2s). The review then delves into the sophisticated signaling networks that regulate these immune responses, with a particular focus on the classic IL-4/STAT6/GATA3 signaling axis and its negative regulatory mechanisms. Building on this, the article further elaborates on the genetic susceptibility architecture of AR, highlighting key risk loci identified by genome-wide association studies (GWAS), such as variants in antigen presentation genes (HLA), epithelial barrier genes (FLG), and genes related to cytokine signaling pathways. To connect genetics with the environment, this review systematically summarizes epigenetic regulatory mechanisms, including DNA methylation, histone modifications, and microRNAs (miRNAs), and discusses the long-range immunomodulatory effects of nasal and gut microbiota dysbiosis on AR via the "gut-nasal axis". Finally, from a translational medicine perspective, the article demonstrates how a profound understanding of these pathophysiological mechanisms has successfully spurred the development of highly effective targeted biologics, such as omalizumab (targeting IgE), dupilumab (targeting the IL-4Rα receptor, thus blocking IL-4/IL-13 signaling), and tezepelumab (targeting TSLP). This review integrates the latest multidimensional research advances in immunology, genetics, epigenetics, and microbiome studies of AR, providing a comprehensive theoretical framework for understanding its complex pathogenesis and for the development of future personalized treatment strategies.},
}

Humans
*Rhinitis, Allergic/genetics/immunology/therapy
Animals
Signal Transduction
Gene Expression Regulation

@article {pmid41608628,
year = {2026},
author = {Jang, HR and Kim, HJ and Kim, BY and Jeong, JH and Kim, JK and Won, JA and Yoo, HH and Lee, YG and Yim, H},
title = {Combining sorafenib with spermine and sphingosine synergistically enhances anticancer efficacy by modulating metabolic pathways and gut microbiome in hepatocellular carcinoma.},
journal = {International journal of biological sciences},
volume = {22},
number = {3},
pages = {1082-1102},
pmid = {41608628},
issn = {1449-2288},
mesh = {*Sorafenib/pharmacology/therapeutic use ; *Spermine/pharmacology/therapeutic use ; *Carcinoma, Hepatocellular/drug therapy/metabolism/microbiology ; Humans ; *Liver Neoplasms/drug therapy/metabolism/microbiology ; Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Sphingosine/pharmacology/therapeutic use ; Cell Line, Tumor ; *Antineoplastic Agents/pharmacology/therapeutic use ; Drug Synergism ; Xenograft Model Antitumor Assays ; Mice, Nude ; Apoptosis/drug effects ; Male ; },
abstract = {Hepatocellular carcinoma (HCC), which makes up about 90% of liver cancer, is the third leading cause of cancer-related death. Recent studies suggest that metabolites derived from the gut microbiome may offer new therapeutic opportunities for HCC. In this study, we explored whether microbial metabolites could enhance the effectiveness of sorafenib, a first-line multi-kinase inhibitor used in advanced HCC. Through a screen of a microbiome metabolite library, we identified spermine and sphingosine as potential candidates that boosted anticancer effects of sorafenib in HepG2, Huh7, and SK-Hep-1 cells. These metabolites worked synergistically with sorafenib to suppress tumor growth in cultured HCC cells, patients-derived HCC organoids, and a xenograft mouse model. Mechanistically, spermine triggered cell cycle arrest at the S phase, while sphingosine and sorafenib induced G1 arrest, contributing to an increased sub-G1 population and apoptosis when combined. Notably, sorafenib treatment led to the downregulation of SMOX (a key catabolic enzyme for spermine), as well as SPHK1 and CERS1 (critical enzymes involved in sphingosine metabolism), whose high expression levels are associated with poorer survival outcomes in liver cancer patients according to TCGA data. A 16S rRNA sequencing analysis revealed that combination of sorafenib with spermine or sphingosine alters the gut microbiome, increasing the relative abundance of Faecalibaculum, inversely correlated with tumor sizes in a xenograft mouse model. Therefore, we propose that combining sorafenib with spermine or sphingosine could enhance its anti-HCC effects by promoting apoptosis and reducing the expression of metabolic enzymes. Moreover, Faecalibaculum may serve as a potential microbiome-based prognostic marker for HCC.},
}

*Sorafenib/pharmacology/therapeutic use
*Spermine/pharmacology/therapeutic use
*Carcinoma, Hepatocellular/drug therapy/metabolism/microbiology
Humans
*Liver Neoplasms/drug therapy/metabolism/microbiology
Animals
Mice
*Gastrointestinal Microbiome/drug effects
*Sphingosine/pharmacology/therapeutic use
Cell Line, Tumor
*Antineoplastic Agents/pharmacology/therapeutic use
Drug Synergism
Xenograft Model Antitumor Assays
Mice, Nude
Apoptosis/drug effects
Male

@article {pmid41608560,
year = {2026},
author = {Wang, N and Ma, L and Huang, Y and Zhou, X and Rong, Y and Long, F and Qiu, W and Wu, S and Hu, Y and He, X and He, J and Tian, S and Hu, W and Yuan, C and Wang, F},
title = {Tumor microbiome-transcriptome crosstalk identifies Prevotella as an immunotherapeutic predictor in NSCLC.},
journal = {Theranostics},
volume = {16},
number = {7},
pages = {3426-3446},
pmid = {41608560},
issn = {1838-7640},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/immunology/drug therapy/genetics/therapy ; *Lung Neoplasms/microbiology/immunology/genetics/drug therapy/therapy ; *Microbiota/immunology/genetics ; *Transcriptome ; Tumor Microenvironment/immunology/genetics ; *Prevotella/isolation & purification/immunology/genetics ; Immunotherapy/methods ; Immune Checkpoint Inhibitors/therapeutic use/pharmacology ; Prognosis ; Female ; Male ; Middle Aged ; Aged ; ErbB Receptors/antagonists & inhibitors ; },
abstract = {Background: The tumor-resident microbiome plays a pivotal role in shaping the tumor immune microenvironment; however, its relationship with the host transcriptome and the response to immune checkpoint inhibitors (ICIs) remains largely uncharacterized in non-small cell lung cancer (NSCLC). This study aimed to elucidate the relationship between tissue-resident microbiota, host transcriptomic alterations, and immunotherapy response in NSCLC. Methods: Paired tumor (T) and paracancerous tissue (PT) samples from patients with NSCLC were analyzed using 2bRAD-M and bulk RNA sequencing to generate comprehensive microbiome and transcriptome profiles. The conditional mutual information algorithm was employed to systematically investigate intratumoral microbe-host interactions. Associations between key microbes and patient prognosis, ICI response, and response to epidermal growth factor receptor (EGFR)-targeted therapy were assessed across four independent local clinical cohorts. Results: Higher microbial richness, α-diversity, and β-diversity were observed in PT samples than in T samples. Specifically, PT-resident Bradyrhizobium and Prevotella were identified as key bacterial taxa significantly associated with immune cell populations, including CD8[+] T cells, natural killer cells, and activated dendritic cells. Among these, PT-resident Prevotella, but not Bradyrhizobium, was independently associated with improved prognosis of patients with NSCLC and ICI response in both local clinical sets and public datasets. Furthermore, a combined diagnostic model integrating PT-resident Prevotella abundance with routine clinical blood indicators demonstrated markedly superior predictive performance for ICI response compared with the conventional biomarker PD-L1. By contrast, PT-resident Prevotella exhibited no association with treatment response in the EGFR-targeted therapy cohort. Conclusion: PT-resident Prevotella is strongly associated with the prognosis and ICI response in patients with NSCLC. Moreover, integration of PT-resident Prevotella with routine clinical blood indicators holds promise as a potential auxiliary diagnostic tool to facilitate personalized immunotherapy in NSCLC.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/microbiology/immunology/drug therapy/genetics/therapy
*Lung Neoplasms/microbiology/immunology/genetics/drug therapy/therapy
*Microbiota/immunology/genetics
*Transcriptome
Tumor Microenvironment/immunology/genetics
*Prevotella/isolation & purification/immunology/genetics
Immunotherapy/methods
Immune Checkpoint Inhibitors/therapeutic use/pharmacology
Prognosis
Female
Male
Middle Aged
Aged
ErbB Receptors/antagonists & inhibitors

@article {pmid41608437,
year = {2025},
author = {De Laffolie, J and Hauer, AC},
title = {Editorial: Advances towards precision medicine in pediatric-onset inflammatory bowel disease.},
journal = {Frontiers in medicine},
volume = {12},
number = {},
pages = {1765757},
pmid = {41608437},
issn = {2296-858X},
}

@article {pmid41608298,
year = {2026},
author = {Aldoori, J and Mitra, S and Davie, A and Toogood, GJ and Edwards, C and Hull, MA},
title = {The effect of omega-3 polyunsaturated fatty acids on short-chain fatty acid production and the gut microbiome in an in vitro colonic fermentation model.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e1},
pmid = {41608298},
issn = {2632-2897},
abstract = {Oral administration of omega-3 polyunsaturated fatty acids (PUFAs) to rodents and humans is associated with an increase in gut bacteria that are predicted to synthesise short-chain fatty acids (SCFAs). We tested the hypothesis that physiological levels of omega-3 PUFAs in the distal intestinal lumen (1-50 μg/mL) are associated with increased SCFA synthesis in an in vitro fermentation model using faecal slurry from 10 healthy participants (mean age 30 years), with and without exogenous dietary fibres. SCFAs were measured by gas chromatography-flame ionisation detection (n = 10), and changes in bacterial composition were analysed by shotgun metagenomic sequencing (n = 6). In the presence of omega-3 PUFAs, there was a mean 9.3% (no inulin; P = 0.03) and 19.3% (+ 0.01 mg/mL inulin; P = 0.01) increase in total SCFA concentration at 24 h compared with paired control fermentations. Omega-3 PUFAs had a limited effect on the fermentation model microbiome in the absence of inulin. However, omega-3 PUFAs (50 μg/mL) were associated with increased abundance of Bifidobacteriaceae compared with paired control fermentations, if inulin (0.01 mg/mL) was present. Prebiotic activity of omega-3 PUFAs drives SCFA synthesis in an in vitro colonic fermentation model and is augmented by the soluble fibre inulin.},
}

@article {pmid41607944,
year = {2025},
author = {Gao, YQ and Hou, QY and Hou, XW and Wei, YJ and Shang, KM and Ma, H and Geng, HL and Liu, R and Yang, LH and Elsheikha, HM and Ni, HB and Huang, YF},
title = {Metagenomics-based characterization of fecal microbiome and resistome of laying hens during the production cycle.},
journal = {Frontiers in veterinary science},
volume = {12},
number = {},
pages = {1740567},
pmid = {41607944},
issn = {2297-1769},
abstract = {The extensive use of antimicrobials in livestock has accelerated the emergence of antimicrobial resistance (AMR), raising serious global concerns. Poultry feces are recognized as important reservoirs of antibiotic resistance genes (ARGs) and their associated mobile genetic elements (MGEs); however, the microbial community characteristics and ARG profiles of laying hens across different laying stages remain poorly understood. In this study, 40 fecal samples were collected from laying hens at five sampling points, including the early laying stage (HE), three peak laying stages (HPI, HPII, and HPIII), and the late laying stage (HL), with eight randomly selected samples per stage. Shotgun metagenomic sequencing was conducted to characterize the taxonomic structure and functional profiles of the intestinal microbiota and to systematically analyze the diversity and distribution patterns of ARGs. The results showed that most ARGs were harbored by bacteria belonging to the phyla Pseudomonadota and Bacillota, with Escherichia coli serving as the primary carrier of antibiotic resistance genes. Moreover, significant correlations were observed between the co-abundance and co-occurrence of ARGs and MGEs, suggesting that MGEs play a key role in facilitating ARG dissemination. Overall, these findings provide novel insights into the prevalence of ARGs in laying hens across different laying stages and may inform strategies to mitigate the spread of antimicrobial resistance in poultry production systems.},
}

@article {pmid41607747,
year = {2026},
author = {Luo, L and Huang, G and Yang, H and Chi, H},
title = {Revisiting multi-region 16S sequencing in gastric cancer.},
journal = {World journal of gastrointestinal oncology},
volume = {18},
number = {1},
pages = {114708},
pmid = {41607747},
issn = {1948-5204},
abstract = {Wu et al recently applied multi-region 16S rRNA sequencing to characterize the gastric cancer microbiome, demonstrating improved taxonomic resolution and detection sensitivity over conventional single-region approaches. While the study represents a valuable methodological step forward, it remains limited by single-center design, lack of quantitative calibration, and insufficient control for contamination and inter-laboratory variability. This editorial critically appraises these methodological gaps and emphasizes that future efforts must focus on harmonized, consensus-driven workflows to ensure reproducibility and clinical reliability. The translational potential of multi-region 16S lies in moving from descriptive microbial profiling to actionable clinical integration, particularly for recurrence prediction, treatment-response monitoring, and perioperative complication risk assessment. By addressing these methodological, economic, and ethical challenges, the field can advance toward evidence-based and clinically deployable microbiome-guided precision oncology.},
}

@article {pmid41607695,
year = {2026},
author = {Dias, HM and Jain, R and Santos, VA and Gonzalez-Hernandez, JL and Solanki, S and Menendez Iii, HM and Graham, C},
title = {Reproducible Emu-Based Workflow for High-Fidelity Soil and Plant Microbiome Profiling on HPC Clusters.},
journal = {Bio-protocol},
volume = {16},
number = {2},
pages = {e5577},
pmid = {41607695},
issn = {2331-8325},
abstract = {Accurate profiling of soil and root-associated bacterial communities is essential for understanding ecosystem functions and improving sustainable agricultural practices. Here, a comprehensive, modular workflow is presented for the analysis of full-length 16S rRNA gene amplicons generated with Oxford Nanopore long-read sequencing. The protocol integrates four standardized steps: (i) quality assessment and filtering of raw reads with NanoPlot and NanoFilt, (ii) removal of plant organelle contamination using a curated Viridiplantae Kraken2 database, (iii) species-level taxonomic assignment with Emu, and (iv) downstream ecological analyses, including rarefaction, diversity metrics, and functional inference. Leveraging high-performance computing resources, the workflow enables parallel processing of large datasets, rigorous contamination control, and reproducible execution across environments. The pipeline's efficiency is demonstrated on full-length 16S rRNA gene datasets from yellow pea rhizosphere and root samples, with high post-filter read retention and high-resolution community profiles. Automated SLURM scripts and detailed documentation are provided in a public GitHub repository (https://github.com/henrimdias/emu-microbiome-HPC; release v1.0.2, emu-pipeline-revised) and archived on Zenodo (DOI: 10.5281/zenodo.17764933). Key features • Implement rigorous quality control (QC) of raw 16S rRNA Nanopore reads and sequencing controls. • Remove plant organelle contamination with a curated Kraken2 database. • Perform high-resolution taxonomic assignment of full-length 16S rRNA reads using Emu. • Integrate downstream statistical analyses, including rarefaction, PERMANOVA, and DESeq2 differential abundance. • Conduct scalable microbiome diversity and functional analyses with FAPROTAX.},
}

@article {pmid41607410,
year = {2026},
author = {Nouso, K and Wakuta, A and Shiota, S and Fujita, R and Kariyama, K and Hiraoka, A and Atsukawa, M and Tani, J and Tada, T and Nakamura, S and Tajiri, K and Kaibori, M and Hirooka, M and Itobayashi, E and Kakizaki, S and Naganuma, A and Ishikawa, T and Imai, M and Aoki, T and Tanaka, H and Hatanaka, T and Tsuji, K and Kawata, K and Takaguchi, K and Tsutsui, A and Ogawa, C and Ochi, H and Yata, Y and Kuroda, H and Matono, T and Yasuda, S and Toyoda, H and Iijima, H and Kudo, M and Kumada, T},
title = {Effect of Butyrate-Producing Enterobacteria and Proton Pump Inhibitors on Advanced Hepatocellular Carcinoma Treatment With Durvalumab and Tremelimumab.},
journal = {JGH open : an open access journal of gastroenterology and hepatology},
volume = {10},
number = {1},
pages = {e70346},
pmid = {41607410},
issn = {2397-9070},
abstract = {AIM: The gut microbiome modulates immune responses, and butyrate-producing bacteria have been linked to improved immune checkpoint inhibitor (ICI) efficacy. Conversely, proton pump inhibitors (PPIs) may negatively impact ICI outcomes by altering gut microbiota. This study aims to elucidate their effects in hepatocellular carcinoma (HCC).

METHODS: This retrospective multicenter cohort study included 208 HCC patients treated with durvalumab plus tremelimumab at 25 hospitals in Japan. Patients were classified into a butyric acid group (n = 27), who ingested drugs containing butyrate-producing enterobacteria, and a non-butyric acid group (n = 181), as well as a PPI group (n = 107) and a non-PPI group (n = 101). Overall survival (OS) was analyzed using inverse probability of treatment weighting, and risk factors were assessed with Cox proportional hazards modeling. Tumor response was evaluated by RECIST v1.1.

RESULTS: No significant OS differences were observed between the butyric acid and non-butyric acid groups (p = 0.921), or between PPI and non-PPI groups (p = 0.917). The objective response rate was 3.7% in the butyric acid group versus 15.5% in the non-butyric acid group (p = 0.543) and 15.8% in the PPI group versus 12.1% in the non-PPI group (p = 0.222). Disease control rates were comparable. Multivariate analysis identified ECOG performance status (p = 0.019) and ALBI score (p < 0.001) as independent prognostic factors, while butyrate-producing bacteria and PPI use were not associated with survival outcomes.

CONCLUSION: Neither butyrate-producing bacteria nor PPI use significantly influenced the efficacy of durvalumab plus tremelimumab in HCC. The liver's immunotolerant microenvironment may limit the impact of microbiome modulation on ICI efficacy.},
}

@article {pmid41607395,
year = {2026},
author = {Uppala, PK and Karanam, SK and Maddi, R},
title = {Science of fecal microbiota transplant: From history to cutting-edge clinical practice.},
journal = {World journal of gastrointestinal endoscopy},
volume = {18},
number = {1},
pages = {113133},
pmid = {41607395},
issn = {1948-5190},
abstract = {Fecal microbiota transplantation (FMT) is a pioneering medical technique designed to re-establish a balanced gut microbiome by transferring processed stool from a rigorously screened donor into the gastrointestinal tract of a recipient. Initially conceived as a last-resort therapy for recurrent Clostridioides difficile (C. difficile) infections - a challenging condition frequently resistant to conventional antibiotics - FMT has achieved impressive clinical response rates, often surpassing 80% in resolving recurrent C. difficile infections. This remarkable success has generated significant enthusiasm for its potential use in addressing a broader spectrum of disorders linked to disrupted gut microbial populations, including inflammatory bowel disease, irritable bowel syndrome, metabolic syndrome, and various autoimmune and neurological conditions. However, the wider clinical integration of FMT is accompanied by several notable challenges. These include the need for optimal donor selection, comprehensive long-term follow-up of recipients, standardization of stool processing and delivery methods, and thorough economic evaluation to establish cost-effectiveness. Safety remains a top priority, with particular attention paid to minimizing the risk of infectious disease transmission and preventing unwanted immune responses. Regulatory standards for FMT vary internationally, with some nations categorizing it as a biologic therapy or experimental treatment, while others have established more formalized approval processes. This article offers a comprehensive examination of FMT, covering its historical evolution, underlying mechanisms, current clinical applications, safety protocols, and regulatory landscape. By consolidating the latest research and clinical guidelines, it aims to educate clinicians, researchers, and policymakers on the expanding role of FMT in modern healthcare.},
}

@article {pmid41607348,
year = {2026},
author = {Abenavoli, L and Yosypenko, K and Yurchyshena, Y and Savytska, M and Lazarieva, O and Shvets, Y and Scarlata, GGM and Lynchak, O and Falalyeyeva, T},
title = {Effect of supplementation with synbiotics in metabolic syndrome: mechanisms and clinical implications.},
journal = {Minerva gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.23736/S2724-5985.25.04054-9},
pmid = {41607348},
issn = {2724-5365},
abstract = {Metabolic syndrome (MetS) is a complex and multifactorial condition that represents a major global health challenge. It is characterized by a cluster of interrelated metabolic abnormalities, including central obesity, insulin resistance, dyslipidemia, and hypertension, all of which substantially increase the risk of developing type 2 diabetes mellitus, cardiovascular diseases, and other related complications. Growing evidence underscores the pivotal role of the gut microbiota in regulating host metabolism, modulating immune responses, and influencing the chronic low-grade inflammatory state associated with MetS. Among emerging therapeutic approaches, synbiotics, defined as synergistic combinations of probiotics and prebiotics, have attracted considerable interest. Therefore, in the present narrative review, we aim to find out the feasibility and effectiveness of synbiotic supplements, as well as to evaluate their impact on people with MetS. By selectively stimulating the growth and activity of beneficial microbial taxa while directly introducing health-promoting strains, synbiotics may restore microbial balance, improve metabolic homeostasis, and attenuate inflammatory pathways. Future research should prioritize personalized nutrition strategies and microbiome-tailored interventions, taking into account individual variability in gut microbial composition and host metabolic responses. Such precision approaches could optimize synbiotic efficacy and safety, positioning them as a viable adjunctive treatment for MetS within an integrated lifestyle and pharmacological framework. Ultimately, large-scale, high-quality randomized controlled trials are essential to confirm current promising findings and to establish clear guidelines for clinical application.},
}

@article {pmid41607234,
year = {2026},
author = {Nasrah, R and Jagoe, RT},
title = {The gut microbiome and dietary interventions in cancer cachexia.},
journal = {Current opinion in clinical nutrition and metabolic care},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCO.0000000000001211},
pmid = {41607234},
issn = {1473-6519},
abstract = {PURPOSE OF REVIEW: The gut microbiome (GM) is altered in cancer cachexia, and it is possible that such GM changes may promote or sustain features of cancer cachexia including changes in host metabolism and anorexia. As a result, there is growing interest in GM-focused interventions to address cancer cachexia. In this review, the factors that likely contribute to changes in GM in cancer cachexia are highlighted. Also, this review presents recent data on GM-derived predictive biomarkers for response to dietary interventions in cachexia.

RECENT FINDINGS: The importance of maintaining or increasing energy intake to combat cancer cachexia has become clearer in recent years. However, there is wide inter-individual variation in response to changes after dietary interventions. Two recent studies have reported GM features which predict response to different types of dietary interventions: enteral feeding in pancreatic cancer patients, and oral nutritional counselling promoting an energy and protein dense diet in a mixed cancer group attending a specialized cancer cachexia clinic. Each study reported that increased abundance of a specific GM taxon predicted a more favourable response to the dietary intervention used.

SUMMARY: GM features may prove to be important in identifying patients with cancer cachexia who are more or less likely to respond well to current dietary interventions. This has clear clinical implications and utility. Further studies will be needed to determine whether GM-targeted interventions can be developed to improve response to dietary interventions and the management of cachexia more generally.},
}

@article {pmid41607112,
year = {2026},
author = {Vasconcelos, DS and Harris, DJ and Tarroso, P and Simões, C and Rato, C and Santos, X and Xavier, R},
title = {Shaped by Fire: Unravelling the Impact of Fire on Lizard Gut Microbiome.},
journal = {Molecular ecology},
volume = {35},
number = {2},
pages = {e70255},
pmid = {41607112},
issn = {1365-294X},
support = {2022.13485.BD//Fundação para a Ciência e a Tecnologia/ ; 2020.00854.CEECIND/CP1601/CT0001//Fundação para a Ciência e a Tecnologia/ ; 2022.07460.PTDC//Fundação para a Ciência e a Tecnologia/ ; },
mesh = {Animals ; *Lizards/microbiology ; *Gastrointestinal Microbiome/genetics ; Portugal ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; *Fires ; Ecosystem ; *Wildfires ; Diet ; Bacteria/genetics/classification ; },
abstract = {In recent decades, wildfire regimes have changed significantly, with increases in frequency, severity and area affected, leading to major habitat alterations that may impact species ecology. While fire's role in plant ecology is well studied, its effects on animal biotic interactions remain poorly understood. In northern Portugal, where wildfires are common, the native rock-dwelling lizard Podarcis lusitanicus may thrive postfire due to its preference for open rocky outcrops, which expand after fires. This suggests not only resilience but also a capacity for persistence in postfire disturbances driven by habitat preferences. However, changes in prey availability after fire induce dietary shifts in this insectivorous lizard, potentially affecting trophic interactions and, consequently, gut microbiota communities. Gut microbiota influence host fitness through effects on nutrition, immunity and behaviour; on the other hand, gut microbiota are affected by variations in diet and environment. This study assessed how fire history affects P. lusitanicus gut microbiota. Sampling occurred across 12 sites in northern Portugal, representing three fire histories: long-unburned, burned in 2016 and burned in 2022. Cloacal swabs were analysed by metabarcoding the V4 region of the 16S rRNA gene. Results showed that gut bacterial composition varied with fire history, as well as with sex, body size and diet. Females had higher microbial richness despite similar diet richness between sexes. While microbiome composition shifted, predicted microbiome function remained relatively stable, indicating both resilience and ecological flexibility in fire-prone environments. These findings enhance understanding of how lizard microbiomes respond to environmental disturbances and may help predict host and microbiota tolerance under changing fire regimes.},
}

Animals
*Lizards/microbiology
*Gastrointestinal Microbiome/genetics
Portugal
RNA, Ribosomal, 16S/genetics
Male
Female
*Fires
Ecosystem
*Wildfires
Diet
Bacteria/genetics/classification

@article {pmid41607069,
year = {2026},
author = {Yang, M and He, Y and Miao, X and Sun, M and Niu, H and Hua, M and Li, D and Xu, H and Wang, J},
title = {Rhodotorula mucilaginosa JAASSRY1 Ameliorates Cyclophosphamide-Induced Immunosuppression by Regulating Gut Microbiota and Activation of Spleen TLR4/MyD88/NF-κB Pathway.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2510031},
doi = {10.4014/jmb.2510.10031},
pmid = {41607069},
issn = {1738-8872},
mesh = {Animals ; *Cyclophosphamide/adverse effects ; Toll-Like Receptor 4/metabolism ; NF-kappa B/metabolism ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Spleen/drug effects/immunology/metabolism ; Myeloid Differentiation Factor 88/metabolism ; *Rhodotorula ; Signal Transduction/drug effects ; *Immunosuppression Therapy ; Cytokines/metabolism ; Immunosuppressive Agents/adverse effects ; Male ; Dysbiosis ; Mice, Inbred BALB C ; },
abstract = {The present study was designed to evaluate the ameliorative effects of Rhodotorula mucilaginosa JAASSRY1 (JAASSRY1) on cyclophosphamide (CTX)-induced immunosuppression in mice. Immunocompromised mice were established by intraperitoneal injection of CTX (80 mg/kg/bw) for three consecutive days, followed by JAASSRY1 orally administered of JAASSRY1 for 21 days. Various immunological parameters, including immune organ indices, spleen cytokine levels, and immunoglobulin profiles, were evaluated. JAASSRY1 prevented CTX-induced immune damage by reversing weight loss and immune organ atrophy, suppressing the expression of IL-6, IL-17, and IFN-γ in the spleen (P< 0.01), and restoring levels of IgA and IgG, while up-regulating IL-4 (P< 0.01). Furthermore, JAASSRY1 attenuated immunosuppressive spleen injury by modulating the TLR4/MyD88/NF-κB pathway and regulating the Bax/Bcl-2 ratio. JAASSRY1 also alleviated CTX-induced dysbiosis by enhancing the abundance of Colidextribacter and reducing the levels of Parabacteroides and Bacteroides. A significant association was observed between specific gut microbiome Bacteroides and immune parameters (P< 0.01). Above all, JAASSRY1 demonstrates efficacy in ameliorating immunosuppression through the modulation of the "gut microbiota-spleen" axis, providing a basis for the development of probiotic formulations with immunomodulatory properties.},
}

Animals
*Cyclophosphamide/adverse effects
Toll-Like Receptor 4/metabolism
NF-kappa B/metabolism
Mice
*Gastrointestinal Microbiome/drug effects
*Spleen/drug effects/immunology/metabolism
Myeloid Differentiation Factor 88/metabolism
*Rhodotorula
Signal Transduction/drug effects
*Immunosuppression Therapy
Cytokines/metabolism
Immunosuppressive Agents/adverse effects
Male
Dysbiosis
Mice, Inbred BALB C

@article {pmid41607051,
year = {2026},
author = {Han, Y and Xie, D and Shan, X and Yang, L},
title = {Glutamine: A spatially precise "GPS Signal" shaping the root microbiota.},
journal = {Journal of integrative plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jipb.70165},
pmid = {41607051},
issn = {1744-7909},
support = {2021YFA1300400//National Key R&D Program of China/ ; 23JCYBJC00540//the Natural Science Foundation of Tianjin, China/ ; No. 32471699//the National Natural Science Foundation of China/ ; },
abstract = {This commentary on Tsai et al. (2025) highlights glutamine's important role in attracting beneficial bacteria to colonize plant roots, deciphers its links to Casparian strip integrity, and explores its dual functions. This finding reveals how plants use chemical signals to shape their root microbiome for better health.},
}

@article {pmid41606855,
year = {2025},
author = {Yang, J and He, Y and Huang, J and Li, M and Wu, X and Pei, X and Yang, X},
title = {Decoding resistome profiles and horizontal transfer of antibiotic resistance genes across the pork production chain under One Health sectors.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117259},
doi = {10.1016/j.foodres.2025.117259},
pmid = {41606855},
issn = {1873-7145},
mesh = {*Gene Transfer, Horizontal ; Animals ; Swine ; Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Microbial/genetics ; *One Health ; *Drug Resistance, Bacterial/genetics ; *Pork Meat/microbiology ; Food Microbiology ; Abattoirs ; Metagenome ; Microbiota/genetics ; Metagenomics ; Bacteria/genetics ; },
abstract = {The emergence of antimicrobial resistance has become a global threat to public health. Intensive antibiotic use in swine farming has accelerated the proliferation of antibiotic resistance genes (ARGs) in animal-derived foods, making the production chain a potential ARG transmission route to humans. However, shared resistome profiles and horizontal gene transfer (HGT) mechanisms along this chain remain unclear. Here, we systematically investigated the resistome profile, ARGs' host, and potential HGT of ARGs across interconnected swine farm, slaughterhouse, and retail market by metagenomic assembly and binning. From 42 metagenomes, 1354 ARG subtypes were identified, with 303 shared across all interfaces. Both microbiome and mobile genetic elements (MGEs) contributed to the variation in ARG profiles. Pseudomonadota were the dominant drivers that shape the resistome through plasmid-mediated HGT. Among the 133 reconstructed ARG-carrying genomes (ACGs), 38 of them carried multiple ARGs, indicating the potential mobility of ARGs. Notably, 3 ACGs taxonomically assigned to Pseudomonas_E alcaligenes, Serratia_J grimesii, and Escherichia coli carrying 9, 13, and 41 ARGs, respectively. Furthermore, MetaCHIP analysis uncovered 445 potential HGT events, and ARGs including CpxR, macB, fusA, and vanR were annotated as potentially transferred subtypes. This study decodes the resistome profiles and tracks horizontal ARG transfer at the community level across the entire pork supply chain - from swine farms to retail outlets. To our knowledge, few studies have explored ARG transmission subtypes and directional flows among humans, pigs, and environmental compartments in the pork production chain using metagenomic approaches. These findings highlight the important role of the pork production chain as a critical transmission vector for ARGs under One Health framework.},
}

*Gene Transfer, Horizontal
Animals
Swine
Anti-Bacterial Agents/pharmacology
*Drug Resistance, Microbial/genetics
*One Health
*Drug Resistance, Bacterial/genetics
*Pork Meat/microbiology
Food Microbiology
Abattoirs
Metagenome
Microbiota/genetics
Metagenomics
Bacteria/genetics

@article {pmid41606854,
year = {2025},
author = {Okoye, CO and Abhadiomhen, SE and Ezenwanne, BC and Chen, X and Jiang, H and Wu, Y and Jiang, J},
title = {Machine learning-based predictive modeling of foodborne pathogens and antimicrobial resistance in food microbiomes using omics techniques: A systematic review.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117255},
doi = {10.1016/j.foodres.2025.117255},
pmid = {41606854},
issn = {1873-7145},
mesh = {*Machine Learning ; *Food Microbiology ; *Foodborne Diseases/microbiology ; *Microbiota ; *Drug Resistance, Bacterial/genetics ; Animals ; Genomics/methods ; Metagenomics ; Salmonella/pathogenicity/genetics ; Food Safety ; Humans ; },
abstract = {The globalization of food systems has heightened the risk of foodborne pathogens such as Salmonella, Listeria monocytogenes, and Campylobacter, exacerbated by rising antimicrobial resistance (AMR). Traditional pathogen identification and AMR risk surveillance methods are often labor-intensive and low-throughput, while single-omics approaches fail to capture microbial complexity. Moreover, reliance on individual machine learning (ML) models limits predictive robustness, posing challenges to food safety and public health. This systematic review evaluates ML-based predictive modeling integrated with omics techniques (genomics, metagenomics, and transcriptomics) for foodborne pathogen and AMR risk surveillance. Following PRISMA guidelines, 1245 articles from PubMed, Scopus, and other databases (2015-2025) were screened, selecting 13 relevant studies. These studies applied ML algorithms, including Random Forest (RF), Extreme Gradient Boosting (XGBoost), and Support Vector Machines (SVM), to enhance predictive accuracy. The selected studies demonstrated predictive accuracies up to 99 % and AUROC scores above 0.90. Key discoveries include genetic markers for Salmonella virulence, Listeria attribution to fruits and dairy, and 145 mobile antimicrobial resistance genes (ARGs) in poultry. Despite these advancements, limitations such as small sample sizes, inconsistent metadata, overfitting, and computational scalability hinder real-world implementation. This review underscores the potential of ML-driven omics frameworks to revolutionize foodborne pathogen and AMR risk monitoring, paving the way for smarter, more resilient food safety systems. However, methodological inconsistencies necessitate standardized protocols, larger datasets, and explainable AI (XAI) to improve reliability and applicability in global food safety monitoring.},
}

*Machine Learning
*Food Microbiology
*Foodborne Diseases/microbiology
*Microbiota
*Drug Resistance, Bacterial/genetics
Animals
Genomics/methods
Metagenomics
Salmonella/pathogenicity/genetics
Food Safety
Humans

@article {pmid41606853,
year = {2025},
author = {Zhang, T and Liao, Z and Bi, J and Li, Z and Liu, Y and Liu, Y and Song, Y and Qin, Y},
title = {Multi-omics analysis reveals microbial community succession and aroma enhancement mechanisms during spontaneous oak-barrel fermentation of chardonnay wine.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117249},
doi = {10.1016/j.foodres.2025.117249},
pmid = {41606853},
issn = {1873-7145},
mesh = {*Wine/analysis/microbiology ; *Fermentation ; *Odorants/analysis ; *Quercus/microbiology ; *Microbiota ; Volatile Organic Compounds/analysis ; *Food Microbiology ; Bacteria/classification/metabolism ; Oxygen/analysis ; *Food Handling/methods ; Fungi/metabolism/classification ; Metabolomics ; Multiomics ; },
abstract = {Spontaneous oak-barrel fermentation contributes to terroir-associated attributes and enhances aroma complexity in wines; however, the microbial succession dynamics and mechanisms underlying aroma enhancement remain unclear. This study comprehensively analyzed the dissolved oxygen concentrations, physicochemical properties, microbial community structures, and aroma compounds during spontaneous oak-barrel fermentation of Chardonnay wine. The results demonstrated that during spontaneous fermentation, dissolved oxygen concentrations varied among different barrel types, with the highest levels observed in new oak barrels, followed by old oak barrels, and the lowest in stainless-steel barrels. Microbiome analysis indicated that the predominant microorganisms included Saccharomyces, Hanseniaspora, Metschnikowia, Fructobacillus, Lactobacillus, and Gluconobacter, all of which were closely associated with aroma compounds formation. The differences in bacterial community composition between different oak barrels were minimal, while the differences in fungal composition were more pronounced. Metabolome analysis identified 15 key differential aroma compounds among the different barrel types, mainly esters, higher alcohols, and acids. Fermentation in new oak barrels exhibited higher concentrations of ester and acid compounds, while fermentation in stainless-steel barrels showed higher levels of higher alcohol compounds. This study elucidates for the first time various oak barrel types influence aroma differentiation during spontaneous fermentation primarily through the interaction between dissolved oxygen and microbial communities. These findings provide valuable insights for optimizing oak barrel usage and enhancing Chardonnay wine quality.},
}

*Wine/analysis/microbiology
*Fermentation
*Odorants/analysis
*Quercus/microbiology
*Microbiota
Volatile Organic Compounds/analysis
*Food Microbiology
Bacteria/classification/metabolism
Oxygen/analysis
*Food Handling/methods
Fungi/metabolism/classification
Metabolomics
Multiomics

@article {pmid41606850,
year = {2025},
author = {Wang, Y and Zhao, L and Huang, S and Peng, J and Wu, K and Wu, M},
title = {High-fat diet-induced obesity disrupts the gut microbiome and mucus secretion to aggravate experimental colitis.},
journal = {Food research international (Ottawa, Ont.)},
volume = {221},
number = {Pt 1},
pages = {117245},
doi = {10.1016/j.foodres.2025.117245},
pmid = {41606850},
issn = {1873-7145},
mesh = {Animals ; *Gastrointestinal Microbiome/physiology ; *Diet, High-Fat/adverse effects ; *Obesity/complications/microbiology ; *Colitis/chemically induced/microbiology/etiology ; Goblet Cells/metabolism ; Mice, Inbred C57BL ; Mice ; *Mucus/metabolism ; Dextran Sulfate ; Male ; Disease Models, Animal ; Intestinal Mucosa/metabolism ; Colon/pathology ; },
abstract = {Obesity and its associated comorbidities have emerged as a major public health crisis. Accumulating evidence indicates that a high fat diet (HFD) may promote intestinal injury. However, the roles of intestinal goblet cells and specific gut microbiota composition in colitis under obesity conditions remain unclear. In this study, we employed a HFD-induced obesity model combined with dextran sulfate sodium (DSS) to induce colitis in mice. Our results reveal that obesity exacerbates DSS-induced colitis in the colon, as evidenced by increased intestinal barrier injury. These changes are associated with impaired goblet cell maturation, reduced mucus production, and a disrupted microbiota composition, notably characterized by an enrichment of pro-inflammatory bacteria Escherichia-Shigella and Helicobacter. In vitro, combined HFD and DSS treatment suppresses mucus secretion and alters the metabolic profile of LS174T cells, particularly affecting amino acid metabolism. Collectively, our findings reveal that HFD-induced obesity aggravates colitis severity, involving disruption of goblet cell function and gut microbial homeostasis, highlighting the importance of dietary intervention in obese individuals to alleviate intestinal inflammation.},
}

Animals
*Gastrointestinal Microbiome/physiology
*Diet, High-Fat/adverse effects
*Obesity/complications/microbiology
*Colitis/chemically induced/microbiology/etiology
Goblet Cells/metabolism
Mice, Inbred C57BL
Mice
*Mucus/metabolism
Dextran Sulfate
Male
Disease Models, Animal
Intestinal Mucosa/metabolism
Colon/pathology

@article {pmid41608402,
year = {2025},
author = {Roth, W and Lo, E and De Leon, O and Suriya, S and Fakhri, F and Brorson, JR and Polster, S and Kass-Hout, T and Prabhakaran, S and Siegler, JE},
title = {Understanding the Relationship Between Cerebrovascular Disease and the Gut Microbiome.},
journal = {Stroke (Hoboken, N.J.)},
volume = {5},
number = {1},
pages = {e001272},
pmid = {41608402},
issn = {2694-5746},
abstract = {While traditional vascular risk factors (eg, hypertension, dyslipidemia, tobacco use) account for 20% of the explained variance in carotid atherosclerosis, they remain a prominent focus for primary and secondary ischemic stroke prevention strategies. Among other potential contributors to atheroma formation and cerebrovascular disease, the gut microbiome has become increasingly implicated as a mediator of vascular risk. The foods we eat, coupled with our physiology and exposures (eg, antibiotics, supplements), directly contribute to atherosclerotic disease in complex ways that are mediated by gastrointestinal flora and metabolic by-products. Proliferation of "pathogenic" gut microbes such as Enterobacteriaceae and Streptococcus spp, decrement of "commensal" species such as Akkermansia spp and the biodiversity of gut flora are directly related to an individual's dietary intake and exposure history. Each of these components of the gut microbiome correlate with the development or progression of many conditions including atherosclerosis. Moreover, the metabolism of certain substrates found in animal products (notably l-carnitine and choline) and of refined sugars by these microorganisms leads to buildup of circulating metabolites with known links to atherogenesis, platelet activation, atrial fibrillation, and other adverse vascular outcomes. Several of these toxic metabolites, including trimethylamine and trimethylamine N-oxide, have been extensively studied in cardiovascular and cerebrovascular disease. Trimethylamine and trimethylamine N-oxide represent not only biomarkers of gut dysbiosis and cardiovascular risk, but they are increasingly recognized as therapeutic targets for novel interventions in atherosclerotic vascular disease. The individualized targeting of one's microbiome, and perhaps more generalized targeting of toxic microbial metabolites, has the potential to revolutionize the treatment of vascular disease. In this review, we summarize the latest evidence illustrating the impact of the microbiome on cerebrovascular disease and highlight the potential applications of this information on individualized and global scales.},
}

@article {pmid41606790,
year = {2026},
author = {Clutter, CH and Leung, DT},
title = {Tracing MR1 expression across tissues to find the perfect MAIT.},
journal = {Journal of leukocyte biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jleuko/qiag014},
pmid = {41606790},
issn = {1938-3673},
abstract = {Mucosal associated invariant T (MAIT) cells are part of a T cell subset that is activated upon presentation of B2 vitamin (riboflavin) metabolites by the major histocompatibility complex, class I related (MR1) protein. Though there is a clear relationship between microbial production of riboflavin and MAIT cell development and persistence, little is known about the cells that primarily communicate with MAIT cells and other MR1-restricted T cells. Elegant work by Deng et al demonstrates that it is macrophages from the lung and peritoneum that express the highest amount of MR1 and are the most efficient at presenting vitamin B antigens to MAIT cells. This landmark study not only definitively identifies and maps the key antigen presenting cell populations involved in MAIT cell activation, it also reveals a bidirectional relationship between MR1 expression and the host microbiome. While further work on how these findings translate to human MAIT cell biology is needed, this study has provided us with unprecedented insights into the mechanistic interplay and microbial ecology of MR1 presentation of riboflavin metabolites.},
}

@article {pmid41606773,
year = {2026},
author = {Ross, SM},
title = {Forever Young, Part 3: Urolithin A: A Gut Microbiome-Derived Metabolite and Its Role in Aging.},
journal = {Holistic nursing practice},
volume = {},
number = {},
pages = {},
pmid = {41606773},
issn = {1550-5138},
}

@article {pmid41606595,
year = {2026},
author = {Luan, J and Zhang, X and Chen, T and Pu, S and Shen, Z and Xu, C and Chen, Z and Zhang, J and Chen, D},
title = {Adolescent exposure to polystyrene nanoplastics induces male reproductive damage via the microbiome-gut-testis axis.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04069-y},
pmid = {41606595},
issn = {1477-3155},
support = {ZDXK202219//Jiangsu Province Capability Improvement Project through Science, Technology and Education/ ; PY2025017//Young Scholars Fostering Fund of the First Affiliated Hospital of Nanjing Medical University/ ; PY2023002//Young Scholars Fostering Fund of the First Affiliated Hospital of Nanjing Medical University/ ; 2022ZB730//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; 82103580//National Natural Science Foundation of China/ ; },
abstract = {Polystyrene nanoplastics (PS-NPs), are increasingly associated with reduced male fertility, yet the underlying mechanisms remain poorly defined. Here, we systematically unraveled a novel microbiome-gut-testis axis mediating PS-NPs-induced reproductive toxicity. Adolescent rats exposed to PS-NPs for 5 weeks induced dose-dependent testicular injury, characterized by disrupted spermatogenesis, and compromised blood-testis barrier. Single-cell atlases revealed spermatogenic arrest, abnormal immune microenvironment, and perturbed testicular cell communication upon exposure to PS-NPs. Furthermore, multi-omics analysis highlighted the activation of NF-κB/IL-17/HIF-1 and inhibition of PPAR-γ signaling, contributing to increased DNA damage and apoptosis, suppressed autophagy, and dysregulated energy-lipid metabolism. Additionally, PS-NPs exposure initiated gut microbial dysbiosis, significantly increasing pro-inflammatory bacteria, while reducing beneficial commensals. This microbial disruption compromised intestinal barrier integrity, leading to elevated circulating LPS levels. Subsequent activation of the TLR4/MyD88/NF-κB signaling pathway propagated inflammatory responses to testes. Crucially, FMT from PS-NPs-exposed donors reproduced the damage in healthy recipients, thus suggesting gut microbiota as a causal mediator. Therapeutically, DI intervention effectively mitigated the reproductive toxicity by restoring gut barrier integrity, rebalancing microbial communities, and suppressing inflammation. Our findings unveil a gut microbiome-centric mechanism for nanoplastic-induced male reproductive toxicity, and identify DI as a promising therapeutic candidate, accordingly providing critical insights for environmental risk assessment.},
}

@article {pmid41606550,
year = {2026},
author = {Zhang, X and Xu, J and Chen, M and Wu, Y and Chen, D and Xu, X and He, X},
title = {Aspergillus fumigatus in mechanically ventilated pneumonia- independent mortality risk and synergistic microbiome signatures from a multicenter mNGS cohort.},
journal = {BMC pulmonary medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12890-026-04131-3},
pmid = {41606550},
issn = {1471-2466},
support = {2022GYX28//Lishui Public Welfare Technology Application Research Program Project/ ; },
}

@article {pmid41606514,
year = {2026},
author = {Hu, S and Luo, C and Wan, S and Zhang, S and Li, N and Liu, G and Zhao, LY},
title = {Modulating the gut microbiome to enhance cancer immunotherapy: a systematic review and Meta-Analysis of probiotics and FMT as adjuncts.},
journal = {BMC cancer},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12885-026-15655-6},
pmid = {41606514},
issn = {1471-2407},
}

@article {pmid41606319,
year = {2026},
author = {Kamitaki, N and Handsaker, RE and Hujoel, MLA and Mukamel, RE and Usher, CL and McCarroll, SA and Loh, PR},
title = {Human and bacterial genetic variation shape oral microbiomes and health.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {41606319},
issn = {1476-4687},
abstract = {Human genetic variation influences all aspects of our biology, including the oral cavity[1-3], through which nutrients and microbes enter the body. Yet it is largely unknown which human genetic variants shape a person's oral microbiome and potentially promote its dysbiosis[3-5]. We characterized the oral microbiomes of 12,519 people by re-analysing whole-genome sequencing reads from previously sequenced saliva-derived DNA. Human genetic variation at 11 loci (10 new) associated with variation in oral microbiome composition. Several of these related to carbohydrate availability; the strongest association (P = 3.0 × 10[-188]) involved the common FUT2 W154X loss-of-function variant, which associated with the abundances of 58 bacterial species. Human host genetics also seemed to powerfully shape genetic variation in oral bacterial species: these 11 host genetic variants also associated with variation of gene dosages in 68 regions of bacterial genomes. Common, multi-allelic copy number variation of AMY1, which encodes salivary amylase, associated with oral microbiome composition (P = 1.5 × 10[-53]) and with dentures use in UK Biobank (P = 5.9 × 10[-35], n = 418,039) but not with body mass index (P = 0.85), suggesting that salivary amylase abundance impacts health by influencing the oral microbiome. Two other microbiome composition-associated loci, FUT2 and PITX1, also significantly associated with dentures risk, collectively nominating numerous host-microbial interactions that contribute to tooth decay.},
}

@article {pmid41606239,
year = {2026},
author = {Salem, GM and Azamor, T and Familiar-Macedo, D and Onwubueke, C and Cambou, MC and Chen, W and Nielsen-Saines, K and Foo, SS},
title = {Mechanistic insights into the impact of prenatal viral infections on maternal and offspring immunity.},
journal = {Npj viruses},
volume = {4},
number = {1},
pages = {7},
pmid = {41606239},
issn = {2948-1767},
support = {N/A//Cleveland Clinic/ ; },
abstract = {Global outbreaks of human immunodeficiency virus (HIV) and respiratory viruses - severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza, accounted for ~50 million infections in 2024. Prenatal exposure to these viruses poses substantial risks to maternal and fetal health, yet the underlying immunological mechanisms remain incompletely understood. Despite differences in viral biology and transmission, mounting evidence reveals a convergent theme of maternal immune activation during pregnancy. Even without vertical transmission, virus-elicted maternal immune responses alter the maternal-fetal interface and gut microbiome, reshaping fetal immunity and birth outcomes. These immune perturbations increase susceptibility to infections, neurodevelopmental disorders, and immune-mediated diseases later in life. Here, we discuss viral immune evasion strategies that modulate maternal immunity and review current clinical and emerging therapeutic approaches aimed at mitigating long-term consequences in exposed children. Understanding how prenatal viral exposure shapes lifelong health is critical for developing targeted interventions and reducing postnatal disease burden.},
}

@article {pmid41606218,
year = {2026},
author = {Abdelhameed, A and Hussein, RH and Hatem, ZA and Bağcı, C and Ziemert, N},
title = {From niche to niche: investigating microbial communities and their specialised metabolite gene clusters in human microbiomes.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {65},
pmid = {41606218},
issn = {1573-0972},
mesh = {Humans ; *Multigene Family ; *Microbiota/genetics ; *Bacteria/genetics/metabolism/classification/isolation & purification ; Metagenomics ; Biosynthetic Pathways/genetics ; Metagenome ; },
abstract = {Diverse microbial communities within the human microbiome perform vital functions which influence both health and disease in hosts. Specialized metabolites produced by microbes via biosynthetic gene clusters (BGCs) drive ecological interactions and offer possibilities for therapeutic application. The biosynthetic capabilities of microorganisms present in human microbiomes are still mostly unexplored despite metagenomics advancements. The study examines the variety of microbial communities and BGC locations through metagenomic data from 1,191 samples across eight human microbiomes taken from the IMG/M database. Kraken2 executed taxonomic classification while antiSMASH v6.1.1 identified BGCs. The study used BiG-SCAPE to build a sequence similarity network while Bracken and Pavian tools analyzed microbial diversity. A total of 25,681 BGCs were identified, of which 97.5%, showed no significant match to existing clusters in MIBIG database, indicating substantial potential for novel biosynthetic discoveries . Showing no match to existing clusters in the MIBiG database which shows huge potential for new biosynthetic discoveries. New strains were discovered that produce unique RiPPs, NRPs, and siderophores primarily within the microbiomes of the large intestine, oral cavity, and skin. The large intestine showed maximum microbial and biosynthetic diversity compared to other areas while the biliary tract and nasal cavity displayed minimal diversity. New BGCs associated with antibiotic, cytotoxic, and immune-modulating functions present potential therapeutic uses. The investigation uncovers essential information about how microbial communities develop specific functions within various body regions. Uncharacterized BGC discoveries present new opportunities for drug development and treatments that target microbiomes.},
}

Humans
*Multigene Family
*Microbiota/genetics
*Bacteria/genetics/metabolism/classification/isolation & purification
Metagenomics
Biosynthetic Pathways/genetics
Metagenome

@article {pmid41606121,
year = {2026},
author = {Duttagupta, S and Messaoudene, M and Hunter, S and Desilets, A and Jamal, R and Mihalcioiu, C and Belkaid, W and Marcoux, N and Fidelle, M and Suissa, D and Ponce, M and Geiger, M and Malo, J and Piccinno, G and Punčochář, M and Filin, A and Heidrich, V and Rusu, D and Mbaye, B and Durand, S and Ben Aissa, I and Puller, V and de Lahondès, R and Blais, N and Tehfe, M and Owen, S and Bélanger, K and Parvathy, SN and Shieh, B and Raphael, J and Lenehan, J and Breadner, D and Rothenstein, J and Rozza, N and Maillou, J and Nili, S and Prifti, DK and Pinto, F and Armanini, F and Kim-Schulze, S and Marron, TU and Kroemer, G and Derosa, L and Zitvogel, L and Silverman, M and Segata, N and Vareki, SM and Routy, B and Elkrief, A},
title = {Fecal microbiota transplantation plus immunotherapy in non-small cell lung cancer and melanoma: the phase 2 FMT-LUMINate trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41606121},
issn = {1546-170X},
abstract = {Immune checkpoint inhibitors (ICI) have improved outcomes for patients with non-small cell lung cancer (NSCLC) and melanoma, yet over half of patients exhibit primary resistance. Fecal microbiota transplantation (FMT) may overcome resistance to anti-programmed cell death protein 1 (PD-1) therapy. The clinical activity and safety of FMT plus anti-PD-1 in NSCLC or anti-PD-1 plus anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) therapy in melanoma have not been evaluated. Here we report results from FMT-LUMINate, a multicenter, open-label, phase 2 trial assessing healthy donor FMT plus anti-PD-1 in NSCLC (n = 20) or anti-PD-1 plus anti-CTLA-4 (dual ICI) in melanoma (n = 20), in the first-line setting. Eligible patients received a single FMT via oral capsules prior to ICI initiation. The primary endpoint was objective response rate (ORR) in NSCLC. Secondary endpoints included ORR in melanoma, safety and donor-host microbiome similarity. In NSCLC, the ORR was 80% (16/20), meeting the study primary endpoint. In melanoma, the ORR was 75% (15/20). FMT was deemed safe in both cohorts by an independent data and safety monitoring committee, with no grade 3 or higher adverse events (AEs) in NSCLC and 13 (65%) patients experiencing grade 3 or higher AEs in melanoma. Shotgun metagenomic sequencing revealed that responders developed a distinct post-FMT gut microbiome composition, independent of acquired donor-recipient similarity or strain-level engraftment. Responders exhibited significantly greater loss of baseline bacterial species compared to non-responders, with frequent depletion of Enterocloster citroniae, E. lavalensis and Clostridium innocuum. This finding was reproduced across three published FMT oncology trials. We recolonized antibiotic-treated, tumor-bearing mice with post-FMT stool from two responder patients, and reintroduction of the specific bacterial species that were lost after FMT abrogated the antitumor effect of ICI. Taken together, these findings confirm the clinical activity of FMT in combination with ICI and suggest that the elimination of deleterious taxa is required for FMT-mediated therapeutic benefit. ClinicalTrials.gov identifier: NCT04951583 .},
}

@article {pmid41606120,
year = {2026},
author = {Fernandes, R and Jabbarizadeh, B and Rajeh, A and Hong, MMY and Baines, KJ and Ernst, S and Winquist, E and Ali, AS and Penny, S and Figueredo, R and Parvathy, SN and Lenehan, JG and Pinto, DM and Silverman, MS and Maleki Vareki, S},
title = {Fecal microbiota transplantation plus immunotherapy in metastatic renal cell carcinoma: the phase 1 PERFORM trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41606120},
issn = {1546-170X},
support = {1-MR_2022_4884//Lotte and John Hecht Memorial Foundation (Lotte & John Hecht Memorial Foundation)/ ; 203745/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Immune checkpoint inhibitors (ICIs) improve outcomes in metastatic renal cell carcinoma (mRCC) but are hindered by immune-related adverse events (irAEs). Modulation of the gut microbiome may enhance efficacy and mitigate toxicity, yet the safety and mechanisms of healthy donor fecal microbiota transplantation (FMT) in mRCC remain unexplored. In this phase 1 trial, 20 treatment-naive patients with mRCC received encapsulated healthy donor FMT (LND101) combined with ipilimumab/nivolumab (n = 16), pembrolizumab/axitinib (n = 3) or pembrolizumab/lenvatinib (n = 1). The primary endpoint was safety, defined by the incidence and severity of irAEs. Secondary endpoints included clinical response (Response Evaluation Criteria in Solid Tumors version 1.1), gut microbiome and immune correlates and patient-reported quality of life. The safety endpoint was met with 50% (10/20) of patients experiencing grade 3 irAEs and no serious FMT-related toxicities or grade 4 or 5 irAEs. Among evaluable patients, the objective response rate was 50% (9/18), including two complete responses (11%, 2/18). Notably, most treatment responders did not develop any grade 3 or higher irAEs. Alpha (α) diversity improvement and durable engraftment of taxa and metabolic functions associated with anti-inflammatory properties correlated with reduced toxicity and improved response. Conversely, patients experiencing grade 3 irAEs exhibited expansion of Segatella copri, particularly with ipilimumab/nivolumab, and elevated levels of donor-derived microbial enzymes previously linked to pro-inflammatory activity. Resilience to toxicity correlated with the maintenance of protective metabolites and increased levels of immune regulatory cells, whereas the presence of grade 3 irAEs and S. copri enrichment was associated with high immune dysregulation. These findings demonstrate the safety and potential for functional microbiome engraftment to optimize response and minimize toxicity in ICI-treated mRCC. ClinicalTrials.gov identifier: NCT04163289 .},
}

@article {pmid41606119,
year = {2026},
author = {Porcari, S and Ciccarese, C and Heidrich, V and Rondinella, D and Quaranta, G and Severino, A and Arduini, D and Buti, S and Fornarini, G and Primi, F and Stumbo, L and Giannarelli, D and Giudice, GC and Damassi, A and Giron Berríos, JR and Punčochář, M and Barbazuk, TB and Piccinno, G and Pinto, F and Armanini, F and Asnicar, F and Schinzari, G and Derosa, L and Kroemer, G and Sanguinetti, M and Masucci, L and Gasbarrini, A and Tortora, G and Cammarota, G and Zitvogel, L and Segata, N and Iacovelli, R and Ianiro, G},
title = {Fecal microbiota transplantation plus pembrolizumab and axitinib in metastatic renal cell carcinoma: the randomized phase 2 TACITO trial.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {41606119},
issn = {1546-170X},
support = {GR-2018-12365734//Ministero della Salute (Ministry of Health, Italy)/ ; PNRR-POC-2023-12377319//Ministero della Salute (Ministry of Health, Italy)/ ; PNRR-POC-2023-12377319//Ministero della Salute (Ministry of Health, Italy)/ ; 30203//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; FIS00001711//Ministero dell'Istruzione, dell'Università e della Ricerca (Ministry of Education, University and Research)/ ; ERC-StG MicroRestore-101221279//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101052444//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; microTOUCH-101045015//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 101168810//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; ONCOBIOME-825410//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; IHMCSA-964590//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; 1U01CA230551//U.S. Department of Health & Human Services | NIH | National Cancer Institute (NCI)/ ; },
abstract = {Renal cell carcinoma (RCC) is a common malignancy with limited durable responses to first-line immune checkpoint inhibitor (ICI)-based therapies. Emerging evidence implicates the gut microbiome in modulating ICI efficacy. In the investigator-initiated, randomized, double-blind placebo-controlled phase 2a TACITO trial, we evaluated whether fecal microbiota transplantation (FMT) from complete ICI responders enhances clinical outcomes in treatment-naive patients with metastatic RCC (mRCC) receiving pembrolizumab + axitinib. The primary endpoint was the rate of patients free from disease progression at 12 months after randomization (12-month progression-free survival (PFS)). Secondary endpoints were median PFS and median overall survival, objective response rate (ORR), safety and microbiome changes, after randomization. Forty-five patients randomly received donor FMT (d-FMT) or placebo FMT (p-FMT). Although the primary endpoint was not met (70% versus 41% for d-FMT versus p-FMT, respectively, P = 0.053), the secondary endpoint of median PFS was significantly longer with d-FMT (24.0 months in the d-FMT arm versus 9.0 months in the p-FMT arm; hazard ratio = 0.50, P = 0.035). The ORR was 52% of patients in the d-FMT arm and 32% of patients receiving placebo. Microbiome analysis confirmed donor strain engraftment and increased α-diversity and larger microbiome shifts (β-diversity) compared with baseline composition in the d-FMT treatment group. Acquisition or loss of specific strains, but not total engraftment, was associated with the primary endpoint. Our findings support the safety and potential efficacy of selected donor FMT to enhance ICI-based treatment in mRCC, which deserves further investigations. ClinicalTrials.gov identifier: NCT04758507 .},
}

@article {pmid41606026,
year = {2026},
author = {Rahat, MTI and Sumi, MSA and Nurejannath, M and Ahmmed, R and Kibria, MK},
title = {Identification of bacterial key genes and therapeutic targets in hypertensive patients with type 2 diabetes through bioinformatics analysis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-36467-5},
pmid = {41606026},
issn = {2045-2322},
abstract = {Hypertension (HTN) coexisting with type 2 diabetes (T2D) significantly increases cardiovascular risk, yet most microbiome studies have focused on these diseases separately and have overlooked their combined microbial gene-level mechanisms. The coexistence of HTN and T2D may create a distinct gut microbial environment where metabolic and vascular pathways intersect but the specific bacterial genes and molecular interactions underlying this dual phenotype remain largely unknown. To address this gap, this study aimed to identify bacterial key genes (bKGs) associated with hypertension coexisting with type-2 diabetes (HTNT2D) and to explore therapeutic agents targeting these bKGs through integrated bioinformatics approaches. A total of 124 gut microbiome samples, including 95 healthy controls (HC) and 29 HTNT2D cases were analyzed. Diversity analysis revealed significantly higher microbial richness and distinct clustering in HTNT2D, indicating altered microbial community structure. Differential abundance analysis identified 19 bacterial genera across four dominant phyla, while functional prediction uncovered 195 enriched metabolic pathways and 257 associated genes. To refine these finding, protein-protein interaction analysis highlighted 10 hub genes (acpP, dnaG, fusA, gltB, guaA, gyrB, lacZ, mdh, purF and tktA) as potential drivers of HTNT2D pathogenesis. Molecular docking analysis of these bKGs revealed binding affinities ranging from - 4.109 to -9.961 kcal/mol and three top-ranked drug candidates named Naringin-fusA (-9.961 kcal/mol), Neohesperidin-mdh (-9.818 kcal/mol), and Bromocriptine-gyrB (-9.446 kcal/mol) were selected as potential drugs based on their binding affinities. Subsequent molecular dynamics simulations performed for 100 ns confirmed the stability of their complexes, supporting their biological relevance. Drug-likeness and ADMET evaluations pointed to Bromocriptine as the most suitable compound though further safety validation will be necessary. Overall, this study provides novel insights into the gut microbiome signatures of HTNT2D and identifies bKGs with therapeutic potential. These computationally identified candidates can be prioritized for experimental validation to advance microbiome-based diagnostics and targeted therapies for HTNT2D management.},
}

@article {pmid41605941,
year = {2026},
author = {Di Grazia, G and Sánchez-Bayona, R and Casals-Pascual, C and Pascual, T and Generali, D and Gennari, A and Vigneri, P and Harbeck, N and Cortés, J and Prat, A and Schettini, F},
title = {Dynamic biomarkers in hormone receptor-positive/HER2-negative breast cancer trials: a new hope for precision oncology.},
journal = {NPJ breast cancer},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41523-026-00904-5},
pmid = {41605941},
issn = {2374-4677},
abstract = {Hormone receptor-positive/HER2-negative breast cancer evolves in response to therapy, demanding smarter, adaptive biomarker-based treatment strategies. We review emerging dynamic biomarkers to guide therapeutic decision-making, spanning tissue and liquid biopsies, metabolic imaging, and microbiome profiling, that capture tumor or host-related changes over time. By contrasting Academic and Industry approaches, we advocate for a cultural shift in clinical trial design and implementation, aiming to move from reactive to proactive Oncology.},
}

@article {pmid41605932,
year = {2026},
author = {Raethong, N and Patumcharoenpol, P and Vongsangnak, W},
title = {Modeling diet-gut microbiome interactions and prebiotic responses in Thai adults.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00921-z},
pmid = {41605932},
issn = {2055-5008},
support = {N42A660907//National Research Council of Thailand/ ; },
abstract = {The impact of diet on gut microbial metabolism is essential for advancing microbiome-based health interventions. This study introduces a novel systems biology pipeline that integrates genome-scale metabolic models (GSMMs) with Thai dietary intake data to simulate gut microbiome metabolism and assess prebiotic responses. Utilizing metagenomic data from healthy Thai adults and an average Thai diet derived from national surveys, community-scale metabolic models (CSMMs) were developed and simulated under both typical dietary and prebiotic-supplemented condition. Flux variability analysis was employed to assess metabolic capacities, short-chain fatty acids (SCFAs) production in relation to microbial taxonomy. The results promisingly revealed inter-individual variability in SCFA profiles, with Bacteroides and Phocaeicola notably linked to isobutyrate production and Bifidobacterium emerged as a key responder to prebiotic supplementation. This integrative framework offers biological insights into diet-gut microbiome interactions and provides a foundation for the development of precision nutrition strategies tailored to the Thai population.},
}

@article {pmid41605865,
year = {2026},
author = {Solis, S and Maldonado, EM and Mukhopadhyay, S and Jan, G and Landete, JM and Maluquer de Motes, C and Gutierrez-Merino, J},
title = {Self-aggregating Lactiplantibacillus plantarum enhances type-I interferon responses via the cytosolic sensors NOD2 and cGAS.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2615490},
doi = {10.1080/19490976.2026.2615490},
pmid = {41605865},
issn = {1949-0984},
mesh = {*Interferon Type I/immunology/metabolism/genetics ; *Nod2 Signaling Adaptor Protein/metabolism/genetics/immunology ; Humans ; Gastrointestinal Microbiome ; *Nucleotidyltransferases/metabolism/genetics/immunology ; Macrophages/immunology/microbiology ; *Lactiplantibacillus plantarum/immunology/physiology ; Animals ; Cytosol ; Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase ; },
abstract = {The gut microbiome plays a critical role in health, disease and immunity. To date, we have access to large datasets describing how the microbial diversity present in the gut correlates with many clinical conditions. However, the microbiome composition is taxonomically complex; influenced by many environmental factors; and variable between individuals and communities, thereby limiting functional and mechanistic insights into the microbiota‒host interactions. We are still unsure of the molecular mechanisms by which gut commensal microbes intrinsically possess to interact with the immune system and induce beneficial responses. This study has addressed this important question by revealing that only certain members of Lactobacillaceae, a bacterial family very well known for its probiotic properties, interact very intimately with macrophages because of their ability to simultaneously overexpress adhesive cell wall proteins and to self-aggregate, leading to significant production of type I interferon (IFN-I) cytokines. IFN-I cytokines are essential to confer protection against viral infections and auto-immune disorders. Specifically, we have proved that this enhanced IFN-I feature is strain-dependent and predominantly driven by cGAS, a molecule that activates the cytosolic sensor STING upon the recognition of bacterial DNA. Furthermore, another cytosolic sensor, NOD2, seems to be an additional stimulus to amplify IFN-I production, suggesting the involvement of successive molecular events for a prominent probiotic response. Our findings provide insight into how specific molecules of probiotic bacteria modulate or stimulate host responses, providing a better understanding of the molecular crosstalk between the microbiome and immune cells.},
}

*Interferon Type I/immunology/metabolism/genetics
*Nod2 Signaling Adaptor Protein/metabolism/genetics/immunology
Humans
Gastrointestinal Microbiome
*Nucleotidyltransferases/metabolism/genetics/immunology
Macrophages/immunology/microbiology
*Lactiplantibacillus plantarum/immunology/physiology
Animals
Cytosol
Cyclic Guanosine Monophosphate-Adenosine Monophosphate Synthase

@article {pmid41605799,
year = {2026},
author = {Lee, H and Lee, MH and Seo, SH and Pak, J and Bae, S and Lee, G and Kim, HS and Kim, K and Kim, JH and Son, HS},
title = {Integrated Microbiome and Metabolomic Profiling to Identify Potential Biomarkers of Major Depressive Disorder.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2512014},
doi = {10.4014/jmb.2512.12014},
pmid = {41605799},
issn = {1738-8872},
mesh = {Humans ; *Major Depressive Disorder/microbiology/diagnosis/blood/metabolism ; *Biomarkers/blood/urine ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Male ; *Metabolomics/methods ; Middle Aged ; Female ; Adult ; *Metabolome ; Bacteria/classification/genetics/isolation & purification/metabolism ; Carnitine/analogs & derivatives/metabolism/blood ; Dysbiosis/microbiology ; Gas Chromatography-Mass Spectrometry ; Fatty Acids/metabolism ; Republic of Korea ; },
abstract = {The pathophysiology of major depressive disorder (MDD) remains incompletely understood, hindering the development of objective diagnostic markers. While the microbiota-gut-brain axis is implicated in MDD, the functional link between gut dysbiosis and systemic metabolism remains largely obscure. To address this, we employed an integrated multi-omics approach combining 16S rRNA gene sequencing, GC-MS analysis of urine and plasma, complemented by UPLC-QTOF-MS profiling of plasma, in a Korean cohort (n = 69). We identified distinct taxonomic shifts, specifically the enrichment of the Eubacterium eligens group and Veillonella in MDD patients. Integrated correlation analysis revealed a functional "gut-lipid axis", where these taxa were strongly associated with alterations in host acylcarnitine and fatty acid metabolism. Notably, diagnostic evaluation demonstrated that the plasma metabolic profile yielded superior predictive accuracy (AUC = 0.862) compared to the gut microbiota (AUC = 0.654). Our findings suggest that while the gut microbiome provides mechanistic insights into lipid dysregulation, the circulating metabolome serves as a more robust, proximal diagnostic readout for MDD.},
}

Humans
*Major Depressive Disorder/microbiology/diagnosis/blood/metabolism
*Biomarkers/blood/urine
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Male
*Metabolomics/methods
Middle Aged
Female
Adult
*Metabolome
Bacteria/classification/genetics/isolation & purification/metabolism
Carnitine/analogs & derivatives/metabolism/blood
Dysbiosis/microbiology
Gas Chromatography-Mass Spectrometry
Fatty Acids/metabolism
Republic of Korea

@article {pmid41605796,
year = {2026},
author = {Park, CK and Bae, SH and Park, HW and Oh, NS and Kim, YJ and Kim, YW and Cho, TJ and Li, Y and Chai, J and Zhao, J and Cho, HT and Jung, JH and Park, J and Kim, TG and Kim, JK},
title = {Development of Large Language Model Specialized into Microbiome Datasets: an Application of Self-Evaluation and Scoring Comparison with Conventional Natural Language Processing Markers.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2511050},
doi = {10.4014/jmb.2511.11050},
pmid = {41605796},
issn = {1738-8872},
mesh = {*Natural Language Processing ; Humans ; Artificial Intelligence ; *Gastrointestinal Microbiome ; *Microbiota ; Computational Biology/methods ; Liver/microbiology/metabolism ; Large Language Models ; },
abstract = {The gut microbiome plays a fundamental role in host metabolism, immune regulation, and disease development. With the rapid accumulation of multi-omics and literature data, the microbiome field now faces the challenge of efficiently extracting scientific insights from massive, heterogeneous datasets. Artificial intelligence (AI) and large language models (LLMs) provide promising tools to address this complexity by enabling integrative analysis and knowledge synthesis across diverse biological sources. In this study, we developed METABOLISM, a microbiome-specialized LLM fine-tuned on 160,000 scientific abstracts to enhance literature-based contextual understanding of microbiome-liver interactions and related biological mechanisms. Using LoRA-based parameter-efficient training, METABOLISM was optimized for domain-specific reasoning and response generation. Model performance was evaluated through both automated Phi-4 scoring (a large language model-based evaluator for relevance, informativeness, and fluency) and structured human expert rubric assessments involving 20 domain specialists. The fine-tuned METABOLISM achieved superior relevance and clarity scores (mean > 7.5 ± 0.06) compared with general-purpose LLMs such as Gemma-3-12B-IT and ChatGPT-4o. Correlation analysis revealed weak to moderate negative relationships (R = -0.65, p < 0.0001) between traditional NLP metrics (BLEU, ROUGE) and human expert rubric scores, with a similar trend observed for correlations with Phi-4-based automated evaluation scores, indicating the limitations of surface-level similarity measures in biomedical contexts. Overall, our findings demonstrate that microbiome-adapted LLMs can effectively distill high-volume scientific data into biologically meaningful insights, supporting more efficient and interpretable research in microbiology and systems biology.},
}

*Natural Language Processing
Humans
Artificial Intelligence
*Gastrointestinal Microbiome
*Microbiota
Computational Biology/methods
Liver/microbiology/metabolism
Large Language Models

@article {pmid41605717,
year = {2026},
author = {Zhang, Y and Zhu, SJ},
title = {Role of bile acid metabolites in regulating viral infections.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2025.12.008},
pmid = {41605717},
issn = {1878-4380},
abstract = {Gut microbiota-derived bile acids are emerging as pivotal regulators of viral pathogenesis. They exhibit dual roles by directly blocking or promoting viral entry, while also systemically tuning immune responses. This forum discusses how spatiotemporal mapping of these interactions can address unresolved questions and inspire novel microbiome-based antiviral strategies.},
}

@article {pmid41605669,
year = {2026},
author = {Shen, X and Li, SB and Gao, MJ and Cao, JJ and Yang, H and Li, WW and Wei, LC and Chen, M and Liu, JY and Shi, YQ},
title = {Relationship Between Fecal Bile Acid Profile and Intestinal Microbiota in Patients With Chronic Radiation Enteritis.},
journal = {Journal of digestive diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/1751-2980.70029},
pmid = {41605669},
issn = {1751-2980},
support = {82330100//National Natural Science Foundation of China/ ; 82200567//National Natural Science Foundation of China/ ; 2024TD-06//Healthcare lnnovation Capability Enhancement Plan in Shaanxi Province/ ; JSYXM04//Booster Plans of Xijing Hospital/ ; },
abstract = {OBJECTIVE: We aimed to investigate the relationship between fecal bile acid (BA) profile and intestinal microbiota in patients with chronic radiation enteritis (CRE).

METHODS: Altogether 60 patients with cervical cancer (CC) who visited Xijing Hospital between December 2022 and September 2023 were enrolled, including 20 patients who did not undergo any treatment (the CC group), 20 patients who developed CRE after radical radiotherapy (the CRE group), and 20 patients who did not experience CRE after radical radiotherapy (the non-CRE [NRE] group). Patients' characteristics and fecal samples were collected. Fecal BA profiles were quantified, and intestinal microbiota were analyzed by using the 16S rRNA gene sequencing. Differentially expressed BAs and microorganisms were identified across groups, and their correlations were assessed using Spearman's correlation analysis.

RESULTS: In patients with CRE, BA metabolism was characterized by increased proportions of primary BAs and decreased proportions of secondary BAs, particularly lithocholic acid and its isomers. In addition, the abundance of beneficial bacterial genera, such as Bifidobacterium and Megasphaera, was reduced, whereas that of potentially pathogenic genera, including Megamonas and Dorea, was increased. Furthermore, a bidirectional relationship between BA metabolism and intestinal microbiota was observed.

CONCLUSIONS: Patients with CRE present notable alterations in BA metabolism and intestinal microbiota. CRE may trigger a harmful feedback mechanism driven by the interaction between these two factors. Targeted regulation of BA metabolism and intestinal microbiota may be a promising therapeutic approach for the management of CRE.

TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT05728060.},
}

@article {pmid41605617,
year = {2026},
author = {Vijay-Kumar, M and Yeoh, BS and Gewirtz, AT},
title = {Hydroxylation matters! Microbial bile acid metabolism and colorectal cancer.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2025-337583},
pmid = {41605617},
issn = {1468-3288},
}

@article {pmid41605597,
year = {2026},
author = {Murcia-Soriano, LF and Venegas-Sanabria, LC and Arias-Blanco, D and Baracaldo Gomez, SDP and Borda, MG and Sanchez, G and Buitrago-Garcia, D},
title = {Microbes and ageing beyond the gut: the oral microbiome and frailty, sarcopenia and neurocognitive disorders in the elderly - a scoping review protocol.},
journal = {BMJ open},
volume = {16},
number = {1},
pages = {e106590},
doi = {10.1136/bmjopen-2025-106590},
pmid = {41605597},
issn = {2044-6055},
mesh = {Humans ; Scoping Reviews as Topic ; *Sarcopenia/microbiology ; Aged ; *Aging/physiology ; *Frailty/microbiology ; *Microbiota ; *Neurocognitive Disorders/microbiology ; *Mouth/microbiology ; Research Design ; },
abstract = {INTRODUCTION: Population ageing is a global phenomenon that has resulted in an increase in the number of patients with chronic diseases and geriatric syndromes. Frailty, sarcopenia and neurocognitive disorders are among the most prevalent conditions affecting older adults and have a direct effect on their quality of life, and can impact the burden and budgets of health systems. Recently, the oral microbiome has gained attention as it may be a factor that potentially influences the onset and progression of these syndromes. However, this is still a new line of research that has not been deeply explored. This scoping review protocol aims to explore how the oral microbiome may be associated with the onset of prevalent geriatric syndromes, frailty, sarcopenia and neurocognitive disorders, providing a picture of the current evidence and potential gaps for future research.

METHODS AND ANALYSIS: The scoping review will follow the Johanna Briggs Institute (JBI) methodology and will be reported accordit to the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews guidelines (PRISMA-ScR). Searches will be conducted in Medline, Embase, Cochrane Central, CINAHL, LILACS and Epistemonikos from inception to December 2025. Independent reviewers will perform the study selection and data extraction. A descriptive analysis of information will be conducted, highlighting oral microorganisms associated with these syndromes and emerging trends in the evidence. Original research studies in any language will be included. We will include randomised controlled trials, cohort studies, case-control studies and other relevant designs if they investigate the oral microbiome and its relation to geriatric syndromes in adults aged 65 or older, regardless of geographic location or setting.

ETHICS AND DISSEMINATION: Ethics approval is not required.},
}

Humans
Scoping Reviews as Topic
*Sarcopenia/microbiology
Aged
*Aging/physiology
*Frailty/microbiology
*Microbiota
*Neurocognitive Disorders/microbiology
*Mouth/microbiology
Research Design

@article {pmid41605486,
year = {2026},
author = {Cai, XX and Zhang, HT and Wang, YX and Li, XJ},
title = {[Role and research progress of dental medicine in physical anthropology studies].},
journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology},
volume = {61},
number = {2},
pages = {266-272},
doi = {10.3760/cma.j.cn112144-20251013-00401},
pmid = {41605486},
issn = {1002-0098},
support = {2023YFC2506300//National Key R&D Program of China/ ; 2024C03241//Key Research and Development Program of Zhejiang Praince/ ; RD2022DXKB03//Exploration and Development Project of School of Stomatolog, Zhejiang University School of Medicine/ ; 202505/WT_/Wellcome Trust/United Kingdom ; },
abstract = {Physical anthropology is a discipline that studies human physical characteristics and their evolutionary patterns through the analysis of human biological remains. Oral tissues such as teeth and jawbones, serving as crucial or even exclusive materials among human biological remains, establish dental medicine's central role in this field. This paper reviewed the advances in dental medicine's research on key physical anthropology topics and methodologies, including human origins and evolution, paleopathology, paleodietary reconstruction, and paleomicrobiology. In human origins and evolution research, dental morphology provides crucial evidence for identifying population relationships. Paleopathology reflects ancient survival pressures, subsistence economies, and cultural behavioral patterns through oral diseases. Paleodietary research reconstructs ancient dietary structures using dental microwear, trace elements, stable isotopes, and calculus microfossils (e.g., starch grains, ancient DNA, ancient proteins). Paleomicrobiology explores the evolution of health and disease through the oral microbiome. Current research faces limitations including narrow observation of oral diseases, inconsistent diagnostic criteria, and insufficient interdisciplinary integration. Future efforts should enhance multidisciplinary collaboration among dental medicine, archaeology, anthropology, and other fields. This multi-perspective approach will systematically elucidate the evolutionary trajectory of oral health and disease, enrich the historical context of dental medicine, and provide insights for contemporary prevention and treatment of oral diseases.},
}