@article {pmid41684751,
year = {2026},
author = {Napier, E and Cinco, I and Stuart, E and Davies, M and Leach, C and Damron, E and Gokmen, M and Leestemaker-Palmer, A and Nuss, S and Bumgardner, C and Kohama, S and Bermudez, L and Winthrop, K and Fuss, C and Spindel, E and Messaoudi, I},
title = {Lung microbial dysregulation and TNF inhibition contribute to worsened nontuberculous mycobacterial lung disease.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8703262/v1},
pmid = {41684751},
issn = {2693-5015},
abstract = {Nontuberculous mycobacteria (NTM) are ubiquitous bacteria that cause a spectrum of diseases, most notably pulmonary disease (NTMPD). The host factors contributing to the heightened susceptibility and severity of NTMPD in elderly individuals are poorly understood. Prior studies have reported increased incidence of NTMPD in individuals receiving immune modulatory biologics such as anti-TNF and JAK-STAT inhibitors. Moreover, we recently described that age-related changes in the lung microbiome, notably the loss of a main commensal Tropheryma species, may contribute to increased severity. Therefore, in this study we explore the hypothesis that TNF-inhibition and a disrupted lung microbiome are key factors that contribute to worse disease outcomes in older NTMPD patients. Young (4-6 years old) rhesus macaques were pretreated with nebulized amikacin and vancomycin to deplete the lung microbiome, pretreated with the TNF inhibitor Inflectra or left untreated. Animals were subsequently inoculated with M. avium subsp. hominissuis (MAH) in the right lung. Bacterial load, radiographic changes, immune responses, and microbiome composition were monitored longitudinally. Antibiotic-treated animals experienced significant dysbiosis including the depletion of Tropheryma from the lung microbiome. One antibiotic-treated animal developed and resolved cavitary disease after the lung microbiome returned to homeostasis. Inflectra-treated animals favored an acute-phase response that persisted up to 114 days after inoculation and one Inflectra-treated animal developed chronic granulomatous disease. No control animals showed granulomas. These data suggest that lung microbiome dysbiosis and TNF inhibition can increase susceptibility to NTM granulomatous disease.},
}

@article {pmid41684743,
year = {2025},
author = {Díaz-Velis, L and Salvador-Sagüez, F and Roach, F and Mancilla, E and Campos, MA and Ruiz-Gil, T and López-Moral, M and Garrido, G and Lázaro-Martínez, JL},
title = {Metagenomic and ribosomal transcript profiles of diabetic foot osteomyelitis in Hispanic patients: underestimated bacteria in biofilm persistence.},
journal = {Frontiers in cellular and infection microbiology},
volume = {15},
number = {},
pages = {1729196},
pmid = {41684743},
issn = {2235-2988},
mesh = {Humans ; *Diabetic Foot/microbiology/complications ; *Osteomyelitis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Biofilms/growth & development ; Male ; Middle Aged ; Female ; Hispanic or Latino ; *Bacteria/classification/genetics/isolation & purification ; Aged ; Chile ; Microbiota/genetics ; Metagenomics ; DNA, Bacterial/genetics ; Adult ; Bone and Bones/microbiology ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; DNA, Ribosomal/genetics ; White ; },
abstract = {BACKGROUND: Diabetic foot osteomyelitis (DFO) is a serious complication of diabetes and a leading cause of lower-limb amputations. Conventional culture-based diagnostics often underestimate the microbial diversity of infected bone tissue. This study represents the first characterization of both total and ribosomally active bone microbiota in Hispanic patients with DFO using high-throughput 16S rRNA gene sequencing. The work aims to contribute to the inclusion of underrepresented populations in microbiome research and informing molecular-based antimicrobial strategies.

METHODS: Bone specimens (n = 13) were collected from seven Chilean patients with histologically confirmed DFO. Samples were analyzed using conventional aerobic culture and 16S rRNA gene sequencing from both genomic DNA (gDNA) and complementary DNA (cDNA) to characterize the total bacterial community and the ribosomally active fraction. In three patients, samples were stratified by bone depth (superficial/top, middle and bottom). Microbial diversity and relative abundance were assessed across patients and bone layers.

RESULTS: Acute osteomyelitis was the predominant histopathological pattern. Culture yielded 19 bacterial isolates, 95% of which were Gram-negative bacilli. Sequencing identified 3,412 operational taxonomic units (OTUs), with Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Enterobacteriaceae and Enterococcaceae were the most ribosomally active families. Microbial community composition varied substantially among patients and across bone depths. Staphylococcus aureus was infrequent (5% of culture isolates; ~1% of sequence reads), whereas low-abundance but ribosomally active taxa, such as Corynebacteriaceae, were consistently detected across all layers.

DISCUSSION: This combined metagenomic and ribosomal transcript analysis reveals a polymicrobial, patient-specific bone microbiota in Chilean patients with DFO, highlighting potentially active bacteria frequently overlooked by standard diagnostic methods. These findings underscore the value of integrating molecular approaches into clinical workflows to improve pathogen detection and support more personalized antimicrobial strategies, while also helping to address gaps in microbiome research among underrepresented populations.},
}

Humans
*Diabetic Foot/microbiology/complications
*Osteomyelitis/microbiology
RNA, Ribosomal, 16S/genetics
*Biofilms/growth & development
Male
Middle Aged
Female
Hispanic or Latino
*Bacteria/classification/genetics/isolation & purification
Aged
Chile
Microbiota/genetics
Metagenomics
DNA, Bacterial/genetics
Adult
Bone and Bones/microbiology
High-Throughput Nucleotide Sequencing
Sequence Analysis, DNA
DNA, Ribosomal/genetics
White

@article {pmid41684710,
year = {2026},
author = {Rahman, S and Sarker, P and Datta, TR and Maysha, TI and Rahman, S and Saha, W and Sarker, A and Mazumder, MAR},
title = {From farm to fork: Microplastic contamination in the meat and dairy supply chain.},
journal = {Current research in food science},
volume = {12},
number = {},
pages = {101334},
pmid = {41684710},
issn = {2665-9271},
abstract = {Microplastics (MPs) are now widespread contaminants in both terrestrial and aquatic ecosystems, leading to increasing worries about food safety and public health. This review offers an in-depth evaluation of the prevalence, pathways, and risks associated with MPs in meat and dairy products, which are significant global sources of animal-based nutrition. Data from different countries shows a persistent presence of MP contamination in livestock tissues, poultry organs, processed meat products, raw milk, and commercial dairy items, with identified polymer types such as polyethylene, polypropylene, polystyrene, nylon, PET, and regenerated cellulose. MPs are primarily found in the form of fibers, fragments, films, and irregular particles, with sizes varying from less than 10 μm to several millimeters. Their concentrations can range from a few particles per gram in raw meat to over 30,000 MP/kg in processed products, and from several MPs per liter in raw milk to more than 1800 MP/kg in cheese. Contamination occurs at various points along the farm-to-fork continuum, encompassing ingestion via tainted feed and water, interaction with agricultural plastics, transfer from milking and processing apparatus, wear during cutting and grinding, and leaching from packaging materials. Recent toxicological findings indicate that MPs and their related chemical additives could lead to gastrointestinal inflammation, oxidative stress, endocrine disruption, immunomodulation, and microbiome dysbiosis, although the long-term health effects are still not fully comprehended. Inconsistencies in methodology related to sampling, particle extraction, and spectroscopic identification impede precise comparisons of exposure and assessments of risk. The review points out significant gaps in current studies and emphasizes the necessity for uniform analytical techniques, enhanced waste and plastic management, as well as sustainable processing and packaging approaches to reduce the entry of MPs into animal-derived foods.},
}

@article {pmid41684696,
year = {2025},
author = {Mundanchira, AV and Wong, A and Klos-Maki, K and Strand, J and Marques, CNH},
title = {Activity of Biocidin[®] against microbial biofilms.},
journal = {Frontiers in antibiotics},
volume = {4},
number = {},
pages = {1692653},
pmid = {41684696},
issn = {2813-2467},
abstract = {Biofilms-microbial communities-are present throughout the environment and interact with humans as part of the resident microbiome or when causing infection and disease. Antibiotics are commonly used to treat bacterial infections, including those due to biofilms. However, antimicrobial tolerance and resistance are common traits of these microbial communities. Resistance to antimicrobials is now widespread, and the search for alternative treatments, such as plant- or herbal-derived extracts, essential oils, and honey, is on the rise. Here, we investigated the effect of Biocidin[®], a botanical supplement, on biofilms of Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Candida albicans. A single (bolus) dose of Biocidin[®] resulted in a significant decrease (> 2 Log) of biofilm and planktonic populations, while a 24-h continuous dose of 25% and 50% Biocidin[®] led to a typical biphasic killing curve, with the latter concentration resulting in biofilm eradication of P. aeruginosa, S. aureus, and E. coli. Exposure to sub-inhibitory concentrations of Biocidin[®] did not affect biofilm viability. Results from this work have implications for the use of Biocidin[®] as a treatment for biofilm-associated infections and as a supplement in natural medicine.},
}

@article {pmid41684282,
year = {2026},
author = {Shangguan, W and Li, W and Huang, W and Wu, J and Yu, Y and Huang, Y and Yang, L and Xie, M and Yang, Q and Zheng, J and Zhu, Y and Sun, Q and Li, B and Li, L and Wang, Z and Zhao, J and Wu, P and Cheng, B},
title = {FomA-Containing Outer Membrane Vesicles of Fusobacterium Nucleatum Facilitate Bladder Cancer Lymphatic Metastasis via IL-6-Dependent M2b Macrophage Polarization.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e23256},
doi = {10.1002/advs.202523256},
pmid = {41684282},
issn = {2198-3844},
support = {82503289//The National Natural Science Foundation of China/ ; 2024A028//President Foundation of Nanfang Hospital, Southern Medical University/ ; 2025M782052//China Postdoctoral Science Foundation/ ; 82570912//National Natural Science Foundation of China/ ; 81870522//National Natural Science Foundation of China/ ; 82173304//National Natural Science Foundation of China/ ; 2023B03J1245//Guangzhou Key Research and Development Program/ ; },
abstract = {Outer membrane vesicles (OMVs) derived from the microbiota have emerged as key modulators of tumor progression and the immune microenvironment. However, the role of urinary microbiota and their associated OMVs proteins in the metastatic processes of bladder cancer (BCa) remains insufficiently understood. In this study, we investigated the impact of urinary microbiota on BCa progression and identified potential biomarkers within the urinary microbiome. We identified Fusobacterium nucleatum (F. nucleatum) as a predominant member of the urinary microbiota. Proteomic analysis of F. nucleatum OMVs revealed the outer membrane protein FomA as the most abundant component. A FomA-deficient F. nucleatum mutant strain was generated to assess the relationship between FomA and lymph node (LN) metastasis. Mechanistically, FomA-containing OMVs directly engage Toll-like receptor 2 (TLR2), triggering the NF-κB signaling pathway and upregulating interleukin-6 (IL-6) expression. Elevated IL-6 induces M2b macrophage polarization, which subsequently promotes the release of VEGF-C to facilitate LN metastasis. Furthermore, we identified pinocembrin, a natural flavonoid, as a potent inhibitor of the FomA-TLR2 interaction, effectively suppressing BCa progression. Collectively, our findings uncover a previously unrecognized microbiota-driven mechanism by which F. nucleatum-derived OMVs reprogram the tumor immune microenvironment toward a pro-metastatic state and highlight FomA as a promising therapeutic target.},
}

@article {pmid41684150,
year = {2026},
author = {Wang, Z and Long, X and Zhang, M and Li, M and Shao, J and Wang, C and Gan, L and Chen, J and Wen, M and Qin, C and Jiang, H},
title = {Amelioration of ammonia-induced oxidative stress, ferroptosis and intestinal damage in Pelteobagrus fulvidraco through dietary tea polyphenols.},
journal = {Journal of fish biology},
volume = {},
number = {},
pages = {},
doi = {10.1111/jfb.70362},
pmid = {41684150},
issn = {1095-8649},
support = {32260912//National Natural Science Foundation of China/ ; QJJ-2024-37//Natural Science Research Project of Guizhou Provincial Department of Education/ ; MS[2025]697//Guizhou Provincial Basic Research Program (Natural Science)/ ; QKHJC[2024]youth105//Guizhou Provincial Science and Technology Project/ ; [2023]15//Cultivation Project of Guizhou University/ ; ZJZX-02//Project of Financial Funds of Ministry of Agriculture and Ruaral Affairs: Investigation of Fishery Resources and Habitat in the Pearl River Basin/ ; 2023NSFSC0241//Sichuan Science and Technology Program/ ; },
abstract = {To investigate the impact of tea polyphenols on the health of Pelteobagrus fulvidraco under ammonia stress, a total of 480 juvenile P. fulvidraco were divided into four groups receiving tea polyphenols supplemented diets at 0 mg kg[-1] (C group), 200 mg kg[-1] (L group), 400 mg kg[-1] (M group) and 600 mg kg[-1] (H group) for 56 days. Ammonia stress was applied from days 28 to 56. The results showed that intestinal histological damage was alleviated in the L and M groups under ammonia stress. In the M group, the levels of total antioxidant capacity and Nrf2, HO-1 and Occludin were the highest. Regarding ferroptosis-related genes, DMT1, FTM and FPN1 exhibited their highest expression in the L group, while TF, TFR1, FTL, SLC7A11 and GPX4 showed their highest expression in the M group. FTH demonstrated its highest expression in the H group. Furthermore, the expression of ACSL4 in the L and M groups was significantly lower than that in the C group. Intestinal microbiome analysis revealed enhanced microbial diversity in the tea polyphenol-added groups, accompanied by reduced relative abundance of dominant phylum Fusobacteriota and genus Cetobacterium compared to the C group. These results suggested that dietary supplementation of 200-400 mg kg[-1] tea polyphenols could alleviate ammonia-induced intestinal ferroptosis and histological damage, as well as protect intestinal health by regulating the compositional structure and diversity of the intestinal microflora. Specifically, the 400 mg kg[-1] dose exerted the most comprehensive protective effects. This study provides mechanistic insights into the development of tea polyphenol-based anti-ammonia feed additives for P. fulvidraco aquaculture.},
}

@article {pmid41684101,
year = {2026},
author = {Yu, F and Tao, Y and Liu, L and Xie, P and Mace, E and Jordan, D and Xie, Q},
title = {Sorghum2035: A decadal vision for sorghum functional genomics and molecular breeding.},
journal = {Molecular plant},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.molp.2026.02.003},
pmid = {41684101},
issn = {1752-9867},
abstract = {Sorghum (Sorghum bicolor L. Moench), the fifth most important cereal crop worldwide, serves as a staple food in arid and semi-arid regions, and a critical resource for livestock forage, bioenergy production, and industrial applications. Given its small genome size and high tolerance to abiotic stresses, such as drought, salt-alkali, and heat, it has become an ideal crop model for abiotic stress research. This review synthesizes recent advances in sorghum genomics, including the development of gapless reference genomes, pan-genome analyses revealing extensive structural variation, and population resequencing studies that have uncovered domestication signatures and stress adaptation loci. Moreover, we summarize progress in sorghum genetic resource collection, selection strategies, and breeding improvement. Genetic functional studies have identified key genes regulating yield-related traits, quality attributes, and tolerance to abiotic/biotic stresses. In molecular breeding, notable achievements include the establishment of efficient transformation systems, CRISPR/Cas9-mediated gene editing enhanced by morphogenic regulators, and mutagenized populations for gene function validation. Notably, challenges persist, such as the functional characterization of complex quantitative traits, integration of multi-omics datasets, and genotype-dependent transformation efficiency. Future research directions emphasize the utilization of wild germplasm, in-depth structural variation analysis, population-level transcriptomics, exploration of microbiome-plant interactions, and AI-driven intelligent breeding approaches. These strategies aim to engineer climate-resilient sorghum varieties to ensure global food security and promote sustainable bioenergy production.},
}

@article {pmid41683949,
year = {2026},
author = {Cao, J and Ma, J and Zha, X and Bian, X and Wang, W and Liu, X},
title = {Gut Microbiota Dysbiosis in Depression: Pathological Correlations, Molecular Pathways, and Therapeutic Interventions.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683949},
issn = {1422-0067},
support = {82073126//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Dysbiosis/microbiology/therapy/complications ; Probiotics/therapeutic use ; *Major Depressive Disorder/microbiology/therapy ; Animals ; *Depression/microbiology ; Prebiotics ; },
abstract = {Major depressive disorder (MDD) ranks as a primary contributor to global ill health and disability, with treatments often proving insufficient. Recent study has increasingly found a strong correlation between gut microbiome diversity and mood-related behaviors, including MDD. Depression can alter gut microbiota (GM) composition, while intentional modulation of the GM may conversely influence depressive symptoms. This phenomenon arises from dynamic bidirectional interactions between the gut and brain, although the exact pathways are not yet fully elucidated. Proposed pathways include, but are not limited to, neural circuits, the endocrine system, immune responses, and metabolic regulation. Clinical data have also shown that regulating the GM through probiotics and prebiotics has the potential to alleviate depressive symptoms. This review summarizes contemporary research on the composition and modulatory functions of GM in MDD, and explores the predictive potential of GM for depression as well as the therapeutic prospects of probiotics, aiming to provide insights and directions for future research.},
}

Humans
*Gastrointestinal Microbiome
*Dysbiosis/microbiology/therapy/complications
Probiotics/therapeutic use
*Major Depressive Disorder/microbiology/therapy
Animals
*Depression/microbiology
Prebiotics

@article {pmid41683934,
year = {2026},
author = {Soundharrajan, I and Ravindran, B and Choi, KC},
title = {Special Issue "Studies on Lactic Acid Bacteria and Their Products in Health and Diseases: 2nd Edition".},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683934},
issn = {1422-0067},
mesh = {Humans ; *Lactobacillales/physiology/metabolism ; *Probiotics ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {Lactic acid bacteria (LAB) provide essential benefits for both animal and human health due to their probiotic potential and their role in maintaining gut microbiome homeostasis [...].},
}

Humans
*Lactobacillales/physiology/metabolism
*Probiotics
*Gastrointestinal Microbiome
Animals

@article {pmid41683908,
year = {2026},
author = {Ben-Laouane, R and Ait-El-Mokhtar, M and Meddich, A and Baslam, M},
title = {Nodule-Microbiome Dynamics: Deciphering the Complexities of Nodule Symbiosis and the Root Microbiome.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683908},
issn = {1422-0067},
mesh = {*Symbiosis ; *Root Nodules, Plant/microbiology ; *Microbiota ; *Plant Roots/microbiology ; Soil Microbiology ; Endophytes ; Rhizobium/physiology ; Plant Root Nodulation ; Fabaceae/microbiology ; Nitrogen Fixation ; },
abstract = {Microbiomes play a pivotal role in sustaining plant function and broader ecosystem processes. Leguminous plants host vast populations of intracellular bacteria within specialized root organs known as nodules. The intricate mutualism between legumes and rhizobia ensures a stable supply of biologically fixed nitrogen (N) essential for plant growth. While rhizobia remain the central actors in this symbiosis, recent discoveries reveal the presence of non-rhizobial endophytes within nodules, suggesting a complex interplay shaped by host selection and compatibility with rhizobial partners. Understanding the structure and dynamics of crop nodule-associated microbial communities is thus critical for optimizing host responses to rhizobia and for leveraging beneficial plant-microbe interactions. This review explores the dualistic nature-both facilitative and inhibitory-of the nodule microbiome in relation to nodulation. We examine the diversity of soil bacteria that stimulate nodulation and those that ultimately colonize nodule tissues, questioning whether these functional groups overlap. Furthermore, we discuss the molecular dialogs and counter-signaling mechanisms that regulate endophyte ingress into nodules, and evaluate how nodule endophytes contribute to plant performance and soil fertility.},
}

*Symbiosis
*Root Nodules, Plant/microbiology
*Microbiota
*Plant Roots/microbiology
Soil Microbiology
Endophytes
Rhizobium/physiology
Plant Root Nodulation
Fabaceae/microbiology
Nitrogen Fixation

@article {pmid41683874,
year = {2026},
author = {Kim, KJ and Zhong, H and Tai, D and Shah, P and Park, D and Goes, V and Li, J and Jung, C and Kim, L and Guzman, S and Brar, G and Castillo, D},
title = {Microbiome Signatures in Advanced Gastric Cancer: Emerging Biomarkers for Risk Stratification, Therapy Guidance, and Prognostic Insight.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683874},
issn = {1422-0067},
mesh = {Humans ; *Stomach Neoplasms/microbiology/therapy/diagnosis/pathology ; *Gastrointestinal Microbiome ; Prognosis ; *Biomarkers, Tumor ; Immunotherapy/methods ; Dysbiosis/microbiology ; Risk Assessment ; },
abstract = {Gastric cancer (GC), often diagnosed at advanced or metastatic stages, remains a significant clinical challenge requiring novel biomarkers for early detection, risk stratification, and effective, personalized treatment optimization. Emerging evidence underscores a strong association between gut microbiome dysbiosis and GC initiation, progression, and therapeutic outcomes. This review explores the potential of the advanced/metastatic gastric microbiome as a source of diagnostic and targetable biomarkers and its role in modulating responses to immunotherapy. Although Helicobacter pylori (H. pylori) is the most significant risk factor for GC, several other gastrointestinal taxa-including Fusobacterium nucleatum (F. nucleatum)-have been implicated in advanced GC (AGC). At its inception, microbial dysbiosis contributes to chronic inflammation and immune evasion, thereby influencing tumor behavior and treatment efficacy. Integrating microbiome-based biomarkers into risk stratification, GC staging, and targetable treatment frameworks may enhance early detection, inform immunotherapy strategies, and improve patient-specific treatment responses. Bifidobacterium and Lactobacillus rhamnosus GG have the potential to change the immunotherapy framework with their direct influence on dendritic cell (DC) and cytotoxic T cell (CTL) activity. However, clinical translation is impeded by methodological heterogeneity, causality limitations, and a lack of clinical trials. Nonetheless, the integration of microbiome profiling and the development of therapeutic microbiome modulation strategies, such as personalized probiotics regimens and fecal microbiota transplantation, hold substantial potential for improving clinical outcomes and reducing treatment-related toxicity in GC management.},
}

Humans
*Stomach Neoplasms/microbiology/therapy/diagnosis/pathology
*Gastrointestinal Microbiome
Prognosis
*Biomarkers, Tumor
Immunotherapy/methods
Dysbiosis/microbiology
Risk Assessment

@article {pmid41683824,
year = {2026},
author = {Bas, TG},
title = {Dietary Polyphenols (Flavonoids) Derived from Plants for Use in Therapeutic Health: Antioxidant Performance, ROS, Molecular Mechanisms, and Bioavailability Limitations.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683824},
issn = {1422-0067},
mesh = {Humans ; *Polyphenols/pharmacology/pharmacokinetics/chemistry/therapeutic use ; *Antioxidants/pharmacology/chemistry/therapeutic use/pharmacokinetics ; Biological Availability ; *Reactive Oxygen Species/metabolism ; Animals ; *Flavonoids/pharmacology/chemistry ; Oxidative Stress/drug effects ; Dietary Supplements ; },
abstract = {Plant polyphenols, particularly flavonoids, are prominent bioactives in preventive/complementary therapeutic strategies. This article analyzes how some polyphenols can mitigate oxidative stress and inflammation. These processes are involved in cardiovascular disease, cancer, neurodegeneration, and metabolic disorders. Polyphenols are explored through the integration of direct antioxidant chemistry (radical scavenging via hydrogen atom transfer/single-electron transfer/metal chelation), redox signaling (Keap1-Nrf2/ARE and inflammatory pathways), endogenous antioxidant enzyme systems, and mitochondrial quality control. Unlike previous descriptive reviews, a novel aspect of this manuscript is its evidence-based synthesis, fully supported by structured summary tables that explicitly detail limitations, contradictions, and context dependencies in in vitro, in vivo, and human studies, and identify clinically interpretable endpoints for their application. We describe relevant flavonoids and dietary sources, along with functional outcomes in cardiometabolic-cognitive/neuroprotective-immunometabolic contexts. We integrate representative clinical interventions and nutraceutical applications, highlighting where reported benefits are supported and where the evidence is preliminary. Bioavailability, microbiota-driven biotransformation, and dose realism are considered the primary determinants of in vivo relevance, rather than secondary or descriptive considerations. Future research should prioritize standardized exposure and metabolite profile, dose-appropriate interventions, harmonized clinical endpoints, and stratification strategies that account for microbiome-driven interindividual variability to improve reproducibility and inform nutraceutical and therapeutic use.},
}

Humans
*Polyphenols/pharmacology/pharmacokinetics/chemistry/therapeutic use
*Antioxidants/pharmacology/chemistry/therapeutic use/pharmacokinetics
Biological Availability
*Reactive Oxygen Species/metabolism
Animals
*Flavonoids/pharmacology/chemistry
Oxidative Stress/drug effects
Dietary Supplements

@article {pmid41683784,
year = {2026},
author = {Tavartkiladze, A and Reiter, RJ and Lou, R and Kasradze, D and Okrostsvaridze, N and Revazishvili, P and Maisuradze, M and Dundua, G and Andronikashvili, I and Nozadze, P and Jinchveladze, D and Tavartkiladze, L and Khutsishvili, R and Potskhoraia, T},
title = {Melatonin Biosynthesis, Receptors, and the Microbiota-Tryptophan-Melatonin Axis: A Shared Dysbiosis Signature Across Cardiac Arrhythmias, Epilepsy, Malignant Proliferation, and Cognitive Trajectories.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683784},
issn = {1422-0067},
mesh = {*Melatonin/biosynthesis/metabolism/analogs & derivatives ; Humans ; *Tryptophan/metabolism ; *Dysbiosis/metabolism/microbiology ; *Gastrointestinal Microbiome ; *Epilepsy/metabolism/microbiology ; Middle Aged ; *Arrhythmias, Cardiac/metabolism/microbiology ; Aged ; Female ; Male ; Adult ; *Receptors, Melatonin/metabolism ; Young Adult ; Cognition ; Neoplasms/metabolism ; },
abstract = {Melatonin, an indolic neuromodulator with putative oncostatic and proposed anti-inflammatory properties, primarily demonstrated in preclinical models, is produced at extrapineal sites-most notably in the gut. Its canonical actions are mediated by high-affinity GPCRs (MT1/MT2) and by NQO2, a cytosolic enzyme with a melatonin-binding site (historically termed "MT3"). A growing body of work highlights a bidirectional interaction between the gut microbiota and host melatonin. We integrated two lines of work: (i) three clinical cohorts-cardiac arrhythmias (n = 111; 46-75 y), epilepsy (n = 77; 20-59 y), and stage III-IV solid cancers (25-79 y)-profiled with stool 16S rRNA sequencing, SCFA measurements, and circulating melatonin/urinary 6-sulfatoxymelatonin and (ii) an age-spanning cognitive cohort with melatonin phenotyping, microbiome analyses, and exploratory immune/metabolite readouts, including a novel observation of melatonin binding on bacterial membranes. Across all three disease cohorts, we observed moderate-to-severe dysbiosis, with reduced alpha-diversity and shifted beta-structure. The core dysbiosis implicated tryptophan-active taxa (Bacteroides/Clostridiales proteolysis and indolic conversions) and depletion of SCFA-forward commensals (e.g., Faecalibacterium, Blautia, Akkermansia, and several Lactobacillus/Bifidobacterium spp.). Synthesised literature indicates that typical human gut commensals rarely secrete measurable melatonin in vitro; rather, their metabolites (SCFAs, lactate, and tryptophan derivatives) regulate host enterochromaffin serotonin/melatonin production. In arrhythmia models, dysbiosis, bile-acid remodelling, and autonomic/inflammatory tone align with melatonin-sensitive antiarrhythmic effects. Epilepsy exhibits circadian seizure patterns and tryptophan-metabolite signatures, with modest and heterogeneous responses to add-on melatonin. Cancer cohorts show broader dysbiosis consistent with melatonin's oncostatic actions. In the cognitive cohort, the absence of dysbiosis tracked with preserved learning across ages, and exploratory immunohistochemistry suggested melatonin-binding sites on bacterial membranes in ~15-17% of samples. A unifying microbiota-tryptophan-melatonin axis plausibly integrates circadian, electrophysiologic, and immune-oncologic phenotypes. Practical levers include fiber-rich diets (to drive SCFAs), light hygiene, and time-aware therapy, with indication-specific use of melatonin. Our conclusions regarding microbiota-melatonin crosstalk rely primarily on local paracrine effects within the gut mucosa (where melatonin concentrations are 10-400× plasma levels), whereas systemic chronotherapy conclusions depend on circulating melatonin amplitude and phase. This original research article presents primary data from four prospectively enrolled clinical cohorts (total n = 577).},
}

*Melatonin/biosynthesis/metabolism/analogs & derivatives
Humans
*Tryptophan/metabolism
*Dysbiosis/metabolism/microbiology
*Gastrointestinal Microbiome
*Epilepsy/metabolism/microbiology
Middle Aged
*Arrhythmias, Cardiac/metabolism/microbiology
Aged
Female
Male
Adult
*Receptors, Melatonin/metabolism
Young Adult
Cognition
Neoplasms/metabolism

@article {pmid41683732,
year = {2026},
author = {Sobczyński, J and Nowaczyński, F and Smolińska, K and Lachowicz-Radulska, J and Serefko, A and Szopa, A},
title = {Natural Bioactive Compounds Targeting FABP4 in Adipogenesis and Obesity: Evidence from In Vitro and In Vivo Studies.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683732},
issn = {1422-0067},
mesh = {*Adipogenesis/drug effects ; Animals ; *Fatty Acid-Binding Proteins/metabolism/genetics ; Humans ; *Obesity/metabolism/drug therapy/etiology ; Adipocytes/metabolism/drug effects ; Signal Transduction/drug effects ; *Biological Products/pharmacology/therapeutic use ; *Phytochemicals/pharmacology ; },
abstract = {FABP4 (fatty acid-binding protein 4) is a lipid chaperone and secreted adipokine linking dysregulated fatty acid handling with inflammation, cellular stress, and insulin resistance in obesity. By modulating nuclear receptor signaling (notably PPARγ) and enhancing NF-κB/MAPK activation in adipocytes and macrophages, FABP4 contributes to maladaptive adipose remodeling and systemic metabolic decline. This review critically summarizes recent preclinical evidence on natural bioactive compounds that regulate FABP4 expression and associated adipogenic programs in models of adipogenesis and diet-induced obesity. Data from 3T3-L1/OP9 adipocytes, rodent studies, and selected alternative models indicate that many plant-derived extracts and phytochemicals (e.g., polyphenols, saponins, coumarins, terpenoids, and fermented products) down-regulate FABP4 at mRNA and/or protein levels. These effects are frequently accompanied by suppression of PPARγ/C/EBPα/SREBP1c signaling, activation of AMPK-related pathways, reduced lipid accumulation, and improved metabolic outcomes including lower weight gain, reduced adipocyte hypertrophy, improved steatosis, and favorable serum lipid profiles. Natural compounds from non-plant sources (animal- and microbe-derived metabolites) further broaden FABP4-targeting strategies, supporting FABP4 as a cross-class therapeutic node. Key translational barriers include poor extract standardization, incomplete identification of active constituents, limited oral bioavailability, microbiome-dependent variability, and scarce clinical validation. Future work should prioritize well-characterized lead scaffolds, targeted delivery, rational combinations, and standardized, adequately powered clinical trials assessing dose, durability of FABP4 suppression, and cardiometabolic safety.},
}

*Adipogenesis/drug effects
Animals
*Fatty Acid-Binding Proteins/metabolism/genetics
Humans
*Obesity/metabolism/drug therapy/etiology
Adipocytes/metabolism/drug effects
Signal Transduction/drug effects
*Biological Products/pharmacology/therapeutic use
*Phytochemicals/pharmacology

@article {pmid41683715,
year = {2026},
author = {Snodgrass, JL and Velayudhan, BT},
title = {Butyrate-Producing Bacteria as a Keystone Species of the Gut Microbiome: A Systemic Review of Dietary Impact on Gut-Brain and Host Health.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683715},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Butyrates/metabolism ; Dysbiosis/microbiology ; *Bacteria/metabolism ; *Brain/metabolism ; Animals ; *Diet ; Prebiotics ; },
abstract = {The human gut microbiome is a complex ecosystem integral to host health, with butyrate-producing bacteria (BPB) playing a critical role in maintaining intestinal homeostasis. This scoping review explores the composition, function, and systemic influence of BPB, focusing on their metabolic product, butyrate, and its implications for gut integrity, immune modulation, and gut-brain axis (GBA) communication. Disruptions to BPB abundance, which is correlated with Western dietary patterns, food additives, and antibiotic exposure, are linked to gut dysbiosis and associated with a wide spectrum of chronic diseases, including inflammatory bowel disease (IBD), obesity, type 2 diabetes, neurodegenerative disorders, and psychiatric conditions. Butyrate supports colonocyte energy metabolism, reinforces epithelial barrier function, regulates goblet cell mucus production, and exerts anti-inflammatory effects via histone deacetylase inhibition and G-protein-coupled receptor signaling. The depletion of BPB and the resultant butyrate deficiency may represent a unifying pathophysiological mechanism underlying these conditions. Therapeutic strategies that restore BPB populations and butyrate levels, such as prebiotics, dietary fiber, and microbiota-targeted interventions, hold promise for mitigating inflammation and enhancing systemic health through microbiome modulation.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Butyrates/metabolism
Dysbiosis/microbiology
*Bacteria/metabolism
*Brain/metabolism
Animals
*Diet
Prebiotics

@article {pmid41683560,
year = {2026},
author = {Lee, SG and Chau, NH and Ham, S and Baek, Y and Nguyen, NH and Kim, SH and Lee, YI},
title = {Microbiome-Derived Indole-3-Lactic Acid Attenuates Cutibacterium Acnes-Induced Inflammation via the Aryl Hydrocarbon Receptor Pathway.},
journal = {International journal of molecular sciences},
volume = {27},
number = {3},
pages = {},
pmid = {41683560},
issn = {1422-0067},
support = {20024192//Technology Innovation Program (or Industrial Strategic Technology Development Program-Novel microbiome therapy for hidradenitis suppurativa and severe acne based on integrative microbi-ome-multiomics approach)/ ; },
mesh = {*Receptors, Aryl Hydrocarbon/metabolism ; Animals ; Humans ; Mice ; *Indoles/pharmacology ; *Acne Vulgaris/microbiology/drug therapy/metabolism ; Keratinocytes/drug effects/metabolism/microbiology ; *Inflammation/drug therapy/microbiology/metabolism ; *Microbiota ; Signal Transduction/drug effects ; Disease Models, Animal ; *Propionibacterium acnes ; },
abstract = {Acne vulgaris is a chronic inflammatory dermatosis where conventional therapies often face limitations in efficacy and safety, necessitating the development of microbiome-targeted interventions. This study investigated the immunomodulatory potential of microbiome-derived tryptophan metabolites as a novel therapeutic strategy for Cutibacterium acnes (C. acnes)-induced inflammation, focusing on the aryl hydrocarbon receptor (AHR) pathway. We evaluated indole-3-lactic acid (ILA), indole-3-acrylic acid (IAA), and indole-3-propionic acid (IPA) in comparison to tapinarof, utilizing C. acnes-stimulated human epidermal keratinocytes and a C. acnes-induced acne mouse model. In vitro, ILA and IPA significantly suppressed C. acnes-driven inflammatory mediators, including Tumor Necrosis Factor-alpha (TNF-α), Interleukin (IL)-1β, and Cyclooxygenase-2 (COX2), whereas IAA demonstrated limited efficacy. In vivo, ILA treatment exhibited superior therapeutic activity, markedly reducing inflammatory cell infiltration, epidermal hyperplasia, and IL-1β expression. Transcriptomic analysis confirmed that ILA attenuates inflammatory signaling (e.g., IL-17 and TNF pathways) while upregulating AHR-responsive genes such as Cytochrome (CYP) 1A1 and CYP1B1. Collectively, these findings establish ILA as a potent postbiotic that mitigates cutaneous inflammation through selective activation of the AHR. Future studies should prioritize the clinical translation of ILA-based topical formulations, with rigorous evaluation of their efficacy and safety in well-designed human trials, to support their development as a non-antibiotic therapeutic alternative for acne management.},
}

*Receptors, Aryl Hydrocarbon/metabolism
Animals
Humans
Mice
*Indoles/pharmacology
*Acne Vulgaris/microbiology/drug therapy/metabolism
Keratinocytes/drug effects/metabolism/microbiology
*Inflammation/drug therapy/microbiology/metabolism
*Microbiota
Signal Transduction/drug effects
Disease Models, Animal
*Propionibacterium acnes

@article {pmid41683463,
year = {2026},
author = {Zhao, Y and Sharfman, NM and Jaber, VR and Taylor, CM and Lukiw, WJ and Bazan, NG},
title = {Down-Regulation of Acyloxyacyl Hydrolase Expression in Alzheimer's Disease Impairs LPS Detoxification and Contributes to Brain Pro-Inflammatory Signaling.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {3},
pages = {},
pmid = {41683463},
issn = {1420-3049},
support = {EY006311/EY/NEI NIH HHS/United States ; AG18031/AG/NIA NIH HHS/United States ; AG038834/AG/NIA NIH HHS/United States ; },
mesh = {Humans ; *Alzheimer Disease/metabolism/genetics/pathology ; *Lipopolysaccharides/metabolism ; *Brain/metabolism/pathology ; Down-Regulation ; Signal Transduction ; MicroRNAs/genetics/metabolism ; *Carboxylic Ester Hydrolases/genetics/metabolism ; Inflammation/metabolism ; },
abstract = {Lipopolysaccharides (LPSs) are potent pro-inflammatory neurotoxins abundant in the gut microbiome and originate primarily from Gram-negative bacteria, such as Escherichia coli. LPS levels increase with brain aging and accumulate around neurons in Alzheimer's disease (AD) brains. Microbiome-generated LPS and other endotoxins cross gut barriers, enter systemic circulation, and translocate across the blood-brain barrier into vascularized brain regions. These processes are exacerbated by aging and neurovascular diseases. Although pro-homeostatic systems mitigate LPS effects, these defenses can fail. This study provides the first evidence that acyloxyacyl hydrolase (AOAH; EC 3.1.1.77), a microglia-enriched LPS detoxifying enzyme, shows reduced expression in AD brain tissue. Analysis of AD patient brains revealed reduced AOAH messenger RNA (mRNA) levels, accompanied by elevated expression of microRNA (hsa-miR-450b-5p), an inflammation regulator. Furthermore, luciferase reporter assays demonstrated that miR-450b-5p specifically targets the AOAH 3'-UTR, leading to a dose-dependent suppression of reporter activity. Also, in vitro experiments on human neuronal glial (HNG) cells further confirmed down-regulation of AOAH expression at protein levels by miR-450b-5p. These findings suggest miR-450b-5p-mediated AOAH deficiency drives LPS-associated neurotoxicity and inflammatory neurodegeneration in AD.},
}

Humans
*Alzheimer Disease/metabolism/genetics/pathology
*Lipopolysaccharides/metabolism
*Brain/metabolism/pathology
Down-Regulation
Signal Transduction
MicroRNAs/genetics/metabolism
*Carboxylic Ester Hydrolases/genetics/metabolism
Inflammation/metabolism

@article {pmid41683364,
year = {2026},
author = {Wesołek-Leszczyńska, A and Rosiejka, D and Bogdańska, K and Bogdański, P},
title = {Fermented Foods and the Gut-Liver Axis: Modulation of MASLD Through Gut Microbiota.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683364},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Fermented Foods ; *Liver/metabolism ; Animals ; Probiotics/administration & dosage ; *Fatty Liver/microbiology ; Prebiotics/administration & dosage ; },
abstract = {Background/Objectives: Metabolic Dysfunction-Associated Steatotic Liver Disease (MASLD) is a prevalent condition defined by hepatic fat accumulation, inflammation, and metabolic dysregulation. Current evidence demonstrates that gut microbiota and their metabolites are associated with MASLD pathogenesis. Fermented foods, rich in live microbes and bioactive compounds, actively modulate the gut-liver axis and influence disease progression. This narrative review provides a comprehensive summary of current evidence on the impact of fermented foods on gut microbiota, intestinal barrier function, and gut-liver interactions, and demonstrates their potential role in preventing or mitigating MASLD. Methods: A comprehensive literature search of preclinical and clinical studies was conducted. Specifically, the review focused on fermented-food interventions, modulation of gut microbiota, metabolite production, and effects on hepatic metabolism and inflammation. Results: This review found that fermented foods provide probiotics, prebiotics, short-chain fatty acid (SCFAs), and bioactive compounds that enhance microbial diversity, improve intestinal barrier integrity, reduce endotoxemia, and modulate bile acid and lipid metabolism. Evidence from animal and human studies indicates that fermented food consumption can attenuate hepatic steatosis, inflammation, and metabolic dysregulation, with variability depending on individual microbiome composition. Conclusions: Altogether, these findings suggest that fermented foods represent a promising adjunctive dietary strategy for MASLD by modulating the gut-liver axis and supporting metabolic and hepatic health. Personalized approaches and further long-term clinical trials are required to optimize interventions and establish evidence-based recommendations.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Fermented Foods
*Liver/metabolism
Animals
Probiotics/administration & dosage
*Fatty Liver/microbiology
Prebiotics/administration & dosage

@article {pmid41683346,
year = {2026},
author = {Fathima, S and Kilgore, PE and Sarkar, T and Sharma, N and Nguyen, HH},
title = {Muno-IgY Supplementation Improves Respiratory Health, Immune Response, and Exercise-Induced Physiological Stress in Healthy Adults: A Randomized Controlled Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683346},
issn = {2072-6643},
mesh = {Humans ; Pilot Projects ; Male ; Adult ; Female ; *Dietary Supplements ; Double-Blind Method ; *Exercise/physiology ; *Respiratory Tract Infections/prevention & control/immunology/epidemiology ; Gastrointestinal Microbiome/drug effects ; *Stress, Physiological/drug effects ; *Immunoglobulins/administration & dosage/pharmacology ; Biomarkers/blood ; Young Adult ; Middle Aged ; },
abstract = {BACKGROUND/OBJECTIVES: Upper respiratory tract infections (URTIs) and exercise-induced immune perturbations are common in adults and may adversely affect quality of life, productivity, and physical performance. Immunoglobulin Y (IgY), a food-derived antibody with broad antimicrobial activity, has demonstrated immunomodulatory potential in preclinical and limited clinical studies. This study evaluated the effects of a multi-pathogen-specific IgY supplement (Muno-IgY) on respiratory health, immune and inflammatory markers, exercise-induced physiological stress, and gut microbiome composition in healthy adults.

METHODS: In this 12-week, double-blind, placebo-controlled trial, 28 healthy adults with a history of URTI were randomly allocated to receive Muno-IgY or placebo and URTI incidence, duration, and severity were recorded daily. Serum immune and inflammatory biomarkers were assessed longitudinally and in response to a standardized exercise challenge. Gut microbiome composition was analyzed using shotgun metagenomic sequencing at baseline and week 12. Safety and tolerability were assessed throughout the study.

RESULTS: URTI incidence was lower in the Muno-IgY group compared with placebo (14.3% vs. 35.7%), with shorter average duration and fewer missed workdays, though differences were not statistically significant (p > 0.05). Following an acute exercise challenge, Muno-IgY supplementation resulted in a significant increase in serum IgA at 24 h post-exercise (p = 0.022) and a significantly greater reduction in lactate dehydrogenase at 1 h post-exercise compared with placebo (p < 0.0001). Exploratory gut microbiome analyses suggested favorable directional shifts, though these changes were not statistically tested.

CONCLUSIONS: In this exploratory pilot study, Muno-IgY supplementation was safe and associated with significant improvements in selected markers of exercise-induced immune response and muscle damage. Numerical trends in URTI incidence and gut microbiome composition were observed but were not statistically significant. These findings are hypothesis-generating and support further evaluation of Muno-IgY in larger, adequately powered clinical trials.},
}

Humans
Pilot Projects
Male
Adult
Female
*Dietary Supplements
Double-Blind Method
*Exercise/physiology
*Respiratory Tract Infections/prevention & control/immunology/epidemiology
Gastrointestinal Microbiome/drug effects
*Stress, Physiological/drug effects
*Immunoglobulins/administration & dosage/pharmacology
Biomarkers/blood
Young Adult
Middle Aged

@article {pmid41683344,
year = {2026},
author = {Chen, Y and Medici, V and Keen, CL and Holt, RR},
title = {The Influence of Daily Honey-Sweetened Yogurt Intake on Outcomes of Low-Grade Inflammation and Microbial Metabolites in Postmenopausal Women.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683344},
issn = {2072-6643},
support = {no grant number//National Honey Board/ ; },
mesh = {Humans ; Female ; *Yogurt ; *Postmenopause ; Middle Aged ; *Honey ; Aged ; Cross-Over Studies ; *Inflammation/blood ; Feces/chemistry ; Fatty Acids, Volatile/analysis ; *Gastrointestinal Microbiome ; Lipids/blood ; Bile Acids and Salts/blood ; Cytokines/blood ; Diet ; },
abstract = {Background/Objectives: After fermentation, yogurt is often supplemented with probiotics, yet sweetened with added sugars that can negatively impact cardiometabolic health. Honey provides rare sugars, oligosaccharides and phenolics that may promote gut and cardiometabolic health. We aimed to determine the impact of yogurt sweetened with commercial clover blossom honey on pro-inflammatory Th17 cytokines and microbial-derived metabolites in healthy postmenopausal women. Methods: In a randomized controlled crossover dietary intervention trial, postmenopausal women (45-65 years of age) consumed two 150 g servings of yogurt for breakfast for 4 weeks, with each serving sweetened with a tablespoon of clover blossom honey or an isocaloric amount of sugar. Blood samples were collected for the measurement of plasma lipids, bile acids (BA) and Th17 cytokines, along with fecal short-chain fatty acids (SCFA). The primary outcome was plasma interleukin (IL)-23. Results: Neither dietary intervention significantly changed IL-23, plasma lipids, fecal SCFA or plasma BA. Compared to sugar-sweetened yogurt, IL-33 was significantly lower after 4 weeks of honey-sweetened yogurt intake. Conclusions: In a healthy population of postmenopausal women, the daily intake for 4 weeks of honey-sweetened yogurt did not significantly impact our primary outcome of IL-23. Instead, lower plasma levels of IL-33 were observed with honey compared to sugar-sweetened yogurt intake. The impact of the intervention on this cytokine was independent of changes in fecal SCFA and plasma BA. Confirmatory studies, in a larger population with levels of honey intake within dietary recommendations for added sugar, are warranted.},
}

Humans
Female
*Yogurt
*Postmenopause
Middle Aged
*Honey
Aged
Cross-Over Studies
*Inflammation/blood
Feces/chemistry
Fatty Acids, Volatile/analysis
*Gastrointestinal Microbiome
Lipids/blood
Bile Acids and Salts/blood
Cytokines/blood
Diet

@article {pmid41683324,
year = {2026},
author = {Zhao, Z and Zhao, S and Li, W and Lai, Z and Zhou, Y and Guan, F and Liang, X and Zhang, J and Wang, L},
title = {Gut Microbiota and Exercise-Induced Fatigue: A Narrative Review of Mechanisms, Nutritional Interventions, and Future Directions.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683324},
issn = {2072-6643},
support = {2022AH040100//The Scientific Research Project of Higher Education Institutions in Anhui Province/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; *Fatigue/microbiology/etiology/physiopathology ; Animals ; Probiotics/administration & dosage ; Prebiotics/administration & dosage ; },
abstract = {Background: Exercise-induced fatigue (EIF) impairs performance and recovery and may contribute to overreaching/overtraining and adverse health outcomes. Beyond classical explanations (substrate depletion, metabolite accumulation, oxidative stress), accumulating evidence indicates that the gut microbiota modulates fatigue-related physiology through metabolic, immune, barrier, and neurobehavioral pathways. Methods: We conducted a structured narrative review of PubMed and Web of Science covering 1 January 2015 to 30 November 2025 using predefined keywords related to EIF, gut microbiota, recovery, and nutritional interventions. Human studies, animal experiments, and mechanistic preclinical work (in vivo/in vitro) were included when they linked exercise load, microbial features (taxa/functions/metabolites), and fatigue-relevant outcomes. Results: Across models, high-intensity or prolonged exercise is consistently associated with disrupted gut homeostasis, including altered community structure, reduced abundance of beneficial taxa, increased intestinal permeability, and shifts in microbial metabolites (e.g., short-chain fatty acids). Evidence converges on four interconnected microbiota-mediated pathways relevant to EIF: (1) energy availability and metabolic by-product clearance; (2) redox balance and inflammation; (3) intestinal barrier integrity and endotoxemia risk; and (4) central fatigue and exercise motivation via microbiota-gut-brain signaling. Nutritional strategies-particularly targeted probiotics, prebiotics/plant polysaccharides, and selected bioactive compounds-show potential to improve fatigue biomarkers and endurance-related outcomes, although effects appear context-dependent (exercise modality, baseline fitness, diet, and baseline microbiota). Conclusions: Current evidence supports a mechanistic role of the gut microbiota in EIF and highlights microbiota-targeted nutrition as a promising adjunct for recovery optimization. Future work should prioritize causal validation (e.g., fecal microbiota transplantation and metabolite supplementation), athlete-focused randomized trials with standardized fatigue endpoints, and precision approaches that stratify individuals by baseline microbiome features and training load.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Exercise/physiology
*Fatigue/microbiology/etiology/physiopathology
Animals
Probiotics/administration & dosage
Prebiotics/administration & dosage

@article {pmid41683320,
year = {2026},
author = {Tamayo, M and Tolosa-Enguis, V and Alabadi, B and Olivares, M and Romera, S and Orti, L and Terrado, E and Flor Duro, A and Morillas, C and Codoñer, P and Real, JT and Sanz, Y},
title = {Safety and Tolerability of the Gut Bacterium Phascolarctobacterium faecium DSM 32890.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683320},
issn = {2072-6643},
support = {PID2020-119536RB-I00 and PID2023-150693OB-I00.//Ministry of Science, Innovation and Universities (MCIU, grants)/ ; EX2021- 001189-S/ MCIN/AEI / 566 10.13039/50110001103//Severo Ochoa 565 Center of Excellence to IATA-CSIC from MCIN/AEI/ ; },
mesh = {Animals ; Male ; Female ; Humans ; Rats, Wistar ; Rats ; *Gastrointestinal Microbiome ; Adult ; *Probiotics/adverse effects/administration & dosage ; Pilot Projects ; Middle Aged ; Overweight/therapy ; Young Adult ; Obesity ; },
abstract = {BACKGROUND/OBJECTIVES: The prevalence of the commensal gut bacterium species, Phascolarctobacterium faecium, has been associated with normal weight in humans. Preclinical evidence suggests that the strain P. faecium DSM 32890 exerts beneficial effects on metabolic and immune function in diet-induced obesity. Herein, we aimed to evaluate the safety and tolerability of this strain in a preclinical study and a pilot interventional trial in humans.

METHODS: A repeated-dose oral toxicity study of 28 days was performed in Wistar rats (male and female), during which adverse signs and clinical outcomes were assessed, along with histological, hematologic, biochemical, and immune markers. Subsequently, a pilot human intervention trial was conducted, including 20 participants (11 overweight and 9 normal weight) who received P. faecium DSM 32890 daily for 15 days. Body composition, dietary intake, physical activity, clinical data, perceived health, gastrointestinal symptoms, and blood analyses were assessed to determine tolerability and identify potential adverse effects.

RESULTS: In rats, the administration of the bacterium did not cause behavioral, physiological, histologic, immune, or biochemical alterations. In humans, there was no evidence of adverse effects on general health, hematological and biochemical profiles, bowel habits, or gastrointestinal symptoms. Overweight participants experienced reductions in flatulence and nausea after the intervention.

CONCLUSIONS: The consumption of P. faecium DSM 32890 did not raise safety concerns and was well tolerated in rats and humans. The findings represent a step forward in the path toward future, longer-term studies to explore the potential efficacy.},
}

Animals
Male
Female
Humans
Rats, Wistar
Rats
*Gastrointestinal Microbiome
Adult
*Probiotics/adverse effects/administration & dosage
Pilot Projects
Middle Aged
Overweight/therapy
Young Adult
Obesity

@article {pmid41683313,
year = {2026},
author = {Fusco, W and De Maio, F and Porcari, S and Severino, A and Salvi, D and Piccirelli, S and Ferrari, C and Sibilla, A and Quaranta, G and Masucci, L and Cammarota, G and Sanguinetti, M and Gasbarrini, A and Ianiro, G},
title = {Informed Therapeutic Microbiome Modulation for Post-Infectious Irritable Bowel Syndrome: Pilot Experience of a Microbiome Clinic.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683313},
issn = {2072-6643},
mesh = {Humans ; *Irritable Bowel Syndrome/therapy/microbiology/etiology ; Pilot Projects ; Female ; Male ; Case-Control Studies ; *Gastrointestinal Microbiome ; Adult ; Middle Aged ; Treatment Outcome ; Severity of Illness Index ; },
abstract = {Background: Untargeted microbiome modulation has achieved conflicting results in post-infectious irritable bowel syndrome (PI-IBS). Methods: In a case-control study of PI-IBS patients, cases received targeted microbial modulation informed by microbiome profiling, while controls were managed by standard therapy. Treatment response was defined as a decrease in IBS-symptom severity scale (IBS-SSS) ≥50 points. Results: All thirteen cases (100%) and 11/20 controls (55%) experienced treatment response (p < 0.0001). The mean IBS-SSS score after treatments was 163 in cases and 231 in controls (p = 0.01). Conclusions: Based on our preliminary results, therapeutic microbiome modulation might be a promising strategy for PI-IBS. Further studies are needed to clarify its role.},
}

Humans
*Irritable Bowel Syndrome/therapy/microbiology/etiology
Pilot Projects
Female
Male
Case-Control Studies
*Gastrointestinal Microbiome
Adult
Middle Aged
Treatment Outcome
Severity of Illness Index

@article {pmid41683263,
year = {2026},
author = {Han, C and Spakowicz, D and Von Ah, D and Noonan, A and Pyter, L},
title = {Gut Microbiota and Nutritional Profiles of Colon Cancer Patients Undergoing Chemotherapy: A Longitudinal Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683263},
issn = {2072-6643},
support = {RE03//Oncology Nursing Foundation/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Pilot Projects ; Male ; Female ; Middle Aged ; *Colonic Neoplasms/drug therapy/microbiology ; Aged ; Longitudinal Studies ; Feces/microbiology ; *Diet ; Fluorouracil/therapeutic use/administration & dosage ; *Nutritional Status ; Bacteria/classification ; Diet, Healthy ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background/Objectives: Nutrition and the gut microbiota influence treatment tolerance and recovery in patients with colon cancer receiving chemotherapy. This pilot study examined changes in diet quality and fecal microbiota over 6 months of chemotherapy and evaluated longitudinal associations between diet quality and gut microbiota diversity and taxa. Methods: 48 adults with stage II-III colon cancer receiving 5-fluorouracil-based chemotherapy were assessed at baseline and 6 months post-initiation. Diet quality was measured using 3-day dietary recalls to calculate Healthy Eating Index (HEI) scores. Stool samples underwent 16S rRNA sequencing to assess Shannon diversity, Beta and taxonomic composition. Pre-post changes were analyzed using paired tests, and associations between HEI and microbiota measures were evaluated using multivariable linear regression adjusting for demographic and clinical covariates. Results: Diet quality declined during chemotherapy, with reduced intake of fiber, fruits and vegetables, and whole grains. Gut microbial alpha diversity decreased over time. At the phylum level, Actinobacteriota decreased, while Bacteroidota and Proteobacteria increased. At the genus level, only Streptococcus (decreased) and Escherichia (increased) remained significantly altered after multiple testing correction. Higher baseline diet quality and improvements over time were associated with greater microbial diversity and lower Proteobacteria abundance. Diet quality was inversely associated with Streptococcus and Escherichia and positively associated with short-chain fatty acid-producing, fiber-responsive genera (Faecalibacterium, Mediterraneibacter, Ruminococcus_E, Fusicatenibacter). Baseline gut microbiota did not significantly associate with changes in diet quality. Conclusions: Chemotherapy was associated with declines in diet quality, gut microbial alpha diversity, along with shifts in beta diversity and microbial taxa. Higher diet quality appeared protective against microbial disruption, supporting a bidirectional relationship between diet and the gut microbiome during chemotherapy. Nutritional and microbiota-focused approaches warrant further investigation in the context of chemotherapy.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Pilot Projects
Male
Female
Middle Aged
*Colonic Neoplasms/drug therapy/microbiology
Aged
Longitudinal Studies
Feces/microbiology
*Diet
Fluorouracil/therapeutic use/administration & dosage
*Nutritional Status
Bacteria/classification
Diet, Healthy
RNA, Ribosomal, 16S/genetics

@article {pmid41683230,
year = {2026},
author = {Elshaghabee, FMF and Hamad, EM and Ebeid, TA and Ibrahim, HS and Al Abdulmonem, W},
title = {Supplementation of Yoghurt with Apilactobacillus kunkeei Strain Ameliorates Non-Alcoholic Fatty Liver Disease in Rat Model.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683230},
issn = {2072-6643},
mesh = {Animals ; *Yogurt/microbiology ; *Non-alcoholic Fatty Liver Disease/prevention & control/microbiology ; *Probiotics/administration & dosage ; Male ; Disease Models, Animal ; Rats ; Rats, Wistar ; Gastrointestinal Microbiome ; Liver/metabolism ; Ethanol/metabolism ; *Dietary Supplements ; Feces/microbiology ; },
abstract = {Background/Objectives: This study evaluated whether yoghurt containing Apilactobacillus kunkeei DSM 12361 protects rats against non-alcoholic fatty liver disease (NAFLD). We hypothesized that this fructophilic probiotic, with anti-inflammatory properties, may affect NAFLD progression by improving the gut microbiome, lowering intestinal ethanol production, and modulating inflammatory and metabolic pathways linked to hepatic fat accumulation. Methods: Wister rats were randomized into three groups; rats in the control group (HFrD) were fed a high-fructose (70%) diet while rats in experimental groups were fed the same diet mixed with 10% of yoghurt containing YC-180 starter culture (HFrD-Y) or yoghurt containing YC-180 and Apilactobacillus kunkeei DSM 12361 (HFrD-Y-A). Results: After six weeks of intervention, levels of plasma triglycerides, cholesterol, glucose, liver enzymes (ALT and AST), interleukin (IL)-6, fecal ethanol, Enterobacteriaceae, and hepatic index were significantly increased (p < 0.05) in the HFrD group as compared to rats in both experimental groups. Moreover, plasma levels of liver enzymes, lipid profile, glucose, and IL-6 were significantly lower (p < 0.05) in rats of the HFrD-Y-A group than those in the HFrD-Y group. Furthermore, plasma levels of IL-10 and fecal Lactobacilli and Bifidobacteria were significantly increased (p < 0.05) in the experimental groups when compared to rats in the control group. Conclusions: In sum, the obtained results indicated that yoghurt containing Apilactobacillus kunkeei could decrease the risk of non-alcoholic fatty liver disease (NAFLD) through (a) blocking the inflammation process associated with NAFLD, (b) enhancing the lipid profile, (c) lowering fecal ethanol, and (III) decreasing the levels of fecal Enterobacteriaceae in comparison with levels of fecal Lactobacilli and Bifidobacteria in rats. More research on molecular mechanisms of the potential effects of the Apilactobacillus kunkeei strain against NAFLD is still required.},
}

Animals
*Yogurt/microbiology
*Non-alcoholic Fatty Liver Disease/prevention & control/microbiology
*Probiotics/administration & dosage
Male
Disease Models, Animal
Rats
Rats, Wistar
Gastrointestinal Microbiome
Liver/metabolism
Ethanol/metabolism
*Dietary Supplements
Feces/microbiology

@article {pmid41683222,
year = {2026},
author = {León, ED and Moriki, D and Artacho, A and Pons, X and Koumpagioti, D and Tsabouri, S and Priftis, KN and Douros, K and Francino, MP},
title = {Disentangling Gut Microbiome Alterations in Children with Cow's Milk Allergy: Impact of Sex, Milk Elimination, and Family History of Allergies.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683222},
issn = {2072-6643},
support = {PID2019- 105969GB-I00//Ministry of Science and Innovation, Spain/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Milk Hypersensitivity/microbiology/immunology ; Male ; Female ; Child, Preschool ; Child ; Sex Factors ; Animals ; RNA, Ribosomal, 16S/genetics ; Milk ; Bacteria/classification/genetics ; },
abstract = {Background: Children with cow's milk allergy (CMA) present alterations in their gut microbiome, but any potential sex-dependency of these has not been addressed. Further, whether eliminating milk from children's diet has similar effects on the gut microbiomes of boys and girls is also not known. Here, our main objective is to analyze how CMA and development of oral tolerance (DOT) to milk proteins affect the gut microbiota in female and male children. We also perform exploratory analyses to investigate whether milk elimination and/or a family history of allergies underlie sex-associated differences. Methods: We obtained 16S rRNA gene sequences of the intestinal microbiota of 32 children aged 5-12 years with CMA, of which 14 had active CMA and 18 had developed oral tolerance, along with 36 age-matched healthy controls (51.5% male). PERMANOVA and differential abundance analyses were employed to evaluate overall compositional differences and to identify bacteria varying between the groups. Results: The effects of CMA on the gut microbiome are more pronounced in girls, including female-specific decreases in bacteria potentially related to protection from allergy, such as Monoglobus and Anaerostipes. The girls' microbiomes were also found to be more influenced by a family history of allergy, remaining farther from the healthy state upon DOT. In contrast, milk elimination affects more taxa in boys in the control group than in girls in the control group, although it alters global microbiome composition in both. In all, milk elimination and family history fail to explain most microbiome alterations observed in CMA, indicating that the latter are specifically linked to disease development. Conclusions: Gut microbiome alterations associated with CMA are sex-dependent, suggesting that sex-specific strategies, dietary and otherwise, may be more effective at modulating them toward healthier states.},
}

Humans
*Gastrointestinal Microbiome
*Milk Hypersensitivity/microbiology/immunology
Male
Female
Child, Preschool
Child
Sex Factors
Animals
RNA, Ribosomal, 16S/genetics
Milk
Bacteria/classification/genetics

@article {pmid41683220,
year = {2026},
author = {Anchidin-Norocel, L and Lobiuc, A and Covasa, M},
title = {Diet-Oral Microbiota Interactions and Salivary Biomarkers of Nutritional Health: A Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683220},
issn = {2072-6643},
mesh = {Humans ; *Saliva/chemistry/microbiology/metabolism ; Biomarkers/analysis/metabolism ; *Diet/adverse effects ; *Microbiota/physiology ; *Nutritional Status ; *Mouth/microbiology ; Metals, Heavy ; Dysbiosis ; Oral Health ; },
abstract = {Diet plays a central role in shaping the composition and metabolic activity of the oral microbiota, thereby influencing both oral and systemic health. Disturbances in this delicate host-microbe balance, triggered by dietary factors, smoking, poor oral hygiene, or antibiotic use, can lead to microbial dysbiosis and increase the risk of oral diseases such as periodontitis, as well as chronic systemic disorders including diabetes, cardiovascular disease, Alzheimer's disease, and certain cancers. Among dietary contaminants, exposure to toxic heavy metals such as cadmium (Cd), lead (Pb), mercury (Hg), nickel (Ni), and arsenic (As) represents an underrecognized modifier of the oral microbial ecosystem. Even at low concentrations, these elements can disrupt microbial diversity, promote inflammation, and impair metabolic homeostasis. Saliva has recently emerged as a promising, non-invasive biofluid for monitoring nutritional status and early metabolic alterations induced by diet and environmental exposures. Salivary biomarkers, including metabolites, trace elements, and microbial signatures, offer potential for assessing the combined effects of diet, microbiota, and toxicant exposure. This review synthesizes current evidence on how diet influences the oral microbiota and modulates susceptibility to heavy metal toxicity. It also examines the potential of salivary biomarkers as integrative indicators of nutritional status and metabolic health, highlights methodological challenges limiting their validation, and outlines future research directions for developing saliva-based tools in personalized nutrition and precision health.},
}

Humans
*Saliva/chemistry/microbiology/metabolism
Biomarkers/analysis/metabolism
*Diet/adverse effects
*Microbiota/physiology
*Nutritional Status
*Mouth/microbiology
Metals, Heavy
Dysbiosis
Oral Health

@article {pmid41683213,
year = {2026},
author = {Kleinová, P and Tímea, B and Matej, V and Graňák, K and Andrej, K and Katarína, Š and Dedinská, I},
title = {Nutritional and Metabolic Interventions to Prevent and Treat Protein-Energy Wasting in Nondialysis CKD-Narrative Review.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683213},
issn = {2072-6643},
support = {09I03-03-V04-00211//The EU NextGenerationEU through the Recovery and Resilience Plan for Slovakia/ ; },
mesh = {Humans ; *Renal Insufficiency, Chronic/complications ; *Protein-Energy Malnutrition/therapy/prevention & control/etiology ; Gastrointestinal Microbiome ; Dietary Supplements ; Exercise ; Acidosis ; Dietary Proteins/administration & dosage ; },
abstract = {Background: Protein-energy wasting (PEW) is a major predictor of morbidity and mortality in patients with chronic kidney disease (CKD), even before the initiation of dialysis. Its multifactorial pathogenesis includes reduced dietary intake, chronic inflammation, metabolic acidosis, hormonal disturbances, and dysbiosis of the gut microbiota. Early recognition and targeted management are crucial for preventing muscle loss, functional decline, and adverse outcomes. Methods: This narrative review summarises and integrates current evidence from the literature on nutritional and metabolic interventions to prevent and treat protein-energy wasting in patients with nondialysis chronic kidney disease. Relevant clinical trials, meta-analyses, and experimental studies published up to date were evaluated, focusing on dietary strategies, metabolic modulation, physical exercise, and gut microbiome-targeted therapies. Results: Adequate energy and protein intake remain the cornerstone of PEW management, based on available clinical and observational evidence. Individualised diets emphasising high-quality and plant-based proteins, oral nutritional supplements, and ketoanalogues can attenuate muscle wasting. Correction of metabolic acidosis and inflammation enhances protein anabolism and nitrogen balance. Physical exercise acts synergistically with dietary interventions to preserve muscle mass and function. Novel approaches-such as modulating the gut-kidney axis with pre-, pro-, and postbiotics or supplementing with short-chain fatty acids-show promise in improving metabolic and inflammatory profiles. Conclusions: The management of PEW in nondialysis CKD requires a personalised approach that integrates nutrition, physical activity, metabolic correction and microbiome modulation. Early, coordinated intervention may help to slow the progression of CKD and improve patient survival and quality of life.},
}

Humans
*Renal Insufficiency, Chronic/complications
*Protein-Energy Malnutrition/therapy/prevention & control/etiology
Gastrointestinal Microbiome
Dietary Supplements
Exercise
Acidosis
Dietary Proteins/administration & dosage

@article {pmid41683210,
year = {2026},
author = {Melenikioti, E and Pavlidou, E and Dakanalis, A and Giaginis, C and Papadopoulou, SK},
title = {Dietary Lithium, Silicon, and Boron: An Updated Critical Review of Their Roles in Metabolic Regulation, Neurobiology, Bone Health, and the Gut Microbiome.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683210},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Silicon/pharmacology/administration & dosage ; *Boron/pharmacology/administration & dosage ; *Bone and Bones/drug effects/metabolism ; *Lithium/pharmacology/administration & dosage ; Animals ; *Diet ; Neurobiology ; },
abstract = {BACKGROUND/OBJECTIVES: Lithium (Li), silicon (Si), and boron (B) are proposed nutritional trace elements with potential roles in metabolic, neurobiological, endocrine, inflammatory, and bone-related processes. This review provides a critical synthesis of data on Li-Si-B, emphasizing (i) physiological and mechanistic pathways, (ii) human clinical relevance, (iii) shared biological domains, and (iv) safety considerations.

METHODS: A narrative review was conducted across PubMed, Scopus, and Web of Science from inception to January 2025. Predefined search strings targeted dietary, environmental, and supplemental exposures of lithium, silicon, or boron in relation to metabolism, endocrine function, neurobiology, inflammation, bone health, and the gut microbiome. Inclusion criteria required peer-reviewed studies in English. Data extraction followed a structured template, and evidence was stratified into human, animal, cellular, and ecological tiers. Methodological limitations were critically appraised.

RESULTS: Li, Si, and B influence overlapping molecular pathways including oxidative stress modulation, mitochondrial stability, inflammatory signaling, endocrine regulation, and epithelial/gut barrier function. Human evidence remains limited: Li is supported primarily by small trials; Si by bone-related observational studies and biomarker-oriented interventions; and B by metabolic, inflammatory, and cognitive studies of modest sample size. Convergence across elements appears in redox control, barrier function, and neuroimmune interactions, but mechanistic synergism remains hypothetical.

CONCLUSIONS: Although Li-Si-B display compelling mechanistic potential, current human data are insufficient to justify dietary recommendations or supplementation. Considerable research gaps-including exposure assessment, dose-response characterization, toxicity thresholds, and controlled human trials-must be addressed before translation into public health policy.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Silicon/pharmacology/administration & dosage
*Boron/pharmacology/administration & dosage
*Bone and Bones/drug effects/metabolism
*Lithium/pharmacology/administration & dosage
Animals
*Diet
Neurobiology

@article {pmid41683193,
year = {2026},
author = {Bagheri, S and Ryszkiel, I and Stanek, A},
title = {Gut Microbiota Impact on Cognitive Function in Humans.},
journal = {Nutrients},
volume = {18},
number = {3},
pages = {},
pmid = {41683193},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Cognition/physiology ; Animals ; },
abstract = {The human gut microbiome and its relationship with both physiological and pathological functions have long intrigued researchers. One of the most fascinating and important areas within this domain is cognitive function. Given that a substantial number of studies, especially interventional ones, have been conducted on animal models, the findings of which are not fully generalizable to humans and may therefore be misinterpreted, the purpose of this study is to synthesize evidence from the most recent human research. Current evidence indicates that the gut microbiota is linked to cognitive function in both healthy and diseased states, with numerous studies suggesting a potential causal relationship between the two. Although the majority of these studies associate changes in cognitive function with differences in the composition of the gut microbiota, some findings also indicate an inverse relationship.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Cognition/physiology
Animals

@article {pmid41683132,
year = {2026},
author = {Zhao, X and Huang, S and Wei, Y and Wang, D and Li, C and Pan, C and Wang, Y and Xiang, H and Yu, G and Zhao, Y},
title = {Marine Bioactive Substances in Precision Nutrient Delivery to the Gut and Advances in Microbiome Regulation: A Narrative Review.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683132},
issn = {2304-8158},
abstract = {Marine bioactive substances exhibit structural diversity and function-specific properties, attracting considerable interest in their potential applications in targeted nutritional delivery to the gut and microbiota regulation. These bioactive components, sourced from seaweed, marine crustaceans, and microorganisms, including polysaccharides, polyphenols, and lipids, demonstrate exceptional biocompatibility and specific recognition capabilities. They serve as an optimal carrier matrix and functional core for developing an efficient, precision-targeted intestinal nutrition delivery system. Research findings demonstrate that optimization via innovative delivery technologies, including nanoencapsulation and polymer microsphere encapsulation, enables marine bioactive substances to navigate various physiological barriers in the gastrointestinal tract effectively. This facilitates targeted, sustained release of nutritional components and enhances bioavailability. Simultaneously, these substances may relieve dysbiosis by modulating the composition of the gut microbiota and the quantity and activity of specific metabolic products, thereby reinforcing intestinal barrier integrity. This narrative review systematically examines the sources and functional attributes of marine bioactive compounds, emphasizing their application strategies in developing targeted delivery systems for the gut and their regulatory effects on gut microbiota. It concludes by delineating future research directions in this field, particularly in optimizing carrier functionalities and clarifying action mechanisms.},
}

@article {pmid41683127,
year = {2026},
author = {Raadani, A and Hamdi, A and Yangui, I and Jiménez-Araujo, A and Rodríguez-Arcos, R and Ben Elhadj Ali, I and Guillén-Bejarano, R and Messaoud, C},
title = {Inter- and Intraspecific Variability in Non-Starch Polysaccharide Composition of Satureja Species from Tunisia: Implications for Functional Food Development.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683127},
issn = {2304-8158},
abstract = {Non-starch polysaccharides, the primary structural component of dietary fiber, play critical roles in metabolic and digestive health through multiple physiological mechanisms, yet their composition in Mediterranean aromatic plants remains poorly characterized, limiting the development of novel functional food ingredients. This study provides the first comprehensive NSP profiling of 22 populations across three Tunisian Satureja species (S. nervosa, S. graeca, and endemic S. barceloi), using enzymatic analysis, gas chromatography, and multivariate statistics. Total non-starch polysaccharides reached exceptional levels (21.5 ± 3.0 g/100 g dry weight (DW)), with several populations exhibiting unprecedented soluble fiber proportions exceeding 50%, including population SG4 achieving 79.7%. Monosaccharide analysis revealed uronic acid dominance (42.9-52.5% of total NSP), indicating pectin-rich cell walls with distinct functional properties. Principal component analysis (explaining 61.5-84.9% of variance) demonstrated that populations cluster by fiber chemotype rather than taxonomic classification. Hierarchical and K-means clustering identified three distinct clusters in the soluble and total fiber fractions, with uronic acid-dominated populations (SG4, SB, SG18, SN8) and arabinose-xylose enriched populations (SN13, SN12, SN22, SG21) as extreme chemotypes. Intraspecific variation (coefficient of variation, CV: 14.0-50.0%) substantially exceeded interspecific differences. These findings establish Tunisian Satureja as an exceptional functional fiber source and demonstrate that population-level chemical screening outperforms taxonomic classification for developing nutraceuticals targeting cholesterol reduction, glycemic control, and gut microbiome modulation.},
}

@article {pmid41683077,
year = {2026},
author = {Jiang, X and Li, X and Song, P and Dou, Y and Xue, J and Wu, Z and Ma, S and Wei, W and Zheng, W and Dou, S and Dong, L},
title = {Analysis of Microbial Interactions During the Production of Chinese Ethnic Fermented Foods.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683077},
issn = {2304-8158},
support = {No.2025-MSLH-016//Liaoning Provincial Science and Technology Plan Joint Plan (Natural Science Foundation-General Program)/ ; 2014020134//Natural Science Foundation of Liaoning Province/ ; JYTMS20230376//Liaoning Provincial Department of Education University Basic Scientific Research Surface Project/ ; },
abstract = {Food fermentation is an ancient bioprocess characterized by complex biochemical transformations driven primarily by microbial communities. Across the diverse regions of China, various ethnic groups have developed a rich array of traditional fermented foods through long-term practical experience. These foods are integral to local culinary heritage and provide valuable systems for studying microbial ecology and function. From the perspective of microbial interactions, this review summarizes key concepts and major interaction types-including mutualism, commensalism, and competition-and describes how bacteria, yeasts, and molds interact via metabolic division of labor to drive substrate conversion, flavor formation, preservation, and biosynthesis of functional compounds. Focusing on four representative ethnic fermented foods-Dong fermented fish, Mongoslian milk curd, Miao sour soup, and Manchurian kombucha-we analyze how microbial interactions contribute to product quality, safety, and sensory attributes. Given current challenges in industrializing traditional fermented foods, such as poor standardization and variable quality, we propose future research directions centered on modern microbiome tools, designed microbial consortia, and process optimization. This work aims to provide a scientific foundation and practical strategies for modernization and quality improvement of traditional fermented foods.},
}

@article {pmid41683004,
year = {2026},
author = {Feng, Q and Li, X and Gong, L and Wei, Y and Bai, Z and Zhou, J and Ma, Y and He, G},
title = {Revealing the Functional Microbiota of Caproic Acid-Producing and Lactic Acid-Utilizing Bacteria in the Pit Muds for Chinese Nong-Xiang Baijiu Fermentation.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {3},
pages = {},
pmid = {41683004},
issn = {2304-8158},
abstract = {Low ethyl caproate and high ethyl lactate contents pose a significant challenge in producing Chinese nong-xiang baijiu. The formation of these esters depends on the metabolism of their precursors-caproic acid and lactic acid-within the pit mud (PM) microbiome. However, the specific taxa driving the metabolic flux from lactate accumulation to caproate synthesis remain unclear. This study aimed to identify potential functional microbes capable of caproate biosynthesis and lactate utilization by systematically analyzing PM samples from the upper, middle, and lower layers of three different pit ages (0, 20, and 50 years). Results showed that 50-year-old PM exhibited significantly higher caproic acid and ammonium nitrogen levels, but lower lactic acid content, compared to the 0- and 20-year-old counterparts. Notably, Petrimonas, Caproiciproducens, and Sedimentibacter were significantly enriched in the 50-year-old PM. Their relative abundances correlated positively with caproic acid and negatively with lactic acid. Furthermore, PICRUSt2 analysis indicated higher abundances of genes associated with caproate synthesis and lactate utilization in the 50-year-old microenvironment. We propose that Petrimonas, Caproiciproducens, and Sedimentibacter are potential functional candidates for lactate degradation and caproate generation. These findings provide a scientific basis for modulating the microbiome for "increasing ethyl caproate and reducing ethyl lactate", thereby enhancing baijiu quality.},
}

@article {pmid41682926,
year = {2026},
author = {Koçak, T and Özbek, YD and Bodur, M and Yeşil, S and Ağagündüz, D},
title = {Intersection of Precision Nutrition and Bladder Cancer: A Narrative State-of-the-Art Review of Potential Applications and Challenges.},
journal = {Journal of clinical medicine},
volume = {15},
number = {3},
pages = {},
pmid = {41682926},
issn = {2077-0383},
support = {02026008001021//Recep Tayyip Erdoğan University/ ; },
abstract = {Bladder cancer (BC) is a biologically heterogeneous tumor affected by genetic, metabolic, environmental, and lifestyle factors. Recent research indicates that nutrition can change the way urothelial cancer forms by affecting inflammation, oxidative stress, cellular energy, and the epigenome. It can also change the risk of BC and how well treatment works. Simultaneous progress in precision nutrition (PN) and nutriomic profiling-encompassing nutrigenomics, nutrigenetics, nutriepigenetics, metabolomics, and microbiome science-presents novel options to tailor dietary regimens beyond universal guidelines. In this review, we consolidate existing knowledge regarding the nutritional factors influencing BC, outline pertinent principles of PN for BC prevention and survival, and explore how urine proteomics and molecular subtyping facilitate the integration of PN into precision oncology. Our review examines the methodological, bioinformatic, biomarker, and clinical translation challenges that impede the implementation of PN in BC management; these challenges include the need for validated nutritional biomarkers with mechanistic endpoints, interoperable data platforms, and rigorously designed clinical trials. Finally, we emphasize future prospects for PN-guided medical nutrition therapy and dietary models during and after systemic treatment recovery. We propose research priorities that will facilitate the integration of PN-informed individualized dietary plans with medical and surgical approaches in BC treatment, aiming to decrease the costs associated with expensive or excessively aggressive treatment methods, thereby supporting long-term survival care. This review seeks to establish a conceptual framework for the integration of PN into BC management by delineating the opportunities and challenges, hence promoting hypothesis-driven research in a promising yet underexplored domain.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

METHODOLOGY: A narrative review.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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