@article {pmid41232540,
year = {2025},
author = {Wieringa, JW and Binyamin, D and Jankelowitz, IA and Schweitzer, R and Turjeman, S and Khatib, S and Esser, MJ and van der Woude, CJ and Fuhler, GM and Koren, O},
title = {Intestinal barrier alterations in mice following fecal microbiota transplant from children of IBD-affected mothers.},
journal = {Med (New York, N.Y.)},
volume = {},
number = {},
pages = {100915},
doi = {10.1016/j.medj.2025.100915},
pmid = {41232540},
issn = {2666-6340},
abstract = {BACKGROUND: Inflammatory bowel disease (IBD) carries a hereditary risk, which is higher through maternal, rather than paternal, inheritance. Like their mothers, children born to mothers with IBD have an altered microbiome shortly after birth.

METHODS: To investigate whether this altered microbiome persists later in life and affects the intestinal mucosa, the fecal microbiome was analyzed in samples from 44 infants ranging from 0 to 10 years of age born to 26 women with IBD. Forty-four age-matched children of 29 women without IBD served as controls. Fecal microbiota transplantation (FMT) to germ-free mice was carried out from 4-year-olds born to mothers with IBD and controls. Markers of inflammation, barrier function, and metabolic changes were investigated.

FINDINGS: Intestinal microbiomes were more similar between women with IBD and their children than between control mothers and their offspring. Microbial changes were noticeable in children from mothers with IBD from the age of 4 years compared to children of controls. No inflammatory response was present in the mucosa of mice receiving FMT from children of mothers with IBD; however, mesenteric lymph node enlargement and decreased expression of barrier genes Zo1 and Ocln were seen in mice receiving FMT from these children compared to controls. Additionally, reduced colonic expression of the immunological tolerance enzyme Ido1 coincided with decreased serum kynurenine/tryptophan ratios.

CONCLUSIONS: Fecal microbiomes of children of mothers with IBD exhibit characteristics that reduce epithelial tight junction barrier genes and tolerogenic tryptophan metabolism. Microbiome-induced gut barrier disruptions may contribute to an enhanced IBD predisposition in infants of mothers with IBD.

FUNDING: This work was funded by ZonMw.},
}

@article {pmid41232537,
year = {2025},
author = {Hu, B and Liu, R and Ramm, E and Tong, P and Dannenmann, M and Chen, Z and Zou, T and Shi, X and Chen, X and Haensch, R and Schloter, M and Rennenberg, H},
title = {Impaired sustainability of thawing permafrost peatland ecosystems by Siberian alder colonization.},
journal = {Current biology : CB},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cub.2025.10.021},
pmid = {41232537},
issn = {1879-0445},
abstract = {Anthropogenic climate warming causes thawing of permafrost soil in pan-Arctic areas of the Northern Hemisphere, thereby triggering changes in ecosystem biodiversity and biogeochemistry. Here, we analyzed the consequences of Siberian alder colonization for the thawing of permafrost soil, soil microbial biodiversity, and the performance of neighboring peatland vegetation. We show, for the first time, that heat dissipation from biological nitrogen fixation (BNF) by alder-Frankia symbiosis in numerous nodule clusters accelerates the thawing of permafrost soil in alder forests. On an areal basis, a rough estimate of heat dissipation from BNF amounts to 4,330-34,630 MJ year[-1] per hectare. The maximum value of this estimate is of the same order of magnitude as the reported areal heat dissipation from microbial organic matter decomposition and accounts for ∼7.6% of the heat dissipation from this decomposition. Colonization by Siberian alder trees strongly modified microbial biodiversity in the top peat and organic soil layers and had nursing effects on dominant peatland plant species neighboring alder forests, as indicated by carbon and nitrogen stable isotope signatures. These results reveal the mechanism of permafrost soil thawing attributed to BNF-mediated heat dissipation by Siberian alder forests at both the site-specific and ecosystem levels. They complement present knowledge on microbial-decomposition-driven soil heating and carbon release in permafrost regions under global warming. In addition, they show that colonization by Siberian alder has significant feedback on climate-change-mediated thawing of permafrost soil, thereby impairing the sustainability of pan-Arctic peatland ecosystems.},
}

@article {pmid41232519,
year = {2025},
author = {Sempeck, CD and Olm, MR},
title = {Mapping the oral microbiome opens links to periodontitis.},
journal = {Cell host & microbe},
volume = {33},
number = {11},
pages = {1832-1833},
doi = {10.1016/j.chom.2025.10.009},
pmid = {41232519},
issn = {1934-6069},
mesh = {Humans ; *Periodontitis/microbiology ; *Microbiota ; *Mouth/microbiology ; *Bacteria/genetics/classification/isolation & purification ; Genome, Bacterial ; },
abstract = {Many microbiome analysis techniques can only detect the microbes present in the reference genome database used. In this issue of Cell Host & Microbe, Cha et al. establish an improved genome database of the human oral microbiome, which they use to discover a connection between periodontitis and an enigmatic bacterial phylum.},
}

Humans
*Periodontitis/microbiology
*Microbiota
*Mouth/microbiology
*Bacteria/genetics/classification/isolation & purification
Genome, Bacterial

@article {pmid41232506,
year = {2025},
author = {Leng, T and de la Fuente-Nunez, C},
title = {The gut's hidden arsenal: A genomics-guided atlas of class II bacteriocins.},
journal = {Cell genomics},
volume = {5},
number = {11},
pages = {101064},
doi = {10.1016/j.xgen.2025.101064},
pmid = {41232506},
issn = {2666-979X},
mesh = {*Bacteriocins/genetics/pharmacology ; Humans ; *Genomics/methods ; *Gastrointestinal Microbiome/genetics/drug effects ; Genome, Bacterial ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Unmodified class II bacteriocins promise precision antimicrobials that spare bystander microbes. Zhang and colleagues introduce IIBacFinder, a genomics-guided pipeline that detects precursor and context genes with a curated pHMM library, infers leader-peptide cleavage, and triages candidates by meta-omics signals. The authors apply it across bacterial genomes, including an atlas of ∼280,000 human-gut genomes, and recover a vast reservoir of narrow-spectrum peptides and prioritize gut-resident candidates for synthesis. Of the 26 synthesized, 16 display activity in vitro, largely via membrane perturbation and with additive effects alongside vancomycin, while ex vivo assays show minimal compositional disruption of fecal communities compared with antibiotic controls. These results position unmodified class II bacteriocins as tractable, microbiome-sparing agents and illustrate how genome-scale mining coupled to meta-omics can bridge sequence to function in complex ecosystems.},
}

*Bacteriocins/genetics/pharmacology
Humans
*Genomics/methods
*Gastrointestinal Microbiome/genetics/drug effects
Genome, Bacterial
Anti-Bacterial Agents/pharmacology

@article {pmid41232381,
year = {2025},
author = {Ozgun Acar, O},
title = {Probiotic modulation of energy metabolism ameliorates experimental autoimmune encephalomyelitis via Nrf2-associated pentose phosphate pathway activation.},
journal = {Biochemical and biophysical research communications},
volume = {791},
number = {},
pages = {152934},
doi = {10.1016/j.bbrc.2025.152934},
pmid = {41232381},
issn = {1090-2104},
abstract = {Alterations in the gut microbiome not only impact immune processes associated with the pathogenesis of multiple sclerosis (MS) but also affect the regulation of metabolic pathways. In MS and experimental autoimmune encephalomyelitis (EAE) models, probiotics are thought to contribute not only to immunomodulatory effects but also to the reprogramming of energy metabolism. In light of these findings, this study assessed the efficacy of the probiotic Lactobacillus acidophilus LA-5 (LA-5) in disorders of pentose phosphate pathway (PPP) energy metabolism during disease processes. LA-5 supplementation markedly improved disease severity in the EAE model, as reflected by reduced clinical scores and increased expression and activity of key pentose phosphate pathway enzymes, including glucose-6-phosphate dehydrogenase (G6PDH) and 6-phosphogluconate dehydrogenase (6-PGD). The treatment also restored diminished transaldolase (TALDO) expression and normalized the NADPH levels in the brain tissue. Moreover, LA-5 reactivated the Nrf2 pathway, which was suppressed under EAE conditions, indicating increased antioxidant capacity. In conclusion, the present findings establish a direct connection between PPP dysfunction and MS pathology, indicating the therapeutic potential of metabolic modulation. This study provides new insights that could inform future strategies for the treatment of MS.},
}

@article {pmid41232361,
year = {2025},
author = {Bishoyi, AK and Al-Hasnaawei, S and Salem, KH and Ganesan, S and Shankhyan, A and Nanda, A and Sinha, A and Ray, S and Nathiya, D and Hammady, FJ},
title = {Gut microbiome metabolites in lung cancer: The emerging importance of short-chain fatty acids.},
journal = {International immunopharmacology},
volume = {168},
number = {Pt 1},
pages = {115821},
doi = {10.1016/j.intimp.2025.115821},
pmid = {41232361},
issn = {1878-1705},
abstract = {Short-chain fatty acids (SCFAs), which are produced from the fermentation by the gut microbiota of dietary fiber, are now proven to play a vital role in the growth control of lung cancer and drug response. SCFAs have mechanisms of action, including the inhibition of histone deacetylases, activation of G-protein-coupled receptors, and metabolic reprogramming. SCFAs suppress tumor growth, induce apoptosis, suppress angiogenesis, and modulate epithelial-mesenchymal transition. Besides the above direct antitumor effects, SCFAs enhance the therapeutic effect of immune checkpoint inhibitors and reduce the toxicity of radiotherapy and chemotherapy by maintaining the mucosal barrier and restoring systemic immune homeostasis. Butyrate function is highly dualistic; it is usually protective but may confer multidrug resistance under certain therapeuticconditions. To reconcile these opposing effects is akey challenge in the translation of microbiota-based therapeutics and interventions. Therapies such as probiotics, fecal microbiota transplantation, and designed microbial consortia all target SCFAs as central mediators of microbiome-host communication. Overall, SCFAs are candidate metabolic co-adjuvants that can maximize therapeutic efficacy, suppress unacceptable side effects, and redirect therapeutic approaches to lung cancer.},
}

@article {pmid41232294,
year = {2025},
author = {Ateş, Ç and Dilbaz, B and Saçıntı, KG},
title = {Deciphering the relationship between adenomyosis and the microbiota: a systematic review.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {316},
number = {},
pages = {114823},
doi = {10.1016/j.ejogrb.2025.114823},
pmid = {41232294},
issn = {1872-7654},
abstract = {Adenomyosis is a benign displacement of endomerial tissue into the uterine myometrium, the exact pathogenesis of which has not yet been established. Recently, there has been increased research on the relationship between microbiota dysbiosis and adenomyosis; however, the details of this interaction are not yet clearly known. We have systematically reviewed all studies focusing on the relationship between microbiota and adenomyosis. The databases Pubmed, Scopus, GoogleScholar and Web of Science were queried up until June 2024. A total of 446 citations were obtained, resulting in the inclusion of a total of 7 papers, one of which was an animal experiment. There were 670 humans and 16 mice. There were 416 adenomyosis patients, 223 healthy controls, and 47 endometriosis-associated controls. 16S rRNA gene amplification and sequencing was used in 6 of 7 studies. Data was collected from the microbiomes of the endometrium, vagina, and gut. In adenomyosis, the abundance of Firmucites, Rhodospirillales, Ruminococcus gauvreauii, Citrobacter freundii, Prevotella copri, Burkholderia cepacia and the predominance of CST-III and CST-IV increase, while the abundance of Clostridiacea, Peptostreptococcaceae, Atopobiacea families and Fastidiosipila, Magasphaera sp. species decrease. This systematic review has revealed distinct bacterial species that are linked to adenomyosis, as well as the microbiome of the female genital tract and gut. Additional research is required to determine if these bacteria are the primary cause or a secondary result of adenomyosis.},
}

@article {pmid41232270,
year = {2025},
author = {Liu, B and Liu, C and Sunggip, C and Pu, G and Deng, D},
title = {Viruses in gastrointestinal cancers: Molecular pathogenesis, oncogenic mechanisms, and translational perspectives.},
journal = {Molecular aspects of medicine},
volume = {106},
number = {},
pages = {101415},
doi = {10.1016/j.mam.2025.101415},
pmid = {41232270},
issn = {1872-9452},
abstract = {Viral pathogens are one of the most significant causes of human carcinogenesis, contributing to up to 15-20 % of worldwide cancers. The gastrointestinal (GI) tract is one of the most vulnerable human organ system to virus-mediated tumorigenesis as a result of frequent exposure to viral infections and various immunological processes. The present review aims to describe the dual roles of viral infections in the development of gastrointestinal cancers (GICs), with a focus on Human Immunodeficiency Virus (HIV) and Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). HIV represents an oncological challenge in the era of effective antiretroviral therapy (ART), where significant immune dysfunction, persistent inflammation, and gut microbiome disruption render infected patients more susceptible to various GICs. On the other hand, SARS-CoV-2 is an emerging viral pathogen whose potential role in oncogenesis remains controversial yet biologically plausible. In this context, SARS-CoV-2 tropism to the gastrointestinal tissues and its capacity to drive cytokine storms, profound dysbiosis, and immune exhaustion raise significant questions regarding its potential to act as a pro-tumorigenic factor. Discussing mechanistic insights from well-known oncogenic viral pathogens, the present review describes the direct and indirect mechanisms by which these two major viruses may affect GI tumorigenesis. Moreover, this review translates these mechanisms into clinical perspectives, underscoring implications for diagnostics, prevention, and therapeutic strategies, while highlighting urgent research priorities for long-term surveillance and biomarker discovery. It highlights the importance of continuous scientific awareness to address the increasing cancer risks presented by emerging and re-emerging viruses through bridging virology and oncology.},
}

@article {pmid41232242,
year = {2025},
author = {Y, K and Isukapatla, AR},
title = {Postmortem microbiome dynamics: Review of forensic microbial clock.},
journal = {Journal of forensic and legal medicine},
volume = {117},
number = {},
pages = {103024},
doi = {10.1016/j.jflm.2025.103024},
pmid = {41232242},
issn = {1878-7487},
abstract = {The postmortem interval (PMI) in Forensic science presents several challenges, including accurate investigation, estimation and reliance on a limited set of physical and microbial markers. However, while these methods have advantages, they are also limited by factors such as environmental variability and temporal constraints. Microbial succession during decomposition, commonly referred to as the "microbial clock", has emerged as a promising and potentially more precise indicator of PMI. It is clear from a thorough examination of more than 30 peer-reviewed studies involving human cadavers and animal models that microbial communities undergo predictable, time-dependent internal and external changes. Controlled studies using murine and porcine models have demonstrated strong temporal correlations between specific microbial taxa and distinct stages of decomposition, with some models capable of predicting PMI within a two-to-three-day accuracy range over several weeks. Similarly, studies on human cadavers have shown consistent patterns of microbial succession within postmortem organs, revealing organ-specific microbial signatures that change over time and can be influenced by variables such as the cause of death, the environment and the health of an individual. These findings suggest that microbial succession can serve as a powerful quantitative and biological tool for determining the time of death. However, to realize its full potential, further research is needed, using diverse datasets and incorporating multiple post-mortem indicators. This review provides a comprehensive summary of current knowledge on the microbial clock and discusses the ecological and practical considerations necessary to develop a robust and reliable post-mortem clock for forensic practice.},
}

@article {pmid41232227,
year = {2025},
author = {Sharma, V and Goel, S and Bisht, K and Kaura, T and Verma, S and Mewara, A and Grover, GS and Biswal, M},
title = {Unveiling the Presence of Coxiella-like bacteria in Rhipicephalus microplus Ticks from Punjab, North India: A 16S rRNA metagenomic study.},
journal = {Veterinary microbiology},
volume = {312},
number = {},
pages = {110783},
doi = {10.1016/j.vetmic.2025.110783},
pmid = {41232227},
issn = {1873-2542},
abstract = {In this study, using 16S rRNA gene-based metagenomics, we aimed to determine the presence of infectious bacteria in the ticks collected from Punjab state in north India. Tick samples were collected from the domesticated animals from the Patiala, Ropar, and Mohali districts of Punjab, India from February 2022- April 2022. DNA was extracted, and the library was prepared by targeting the V3-V4 hypervariable region of the 16S rRNA gene. The sequencing was conducted in Illumina using the 300 bp paired-end chemistry. Eight tick samples were analyzed from the Patiala, Ropar and Mohali districts of Punjab, India, revealing a diverse range of bacterial species within the tick microbiome. Seven out of eight samples were found to harbour Coxiella-like bacteria (46-181,607 reads; closely related to C. burnetii based on 16S rRNA [V3-V4] sequence similarity), indicating their abundance in the tick population. Furthermore, the analysis uncovered the presence of other pathogenic bacterial genera, including Staphylococcus, Streptococcus, Corynebacterium, Enterococcus, Pseudomonas, Bordetella, and Micrococcus in the tick microbiome, highlighting the abundance and diversity of infectious organisms within ticks. 16S rRNA gene-based metagenomics enables valuable insights into infectious agents in disease-transmitting vectors. Coxiella-like bacteria were found to be predominant bacterial species in the tick microbiomes in this study. The public health significance of this finding in animals and humans needs to be explored in this region. However, as 16S rRNA sequencing offers limited resolution for distinguishing closely related taxa, further confirmation using additional loci or whole-genome sequencing is warranted.},
}

@article {pmid41232211,
year = {2025},
author = {Bai, X and He, Y and Ge, Y and Gao, S and Li, A and Guo, T and Hu, H and Pan, H},
title = {Crosstalk between liver gene expression and enteric microbiome regulates laying performance and lipid metabolism in different breeds of layer hens during growing and pre-laying periods.},
journal = {Poultry science},
volume = {104},
number = {12},
pages = {106068},
doi = {10.1016/j.psj.2025.106068},
pmid = {41232211},
issn = {1525-3171},
abstract = {The present work was conducted to investigate the interaction between liver gene profile and enteric microbiome on regulation of laying performance and lipid metabolism in different breeds of layer hens during the growth and pre-laying periods. A total of 192 7-w-old laying hens (six replicates per breed, 16 hens per replicate), including 96 Jingfen-1 (JF-1) and 96 Jingfen-2 (JF-2) hens, were selected and fed the same feed under identical environments. The experiment lasted from 7 to 20 w-of-age. JF-1 initiated egg production at 16 w, whereas JF-2 started at 18 w. From 17 w, JF-1 exhibited higher egg production rates than JF-2 (P < 0.05). Compared with JF-2, egg weight, Haugh unit, egg shape index, albumen height, and yolk mass were higher in JF-1 eggs (P < 0.05). Hepatic triglyceride, cholesterol, fatty acid synthase, and acetyl-CoA carboxylase contents were higher, whereas lipoprotein lipase and total lipase levels were lower in JF-1 (P < 0.05). There were 363 downregulated and 385 upregulated genes in the liver of the JF-2. Kyoto Encyclopedia of Genes and Genomes analysis indicated that pathways enriched in the downregulated genes of JF-2 hens included fatty acid biosynthesis, elongation, and metabolism and peroxisome proliferator-activated receptor signaling. Lipid synthesis-related genes such as FASN, ACACA, ELOVL2, and ACSL5 were upregulated in JF-1 hens. The cecal Firmicutes abundance in JF-1 was higher, whereas the Bacteroidetes abundance was lower than that in JF-2 hens (P < 0.05). Firmicutes/Bacteroidetes ratio in the cecum of JF-1 hens was higher than in JF-2 hens (P < 0.05). Phocaeicola, Lactobacillus, Mediterraneibacter, and Phascolarctobacterium were more abundant (P < 0.05) in the cecum of JF-1 hens. Correlation analysis suggested that higher Firmicutes/Bacteroidetes ratio in the cecum might activate the liver gene expression associated with lipid synthesis, and then improved egg quality in JF-1 hens. Summary, the liver genes and intestinal flora coordinated to promote laying performance and egg quality by modulating physiological fat deposition in JF-1 during the growing and pre-lay periods.},
}

@article {pmid41232182,
year = {2025},
author = {Guo, P and Li, Z and Luo, J and Xu, X and Liu, H and Cao, Y and Wei, Y and Liu, Z and Qing, Y and Wu, Y},
title = {Synergistic Se/S functionalization of biochar for effective immobilization of multi-target heavy metals in water and soil.},
journal = {Journal of hazardous materials},
volume = {500},
number = {},
pages = {140453},
doi = {10.1016/j.jhazmat.2025.140453},
pmid = {41232182},
issn = {1873-3336},
abstract = {Cadmium (Cd) and lead (Pb) contaminate aquatic environments and soil systems, threatening ecosystems and human health via bioaccumulation, while current remediation materials are often limited by insufficient adsorption capacity and restriction to a single medium. To address these challenges, a novel almond shell biochar co-functionalized with L-cysteine (L-Cys) and selenium (Se) was prepared (L-SeBC). This synergistic integration endows L-SeBC with abundant active sites for effective remediation. Adsorption thermodynamics demonstrated the maximum of 147.7 mg/g (Cd[2 +]) and 203.4 mg/g (Pb[2+]). Density functional theory (DFT) calculations indicated that the enhanced adsorption occurred via chemisorption-physisorption synergy. In soil remediation experiments (5 % w/wL-SeBC application), the available Cd and Pb decreased by 45.1 % and 52.1 %. The addition of L-SeBC promoted soybean growth in contaminated soil, and reduced Cd and Pb contents in leaves (by 55.6 % and 68.9 %) and roots (by 28.6 % and 29.0 %). Furthermore, L-SeBC increased the activities of plant enzymes and soil enzymes, enhancing nutrient cycling and stress resistance of plants. Microbial analysis revealed that L-SeBC reshaped the soil microbiome by enriching functional genera (e.g., Pseudomonas spp.). Overall, the waste-derived, multifunctional adsorbent L-SeBC is cost-effective and eco-friendly, enables multi-scenario remediation, and exhibits great practical potential in sustainable pollution control.},
}

@article {pmid41231980,
year = {2025},
author = {Gelsinger, DR and Ronda, C and Ma, J and Kar, OB and Edwards, M and Huang, Y and Mavros, CF and Sun, Y and Perdue, T and Vo, PL and Ivanov, II and Sternberg, SH and Wang, HH},
title = {Metagenomic editing of commensal bacteria in vivo using CRISPR-associated transposases.},
journal = {Science (New York, N.Y.)},
volume = {390},
number = {6774},
pages = {eadx7604},
doi = {10.1126/science.adx7604},
pmid = {41231980},
issn = {1095-9203},
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Gene Editing/methods ; *Bacteroides/genetics/growth & development ; Humans ; Metagenomics/methods ; *CRISPR-Cas Systems ; Symbiosis ; Mice, Inbred C57BL ; Metagenome ; Clustered Regularly Interspaced Short Palindromic Repeats ; },
abstract = {Although metagenomic sequencing has revealed a rich microbial biodiversity in the mammalian gut, methods to genetically alter specific species in the microbiome are highly limited. Here, we introduce Metagenomic Editing (MetaEdit) as a platform technology for microbiome engineering that uses optimized CRISPR-associated transposases delivered by a broadly conjugative vector to directly modify diverse native commensal bacteria from mice and humans with new pathways at single-nucleotide genomic resolution. Using MetaEdit, we achieved in vivo genetic capture of native murine Bacteroides by integrating a metabolic payload that enables tunable growth control in the mammalian gut with dietary inulin. We further show in vivo editing of segmented filamentous bacteria, an immunomodulatory small-intestinal microbial species recalcitrant to cultivation. Collectively, this work provides a paradigm to precisely manipulate individual bacteria in native communities across gigabases of their metagenomic repertoire.},
}

Animals
Mice
*Gastrointestinal Microbiome/genetics
*Gene Editing/methods
*Bacteroides/genetics/growth & development
Humans
Metagenomics/methods
*CRISPR-Cas Systems
Symbiosis
Mice, Inbred C57BL
Metagenome
Clustered Regularly Interspaced Short Palindromic Repeats

@article {pmid41231970,
year = {2025},
author = {Coelho, C and Taborda, A and Lorena, C and Frazão, T and Veríssimo, A and Borges, PT and Brissos, V and Tiago, I and Martins, LO},
title = {Shotgun metagenomic mining reveals a new FAD-dependent D-lactate dehydrogenase in an isopod gut microbiome.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0148025},
doi = {10.1128/aem.01480-25},
pmid = {41231970},
issn = {1098-5336},
abstract = {UNLABELLED: Shotgun metagenomic sequencing has emerged as a powerful tool for exploring microbial diversity and uncovering genes encoding novel biocatalysts from complex environments. Here, we report the discovery and characterization of a new FAD-dependent D-lactate dehydrogenase (PdG-D-LDH) from the gut microbiome of the isopod Porcellio dilatatus. The enzyme was identified through in silico screening using BLAST and AlphaFold3 and functionally characterized as a homodimeric, thermoactive, and thermostable protein, demonstrating the robustness required for biotechnological applications. PdG-D-LDH exhibits a strong catalytic preference toward D-lactate and preferentially reduces quinones over cytochrome c or molecular oxygen. X-ray crystallography revealed a VAO/PCMH-like fold with a solvent-accessible active site that harbors both a FAD cofactor and an Fe(II) ion. Molecular docking studies provided insights into the structural determinants of its stereoselective substrate recognition. Under mild conditions, the enzyme catalyzed the oxidation of D-lactate to pyruvate with a 90% yield after 24 h of reaction, using molecular oxygen as the electron acceptor.

IMPORTANCE: This study illustrates how metagenomics, structural biology, and computational tools can jointly drive the discovery of new enzymes with valuable biotechnological applications aligned with circular economic principles. The newly identified D-lactate dehydrogenase, PdG-D-LDH, exhibits thermostability, stereoselectivity, and high catalytic efficiency, providing new insights into the structure-function relationships of lactate-metabolizing enzymes.},
}

@article {pmid41231796,
year = {2025},
author = {Baral, T and Maile, A and Adimurthy, NH and Saravu, K and Kudru, CU and Singh, J and Mukhopadhyay, C and Rao, M and Manu, MK and Sekhar Miraj, S},
title = {Exploring gut microbiota and its predicted functions in pulmonary tuberculosis: A multi-regional study using public 16S datasets.},
journal = {PloS one},
volume = {20},
number = {11},
pages = {e0336337},
doi = {10.1371/journal.pone.0336337},
pmid = {41231796},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/genetics/drug effects ; *Tuberculosis, Pulmonary/microbiology/drug therapy ; Phylogeny ; *RNA, Ribosomal, 16S/genetics ; Antitubercular Agents/therapeutic use ; Male ; Female ; Mycobacterium tuberculosis/genetics ; Middle Aged ; Adult ; },
abstract = {BACKGROUND: Pulmonary tuberculosis, caused by the bacillus Mycobacterium tuberculosis, remains a major global health challenge, particularly in developing countries. In this study, we analyzed publicly available 16S amplicon sequencing datasets from four geographical locations using a single workflow.

METHODS: We employed Quantitative Insights Into Microbial Ecology v.2 for microbial diversity analysis and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States v.2 for functional pathway predictions of the gut microbiota in patients with PTB and antitubercular therapy.

RESULTS: Our analysis revealed statistically significant alpha diversity differences in West Africa with decreased microbial diversity in pulmonary tuberculosis patients after two months of antitubercular therapy. Additionally, there were no statistically significant differences observed in pairwise comparisons within the same location or in the aggregate beta diversity of the datasets. The predicted microbial metabolic pathways related to vitamin biosynthesis, amino acid synthesis, and energy production were depleted in pulmonary tuberculosis patients following antitubercular therapy.

CONCLUSIONS: The observed alterations of gut microbial diversity and predicted functional profile underscores the influence of antitubercular therapy on gut health, suggesting that longer treatment durations may aggravate these alterations in gut microbial function. Moreover, geographical location exerts a more significant impact on microbial diversity than the disease state in a specific location, highlighting the potential for precision medicine to tailor interventions based on individual or regional microbiome characteristics.},
}

Humans
*Gastrointestinal Microbiome/genetics/drug effects
*Tuberculosis, Pulmonary/microbiology/drug therapy
Phylogeny
*RNA, Ribosomal, 16S/genetics
Antitubercular Agents/therapeutic use
Male
Female
Mycobacterium tuberculosis/genetics
Middle Aged
Adult

@article {pmid41231731,
year = {2025},
author = {van Hout, NE and Nevot, G and Jansen, PAM and Mannan, AA and Zeeuwen, PLJM and Hijnen, DJ and Tanaka, RJ and Güell, M and van den Bogaard, EH},
title = {From prebiotics to engineered microbes: microbe-inspired therapies for atopic dermatitis.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljaf451},
pmid = {41231731},
issn = {1365-2133},
abstract = {Atopic dermatitis (AD) is a common chronic inflammatory skin disease with diverse clinical and histological features. While primarily immune-mediated, genetic studies have also highlighted the role of epithelium-expressed gene abnormalities (e.g., filaggrin mutations) as a key factor. The approaches to treat AD are multifaceted, involving barrier restoration, local anti-inflammatory treatment, and, if needed, systemic immunosuppressive therapy. Genetic variations in the stratum corneum and the immune system are linked to an unbalance between the host and its microbiota, known as dysbiosis. An impaired skin barrier and immune responses can alter the microbial composition, while the skin microbiota itself can influence skin immunity and barrier formation. A hallmark of AD is increased bacterial colonization with Staphylococcus aureus (S. aureus), which is found on lesional skin in over 90% of patients. It contributes to disease severity driving further breakdown of the skin barrier and immune stimulation. The most common treatment for S. aureus infections in AD is topical or systemic antibiotic administration. While these treatments are typically reserved for active infections, they are sometimes prescribed to AD patients without clear skin infection. However, these treatments can disrupt commensal skin and gut microbiota, which play a critical role in maintaining skin and gut health. In this review we describe various therapies targeting the skin microbiome to reduce infection and inflammation in AD, including transplantation of microbiota, and the use of prebiotics, probiotics, and postbiotics. In addition, we provide a perspective to engineer and to harness bacteria of the skin microbiome as next-generation probiotics, also known as engineered live biotherapeutic products (eLBPs), using synthetic biology to create strains that can sense skin signals, such as immune signals, and environmental factors, and produce therapeutic treatments for AD on demand.},
}

@article {pmid41231537,
year = {2025},
author = {Cao, H and de la Fuente-Nunez, C},
title = {Microbial Primer: Artificial intelligence for microbiologists.},
journal = {Microbiology (Reading, England)},
volume = {171},
number = {11},
pages = {},
doi = {10.1099/mic.0.001629},
pmid = {41231537},
issn = {1465-2080},
mesh = {*Artificial Intelligence ; Machine Learning ; Humans ; Anti-Bacterial Agents/pharmacology ; Microbiota ; Genomics ; Drug Discovery/methods ; Bacteria/genetics/drug effects ; *Microbiology ; Algorithms ; },
abstract = {Artificial intelligence (AI) and machine learning (ML) are reshaping microbiology, enabling rapid antibiotic discovery, resistance prediction and clinical diagnostics. For microbiologists, the goal is not to build new algorithms but to recognize when ML is appropriate, how to prepare data and how to interpret outputs responsibly. This primer takes that practical stance - driving the ML car rather than rebuilding the engine. At a high level, ML learns from complex patterns, often noisy data. In antibiotic discovery, ML models help identify compounds in biological data and design new ones from scratch using generative AI. In microbiome studies, where measurements are compositional, sparse and often confounded, ML helps uncover community structure and link taxa or functions to phenotypes. In pathogen genomics, supervised models map sequence-derived features (e.g. k‑mers, SNPs and gene presence/absence) to outcomes such as species identity, antimicrobial susceptibility or MIC. Unsupervised learning supports exploration, including clustering, latent gradients and dimensionality reduction for visualization. Across these settings, success hinges less on exotic architectures than on sound problem framing, careful preprocessing and experimental validation.},
}

*Artificial Intelligence
Machine Learning
Humans
Anti-Bacterial Agents/pharmacology
Microbiota
Genomics
Drug Discovery/methods
Bacteria/genetics/drug effects
*Microbiology
Algorithms

@article {pmid41231416,
year = {2025},
author = {McAlister, FA and Lin, M and Youngson, E and Lethebe, BC and Leslie, M},
title = {Prior antibiotic exposure is associated with worse outcomes in adults with COVID-19.},
journal = {Infectious diseases (London, England)},
volume = {},
number = {},
pages = {1-9},
doi = {10.1080/23744235.2025.2585984},
pmid = {41231416},
issn = {2374-4243},
abstract = {BACKGROUND: Antibiotic-induced perturbations of the gut microbiome impair immunologic responses but whether they influence disease severity is unknown. The COVID-19 pandemic provided a unique opportunity to explore this question given widespread testing for SARS-CoV-2 infections.

OBJECTIVE: To determine whether prior antibiotic exposure was associated with outcomes in patients with COVID-19.

METHODS: Retrospective cohort study of all community-dwelling adults in Alberta, Canada with COVID-19 between March 2020 and June 2023. Subjects with antibiotic dispensations in the prior 3 months were compared (using multivariable logistic regression and propensity score (PS)-matching) to those without antibiotic exposure for differences in 30-day outcomes.

RESULTS: Of 445,646 adults with COVID-19, 49,581 (11.1%) were exposed to at least one antibiotic course in the prior 3 months. Those exposed to antibiotics were more likely to present to an emergency department (13.4% vs. 7.4%, aOR 1.52, 95%CI 1.48-1.57, PS-matched OR 1.48, 1.42-1.54), be hospitalised (5.8% vs. 2.8%, aOR 1.40,1.33-1.46, PS-matched OR 1.37, 1.29-1.45), or die (1.7% vs. 0.6%, aOR 1.28, 1.18-1.40, PS-matched OR 1.27, 1.14-1.42) than patients without prior antibiotic exposure. The associations were similar whether the antibiotic prescriptions were appropriate or not or whether antibiotic exposure periods were 6 weeks, 6 months, or 12 months prior to the positive RT-PCR test. The associations were stronger in those individuals with the highest tertile of antibiotic exposure, or those exposed to broad-spectrum antibiotics, or younger patients.

CONCLUSION: Prior antibiotic exposure is associated with worsened disease severity in patients infected with SARS-CoV-2. These findings support efforts to reduce antibiotic use.},
}

@article {pmid41231387,
year = {2025},
author = {Miller, CA and Pirotta, E and Grim, S and Moore, MJ and Durban, JW and Tyack, PL and Fearnbach, H and Leander, SGM and Knowlton, AR and Warren, AM and Zani, MA and Asmutis-Silvia, R and Pettis, HM and Apprill, A},
title = {Respiratory microbiomes reflect whale health.},
journal = {The ISME journal},
volume = {19},
number = {1},
pages = {},
doi = {10.1093/ismejo/wraf231},
pmid = {41231387},
issn = {1751-7370},
support = {NA19OAR4320074, NA24OARX432C0008//NOAA Cooperative Institute agreement/ ; N000142012697//Office of Naval Research/ ; N000142112096//Office of Naval Research/ ; RC20-1097//Strategic Environmental Research and Development Program/ ; RC20-7188//Strategic Environmental Research and Development Program/ ; RC21-3091//Strategic Environmental Research and Development Program/ ; },
mesh = {Animals ; *Microbiota ; *Whales/microbiology/physiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Female ; Archaea/classification/isolation & purification/genetics ; *Respiratory System/microbiology ; },
abstract = {As important members of the marine ecosystem, baleen whales are frequently managed and protected, but methodology to assess their health remains limited. Recent technological advances, such as the use of drones, support the non-invasive collection of promising health-associated data, including respiratory exhalant microbiota. Here, we considered five health metrics paired with respiratory exhalant samples to examine the utility of characterizing respiratory microorganisms for health diagnostics of North Atlantic right whales (Eubalaena glacialis), one of the most endangered baleen whale species. In 2016-2024, we used drones to collect 103 exhalant samples from 85 individuals to examine the associated microbiome, using amplicon sequencing methods targeting bacteria and archaea. The health status of sampled whales was characterized using an index of body condition derived from full-body vertical drone images, three qualitative assessments obtained from photo-identification imagery, and an existing health and vital rates model. Using an elastic net penalized regression approach, we demonstrate significant relationships between these health metrics and respiratory-associated microorganisms. Bacterial taxa that significantly contributed to the model for the body condition index differed between the thinnest and most robust males in the dataset. The thin whale harbored taxa belonging to the same genus as mammalian pathogens, Clostridium and Peptoniphilus, whereas the robust whale harbored taxa commonly observed in lipid-rich environments, Sediminispirochaeta and Candidatus Gracilibacteria. These differences warrant further investigation into the mechanisms by which bacteria contribute to whale health. Our findings demonstrate the utility of non-invasive multi-metric health models that include respiratory exhalant microbiota for whale health assessment and management.},
}

Animals
*Microbiota
*Whales/microbiology/physiology
*Bacteria/classification/genetics/isolation & purification
Male
Female
Archaea/classification/isolation & purification/genetics
*Respiratory System/microbiology

@article {pmid41231285,
year = {2025},
author = {Padur Sankaranarayanan, A and Dhanapal, S and Valliyappan, M and Shyu, DJH and Parthasarathy, TN},
title = {Intestinal microbiome diversity and disparity between wild and captive endangered Asian elephants (Elephas maximus indicus) in southern India.},
journal = {Antonie van Leeuwenhoek},
volume = {118},
number = {12},
pages = {191},
pmid = {41231285},
issn = {1572-9699},
support = {31950410559//National Natural Science Foundation [NSFC] of China/ ; },
mesh = {Animals ; *Elephants/microbiology ; *Gastrointestinal Microbiome/genetics ; India ; RNA, Ribosomal, 16S/genetics ; *Animals, Wild/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Endangered Species ; Biodiversity ; Phylogeny ; Animals, Zoo/microbiology ; Male ; DNA, Bacterial/genetics/chemistry ; Feces/microbiology ; Female ; },
abstract = {The gut microbiome affects the physical and mental wellbeing of an animal. Several factors, including diet, host physiology, age, sex, lifestyle, and environmental factors, influence the dynamic gut microbiome. We studied the gut microbiome composition of the endangered Asian elephants (Elephas maximus) kept under prolonged captive conditions (15.8 ± 3.9 years) and their wild counterparts, as both were exposed to two different environmental pressures. A total of 648,581 high-quality sequences were obtained, comprising 208 microbial families from 22 phyla and 97 orders, as determined by high-throughput 16S rRNA gene sequencing. Among them, 90% of the microbes belonged to the phyla Firmicutes, Proteobacteria and Bacteroidetes. Our analysis revealed a distinct variation in the gut microbiome between captive and wild elephants. The captive elephants had a higher abundance of the microbial phyla Kiritimatiellaeota, Tenericutes, Euryarchaeota, and Verrucomicrobia, which suggests that captivity alters the gut microbiome. These findings reveal distinct patterns of gut microbiome diversity between captive and wild elephants, underscoring the role of diet and environmental conditions in shaping the elephant gut microbiome.},
}

Animals
*Elephants/microbiology
*Gastrointestinal Microbiome/genetics
India
RNA, Ribosomal, 16S/genetics
*Animals, Wild/microbiology
*Bacteria/classification/genetics/isolation & purification
Endangered Species
Biodiversity
Phylogeny
Animals, Zoo/microbiology
Male
DNA, Bacterial/genetics/chemistry
Feces/microbiology
Female

@article {pmid41231233,
year = {2025},
author = {Absolon, DE and Jackson, VLN and Monier, A and Smith, AG and Helliwell, KE},
title = {Metagenomics of the MAST-3 stramenopile, Incisomonas, and its associated microbiome reveals unexpected metabolic attributes and extensive nutrient dependencies.},
journal = {Microbial genomics},
volume = {11},
number = {11},
pages = {},
doi = {10.1099/mgen.0.001510},
pmid = {41231233},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Microbiota/genetics ; *Stramenopiles/genetics/metabolism/classification ; Bacteria/genetics/metabolism/classification ; Phylogeny ; },
abstract = {Protists are polyphyletic single-celled eukaryotes that underpin global ecosystem functioning, particularly in the oceans. Most remain uncultured, limiting the investigation of their physiology and cell biology. MArine STramenopiles (MASTs) are heterotrophic protists that, although related to well-characterized photosynthetic diatoms and parasitic oomycetes, are poorly studied. The Nanomonadea (MAST-3) species Incisomonas marina has been maintained in co-culture with a bacterial consortium, offering opportunities to investigate the metabolic attributes and nutritional dependencies of the community. Employing a metagenomics approach, the 68 Mbp haploid genome of I. marina was retrieved to an estimated completeness of 93%, representing the most complete MAST genome so far. We also characterized the diversity of, and assembled genomes for, 23 co-cultured bacteria. Auxotrophy of I. marina for B vitamins (B1, B2, B6, B7 and B12), but not vitamins C, B3, B5 and B9, was predicted. Several bacteria also lacked complete B-vitamin biosynthesis pathways, suggesting that vitamins and/or their precursors are exchanged in the consortium. Moreover, I. marina lacked the ability to synthesize half the protein amino acids, although genes encoding the complete urea cycle were identified, like diatoms; this may play a role in recycling organic nitrogen compounds. Unexpectedly, we also identified the gene DSYB for dimethylsulphoniopropionate biosynthesis. Biosynthesis of this important stress protectant and bacterial chemoattractant is typically found in photosynthetic eukaryotes and has not been identified before in heterotrophic stramenopiles. Together, our study reveals the metabolic attributes of a hitherto understudied organism, advancing knowledge of the evolution and adaptations of the stramenopiles and informing future culturing efforts.},
}

*Metagenomics/methods
*Microbiota/genetics
*Stramenopiles/genetics/metabolism/classification
Bacteria/genetics/metabolism/classification
Phylogeny

@article {pmid41231220,
year = {2025},
author = {Jones, DG and Grimminger, P and Reynolds, J and Rosati, R and Hanna, G and Nilsson, M and Markar, S and van Hillegersberg, R and van Berge Henegouwen, M and Gisbertz, S and Ferri, L and Seely, AJE},
title = {Toward standardization in esophageal cancer surgery: patterns of practice across high-volume European centers.},
journal = {Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus},
volume = {38},
number = {6},
pages = {},
doi = {10.1093/dote/doaf100},
pmid = {41231220},
issn = {1442-2050},
mesh = {Humans ; *Esophageal Neoplasms/surgery ; *Esophagectomy/standards/methods/statistics & numerical data ; Europe ; *Practice Patterns, Physicians'/statistics & numerical data/standards ; *Adenocarcinoma/surgery ; Esophagogastric Junction/surgery ; Hospitals, High-Volume/statistics & numerical data ; Perioperative Care/standards/methods ; Surveys and Questionnaires ; Lymph Node Excision/standards/methods ; Carcinoma, Squamous Cell/surgery ; },
abstract = {Esophageal cancer (EC) remains a leading cause of cancer-related mortality worldwide. For patients with locally advanced, non-metastatic EC, advances in perioperative care, and surgical techniques have led to improved outcomes; however, significant variation persists, and standardization remains limited. This study aimed to characterize current practice patterns among expert surgeons at high-volume European centers through a structured, in-depth survey. Eight expert upper gastrointestinal surgeons from European centers performing >60 esophagectomies annually participated in comprehensive interviews. Topics included preoperative care pathways for distal esophageal/gastroesophageal junction adenocarcinoma, technical aspects of Ivor Lewis esophagectomy, and postoperative recovery protocols. Additional focus areas included multidisciplinary team involvement, allied health integration, research program participation, and follow-up strategies. Widespread agreement (7-8 of 8 centers) was observed in several domains: national EC care regionalization, multidisciplinary cancer conference review of all patients, institutional EC research programs, use of prospective national/international databases, application of CROSS chemoradiotherapy for squamous cell carcinoma, and perioperative FLOT chemotherapy for adenocarcinoma. Common surgical techniques included minimally invasive Ivor Lewis esophagectomy, two-field lymphadenectomy with en-bloc thoracic duct ligation, nasogastric tube placement, omental wrap of the anastomosis, and Enhanced Recovery After Surgery-based postoperative protocols. The majority of centers (5-6/8) performed routine preoperative optimization (nutrition, smoking cessation, frailty screening, oral hygiene/microbiome assessment), jejunostomy placement, and postoperative contrast swallow studies. Areas with notable variability (≤4/8 centers) included intraoperative crural closure, pyloric drainage procedures, gastric conduit sizing, postoperative pain management, and follow-up imaging timelines. High-volume European centers demonstrated strong alignment in several programmatic and perioperative elements of EC care, particularly around enhanced recovery pathways and preoperative optimization. Nonetheless, key intraoperative and postoperative variations persist, highlighting opportunities for future research, consensus building, and standardization to improve patient outcomes.},
}

Humans
*Esophageal Neoplasms/surgery
*Esophagectomy/standards/methods/statistics & numerical data
Europe
*Practice Patterns, Physicians'/statistics & numerical data/standards
*Adenocarcinoma/surgery
Esophagogastric Junction/surgery
Hospitals, High-Volume/statistics & numerical data
Perioperative Care/standards/methods
Surveys and Questionnaires
Lymph Node Excision/standards/methods
Carcinoma, Squamous Cell/surgery

@article {pmid41231122,
year = {2025},
author = {Brandl, P and Lüthy, L and Pultar, F and Hansen, ME and Jelmini, N and Faris, J and Yasmin, SO and Kamenik, AS and Arnold, R and Ebert, MO and Wolfrum, S and Lokey, RS and Riniker, S and Carreira, EM},
title = {Mutanobactin D from the Human Microbiome: Chemistry, Biology, and Molecular Dynamics Studies.},
journal = {Journal of the American Chemical Society},
volume = {},
number = {},
pages = {},
doi = {10.1021/jacs.5c08850},
pmid = {41231122},
issn = {1520-5126},
abstract = {Mutanobactin D is an interkingdom communicator derived from the human oral microbiome. The lipopeptide prevents yeast-to-hyphae morphogenesis in Candida albicans, notably without fungicidal or fungistatic activity. The mode of action and structure-activity relationship of mutanobactin D are unknown and prompt an interdisciplinary program of study. Stereoselective synthesis of designed mutanobactin D analogs reveals that the C26 configuration is crucial for bioactivity associated with inhibition of pathogenesis, or yeast-to-hyphae transition, in C. albicans. To shed light on this finding, we employ molecular dynamics (MD) simulations of mutanobactin D and selected analogs in increasingly complex environments: Monophasic (water or CHCl3), interfacial (water/CHCl3), and explicit lipid membrane (phosphatidylcholine) models. Monophasic MD simulations do not distinguish between bioactive and inactive compounds. In contrast, at a polar/apolar interphase, a dominant, stable conformation emerges for mutanobactin D and bioactive analogs. Explicit lipid membrane simulations reinforce these results and further reveal the formation of a continuous, structured water cushion, which is not found for inactive analogs. Our studies collectively reveal how the stereodefined attachment of the lipid in the C26-C28 motif governs activity against C. albicans and provide a framework for understanding the membrane behavior of mutanobactin D, which may be coupled to its role in the human oral microbiome. The approach described herein, consisting of synthesis and evaluation of designed analogs complemented by MD simulations, provides a blueprint for the study of bioactive natural products in various contexts, including the human microbiome.},
}

@article {pmid41230671,
year = {2025},
author = {Portillo-Miño, JD and Cifuentes, S and Morales, J and Bastidas, M and Otero, W and Pimentel de Assumpção, P and Latorre, G and Neuman, M and Riquelme, A},
title = {Gastric remnant cancer: a comprehensive narrative review from carcinogenesis to treatment.},
journal = {Revista de gastroenterologia del Peru : organo oficial de la Sociedad de Gastroenterologia del Peru},
volume = {45},
number = {3},
pages = {282-294},
pmid = {41230671},
issn = {1609-722X},
mesh = {Humans ; *Stomach Neoplasms/etiology/therapy/pathology ; *Gastric Stump/pathology ; *Gastrectomy/adverse effects ; Helicobacter Infections/complications ; Risk Factors ; Helicobacter pylori ; Bariatric Surgery/adverse effects ; Epstein-Barr Virus Infections/complications ; Carcinogenesis ; },
abstract = {Gastric remnant cancer is cancer secondary to partial gastrectomy after five years. Peculiarities due to the gastrectomy status may influence this type of GC. Modifications in the gastric microbiome, luminal pH, dietary habits, increased bile reflux, and Epstein-Barr virus infection, together with the traditional GC risk factors, cooperate to increase the risk of cancer in the remnant stomach. H. pylori infection has been widely associated with GC, and its role in the pathogenesis of the remnant stomach, as well as the preventive effect of its eradication after gastrectomy, are issues of great scientific interest. Bariatric surgery is another condition potentially related to increased GC risk and challenges to its diagnosis. In this scenario, this article aims to review the current evidence of the fundamental aspects involved in developing the gastric remnant cancer.},
}

Humans
*Stomach Neoplasms/etiology/therapy/pathology
*Gastric Stump/pathology
*Gastrectomy/adverse effects
Helicobacter Infections/complications
Risk Factors
Helicobacter pylori
Bariatric Surgery/adverse effects
Epstein-Barr Virus Infections/complications
Carcinogenesis

@article {pmid41230548,
year = {2025},
author = {Mukherjee, A and Tan, BH and Swarup, S},
title = {In Silico Prediction and In Vitro Validation of Bacterial Interactions in the Plant Rhizosphere Using a Synthetic Bacterial Community.},
journal = {Bio-protocol},
volume = {15},
number = {21},
pages = {e5496},
pmid = {41230548},
issn = {2331-8325},
abstract = {The rhizosphere, a 2-10 mm region surrounding the root surface, is colonized by numerous microorganisms, known as the rhizosphere microbiome. These microorganisms interact with each other, leading to emergent properties that affect plant fitness. Mapping these interactions is crucial to understanding microbial ecology in the rhizosphere and predicting and manipulating plant health. However, current methods do not capture the chemistry of the rhizosphere environment, and common plant-microbe interaction study setups do not map bacterial interactions in this niche. Additionally, studying bacterial interactions may require the creation of transgenic bacterial lines with markers for antibiotic resistance/fluorescent probes and even isotope labeling. Here, we describe a protocol for both in silico prediction and in vitro validation of bacterial interactions that closely recapitulate the major chemical constituents of the rhizosphere environment using a widely used Murashige & Skoog (MS)-based gnotobiotic plant growth system. We use the auto-fluorescent Pseudomonas, abundantly found in the rhizosphere, to estimate their interactions with other strains, thereby avoiding the need for the creation of transgenic bacterial strains. By combining artificial root exudate medium, plant cultivation medium, and a synthetic bacterial community (SynCom), we first simulate their interactions using genome-scale metabolic models (GSMMs) and then validate these interactions in vitro, using growth assays. We show that the GSMM-predicted interaction scores correlate moderately, yet significantly, with their in vitro validation. Given the complexity of interactions among rhizosphere microbiome members, this reproducible and efficient protocol will allow confident mapping of interactions of fluorescent Pseudomonas with other bacterial strains within the rhizosphere microbiome. Key features • This method builds upon the widely used MS-based gnotobiotic system for growing plants and a synthetic bacterial community (SynCom) for plant-microbe interaction studies. • It considers the chemical composition of plant growth media (MS) and root exudates to map bacterial interactions. • It provides a method to both predict and validate interactions of fluorescent Pseudomonas with other strains within a SynCom. • This method is scalable for any bacterial pair with distinguishing markers (e.g., fluorescence, antibiotic resistance).},
}

@article {pmid41230539,
year = {2025},
author = {Lopes, S and Lopes, PC and Fidalgo-Pereira, R and Flores-Fraile, J and Veiga, N and Gomes, ATPC},
title = {Antimicrobial potential of bioactive resin composites in caries management: a systematic review of in vitro studies.},
journal = {Frontiers in oral health},
volume = {6},
number = {},
pages = {1625977},
pmid = {41230539},
issn = {2673-4842},
abstract = {INTRODUCTION: Secondary caries is the leading cause of failure in resin composite restorations due to biofilm accumulation. Bioactive resin composites (BRCs) release ions that promote remineralization and inhibit bacterial growth. This review compares microbial adhesion and antimicrobial effectiveness between BRCs and conventional resin composites.

METHODS: A systematic search was conducted in databases PubMed, Scopus, and Cochrane Library to identify in vitro studies evaluating bacterial adhesion and antimicrobial effect of commercially available bioactive resin composites and their comparison with conventional resin composites. Studies reporting on microbial adhesion and/or antimicrobial effects were included.

RESULTS: A total of 272 potentially relevant articles were identified. Following PRISMA guidelines, eight articles met the inclusion criteria. The studies focused on five commercially available BRCs: Activa Bioactive Restorative (ACT), Beautifil II (BE), Cention N (CN), Equia Forte (EF), and SDR Flow Plus. Most studies assessed the adhesion of Streptococcus mutans in isolation. While microbial adhesion was observed on both bioactive and conventional resin composites, cell viability differed, with BRCs demonstrating superior antimicrobial effects.

CONCLUSION: Bacterial adhesion to dental restorative materials is influenced by surface roughness, hydrophilicity, chemical composition, and ion release. This review suggests that BRCs and conventional resin composites exhibit similar surface characteristics, resulting in comparable bacterial adhesion. However, BRCs show greater efficacy in reducing bacterial viability, probably due to ion release, which modulates the local microenvironment and microbial dynamics. Further research is needed to explore the broader impact of ion release on the oral microbiome and its potential role in dysbiosis and disease progression.

OSF Registries, https://doi.org/10.17605/OSF.IO/HRKFV.},
}

@article {pmid41230492,
year = {2025},
author = {Rodriguez-Fernandez, IA and Santiago-Rodriguez, TM and Figueroa-Pratts, PG and Cintrón-Berríos, K and Rodriguez-Cornier, ND and Toranzos, GA},
title = {Gut microbial community structure of the adult citrus root weevil Diaprepes abbreviatus.},
journal = {Frontiers in insect science},
volume = {5},
number = {},
pages = {1676003},
pmid = {41230492},
issn = {2673-8600},
abstract = {Diaprepes abbreviatus is an agricultural pest known to affect around 270 plant species across the Caribbean and the United States, posing significant challenges to pest management. Chemical control dominates management, but environmental and health concerns motivate microbiome-informed alternatives. However, limited information exists on the gut anatomy, physicochemical environment, and microbial composition of D. abbreviatus. In this study, we provide the first comprehensive characterization of the gut morphology, pH, and microbiota of adult D. abbreviatus in both females and males collected in Puerto Rico. Using dye-based gut tracing, we identified foregut, midgut, and hindgut or posterior gut compartments, and confirmed the presence of a muscular, sclerotized gizzard. Colorimetric analysis revealed a mildly acidic gut environment (approximately pH 4-5, based on qualitative ranges), consistent across sexes and regions. Shotgun metagenomic sequencing of dissected guts from males and females revealed microbial communities distinct from the leaf samples microbiota. While alpha and beta diversity did not differ significantly between sexes, co-occurrence analyses identified sex-specific correlation patterns among bacterial taxa. Notably, Enterobacter cloacae, Pantoea vagans, Lactococcus lactis, and Pseudomonas monteilii were repeatedly detected across individuals and generated metagenomic datasets, and some were localized to the hindgut, suggesting possible niche specialization. The presence of taxa, such as Enterobacter cloacae, previously reported as symbionts in other phytophagous insects further supports the hypothesis that certain bacteria may contribute to host digestion or adaptation. These findings establish a framework for understanding the gut environment and microbial community of D. abbreviatus, and highlight candidate taxa for future functional studies. More broadly, this work supports further research into the potential roles of gut microbiota in the ecology and management of this pest.},
}

@article {pmid41230376,
year = {2025},
author = {Triva, F and Borghi, E and Marsiglia, MD and Ottaviano, E and Ricci, E and Tognini, P and Montecucco, M and Vignoli, A},
title = {Targeting the gut to improve seizure control in CDKL5 deficiency disorder (CDD): study protocol for a single-arm, open-label clinical trial.},
journal = {Frontiers in neurology},
volume = {16},
number = {},
pages = {1642329},
pmid = {41230376},
issn = {1664-2295},
abstract = {INTRODUCTION: Cyclin-dependent kinase-like 5 deficiency disorder (CDD) is a neurodevelopmental condition characterized by infantile-onset epilepsy, developmental delay, intellectual and motor disabilities, sleep disturbances, and cortical visual impairment. Currently, there is no treatment for CDD, and epilepsy is a prominent and severe feature of the disorder. Standard anti-seizure medications have limited efficacy in seizure control, leading to detrimental effects on cognitive and motor development in CDD. The gut-brain axis has gained attention in epilepsy research, prompted by evidence of gastrointestinal (GI) symptoms in people with epilepsy. Notably, CDD patients experience GI problems and exhibit alterations in their gut microbiota compared to healthy individuals. We propose targeting the gut-microbiota-brain axis in CDD patients to alleviate seizures and potentially ameliorate other symptoms.

METHODS AND ANALYSIS: The protocol involves a two-step treatment strategy: a 12-week supplementation with alpha-lactalbumin (ALAC), fructooligosaccharides (FOS), and inulin to reduce inflammation, followed by a 12-week supplementation with ALAC/FOS/Inulin plus Sodium butyrate (NaB), to restore the balance of the gut microbiota. Clinical parameters, including seizure frequency, sleep disturbances, and GI discomfort, will be evaluated. Stool samples will be collected to analyse the gut microbiome. Primary objectives are to determine whether supplementation with ALAC/FOS/inulin alone or in combination with NaB can improve neurological features in CDD and to explore their effects on gut microbiota composition. Our study aims to provide insights into the potential benefits of targeting the gut-brain axis in CDD and offer new therapeutic options to improve seizure control and associated comorbidities.

ETHICS AND DISSEMINATION: The study protocol was approved by the local ethics committee (CET 3, n° 4189_17.04.2024_N_bis). Study results will be disseminated by the investigators through presentations at international scientific conferences and reported in peer-reviewed scientific journals.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, Identifier NCT06448663.},
}

@article {pmid41230235,
year = {2025},
author = {Tardivo, C and Monus, B and Pugina, G and Strauss, SL and Alferez, F and Albrecht, U},
title = {Delaying Candidatus Liberibacter asiaticus infection of citrus trees through use of individual protective covers and systemic delivery of oxytetracycline.},
journal = {Frontiers in plant science},
volume = {16},
number = {},
pages = {1671217},
pmid = {41230235},
issn = {1664-462X},
abstract = {Huanglongbing (HLB), or citrus greening, remains one of the most destructive diseases affecting citrus production globally. Associated with the phloem-limited bacterium Candidatus Liberibacter asiaticus (CLas) and vectored by Diaphorina citri, HLB leads to canopy decline, fibrous root loss, and reductions in fruit yield and quality. Recently, the systemic delivery of oxytetracycline (OTC) via trunk injection was approved in Florida as a targeted therapy to reduce CLas titers and improve tree health. In parallel, Individual Protective Covers (IPCs) have been adopted to delay CLas infection in newly planted citrus trees by vector exclusion. This study investigates the combined use of IPCs and trunk injection of OTC for post-IPC therapy. 'Valencia' sweet orange trees grafted on US-812 and US-942 rootstocks were planted in December 2020 under HLB-endemic conditions in southwest Florida. IPCs were installed at planting and removed after 18 months. The first OTC injection was performed in May 2023, 10 months after IPC removal. A second injection was performed in May 2024. A 2 × 2 × 2 factorial experimental design evaluated the effects of infection history (early-infected and late-infected), rootstock cultivar (US-812 and US-942), and injection treatment (OTC-injected and non-injected) on tree responses over two consecutive production seasons. In year 1, infection history significantly influenced tree size, fruit yield, total soluble solids (TSS), TSS/titratable acidity ratio, and peel color. Late-infected trees outperformed early-infected trees, regardless of injection treatment and rootstock cultivar. In year 2, OTC-injected trees exhibited significantly higher yields, improved juice quality, and enhanced canopy health regardless of infection history and rootstock cultivar. Fibrous root microbiome analyses based on 16S rRNA sequencing revealed no significant effects of OTC injection on bacterial alpha or beta diversity, with stable community structure observed across treatments and time points. This suggests that targeted vascular delivery of OTC may not cause any major disruption to the root endorhizosphere microbiome. Together, the results from this study demonstrate the efficacy of integrating preventative (use of IPCs) and therapeutic (OTC vascular delivery) strategies for sustainable HLB management while preserving microbial integrity and offering a model for citrus production in parts of the world where HLB is prevalent.},
}

@article {pmid41230178,
year = {2025},
author = {Nami, Y and Shaghaghi Ranjbar, M and Modarres Aval, M and Haghshenas, B},
title = {Harnessing Lactobacillus-derived SCFAs for food and health: Pathways, genes, and functional implications.},
journal = {Current research in microbial sciences},
volume = {9},
number = {},
pages = {100496},
pmid = {41230178},
issn = {2666-5174},
abstract = {Short-chain fatty acids (SCFAs) are crucial microbial metabolites that mediate host-microbiota interactions, regulate immune responses, and maintain gut homeostasis. While most studies focus on SCFA production by obligate anaerobes, recent evidence highlights Lactobacillus spp. as potential SCFA-producing microorganisms that remain understudied in terms of SCFA-based health and food-related effects. This research review compiles what is currently known about species- and strain-specific biosynthetic capabilities of Lactobacillus for SCFA production, particularly acetate, and lactate, which, while produced by Lactobacillus, is not classified as a SCFA but plays similar metabolic roles (e.g., activation of G-protein-coupled receptors, inhibition of histone deacetylases, and immune cell metabolism). We additionally assess new synthetic biology and metabolic engineering approaches to improving SCFA yield in Lactobacillus, including gene circuit design, CRISPR editing, and co-culture optimization. Importantly, we discuss translational opportunities not only in inflammatory, metabolic, and neuroimmune diseases but also in the development of functional foods, synbiotics, and nutraceutical applications. Finally, we highlight key challenges-strain variability, delivery strategies, and regulatory oversight-that preclude both clinical and food system translation. By integrating perspectives from microbiology, immunology, food science, and bioengineering, this review provides a broad framework for the rational design of SCFA-producing Lactobacillus strains as next-generation probiotics and food-grade biotherapeutics.},
}

@article {pmid41229982,
year = {2025},
author = {Chen, Z and Li, L and Jin, D and Zhao, Y and Malard, F and Huang, H and Ye, Y and Mohty, M},
title = {Gut microbiota and acute graft-versus-host disease.},
journal = {Chinese journal of cancer research = Chung-kuo yen cheng yen chiu},
volume = {37},
number = {5},
pages = {657-666},
pmid = {41229982},
issn = {1000-9604},
abstract = {Acute graft-versus-host disease (aGVHD) is an important complication which critically impacts the prognosis of patients undergoing allogeneic hematopoietic stem cell transplantation. Increasing evidence suggests that dysbiosis of the gut microbiota plays a key role in aGVHD pathogenesis. The biological process involves compromised intestinal barrier integrity, amplified inflammation driven by the translocation of microbial products like lipopolysaccharide, and finally the dysregulated immune response centralized by T cell activation and differentiation. Meanwhile, certain microbial metabolites such as short-chain fatty acids and secondary bile acids exert protective effects. The clinical relevance of these findings is underscored by studies establishing that specific gut microbial signatures, such as low diversity and single pathogen dominance, independently predict aGVHD morbidity and mortality. From a therapeutic perspective, the microbiome has emerged as an important therapeutic target for aGVHD. Fecal microbiota transplantation has shown significant efficacy in clinical trials for prophylaxis and treatment of aGVHD, providing definitive proof-of-concept for ecological restoration. This review synthesizes these foundational mechanistic insights, from metabolic disruption to host-microbe crosstalk at the mucosal barrier, and details the rapidly advancing clinical landscape of microbiome-targeted diagnostics and therapeutics for aGVHD.},
}

@article {pmid41229801,
year = {2025},
author = {Li, S and Xu, Y and Wu, Y and Zhao, Z},
title = {16S rRNA sequencing-based analysis of sputum microbiome in patients with acute exacerbations of chronic obstructive pulmonary disease: retrospective cohort study.},
journal = {Journal of thoracic disease},
volume = {17},
number = {10},
pages = {8876-8886},
pmid = {41229801},
issn = {2072-1439},
abstract = {BACKGROUND: Chronic obstructive pulmonary disease (COPD) is characterized mainly by persistent airflow limitation. Its acute exacerbation of COPD (AECOPD) significantly accelerates the progression of the disease. Current studies have shown that dysregulation of the airway microbiota may be related to the occurrence of AECOPD. However, the dynamic changes of the microbiota in sputum during AECOPD and their correlations with clinical indicators still need to be further clarified. This study aimed to investigate sputum microbiome characteristics and differences between healthy people and patients with AECOPD, and to analyse the correlation between the microecological structural characteristics of the sputum of AECOPD patients and clinical indicators.

METHODS: A total of 35 sputum samples from patients with AECOPD, 13 sputum samples from patients in the recovery stage, and 20 sputum samples from healthy controls were collected. The 16S ribosomal RNA (rRNA) sequencing method was used to analyse the differences in respiratory microecology. The characteristics of sputum microbiome in healthy people and patients with AECOPD were revealed through the analysis of alpha diversity, beta diversity, and linear discriminant analysis (LDA) effect size (LEfSe) differences.

RESULTS: Sputum microbiome structures were differences between COPD patients and healthy population. Compared with the healthy control group, the diversity and abundance of AECOPD patients and the recovery group was significantly reduced. The dominant phyla in the AECOPD group are the Firmicutes, followed by the Proteobacteria. The microbiome in the AECOPD group was characterized by a predominance of Streptococcus and Neisseria at the genus level. Relative abundances of Neisseria and Actinomyces were higher in the AECOPD group than in the control group. Furthermore, Corynebacterium and Haemophilus were identified as the unique microbiota of AECOPD patients. The inflammatory indicators of AECOPD patients were positively correlated with Staphylococcus in the respiratory tract.

CONCLUSIONS: Our study reveals changes in the sputum microbiome of AECOPD and analyses its correlation with clinical indicators. The results suggested that ecological dysregulation of the microbiota may contribute to disease progression. This study contributes potential microbial biomarkers that could aid in the diagnosis of AECOPD.},
}

@article {pmid41229691,
year = {2025},
author = {Hurd, PJ and Veto, V and Bell, G and Jackson, JJ},
title = {KtrB-mediated alkaline adaptation drives Enterococcus faecalis persistence in the gastrointestinal tract of Helicoverpa zea.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1641331},
pmid = {41229691},
issn = {1664-302X},
abstract = {Enterococcus faecalis is a commensal enteric bacterium capable of surviving in extreme and diverse environments. Here, we characterized the role of the gene ntpJ, which encodes the KtrB subunit of the KtrAB Na[+]/K[+] symporter, during the adaptation of E. faecalis to alkaline stress and persistence in Helicoverpa zea (corn earworm). We assessed growth kinetics, biofilm formation, surface adhesion, and gastrointestinal persistence in vivo using an E. faecalis OG1RF mariner transposon mutant (ntpJ-Tn). The ntpJ-Tn mutant showed delayed entry into mid-log phase growth and biofilm formation under standard and alkaline-adjusted conditions relative to the wild-type strain, while adherence to a low-density substrate was not affected, indicating KtrB-mediated transport was important for early-stage planktonic growth but unnecessary for surface attachment. Interestingly, elevated K[+] and Na[+] ions differentially influenced biofilm morphology and the distribution of adherent cells, highlighting an ion-specific response to alkalinity. The ntpJ-Tn mutant was undetectable 48 hours following ingestion in the novel non-destructive H. zea model, suggesting the loss of KtrB resulted in a persistence defect. These findings reinforce the significance of KtrB-mediated transport in sustaining optimal ionic homeostasis during microbial survival of alkaline stress and demonstrate the efficacy of lepidopteran models for interrogating host-microbe interactions.},
}

@article {pmid41229688,
year = {2025},
author = {Zhao, J and Zeng, R and Zhang, C and He, B and Zhang, Q and Zhou, Q and Gong, Z and Liu, H and Liu, S},
title = {Comparative analysis of soil properties before and after Morchella sextelata cultivation across various soil types.},
journal = {Frontiers in microbiology},
volume = {16},
number = {},
pages = {1700246},
pmid = {41229688},
issn = {1664-302X},
abstract = {Morchella, a highly nutritious edible fungus, has been successfully cultivated through artificial means. However, as cultivation areas have expanded, declining yield have emerged more prominently. Soil physicochemical characteristics and microbial communities were critical to production on cultivating morels. In this study, our results reveals that cultivation significantly alters soil properties and microbial communities in a soil type-dependent manner. In sandy soil, pH and key nutrients (total nitrogen, total phosphorus, available phosphorus) increased, while potassium and calcium levels decreased. Microbial diversity decreased in sandy soil but increased in paddy soil, with the overall community structure in sandy soil being more drastically reshaped. Metagenomic profiling identified distinct differential taxa and functional shifts, showing that sandy soil exhibited greater enrichment of microbial genes, including soil-borne diseases. These findings demonstrate that M. sextelata cultivation induces considerable and contrasting changes in soil nutrient profiles and microbiome composition, with sandy soil being more susceptible to microbial restructuring and potential pathogen enrichment.},
}

@article {pmid41229416,
year = {2025},
author = {Gupta, S and Raghav, SK and Chauhan, NS},
title = {Editorial: Host-microbiota immuno-interactions for personalized microbial therapeutics.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1716098},
pmid = {41229416},
issn = {1664-3224},
}

@article {pmid41229402,
year = {2025},
author = {Tola, YH and Wagoner, K and Strand, MK and Rueppell, O and Tarpy, DR},
title = {The gut microbiome differs between hygiene-performing and non-hygiene-performing worker honey bees.},
journal = {Insectes sociaux},
volume = {72},
number = {4},
pages = {397-404},
pmid = {41229402},
issn = {0020-1812},
abstract = {UNLABELLED: Gut microbiomes play a significant role in the health, development, and behavior of numerous species, including honey bees (Apis mellifera). Worker honey bees exhibit varying degrees of hygienic behavior, which involves the removal of unhealthy brood to mitigate disease within their colony. However, the potential relationship between hygienic behavior and the honey bee gut microbiome has not been previously investigated. In this study, we compared gut microbiota in honey bees engaged in hygienic behavior (hygiene performers) versus those not exhibiting this behavior (non-hygiene performers) using 16S rRNA gene amplicon sequencing. Proteobacteria, Firmicutes, and Actinobacteria were identified as the predominant phyla. Notably, three bacterial species (Apilactobacillus kunkeei, Bartonella apis, and Frischella perrara) were found to be more abundant in hygiene performer bees compared to non-hygiene performer bees. Additionally, hygiene performer bees showed a higher diversity of amplicon sequence variants, with Apibacter mensalis being exclusively present in hygiene performer bees and absent in non-hygiene performer bees. These findings reveal an association between gut microbiota composition and hygienic behavior in honey bees, which may provide a foundation for future research exploring probiotic development and other strategies to enhance honey bee health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00040-025-01029-x.},
}

@article {pmid41229186,
year = {2025},
author = {Park, JW and Park, JS and Kook, PR and Cho, YH and Park, SK and Lee, JH and Kang, SK and Kim, SW and Kim, SR},
title = {Impact of Artificial Diet Versus Mulberry Leaves on Silkworm Growth, Nutrient Composition, and Gut Microbiota.},
journal = {Archives of insect biochemistry and physiology},
volume = {120},
number = {3},
pages = {e70113},
doi = {10.1002/arch.70113},
pmid = {41229186},
issn = {1520-6327},
support = {PJ01721401.//This study was supported by the 2025 RDA Fellowship Program of the National Institute of Agricultural Science./ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Morus/chemistry ; *Bombyx/growth & development/microbiology/metabolism ; Plant Leaves/chemistry ; Larva/growth & development/microbiology ; *Diet ; *Animal Feed/analysis ; Nutrients/analysis ; RNA, Ribosomal, 16S ; },
abstract = {Silkworms (Bombyx Mori) are traditionally reared on mulberry leaves; however, artificial diets have been developed to enable year-round rearing and automation. The physiological performance and cocoon yield of silkworms fed artificial diets remain inferior to those reared on mulberry leaves. We compared growth and nutrient composition in larvae reared on mulberry leaves (ML) and antibiotic-free artificial diet (ADS), and profiled gut microbiota in ML, ADS, and antibiotic-supplemented artificial diet (ADSA) to assess dietary effects on host physiology and microbial ecology. Proximate analysis revealed that protein accumulation was greater in ML-fed larvae, while ADS-fed larvae showed relatively higher fat content at the late fifth instar. Amino acid profiling showed consistently higher silk-related residues (Gly, Ala, Ser) and the derived Silk Amino Acid Index in ML-fed larvae, indicating enhanced fibroin synthesis potential. Microbiome analysis using 16S rRNA amplicon sequencing demonstrated dominance of Enterococcus mundtii in ADS groups, resulting in reduced alpha diversity and uneven community structure. In contrast, ML-fed larvae harbored diverse taxa, including Methylorubrum and Methylobacterium, while ADSA groups exhibited intermediate profiles with occasional dominance of Bacillus cereus. These findings highlight that artificial diet alters host nutrient metabolism and drives dysbiosis of gut microbiota, underscoring the need for optimized formulations and microbiome-stabilizing strategies, such as probiotics or prebiotics.},
}

Animals
*Gastrointestinal Microbiome
*Morus/chemistry
*Bombyx/growth & development/microbiology/metabolism
Plant Leaves/chemistry
Larva/growth & development/microbiology
*Diet
*Animal Feed/analysis
Nutrients/analysis
RNA, Ribosomal, 16S

@article {pmid41229051,
year = {2025},
author = {Naseeb, J and Sarwar, A and Zhennai, Y and Aziz, T and Elkhadragy, MF and Alwethaynani, MS and Alhhazmi, AA and Fallatah, D and Almsaud, MM and Alshehri, WA and Alsanie, SA and Alharbi, NA},
title = {Network pharmacology-guided probiotic metabolite therapy for acne vulgaris to target Cutibacterium acnes CAMP factors through Pediococcus acidilactici BCBH1 fatty acids.},
journal = {Allergologia et immunopathologia},
volume = {53},
number = {6},
pages = {126-140},
pmid = {41229051},
issn = {1578-1267},
support = {//This research was financially supported by the National Natural Science Foundation of China (Project No. 32272296). The authors are thankful to Princess Nourah bint Abdulrahman University Researchers Supporting Project number (PNURSP2025R23), Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia./ ; },
mesh = {*Acne Vulgaris/therapy/microbiology ; Humans ; *Probiotics/therapeutic use ; *Pediococcus acidilactici/metabolism ; Molecular Docking Simulation ; Network Pharmacology ; *Propionibacterium acnes ; *Fatty Acids/metabolism ; *Oleic Acids/metabolism/pharmacology ; Virulence Factors/metabolism ; *Bacterial Proteins/metabolism ; },
abstract = {Acne vulgaris is a chronic inflammatory skin disorder predominantly caused by Cutibacterium acnes and its virulence-associated CAMP (Christie-Atkins-Munch-Petersen) factors, particularly CAMP1 and CAMP2, which contribute to inflammation and bacterial survival. With increasing antibiotic resistance and concerns over microbiome disruption from conventional treatments, probiotic-derived postbiotics present a promising alternative. This study aimed to investigate the anti-acne potential of fatty acids produced by Pediococcus acidilactici BCBH1, targeting CAMP1 and CAMP2 proteins of C. acnes using a network pharmacology-guided approach. Metabolite profiling via GC-MS identified vaccenic acid as a major fatty acid metabolite (4.88 mg/L at 48 h under 10% linoleic acid stress). Virulence prediction confirmed high pathogenicity of CAMP1 (score 0.9055) and CAMP2 (score 0.9927). Molecular docking revealed strong binding affinities of vaccenic acid to CAMP1 and CAMP2 with binding energies of -9.6 kJ/mol and -9.3 kJ/mol, respectively, outperforming traditional anti-acne compound 4-terpineol (-9.0 kJ/mol and -8.7 kJ/mol). Molecular dynamics simulations further validated the stable interaction of vaccenic acid with CAMP proteins over 100 ns. Pharmacokinetic analyses indicated vaccenic acid's favorable absorption and safety profiles with no blood-brain barrier permeability. These findings highlight vaccenic acid as a potent, microbiome-friendly therapeutic candidate for acne management. Future work should focus on experimental validation, formulation development, and combinatorial strategies to enhance clinical efficacy and safety.},
}

*Acne Vulgaris/therapy/microbiology
Humans
*Probiotics/therapeutic use
*Pediococcus acidilactici/metabolism
Molecular Docking Simulation
Network Pharmacology
*Propionibacterium acnes
*Fatty Acids/metabolism
*Oleic Acids/metabolism/pharmacology
Virulence Factors/metabolism
*Bacterial Proteins/metabolism

@article {pmid41228567,
year = {2025},
author = {Brough, L and Rees, G and Drummond-Clarke, L and McCallum, JE and Taylor, E and Kozhevnikov, O and Walker, S},
title = {Can Dietary Supplements Support Muscle Function and Physical Activity? A Narrative Review.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213495},
pmid = {41228567},
issn = {2072-6643},
mesh = {Humans ; *Dietary Supplements/adverse effects ; *Exercise/physiology ; *Muscle, Skeletal/physiology/drug effects ; Muscle Strength ; Activities of Daily Living ; Female ; Quality of Life ; },
abstract = {Dietary supplementation is commonly used by athletes to gain muscle mass, enhance performance, and improve recovery. Most adults engage in insufficient physical activity. Yet healthy muscles are also critical for activities of daily living (ADLs), maintaining a good quality of life and positive ageing. There is growing interest in whether dietary supplementation is of value, particularly among subgroups such as the occasionally active, the ill and elderly, and peri- and menopausal women. By focusing on function, performance, mass and strength, ADLs, exercise-induced muscle damage and delayed onset muscle soreness, this review sought to examine muscle health through a nutritional lens. Further, to look at the potential benefits and harms of some commonly proposed dietary supplements in non-athlete adults, while exploring the emerging role of the gut-muscle axis. Inflammation appears central to cellular events. Several supplements were identified that, alone or in combination, may help optimise muscle health, particularly when combined with exercise or where a deficit may exist. Although supportive evidence is emerging, real-world clinical benefits remain to be substantiated. Though dietary supplements are generally safe, their regulation is less stringent than for medicines. Adherence to recommended dosage, seeking medical advice regarding possible side effects/interactions, and obtaining supplies from reliable sources are recommended.},
}

Humans
*Dietary Supplements/adverse effects
*Exercise/physiology
*Muscle, Skeletal/physiology/drug effects
Muscle Strength
Activities of Daily Living
Female
Quality of Life

@article {pmid41228565,
year = {2025},
author = {Loomba, M and Bansal, S and Singh, KK and Mishra, PK and Ghosh, S and Raghunath, M and Mishra, AK and Sinha, JK},
title = {The Diet-Obesity-Brain Axis: Metabolic, Epigenetic, and DNA-Repair Pathways Linking Eating Patterns to Cognitive Aging, with an AI-Enabled Translational Perspective.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213493},
pmid = {41228565},
issn = {2072-6643},
mesh = {Humans ; *Obesity/metabolism/complications ; *Brain/metabolism ; *Cognitive Aging/physiology ; *Artificial Intelligence ; *Diet/adverse effects ; *DNA Repair ; *Epigenesis, Genetic ; Cognitive Dysfunction/etiology ; *Feeding Behavior ; Translational Research, Biomedical ; },
abstract = {Diet influences brain health through many connected metabolic and molecular pathways, and these effects are stronger in obesity. This review links diet quality with cognitive decline and dementia risk. Ultra-processed, high-fat, high-sugar diets drive weight gain, insulin resistance, and chronic inflammation. These changes trigger brain oxidative stress, reduce DNA repair, deplete NAD[+], disturb sirtuin/PARP balance, and alter epigenetic marks. Gut dysbiosis and leaky gut add inflammatory signals, weaken the blood-brain barrier, and disrupt microglia. Mediterranean and MIND diets, rich in plants, fiber, polyphenols, and omega-3 fats, slow cognitive decline and lower dementia risk. Trials show extra benefit when diet improves alongside exercise and vascular risk control. Specific nutrients can help in certain settings. DHA and EPA support brain health in people with low omega-3 status or early disease. B-vitamins slow brain shrinkage in mild cognitive impairment when homocysteine is high. Vitamin D correction is beneficial when levels are low. A practical plan emphasizes healthy eating and good metabolic control. It includes screening for deficiencies and supporting the microbiome with fiber and fermented foods. Mechanism-based add-ons, such as NAD[+] boosters, deserve testing in lifestyle-focused trials. Together, these measures may reduce diet-related brain risk across the life span. At the same time, artificial intelligence can integrate diet exposures, adiposity, metabolic markers, multi-omics, neuroimaging, and digital phenotyping. This can identify high-risk phenotypes, refine causal links along the diet-obesity-brain axis, and personalize nutrition-plus-lifestyle interventions. It can also highlight safety, equity, and privacy considerations. Translationally, a pattern-first strategy can support early screening and personalized risk reduction by integrating diet quality, adiposity, vascular risk, micronutrient status, and microbiome-responsive behaviors. AI can aid measurement and risk stratification when developed with privacy, equity, and interpretability safeguards, but clinical decisions should remain mechanism-aligned and trial-anchored.},
}

Humans
*Obesity/metabolism/complications
*Brain/metabolism
*Cognitive Aging/physiology
*Artificial Intelligence
*Diet/adverse effects
*DNA Repair
*Epigenesis, Genetic
Cognitive Dysfunction/etiology
*Feeding Behavior
Translational Research, Biomedical

@article {pmid41228562,
year = {2025},
author = {Paredes-Marin, A and He, Y and Zhang, X},
title = {Dietary Interventions in Metabolic Dysfunction-Associated Steatotic Liver Disease: A Narrative Review of Evidence, Mechanisms, and Translational Challenges.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213491},
pmid = {41228562},
issn = {2072-6643},
mesh = {Humans ; *Fatty Liver/diet therapy ; Diet, Mediterranean ; Gastrointestinal Microbiome ; *Non-alcoholic Fatty Liver Disease/diet therapy ; Prebiotics/administration & dosage ; },
abstract = {Background/Objectives: Metabolic dysfunction-associated steatotic liver disease (MASLD) is rapidly attracting growing concern around the world. While there has been progress in the development of pharmacologic treatments, lifestyle and dietary interventions remain as the first-line approach for management. This scoping review aimed to identify dietary strategies for managing MASLD and to highlight current research gaps and challenges. Methods: A systematic search of PubMed and Science Direct was conducted up to 10 July 2025, for relevant studies on dietary modifications and MASLD. Data extracted included types of interventions, outcomes related to liver health, and research limitations. Results: Dietary interventions were shown to consistently improve hepatic and metabolic outcomes. In a randomized controlled trial of 12 weeks (n = 259), a Mediterranean diet reduced hepatic steatosis by 39% and improved insulin sensitivity. A calorie-restricted lifestyle program in adults with MASLD (n = 196) reduced liver fat by 25% over 52 weeks. Resistant starch supplementation (n = 200) lowered intrahepatic triglyceride content by 8% through gut microbiome modulation. A pilot RCT of medically tailored meals in cirrhosis (n = 40) reduced ascites symptoms and improved quality of life. Finally, prebiotic supplementation in MASLD (n = 200) lowered systemic inflammation and increased immune-regulating microbes. In contrast, Western dietary patterns and ultra-processed foods were consistently linked to lipotoxicity and inflammation. Conclusions: Dietary interventions remain critical for the management of chronic liver disease and continue to play a vital role even as pharmacotherapy options emerge. Further research should explore precision nutrition and microbiome-based therapies while also addressing the methodological limitations like the underutilization of causal inference frameworks. Finally, it is also important to consider culturally tailored interventions to account for barriers in access and equity in underserved populations.},
}

Humans
*Fatty Liver/diet therapy
Diet, Mediterranean
Gastrointestinal Microbiome
*Non-alcoholic Fatty Liver Disease/diet therapy
Prebiotics/administration & dosage

@article {pmid41228547,
year = {2025},
author = {Di Benedetto, G and Sorge, G and Sarchiapone, M and Di Martino, L},
title = {Dietary Patterns, Not Gut Microbiome Composition, Are Associated with Behavioral Challenges in Children with Autism: An Observational Study.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213476},
pmid = {41228547},
issn = {2072-6643},
support = {RES605229/NH/NIH HHS/United States ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; Male ; Child ; Female ; *Autism Spectrum Disorder/microbiology/psychology ; *Diet ; *Feeding Behavior ; Child, Preschool ; Mycobiome ; Siblings ; },
abstract = {Background/Objectives: Autism Spectrum Disorder (ASD) is a complex neurodevelopmental condition characterized by persistent social communication difficulties and restricted, repetitive behaviors, with prevalence estimates continuing to rise worldwide. The gut-brain axis has been proposed as a potential contributor to ASD, yet human studies yield inconsistent findings, partly due to confounding effects of diet and behavior. Methods: Here, we investigated the gut bacteriome and mycobiome of children with ASD (n = 17) compared with their non-ASD siblings (n = 9) and parents without ASD (n = 27), alongside detailed assessment of dietary intake (n = 79) using 7-day food diaries. Results: Multi-kingdom microbiome profiling revealed no significant differences in α- or β- diversity across ASD, sibling, and parental groups, with only minor taxonomic variation observed. Similarly, fungal community composition showed negligible group-level differences. By contrast, dietary patterns strongly differentiated ASD from non-ASD participants: children with ASD consumed higher levels of sweets and sugary foods, lower portions of vegetables, and exhibited reduced overall dietary diversity. Statistical analyses confirmed that dietary factors, rather than microbial composition, explained variation in ASD diagnosis. Conclusions: These findings suggest that selective and repetitive eating behaviors are characteristic of ASD shape dietary intake, which in turn influences gut microbial diversity. Thus, in humans, the directionality may run primarily from behavior to diet to microbiome, rather than from microbiome to behavior. Our results underscore the importance of incorporating dietary variables into microbiome research and highlight the need for targeted nutritional interventions to improve health outcomes in individuals with ASD.},
}

Humans
*Gastrointestinal Microbiome
Male
Child
Female
*Autism Spectrum Disorder/microbiology/psychology
*Diet
*Feeding Behavior
Child, Preschool
Mycobiome
Siblings

@article {pmid41228504,
year = {2025},
author = {Aslan Gönül, B and Delikan, E and Çiçek, B and Yılmaz Cankılıç, M},
title = {Associations of Salivary Microbiota with Diet Quality, Body Mass Index, and Oral Health Status in Turkish Adolescents.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213434},
pmid = {41228504},
issn = {2072-6643},
support = {TDK-2023-12772//Erciyes University Scientific Research Fund/ ; },
mesh = {Humans ; Adolescent ; *Oral Health ; *Saliva/microbiology ; Female ; Male ; *Body Mass Index ; Turkey ; Cross-Sectional Studies ; *Microbiota ; *Diet ; Thinness/microbiology ; Periodontal Index ; RNA, Ribosomal, 16S/genetics ; },
abstract = {Background: The oral microbiota is the largest and most diverse microbial community in the human body, shaped by numerous factors such as body composition, dietary habits, and oral health status. However, relationships between these parameters and the salivary microbiota in adolescents are not yet well understood. Objectives: This study aimed to characterize the salivary microbiota of healthy Turkish adolescents and to examine its associations with body mass index (BMI), diet quality, decayed-missing filled teeth (DMFT) index, and community periodontal index of treatment needs (CPITN). Methods: A descriptive, cross-sectional study was conducted among 40 adolescents aged 14-18 years, classified into four BMI z-score categories (underweight, normal weight, overweight, and obese). Anthropometric measurements, nutritional information, and oral health parameters (DMFT, CPITN) were assessed. Unstimulated saliva samples were collected, and the V3-V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Alpha and beta diversity, differential abundance (LEfSe), and correlations with HEI components were analyzed. Results: Underweight adolescents exhibited significantly higher alpha diversity than obese participants (p = 0.024), while beta diversity did not differ across BMI, HEI, DMFT, or CPITN categories. LEfSe analysis revealed BMI-specific taxa: Leptotrichia sp., Haemophilus sp., and Treponema socranskii were enriched in the underweight group; Prevotella denticola in the obese group; and Selenomonas sputigena in the normal-weight group. HEI components, including whole fruits, whole grains, and plant-based proteins, showed positive correlations with Desulfobacterota and Proteobacteria. Poor oral hygiene was associated with higher species richness but not with large shifts in community structure. Conclusions: Salivary microbiota diversity and composition in adolescents vary with BMI, diet quality, and oral hygiene. These patterns are consistent with the idea that targeted nutritional and oral health interventions could influence the salivary microbiome during adolescence.},
}

Humans
Adolescent
*Oral Health
*Saliva/microbiology
Female
Male
*Body Mass Index
Turkey
Cross-Sectional Studies
*Microbiota
*Diet
Thinness/microbiology
Periodontal Index
RNA, Ribosomal, 16S/genetics

@article {pmid41228494,
year = {2025},
author = {Liang, X and Wang, L},
title = {The Mediating Role of Bioactive Molecules in Gut Microbiota-Bone Metabolism Crosstalk.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213421},
pmid = {41228494},
issn = {2072-6643},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Bone and Bones/metabolism ; Fatty Acids, Volatile/metabolism ; Vitamin D/metabolism ; *Osteoporosis/metabolism/microbiology ; Estrogens/metabolism ; Animals ; Signal Transduction ; },
abstract = {The interaction between the gut microbiota and the skeletal system has evolved into a new research focus. Studies underscore the role of bioactive metabolites in sustaining systemic balance via the "gut microbiota-endocrine-skeleton" axis, where they modulate metabolic processes and organ morphology through intracellular signaling. A key bidirectional relationship exists with the gut: shifts in gut microbiota affect host metabolism and subsequent metabolite profiles, while these metabolites can, in turn, reshape the intestinal microenvironment. This review explores how short-chain fatty acids (SCFAs), estrogen, and vitamin D modulate osteoporosis via the gut-bone axis. It synthesizes evidence of their signaling pathways and metabolic roles, identifies research gaps from recent clinical studies, and evaluates gut microbiota-targeted therapeutic strategies for potential clinical translation.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Bone and Bones/metabolism
Fatty Acids, Volatile/metabolism
Vitamin D/metabolism
*Osteoporosis/metabolism/microbiology
Estrogens/metabolism
Animals
Signal Transduction

@article {pmid41228422,
year = {2025},
author = {Diotaiuti, P and Misiti, F and Marotta, G and Falese, L and Calabrò, GE and Mancone, S},
title = {The Gut Microbiome and Its Impact on Mood and Decision-Making: A Mechanistic and Therapeutic Review.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213350},
pmid = {41228422},
issn = {2072-6643},
support = {MUR Decree n. 105123.06.2022 PNRR Missione 4 Componente 2 Investimento 1.5-CUP H33C22000420001//Project ECS0000024 "Ecosistema dell'innovazione-Rome Technopole" financed by EU NextGeneration EU plan/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; *Affect/physiology ; *Decision Making/physiology ; Animals ; Cognition ; Probiotics ; Dysbiosis/microbiology ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; },
abstract = {Background/Objectives: The gut microbiome is increasingly recognized as a key modulator of central nervous system function through the gut-brain axis. Dysbiosis has been associated with neuropsychiatric disorders such as depression, anxiety, impulsivity, cognitive decline, and addiction. This review aims to synthesize mechanistic insights and therapeutic perspectives on how gut microbiota influence mood regulation, decision-making, and cognitive processes. Methods: A comprehensive narrative review was conducted using peer-reviewed articles retrieved from PubMed, Scopus, and Web of Science up to August 2025. Studies were included if they explored microbiota-related effects on behavior, mood, cognition, or decision-making using human or animal models. Emphasis was placed on molecular mechanisms, microbiome-targeted therapies, and multi-omics approaches. Results: Evidence indicates that gut microbiota modulate neurochemical pathways involving serotonin, dopamine, GABA, and glutamate, as well as immune and endocrine axes. Microbial imbalance contributes to low-grade systemic inflammation, impaired neuroplasticity, and altered stress responses, all of which are linked to mood and cognitive disturbances. Specific microbial taxa, dietary patterns, and interventions such as probiotics, prebiotics, psychobiotics, and fecal microbiota transplantation (FMT) have shown promise in modulating these outcomes. The review highlights methodological advances including germ-free models, metagenomic profiling, and neuroimaging studies that clarify causal pathways. Conclusions: Gut microbiota play a foundational role in shaping emotional and cognitive functions through complex neuroimmune and neuroendocrine mechanisms. Microbiome-based interventions represent a promising frontier in neuropsychiatric care, although further translational research is needed to define optimal therapeutic strategies and address individual variability.},
}

*Gastrointestinal Microbiome/physiology
Humans
*Affect/physiology
*Decision Making/physiology
Animals
Cognition
Probiotics
Dysbiosis/microbiology
Fecal Microbiota Transplantation
Prebiotics/administration & dosage

@article {pmid41228418,
year = {2025},
author = {Ribeiro, PR and Ferreira, C and Antunes, C and Dias, G and Lima, MJ and Guiné, R and Teixeira-Lemos, E},
title = {Nutritional Approaches in Neurodegenerative Disorders: A Mini Scoping Review with Emphasis on SPG11-Related Conditions.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213344},
pmid = {41228418},
issn = {2072-6643},
mesh = {Humans ; *Spastic Paraplegia, Hereditary/diet therapy/genetics ; *Neurodegenerative Diseases/diet therapy/genetics ; Precision Medicine ; Autophagy ; Proteins ; },
abstract = {Background: Neurodegenerative diseases, including spastic paraplegia type 11 (SPG11), are complex disorders characterized by progressive neurological decline and significant metabolic disturbances. Spatacsin, the protein encoded by the SPG11 gene, plays a critical role in autophagy and lysosomal homeostasis, which are essential for neuronal health. Its impairment leads to defective cellular clearance and neurodegeneration. Recently, personalized and precision nutrition have emerged as promising approaches to enhance clinical outcomes by tailoring dietary interventions to individual genetic, metabolic, and phenotypic profiles. Objectives: This mini scoping review aimed to synthesize current evidence on the application of personalized and precision nutrition in SPG11 and to explore how insights from related neurodegenerative diseases could inform the development of future dietary and metabolic interventions for this rare disorder. Methods: Following PRISMA-ScR guidelines, a scoping review was conducted using PubMed, Scopus, and Web of Science databases (2020-2024). Eligible studies included investigations addressing nutritional, genomic, or metabolic interventions in neurodegenerative diseases. Of 30 screened papers, nine met the inclusion criteria, primarily focusing on nutritional and metabolic interventions related to neurodegenerative and neuromuscular conditions. Results: To date, no dietary intervention trials have been conducted specifically for SPG11. However, evidence from studies on related neurodegenerative diseases suggests that antioxidant, mitochondrial-supportive, and microbiota-targeted dietary approaches may beneficially influence key pathological processes such as oxidative stress, lipid dysregulation, and autophagy-core mechanisms that are also central to SPG11 pathophysiology. Conclusions: Although current evidence remains preliminary, personalized nutrition is a promising supplementary strategy for managing neurodegenerative diseases, including SPG11. Future research should incorporate systems-based approaches that combine dietary, metabolic, and neuroimaging assessments, with sex and comorbidity-stratified analyses, multi-omics profiling, and predictive modeling. These frameworks could help design safe, effective, and personalized nutritional interventions aimed at enhancing metabolic resilience and slowing disease progression in SPG11.},
}

Humans
*Spastic Paraplegia, Hereditary/diet therapy/genetics
*Neurodegenerative Diseases/diet therapy/genetics
Precision Medicine
Autophagy
Proteins

@article {pmid41228416,
year = {2025},
author = {Robinson, LA and Lennon, S and Pegel, AR and Strickland, KP and Feeley, CA and Watts, SO and J Van Der Pol, W and Roberts, MD and Greene, MW and Frugé, AD},
title = {A Randomized Controlled Crossover Lifestyle Intervention to Improve Metabolic and Mental Health in Female Healthcare Night-Shift Workers.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213342},
pmid = {41228416},
issn = {2072-6643},
mesh = {Humans ; Female ; Adult ; Cross-Over Studies ; Middle Aged ; Young Adult ; Adolescent ; *Mental Health ; *Shift Work Schedule/psychology/adverse effects ; *Life Style ; Exercise ; *Health Personnel/psychology ; Quality of Life ; Sleep ; *Work Schedule Tolerance/physiology/psychology ; Circadian Rhythm ; },
abstract = {Background: Circadian rhythm disruption caused by shift work alters metabolic and hormonal pathways, which accelerates chronic disease onset, leading to decreased quality and quantity of life. This study aimed to determine whether a practical lifestyle intervention emphasizing nutrition timing and recovery habits could mitigate the metabolic and psychological effects of night-shift work. We conducted a randomized, open-label, crossover trial with two 8-week periods. Methods: Female healthcare workers (n = 13) aged 18-50 years with a body mass index (BMI) between 27 and 40 kg/m[2] and working predominantly night shifts (≥30 h/week for ≥6 months) were randomized. During the 8-week intervention phase, participants received daily text messages with guidance on food, sleep/rest, and physical activity and were provided with whey protein isolate powder and grain-based snack bars to consume during work shifts. The program targeted improved nutrient timing, adequate protein intake, and structured rest without formal exercise training, allowing evaluation of dietary and behavioral effects feasible for this population. Total caloric (~30 kcal/kg lean mass) and protein (2 g/kg lean mass) needs were measured, along with sleep/rest goals of 6-8 h/24 h. Primary outcome measures were change in visceral fat percentage (VF%) by DXA and mental/physical quality of life (RAND SF-12). Secondary outcomes included fasting triglycerides, ALT, blood glucose, LDL, actigraphy, and fecal microbiome. Mixed-design two-way ANOVA was conducted to assess the effects of group (immediate [IG] and delayed [DG]), time (baseline, 8-week crossover, and week 16), and Group × Time (GxT) interactions, and Bonferroni correction was applied to post hoc t-tests. Results: Eleven participants completed the study. Both groups increased dietary protein intake (p < 0.001), and a GxT interaction for VF% (p = 0.039) indicated DG reduced VF% to a greater extent (-0.335 ± 0.114% (p = 0.003) vs. 0.279 ± 0.543% (p = 0.158)). Mental and physical QOL, objectively measured physical activity and sleep, serum lipids and inflammatory markers, and fecal microbiota remained unchanged (p > 0.05 for all GxT). Conclusions: The findings suggest that targeted nutrition and recovery strategies can modestly improve dietary intake and visceral fat; however, consistent with prior work, interventions without structured exercise may be insufficient to reverse broader metabolic effects of circadian disruption. This trial was registered at ClinicalTrials.gov, identifier: NCT06158204, first registered: 28 November 2023.},
}

Humans
Female
Adult
Cross-Over Studies
Middle Aged
Young Adult
Adolescent
*Mental Health
*Shift Work Schedule/psychology/adverse effects
*Life Style
Exercise
*Health Personnel/psychology
Quality of Life
Sleep
*Work Schedule Tolerance/physiology/psychology
Circadian Rhythm

@article {pmid41228392,
year = {2025},
author = {Nurain Binti, MA and Varga, JT},
title = {Nutrition and Gut Microbiome in the Prevention of Food Allergy.},
journal = {Nutrients},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/nu17213320},
pmid = {41228392},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Food Hypersensitivity/prevention & control/microbiology/immunology ; *Probiotics/administration & dosage ; Prebiotics/administration & dosage ; Infant ; Female ; Synbiotics/administration & dosage ; Pregnancy ; Randomized Controlled Trials as Topic ; Child ; Child, Preschool ; Male ; },
abstract = {Background: Food allergies are increasingly recognized as a global health concern, influenced by early-life nutrition and the gut microbiome. This systematic review examined randomized controlled trials from 2005 to 2025 assessing the effects of probiotics, prebiotics, and synbiotics in preventing food allergies. Methods: Fourteen studies involving 5685 participants, including pregnant women, infants, and children with or without diagnosed food allergies, were analyzed. While several interventions demonstrated modulation of gut microbiota and immune responses, most trials reported no statistically significant reduction in IgE-mediated food allergy compared with placebo. Results: Some evidence suggested benefits from early exposure to allergenic foods and specific probiotic strains, such as Lactobacillus rhamnosus GG, particularly in cow's milk allergy. However, heterogeneity in study designs, strains, dosages, and diagnostic criteria limited generalizability. Conclusions: Overall, microbiome-targeted nutritional interventions show biological plausibility but inconsistent clinical efficacy. Future large-scale, standardized, and mechanistic studies integrating microbiome, genetic, and environmental data are warranted to define optimal strategies for allergy prevention.},
}

Humans
*Gastrointestinal Microbiome
*Food Hypersensitivity/prevention & control/microbiology/immunology
*Probiotics/administration & dosage
Prebiotics/administration & dosage
Infant
Female
Synbiotics/administration & dosage
Pregnancy
Randomized Controlled Trials as Topic
Child
Child, Preschool
Male

@article {pmid41228271,
year = {2025},
author = {Starska-Kowarska, K},
title = {The Role of Porphyromonas gingivalis in Oral Carcinogenesis and Progression by Remodelling the Tumour Microenvironment: A Narrative Review.},
journal = {Cancers},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/cancers17213478},
pmid = {41228271},
issn = {2072-6694},
abstract = {(1) Background: Oral squamous cell carcinoma (OSCC) is the most common type of head and neck malignancy worldwide. Despite the prevalence of modern diagnostic and prognostic techniques, late diagnosis and resistance to treatment still result in a low 5-year survival rate, high recurrence rate, and frequent malignant metastases. Increasing evidence indicates that bacteria of the oral microbiome, such as the Gram-negative anaerobic Porphyromonas gingivalis, may play a crucial role in the initiation and development of OSCC by inducing periodontitis. Indeed, epithelial-to-mesenchymal transition (EMT) and dysregulated immune response have been attributed to the activity of a dysbiotic microbiota. This comprehensive review examines the influence of P. gingivalis on oral carcinogenesis and progression, which has been associated with tumour microenvironment remodelling and the dysregulation of key signalling pathways related to epithelial-to-mesenchymal transition (EMT), cell-cycling, autophagy, and apoptosis. (2) Methods: The article reviews current literature on the possible role of P. gingivalis and induced dysbiosis, periodontitis and a pro-inflammatory environment as key mechanisms driving neoplastic epithelial changes and chemoresistance to anticancer agents in patients with OSCC; the research corpus was acquired from the Pub-Med/Medline/EMBASE/Cochrane Library databases. (3) Results: The identification of virulence factors and key mechanisms used by P. gingivalis to promote the development and progression of OSCC may support traditional diagnostic methods and factors related to treatment response and prevention of OSCC. (4) Conclusions: Emerging evidence suggests a possible association between periodontal bacteria and oral carcinogenesis. P. gingivalis may be an important potential target for future strategies aimed at treating oral cancer.},
}

@article {pmid41228253,
year = {2025},
author = {Lin, S and Zhou, C and Chen, H and Zhou, X and Yang, H and Sun, L and Zhang, L and Zhang, Y},
title = {Advances in Hereditary Colorectal Cancer: How Precision Medicine Is Changing the Game.},
journal = {Cancers},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/cancers17213461},
pmid = {41228253},
issn = {2072-6694},
support = {2024KY1226//Medical Health Science and Technology Project of Zhejiang Provincial Health Commission/ ; },
abstract = {Only about 5% of colorectal cancers are hereditary, which is due to the low carrier rate of pathogenic gene mutations. The typical pattern of these cases is intergenerational aggregation within families and early onset. But public awareness of early diagnosis and intervention of HCRC is insufficient, resulting in most patients being diagnosed only after developing cancer, thereby missing the optimal window for treatment. This article reviews the latest developments in precision screening, treatment, evaluation and prevention strategies for HCRC, including innovative uses of artificial intelligence (AI) in molecular diagnostics, imaging technology advances, and potential application prospects. Regarding precision screening, tests of genomics, transcriptomics, microbiome, etc., combined with personalised risk stratification, can, respectively, effectively detect pathogenic mutations and "cancer-promoting" intestinal environments in the preclinical stage. AI combined with endoscopic and imaging tools has improved the accuracy of polyp detection and tumor profiling. Liquid biopsy and molecular marker detection provide new non-invasive monitoring solutions. In precision treatment, beyond traditional approaches like surgery and chemotherapy, immunotherapy with checkpoint inhibitors may be considered for HCRC patients with mismatch repair deficiency (dMMR). For patients harboring somatic mutations such as KRAS or BRAF V600E, targeted therapy can be guided by these specific mutations. Regarding precision assessment, AI incorporates microsatellite instability (MSI) detection and imaging diagnostic techniques, crucial for integrating genetic, environmental, and lifestyle data in follow-up. This helps assess the risk of recurrence and adjust the long-term medication regimens, as well as provide effective nutritional support and psychological counselling. In summary, the rapid development of precision medicine is driving the clinical management of HCRC into the era of tailored care, aiming to optimise patient outcomes.},
}

@article {pmid41228220,
year = {2025},
author = {Szabó, PJ and Sági, V and Kassai, LK and Kiss-Miki, RM and Makra, N and Szabó, D and Garami, M},
title = {Parallel Alterations in Gut and Tumor Microbiota in Pediatric Oncology: Potential Impacts on Disease Progression and Treatment Response.},
journal = {Cancers},
volume = {17},
number = {21},
pages = {},
doi = {10.3390/cancers17213426},
pmid = {41228220},
issn = {2072-6694},
abstract = {In the last decade, knowledge of gut microbiota has expanded. Several studies have demonstrated a correlation between certain diseases and alterations in gut microbiota. A comprehensive understanding of this complex ecosystem is still lacking; however, this review highlights the importance of microorganisms in oncology. Recently, several studies have demonstrated that the gut microbiota influences therapeutic efficacy and tumor formation, also known as tumorigenesis. We must remember that these microorganisms also play a crucial role in tumor prognosis. Since the discovery of Fusobacterium nucleatum in colorectal carcinoma (CRC), it has been established that tumor tissues are not sterile and contain microorganisms that can lead to either beneficial or harmful pathways, affecting tumor size and response to chemotherapeutic agents. Additionally, it should be noted that data on the pediatric population are limited, as this area has not been widely researched due to the low number of cases and the complexity of therapeutic approaches. In children, the only available data are mainly based on hematological malignancies, such as acute lymphoblastic leukemia (ALL). For a better understanding, larger cohorts are required.},
}

@article {pmid41228079,
year = {2025},
author = {Williams, C and Labyak, C and Arikawa, A and Watermann, A and Chou, W and James, A and Holland, P and Dangiolo, M and Masternak, MM and Golden, A and Jain, S and Yadav, H},
title = {Activity Engagement Across Stages of Cognitive Health.},
journal = {Healthcare (Basel, Switzerland)},
volume = {13},
number = {21},
pages = {},
pmid = {41228079},
issn = {2227-9032},
support = {22A17//Florida Department of Health- (Ed and Ethel Moore Alzheimer's Disease Consortium grant-22A17/ ; },
abstract = {Objective: This study aims to examine activity engagement across stages of cognitive health among older adults. Methods: We used a cross-sectional study analysis of baseline data collected as part of the prospective Microbiome in Aging of Gut and Brain (MiaGB) longitudinal study; the study period was August 2022 to December 2023. Health history and activity engagement questionnaires and the Montreal Cognitive Assessment (MoCA) were used to examine the study objective. One-way ANOVA and chi-squared tests, with Bonferroni post hoc analyses, assessed group differences. Results: The weighted samples reflected 417 participants: 54% females, 70.7% White, with an average age of 72 (±8.7) years, 90% with at least high school education, and 75% self-reported medium income status. Results suggested that individuals who scored ≤17 points on the MoCA had an average age of 84 years, were White, non-Hispanic, female, had less than a high school education, and medium income status (p < 0.001). Significant differences were found in active engagement in all health behaviors (p < 0.05). The frequency of engagement in activities was all statistically significant (p < 0.05), except the frequency of looking after grandchildren (p > 0.05). Older adults who scored ≤17 MoCA points reported higher rates of hypertension, osteoarthritis, and depression compared with individuals who scored higher on the MoCA assessment. Conclusions: Older adults with lower cognitive status report a higher rate of clinical ailments and have less engagement in meaningful activities. We should promote meaningful activities to improve the quality of life in older adults with decreased cognition. We make recommendations for appropriate modifications for activity engagement across cognitive health levels.},
}

@article {pmid41227654,
year = {2025},
author = {Liscano, Y and Caicedo, N and Oñate-Garzón, J},
title = {Unlocking New Bioactive Peptides from Coffee Pulp: A Metagenomics and AI-Driven Discovery Paradigm.},
journal = {Foods (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41227654},
issn = {2304-8158},
support = {call No. DGI-01-2025//Universidad Santiago de Cali/ ; },
abstract = {This perspective reframes Colombian coffee pulp from an environmental liability into a strategic asset by proposing a new discovery paradigm. We argue that the pulp's challenging chemical environment is not a barrier but its key advantage, having acted as a natural evolutionary filter that has sculpted a unique, highly resilient microbiome. Our vision is a technology pipeline that harnesses this natural pre-selection. By converging deep metagenomic data from the pulp's microbiome with generative artificial intelligence, we can create and validate novel, high-performance bioactive peptides and enzymes that are already pre-optimized for industrial robustness. This approach transcends traditional waste valorization, establishing a new framework for "biointelligence" in action. It offers a strategic roadmap for Colombia to generate knowledge-intensive value chains from its most iconic agricultural product, turning a national challenge into a global opportunity in the bioeconomy.},
}

@article {pmid41227517,
year = {2025},
author = {Li, H and Gao, Q and Han, J and Song, Q and Yan, F and Xu, Y and Zhang, C and Wang, X and Li, Y},
title = {Gut Microbiome of Two Rodent Species (Niviventer confucianus and Apodemus agrarius) from Two Regions Exhibit Different Structures and Assembly Mechanisms.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227517},
issn = {2076-2615},
support = {32270480//National Natural Science Foundation of China/ ; ZR2023QC255//Natural Science Foundation of Shandong Province, China/ ; },
abstract = {The structure and assembly mechanism of wild animal gut microbiota represent persistent research hotspots. Among, the impact of geographic factors on the bacterial co-occurrence network characteristics and assembly mechanism of the gut microbiome remains unclear. Therefore, this study analyzed the gut microbiome of Niviventer confucianus and Apodemus agrarius from Anhui and Hubei provinces. The same alpha diversity pattern was found in the gut microbiome of species from the same region. The gut microbiome of the two rodent species in Anhui region exhibited "small world" characteristics, such as nodes with more local connections to allow interaction information (such as metabolites) to rapidly spread throughout the entire microbial community. In addition, dispersal limitations and heterogeneous selection accounted for higher proportions of the gut microbiome in the rodents from the Anhui and Hubei regions, respectively. The higher proportion of heterogeneous selection may exacerbate selection pressure in the Hubei region. Multiple regression on distance matrices analysis revealed that geographic region exerted a limited but significant influence (0 < R[2] < 0.2, * p < 0.05) on the gut microbiome, surpassing the effects of host phylogeny, gender, and weight. Nevertheless, the roles of regional factors-such as environmental microbes, pollutants, and diet-remain unexamined, and their potential as key drivers of microbiota variation in these rodents warrants further investigation.},
}

@article {pmid41227457,
year = {2025},
author = {Soto-López, JD and Fernández-Soto, P and Muro, A},
title = {Bacterial Composition Across Bat Species: A Human Health Perspective.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227457},
issn = {2076-2615},
abstract = {Bats are widely recognized as reservoirs of diverse bacterial pathogens with important implications for human health. Recent zoonotic disease outbreaks have intensified interest in bat microbiomes, with high-throughput sequencing increasingly used to assess microbial diversity. In this article, we review literature from the past five years on bacterial species associated with bats and their potential clinical relevance. Using automated searches and manual filtering, we extracted data from 47 peer-reviewed studies. Most research has focused on guano samples, though interest in skin microbiomes is rising, particularly in relation to Pseudogymnoascus destructans, the agent of white-nose syndrome. China leads in the number of publications, followed by the United States, and amplicon sequencing remains the predominant metagenomic method. Across studies, 4700 bacterial species were reported, including several known human pathogens capable of aerosol transmission or opportunistic infections in immunocompromised individuals. Many of these taxa are classified as global priority targets for antimicrobial drug development by the World Health Organization and the U.S. Centers for Disease Control and Prevention. Given the clinical severity of diseases linked to some species, bats should be integrated into epidemiological surveillance systems. However, the lack of standardized reporting practices significantly limits the comparability and utility of bat microbiome data for robust ecological and epidemiological analyses.},
}

@article {pmid41227435,
year = {2025},
author = {Liu, J and Bai, M and Wang, S and Zhang, Y and Peng, C and Shao, Y and Xiong, X and Xing, Y and Liu, H},
title = {Modulation of Milk Source Differences on Immunity, Nutritional Physiology and Intestinal Microbiota in Neonatal Piglets.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227435},
issn = {2076-2615},
support = {2022YFD1300704//The National Key Research and Development Program of China/ ; 2023JJ40643//The Natural Science Foundation of Hunan Province/ ; 32402793//The National Natural Science Foundation of China/ ; },
abstract = {Milk sources directly influence digestion, absorption, and overall nutrient utilization during early infant nutrition. Goat milk features a nutritional composition and digestive properties that are more similar to human breast milk. This study aimed to investigate the effects of different milk sources on the immunity, amino acid and fatty acid metabolism, and intestinal microbiota in neonatal piglets. Sixteen 7-day-old suckling piglets were randomly allocated into two groups (eight replicates/group, one piglet/replicate) and fed with standard formula milk powder (CON) and goat milk formula powder (GMF). The formal experiment lasted for 14 days. Results showed that compared with the CON group, the GMF group showed a significant increase (p < 0.05) in the final weight, the serum levels of immunoglobulin A (IgA), IgG, IgM and C-reactive protein (CRP4), and intestinal trypsin content. Additionally, the GMF group had higher (p < 0.05) serum essential and non-essential amino acid and fatty acid levels, and had trends toward upregulation (0.05 < p < 0.1) in hepatic mRNA expression of spermine N1-acetyltransferase 1 (SAT1), duodenal peptide transporter 1 (PePT1), and jejunal cationic amino acid transporter 1 (CAT1). Microbiome sequencing revealed that GMF enhanced intestinal microbial richness and diversity and increased concentrations of acetic and propionic acids (p < 0.05). In conclusion, GMF suggests a potential improvement in the growth performance by enhancing immunity, amino acid and fatty acid metabolism and optimizing intestinal microbiota composition in neonatal piglets. These findings further support the favorable nutritional properties and tolerability of GMF in early-life nutrition.},
}

@article {pmid41227430,
year = {2025},
author = {Deng, L and Yao, Y and Li, H and Lu, Q and Wu, R},
title = {Effects of Antimicrobial Peptides on the Growth Performance of Squabs Were Investigated Based on Microbiomics and Non-Targeted Metabolomics.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227430},
issn = {2076-2615},
support = {2023B02036//Xinjiang Uygur Autonomous Region Key Research and Development Project/ ; XJARS-12-01//Xinjiang Uygur Autonomous Region Modern Agricultural Industrial Technology System/ ; 2025XJJQ-z-01//Xinjiang Uygur Autonomous Region Modern Livestock and Poultry Breeding Industry Promotion Project/ ; },
abstract = {This study aims to investigate the effects of dietary supplementation with AMPs on the growth performance, antioxidant capacity, and intestinal health of squabs. Furthermore, metagenomic and metabolomic approaches were employed to identify key differential bacterial species and metabolites associated with growth performance, and thereby the potential mechanisms underlying the enhancement of squab growth and development by AMPs being elucidated. One hundred and twenty pairs of healthy adult White Carneau pigeons (2 years old) were randomly divided into two groups, the control group (CK, fed with basal diet) and antimicrobial peptide group (AP, fed with basal diet +200 mg/kg antimicrobial peptide), with 10 replicates per group and 6 pairs of breeding pigeons per replicate. The experiment lasted for 53 days, including 7 days of prefeeding, 18 days of incubation and 28 days of feeding. In this study, squabs were weighed at 0 and 28 days of age to evaluate growth performance. At 28 days of age, duodenal contents were collected to assess digestive enzyme activities, while jejunal and liver tissues were harvested to determine antioxidant capacity. Intestinal morphology was examined using tissue samples from the duodenum, jejunum, and ileum. Finally, ileal contents were collected for a comprehensive analysis of microbial composition and metabolite profiles in the two experimental groups, employing high-throughput sequencing and LC-MS/MS techniques. The results showed that body weight, liver total antioxidant capacity (T-AOC), jejunal malondialdehyde (MDA) content, jejunum and ileum villus height-to-crypt depth ratio (VH/CD) were significantly increased, and jejunal crypt depth (CD) was significantly decreased in the AP group at 28 days of age (p < 0.05). In addition, the microbiome data showed that Lactobacillus in the AP group was a biomarker with significant differences (p < 0.05). Metabolomics analysis showed that the steroid hormone biosynthesis pathway was significantly different between the two groups (p < 0.01). In addition, the content of potentially beneficial metabolites (Biotin, beta-Tocotrienol, 7-Chloro-L-tryptophan and Dihydrozeatin) was significantly increased in the AP group (p < 0.05). These results indicate that dietary AMPs can significantly improve the body weights, liver antioxidant capacity and jejunum and ileum VH/CD of squabs.},
}

@article {pmid41227429,
year = {2025},
author = {Huang, HW and Yeh, TC and Hsieh, JC and Tsai, CW and Lee, YJ and Chen, MJ},
title = {Evaluating the Adjuvant Therapeutic Effects of Probiotic Strains Lactococcus cremoris and Lacticaseibacillus paracasei on Canine Atopic Dermatitis and Their Impact on the Gut and Skin Microbiome.},
journal = {Animals : an open access journal from MDPI},
volume = {15},
number = {21},
pages = {},
pmid = {41227429},
issn = {2076-2615},
support = {110AS-10.1.7-AD-U1//Council of Agriculture of Taiwan, Executive Yuan/ ; },
abstract = {This study investigated the therapeutic potential of a novel probiotic combination consisting of Lactococcus cremoris subsp. cremoris MP01 and Lacticaseibacillus paracasei subsp. paracasei MP02, collectively referred to as LCP, in the treatment of canine atopic dermatitis (CAD). In a 60-day open-label, single-arm trial involving eight dogs, notable clinical improvements were observed following daily LCP treatment, as evidenced by decreasing trends in Canine Atopic Dermatitis Extent and Severity Index and Pruritus Visual Analogue Scale scores, as well as a significant reduction in serum immunoglobulin E levels (p < 0.05). Microbiome and short-chain fatty acid (SCFA) analyses were subsequently conducted in a representative subset of six dogs to explore the effects of LCP on the fecal and skin microbial ecosystems. Concomitant alterations in gut and skin microbiome were observed, including a significant reduction in abundance of Erysipelotrichaceae (p < 0.05) and non-significant decreasing trends in Romboutsia, Escherichia/Shigella spp., and Shigella flexneri, along with a trend toward increased SCFA production. Functional prediction using PICRUSt suggested potential involvement of immune- and infection-related signaling pathways, including those associated with nucleotide-binding oligomerization domain-like receptors, retinoic acid-inducible gene I-like receptors and Shigellosis, supporting the hypothesis that LCP may exert its effects through modulation of the gut-skin axis. These findings support LCP as a safe and promising adjunct therapy for CAD, offering a novel microbiome-targeted approach targeting both clinical symptoms and underlying dysbiosis. Further investigation is warranted to optimize probiotic formulations and better understand the mechanisms underlying microbiome-mediated immune modulation in canine allergy.},
}

@article {pmid41227299,
year = {2025},
author = {Łuczak, JW and Palusińska, M and Maślińska-Gromadka, K and Pietrzak, D and Szopiński, T and Lewicki, S and Schenk, T and Szymański, Ł},
title = {The Next Generation of Skin Care: Transforming Retinoid Therapeutics.},
journal = {Cells},
volume = {14},
number = {21},
pages = {},
doi = {10.3390/cells14211650},
pmid = {41227299},
issn = {2073-4409},
support = {0176/L-14/2023//The National Centre for Research and Development/ ; },
mesh = {Humans ; *Retinoids/therapeutic use/pharmacology ; *Skin/drug effects/metabolism ; Animals ; *Skin Care/methods ; Receptors, Retinoic Acid/metabolism ; *Skin Diseases/drug therapy ; },
abstract = {Retinoids are central regulators of skin biology, influencing keratinocyte proliferation, differentiation, immune modulation, and barrier maintenance. Their therapeutic relevance has long been attributed to retinoic acid receptor (RAR)-mediated transcriptional activity; however, recent studies have revealed additional layers of regulation, including epigenetic modifications, kinase signaling networks, and interactions with the skin microbiome. These mechanisms not only refine our understanding of retinoid function but also inform strategies to overcome therapeutic limitations such as resistance, irritation, and systemic toxicity. Advances in medicinal chemistry have yielded synthetic retinoids with enhanced receptor selectivity, particularly for RAR-γ agonists such as trifarotene, as well as inhibitors of cytochrome P450-mediated retinoic acid metabolism, which sustain endogenous activity and mitigate resistance (DX314 and other RAMBAs). In parallel, the development of nanocarriers, stimuli-responsive gels, and other targeted delivery systems has improved drug stability, bioavailability, and tolerability. Together, these innovations underscore the evolving role of retinoid-based interventions in precision dermatology, providing opportunities to optimize treatment outcomes for acne, psoriasis, photoaging, and other dermatological disorders while addressing the shortcomings of earlier generations.},
}

Humans
*Retinoids/therapeutic use/pharmacology
*Skin/drug effects/metabolism
Animals
*Skin Care/methods
Receptors, Retinoic Acid/metabolism
*Skin Diseases/drug therapy

@article {pmid41227212,
year = {2025},
author = {Fousekis, FS and Mpakogiannis, K and Lianos, GD and Antonelli, E and Bassotti, G and Katsanos, KH},
title = {Gut-Liver Axis, Microbiota, Bile Acids, and Immune Response in Pathogenesis of Primary Sclerosing Cholangitis: An Overview.},
journal = {Journal of clinical medicine},
volume = {14},
number = {21},
pages = {},
pmid = {41227212},
issn = {2077-0383},
abstract = {Primary sclerosing cholangitis (PSC) is a chronic, immune-mediated cholestatic liver disease characterized by progressive bile duct inflammation and fibrosis. Its strong association with inflammatory bowel disease (IBD) highlights the possible role of the gut-liver axis in disease pathogenesis. Here, we review the mechanisms that may contribute to the disruption of the gut-liver axis, leading to liver injury and the development of PSC. In particular, disruption of the intestinal barrier allows microbial products to enter the portal circulation, stimulating hepatic immune cells and triggering biliary inflammation. Concurrently, gut-primed lymphocytes expressing mucosal homing receptors migrate aberrantly to the liver, where they may contribute to biliary epithelial cell injury. Dysbiosis, characterized by reduced microbial diversity and the expansion of bile-tolerant and pro-inflammatory taxa, amplifies this immune activation and disturbs gut-liver homeostasis. Moreover, bile acids act as signaling molecules, regulating metabolism and immune responses through receptors such as FXR and TGR5. Dysregulation of these pathways may promote cholestasis, inflammation, and fibrosis. By understanding these interactions, we may identify novel therapeutic targets for PSC.},
}

@article {pmid41227067,
year = {2025},
author = {Zygmunt, Ł and Kiryk, S and Wesołek, K and Kiryk, J and Nawrot-Hadzik, I and Rybak, Z and Sztyler, K and Małyszek, A and Matys, J and Dobrzyński, M},
title = {The Role of the Oral Microbiome and Dental Caries in Respiratory Health: A Systematic Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {21},
pages = {},
pmid = {41227067},
issn = {2077-0383},
abstract = {Objectives: This systematic review aimed to evaluate the association between oral health-particularly dental caries and dysbiosis of the oral microbiome-and respiratory diseases across different age groups and clinical settings, with emphasis on microbial overlap, clinical outcomes, and preventive strategies. Methods: A systematic search was conducted in PubMed, Scopus, Embase, Web of Science, and the Cochrane Library up to June 2025. Eligible studies included randomized controlled trials, cohort, case-control, and cross-sectional investigations examining the relationship between oral diseases or microbiome alterations and respiratory outcomes. Data on study design, population, oral health parameters, microbial taxa, and respiratory endpoints were extracted. Study quality was assessed using the Mixed Methods Appraisal Tool (MMAT, 2018). Results: Twenty studies met the inclusion criteria, encompassing pediatric, adult, and elderly populations. Poor oral health, reflected by higher caries indices and periodontal inflammation, was consistently associated with increased risk of lower respiratory tract infections (LRTI), aspiration events, ventilator-associated pneumonia (VAP), and impaired pulmonary function. Oral microbiome analyses revealed enrichment of Veillonella, Prevotella, Klebsiella, and Pseudomonas species in both oral and airway samples, supporting the oral cavity as a reservoir for respiratory pathogens. Interventional evidence from intensive care and nursing home settings demonstrated that structured oral care-particularly daily toothbrushing and chlorhexidine-based plaque control-significantly reduced pneumonia incidence. Conclusions: This review confirms a clinically relevant and biologically plausible link between oral dysbiosis, dental caries, and respiratory disease. Oral biofilms contribute to infection risk through microaspiration and microbial seeding of the lower airways. Integrating oral screening, hygiene maintenance, and treatment of active oral disease into respiratory care pathways may reduce respiratory morbidity and mortality, particularly among high-risk populations such as ICU patients, older adults, and individuals with chronic lung disease.},
}

@article {pmid41226976,
year = {2025},
author = {Bharadwaj, HR and Koo, TH and Dahiya, DS and Dalal, P and Fuad, M and Arab, S and Chhatwal, K and Bhatti, T and Malik, M and Singh, S and Hasan, F and Tofani, C and Infantolino, A},
title = {Gastric Motility Disorders Post Organ Transplantation-A Comprehensive Review.},
journal = {Journal of clinical medicine},
volume = {14},
number = {21},
pages = {},
pmid = {41226976},
issn = {2077-0383},
abstract = {Motility disorders, particularly gastroparesis, are prevalent complications following solid organ transplantation, significantly impacting quality of life, nutritional status, graft survival, and mortality. This comprehensive review synthesises evidence from PubMed, Scopus, and Embase databases on pathophysiology, clinical manifestations, diagnosis, management, and prognostic factors across transplant types. Mechanisms include vagal nerve injury (highest in lung transplants, prevalence 40-91%), immunosuppressive effects (e.g., tacrolimus accelerates motility; mycophenolate impairs it), surgical trauma, microbiome dysbiosis (reduced Firmicutes/Bacteroidetes ratio), and metabolic factors like post-transplant diabetes (OR 5.17 in kidney recipients). Pediatric and thoracic recipients face the highest risks, with lung transplant gastroparesis conferring a 2.7-fold increased mortality/retransplantation hazard (p < 0.05). Diagnosis relies on gastric emptying scintigraphy (gold standard, sensitivity 85-95%) and wireless motility capsules (100% sensitivity for delay), while management encompasses prokinetics (60-80% response), endoscopic G-POEM (85% success), gastric electrical stimulation (100% quality-of-life improvement in series), and nutritional support. Prognostic factors include younger age (better intervention response), aetiology (anatomical worse than metabolic), and early therapy success. Outcomes vary: lung recipients experience severe impacts on chronic allograft dysfunction (83% oesophageal motility abnormalities correlate with 66-67% rejection). Future directions emphasise microbiome therapies, AI predictive models (AUC 0.85), and wearables for continuous monitoring. Multidisciplinary approaches are essential to balance immunosuppression with GI management, addressing ethical dilemmas like drug interactions and access disparities. Ultimately, early screening and personalised interventions can mitigate complications, enhancing long-term transplant success.},
}

@article {pmid41226831,
year = {2025},
author = {Stoyancheva, G and Mihaylova, N and Gerginova, M and Krumova, E},
title = {Endometrial Microbiome and Reproductive Receptivity: Diverse Perspectives.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110796},
pmid = {41226831},
issn = {1422-0067},
support = {КП-06-Н83/6//Scientific Research Fund at the Ministry of Education and Science, Bulgaria/ ; },
mesh = {Humans ; Female ; *Endometrium/microbiology ; *Microbiota ; *Embryo Implantation ; Dysbiosis/microbiology ; *Reproduction ; },
abstract = {The human endometrium, previously considered a sterile environment, is now recognized as a low-biomass but biologically active microbial niche critical to reproductive health. Advances in sequencing technologies, particularly shotgun metagenomics, have provided unprecedented insights into the taxonomic and functional complexity of the endometrial microbiome. While 16S rRNA sequencing has delineated the distinction between Lactobacillus-dominant and non-dominant microbial communities, shotgun metagenomics has revealed additional diversity at the species and strain level, uncovering microbial signatures that remain undetected by amplicon-based approaches. Current evidence supports the association of Lactobacillus dominance with endometrial homeostasis and favorable reproductive outcomes. Dysbiosis, characterized by increased microbial diversity and enrichment of anaerobic taxa such as Gardnerella, Atopobium, Prevotella, and Streptococcus, is linked to chronic endometritis, implantation failure, and adverse IVF results. Beyond compositional differences, the endometrial microbiome interacts with the host through immunological, metabolic, and epigenetic mechanisms. These interactions modulate cytokine signaling, epithelial barrier integrity, and receptivity-associated gene expression, ultimately influencing embryo implantation. However, discrepancies between published studies reflect the lack of standardized protocols for sampling, DNA extraction, and bioinformatic analysis, as well as the inherent challenges of studying low-biomass environments. Factors such as geography, ethnicity, hormonal status, and antibiotic exposure further contribute to interindividual variability. Culturomics approaches complement sequencing by enabling the isolation of viable bacterial strains, offering perspectives for microbiome-based biotherapeutics. Emerging 3D endometrial models provide additional tools to dissect microbiome-host interactions under controlled conditions. Taken together, the growing body of data highlights the potential of endometrial microbiome profiling as a biomarker for reproductive success and as a target for personalized interventions. Future research should focus on integrating multi-omics approaches and functional analyses to establish causal relationships and translate findings into clinical practice. This review gives a new insight into current knowledge on the uterine microbiome and its impact on implantation success, analyzed through the lenses of microbiology, immunology, and oxidative stress.},
}

Humans
Female
*Endometrium/microbiology
*Microbiota
*Embryo Implantation
Dysbiosis/microbiology
*Reproduction

@article {pmid41226824,
year = {2025},
author = {de Groen, P and Blok, LCHM and Fuhri Snethlage, CM and Hanssen, NMJ and Rampanelli, E and Nieuwdorp, M},
title = {Unraveling Type 1 Diabetes: Integrating Microbiome, Metabolomics, and Immunomodulation for Next-Generation Therapies.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110788},
pmid = {41226824},
issn = {1422-0067},
support = {09150182010020//Personal NWO-VICI grant 2020/ ; 101141346//ERC Advanced grant/ ; 4-SRA-2025-1766-M-B//BREAKTHROUGH T1D Grant/ ; 09150172210050//ZonMw-VIDI grant 2023/ ; 2021T055//Senior Clinical Dekker grant by the Dutch Heart Foundation/ ; 09150172210019//ZONMW-VIDI grant 2023/ ; },
mesh = {Humans ; *Diabetes Mellitus, Type 1/therapy/immunology/metabolism/microbiology ; *Gastrointestinal Microbiome/immunology ; *Metabolomics/methods ; *Immunomodulation ; Animals ; Fecal Microbiota Transplantation ; Autoimmunity ; },
abstract = {Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by T-cell-mediated destruction of pancreatic beta cells, resulting in insulin deficiency. Both genetic predisposition and environmental factors contribute to T1D development, with growing evidence implicating the gut microbiome as a critical environmental modulator in disease pathogenesis. Gut microbial composition and derived metabolites influence immune homeostasis and autoimmunity. This review summarizes recent advances elucidating immune dysregulations in T1D and novel therapeutic strategies to preserve beta cell function. We discuss approaches such as immune cell engineering, including CAR-Treg therapy, and targeted modulation of immune signaling pathways like JAK-STAT. Furthermore, we explore the role of the gut microbiota and its metabolites in modulating host immunity and describe emerging microbiome-targeting interventions, including fecal microbiota transplantation and metabolite supplementation. These interventions show promise in modulating disease progression in preclinical and early clinical studies. An integrated understanding of immune and microbiome-related mechanisms is critical for developing next-generation therapies. Further research and clinical trials are needed to optimize these approaches and translate them into durable, personalized treatments for individuals with T1D.},
}

Humans
*Diabetes Mellitus, Type 1/therapy/immunology/metabolism/microbiology
*Gastrointestinal Microbiome/immunology
*Metabolomics/methods
*Immunomodulation
Animals
Fecal Microbiota Transplantation
Autoimmunity

@article {pmid41226760,
year = {2025},
author = {Nowacka, A and Śniegocki, M and Bożiłow, D and Ziółkowska, E},
title = {Gut Microbiota and Central Nervous System Tumors: A Comprehensive Systematic Review and Meta-Analysis of Microbiome-CNS Interactions.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110721},
pmid = {41226760},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Central Nervous System Neoplasms/microbiology/metabolism ; Central Nervous System ; },
abstract = {The gut-brain axis has emerged as a critical pathway influencing central nervous system (CNS) tumor biology through complex microbiome-mediated mechanisms. Understanding these interactions is essential for developing novel therapeutic strategies and biomarkers for CNS tumors. To systematically review and meta-analyze current evidence on gut microbiota interactions with CNS tumors, examining mechanisms, clinical correlations, therapeutic implications, and biomarker potential. We conducted a comprehensive systematic review following PRISMA guidelines, searching PubMed, EMBASE, Google Scholar, and Cochrane Library databases for studies published from 2010-2025. A random-effects meta-analysis of reported statistical outcomes was performed to quantify microbiome alterations using standardized mean differences (Cohen's d) and diagnostic accuracy measures. Analyses were based on published summary statistics rather than reprocessed raw sequencing data, acknowledging cross-study heterogeneity. From 161 identified records, 12 studies met inclusion criteria (6 clinical studies, n = 387 participants; 6 preclinical studies). Meta-analysis revealed significant Shannon diversity reduction in CNS tumor patients (Cohen's d = -1.237 [95% CI: -1.614, -0.860; 95% PI: -2.48, -0.12]) with moderate heterogeneity (I[2] = 60.5%). Evidence demonstrated significant gut microbiome alterations with reduced microbial diversity, increased pathogenic bacteria (Akkermansia muciniphila: 2.23-fold increase, Fusobacterium spp.: 2.04-fold increase), and decreased beneficial bacteria (Bifidobacterium spp.: 47% reduction, Lachnospira spp.: 56% reduction). Diagnostic performance showed fair discrimination (pooled AUC = 0.786 [95% CI: 0.781, 0.791]). Key mechanisms include bidirectional tumor-microbiota interactions through immune system modulation, metabolic pathway alterations involving short-chain fatty acids, and inflammatory response modifications within the altered CNS immune privilege environment. Preliminary evidence suggests gut microbiota alterations in CNS tumor patients, but findings require validation in large, standardized cohorts before clinical application. Current evidence quality is low (GRADE assessment), necessitating substantial additional research.},
}

Humans
*Gastrointestinal Microbiome
*Central Nervous System Neoplasms/microbiology/metabolism
Central Nervous System

@article {pmid41226742,
year = {2025},
author = {Suliman, IL and Panculescu, FG and Fasie, D and Cimpineanu, B and Alexandru, A and Gafar, N and Popescu, S and Nitu, TS and Enache, FD and Chisnoiu, T and Cozaru, GC and Tuta, LA},
title = {Gut Microbiome in Patients with Chronic Kidney Disease Stages 4 and 5: A Systematic Literature Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110706},
pmid = {41226742},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/microbiology/pathology ; Dysbiosis/microbiology ; Uremic Toxins/metabolism ; Disease Progression ; Inflammation/microbiology ; },
abstract = {This systematic review investigates the role of the gut microbiota in patients with advanced chronic kidney disease (CKD), specifically stages 4 and 5. Increasing evidence suggests that dysbiosis-an alteration in the normal balance of gut microbial populations-is not merely a secondary consequence of renal decline but a significant driver of disease progression. Such microbial imbalances are closely linked to a range of CKD-associated complications, including systemic inflammation, accumulation of uremic toxins, and heightened cardiovascular risk. Using PRISMA 2020 guidelines, we analyzed 87 peer-reviewed studies published between 2019 and 2025. The review revealed a consistent decline in beneficial microbes such as short-chain fatty acid-producing bacteria were markedly reduced, while populations of uremic toxin-generating microbes were notably increased. This microbial imbalance was associated with elevated concentrations of indoxyl sulfate and p-cresyl sulfate, heightened systemic inflammation, and impaired intestinal barrier integrity. Five conceptual frameworks-including the gut-kidney axis and endotoxemia-inflammation loop-were discussed. Ten microbiome assessment tools were reviewed, including 16S rRNA sequencing and LC-MS/MS for uremic toxin detection. Although probiotics, prebiotics, and synbiotics are gaining attention as potential therapeutic options, questions remain regarding their long-term efficacy and incorporation into standard clinical practice. Increasing scientific evidence underscores the gut microbiome's pivotal role in CKD progression and management, reinforcing the need for carefully designed, long-term interventions aimed at restoring a healthier microbial balance to support renal function.},
}

Humans
*Gastrointestinal Microbiome
*Renal Insufficiency, Chronic/microbiology/pathology
Dysbiosis/microbiology
Uremic Toxins/metabolism
Disease Progression
Inflammation/microbiology

@article {pmid41226678,
year = {2025},
author = {Dini, I and Mancusi, R and De Biasi, MG},
title = {The Role of Omics Technology in Evaluating Plastic Pollution's Effects on Plants: A Comprehensive Review.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110646},
pmid = {41226678},
issn = {1422-0067},
mesh = {*Plants/drug effects/genetics/metabolism ; *Plastics/toxicity/adverse effects ; *Soil Pollutants/toxicity ; *Microplastics/toxicity ; Soil Microbiology ; Metabolomics/methods ; Soil/chemistry ; },
abstract = {Micro and nano-plastics pose a significant threat to the global environment, affecting agricultural systems, food security, and human health. Some studies indicate that microplastics can induce physiological damage in plants, including oxidative stress, reduced germination, stunted biomass growth, and impaired photosynthesis. The extent of the damage varies depending on the type of microplastics, their size, and concentration. Moreover, micro- and nano-plastics can disturb the delicate balance of the soil microbiome. Microbial communities play a significant role in the health and functioning of ecosystems by facilitating nutrient turnover, breaking down organic matter, preserving soil integrity, and controlling diseases caused by soil-dwelling pathogens. This review highlights the role of omics technologies in elucidating the molecular mechanisms underlying plant responses to micro- and nanoplastics. The findings can enhance our comprehension of how micro- and nanoplastics affect agricultural systems when they contaminate soil.},
}

*Plants/drug effects/genetics/metabolism
*Plastics/toxicity/adverse effects
*Soil Pollutants/toxicity
*Microplastics/toxicity
Soil Microbiology
Metabolomics/methods
Soil/chemistry

@article {pmid41226666,
year = {2025},
author = {Rodrigues, R and Silva, AR and Sousa, C and Vale, N},
title = {Disrupted Cervicovaginal Microbiota: Its Role in Chlamydia trachomatis Genital Infection and Associated Reproductive Outcomes.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110635},
pmid = {41226666},
issn = {1422-0067},
mesh = {Female ; Humans ; *Chlamydia trachomatis/pathogenicity ; *Chlamydia Infections/microbiology/complications ; *Microbiota ; *Vagina/microbiology ; *Cervix Uteri/microbiology ; Pregnancy ; Dysbiosis/microbiology ; },
abstract = {Chlamydia trachomatis (CT) remains the most commonly reported bacterial sexually transmitted infection (STI) globally, with particularly high incidence among adolescents and young adults. In Europe, CT cases have continued to rise over the past decade, despite ongoing public health efforts in prevention and screening. Screening coverage, however, remains inconsistent across countries. CT infections are often asymptomatic, especially in women, yet can lead to serious CT-related reproductive complications if left untreated, including pelvic inflammatory disease (PID), tubal factor infertility, and ectopic pregnancy. Emerging evidence highlights the cervicovaginal microbiota as a key factor influencing susceptibility to STIs, including CT infection, its progression, and associated outcomes. A Lactobacillus-dominated microbiota, particularly L. crispatus, is well-known to be a protective factor against CT acquisition, whereas vaginal dysbiosis, characterized by a depletion of these species and an overgrowth of anaerobes, such as Gardnerella vaginalis, Atopobium vaginae, and Prevotella spp., has been linked to increased CT acquisition risk, reduced immune control, and impaired infection resolution. Interaction between microbial communities and host immunity may modulate whether CT infections spontaneously clear, persist, or progress into pathological conditions. This review explores the natural history of CT genital infection in women, emphasizing the role of cervicovaginal dysbiosis in disease progression and reproductive sequelae. By integrating current knowledge about resident cervicovaginal microbes, host-microbe interaction, and CT-related reproductive outcomes, we discuss how microbiota-targeted strategies, including probiotic or microbiome-modulating strategies, may complement current CT prevention, diagnosis, and treatment approaches.},
}

Female
Humans
*Chlamydia trachomatis/pathogenicity
*Chlamydia Infections/microbiology/complications
*Microbiota
*Vagina/microbiology
*Cervix Uteri/microbiology
Pregnancy
Dysbiosis/microbiology

@article {pmid41226642,
year = {2025},
author = {Leonetti, P and Di Palma, PR and Gazzola, G and Molinari, S},
title = {Food Waste Compost as a Tool of Microbiome-Assisted Agri-Culture for Sustainable Protection of Vegetable Crops Against Soil-Borne Parasites.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110606},
pmid = {41226642},
issn = {1422-0067},
support = {Investimento 1.4-D.D. 1032 17/06/2022, CN00000022//European Union Next-Generation/ ; },
mesh = {*Composting/methods ; Animals ; *Microbiota ; *Soil/parasitology/chemistry ; *Vegetables/parasitology/growth & development/microbiology ; Fertilizers ; Plant Roots/parasitology/microbiology ; *Crops, Agricultural/parasitology/growth & development ; Soil Microbiology ; Tylenchoidea ; *Plant Diseases/parasitology/prevention & control ; Mycorrhizae ; Food Loss and Waste ; },
abstract = {A low-scale Food Waste Compost (FWC1), characterized by optimal physic-chemical parameters and high organic matter percentages, was used as a fertilizer and a bio-stimulant for vegetable plants. Groups of treated plants were inoculated with active juveniles of root-knot nematodes to detect the effect on plant defense. Optimal amounts of compost mixed with soil increased plant biomass 30% compared to untreated plants. Moreover, when plants were inoculated, treated roots contained about 50% less sedentary forms (SFs) of nematodes and a lower reproduction rate of the parasites than untreated plants. Although the performance of FWC1 as defense activator was similar to other microbiome-generating commercial formulations, the compost was found to be the best fertilizer in both un- and inoculated plants. Diffuse root colonization by arbuscular mycorrhizal fungi (AMF) was observed after treatments with FWC1. FWC1 water extracts did not show any toxic effect on living nematode juveniles. Expression of the marker gene of immune response PR4b was found to be 3-5-fold higher in the roots of inoculated plants treated with FWC1 with respect to untreated plants, thus indicating that FWC1 primes plants against RKNs (root-knot nematodes, Meloidogyne incognita (Kofoid White) Chitw). Data are reported to associate immunization of plants with mycorrhization occurring in FWC1-treated plants. The proposed compost is indicated as having optimal performance both as a bio-fertilizer and a bio-stimulant.},
}

*Composting/methods
Animals
*Microbiota
*Soil/parasitology/chemistry
*Vegetables/parasitology/growth & development/microbiology
Fertilizers
Plant Roots/parasitology/microbiology
*Crops, Agricultural/parasitology/growth & development
Soil Microbiology
Tylenchoidea
*Plant Diseases/parasitology/prevention & control
Mycorrhizae
Food Loss and Waste

@article {pmid41226638,
year = {2025},
author = {Xue, K and Wang, T and Shi, P and Wang, J},
title = {The Role of Carbon Dots in Regulating the Periodontal Immune Microenvironment: Progress and Perspectives.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110600},
pmid = {41226638},
issn = {1422-0067},
support = {82270990//National Natural Science Foundation of China/ ; 2023YFC2506300//National Key R&D Program of China/ ; 2025ZNSFSC1580//Sichuan Science and Technology Program/ ; },
mesh = {Humans ; *Carbon/chemistry/pharmacology ; Animals ; *Periodontitis/immunology/drug therapy ; *Quantum Dots/chemistry ; Oxidative Stress/drug effects ; *Cellular Microenvironment/drug effects/immunology ; Macrophages/immunology/drug effects ; Microbiota/drug effects ; },
abstract = {As a prevalent oral chronic infectious disease, periodontitis is characterized by a complex pathogenesis, including microbial infection, host immune dysregulation, oxidative stress, and abnormal bone metabolism. Given their excellent biocompatibility, multifunctionality, and structural tunability, carbon dots (CDs) have emerged as a novel nanomaterial offering fresh approaches for the pharmacological management of periodontitis. This review systematically summarizes the application characteristics of CDs in biology and the various mechanisms in modulating the periodontal immune microenvironment. These include the roles in antimicrobial and microbiome modulation, regulation of oxidative stress balance, modulation of macrophage polarization, regulation of stem cell functions, and maintenance of bone homeostasis. The unique advantages of CDs in improving the periodontal immune microenvironment through multi-target, multi-pathway mechanisms are emphasized, thereby providing a theoretical foundation for future clinical applications.},
}

Humans
*Carbon/chemistry/pharmacology
Animals
*Periodontitis/immunology/drug therapy
*Quantum Dots/chemistry
Oxidative Stress/drug effects
*Cellular Microenvironment/drug effects/immunology
Macrophages/immunology/drug effects
Microbiota/drug effects

@article {pmid41226634,
year = {2025},
author = {Aggeletopoulou, I and Papantoniou, K and Pastras, P and Triantos, C},
title = {Unraveling the Pathophysiology of Irritable Bowel Syndrome: Mechanisms and Insights.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110598},
pmid = {41226634},
issn = {1422-0067},
mesh = {Humans ; *Irritable Bowel Syndrome/physiopathology/microbiology/etiology/metabolism ; Gastrointestinal Microbiome ; Animals ; Hypothalamo-Hypophyseal System ; Quality of Life ; Brain-Gut Axis ; },
abstract = {Irritable Bowel Syndrome (IBS) is one of the most prevalent gastrointestinal disorders, affecting about 11% of the global population and exerting a substantial burden on quality of life and healthcare systems. Despite the emerging interest in this disease, its pathophysiology remains elusive, reflecting the interplay between the brain-gut axis, neuroendocrine dysregulation, immune activation, barrier dysfunction, microbial imbalance, and environmental triggers. Disruptions in the hypothalamic-pituitary-adrenal axis, impaired serotonin signaling, bile acid malabsorption, and altered intestinal permeability collectively result in the emergence of abnormal motility, visceral hypersensitivity, and chronic inflammation. The gut microbiome further modulates these processes by influencing neurotransmitter metabolism, immune responses, and epithelial integrity, positioning it as both a driver of symptoms and a promising therapeutic target. The aim of this review is to synthesize current mechanistic insights into IBS, highlighting the interconnected roles of the brain-gut axis, immune modulation, and microbial dynamics, and to explore how these pathways may be translated into precision medicine approaches. This review integrates molecular, microbial, and neuroimmune perspectives to propose a systems-level understanding of IBS pathophysiology and its implications for precision medicine. By integrating host-microbe interactions, dietary influences, and genetic predispositions, we highlight the mechanistic complexity underlying IBS and the potential for translating these insights into personalized strategies for symptom control and improved quality of life.},
}

Humans
*Irritable Bowel Syndrome/physiopathology/microbiology/etiology/metabolism
Gastrointestinal Microbiome
Animals
Hypothalamo-Hypophyseal System
Quality of Life
Brain-Gut Axis

@article {pmid41226627,
year = {2025},
author = {Xue, M and Wang, H and Campos, F and Jackson, CJ and March, L},
title = {Rheumatoid Arthritis: Biomarkers and the Latest Breakthroughs.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110594},
pmid = {41226627},
issn = {1422-0067},
mesh = {Humans ; *Arthritis, Rheumatoid/metabolism/diagnosis/genetics ; *Biomarkers/metabolism ; Proteomics/methods ; Metabolomics/methods ; Genomics/methods ; Gastrointestinal Microbiome ; Animals ; },
abstract = {Rheumatoid arthritis (RA) is a heterogeneous autoimmune disease characterized by variable clinical manifestations and a complex, often unpredictable disease trajectory, which hinders early diagnosis and personalized treatment. This review highlights recent breakthroughs in biomarker discovery, emphasizing the transformative impact of multi-omics technologies and deep profiling of the synovial microenvironment. Advances in genomics and transcriptomics have identified key genetic variants and expression signatures associated with disease susceptibility, progression, and therapeutic response. Complementary insights from proteomics and metabolomics have elucidated dynamic molecular patterns linked to inflammation and joint destruction. Concurrently, microbiome research has positioned gut microbiota as a compelling source of non-invasive biomarkers with both diagnostic and immunomodulatory relevance. The integration of these diverse data modalities through advanced bioinformatics platforms enables the construction of comprehensive biomarker panels, offering a multidimensional molecular portrait of RA. When coupled with synovial tissue profiling, these approaches facilitate the identification of spatially resolved biomarkers essential for localized disease assessment and precision therapeutics. These innovations are transforming RA care by enabling earlier detection, improved disease monitoring, and personalized treatment strategies that aim to optimize patient outcomes.},
}

Humans
*Arthritis, Rheumatoid/metabolism/diagnosis/genetics
*Biomarkers/metabolism
Proteomics/methods
Metabolomics/methods
Genomics/methods
Gastrointestinal Microbiome
Animals

@article {pmid41226606,
year = {2025},
author = {Murphy, CE and Coffey, MJ and Chen, Q and Adams, S and Ooi, CY and van Dorst, J},
title = {Altered Development of Gut Microbiota and Gastrointestinal Inflammation in Children with Post-Operative Hirschsprung's Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110570},
pmid = {41226606},
issn = {1422-0067},
support = {2020/GNT1194358//National Health and Medical Research Council, Australia (NHMRC) Investigator Grant/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Hirschsprung Disease/microbiology/surgery/complications ; Female ; Male ; Feces/microbiology/chemistry ; Child ; Leukocyte L1 Antigen Complex/analysis/metabolism ; Child, Preschool ; RNA, Ribosomal, 16S/genetics ; *Inflammation/microbiology ; Infant ; *Enterocolitis/microbiology/etiology ; Dysbiosis/microbiology ; Case-Control Studies ; },
abstract = {Gastrointestinal symptoms often persist in children with Hirschsprung's disease (HD) even after "corrective" pull-through surgery. Alteration of the gut microbiota ("dysbiosis") has emerged as a potential contributing factor. Animal studies show gut ecosystem changes that are both intrinsic to HD and caused by bowel resection itself, but human studies comparing the intestinal microbiota of children with HD and healthy children are limited. We collected food frequency dietary surveys, clinical and symptom data, and stool samples from 15 post-operative children with HD and 15 healthy controls (HCs). We performed 16S rRNA gene sequencing from the stool samples and quantified faecal calprotectin as a measure of gastrointestinal inflammation. Despite no global changes in the microbiota between HD and HC cohorts and no differences between individuals with and without a history of HD-associated enterocolitis (HAEC), we identified evidence of altered microbiota development and inflammatory trajectories in HD. In HCs, alpha diversity increased with age (r = 0.83, p < 0.001), while calprotectin levels declined (Spearman's ρ = -0.53, p = 0.04). These age-related patterns were absent in HD. Across the combined cohort, lower alpha diversity was associated with higher faecal calprotectin (Spearman's ρ = -0.47, p = 0.01). In HD, Fusobacteria abundance showed a strong positive correlation with calprotectin (Spearman's ρ = 0.76, adjusted p = 0.02). Pediatric Quality of Life (PedsQL) and gastrointestinal disease-specific symptom scores were lower in HD compared to HC but were not directly linked to microbial diversity or inflammation. Overall, we observed a divergence from healthy peers in the typical developmental trajectory of gut microbial communities and inflammation in children with HD that may involve Fusobacteria. Children with HD reported reduced health-related quality of life compared with HC, consistent with ongoing gastrointestinal symptoms. No microbiota differences were associated with HAEC history, though this may reflect limited sample size.},
}

Humans
*Gastrointestinal Microbiome/genetics
*Hirschsprung Disease/microbiology/surgery/complications
Female
Male
Feces/microbiology/chemistry
Child
Leukocyte L1 Antigen Complex/analysis/metabolism
Child, Preschool
RNA, Ribosomal, 16S/genetics
*Inflammation/microbiology
Infant
*Enterocolitis/microbiology/etiology
Dysbiosis/microbiology
Case-Control Studies

@article {pmid41226570,
year = {2025},
author = {Post, A and Connelly, MA and Bakker, SJL and Dullaart, RPF},
title = {Lower Thyroid Function and Higher Plasma Choline: Effect Modification by Metabolic Dysfunction-Associated Steatotic Liver Disease.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110525},
pmid = {41226570},
issn = {1422-0067},
support = {Grant E.033//The Dutch Kidney Foundation funded the infrastructure of the PREVEND program from 1997 to 2003/ ; grant 2001-005//The Netherlands Heart Foundation/ ; },
mesh = {Humans ; *Choline/blood ; Male ; Female ; Middle Aged ; Methylamines/blood ; Gastrointestinal Microbiome ; Thyrotropin/blood ; Betaine/blood ; *Thyroid Gland/metabolism/physiopathology ; Aged ; Thyroid Function Tests ; *Fatty Liver/blood/metabolism ; Thyroxine/blood ; Cohort Studies ; Adult ; },
abstract = {Evidence is accumulating that there is a bidirectional relationship between thyroid function and the gut microbiome. We assessed associations of gut microbiome-derived circulating metabolites, choline, trimethylamine N-oxide (TMAO), and betaine with thyroid function status. Among 4771 euthyroid participants of the community-dwelling PREVEND cohort study (thyroid stimulating hormone (TSH), free thyroxine, and free triiodothyronine levels within the reference range; no use of thyroid function altering medication), associations of TSH (higher levels indicating low-normal thyroid function) with choline, TMAO, and betaine (determined by nuclear magnetic resonance spectroscopy) were assessed. Plasma choline varied by TSH category with the highest values observed in the highest TSH quartile (p < 0.001). Such a trend was also found for TMAO (p = 0.10) but not for betaine (p = 0.68). Linear regression analysis showed a positive association of choline with TSH in fully adjusted analysis (std β: 0.04 (95% CI, 0.01; 0.07; p = 0.012)). TMAO was associated with TSH in unadjusted analysis (std β: 0.03 (95% CI, 0.01; 0.06; p = 0.031)), but not in a fully adjusted model (0.03 (95% CI, -0.01; 0.06; p = 0.094)). Betaine was not associated with TSH. The association of choline with TSH was more pronounced in participants with an elevated fatty liver index, a proxy of metabolic dysfunction-associated steatotic liver disease (fully adjusted std β: 0.08; 95% CI, 0.03; 0.13; p = 0.003). Given associations of higher plasma choline and TMAO with cardiovascular disease and mortality, low-normal thyroid function could influence cardiometabolic health via effects on gut microbiome-derived circulating metabolites.},
}

Humans
*Choline/blood
Male
Female
Middle Aged
Methylamines/blood
Gastrointestinal Microbiome
Thyrotropin/blood
Betaine/blood
*Thyroid Gland/metabolism/physiopathology
Aged
Thyroid Function Tests
*Fatty Liver/blood/metabolism
Thyroxine/blood
Cohort Studies
Adult

@article {pmid41226514,
year = {2025},
author = {Hammad, AS and Zahedy, SH and Elqasass, SS and Said, SS and Elgamal, AM and Mahmoud, NN and Al-Asmakh, M},
title = {In Vitro Analysis of the Dynamic Role of the Bacterial Virulence Factors in Skin Wound Healing.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110472},
pmid = {41226514},
issn = {1422-0067},
support = {QU Student Grant: (QUST -1-CHS-2024-1813) and (QU Grant: QUPD-CHS-23-24-563//Qatar University/ ; },
mesh = {*Virulence Factors/metabolism/pharmacology ; *Wound Healing/drug effects ; Humans ; *Skin/microbiology/pathology/injuries ; Pseudomonas aeruginosa/pathogenicity ; Staphylococcus aureus/pathogenicity ; Cell Survival/drug effects ; Enterococcus faecalis/pathogenicity ; Streptococcus pyogenes/pathogenicity ; Cell Line ; *Bacteria/pathogenicity/metabolism ; Fibroblasts/metabolism/drug effects ; },
abstract = {The skin acts as a primary barrier against environmental insults and maintains homeostasis. Injury initiates a wound healing cascade of hemostasis, inflammation, proliferation, and remodeling. In chronic wounds, persistent microbial colonization and inflammation disrupt this process, with bacterial virulence factors acting as key drivers. While the microbiome's role in chronic wounds is recognized, the effects of individual virulence factors on acute repair remain unclear. Therefore, this study investigated the differential effects of virulence factors derived from five skin-associated bacterial species on acute wound healing dynamics. In this context, virulence factors from Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pyogenes, Lactobacillus plantarum, and Enterococcus faecalis were tested on HDF-n cell viability and wound closure, with multiplex ELISA used to assess inflammatory mediator secretion and underlying mechanisms. Overall, virulence factors were generally well tolerated across concentrations (0.05-16 µg/mL) and time points (24, 48 h), with cell viability >80%, except for S. aureus, which reduced viability to ~70% at higher concentrations by 48 h. Wound healing responses varied markedly: S. aureus significantly impaired closure in a dose-dependent manner (~10% closure at 16 µg/µL, 48 h), and E. faecalis similarly delayed repair. In contrast, factors from P. aeruginosa, S. pyogenes, and L. plantarum showed neutral or mildly pro-healing effects. Notably, co-treatment with S. pyogenes partially rescued impairment caused by S. aureus and E. faecalis. Collectively, these findings highlight that bacterial virulence factors have variable impacts on acute wound healing. These findings suggest potential therapeutic applications through targeted modulation or combinations of bacterial factors.},
}

*Virulence Factors/metabolism/pharmacology
*Wound Healing/drug effects
Humans
*Skin/microbiology/pathology/injuries
Pseudomonas aeruginosa/pathogenicity
Staphylococcus aureus/pathogenicity
Cell Survival/drug effects
Enterococcus faecalis/pathogenicity
Streptococcus pyogenes/pathogenicity
Cell Line
*Bacteria/pathogenicity/metabolism
Fibroblasts/metabolism/drug effects

@article {pmid41226502,
year = {2025},
author = {Kuo, TH and Wu, PH and Liu, PY and Chuang, YS and Tai, CJ and Kuo, MC and Chiu, YW and Lin, YT},
title = {Identification of Gut Microbiome Signatures Associated with Serotonin Pathway in Tryptophan Metabolism of Patients Undergoing Hemodialysis.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110463},
pmid = {41226502},
issn = {1422-0067},
support = {MOST 111-2314-B-037-032-MY3//Ministry of Science and Technology, Taiwan/ ; MOST 111-2314-B-037 -083 -MY3//Ministry of Science and Technology, Taiwan/ ; KMUH-DK(C)113003//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH-DK(B)110003-4//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2M08//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R21//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH112-2R76//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1M60//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH111-1R73//Kaohsiung Medical University Hospital, Taiwan/ ; KMUH110-0M73//Kaohsiung Medical University Hospital, Taiwan/ ; NHRIKMU-111-I003-2//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-113-I005//Kaohsiung Medical University, Taiwan/ ; NYCUKMU-112-I006//Kaohsiung Medical University, Taiwan/ ; KT112P012//Kaohsiung Medical University, Taiwan/ ; KT113P006//Kaohsiung Medical University, Taiwan/ ; NHRIKMU-114-I001//Kaohsiung Medical University, Taiwan/ ; S11209//Kaohsiung Medical University, Taiwan/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Tryptophan/metabolism ; *Serotonin/metabolism ; Male ; Female ; Middle Aged ; *Renal Dialysis ; Aged ; Melatonin/metabolism ; Metagenomics/methods ; Adult ; },
abstract = {Serotonin, a tryptophan metabolite, exerts a significant influence on both brain and gut functionality. While previous research has elucidated the intricate dynamics of the gut-brain axis, the interplay between serotonin pathway metabolites and gut microbiota in individuals undergoing hemodialysis remains largely unexplored. Therefore, this study aimed to investigate gut microbiota composition corresponding to serotonin pathway metabolite levels among patients with hemodialysis. A total of 85 patients undergoing hemodialysis were selected. Their gut microbiota was analyzed using shotgun metagenomic sequencing profiling. The serotonin pathway metabolites, including 5-hydroxytryptophan (5-HTP), serotonin, 5-methoxytryptophan (5-MTP), 5-methoxytryptamine, melatonin, and 6-hydroxymelatonin, were analyzed with the liquid chromatograph-tandem mass spectrometer. The robust linear discriminant analysis Effect Size (LEfSe) was employed to reveal the gut microbiota signature according to levels of serotonin pathway metabolites. A significant β-diversity difference in 5-Methoxytryptamine (p = 0.037) was found, while no variance in α-diversity was detected. Using LefSe analysis, we identified an enriched Tannerellaceae family in the high-hydroxytryptophan (5-HTP) group, the Odoribacteraceae family in the high-serotonin group, the Eubacteriales order in the high-5-methoxytryptophan (5-MTP) group, the Prevotella copri species in the high-5-Methoxytryptamine group, and the Clostridium genus in the high-melatonin group. In contrast, an enriched Clostridiaceae family in the low-5-HTP group, the Clostridiaceae family in the low-serotonin group, and the Bacteroides ovatus species in the low-5-MTP group were found. Distinct gut microbiota signatures linked to serotonin pathway metabolites were identified in patients undergoing hemodialysis. These findings provide insights for future gut-brain axis research and may guide methods to modulate gut microbiota to influence serotonin metabolites.},
}

Humans
*Gastrointestinal Microbiome
*Tryptophan/metabolism
*Serotonin/metabolism
Male
Female
Middle Aged
*Renal Dialysis
Aged
Melatonin/metabolism
Metagenomics/methods
Adult

@article {pmid41226494,
year = {2025},
author = {Kiang, JG and Cannon, G},
title = {An Update on Dynamic Changes in Cytokine Expression and Dysbiosis Due to Radiation Combined Injury.},
journal = {International journal of molecular sciences},
volume = {26},
number = {21},
pages = {},
doi = {10.3390/ijms262110456},
pmid = {41226494},
issn = {1422-0067},
support = {AFR-B2-12812//Armed Forces Radiobiology Research Institute/ ; 5U19AI06777-18//National Institute of Allergy and Infectious Diseases/ ; R21/33AI08553//National Institute of Allergy and Infectious Diseases/ ; },
mesh = {Animals ; *Cytokines/metabolism/genetics ; *Dysbiosis/etiology/metabolism ; Gastrointestinal Microbiome/radiation effects ; *Radiation Injuries/metabolism/microbiology ; Humans ; Mice ; },
abstract = {The complexity of adverse responses from radiation injury (RI) followed by physical trauma, namely, radiation combined injury (RCI), is unique and more pronounced than either insult alone due to a poor understanding of the integration of these insults at the molecular/cellular/tissue and/or organ levels. It was shown that mice receiving [60]Co γ-photon RCI with wounding had a lower LD50/30 than RI alone. This survival synergism was observed in bone marrow and the gastrointestinal system, as evidenced by an increase in γ-H2AX expression in bone marrow cell DNA, loss of circulatory blood cells, elevation of serum cytokine concentration, and activation of nuclear factor-κB/inducible nitric oxide synthase, and an earlier onset of bacterial infection and sepsis after RCI than after RI was detected. Dysbiosis (imbalance of the gut microbiota) was observed. There remains a pressing need for both prophylactic countermeasures and therapeutic remedies to deal with RCI threats. Investigations of how RCI can affect this important network of communication between the gut microbiota and other organs, including the brain, lung, heart, liver, kidney, and skin, could lead to new and critical interventions and prevention strategies. This review provides an update on new RCI animal models, dynamic changes in cytokine expression, dysbiosis, as well as links between the gut microbiome and other organs after RCI.},
}

Animals
*Cytokines/metabolism/genetics
*Dysbiosis/etiology/metabolism
Gastrointestinal Microbiome/radiation effects
*Radiation Injuries/metabolism/microbiology
Humans
Mice

@article {pmid41226173,
year = {2025},
author = {Łukaszyk, A and Kwiecień, I and Kanik, A and Blicharska, E and Tatarczak-Michalewska, M and Białowąs, W and Czarnek, K and Szopa, A},
title = {Nutritional, Therapeutic, and Functional Food Perspectives of Kale (Brassica oleracea var. acephala): An Integrative Review.},
journal = {Molecules (Basel, Switzerland)},
volume = {30},
number = {21},
pages = {},
pmid = {41226173},
issn = {1420-3049},
support = {2023/49/B/NZ7/02428//National Science Centre/ ; },
mesh = {*Brassica/chemistry ; Humans ; *Functional Food/analysis ; Phytochemicals/chemistry/pharmacology ; Antioxidants/chemistry/pharmacology ; Glucosinolates/chemistry ; Animals ; },
abstract = {Kale (Brassica oleracea var. acephala) is a non-heading leafy vegetable of the Brassicaceae family, widely recognized for its dense nutritional profile and diverse phytochemical composition. This review provides a comprehensive and up-to-date synthesis of kale's botanical characteristics, cultivation practices, chemical constituents, biological activities, and applications in pharmacy, functional foods, and cosmetics. Importantly, this work highlights the novelty of kale's multifunctional role. Kale is particularly rich in vitamins (A, C, K), minerals (Ca, Fe, K), dietary fiber, glucosinolates, polyphenols, carotenoids, flavonoids, and chlorophylls, which contribute to its classification as a "superfood." In this article the discussion of the health-promoting effects of glucosinolates and their enzymatic degradation products, such as isothiocyanates, indoles, and nitriles, highlighting their antioxidant, anti-inflammatory, anticancer, antimicrobial, and lipid-lowering properties, was performed. Moreover, key compounds including sulforaphane, indole-3-carbinol (I3C), and diindolylmethane (DIM) are emphasized for their roles in chemoprevention, hormonal regulation, and cellular protection. The review also summarizes recent in vivo and clinical studies demonstrating kale's potential in reducing the risk of chronic diseases such as cardiovascular disorders, type 2 diabetes, and hormone-related cancers. The effects of kale on the composition of the gut microbiome, glycemic control, and cholesterol metabolism are also discussed. Advances in plant biotechnology, including micropropagation, somatic embryogenesis, and metabolite enhancement, are also discussed. Overall, this review supports the integration of kale into health-oriented dietary strategies and highlights its relevance in preventive medicine, food innovation, and cosmeceutical development.},
}

*Brassica/chemistry
Humans
*Functional Food/analysis
Phytochemicals/chemistry/pharmacology
Antioxidants/chemistry/pharmacology
Glucosinolates/chemistry
Animals

@article {pmid41226077,
year = {2025},
author = {Harrandah, AM},
title = {The Oral-Gut-Systemic Axis: Emerging Insights into Periodontitis, Microbiota Dysbiosis, and Systemic Disease Interplay.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {15},
number = {21},
pages = {},
pmid = {41226077},
issn = {2075-4418},
abstract = {The oral cavity harbors one of the most diverse microbial ecosystems in the human body, second only to the gut. Periodontitis, a chronic inflammatory disease arising from oral microbiota dysbiosis, has been increasingly associated with systemic disorders such as diabetes mellitus, atherosclerosis, rheumatoid arthritis, inflammatory bowel disease, and neurodegenerative conditions. Although hematogenous dissemination of oral pathogens and inflammatory mediators has long been proposed as a mechanistic link, emerging evidence identifies the oral-gut axis as a novel bidirectional pathway. Swallowed oral pathobionts, such as Porphyromonas gingivalis and Fusobacterium nucleatum, can colonize the gut, disrupt the intestinal barrier, and induce dysbiosis, immune imbalance, and metabolic alterations that aggravate systemic inflammation and disease progression. In contrast, gut dysbiosis, especially in obesity or high-fat-diet models, can exacerbate periodontal tissue destruction through hyperuricemia, altered bone metabolism, and Th17/Treg immune imbalance. Experimental and clinical studies further support this reciprocal relationship, implicating microbial, metabolic, and immune crosstalk in both oral and systemic pathology. Understanding this oral-gut-systemic axis offers a paradigm shift in diagnostics and therapeutics, focusing on precision interventions such as microbiome modulation, probiotics, and integrated oral care to mitigate systemic inflammatory burden and improve overall health outcomes.},
}

@article {pmid41225903,
year = {2025},
author = {Zhang, L and Bellotti, G and Salehi, H and Puglisi, E and Lucini, L},
title = {Effects of Arbuscular Mycorrhizal Fungi and Metal-Tolerant Pseudomonas fluorescens on Mitigating Cadmium and Zinc Stress in Tomato.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41225903},
issn = {2223-7747},
abstract = {Heavy metal (HM) contamination in agricultural soils poses a significant threat to soil health and plant productivity. This study investigates the impact of cadmium (Cd) and zinc (Zn) stress on tomato plants (Solanum lycopersicum) and explores the mitigation potential of microbial biostimulants (MBs), including arbuscular mycorrhizal fungi (AMF) and Pseudomonas fluorescens So_08 (PGPR), over a 52-day period using multi-omics approaches. Root exudate profiling revealed distinct metabolic changes under HM stress, which compromised soil-plant interactions. Cd stress reduced the secretion of phenylpropanoids (sum LogFC: -45.18), lipids (sum LogFC: -27.67), and isoprenoids (sum LogFC: -11-67), key metabolites in antioxidative defense, while also suppressing rhizosphere fungal populations. Conversely, Zn stress enhanced lipid exudation (such as sphingolipids and sterols, as sum LogFC of 8.72 and 9.99, respectively) to maintain membrane integrity and reshaped rhizobacterial communities. The MBs application mitigated HM-induced stress by enhancing specialized metabolite syntheses, including cinnamic acids, terpenoids, and flavonoids, which promoted crop resilience. MBs also reshaped microbial diversity, fostering beneficial species like Portibacter spp., Alkalitalea saponilacus under Cd stress, and stimulating rhizobacteria like Aggregatilinea spp. under Zn stress. Specifically, under Cd stress, bacterial diversity remained relatively stable, suggesting their resilience to Cd. However, fungal communities exhibited greater sensitivity, with a decline in diversity in Cd-treated soils and partial recovery when MBs were applied. Conversely, Zn stress caused decline in bacterial α-diversity, while fungal diversity was maintained, indicating that Zn acts as an ecological filter that suppresses sensitive bacterial taxa and favors Zn-tolerant fungal species. Multi-omics data integration combined with network analysis highlighted key features associated with improved nutrient availability and reduced HM toxicity under MB treatments, including metabolites and microbial taxa linked to sulfur cycling, nitrogen metabolism, and iron reduction pathways. These findings demonstrate that MBs can modulate plant metabolic responses and restore rhizosphere microbial communities under Cd and Zn stress, with PGPR showing broader metabolomic recovery effects and AMF influencing specific metabolite pathways. This study provides new insights into plant-microbe interactions in HM-contaminated environments, supporting the potential application of biostimulants for sustainable soil remediation and plant health improvement.},
}

@article {pmid41225883,
year = {2025},
author = {Lu, J and Zhang, X and Mu, Y and Gao, J and Yi, F and Wang, P and Jin, D and Tang, F and Fan, W},
title = {Effects of Organic Fertilizer Type and Application Rate on Soil-Microbe Interactions, Yield, and Quality of Greenhouse Tomato.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41225883},
issn = {2223-7747},
abstract = {Soil nutrient imbalance and the decline of microbial diversity threaten the long-term sustainability of crop production in intensive agriculture. Organic fertilizers provide a promising means to improve soil-microbe-plant interactions, yet the combined effects of fertilizer type and application rate on soil function and crop productivity remain insufficiently understood. In this study, we investigated the agronomic and ecological responses of greenhouse tomato (Solanum lycopersicum L.) to three organic fertilizers-bone calcium fertilizer (BCF), bone mud fertilizer (BMF), and bio-organic fertilizer (BOF)-each applied at four rates (7500, 15,000, 30,000, and 45,000 kg·ha[-1]). The highest tested BOF rate (45,000 kg·ha[-1]) significantly increased net photosynthesis by 29.5%, stomatal conductance by 50.0%, and fruit yield by 40.8% compared with the unfertilized control. It also enhanced soil organic matter by 42.6% and total nitrogen by 82.0%, while increasing the relative abundance of Proteobacteria, a phylum closely associated with nutrient cycling and plant growth promotion. Network and path modeling revealed that changes in microbial diversity were positively associated with improved soil properties, which were subsequently linked to higher photosynthetic efficiency and yield formation, suggesting a potential microbiome-mediated pathway from fertilization to productivity. These effects were statistically consistent across measured endpoints. Our findings highlight that optimizing both the type and rate of organic fertilizer-particularly bio-organic fertilizer under greenhouse conditions-can enhance soil fertility, microbial function, and crop yield simultaneously. This study provides an evidence-based framework for precision fertilization strategies aimed at improving agroecosystem resilience and advancing sustainable tomato production.},
}

@article {pmid41225793,
year = {2025},
author = {Aina, O and Donaldson, L},
title = {Harnessing the Sorghum Microbiome for Enhancing Crop Productivity and Food Security Towards Sustainable Agriculture in Smallholder Farming.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41225793},
issn = {2223-7747},
abstract = {Smallholder farming plays a crucial role in global food security, contributing more than half of the world's food supply. However, it is increasingly threatened by climate variability, declining soil fertility, and financial constraints, all of which suppress plant growth, reduce yields, and endanger livelihood stability. Addressing these challenges requires sustainable, eco-friendly alternatives to costly and environmentally damaging agrochemicals. Sorghum, a climate-resilient cereal, harbours a diverse microbiome that contributes significantly to its remarkable adaptability under adverse conditions. Harnessing the sorghum-associated microbiome, therefore, represents a promising, low-cost, and sustainable strategy to enhance sorghum productivity and resilience in smallholder farming systems. However, despite its potential, the adoption of microbiome-based technologies among smallholders remains limited due to a lack of local production units, poor government policies, knowledge gaps, and perceived risks. Although many studies report positive outcomes from microbiome-based interventions, translating this potential from controlled experiments to real-world field applications requires a critical evaluation of the efficacy, practicality, and limitations of microbial interventions. Furthermore, the outcomes of these studies are uneven, highly context-dependent, and often restricted to short-term or small-scale trials. This review, therefore, seeks to highlight current understanding of the sorghum microbiome, including its composition and the procedures for isolating and characterising beneficial microbes. It further evaluates the key challenges hindering adoption and proposes strategies to overcome them. Ultimately, this review advocates for integrating sorghum-associated microbiome technologies within integrated farming systems, underscoring their potential to enhance sustainable crop production, strengthen smallholder resilience, and contribute to the global sustainable development goals.},
}

@article {pmid41225787,
year = {2025},
author = {Díaz-González, S and González-Sanz, C and González-Bodí, S and Marín, P and Brunner, F and Sacristán, S},
title = {Microbiome Analysis Reveals Biocontrol of Aspergillus and Mycotoxin Mitigation in Maize by the Growth-Promoting Fungal Endophyte Colletotrichum tofieldiae Ct0861.},
journal = {Plants (Basel, Switzerland)},
volume = {14},
number = {21},
pages = {},
pmid = {41225787},
issn = {2223-7747},
support = {DI-15-07906//MCIN/AEI/10.13039/501100011033/ ; PID2021-123697OB-I00//MCIU/AEI/10.13039/501100011033 and "ERDF/EU"/ ; PTA2021-020636-I//MCIU/AEI/ https://dx.doi.org/10.13039/501100011033 and the European Social Fund Plus (FSE +)/ ; PEJ-2020-AI/BIO-19580//Comunidad de Madrid/ ; PRE2022-103983//MCIU/AEI/ https://dx.doi.org/10.13039/501100011033 and "ESF Investing in your future"/ ; CEX2020-000999-S-20-3//MCIU/AEI/ https://dx.doi.org/10.13039/501100011033 and "ESF Investing in your future"/ ; },
abstract = {Maize (Zea mays L.) is a globally critical crop that faces numerous challenges, including contamination by mycotoxigenic fungi such as Aspergillus spp. The use of fungal endophytes as bioinoculants offers a sustainable strategy to improve plant resilience against biotic and abiotic stresses. Here, we evaluate the potential of Colletotrichum tofieldiae strain Ct0861 as a bioinoculant and its impact on maize-associated bacterial and fungal microbiomes. Field trials demonstrated that Ct0861 enhanced biomass and yield compared to controls, regardless of the application method (seed or foliar). Microbiome profiling showed that Ct0861 induced subtle, compartment-specific changes in microbial diversity and composition, while preserving the stability of core microbiome assemblages. Both microbiome data and qPCR quantification confirmed a significant reduction in Aspergillus spp. abundance in Ct0861-treated plants. Greenhouse assays corroborated these results: Ct0861 reduced A. flavus biomass by up to 90% and significantly lowered aflatoxin levels in infected grains. Dual-culture assays and the absence of Ct0861 in grain samples suggest an indirect biocontrol mechanism, potentially mediated by plant-induced resistance. This study provides the first evidence that Ct0861 acts as a biocontrol agent against mycotoxigenic Aspergillus spp. in maize. Beyond promoting plant growth, Ct0861 enhances food safety by reducing mycotoxin accumulation without disrupting the native microbiome, supporting its potential as a tool for sustainable crop protection.},
}

@article {pmid41225505,
year = {2025},
author = {Motte, LR and Giarritiello, F and Sala, L and Drago, L},
title = {A systematic review of TMAO, microRNAs, and the oral/gut microbiomes in atherosclerosis and myocardial infarction: mechanistic insights and translational opportunities.},
journal = {Journal of translational medicine},
volume = {23},
number = {1},
pages = {1269},
pmid = {41225505},
issn = {1479-5876},
mesh = {Humans ; *MicroRNAs/metabolism/genetics ; *Methylamines/metabolism ; *Gastrointestinal Microbiome ; *Atherosclerosis/microbiology/genetics/metabolism ; *Myocardial Infarction/microbiology/genetics/metabolism ; *Translational Research, Biomedical ; *Mouth/microbiology ; Animals ; },
abstract = {Cardiovascular disease (CVD) is the leading cause of death worldwide, driven by complex interactions among atherosclerosis, inflammation, and metabolic dysregulation. Recent studies have identified the gut and oral microbiomes-through their metabolism of dietary precursors into trimethylamine (TMA) and its hepatic conversion to trimethylamine-N-oxide (TMAO)-as pivotal contributors to CVD risk. In parallel, microRNAs (miRNAs) have emerged as crucial regulators of inflammatory and metabolic pathways that further modulate these processes. This review examines recent human studies (2020-2025) to explore how microbiota-derived TMAO, miRNA regulatory networks, and changes in the oral microbiome contribute to the development of atherosclerosis and myocardial infarction. It also highlights potential therapeutic strategies targeting these pathways, providing insights for precision medicine in cardiovascular disease management.},
}

Humans
*MicroRNAs/metabolism/genetics
*Methylamines/metabolism
*Gastrointestinal Microbiome
*Atherosclerosis/microbiology/genetics/metabolism
*Myocardial Infarction/microbiology/genetics/metabolism
*Translational Research, Biomedical
*Mouth/microbiology
Animals

@article {pmid41225454,
year = {2025},
author = {Ohmichi-Tomiwa, M and Kato-Kogoe, N and Kudo, A and Fujita, D and Sakaguchi, S and Tsuda, K and Omori, M and Hayashi, E and Nakamura, S and Nakano, T and Ohmichi, M and Tamaki, J and Ueno, T},
title = {Exploratory study of the oral microbiota in pregnant women with hypothyroidism and their infants.},
journal = {BMC pregnancy and childbirth},
volume = {25},
number = {1},
pages = {1198},
pmid = {41225454},
issn = {1471-2393},
mesh = {Humans ; Female ; Pregnancy ; *Hypothyroidism/microbiology ; *Microbiota ; *Mouth/microbiology ; Adult ; Prospective Studies ; Infant ; Infant, Newborn ; *Pregnancy Complications/microbiology ; Case-Control Studies ; Postpartum Period ; },
abstract = {BACKGROUND: Hypothyroidism is a metabolic disorder associated with potentially adverse maternal and neonatal outcomes. Emerging evidence suggests a link between thyroid function and the microbiota; however, little is known about the oral microbiota of pregnant women with hypothyroidism and its potential impact on that of their offspring. This study aimed to characterize the oral microbiota of pregnant women with hypothyroidism and their children as part of the Oral Microbiome Prospective Unicenter Cohort Study (OMPU-CS).

METHODS: Pregnant women with hypothyroidism (Hypothyroid group, n = 31) and those with normal thyroid function (Control group, n = 30) were selected from participants in the ongoing OMPU-CS. Oral samples were collected from the women during pregnancy and at one month postpartum, and from their one-month-old infants. Microbiota composition was analyzed using 16 S rRNA metagenomic sequencing.

RESULTS: Compared with pregnant women in the Control group, those in the Hypothyroid group exhibited significantly reduced richness and evenness of the oral microbiota (observed operational taxonomic units, p = 0.034; Shannon index, p = 0.034). The overall structure of the oral microbiota differed significantly between groups at all phases-in pregnant women, postpartum women, and their infants (unweighted UniFrac distances, p = 0.002, p = 0.049, and p = 0.019, respectively). Linear discriminant analysis effect size (LEfSe) identified several differentially abundant taxa, including a consistently reduced abundance of members of the Rhizobiaceae family in the Hypothyroid group across all three phases compared with that in the Control group.

CONCLUSIONS: The oral microbiota of pregnant women with hypothyroidism and their one-month-old infants exhibited disease-specific characteristics. These findings suggest that maternal hypothyroidism may influence the oral microbiota of offspring, underscoring the importance of monitoring oral microbiota in mothers with hypothyroidism and their children.},
}

Humans
Female
Pregnancy
*Hypothyroidism/microbiology
*Microbiota
*Mouth/microbiology
Adult
Prospective Studies
Infant
Infant, Newborn
*Pregnancy Complications/microbiology
Case-Control Studies
Postpartum Period

@article {pmid41225359,
year = {2025},
author = {He, C and Wang, J and Ding, L and Li, X and Hu, Y and He, W and Xia, L and Xiong, H and Huang, X and Lei, Y and Luo, L and Lu, N and Zhu, Y},
title = {Longitudinal dysbiosis of gut bacteriome and mycobiome in patients with severe acute pancreatitis and its association with mortality.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {730},
pmid = {41225359},
issn = {1471-2180},
support = {82400761//National Natural Science Foundation of China/ ; 82370661//National Natural Science Foundation of China/ ; YFYKCTDPY202202//Science and Technology Innovation Team cultivation project of the First Affiliated Hospital of Nanchang University/ ; jxsp2019201028//Jiangxi Province's Thousand Talents Plan for introducing and cultivating high-level talents in innovation and entrepreneurship/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/mortality ; *Gastrointestinal Microbiome ; *Mycobiome ; Male ; Middle Aged ; *Bacteria/classification/genetics/isolation & purification ; Female ; Feces/microbiology ; *Pancreatitis/microbiology/mortality ; *Fungi/classification/genetics/isolation & purification ; Aged ; Adult ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The dysbiosis of gut microbiome is known to have a significant impact on the progression of sever acute pancreatitis (SAP). This study intends to investigate the alteration of gut microbiome in SAP patients during hospitalization and its association with mortality. Bacterial and fungal compositions of the fecal microbiota were determined via 16S and ITS1 sequencing, respectively.

RESULTS: Our findings indicated that SAP patients exhibited bacterial and fungal dysbiosis either at the time of admission or within the first 72 h of admission prior to any antibiotic treatment, characterized by reduced biodiversity, lower abundances of Blautia, Bifidobacterium, and increased Escherichia-Shigella, Enterococcus, and Candida. The overall microbiome was partially restored post-treatment in survivors, including commensal Bifidobacterium enhancement. In contrast, non-survivors experienced sustained perturbations during hospitalization, with over-representation of pathogenic Enterococcus and Candida. A classifier based on 20 optimal bacteria markers showed superior efficiency for predicting mortality. Interestingly, the abundances of Acinetobacter, Klebsiella and Candida were considerably elevated in the gut of patients who subsequently developed infectious complications.

CONCLUSIONS: Our study provided a comprehensive profile of gut bacteriome and mycobiome in SAP patients and identified the temporal trajectory alterations of microbiome associated with mortality. These findings underscore the importance of early recognition of pathobiome states and the potential role for the modulation of microbiota during the development of SAP.},
}

Humans
*Dysbiosis/microbiology/mortality
*Gastrointestinal Microbiome
*Mycobiome
Male
Middle Aged
*Bacteria/classification/genetics/isolation & purification
Female
Feces/microbiology
*Pancreatitis/microbiology/mortality
*Fungi/classification/genetics/isolation & purification
Aged
Adult
Longitudinal Studies
RNA, Ribosomal, 16S/genetics

@article {pmid41225348,
year = {2025},
author = {Huang, X and Chen, M and Huang, P and Zhou, Q and Ling, Z and Wu, Y and Mu, D and Xu, L and Peng, Y and Cai, X},
title = {Phenotypic and genomic characterization of Paenibacillus salivarius sp. nov., isolated from the human oral cavity.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {737},
pmid = {41225348},
issn = {1471-2180},
support = {2024AH051076//University Research Projects of Anhui Provincial/ ; Wxn202403//Open Project of Key Lab. of Provincial Key Laboratory/ ; 202410372016//Undergraduate Innovation and Entrepreneurship Training Program/ ; 202410372004S//Undergraduate Innovation and Entrepreneurship Training Program/ ; H20250225//Industry Academia-Research Project of Demonstration Research on Fungal Genome Analysis and Technological Innovation in Microbial Agricultural Wastewater Treatment/ ; (Industry-University Co-constructed Demonstration Course: Restoration Ecology, X2025xqkc007)//Anqing Normal University Graduate Student Industry-University Collaborative Practice Program Special Fund Grant/ ; 202305A12020022//Major Science and Technology Projects of the Scientific and Technological Innovation Platform/ ; ZT-2410372012//Ministry of Education's 2024 Themed Case Study Project/ ; JCYJ20230808105208017//Shenzhen Science and Technology Program/ ; },
mesh = {Humans ; *Paenibacillus/genetics/classification/isolation & purification/physiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Base Composition ; *Genome, Bacterial ; *Mouth/microbiology ; Aged ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Whole Genome Sequencing ; Bacterial Typing Techniques ; Nucleic Acid Hybridization ; China ; Sequence Analysis, DNA ; Phenotype ; Chronic Periodontitis/microbiology ; Saliva/microbiology ; },
abstract = {A novel Gram-stain-negative, facultatively anaerobic, endospore-forming bacterium, designated DYY-L-2[T], was isolated from the saliva of a 69-year-old patient with chronic periodontitis in Hengyang, China. Phylogenetic analysis based on the 16S rRNA gene sequences revealed that strain DYY-L-2[T] belonged to the genus Paenibacillus, with the highest similarity to Paenibacillus konsidensis LBY[T] (98.6%), followed by Paenibacillus vini LAM0504[T] (97.2%). Whole-genome sequencing yielded a complete circular chromosome of 5,642,305 bp with a genomic DNA G + C content of 50.8%. Overall genome relatedness index analysis indicated low average nucleotide identity (ANI < 80%) and in silico DNA-DNA hybridization (isDDH < 25%) values between strain DYY-L-2[T] and its closely related type strains, supporting its status as a novel genospecies. The strain grew optimally at 37 °C, in pH 7.0, and tolerated up to 5% (w/v) NaCl. Major cellular fatty acids were C16:0 and anteiso-C15:0. The genomic functional annotation identified unique regions enriched with mobile genetic elements and Type I restriction-modification systems (e.g. hsdR and hsdM), suggesting adaptive mechanisms for genomic stability in the oral environment. Based on polyphasic taxonomic data, strain DYY-L-2[T] represents a novel species within the genus Paenibacillus, for which the name Paenibacillus salivarius sp. nov. is proposed. The type strain is DYY-L-2[T] (= GDMCC 1.6010[T] = KCTC 43851[T]). This study expands the understanding of the Paenibacillus diversity in host-associated environments and provides insights into its ecological role in the human oral microbiome.},
}

Humans
*Paenibacillus/genetics/classification/isolation & purification/physiology
Phylogeny
RNA, Ribosomal, 16S/genetics
Base Composition
*Genome, Bacterial
*Mouth/microbiology
Aged
DNA, Bacterial/genetics
Fatty Acids/analysis
Whole Genome Sequencing
Bacterial Typing Techniques
Nucleic Acid Hybridization
China
Sequence Analysis, DNA
Phenotype
Chronic Periodontitis/microbiology
Saliva/microbiology

@article {pmid41225338,
year = {2025},
author = {Xie, H and Dong, C and Li, Y and Guo, J and Yang, Y and Yang, J and Li, X and Cha, J and Hu, S and Lin, C},
title = {XGBoost-based urinary microbial signatures enable non-invasive diagnosis and prognosis for urothelial carcinoma.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {732},
pmid = {41225338},
issn = {1471-2180},
support = {no. Tsqn202103198//Taishan Scholar Program of Shandong Province/ ; ZR2024MH305//Shandong Provincial Natural Science Foundation/ ; 2024YT06000818//The development of scientific and technological innovation in Yantai/ ; },
mesh = {Humans ; Male ; Female ; Prognosis ; Middle Aged ; Aged ; *Microbiota/genetics ; *Urinary Bladder Neoplasms/diagnosis/microbiology/urine ; *Bacteria/classification/genetics/isolation & purification ; Machine Learning ; *Urologic Neoplasms/diagnosis/microbiology ; *Carcinoma, Transitional Cell/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Aged, 80 and over ; Biomarkers, Tumor/urine ; *Urine/microbiology ; Boosting Machine Learning Algorithms ; },
abstract = {BACKGROUND: Urothelial carcinoma (UC) is the most common malignant tumor of the urinary system, characterized by high incidence and recurrence rates, posing a serious threat to human health. While previous studies have linked urinary microbiota alterations to bladder cancer, little is known about the broader spectrum of UC subtypes or their clinical implications. To address this gap, we analyzed microbiota profiles across multiple UC subtypes, incorporating microbial network analyses and machine learning to establish diagnostic models and identify prognostic biomarkers.

METHOD: A total of 112 subjects were enrolled for 16 S rDNA sequencing of clean-catch midstream urine samples, including 63 patients with bladder cancer (BCA), 29 with Upper Tract Urothelial Carcinoma (UTUC), 9 with renal pelvis cancer (RPC), and 40 healthy controls (HC). Microbial diversity, community networks, and clinical associations were analyzed. An XGBoost-based diagnostic model was developed with a 70/30 train-test split, cross-validation, and external validation. Model interpretability was assessed with the SHAP algorithm.

RESULTS: UC groups showed elevated α-diversity versus HC, with consistent enrichment of Streptococcus and Clostridium. Microbial structure networks significantly differed in tumors. A urinary microbiota-based diagnostic model achieved high accuracy for BCA detection (AUC = 0.927), and Lachnospiraceae family members showed potential prognostic value.

CONCLUSION: Our study illuminates the microbial profiles in the UC and suggests that urinary microbiota signatures represent promising non-invasive independent biomarker for the diagnosis and prognosis of UC.},
}

Humans
Male
Female
Prognosis
Middle Aged
Aged
*Microbiota/genetics
*Urinary Bladder Neoplasms/diagnosis/microbiology/urine
*Bacteria/classification/genetics/isolation & purification
Machine Learning
*Urologic Neoplasms/diagnosis/microbiology
*Carcinoma, Transitional Cell/diagnosis/microbiology
RNA, Ribosomal, 16S/genetics
Aged, 80 and over
Biomarkers, Tumor/urine
*Urine/microbiology
Boosting Machine Learning Algorithms

@article {pmid41225325,
year = {2025},
author = {Debbagh-Nour, H and Khourchi, S and Mouttaqi, AE and Elfermi, R and Bourazza, A and Malou, OP and Ducousso, M and Boukcim, H and Hijri, M and Hirich, A},
title = {Plant identity and environmental filtering are the key drivers of bacterial community structure in four desert plant species from the Sahara Desert in Morocco.},
journal = {BMC microbiology},
volume = {25},
number = {1},
pages = {734},
pmid = {41225325},
issn = {1471-2180},
mesh = {Morocco ; *Soil Microbiology ; Desert Climate ; *Bacteria/classification/genetics/isolation & purification ; Plant Roots/microbiology ; Soil/chemistry ; Rhizosphere ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Plants/microbiology/classification ; Carbon/analysis ; DNA, Bacterial/genetics ; },
abstract = {BACKGROUND: Plant microbiome is a very wide research area playing a major role in agriculture and plant health. This study investigates the interactions between root-associated bacterial communities and soil physico-chemical characteristics of four Moroccan desert plant species: Lavandula coronopifolia Poir. (n = 20), Lycium intricatum Boiss. (n = 20), Nitraria retusa Asch. (n = 20) and Searsia tripartita (Ucria) Moffett. (n = 20). Soil samples were collected in the rhizosphere of each plant species, and root samples from four different sites, with five random samples per site. Elemental chemical composition of soil sample was analyzed using the X-Ray fluorescence spectrometry and soil carbon, i.e., organic carbon (SOC) and inorganic carbon (SIC) were measured using the Rock-Eval® Oxypure method. Roots were assessed for their microbial community, using the 16S rDNA metabarcoding analysis.

RESULTS: Significant variation in soil parameters was observed across sites and among the four desert plant species. SOC and SIC contents were highest in soils associated with S. tripartita, N. retusa, and Ly. intricatum, while La. coronopifolia was associated with elevated levels of Si, Al, K, and Mn. Soil EC was highest in N. retusa and S. tripartita. Microbial analysis revealed that Pseudomonadota and Actinomycetota dominated the root-associated bacterial communities, comprising around 60% of total abundance. Alpha diversity (Shannon and Simpson indices) varied significantly across species and sites, especially in La. coronopifolia. Beta diversity analyzes confirmed that geographic location significantly influenced microbial community structure. Rhizosphere network complexity and composition varied by species, with N. retusa showing broad ecological tolerance, while S. tripartita communities were strongly shaped by SOC, SIC, K, Ca, Mn, and Fe. Mantel test results further highlighted that plant identity and environmental factors differentially influence root microbial composition across sites.

CONCLUSION: Each plant species showed unique responses in terms of soil characteristics and microbial communities, highlighting the importance of adopting a species-specific approach.},
}

Morocco
*Soil Microbiology
Desert Climate
*Bacteria/classification/genetics/isolation & purification
Plant Roots/microbiology
Soil/chemistry
Rhizosphere
*Microbiota
RNA, Ribosomal, 16S/genetics
*Plants/microbiology/classification
Carbon/analysis
DNA, Bacterial/genetics

@article {pmid41225294,
year = {2025},
author = {Osman, NA and Mohd-Ridwan, AR and Gani, M and Karuppannan, KV and Abdul-Latiff, MAB and Aifat, NR and Md-Zain, BM},
title = {Comparative Metabarcoding Analysis of Gut Microbiome in Wild and Captive Stump-Tailed Macaques (Macaca arctoides).},
journal = {Journal of medical primatology},
volume = {54},
number = {6},
pages = {e70043},
doi = {10.1111/jmp.70043},
pmid = {41225294},
issn = {1600-0684},
support = {ST-2021-017//TNB Research/ ; ST-2022-027//The National Conservation Trust Fund for Natural Resources/ ; GUP-2019-037//Universiti Kebangsaan Malaysia/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Malaysia ; *Macaca/microbiology ; RNA, Ribosomal, 16S/analysis/genetics ; *DNA Barcoding, Taxonomic/veterinary ; Animals, Wild/microbiology ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Male ; Animals, Zoo/microbiology ; Female ; },
abstract = {The primate gastrointestinal tract is home to bacteria, which may be associated with its habitat. In Malaysia, wild stump-tailed macaques (Macaca arctoides) are found solely in the northern region of Peninsular Malaysia. No information is currently available regarding the intestinal microbiota of wild or captive Malaysian stump-tailed macaques. In this study, a fecal metabarcoding approach was utilized to determine the gut microbiome composition of wild and captive M. arctoides and how these microbial communities respond to the host's external environment. To elucidate these relationships, 16S rRNA was amplified and sequenced using the MiSeq platform, with 300 paired-end sequences. We identified 18 phyla, 38 orders, 46 families, 76 genera, and 131 species in the stump-tailed macaque samples. The most prevalent bacterial families in the gut of M. arctoides were Firmicutes (4.69%), Spirochaetes (2.87%), and Proteobacteria (2.40%). Our analysis did not reveal any substantial differences between the habitat environment and gut microbiome composition in M. arctoides. Nonetheless, to the best of our knowledge, this study is the first to document the gut microbiome of the wild M. arctoides population in Peninsular Malaysia. Future studies are required to explore and better understand potential zoonotic pathogens harbored in stump-tailed macaques.},
}

Animals
*Gastrointestinal Microbiome
Malaysia
*Macaca/microbiology
RNA, Ribosomal, 16S/analysis/genetics
*DNA Barcoding, Taxonomic/veterinary
Animals, Wild/microbiology
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Male
Animals, Zoo/microbiology
Female

@article {pmid41225248,
year = {2025},
author = {Bignami, G and Monzón-Atienza, L and Leuzzi, D and Scicchitano, D and Candela, M and Gómez-Mercader, A and Jlidi, M and Gustinelli, A and Tedesco, P and Fioravanti, ML and Castro, PL and Acosta, F},
title = {"Effects of Bacillus Velezensis D-18 on Health Status of European Seabass (Dicentrarchus labrax) Experimentally Challenged with Vibrio harveyi".},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41225248},
issn = {1867-1314},
support = {28740//Horizon 2020/ ; },
abstract = {In recent years, the use of probiotics as a possible alternative to antibiotics has generated a growing interest in the global aquaculture field. In this study, the probiotic Bacillus velezensis D-18 was evaluated for its potential protective effect against the marine pathogen Vibrio harveyi. The probiotic was administered through the diet of European seabass (Dicentrarchus labrax) for 30 days, followed by an in vivo challenge with V. harveyi to assess whether the D-18 strain could enhance host resistance to infection. Biofilm formation in tanks was also investigated to analyze its composition and if there are antagonistic interactions between the two bacterial species. From a histological perspective, significant changes were observed in intestinal morphological parameters after infection, the area and base of the villi appeared to increase in the probiotic-fed groups as did the number of goblet cells and in the serum antibacterial activity which was increased in the infected group that received the probiotic compared to baseline levels. The intestinal microbiome was also analyzed to monitor the composition and determine whether different diets before and after infection induced any changes. Although no significant differences were found in the metagenomics of the tank biofilm and the gut microbiome, mortality rates showed that the probiotic provided effective protection against the pathogen. These findings support the potential of B. velezensis D-18 as a viable alternative to antibiotics, particularly when included in the diet prior to disease onset.},
}

@article {pmid41225127,
year = {2026},
author = {Gasmi, A and Benahmed, AG and Nehaoua, A and Noor, S and Menzel, A},
title = {Innovative Biomarkers for Oral Immunity: Advancements and Clinical Applications.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {795-814},
pmid = {41225127},
issn = {0065-2598},
mesh = {Humans ; *Biomarkers/metabolism/analysis ; Microbiota/immunology ; *Mouth Diseases/immunology/genetics/microbiology/diagnosis ; *Oral Health ; Metabolomics ; Proteomics ; Polymorphism, Single Nucleotide ; },
abstract = {Oral immunity is an essential barrier for protection against pathogens, supporting oral health, and overall health-related challenges. Nevertheless, dysregulation of oral immunity results in different pathological conditions that are often challenging to diagnose and manage. Biomarkers have revolutionized the management of oral health by offering information about molecular and cellular immune events, disease etiology, and treatment outcomes. This review focuses on the biomarkers for oral immunity in the context of the existing trends and includes genetic, proteomic, metabolomic, and microbiome biomarkers. Single-nucleotide polymorphism (SNP) and copy number variation (CNV) have improved the knowledge of the genetic risk factors for oral diseases and the treatment plan for patients. Cytokines, matrix metalloproteinases (MMPs), and antimicrobial peptides (AMPs) have enhanced the diagnostic accuracy of diseases, prognostication, and evaluation of therapeutic efficacy. Metabolomic biomarkers have provided valuable insights into the biochemical pathways related to oral health and diseases, while microbiome-derived biomarkers have revealed the intricate host-microbiota interactions. Recent developments in high-throughput screening, multi-omics, and computational biology have facilitated the identification of biomarkers of oral immunity. These molecular markers have been proven to have the potential for screening, prognosis, and targeted therapy of oral diseases such as periodontitis, oral cancer, and autoimmune diseases. However, some issues are still to be solved, such as standardization of biomarker usage, obtaining the approval of biomarkers by different authorities, and the economic issues regarding the application of biomarkers for clinical diagnostics.},
}

Humans
*Biomarkers/metabolism/analysis
Microbiota/immunology
*Mouth Diseases/immunology/genetics/microbiology/diagnosis
*Oral Health
Metabolomics
Proteomics
Polymorphism, Single Nucleotide

@article {pmid41225119,
year = {2026},
author = {Suárez, LJ and Mera, J and Garzón, HS and Arce, RM and S Souza, JG and Shibli, JA},
title = {Immunomodulation Strategies in Oral Diseases: From Microbiome Manipulation to Pro-resolution Therapies.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {627-649},
pmid = {41225119},
issn = {0065-2598},
mesh = {Humans ; *Immunomodulation/drug effects ; *Microbiota/immunology/drug effects ; *Periodontitis/immunology/microbiology/therapy ; Animals ; *Mouth Diseases/immunology/microbiology/therapy ; Biofilms ; Peri-Implantitis/immunology/microbiology ; },
abstract = {Host-response and inflammatory processes commonly triggered by dental biofilms play a crucial role in the pathogenesis pathways of prevalent oral diseases, such as periodontitis and implant-related infections, which have been widely explored by scientific evidence. The role of the oral microbiome and the interaction between microorganisms and immune components in the onset and development of such inflammatory conditions has been a primary focus for scientists and clinicians and has opened new possibilities for therapeutic targets to modulate disease progression. Such knowledge and new strategies with the aim of promoting microbial transition to a symbiotic state or modulating immune response have paved the way for innovative approaches to control, treat, and prevent oral diseases. This chapter presents the concepts of immunomodulation related to oral diseases, including the initial changes in resolving the inflammatory response (pro-resolution of inflammation) and how inflammatory processes can be modulated by immune modulatory agents in periodontal and peri-implant diseases.},
}

Humans
*Immunomodulation/drug effects
*Microbiota/immunology/drug effects
*Periodontitis/immunology/microbiology/therapy
Animals
*Mouth Diseases/immunology/microbiology/therapy
Biofilms
Peri-Implantitis/immunology/microbiology

@article {pmid41225118,
year = {2026},
author = {Esmaeili, S and Shahbazi, S and Ziaei, H and Younessian, F},
title = {Evaluating the Impact of Clear Dental Aligners on Dental and Periodontal Conditions, Oral Microbial Patterns, and the Immune System.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {605-624},
pmid = {41225118},
issn = {0065-2598},
abstract = {Clear aligner therapy (CAT) has gained widespread adoption for managing malocclusions, primarily due to its aesthetic advantages, improved access for hygiene, and enhanced patient comfort relative to fixed appliances (FAs). However, CAT introduces a distinct intraoral environment that can influence microbial composition, biofilm development, and host immune responses. This chapter explores the effects of clear aligners on dental and periodontal health, oral microbial communities, and immunological parameters. Evidence indicates that CAT may facilitate plaque and biofilm accumulation, particularly on composite attachments, thereby increasing the risk of white spot lesions (WSLs), gingivitis, and dental caries. Despite these risks, aligners are generally associated with lower levels of pathogenic bacteria compared to FAs. Microbiome analyses of subgingival plaque and saliva reveal shifts in bacterial genera and phyla, although these changes are frequently non-pathogenic. CAT has demonstrated minimal negative effects on clinical periodontal indices, including the plaque index and gingival bleeding index, particularly when effective oral hygiene is maintained. Furthermore, aligners may reduce sustained immune activation by limiting plaque retention and aseptic inflammation, potentially decreasing the expression of pro-inflammatory cytokines such as IL-1β, IL-6, and TNF-α. Although hypersensitivity reactions to aligner materials are infrequent, they warrant consideration. Overall, CAT appears to support periodontal health and promote a more stable oral microbial environment compared to FAs. Continued patient adherence to hygiene protocols and further long-term studies are necessary to fully evaluate systemic implications and optimize clinical outcomes.},
}

@article {pmid41225098,
year = {2026},
author = {Contaldo, M},
title = {Periodontal Disease and Osteoporosis: A Bidirectional Relationship.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {163-178},
pmid = {41225098},
issn = {0065-2598},
abstract = {Osteoporosis (OP) and periodontitis (PD) are two prevalent diseases with significant public health implications, particularly among aging populations. Osteoporosis is a condition that can affect any bone, characterized by decreased bone mineral density (BMD) and deterioration of the bone architecture, resulting in weaker bones and a higher risk of fractures. Periodontitis is a chronic inflammatory condition affecting the supporting structures of the teeth, such as the gingiva, periodontal ligament, and alveolar bone, often leading to tooth loss if left untreated.Recent studies have suggested an interrelationship between these conditions, rooted in shared biological mechanisms. Both diseases involve an imbalance in bone remodeling processes, with excessive activity of osteoclasts over osteoblasts, leading to bone resorption. In osteoporosis, this imbalance is systemic, while in periodontitis, it is localized to the jawbone.Shared risk factors, such as aging, hormonal changes (e.g., postmenopausal estrogen deficiency), and lifestyle factors, like smoking and poor nutrition, further strengthen this association. Additionally, osteoporosis may exacerbate periodontitis by reducing alveolar bone density, while periodontal inflammation can elevate the expression of systemic biomarkers of bone resorption, influencing osteoporosis progression. Furthermore, dysbiosis of the gut and oral cavity microbial communities plays a critical role in both conditions. Gut dysbiosis can influence systemic inflammation and bone metabolism, exacerbating osteoporosis, while oral dysbiosis, marked by pathogenic shifts in the microbiota, triggers and perpetuates periodontal inflammation and alveolar bone loss. Understanding these interrelationships emphasizes the need for an integrated approach to preventing and managing these interconnected conditions.},
}

@article {pmid41225096,
year = {2026},
author = {Nehaoua, A and Gasmi, A and Noor, S and Benahmed, AG},
title = {Diabesity and Oral Immunity: Exploring the Interconnection.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {121-139},
pmid = {41225096},
issn = {0065-2598},
abstract = {Diabesity-obesity and type 2 diabetes mellitus (T2DM)-has a profound effect on oral health, and modulation of the oral immune system may help in managing it. This review aims to elucidate the complex interconnection between diabesity, oral immunity, and oral health consequences. Diabesity affects metabolic homeostasis, leading to changes in the immune system within the oral cavity, and increases the incidence of chronic low-grade inflammation and oral diseases. Alterations in the oral microbiome and the breakdown of immune homeostasis further contribute to oral health problems. The reciprocal relationship between diabesity and oral diseases and how inflammation in the oral cavity can worsen systemic metabolic diseases are also described. Apart from periodontal diseases, diabesity increases susceptibility to dental caries, xerostomia, and oral mucosal lesions. Novel treatment strategies are presented with special emphasis on nutrition, lifestyle changes, new drugs, and immunomodulating therapies. The possibility of using a personalized medicine approach in the prevention and treatment of oral diseases in diabesity patients is discussed with regard to genetic and epigenetic factors, biomarkers, and genetic profiles. A combined strategy focusing on both systemic metabolic and oral immunomodulation is recommended to advance the knowledge of diabesity in oral health and thus improve the oral health and quality of life (QoL) of patients with diabesity.},
}

@article {pmid41225095,
year = {2026},
author = {Nehaoua, A and Gasmi, A and Noor, S and Benahmed, AG},
title = {The Oral Microbiome, Oral Hyperpermeability, and Periodontitis in Metabolic Syndrome.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {101-120},
pmid = {41225095},
issn = {0065-2598},
abstract = {The links between the oral microbiome, oral hyperpermeability, periodontitis, and metabolic syndrome (MetS) are good examples of the oral-systemic health connection. The oral microbiota is involved in host defense and metabolism. Oral dysbiosis disrupts periodontal homeostasis, increases the permeability of the oral mucosa, and triggers systemic inflammation, thus leading to MetS. On the other hand, metabolic disorders can change the environmental conditions in the oral cavity and exacerbate dysbiosis and periodontitis. Oral hyperpermeability is evidently a key player in this oral-systemic connection, allowing passage of oral bacteria, their by-products, and inflammatory mediators into the systemic circulation. It triggers the low-grade, chronic inflammation commonly seen in MetS and may exacerbate insulin resistance and other metabolic changes. Thus, periodontitis-a chronic inflammatory disease-is both a result and a cause of MetS. The classification of periodontitis as both a diagnostic marker and a treatment target in metabolic risk enhances the opportunity for the assessment and control of MetS. New-generation therapies targeting oral permeability and dysbiosis, such as barrier-strengthening agents, precision probiotics, and advanced antimicrobial agents, are potential strategies to address the oral-systemic health link. The concept of oral-systemic healthcare, incorporating both dental and medical care, is an emerging model of care delivery systems. Such strategies, including salivary risk management (SRM), targeted interventions, and patient education, may contribute to the enhancement of general health, particularly among individuals with or at risk of MetS.},
}

@article {pmid41225090,
year = {2026},
author = {Ziaei, H and Rezaei, N},
title = {Introduction to Oral Immunity.},
journal = {Advances in experimental medicine and biology},
volume = {1492},
number = {},
pages = {3-21},
pmid = {41225090},
issn = {0065-2598},
abstract = {The oral immune system functions as a primary line of defense, composed of oral epithelial barriers, salivary antimicrobial factors, and various innate and adaptive immune components to prevent pathogen entry. Resident immune cells in oral tissues help maintain tolerance to commensal microorganisms while simultaneously responding to harmful external stimuli and contributing to systemic immune regulation. This chapter provides a comprehensive overview of the immunological components and their functions in the oral cavity, emphasizing the dual role of maintaining tolerance to commensal microbes and dietary antigens while initiating protective responses against pathogens. Any disruptions in this balance, such as oral dysbiosis or immune dysregulation, can lead to the development of local inflammatory conditions; it may also contribute to systemic immune disturbances and related pathologies. Immune mechanisms also regulate craniofacial development and postnatal bone remodeling and regeneration, mainly through cytokine-mediated signaling pathways and interactions between stem cells and immune cells. Several local and systemic immunological pathways are often dysregulated in oral inflammatory conditions, which makes them important therapeutic targets. Therapeutic strategies targeting these pathways include immune checkpoint inhibitors, microbiome-directed interventions, stem cell-based therapies, and salivary diagnostics for real-time and noninvasive immune profiling. These offer promising approaches for restoring oral and systemic immune balance. Finally, this chapter has reviewed recent technological advances, such as single-cell RNA sequencing (scRNA-seq), spatial transcriptomics, metagenomics, and multi-omics integration, in the context of oral immunity. These novel techniques are transforming oral immunology, since they enable high-resolution characterization of cellular, microbial, and molecular interactions, and support the transition toward establishing more precise diagnosis and treatment plans. These findings suggest that oral immunity plays a critical role in linking local mucosal defense and systemic immune responses. Therefore, understanding oral immune mechanisms in health and inflammatory conditions is important for revealing disease pathogenesis and guiding targeted interventions.},
}

@article {pmid41224847,
year = {2025},
author = {Gu, X and Ruan, X and Yang, W and He, J and Tang, L and Niu, D and Ma, B},
title = {Integrative multi-omics identifies coordinated alterations in the gut microbiome and in plasma and aqueous humor metabolomes in high myopic cataract.},
journal = {Scientific reports},
volume = {15},
number = {1},
pages = {39636},
pmid = {41224847},
issn = {2045-2322},
support = {2025JC-YBQN-1258//Natural Science Foundation of Shaanxi Province/ ; 2023-JC-QN-0885//Natural Science Foundation of Shaanxi Province/ ; ZR2023QH479//Natural Science Foundation of Shandong Province/ ; },
abstract = {Growing evidence suggests that chronic inflammation contributes to the development of myopia, but the biological link between systemic processes and ocular changes remains poorly understood. In this study, we explored the gut-retina axis using a multi-omics approach in patients with high myopic cataract (HMC) compared with age-related cataract (ARC) controls. Fecal 16S rDNA sequencing revealed distinct microbial signatures in HMC, notably the enrichment of Lactobacillales and depletion of Roseburia, taxa associated with systemic inflammatory status. Metabolomic profiling of plasma and aqueous humor (AH) identified widespread alterations, with enrichment analyses highlighting pathways related to steroid hormone biosynthesis, PPAR signaling, and amino acid metabolism. Several metabolites correlated with axial length, and 4-phenolsulfonic acid in plasma and 5'-N-ethylcarboxamidoadenosine in AH showed the strongest discriminatory potential between HMC and ARC groups. While these findings are associative and require validation in larger, longitudinal cohorts, they suggest that systemic and ocular metabolic disturbances are closely linked to established high myopia. This study provides novel insights into the potential role of the gut-retina axis in myopia pathogenesis.},
}

@article {pmid41224658,
year = {2025},
author = {Vonder Haar, C and Celorrio, M and Martens, KM and Friess, SH and Villapol, S and Urban, RJ and Pyles, R and Mychasiuk, R and Simon, D and Dave, A},
title = {The Gut Microbiome as a Modulator of Traumatic Brain Injury Pathology and Symptoms.},
journal = {The Journal of neuroscience : the official journal of the Society for Neuroscience},
volume = {45},
number = {46},
pages = {},
doi = {10.1523/JNEUROSCI.1337-25.2025},
pmid = {41224658},
issn = {1529-2401},
abstract = {Traumatic brain injuries (TBIs) affect millions annually, leading to devastating neurobehavioral consequences and increasing risk for neurodegenerative and psychiatric diseases. However, therapies are lacking. Starting in 2018, dysbiosis of the gut microbiome was identified as an acute, and potentially chronic, pathology originating from TBI. Recent studies established that the microbiome contributes to the evolution of TBI pathology and functional impairments. The gut microbiome is the collection of microorganisms that inhabit the stomach through colon and is indicated as a contributor to myriad neurological and psychiatric conditions. This makes it an intriguing target to understand in the context of TBI. Thus, this review focuses on the evidence establishing the gut as a modulator of TBI and the major potential mechanisms by which this occurs. This includes regulation of food processing into host-usable nutrients, inflammatory signaling, and vagus nerve modulation. Each of these areas provides potential for future therapeutic development and intervention but there are also multiple areas where microbiome-TBI science could be improved.},
}